forcefield.py 209 KB
Newer Older
1
2
"""
forcefield.py: Constructs OpenMM System objects based on a Topology and an XML force field description
3
4
5
6
7
8

This is part of the OpenMM molecular simulation toolkit originating from
Simbios, the NIH National Center for Physics-Based Simulation of
Biological Structures at Stanford, funded under the NIH Roadmap for
Medical Research, grant U54 GM072970. See https://simtk.org.

9
Portions copyright (c) 2012-2015 Stanford University and the Authors.
10
11
12
Authors: Peter Eastman, Mark Friedrichs
Contributors:

Justin MacCallum's avatar
Justin MacCallum committed
13
Permission is hereby granted, free of charge, to any person obtaining a
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
copy of this software and associated documentation files (the "Software"),
to deal in the Software without restriction, including without limitation
the rights to use, copy, modify, merge, publish, distribute, sublicense,
and/or sell copies of the Software, and to permit persons to whom the
Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
USE OR OTHER DEALINGS IN THE SOFTWARE.
30
"""
31
32
from __future__ import absolute_import, print_function

33
34
35
36
37
38
__author__ = "Peter Eastman"
__version__ = "1.0"

import os
import itertools
import xml.etree.ElementTree as etree
39
import math
40
41
42
from math import sqrt, cos
import simtk.openmm as mm
import simtk.unit as unit
43
from . import element as elem
44
45
from simtk.openmm.app import Topology

46
47
def _convertParameterToNumber(param):
    if unit.is_quantity(param):
48
49
50
        if param.unit.is_compatible(unit.bar):
            return param / unit.bar
        return param.value_in_unit_system(unit.md_unit_system)
51
52
    return float(param)

53
54
# Enumerated values for nonbonded method

55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
class NoCutoff(object):
    def __repr__(self):
        return 'NoCutoff'
NoCutoff = NoCutoff()

class CutoffNonPeriodic(object):
    def __repr__(self):
        return 'CutoffNonPeriodic'
CutoffNonPeriodic = CutoffNonPeriodic()

class CutoffPeriodic(object):
    def __repr__(self):
        return 'CutoffPeriodic'
CutoffPeriodic = CutoffPeriodic()

class Ewald(object):
    def __repr__(self):
        return 'Ewald'
Ewald = Ewald()

class PME(object):
    def __repr__(self):
        return 'PME'
PME = PME()
79
80
81

# Enumerated values for constraint type

82
83
84
85
86
87
88
89
90
91
92
93
94
95
class HBonds(object):
    def __repr__(self):
        return 'HBonds'
HBonds = HBonds()

class AllBonds(object):
    def __repr__(self):
        return 'AllBonds'
AllBonds = AllBonds()

class HAngles(object):
    def __repr__(self):
        return 'HAngles'
HAngles = HAngles()
96
97
98
99
100
101
102
103
104
105

# A map of functions to parse elements of the XML file.

parsers = {}

class ForceField(object):
    """A ForceField constructs OpenMM System objects based on a Topology."""

    def __init__(self, *files):
        """Load one or more XML files and create a ForceField object based on them.
Justin MacCallum's avatar
Justin MacCallum committed
106

Robert McGibbon's avatar
Robert McGibbon committed
107
108
109
110
111
112
113
114
        Parameters
        ----------
        files : list
            A list of XML files defining the force field.  Each entry may
            be an absolute file path, a path relative to the current working
            directory, a path relative to this module's data subdirectory
            (for built in force fields), or an open file-like object with a
            read() method from which the forcefield XML data can be loaded.
115
116
117
        """
        self._atomTypes = {}
        self._templates = {}
118
        self._templateSignatures = {None:[]}
119
        self._atomClasses = {'':set()}
120
        self._forces = []
121
        self._scripts = []
122
        self._templateGenerators = []
123
        self.loadFile(files)
124

125
    def loadFile(self, files):
126
        """Load an XML file and add the definitions from it to this ForceField.
127

Robert McGibbon's avatar
Robert McGibbon committed
128
129
        Parameters
        ----------
130
131
132
        files : string or file or tuple
            An XML file or tuple of XML files containing force field definitions.
            Each entry may be either an absolute file path, a path relative to the current working
Robert McGibbon's avatar
Robert McGibbon committed
133
134
135
            directory, a path relative to this module's data subdirectory (for
            built in force fields), or an open file-like object with a read()
            method from which the forcefield XML data can be loaded.
peastman's avatar
peastman committed
136
        """
137

138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
        if not isinstance(files, tuple):
            files = (files,)

        trees = []

        for file in files:
            try:
                # this handles either filenames or open file-like objects
                tree = etree.parse(file)
            except IOError:
                tree = etree.parse(os.path.join(os.path.dirname(__file__), 'data', file))
            except Exception as e:
                # Fail with an error message about which file could not be read.
                # TODO: Also handle case where fallback to 'data' directory encounters problems,
                # but this is much less worrisome because we control those files.
                msg  = str(e) + '\n'
                if hasattr(file, 'name'):
                    filename = file.name
                else:
                    filename = str(file)
                msg += "ForceField.loadFile() encountered an error reading file '%s'\n" % filename
                raise Exception(msg)

            trees.append(tree)

peastman's avatar
peastman committed
163
164
165

        # Load the atom types.

166
167
168
169
        for tree in trees:
            if tree.getroot().find('AtomTypes') is not None:
                for type in tree.getroot().find('AtomTypes').findall('Type'):
                    self.registerAtomType(type.attrib)
peastman's avatar
peastman committed
170
171
172

        # Load the residue templates.

173
174
175
176
177
        for tree in trees:
            if tree.getroot().find('Residues') is not None:
                for residue in tree.getroot().find('Residues').findall('Residue'):
                    resName = residue.attrib['name']
                    template = ForceField._TemplateData(resName)
178
179
                    if 'overload' in residue.attrib:
                        template.overloadLevel = int(residue.attrib['overload'])
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
                    atomIndices = {}
                    for atom in residue.findall('Atom'):
                        params = {}
                        for key in atom.attrib:
                            if key not in ('name', 'type'):
                                params[key] = _convertParameterToNumber(atom.attrib[key])
                        atomName = atom.attrib['name']
                        if atomName in atomIndices:
                            raise ValueError('Residue '+resName+' contains multiple atoms named '+atomName)
                        atomIndices[atomName] = len(template.atoms)
                        typeName = atom.attrib['type']
                        template.atoms.append(ForceField._TemplateAtomData(atomName, typeName, self._atomTypes[typeName].element, params))
                    for site in residue.findall('VirtualSite'):
                        template.virtualSites.append(ForceField._VirtualSiteData(site, atomIndices))
                    for bond in residue.findall('Bond'):
                        if 'atomName1' in bond.attrib:
                            template.addBondByName(bond.attrib['atomName1'], bond.attrib['atomName2'])
                        else:
                            template.addBond(int(bond.attrib['from']), int(bond.attrib['to']))
                    for bond in residue.findall('ExternalBond'):
                        if 'atomName' in bond.attrib:
                            template.addExternalBondByName(bond.attrib['atomName'])
                        else:
                            template.addExternalBond(int(bond.attrib['from']))
                    self.registerResidueTemplate(template)
peastman's avatar
peastman committed
205
206
207

        # Load force definitions

208
209
210
211
        for tree in trees:
            for child in tree.getroot():
                if child.tag in parsers:
                    parsers[child.tag](child, self)
peastman's avatar
peastman committed
212
213
214

        # Load scripts

215
216
217
        for tree in trees:
            for node in tree.getroot().findall('Script'):
                self.registerScript(node.text)
218

219
220
221
    def getGenerators(self):
        """Get the list of all registered generators."""
        return self._forces
222

223
224
225
    def registerGenerator(self, generator):
        """Register a new generator."""
        self._forces.append(generator)
226

227
228
229
230
231
232
233
234
235
236
237
238
    def registerAtomType(self, parameters):
        """Register a new atom type."""
        name = parameters['name']
        if name in self._atomTypes:
            raise ValueError('Found multiple definitions for atom type: '+name)
        atomClass = parameters['class']
        mass = _convertParameterToNumber(parameters['mass'])
        element = None
        if 'element' in parameters:
            element = parameters['element']
            if not isinstance(element, elem.Element):
                element = elem.get_by_symbol(element)
239
        self._atomTypes[name] = ForceField._AtomType(name, atomClass, mass, element)
240
241
242
243
244
245
246
        if atomClass in self._atomClasses:
            typeSet = self._atomClasses[atomClass]
        else:
            typeSet = set()
            self._atomClasses[atomClass] = typeSet
        typeSet.add(name)
        self._atomClasses[''].add(name)
247

248
249
250
251
252
    def registerResidueTemplate(self, template):
        """Register a new residue template."""
        self._templates[template.name] = template
        signature = _createResidueSignature([atom.element for atom in template.atoms])
        if signature in self._templateSignatures:
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
            registered = False
            for regtemplate in self._templateSignatures[signature]:
                if regtemplate.name == template.name:
                    if regtemplate.overloadLevel > template.overloadLevel:
                        # ok to break - this is done every time a template is
                        # registered so there can only be one already existing
                        # with same name at a time
                        registered = True
                        break
                    elif regtemplate.overloadLevel < template.overloadLevel:
                        self._templateSignatures[signature].remove(regtemplate)
                        self._templateSignatures[signature].append(template)
                        registered = True
                    else:
                        raise Exception('Residue template %s with the same overloadLevel %d already exists.' %
                                         (template.name, template.overloadLevel)
                                         )
            if not registered:
                self._templateSignatures[signature].append(template)
272
273
        else:
            self._templateSignatures[signature] = [template]
274

275
276
277
    def registerScript(self, script):
        """Register a new script to be executed after building the System."""
        self._scripts.append(script)
278

John Chodera (MSKCC)'s avatar
John Chodera (MSKCC) committed
279
    def registerTemplateGenerator(self, generator):
280
281
282
283
        """Register a residue template generator that can be used to parameterize residues that do not match existing forcefield templates.

        This functionality can be used to add handlers to parameterize small molecules or unnatural/modified residues.

John Chodera (MSKCC)'s avatar
John Chodera (MSKCC) committed
284
285
        .. CAUTION:: This method is experimental, and its API is subject to change.

286
287
        Parameters
        ----------
John Chodera (MSKCC)'s avatar
John Chodera (MSKCC) committed
288
        generator : function
289
290
            A function that will be called when a residue is encountered that does not match an existing forcefield template.

John Chodera (MSKCC)'s avatar
John Chodera (MSKCC) committed
291
        When a residue without a template is encountered, the `generator` function is called with:
292

John Chodera (MSKCC)'s avatar
John Chodera (MSKCC) committed
293
294
        ::
           success = generator(forcefield, residue)
295
296
        ```

John Chodera (MSKCC)'s avatar
John Chodera (MSKCC) committed
297
298
299
300
301
302
303
304
305
306
        where `forcefield` is the calling `ForceField` object and `residue` is a simtk.openmm.app.topology.Residue object.

        `generator` must conform to the following API:
        ::
          Parameters
           ----------
           forcefield : simtk.openmm.app.ForceField
               The ForceField object to which residue templates and/or parameters are to be added.
           residue : simtk.openmm.app.Topology.Residue
               The residue topology for which a template is to be generated.
307

John Chodera (MSKCC)'s avatar
John Chodera (MSKCC) committed
308
309
310
311
312
           Returns
           -------
           success : bool
               If the generator is able to successfully parameterize the residue, `True` is returned.
               If the generator cannot parameterize the residue, it should return `False` and not modify `forcefield`.
313

John Chodera (MSKCC)'s avatar
John Chodera (MSKCC) committed
314
315
316
317
318
           The generator should either register a residue template directly with `forcefield.registerResidueTemplate(template)`
           or it should call `forcefield.loadFile(file)` to load residue definitions from an ffxml file.

           It can also use the `ForceField` programmatic API to add additional atom types (via `forcefield.registerAtomType(parameters)`)
           or additional parameters.
319
320

        """
321
        self._templateGenerators.append(generator)
322

323
    def _findAtomTypes(self, attrib, num):
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
        """Parse the attributes on an XML tag to find the set of atom types for each atom it involves.

        Parameters
        ----------
        attrib : dict of attributes
            The dictionary of attributes for an XML parameter tag.
        num : int
            The number of atom specifiers (e.g. 'class1' through 'class4') to extract.

        Returns
        -------
        types : list
            A list of atom types that match.

        """
339
340
341
342
343
344
345
        types = []
        for i in range(num):
            if num == 1:
                suffix = ''
            else:
                suffix = str(i+1)
            classAttrib = 'class'+suffix
346
            typeAttrib = 'type'+suffix
347
            if classAttrib in attrib:
348
                if typeAttrib in attrib:
349
                    raise ValueError('Specified both a type and a class for the same atom: '+str(attrib))
350
                if attrib[classAttrib] not in self._atomClasses:
peastman's avatar
peastman committed
351
352
353
                    types.append(None) # Unknown atom class
                else:
                    types.append(self._atomClasses[attrib[classAttrib]])
354
355
            elif typeAttrib in attrib:
                if attrib[typeAttrib] == '':
Rafal P. Wiewiora's avatar
Rafal P. Wiewiora committed
356
                    types.append(self._atomClasses[''])
357
                elif attrib[typeAttrib] not in self._atomTypes:
peastman's avatar
peastman committed
358
359
360
                    types.append(None) # Unknown atom type
                else:
                    types.append([attrib[typeAttrib]])
361
362
            else:
                types.append(None) # Unknown atom type
363
364
        return types

365
    def _parseTorsion(self, attrib):
366
        """Parse the node defining a torsion."""
367
        types = self._findAtomTypes(attrib, 4)
peastman's avatar
peastman committed
368
        if None in types:
369
370
371
372
373
            return None
        torsion = PeriodicTorsion(types)
        index = 1
        while 'phase%d'%index in attrib:
            torsion.periodicity.append(int(attrib['periodicity%d'%index]))
374
375
            torsion.phase.append(_convertParameterToNumber(attrib['phase%d'%index]))
            torsion.k.append(_convertParameterToNumber(attrib['k%d'%index]))
376
            index += 1
Justin MacCallum's avatar
Justin MacCallum committed
377
378
        return torsion

379
    class _SystemData(object):
380
381
382
        """Inner class used to encapsulate data about the system being created."""
        def __init__(self):
            self.atomType = {}
383
            self.atomParameters = {}
384
            self.atoms = []
385
            self.excludeAtomWith = []
386
            self.virtualSites = {}
387
388
389
390
391
392
            self.bonds = []
            self.angles = []
            self.propers = []
            self.impropers = []
            self.atomBonds = []
            self.isAngleConstrained = []
393
394
395
396
397
398
399
400
401
402
403
            self.constraints = {}

        def addConstraint(self, system, atom1, atom2, distance):
            """Add a constraint to the system, avoiding duplicate constraints."""
            key = (min(atom1, atom2), max(atom1, atom2))
            if key in self.constraints:
                if self.constraints(key) != distance:
                    raise ValueError('Two constraints were specified between atoms %d and %d with different distances' % (atom1, atom2))
            else:
                self.constraints[key] = distance
                system.addConstraint(atom1, atom2, distance)
404

405
    class _TemplateData(object):
406
407
408
409
        """Inner class used to encapsulate data about a residue template definition."""
        def __init__(self, name):
            self.name = name
            self.atoms = []
410
            self.virtualSites = []
411
412
            self.bonds = []
            self.externalBonds = []
413
            self.overloadLevel = 0
414

415
416
417
418
419
420
421
        def getAtomIndexByName(self, atom_name):
            """Look up an atom index by atom name, providing a helpful error message if not found."""
            for (index, atom) in enumerate(self.atoms):
                if atom.name == atom_name:
                    return index

            # Provide a helpful error message if atom name not found.
John Chodera (MSKCC)'s avatar
John Chodera (MSKCC) committed
422
423
            msg =  "Atom name '%s' not found in residue template '%s'.\n" % (atom_name, self.name)
            msg += "Possible atom names are: %s" % str(atomIndices.keys())
424
425
            raise ValueError(msg)

426
        def addBond(self, atom1, atom2):
John Chodera (MSKCC)'s avatar
John Chodera (MSKCC) committed
427
            """Add a bond between two atoms in a template given their indices in the template."""
428
429
430
            self.bonds.append((atom1, atom2))
            self.atoms[atom1].bondedTo.append(atom2)
            self.atoms[atom2].bondedTo.append(atom1)
431

432
        def addBondByName(self, atom1_name, atom2_name):
John Chodera (MSKCC)'s avatar
John Chodera (MSKCC) committed
433
            """Add a bond between two atoms in a template given their atom names."""
434
435
436
437
438
            atom1 = self.getAtomIndexByName(atom1_name)
            atom2 = self.getAtomIndexByName(atom2_name)
            self.addBond(atom1, atom2)

        def addExternalBond(self, atom_index):
John Chodera (MSKCC)'s avatar
John Chodera (MSKCC) committed
439
            """Designate that an atom in a residue template has an external bond, using atom index within template."""
440
441
442
443
            self.externalBonds.append(atom_index)
            self.atoms[atom_index].externalBonds += 1

        def addExternalBondByName(self, atom_name):
John Chodera (MSKCC)'s avatar
John Chodera (MSKCC) committed
444
            """Designate that an atom in a residue template has an external bond, using atom name within template."""
445
446
447
            atom = self.getAtomIndexByName(atom_name)
            self.addExternalBond(atom)

448
    class _TemplateAtomData(object):
449
        """Inner class used to encapsulate data about an atom in a residue template definition."""
450
        def __init__(self, name, type, element, parameters={}):
451
452
453
            self.name = name
            self.type = type
            self.element = element
454
            self.parameters = parameters
455
456
457
            self.bondedTo = []
            self.externalBonds = 0

458
    class _BondData(object):
459
460
461
462
463
464
        """Inner class used to encapsulate data about a bond."""
        def __init__(self, atom1, atom2):
            self.atom1 = atom1
            self.atom2 = atom2
            self.isConstrained = False
            self.length = 0.0
Justin MacCallum's avatar
Justin MacCallum committed
465

466
    class _VirtualSiteData(object):
467
        """Inner class used to encapsulate data about a virtual site."""
468
        def __init__(self, node, atomIndices):
469
470
471
            attrib = node.attrib
            self.type = attrib['type']
            if self.type == 'average2':
472
                numAtoms = 2
473
474
                self.weights = [float(attrib['weight1']), float(attrib['weight2'])]
            elif self.type == 'average3':
475
                numAtoms = 3
476
477
                self.weights = [float(attrib['weight1']), float(attrib['weight2']), float(attrib['weight3'])]
            elif self.type == 'outOfPlane':
478
                numAtoms = 3
479
                self.weights = [float(attrib['weight12']), float(attrib['weight13']), float(attrib['weightCross'])]
480
            elif self.type == 'localCoords':
481
                numAtoms = 3
482
483
484
485
                self.originWeights = [float(attrib['wo1']), float(attrib['wo2']), float(attrib['wo3'])]
                self.xWeights = [float(attrib['wx1']), float(attrib['wx2']), float(attrib['wx3'])]
                self.yWeights = [float(attrib['wy1']), float(attrib['wy2']), float(attrib['wy3'])]
                self.localPos = [float(attrib['p1']), float(attrib['p2']), float(attrib['p3'])]
486
487
            else:
                raise ValueError('Unknown virtual site type: %s' % self.type)
488
489
490
491
492
493
            if 'siteName' in attrib:
                self.index = atomIndices[attrib['siteName']]
                self.atoms = [atomIndices[attrib['atomName%d'%(i+1)]] for i in range(numAtoms)]
            else:
                self.index = int(attrib['index'])
                self.atoms = [int(attrib['atom%d'%(i+1)]) for i in range(numAtoms)]
494
495
496
497
            if 'excludeWith' in attrib:
                self.excludeWith = int(attrib['excludeWith'])
            else:
                self.excludeWith = self.atoms[0]
498

499
    class _AtomType(object):
500
501
502
503
504
505
506
        """Inner class used to record atom types and associated properties."""
        def __init__(self, name, atomClass, mass, element):
            self.name = name
            self.atomClass = atomClass
            self.mass = mass
            self.element = element

507
    class _AtomTypeParameters(object):
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
        """Inner class used to record parameter values for atom types."""
        def __init__(self, forcefield, forceName, atomTag, paramNames):
            self.ff = forcefield
            self.forceName = forceName
            self.atomTag = atomTag
            self.paramNames = paramNames
            self.paramsForType = {}
            self.extraParamsForType = {}

        def registerAtom(self, parameters, expectedParams=None):
            if expectedParams is None:
                expectedParams = self.paramNames
            types = self.ff._findAtomTypes(parameters, 1)
            if None not in types:
                values = {}
                extraValues = {}
                for key in parameters:
                    if key in expectedParams:
                        values[key] = _convertParameterToNumber(parameters[key])
                    else:
                        extraValues[key] = parameters[key]
                if len(values) < len(expectedParams):
                    for key in expectedParams:
                        if key not in values:
                            raise ValueError('%s: No value specified for "%s"' % (self.forceName, key))
                for t in types[0]:
                    self.paramsForType[t] = values
                    self.extraParamsForType[t] = extraValues

        def parseDefinitions(self, element):
            """"Load the definitions from an XML element."""
            expectedParams = list(self.paramNames)
            excludedParams = [node.attrib['name'] for node in element.findall('UseAttributeFromResidue')]
            for param in excludedParams:
                if param not in expectedParams:
                    raise ValueError('%s: <UseAttributeFromResidue> specified an invalid attribute: %s' % (self.forceName, param))
                expectedParams.remove(param)
            for atom in element.findall(self.atomTag):
                for param in excludedParams:
                    if param in atom.attrib:
                        raise ValueError('%s: The attribute "%s" appeared in both <%s> and <UseAttributeFromResidue> tags' % (self.forceName, param, self.atomTag))
                self.registerAtom(atom.attrib, expectedParams)

        def getAtomParameters(self, atom, data):
            """Get the parameter values for a particular atom."""
            t = data.atomType[atom]
            p = data.atomParameters[atom]
            if t in self.paramsForType:
                values = self.paramsForType[t]
                result = [None]*len(self.paramNames)
                for i, name in enumerate(self.paramNames):
                    if name in values:
                        result[i] = values[name]
                    elif name in p:
                        result[i] = p[name]
                    else:
                        raise ValueError('%s: No value specified for "%s"' % (self.forceName, name))
                return result
            else:
                raise ValueError('%s: No parameters defined for atom type %s' % (self.forceName, t))

        def getExtraParameters(self, atom, data):
            """Get extra parameter values for an atom that appeared in the <Atom> tag but were not included in paramNames."""
            t = data.atomType[atom]
            if t in self.paramsForType:
                return self.extraParamsForType[t]
            else:
                raise ValueError('%s: No parameters defined for atom type %s' % (self.forceName, t))


578
    def _getResidueTemplateMatches(self, res, bondedToAtom):
579
580
581
582
583
584
        """Return the residue template matches, or None if none are found.

        Parameters
        ----------
        res : Topology.Residue
            The residue for which template matches are to be retrieved.
585
586
        bondedToAtom : list of set of int
            bondedToAtom[i] is the set of atoms bonded to atom index i
587
588
589
590
591
592
593
594
595
596
597
598
599
600

        Returns
        -------
        template : _ForceFieldTemplate
            The matching forcefield residue template, or None if no matches are found.
        matches : list
            a list specifying which atom of the template each atom of the residue
            corresponds to, or None if it does not match the template

        """
        template = None
        matches = None
        signature = _createResidueSignature([atom.element for atom in res.atoms()])
        if signature in self._templateSignatures:
601
            allMatches = []
602
            for t in self._templateSignatures[signature]:
603
604
605
606
607
608
609
610
                match = _matchResidue(res, t, bondedToAtom)
                if match is not None:
                    allMatches.append((t, match))
            if len(allMatches) == 1:
                template = allMatches[0][0]
                matches = allMatches[0][1]
            elif len(allMatches) > 1:
                raise Exception('Multiple matching templates found for residue %d (%s).' % (res.index+1, res.name))
611
612
        return [template, matches]

613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
    def _buildBondedToAtomList(self, topology):
        """Build a list of which atom indices are bonded to each atom.

        Parameters
        ----------
        topology : Topology
            The Topology whose bonds are to be indexed.

        Returns
        -------
        bondedToAtom : list of set of int
            bondedToAtom[index] is the set of atom indices bonded to atom `index`

        """
        bondedToAtom = []
        for atom in topology.atoms():
            bondedToAtom.append(set())
630
631
632
        for (atom1, atom2) in topology.bonds():
            bondedToAtom[atom1.index].add(atom2.index)
            bondedToAtom[atom2.index].add(atom1.index)
633
        return bondedToAtom
634

635
636
637
    def getUnmatchedResidues(self, topology):
        """Return a list of Residue objects from specified topology for which no forcefield templates are available.

638
639
        .. CAUTION:: This method is experimental, and its API is subject to change.

640
641
642
        Parameters
        ----------
        topology : Topology
643
            The Topology whose residues are to be checked against the forcefield residue templates.
644
645
646
647

        Returns
        -------
        unmatched_residues : list of Residue
648
            List of Residue objects from `topology` for which no forcefield residue templates are available.
649
650
651
652
653
            Note that multiple instances of the same residue appearing at different points in the topology may be returned.

        This method may be of use in generating missing residue templates or diagnosing parameterization failures.
        """
        # Find the template matching each residue, compiling a list of residues for which no templates are available.
654
        bondedToAtom = self._buildBondedToAtomList(topology)
655
        unmatched_residues = list() # list of unmatched residues
656
657
658
659
660
661
        for res in topology.residues():
            # Attempt to match one of the existing templates.
            [template, matches] = self._getResidueTemplateMatches(res, bondedToAtom)
            if matches is None:
                # No existing templates match.
                unmatched_residues.append(res)
662
663
664

        return unmatched_residues

665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
    def getMatchingTemplates(self, topology):
        """Return a list of forcefield residue templates matching residues in the specified topology.

        .. CAUTION:: This method is experimental, and its API is subject to change.

        Parameters
        ----------
        topology : Topology
            The Topology whose residues are to be checked against the forcefield residue templates.

        Returns
        -------
        templates : list of _TemplateData
            List of forcefield residue templates corresponding to residues in the topology.
            templates[index] is template corresponding to residue `index` in topology.residues()

        This method may be of use in debugging issues related to parameter assignment.
        """
        # Find the template matching each residue, compiling a list of residues for which no templates are available.
        bondedToAtom = self._buildBondedToAtomList(topology)
        templates = list() # list of templates matching the corresponding residues
        for res in topology.residues():
            # Attempt to match one of the existing templates.
            [template, matches] = self._getResidueTemplateMatches(res, bondedToAtom)
            # Raise an exception if we have found no templates that match.
            if matches is None:
                raise ValueError('No template found for residue %d (%s).  %s' % (res.index+1, res.name, _findMatchErrors(self, res)))
            else:
                templates.append(template)

        return templates

697
698
    def generateTemplatesForUnmatchedResidues(self, topology):
        """Generate forcefield residue templates for residues in specified topology for which no forcefield templates are available.
699

700
701
        .. CAUTION:: This method is experimental, and its API is subject to change.

702
703
704
        Parameters
        ----------
        topology : Topology
705
            The Topology whose residues are to be checked against the forcefield residue templates.
706
707
708

        Returns
        -------
709
710
711
712
713
714
        templates : list of _TemplateData
            List of forcefield residue templates corresponding to residues in `topology` for which no forcefield templates are currently available.
            Atom types will be set to `None`, but template name, atom names, elements, and connectivity will be taken from corresponding Residue objects.
        residues : list of Residue
            List of Residue objects that were used to generate the templates.
            `residues[index]` is the Residue that was used to generate the template `templates[index]`
715
716
717
718
719

        """
        # Get a non-unique list of unmatched residues.
        unmatched_residues = self.getUnmatchedResidues(topology)
        # Generate a unique list of unmatched residues by comparing fingerprints.
720
        bondedToAtom = self._buildBondedToAtomList(topology)
721
722
        unique_unmatched_residues = list() # list of unique unmatched Residue objects from topology
        templates = list() # corresponding _TemplateData templates
723
724
725
        signatures = set()
        for residue in unmatched_residues:
            signature = _createResidueSignature([ atom.element for atom in residue.atoms() ])
726
            template = _createResidueTemplate(residue)
727
728
729
730
731
732
733
734
735
736
737
            is_unique = True
            if signature in signatures:
                # Signature is the same as an existing residue; check connectivity.
                for check_residue in unique_unmatched_residues:
                    matches = _matchResidue(check_residue, template, bondedToAtom)
                    if matches is not None:
                        is_unique = False
            if is_unique:
                # Residue is unique.
                unique_unmatched_residues.append(residue)
                signatures.add(signature)
738
                templates.append(template)
739

740
        return [templates, unique_unmatched_residues]
741

742
    def createSystem(self, topology, nonbondedMethod=NoCutoff, nonbondedCutoff=1.0*unit.nanometer,
743
                     constraints=None, rigidWater=True, removeCMMotion=True, hydrogenMass=None, residueTemplates=dict(), **args):
744
        """Construct an OpenMM System representing a Topology with this force field.
Justin MacCallum's avatar
Justin MacCallum committed
745

Robert McGibbon's avatar
Robert McGibbon committed
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
        Parameters
        ----------
        topology : Topology
            The Topology for which to create a System
        nonbondedMethod : object=NoCutoff
            The method to use for nonbonded interactions.  Allowed values are
            NoCutoff, CutoffNonPeriodic, CutoffPeriodic, Ewald, or PME.
        nonbondedCutoff : distance=1*nanometer
            The cutoff distance to use for nonbonded interactions
        constraints : object=None
            Specifies which bonds and angles should be implemented with constraints.
            Allowed values are None, HBonds, AllBonds, or HAngles.
        rigidWater : boolean=True
            If true, water molecules will be fully rigid regardless of the value
            passed for the constraints argument
        removeCMMotion : boolean=True
            If true, a CMMotionRemover will be added to the System
        hydrogenMass : mass=None
            The mass to use for hydrogen atoms bound to heavy atoms.  Any mass
            added to a hydrogen is subtracted from the heavy atom to keep
            their total mass the same.
767
768
769
770
771
772
773
        residueTemplates : dict=dict()
           Key: Topology Residue object
           Value: string, name of _TemplateData residue template object to use for
                  (Key) residue
           This allows user to specify which template to apply to particular Residues
           in the event that multiple matching templates are available (e.g Fe2+ and Fe3+
           templates in the ForceField for a monoatomic iron ion in the topology).
Robert McGibbon's avatar
Robert McGibbon committed
774
775
776
777
778
779
780
781
782
        args
             Arbitrary additional keyword arguments may also be specified.
             This allows extra parameters to be specified that are specific to
             particular force fields.

        Returns
        -------
        system
            the newly created System
783
784
        """
        data = ForceField._SystemData()
785
        data.atoms = list(topology.atoms())
786
787
        for atom in data.atoms:
            data.excludeAtomWith.append([])
788
789

        # Make a list of all bonds
Justin MacCallum's avatar
Justin MacCallum committed
790

791
        for bond in topology.bonds():
792
            data.bonds.append(ForceField._BondData(bond[0].index, bond[1].index))
793
794

        # Record which atoms are bonded to each other atom
Justin MacCallum's avatar
Justin MacCallum committed
795

796
797
798
799
800
801
802
803
804
805
806
807
        bondedToAtom = []
        for i in range(len(data.atoms)):
            bondedToAtom.append(set())
            data.atomBonds.append([])
        for i in range(len(data.bonds)):
            bond = data.bonds[i]
            bondedToAtom[bond.atom1].add(bond.atom2)
            bondedToAtom[bond.atom2].add(bond.atom1)
            data.atomBonds[bond.atom1].append(i)
            data.atomBonds[bond.atom2].append(i)

        # Find the template matching each residue and assign atom types.
John Chodera (MSKCC)'s avatar
John Chodera (MSKCC) committed
808
        # If no templates are found, attempt to use residue template generators to create new templates (and potentially atom types/parameters).
Justin MacCallum's avatar
Justin MacCallum committed
809

810
811
        for chain in topology.chains():
            for res in chain.residues():
812
813
814
815
816
817
818
819
820
                if res in residueTemplates:
                    tname = residueTemplates[res]
                    template = self._templates[tname]
                    matches = _matchResidue(res, template, bondedToAtom)
                    if matches is None:
                        raise Exception('User-supplied template %s does not match the residue %d (%s)' % (tname, res.index+1, res.name))
                else:
                    # Attempt to match one of the existing templates.
                    [template, matches] = self._getResidueTemplateMatches(res, bondedToAtom)
821
822
                if matches is None:
                    # No existing templates match.  Try any registered residue template generators.
823
                    for generator in self._templateGenerators:
824
                        if generator(self, res):
825
                            # This generator has registered a new residue template that should match.
826
                            [template, matches] = self._getResidueTemplateMatches(res, bondedToAtom)
827
828
829
830
831
832
833
834
                            if matches is None:
                                # Something went wrong because the generated template does not match the residue signature.
                                raise Exception('The residue handler %s indicated it had correctly parameterized residue %s, but the generated template did not match the residue signature.' % (generator.__class__.__name__, str(res)))
                            else:
                                # We successfully generated a residue template.  Break out of the for loop.
                                break

                # Raise an exception if we have found no templates that match.
835
                if matches is None:
836
                    raise ValueError('No template found for residue %d (%s).  %s' % (res.index+1, res.name, _findMatchErrors(self, res)))
837
838

                # Store parameters for the matched residue template.
839
                matchAtoms = dict(zip(matches, res.atoms()))
840
841
                for atom, match in zip(res.atoms(), matches):
                    data.atomType[atom] = template.atoms[match].type
842
                    data.atomParameters[atom] = template.atoms[match].parameters
843
844
                    for site in template.virtualSites:
                        if match == site.index:
845
                            data.virtualSites[atom] = (site, [matchAtoms[i].index for i in site.atoms], matchAtoms[site.excludeWith].index)
846
847

        # Create the System and add atoms
Justin MacCallum's avatar
Justin MacCallum committed
848

849
850
        sys = mm.System()
        for atom in topology.atoms():
John Chodera (MSKCC)'s avatar
John Chodera (MSKCC) committed
851
            # Look up the atom type name, returning a helpful error message if it cannot be found.
852
853
854
855
            if atom not in data.atomType:
                raise Exception("Could not identify atom type for atom '%s'." % str(atom))
            typename = data.atomType[atom]

John Chodera (MSKCC)'s avatar
John Chodera (MSKCC) committed
856
            # Look up the type name in the list of registered atom types, returning a helpful error message if it cannot be found.
857
858
859
860
            if typename not in self._atomTypes:
                msg  = "Could not find typename '%s' for atom '%s' in list of known atom types.\n" % (typename, str(atom))
                msg += "Known atom types are: %s" % str(self._atomTypes.keys())
                raise Exception(msg)
John Chodera (MSKCC)'s avatar
John Chodera (MSKCC) committed
861
862

            # Add the particle to the OpenMM system.
863
            mass = self._atomTypes[typename].mass
864
            sys.addParticle(mass)
865

866
        # Adjust hydrogen masses if requested.
867

868
        if hydrogenMass is not None:
869
870
            if not unit.is_quantity(hydrogenMass):
                hydrogenMass *= unit.dalton
871
872
873
874
875
876
877
            for atom1, atom2 in topology.bonds():
                if atom1.element == elem.hydrogen:
                    (atom1, atom2) = (atom2, atom1)
                if atom2.element == elem.hydrogen and atom1.element not in (elem.hydrogen, None):
                    transferMass = hydrogenMass-sys.getParticleMass(atom2.index)
                    sys.setParticleMass(atom2.index, hydrogenMass)
                    sys.setParticleMass(atom1.index, sys.getParticleMass(atom1.index)-transferMass)
Justin MacCallum's avatar
Justin MacCallum committed
878

879
        # Set periodic boundary conditions.
Justin MacCallum's avatar
Justin MacCallum committed
880

881
882
883
        boxVectors = topology.getPeriodicBoxVectors()
        if boxVectors is not None:
            sys.setDefaultPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2])
John Chodera (MSKCC)'s avatar
John Chodera (MSKCC) committed
884
        elif nonbondedMethod not in [NoCutoff, CutoffNonPeriodic]:
885
886
887
            raise ValueError('Requested periodic boundary conditions for a Topology that does not specify periodic box dimensions')

        # Make a list of all unique angles
Justin MacCallum's avatar
Justin MacCallum committed
888

889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
        uniqueAngles = set()
        for bond in data.bonds:
            for atom in bondedToAtom[bond.atom1]:
                if atom != bond.atom2:
                    if atom < bond.atom2:
                        uniqueAngles.add((atom, bond.atom1, bond.atom2))
                    else:
                        uniqueAngles.add((bond.atom2, bond.atom1, atom))
            for atom in bondedToAtom[bond.atom2]:
                if atom != bond.atom1:
                    if atom > bond.atom1:
                        uniqueAngles.add((bond.atom1, bond.atom2, atom))
                    else:
                        uniqueAngles.add((atom, bond.atom2, bond.atom1))
        data.angles = sorted(list(uniqueAngles))
Justin MacCallum's avatar
Justin MacCallum committed
904

905
        # Make a list of all unique proper torsions
Justin MacCallum's avatar
Justin MacCallum committed
906

907
908
909
        uniquePropers = set()
        for angle in data.angles:
            for atom in bondedToAtom[angle[0]]:
pgrinaway's avatar
pgrinaway committed
910
                if atom not in angle:
911
912
913
914
915
                    if atom < angle[2]:
                        uniquePropers.add((atom, angle[0], angle[1], angle[2]))
                    else:
                        uniquePropers.add((angle[2], angle[1], angle[0], atom))
            for atom in bondedToAtom[angle[2]]:
pgrinaway's avatar
pgrinaway committed
916
                if atom not in angle:
917
918
919
920
921
                    if atom > angle[0]:
                        uniquePropers.add((angle[0], angle[1], angle[2], atom))
                    else:
                        uniquePropers.add((atom, angle[2], angle[1], angle[0]))
        data.propers = sorted(list(uniquePropers))
Justin MacCallum's avatar
Justin MacCallum committed
922

923
        # Make a list of all unique improper torsions
Justin MacCallum's avatar
Justin MacCallum committed
924

925
926
927
928
929
        for atom in range(len(bondedToAtom)):
            bondedTo = bondedToAtom[atom]
            if len(bondedTo) > 2:
                for subset in itertools.combinations(bondedTo, 3):
                    data.impropers.append((atom, subset[0], subset[1], subset[2]))
Justin MacCallum's avatar
Justin MacCallum committed
930

931
        # Identify bonds that should be implemented with constraints
Justin MacCallum's avatar
Justin MacCallum committed
932

933
934
935
936
937
938
939
940
941
942
943
944
945
946
        if constraints == AllBonds or constraints == HAngles:
            for bond in data.bonds:
                bond.isConstrained = True
        elif constraints == HBonds:
            for bond in data.bonds:
                atom1 = data.atoms[bond.atom1]
                atom2 = data.atoms[bond.atom2]
                bond.isConstrained = atom1.name.startswith('H') or atom2.name.startswith('H')
        if rigidWater:
            for bond in data.bonds:
                atom1 = data.atoms[bond.atom1]
                atom2 = data.atoms[bond.atom2]
                if atom1.residue.name == 'HOH' and atom2.residue.name == 'HOH':
                    bond.isConstrained = True
Justin MacCallum's avatar
Justin MacCallum committed
947

948
        # Identify angles that should be implemented with constraints
Justin MacCallum's avatar
Justin MacCallum committed
949

950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
        if constraints == HAngles:
            for angle in data.angles:
                atom1 = data.atoms[angle[0]]
                atom2 = data.atoms[angle[1]]
                atom3 = data.atoms[angle[2]]
                numH = 0
                if atom1.name.startswith('H'):
                    numH += 1
                if atom3.name.startswith('H'):
                    numH += 1
                data.isAngleConstrained.append(numH == 2 or (numH == 1 and atom2.name.startswith('O')))
        else:
            data.isAngleConstrained = len(data.angles)*[False]
        if rigidWater:
            for i in range(len(data.angles)):
                angle = data.angles[i]
                atom1 = data.atoms[angle[0]]
                atom2 = data.atoms[angle[1]]
                atom3 = data.atoms[angle[2]]
                if atom1.residue.name == 'HOH' and atom2.residue.name == 'HOH' and atom3.residue.name == 'HOH':
                    data.isAngleConstrained[i] = True
Justin MacCallum's avatar
Justin MacCallum committed
971

972
        # Add virtual sites
Justin MacCallum's avatar
Justin MacCallum committed
973

974
        for atom in data.virtualSites:
975
            (site, atoms, excludeWith) = data.virtualSites[atom]
976
            index = atom.index
977
            data.excludeAtomWith[excludeWith].append(index)
978
            if site.type == 'average2':
979
                sys.setVirtualSite(index, mm.TwoParticleAverageSite(atoms[0], atoms[1], site.weights[0], site.weights[1]))
980
            elif site.type == 'average3':
981
                sys.setVirtualSite(index, mm.ThreeParticleAverageSite(atoms[0], atoms[1], atoms[2], site.weights[0], site.weights[1], site.weights[2]))
982
            elif site.type == 'outOfPlane':
983
984
985
986
987
988
989
                sys.setVirtualSite(index, mm.OutOfPlaneSite(atoms[0], atoms[1], atoms[2], site.weights[0], site.weights[1], site.weights[2]))
            elif site.type == 'localCoords':
                sys.setVirtualSite(index, mm.LocalCoordinatesSite(atoms[0], atoms[1], atoms[2],
                                                                  mm.Vec3(site.originWeights[0], site.originWeights[1], site.originWeights[2]),
                                                                  mm.Vec3(site.xWeights[0], site.xWeights[1], site.xWeights[2]),
                                                                  mm.Vec3(site.yWeights[0], site.yWeights[1], site.yWeights[2]),
                                                                  mm.Vec3(site.localPos[0], site.localPos[1], site.localPos[2])))
Justin MacCallum's avatar
Justin MacCallum committed
990

991
        # Add forces to the System
Justin MacCallum's avatar
Justin MacCallum committed
992

993
994
        for force in self._forces:
            force.createForce(sys, data, nonbondedMethod, nonbondedCutoff, args)
995
996
        if removeCMMotion:
            sys.addForce(mm.CMMotionRemover())
Justin MacCallum's avatar
Justin MacCallum committed
997

John Chodera (MSKCC)'s avatar
John Chodera (MSKCC) committed
998
        # Let force generators do postprocessing
Justin MacCallum's avatar
Justin MacCallum committed
999

peastman's avatar
peastman committed
1000
1001
1002
        for force in self._forces:
            if 'postprocessSystem' in dir(force):
                force.postprocessSystem(sys, data, args)
Justin MacCallum's avatar
Justin MacCallum committed
1003

1004
        # Execute scripts found in the XML files.
Justin MacCallum's avatar
Justin MacCallum committed
1005

1006
        for script in self._scripts:
1007
            exec(script, locals())
1008
1009
1010
        return sys


1011
1012
def _countResidueAtoms(elements):
    """Count the number of atoms of each element in a residue."""
1013
1014
    counts = {}
    for element in elements:
1015
        if element in counts:
1016
1017
1018
            counts[element] += 1
        else:
            counts[element] = 1
1019
1020
1021
1022
1023
1024
    return counts


def _createResidueSignature(elements):
    """Create a signature for a residue based on the elements of the atoms it contains."""
    counts = _countResidueAtoms(elements)
1025
1026
    sig = []
    for c in counts:
1027
1028
        if c is not None:
            sig.append((c, counts[c]))
1029
    sig.sort(key=lambda x: -x[0].mass)
Justin MacCallum's avatar
Justin MacCallum committed
1030

1031
    # Convert it to a string.
1032
1033

    s = ''
1034
    for element, count in sig:
1035
1036
1037
        s += element.symbol+str(count)
    return s

1038
def _matchResidue(res, template, bondedToAtom):
1039
    """Determine whether a residue matches a template and return a list of corresponding atoms.
Justin MacCallum's avatar
Justin MacCallum committed
1040

Robert McGibbon's avatar
Robert McGibbon committed
1041
1042
1043
1044
1045
1046
1047
1048
1049
1050
1051
    Parameters
    ----------
    res : Residue
        The residue to check
    template : _TemplateData
        The template to compare it to
    bondedToAtom : list
        Enumerates which other atoms each atom is bonded to

    Returns
    -------
1052
1053
1054
    list
        a list specifying which atom of the template each atom of the residue
        corresponds to, or None if it does not match the template
1055
1056
    """
    atoms = list(res.atoms())
peastman's avatar
peastman committed
1057
1058
    numAtoms = len(atoms)
    if numAtoms != len(template.atoms):
1059
        return None
Justin MacCallum's avatar
Justin MacCallum committed
1060

1061
    # Translate from global to local atom indices, and record the bonds for each atom.
Justin MacCallum's avatar
Justin MacCallum committed
1062

1063
    renumberAtoms = {}
peastman's avatar
peastman committed
1064
    for i in range(numAtoms):
1065
        renumberAtoms[atoms[i].index] = i
1066
1067
1068
    bondedTo = []
    externalBonds = []
    for atom in atoms:
1069
        bonds = [renumberAtoms[x] for x in bondedToAtom[atom.index] if x in renumberAtoms]
1070
        bondedTo.append(bonds)
1071
        externalBonds.append(len([x for x in bondedToAtom[atom.index] if x not in renumberAtoms]))
1072
1073
1074
1075
1076
1077
1078
1079
1080
1081
1082
1083
1084
1085
1086
1087
1088
1089

    # For each unique combination of element and number of bonds, make sure the residue and
    # template have the same number of atoms.

    residueTypeCount = {}
    for i, atom in enumerate(atoms):
        key = (atom.element, len(bondedTo[i]), externalBonds[i])
        if key not in residueTypeCount:
            residueTypeCount[key] = 1
        residueTypeCount[key] += 1
    templateTypeCount = {}
    for i, atom in enumerate(template.atoms):
        key = (atom.element, len(atom.bondedTo), atom.externalBonds)
        if key not in templateTypeCount:
            templateTypeCount[key] = 1
        templateTypeCount[key] += 1
    if residueTypeCount != templateTypeCount:
        return None
peastman's avatar
peastman committed
1090
1091
1092
1093
1094
1095
1096
1097
1098
1099
1100
1101
1102
1103
1104
1105
1106
1107
1108
1109
1110
1111
1112
1113
1114
1115
1116
1117
1118
1119
1120
1121
1122
1123
1124
1125
1126
1127
1128
        
    # Identify template atoms that could potentially be matches for each atom.
    
    candidates = [[] for i in range(numAtoms)]
    for i in range(numAtoms):
        for j, atom in enumerate(template.atoms):
            if (atom.element is not None and atom.element != atoms[i].element) or (atom.element is None and atom.name != atoms[i].name):
                continue
            if len(atom.bondedTo) != len(bondedTo[i]):
                continue
            if atom.externalBonds != externalBonds[i]:
                continue
            candidates[i].append(j)

    # Find an optimal ordering for matching atoms.  This means 1) start with the one that has the fewest options,
    # and 2) follow with ones that are bonded to an already matched atom.
    
    searchOrder = []
    atomsToOrder = set(range(numAtoms))
    efficientAtoms = set()
    while len(atomsToOrder) > 0:
        if len(efficientAtoms) == 0:
            fewestNeighbors = numAtoms+1
            for i in atomsToOrder:
                if len(candidates[i]) < fewestNeighbors:
                    nextAtom = i
                    fewestNeighbors = len(candidates[i])
        else:
            nextAtom = efficientAtoms.pop()
        searchOrder.append(nextAtom)
        atomsToOrder.remove(nextAtom)
        for i in bondedTo[nextAtom]:
            if i in atomsToOrder:
                efficientAtoms.add(i)
    inverseSearchOrder = [0]*numAtoms
    for i in range(numAtoms):
        inverseSearchOrder[searchOrder[i]] = i
    bondedTo = [[inverseSearchOrder[bondedTo[i][j]] for j in range(len(bondedTo[i]))] for i in searchOrder]
    candidates = [candidates[i] for i in searchOrder]
1129
1130
1131

    # Recursively match atoms.

peastman's avatar
peastman committed
1132
1133
1134
1135
    matches = numAtoms*[0]
    hasMatch = numAtoms*[False]
    if _findAtomMatches(template, bondedTo, matches, hasMatch, candidates, 0):
        return [matches[inverseSearchOrder[i]] for i in range(numAtoms)]
1136
1137
1138
    return None


peastman's avatar
peastman committed
1139
1140
1141
1142
1143
1144
1145
1146
1147
1148
1149
def _getAtomMatchCandidates(template, bondedTo, matches, candidates, position):
    """Get a list of template atoms that are potential matches for the next atom."""
    for bonded in bondedTo[position]:
        if bonded < position:
            # This atom is bonded to another one for which we already have a match, so only consider
            # template atoms that *that* one is bonded to.
            return template.atoms[matches[bonded]].bondedTo
    return candidates[position]


def _findAtomMatches(template, bondedTo, matches, hasMatch, candidates, position):
1150
    """This is called recursively from inside _matchResidue() to identify matching atoms."""
peastman's avatar
peastman committed
1151
    if position == len(matches):
1152
        return True
peastman's avatar
peastman committed
1153
    for i in _getAtomMatchCandidates(template, bondedTo, matches, candidates, position):
1154
        atom = template.atoms[i]
peastman's avatar
peastman committed
1155
        if not hasMatch[i] and i in candidates[position]:
1156
            # See if the bonds for this identification are consistent
Justin MacCallum's avatar
Justin MacCallum committed
1157

1158
1159
            allBondsMatch = all((bonded > position or matches[bonded] in atom.bondedTo for bonded in bondedTo[position]))
            if allBondsMatch:
peastman's avatar
peastman committed
1160
                # This is a possible match, so try matching the rest of the residue.
Justin MacCallum's avatar
Justin MacCallum committed
1161

1162
1163
                matches[position] = i
                hasMatch[i] = True
peastman's avatar
peastman committed
1164
                if _findAtomMatches(template, bondedTo, matches, hasMatch, candidates, position+1):
1165
1166
1167
1168
1169
                    return True
                hasMatch[i] = False
    return False


1170
1171
1172
def _findMatchErrors(forcefield, res):
    """Try to guess why a residue failed to match any template and return an error message."""
    residueCounts = _countResidueAtoms([atom.element for atom in res.atoms()])
1173
    numResidueAtoms = sum(residueCounts.values())
1174
    numResidueHeavyAtoms = sum(residueCounts[element] for element in residueCounts if element not in (None, elem.hydrogen))
1175

1176
    # Loop over templates and see how closely each one might match.
1177

1178
1179
1180
1181
1182
1183
    bestMatchName = None
    numBestMatchAtoms = 3*numResidueAtoms
    numBestMatchHeavyAtoms = 2*numResidueHeavyAtoms
    for templateName in forcefield._templates:
        template = forcefield._templates[templateName]
        templateCounts = _countResidueAtoms([atom.element for atom in template.atoms])
1184

1185
        # Does the residue have any atoms that clearly aren't in the template?
1186

1187
1188
        if any(element not in templateCounts or templateCounts[element] < residueCounts[element] for element in residueCounts):
            continue
1189

1190
        # If there are too many missing atoms, discard this template.
1191

1192
        numTemplateAtoms = sum(templateCounts.values())
1193
        numTemplateHeavyAtoms = sum(templateCounts[element] for element in templateCounts if element not in (None, elem.hydrogen))
1194
1195
1196
1197
        if numTemplateAtoms > numBestMatchAtoms:
            continue
        if numTemplateHeavyAtoms > numBestMatchHeavyAtoms:
            continue
1198

1199
1200
        # If this template has the same number of missing atoms as our previous best one, look at the name
        # to decide which one to use.
1201

1202
1203
1204
        if numTemplateAtoms == numBestMatchAtoms:
            if bestMatchName == res.name or res.name not in templateName:
                continue
1205

1206
        # Accept this as our new best match.
1207

1208
1209
1210
        bestMatchName = templateName
        numBestMatchAtoms = numTemplateAtoms
        numBestMatchHeavyAtoms = numTemplateHeavyAtoms
1211
        numBestMatchExtraParticles = len([atom for atom in template.atoms if atom.element is None])
1212

1213
    # Return an appropriate error message.
1214

1215
    if numBestMatchAtoms == numResidueAtoms:
1216
1217
        chainResidues = list(res.chain.residues())
        if len(chainResidues) > 1 and (res == chainResidues[0] or res == chainResidues[-1]):
1218
1219
1220
1221
            return 'The set of atoms matches %s, but the bonds are different.  Perhaps the chain is missing a terminal group?' % bestMatchName
        return 'The set of atoms matches %s, but the bonds are different.' % bestMatchName
    if bestMatchName is not None:
        if numBestMatchHeavyAtoms == numResidueHeavyAtoms:
1222
1223
1224
1225
1226
            numResidueExtraParticles = len([atom for atom in res.atoms() if atom.element is None])
            if numResidueExtraParticles == 0 and numBestMatchExtraParticles == 0:
                return 'The set of atoms is similar to %s, but it is missing %d hydrogen atoms.' % (bestMatchName, numBestMatchAtoms-numResidueAtoms)
            if numBestMatchExtraParticles-numResidueExtraParticles == numBestMatchAtoms-numResidueAtoms:
                return 'The set of atoms is similar to %s, but it is missing %d extra particles.  You can add them with Modeller.addExtraParticles().' % (bestMatchName, numBestMatchAtoms-numResidueAtoms)
1227
1228
1229
        return 'The set of atoms is similar to %s, but it is missing %d atoms.' % (bestMatchName, numBestMatchAtoms-numResidueAtoms)
    return 'This might mean your input topology is missing some atoms or bonds, or possibly that you are using the wrong force field.'

1230
1231
1232
1233
1234
1235
1236
1237
1238
1239
1240
1241
1242
1243
1244
1245
1246
1247
def _createResidueTemplate(residue):
    """Create a _TemplateData template from a Residue object.

    Parameters
    ----------
    residue : Residue
        The Residue from which the template is to be constructed.

    Returns
    -------
    template : _TemplateData
        The residue template, with atom types set to None.

    This method may be useful in creating new residue templates for residues without templates defined by the ForceField.

    """
    template = ForceField._TemplateData(residue.name)
    for atom in residue.atoms():
John Chodera (MSKCC)'s avatar
John Chodera (MSKCC) committed
1248
        template.atoms.append(ForceField._TemplateAtomData(atom.name, None, atom.element))
1249
1250
1251
1252
1253
1254
1255
1256
1257
    for (atom1,atom2) in residue.internal_bonds():
        template.addBondByName(atom1.name, atom2.name)
    residue_atoms = [ atom for atom in residue.atoms() ]
    for (atom1,atom2) in residue.external_bonds():
        if atom1 in residue_atoms:
            template.addExternalBondByName(atom1.name)
        elif atom2 in residue_atoms:
            template.addExternalBondByName(atom2.name)
    return template
1258

1259
1260
1261
1262
1263
# The following classes are generators that know how to create Force subclasses and add them to a System that is being
# created.  Each generator class must define two methods: 1) a static method that takes an etree Element and a ForceField,
# and returns the corresponding generator object; 2) a createForce() method that constructs the Force object and adds it
# to the System.  The static method should be added to the parsers map.

1264
## @private
1265
class HarmonicBondGenerator(object):
1266
    """A HarmonicBondGenerator constructs a HarmonicBondForce."""
Justin MacCallum's avatar
Justin MacCallum committed
1267

1268
1269
    def __init__(self, forcefield):
        self.ff = forcefield
1270
1271
1272
1273
        self.types1 = []
        self.types2 = []
        self.length = []
        self.k = []
1274

1275
1276
1277
1278
1279
1280
1281
    def registerBond(self, parameters):
        types = self.ff._findAtomTypes(parameters, 2)
        if None not in types:
            self.types1.append(types[0])
            self.types2.append(types[1])
            self.length.append(_convertParameterToNumber(parameters['length']))
            self.k.append(_convertParameterToNumber(parameters['k']))
Justin MacCallum's avatar
Justin MacCallum committed
1282

1283
1284
    @staticmethod
    def parseElement(element, ff):
Rafal P. Wiewiora's avatar
Rafal P. Wiewiora committed
1285
1286
1287
1288
1289
1290
        existing = [f for f in ff._forces if isinstance(f, HarmonicBondGenerator)]
        if len(existing) == 0:
            generator = HarmonicBondGenerator(ff)
            ff.registerGenerator(generator)
        else:
            generator = existing[0]
1291
        for bond in element.findall('Bond'):
1292
            generator.registerBond(bond.attrib)
Justin MacCallum's avatar
Justin MacCallum committed
1293

1294
1295
1296
1297
1298
1299
1300
1301
1302
1303
1304
1305
1306
1307
1308
1309
1310
    def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
        existing = [sys.getForce(i) for i in range(sys.getNumForces())]
        existing = [f for f in existing if type(f) == mm.HarmonicBondForce]
        if len(existing) == 0:
            force = mm.HarmonicBondForce()
            sys.addForce(force)
        else:
            force = existing[0]
        for bond in data.bonds:
            type1 = data.atomType[data.atoms[bond.atom1]]
            type2 = data.atomType[data.atoms[bond.atom2]]
            for i in range(len(self.types1)):
                types1 = self.types1[i]
                types2 = self.types2[i]
                if (type1 in types1 and type2 in types2) or (type1 in types2 and type2 in types1):
                    bond.length = self.length[i]
                    if bond.isConstrained:
1311
                        data.addConstraint(sys, bond.atom1, bond.atom2, self.length[i])
1312
1313
1314
1315
1316
1317
1318
                    elif self.k[i] != 0:
                        force.addBond(bond.atom1, bond.atom2, self.length[i], self.k[i])
                    break

parsers["HarmonicBondForce"] = HarmonicBondGenerator.parseElement


1319
## @private
1320
class HarmonicAngleGenerator(object):
1321
    """A HarmonicAngleGenerator constructs a HarmonicAngleForce."""
Justin MacCallum's avatar
Justin MacCallum committed
1322

1323
1324
    def __init__(self, forcefield):
        self.ff = forcefield
1325
1326
1327
1328
1329
        self.types1 = []
        self.types2 = []
        self.types3 = []
        self.angle = []
        self.k = []
Justin MacCallum's avatar
Justin MacCallum committed
1330

1331
1332
1333
1334
1335
1336
1337
1338
1339
    def registerAngle(self, parameters):
        types = self.ff._findAtomTypes(parameters, 3)
        if None not in types:
            self.types1.append(types[0])
            self.types2.append(types[1])
            self.types3.append(types[2])
            self.angle.append(_convertParameterToNumber(parameters['angle']))
            self.k.append(_convertParameterToNumber(parameters['k']))

1340
1341
    @staticmethod
    def parseElement(element, ff):
Rafal P. Wiewiora's avatar
Rafal P. Wiewiora committed
1342
1343
1344
1345
1346
1347
        existing = [f for f in ff._forces if isinstance(f, HarmonicAngleGenerator)]
        if len(existing) == 0:
            generator = HarmonicAngleGenerator(ff)
            ff.registerGenerator(generator)
        else:
            generator = existing[0]
1348
        for angle in element.findall('Angle'):
1349
            generator.registerAngle(angle.attrib)
Justin MacCallum's avatar
Justin MacCallum committed
1350

1351
1352
1353
1354
1355
1356
1357
1358
1359
1360
1361
1362
1363
1364
1365
1366
1367
1368
1369
    def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
        existing = [sys.getForce(i) for i in range(sys.getNumForces())]
        existing = [f for f in existing if type(f) == mm.HarmonicAngleForce]
        if len(existing) == 0:
            force = mm.HarmonicAngleForce()
            sys.addForce(force)
        else:
            force = existing[0]
        for (angle, isConstrained) in zip(data.angles, data.isAngleConstrained):
            type1 = data.atomType[data.atoms[angle[0]]]
            type2 = data.atomType[data.atoms[angle[1]]]
            type3 = data.atomType[data.atoms[angle[2]]]
            for i in range(len(self.types1)):
                types1 = self.types1[i]
                types2 = self.types2[i]
                types3 = self.types3[i]
                if (type1 in types1 and type2 in types2 and type3 in types3) or (type1 in types3 and type2 in types2 and type3 in types1):
                    if isConstrained:
                        # Find the two bonds that make this angle.
Justin MacCallum's avatar
Justin MacCallum committed
1370

1371
1372
1373
1374
1375
1376
1377
1378
1379
                        bond1 = None
                        bond2 = None
                        for bond in data.atomBonds[angle[1]]:
                            atom1 = data.bonds[bond].atom1
                            atom2 = data.bonds[bond].atom2
                            if atom1 == angle[0] or atom2 == angle[0]:
                                bond1 = bond
                            elif atom1 == angle[2] or atom2 == angle[2]:
                                bond2 = bond
Justin MacCallum's avatar
Justin MacCallum committed
1380

1381
                        # Compute the distance between atoms and add a constraint
Justin MacCallum's avatar
Justin MacCallum committed
1382

1383
1384
1385
1386
1387
                        if bond1 is not None and bond2 is not None:
                            l1 = data.bonds[bond1].length
                            l2 = data.bonds[bond2].length
                            if l1 is not None and l2 is not None:
                                length = sqrt(l1*l1 + l2*l2 - 2*l1*l2*cos(self.angle[i]))
1388
                                data.addConstraint(sys, angle[0], angle[2], length)
1389
1390
1391
1392
1393
1394
1395
                    elif self.k[i] != 0:
                        force.addAngle(angle[0], angle[1], angle[2], self.angle[i], self.k[i])
                    break

parsers["HarmonicAngleForce"] = HarmonicAngleGenerator.parseElement


1396
## @private
1397
class PeriodicTorsion(object):
1398
1399
1400
1401
1402
1403
1404
1405
1406
1407
1408
    """A PeriodicTorsion records the information for a periodic torsion definition."""

    def __init__(self, types):
        self.types1 = types[0]
        self.types2 = types[1]
        self.types3 = types[2]
        self.types4 = types[3]
        self.periodicity = []
        self.phase = []
        self.k = []

1409
## @private
1410
class PeriodicTorsionGenerator(object):
1411
    """A PeriodicTorsionGenerator constructs a PeriodicTorsionForce."""
Justin MacCallum's avatar
Justin MacCallum committed
1412

1413
1414
    def __init__(self, forcefield):
        self.ff = forcefield
1415
1416
        self.proper = []
        self.improper = []
Justin MacCallum's avatar
Justin MacCallum committed
1417

1418
1419
1420
1421
1422
1423
1424
1425
1426
1427
    def registerProperTorsion(self, parameters):
        torsion = self.ff._parseTorsion(parameters)
        if torsion is not None:
            self.proper.append(torsion)

    def registerImproperTorsion(self, parameters):
        torsion = self.ff._parseTorsion(parameters)
        if torsion is not None:
            self.improper.append(torsion)

1428
1429
    @staticmethod
    def parseElement(element, ff):
Rafal P. Wiewiora's avatar
Rafal P. Wiewiora committed
1430
1431
1432
1433
1434
1435
        existing = [f for f in ff._forces if isinstance(f, PeriodicTorsionGenerator)]
        if len(existing) == 0:
            generator = PeriodicTorsionGenerator(ff)
            ff.registerGenerator(generator)
        else:
            generator = existing[0]
1436
        for torsion in element.findall('Proper'):
1437
            generator.registerProperTorsion(torsion.attrib)
1438
        for torsion in element.findall('Improper'):
1439
            generator.registerImproperTorsion(torsion.attrib)
Justin MacCallum's avatar
Justin MacCallum committed
1440

1441
1442
1443
1444
1445
1446
1447
1448
1449
1450
1451
1452
1453
1454
1455
1456
1457
1458
1459
1460
1461
1462
1463
1464
1465
1466
1467
1468
1469
1470
1471
1472
1473
1474
1475
    def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
        existing = [sys.getForce(i) for i in range(sys.getNumForces())]
        existing = [f for f in existing if type(f) == mm.PeriodicTorsionForce]
        if len(existing) == 0:
            force = mm.PeriodicTorsionForce()
            sys.addForce(force)
        else:
            force = existing[0]
        wildcard = self.ff._atomClasses['']
        for torsion in data.propers:
            type1 = data.atomType[data.atoms[torsion[0]]]
            type2 = data.atomType[data.atoms[torsion[1]]]
            type3 = data.atomType[data.atoms[torsion[2]]]
            type4 = data.atomType[data.atoms[torsion[3]]]
            match = None
            for tordef in self.proper:
                types1 = tordef.types1
                types2 = tordef.types2
                types3 = tordef.types3
                types4 = tordef.types4
                if (type2 in types2 and type3 in types3 and type4 in types4 and type1 in types1) or (type2 in types3 and type3 in types2 and type4 in types1 and type1 in types4):
                    hasWildcard = (wildcard in (types1, types2, types3, types4))
                    if match is None or not hasWildcard: # Prefer specific definitions over ones with wildcards
                        match = tordef
                    if not hasWildcard:
                        break
            if match is not None:
                for i in range(len(match.phase)):
                    if match.k[i] != 0:
                        force.addTorsion(torsion[0], torsion[1], torsion[2], torsion[3], match.periodicity[i], match.phase[i], match.k[i])
        for torsion in data.impropers:
            type1 = data.atomType[data.atoms[torsion[0]]]
            type2 = data.atomType[data.atoms[torsion[1]]]
            type3 = data.atomType[data.atoms[torsion[2]]]
            type4 = data.atomType[data.atoms[torsion[3]]]
1476
            match = None
1477
1478
1479
1480
1481
            for tordef in self.improper:
                types1 = tordef.types1
                types2 = tordef.types2
                types3 = tordef.types3
                types4 = tordef.types4
1482
1483
1484
1485
                hasWildcard = (wildcard in (types1, types2, types3, types4))
                if match is not None and hasWildcard:
                    # Prefer specific definitions over ones with wildcards
                    continue
1486
1487
1488
                if type1 in types1:
                    for (t2, t3, t4) in itertools.permutations(((type2, 1), (type3, 2), (type4, 3))):
                        if t2[0] in types2 and t3[0] in types3 and t4[0] in types4:
1489
1490
1491
1492
1493
1494
1495
1496
1497
1498
1499
                            # Workaround to be more consistent with AMBER.  It uses wildcards to define most of its
                            # impropers, which leaves the ordering ambiguous.  It then follows some bizarre rules
                            # to pick the order.
                            a1 = torsion[t2[1]]
                            a2 = torsion[t3[1]]
                            e1 = data.atoms[a1].element
                            e2 = data.atoms[a2].element
                            if e1 == e2 and a1 > a2:
                                (a1, a2) = (a2, a1)
                            elif e1 != elem.carbon and (e2 == elem.carbon or e1.mass < e2.mass):
                                (a1, a2) = (a2, a1)
1500
                            match = (a1, a2, torsion[0], torsion[t4[1]], tordef)
1501
                            break
1502
1503
1504
1505
1506
            if match is not None:
                (a1, a2, a3, a4, tordef) = match
                for i in range(len(tordef.phase)):
                    if tordef.k[i] != 0:
                        force.addTorsion(a1, a2, a3, a4, tordef.periodicity[i], tordef.phase[i], tordef.k[i])
1507
1508
1509
1510

parsers["PeriodicTorsionForce"] = PeriodicTorsionGenerator.parseElement


1511
## @private
1512
class RBTorsion(object):
1513
1514
1515
1516
1517
1518
1519
1520
1521
    """An RBTorsion records the information for a Ryckaert-Bellemans torsion definition."""

    def __init__(self, types, c):
        self.types1 = types[0]
        self.types2 = types[1]
        self.types3 = types[2]
        self.types4 = types[3]
        self.c = c

1522
## @private
1523
class RBTorsionGenerator(object):
1524
    """An RBTorsionGenerator constructs an RBTorsionForce."""
Justin MacCallum's avatar
Justin MacCallum committed
1525

1526
1527
    def __init__(self, forcefield):
        self.ff = forcefield
1528
1529
        self.proper = []
        self.improper = []
Justin MacCallum's avatar
Justin MacCallum committed
1530

1531
1532
    @staticmethod
    def parseElement(element, ff):
Rafal P. Wiewiora's avatar
Rafal P. Wiewiora committed
1533
1534
1535
1536
1537
1538
        existing = [f for f in ff._forces if isinstance(f, RBTorsionGenerator)]
        if len(existing) == 0:
            generator = RBTorsionGenerator(ff)
            ff.registerGenerator(generator)
        else:
            generator = existing[0]
1539
        for torsion in element.findall('Proper'):
1540
            types = ff._findAtomTypes(torsion.attrib, 4)
peastman's avatar
peastman committed
1541
            if None not in types:
1542
1543
                generator.proper.append(RBTorsion(types, [float(torsion.attrib['c'+str(i)]) for i in range(6)]))
        for torsion in element.findall('Improper'):
1544
            types = ff._findAtomTypes(torsion.attrib, 4)
peastman's avatar
peastman committed
1545
            if None not in types:
1546
                generator.improper.append(RBTorsion(types, [float(torsion.attrib['c'+str(i)]) for i in range(6)]))
Justin MacCallum's avatar
Justin MacCallum committed
1547

1548
1549
1550
1551
1552
1553
1554
1555
1556
1557
1558
1559
1560
1561
1562
1563
1564
1565
1566
1567
1568
1569
1570
1571
1572
1573
1574
1575
1576
1577
1578
1579
1580
    def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
        existing = [sys.getForce(i) for i in range(sys.getNumForces())]
        existing = [f for f in existing if type(f) == mm.RBTorsionForce]
        if len(existing) == 0:
            force = mm.RBTorsionForce()
            sys.addForce(force)
        else:
            force = existing[0]
        wildcard = self.ff._atomClasses['']
        for torsion in data.propers:
            type1 = data.atomType[data.atoms[torsion[0]]]
            type2 = data.atomType[data.atoms[torsion[1]]]
            type3 = data.atomType[data.atoms[torsion[2]]]
            type4 = data.atomType[data.atoms[torsion[3]]]
            match = None
            for tordef in self.proper:
                types1 = tordef.types1
                types2 = tordef.types2
                types3 = tordef.types3
                types4 = tordef.types4
                if (type2 in types2 and type3 in types3 and type4 in types4 and type1 in types1) or (type2 in types3 and type3 in types2 and type4 in types1 and type1 in types4):
                    hasWildcard = (wildcard in (types1, types2, types3, types4))
                    if match is None or not hasWildcard: # Prefer specific definitions over ones with wildcards
                        match = tordef
                    if not hasWildcard:
                        break
            if match is not None:
                force.addTorsion(torsion[0], torsion[1], torsion[2], torsion[3], match.c[0], match.c[1], match.c[2], match.c[3], match.c[4], match.c[5])
        for torsion in data.impropers:
            type1 = data.atomType[data.atoms[torsion[0]]]
            type2 = data.atomType[data.atoms[torsion[1]]]
            type3 = data.atomType[data.atoms[torsion[2]]]
            type4 = data.atomType[data.atoms[torsion[3]]]
1581
            match = None
1582
1583
1584
1585
1586
            for tordef in self.improper:
                types1 = tordef.types1
                types2 = tordef.types2
                types3 = tordef.types3
                types4 = tordef.types4
1587
1588
1589
1590
                hasWildcard = (wildcard in (types1, types2, types3, types4))
                if match is not None and hasWildcard:
                    # Prefer specific definitions over ones with wildcards
                    continue
1591
1592
1593
                if type1 in types1:
                    for (t2, t3, t4) in itertools.permutations(((type2, 1), (type3, 2), (type4, 3))):
                        if t2[0] in types2 and t3[0] in types3 and t4[0] in types4:
1594
                            if hasWildcard:
1595
1596
1597
1598
1599
1600
1601
1602
1603
1604
1605
                                # Workaround to be more consistent with AMBER.  It uses wildcards to define most of its
                                # impropers, which leaves the ordering ambiguous.  It then follows some bizarre rules
                                # to pick the order.
                                a1 = torsion[t2[1]]
                                a2 = torsion[t3[1]]
                                e1 = data.atoms[a1].element
                                e2 = data.atoms[a2].element
                                if e1 == e2 and a1 > a2:
                                    (a1, a2) = (a2, a1)
                                elif e1 != elem.carbon and (e2 == elem.carbon or e1.mass < e2.mass):
                                    (a1, a2) = (a2, a1)
1606
                                match = (a1, a2, torsion[0], torsion[t4[1]], tordef)
1607
1608
                            else:
                                # There are no wildcards, so the order is unambiguous.
1609
                                match = (torsion[0], torsion[t2[1]], torsion[t3[1]], torsion[t4[1]], tordef)
1610
                            break
1611
1612
1613
            if match is not None:
                (a1, a2, a3, a4, tordef) = match
                force.addTorsion(a1, a2, a3, a4, tordef.c[0], tordef.c[1], tordef.c[2], tordef.c[3], tordef.c[4], tordef.c[5])
1614
1615
1616
1617

parsers["RBTorsionForce"] = RBTorsionGenerator.parseElement


1618
## @private
1619
class CMAPTorsion(object):
1620
1621
1622
1623
1624
1625
1626
1627
1628
1629
    """A CMAPTorsion records the information for a CMAP torsion definition."""

    def __init__(self, types, map):
        self.types1 = types[0]
        self.types2 = types[1]
        self.types3 = types[2]
        self.types4 = types[3]
        self.types5 = types[4]
        self.map = map

1630
## @private
1631
class CMAPTorsionGenerator(object):
1632
    """A CMAPTorsionGenerator constructs a CMAPTorsionForce."""
Justin MacCallum's avatar
Justin MacCallum committed
1633

1634
1635
    def __init__(self, forcefield):
        self.ff = forcefield
1636
1637
        self.torsions = []
        self.maps = []
Justin MacCallum's avatar
Justin MacCallum committed
1638

1639
1640
    @staticmethod
    def parseElement(element, ff):
Rafal P. Wiewiora's avatar
Rafal P. Wiewiora committed
1641
1642
1643
1644
1645
1646
        existing = [f for f in ff._forces if isinstance(f, CMAPTorsionGenerator)]
        if len(existing) == 0:
            generator = CMAPTorsionGenerator(ff)
            ff.registerGenerator(generator)
        else:
            generator = existing[0]
1647
1648
1649
1650
1651
1652
1653
        for map in element.findall('Map'):
            values = [float(x) for x in map.text.split()]
            size = sqrt(len(values))
            if size*size != len(values):
                raise ValueError('CMAP must have the same number of elements along each dimension')
            generator.maps.append(values)
        for torsion in element.findall('Torsion'):
1654
            types = ff._findAtomTypes(torsion.attrib, 5)
peastman's avatar
peastman committed
1655
            if None not in types:
1656
                generator.torsions.append(CMAPTorsion(types, int(torsion.attrib['map'])))
Justin MacCallum's avatar
Justin MacCallum committed
1657

1658
1659
1660
1661
1662
1663
1664
1665
1666
1667
    def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
        existing = [sys.getForce(i) for i in range(sys.getNumForces())]
        existing = [f for f in existing if type(f) == mm.CMAPTorsionForce]
        if len(existing) == 0:
            force = mm.CMAPTorsionForce()
            sys.addForce(force)
        else:
            force = existing[0]
        for map in self.maps:
            force.addMap(int(sqrt(len(map))), map)
Justin MacCallum's avatar
Justin MacCallum committed
1668

1669
        # Find all chains of length 5
Justin MacCallum's avatar
Justin MacCallum committed
1670

1671
1672
1673
1674
1675
1676
1677
1678
1679
1680
1681
1682
1683
1684
1685
1686
1687
1688
1689
1690
1691
1692
1693
1694
1695
1696
1697
1698
1699
1700
1701
1702
1703
1704
1705
1706
1707
1708
1709
1710
1711
1712
1713
        uniqueTorsions = set()
        for torsion in data.propers:
            for bond in (data.bonds[x] for x in data.atomBonds[torsion[0]]):
                if bond.atom1 == torsion[0]:
                    atom = bond.atom2
                else:
                    atom = bond.atom1
                if atom != torsion[1]:
                    uniqueTorsions.add((atom, torsion[0], torsion[1], torsion[2], torsion[3]))
            for bond in (data.bonds[x] for x in data.atomBonds[torsion[3]]):
                if bond.atom1 == torsion[3]:
                    atom = bond.atom2
                else:
                    atom = bond.atom1
                if atom != torsion[2]:
                    uniqueTorsions.add((torsion[0], torsion[1], torsion[2], torsion[3], atom))
        torsions = sorted(list(uniqueTorsions))
        wildcard = self.ff._atomClasses['']
        for torsion in torsions:
            type1 = data.atomType[data.atoms[torsion[0]]]
            type2 = data.atomType[data.atoms[torsion[1]]]
            type3 = data.atomType[data.atoms[torsion[2]]]
            type4 = data.atomType[data.atoms[torsion[3]]]
            type5 = data.atomType[data.atoms[torsion[4]]]
            match = None
            for tordef in self.torsions:
                types1 = tordef.types1
                types2 = tordef.types2
                types3 = tordef.types3
                types4 = tordef.types4
                types5 = tordef.types5
                if (type1 in types1 and type2 in types2 and type3 in types3 and type4 in types4 and type5 in types5) or (type1 in types5 and type2 in types4 and type3 in types3 and type4 in types2 and type5 in types1):
                    hasWildcard = (wildcard in (types1, types2, types3, types4, types5))
                    if match is None or not hasWildcard: # Prefer specific definitions over ones with wildcards
                        match = tordef
                    if not hasWildcard:
                        break
            if match is not None:
                force.addTorsion(match.map, torsion[0], torsion[1], torsion[2], torsion[3], torsion[1], torsion[2], torsion[3], torsion[4])

parsers["CMAPTorsionForce"] = CMAPTorsionGenerator.parseElement


1714
## @private
1715
class NonbondedGenerator(object):
1716
    """A NonbondedGenerator constructs a NonbondedForce."""
Justin MacCallum's avatar
Justin MacCallum committed
1717

1718
1719
    SCALETOL = 1e-5

1720
1721
    def __init__(self, forcefield, coulomb14scale, lj14scale):
        self.ff = forcefield
1722
1723
        self.coulomb14scale = coulomb14scale
        self.lj14scale = lj14scale
1724
        self.params = ForceField._AtomTypeParameters(forcefield, 'NonbondedForce', 'Atom', ('charge', 'sigma', 'epsilon'))
1725

1726
    def registerAtom(self, parameters):
1727
        self.params.registerAtom(parameters)
1728

1729
1730
1731
1732
    @staticmethod
    def parseElement(element, ff):
        existing = [f for f in ff._forces if isinstance(f, NonbondedGenerator)]
        if len(existing) == 0:
1733
1734
            generator = NonbondedGenerator(ff, float(element.attrib['coulomb14scale']), float(element.attrib['lj14scale']))
            ff.registerGenerator(generator)
1735
1736
1737
        else:
            # Multiple <NonbondedForce> tags were found, probably in different files.  Simply add more types to the existing one.
            generator = existing[0]
1738
1739
            if abs(generator.coulomb14scale - float(element.attrib['coulomb14scale'])) > NonbondedGenerator.SCALETOL or \
                    abs(generator.lj14scale - float(element.attrib['lj14scale'])) > NonbondedGenerator.SCALETOL:
Justin MacCallum's avatar
Justin MacCallum committed
1740
                raise ValueError('Found multiple NonbondedForce tags with different 1-4 scales')
1741
        generator.params.parseDefinitions(element)
Justin MacCallum's avatar
Justin MacCallum committed
1742

1743
1744
1745
1746
1747
1748
1749
    def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
        methodMap = {NoCutoff:mm.NonbondedForce.NoCutoff,
                     CutoffNonPeriodic:mm.NonbondedForce.CutoffNonPeriodic,
                     CutoffPeriodic:mm.NonbondedForce.CutoffPeriodic,
                     Ewald:mm.NonbondedForce.Ewald,
                     PME:mm.NonbondedForce.PME}
        if nonbondedMethod not in methodMap:
Justin MacCallum's avatar
Justin MacCallum committed
1750
            raise ValueError('Illegal nonbonded method for NonbondedForce')
1751
1752
        force = mm.NonbondedForce()
        for atom in data.atoms:
1753
1754
            values = self.params.getAtomParameters(atom, data)
            force.addParticle(values[0], values[1], values[2])
peastman's avatar
peastman committed
1755
1756
1757
1758
        force.setNonbondedMethod(methodMap[nonbondedMethod])
        force.setCutoffDistance(nonbondedCutoff)
        if 'ewaldErrorTolerance' in args:
            force.setEwaldErrorTolerance(args['ewaldErrorTolerance'])
1759
1760
        if 'useDispersionCorrection' in args:
            force.setUseDispersionCorrection(bool(args['useDispersionCorrection']))
peastman's avatar
peastman committed
1761
        sys.addForce(force)
Justin MacCallum's avatar
Justin MacCallum committed
1762

peastman's avatar
peastman committed
1763
    def postprocessSystem(self, sys, data, args):
1764
        # Create exceptions based on bonds.
1765

1766
1767
1768
        bondIndices = []
        for bond in data.bonds:
            bondIndices.append((bond.atom1, bond.atom2))
1769
1770
1771

        # If a virtual site does *not* share exclusions with another atom, add a bond between it and its first parent atom.

1772
1773
        for i in range(sys.getNumParticles()):
            if sys.isVirtualSite(i):
1774
1775
1776
                (site, atoms, excludeWith) = data.virtualSites[data.atoms[i]]
                if excludeWith is None:
                    bondIndices.append((i, site.getParticle(0)))
1777

1778
1779
        # Certain particles, such as lone pairs and Drude particles, share exclusions with a parent atom.
        # If the parent atom does not interact with an atom, the child particle does not either.
1780

1781
1782
1783
1784
1785
1786
1787
1788
1789
1790
        for atom1, atom2 in bondIndices:
            for child1 in data.excludeAtomWith[atom1]:
                bondIndices.append((child1, atom2))
                for child2 in data.excludeAtomWith[atom2]:
                    bondIndices.append((child1, child2))
            for child2 in data.excludeAtomWith[atom2]:
                bondIndices.append((atom1, child2))

        # Create the exceptions.

peastman's avatar
peastman committed
1791
        nonbonded = [f for f in sys.getForces() if isinstance(f, mm.NonbondedForce)][0]
Justin MacCallum's avatar
Justin MacCallum committed
1792
        nonbonded.createExceptionsFromBonds(bondIndices, self.coulomb14scale, self.lj14scale)
1793
1794
1795
1796

parsers["NonbondedForce"] = NonbondedGenerator.parseElement


1797
## @private
1798
class GBSAOBCGenerator(object):
1799
    """A GBSAOBCGenerator constructs a GBSAOBCForce."""
Justin MacCallum's avatar
Justin MacCallum committed
1800

1801
1802
    def __init__(self, forcefield):
        self.ff = forcefield
1803
        self.params = ForceField._AtomTypeParameters(forcefield, 'GBSAOBCForce', 'Atom', ('charge', 'radius', 'scale'))
1804

1805
    def registerAtom(self, parameters):
1806
        self.params.registerAtom(parameters)
1807

1808
1809
    @staticmethod
    def parseElement(element, ff):
1810
1811
        existing = [f for f in ff._forces if isinstance(f, GBSAOBCGenerator)]
        if len(existing) == 0:
1812
1813
            generator = GBSAOBCGenerator(ff)
            ff.registerGenerator(generator)
1814
1815
1816
        else:
            # Multiple <GBSAOBCForce> tags were found, probably in different files.  Simply add more types to the existing one.
            generator = existing[0]
1817
        generator.params.parseDefinitions(element)
Justin MacCallum's avatar
Justin MacCallum committed
1818

1819
1820
1821
1822
1823
    def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
        methodMap = {NoCutoff:mm.NonbondedForce.NoCutoff,
                     CutoffNonPeriodic:mm.NonbondedForce.CutoffNonPeriodic,
                     CutoffPeriodic:mm.NonbondedForce.CutoffPeriodic}
        if nonbondedMethod not in methodMap:
Justin MacCallum's avatar
Justin MacCallum committed
1824
            raise ValueError('Illegal nonbonded method for GBSAOBCForce')
1825
1826
        force = mm.GBSAOBCForce()
        for atom in data.atoms:
1827
1828
            values = self.params.getAtomParameters(atom, data)
            force.addParticle(values[0], values[1], values[2])
1829
1830
        force.setNonbondedMethod(methodMap[nonbondedMethod])
        force.setCutoffDistance(nonbondedCutoff)
1831
1832
1833
1834
        if 'soluteDielectric' in args:
            force.setSoluteDielectric(float(args['soluteDielectric']))
        if 'solventDielectric' in args:
            force.setSolventDielectric(float(args['solventDielectric']))
1835
1836
        sys.addForce(force)

1837
1838
    def postprocessSystem(self, sys, data, args):
        # Disable the reaction field approximation, since it produces bad results when combined with GB.
Justin MacCallum's avatar
Justin MacCallum committed
1839

1840
1841
1842
1843
        for force in sys.getForces():
            if isinstance(force, mm.NonbondedForce):
                force.setReactionFieldDielectric(1.0)

1844
1845
1846
parsers["GBSAOBCForce"] = GBSAOBCGenerator.parseElement


1847
## @private
1848
class CustomBondGenerator(object):
1849
    """A CustomBondGenerator constructs a CustomBondForce."""
Justin MacCallum's avatar
Justin MacCallum committed
1850

1851
1852
    def __init__(self, forcefield):
        self.ff = forcefield
1853
1854
1855
1856
1857
        self.types1 = []
        self.types2 = []
        self.globalParams = {}
        self.perBondParams = []
        self.paramValues = []
Justin MacCallum's avatar
Justin MacCallum committed
1858

1859
1860
    @staticmethod
    def parseElement(element, ff):
1861
1862
        generator = CustomBondGenerator(ff)
        ff.registerGenerator(generator)
1863
1864
1865
1866
1867
1868
        generator.energy = element.attrib['energy']
        for param in element.findall('GlobalParameter'):
            generator.globalParams[param.attrib['name']] = float(param.attrib['defaultValue'])
        for param in element.findall('PerBondParameter'):
            generator.perBondParams.append(param.attrib['name'])
        for bond in element.findall('Bond'):
1869
            types = ff._findAtomTypes(bond.attrib, 2)
peastman's avatar
peastman committed
1870
            if None not in types:
1871
1872
1873
                generator.types1.append(types[0])
                generator.types2.append(types[1])
                generator.paramValues.append([float(bond.attrib[param]) for param in generator.perBondParams])
Justin MacCallum's avatar
Justin MacCallum committed
1874

1875
1876
1877
1878
1879
1880
1881
1882
1883
1884
1885
1886
1887
1888
1889
1890
1891
1892
1893
1894
    def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
        force = mm.CustomBondForce(self.energy)
        sys.addForce(force)
        for param in self.globalParams:
            force.addGlobalParameter(param, self.globalParams[param])
        for param in self.perBondParams:
            force.addPerBondParameter(param)
        for bond in data.bonds:
            type1 = data.atomType[data.atoms[bond.atom1]]
            type2 = data.atomType[data.atoms[bond.atom2]]
            for i in range(len(self.types1)):
                types1 = self.types1[i]
                types2 = self.types2[i]
                if (type1 in types1 and type2 in types2) or (type1 in types2 and type2 in types1):
                    force.addBond(bond.atom1, bond.atom2, self.paramValues[i])
                    break

parsers["CustomBondForce"] = CustomBondGenerator.parseElement


1895
## @private
1896
class CustomAngleGenerator(object):
1897
    """A CustomAngleGenerator constructs a CustomAngleForce."""
Justin MacCallum's avatar
Justin MacCallum committed
1898

1899
1900
    def __init__(self, forcefield):
        self.ff = forcefield
1901
1902
1903
1904
1905
1906
        self.types1 = []
        self.types2 = []
        self.types3 = []
        self.globalParams = {}
        self.perAngleParams = []
        self.paramValues = []
Justin MacCallum's avatar
Justin MacCallum committed
1907

1908
1909
    @staticmethod
    def parseElement(element, ff):
1910
1911
        generator = CustomAngleGenerator(ff)
        ff.registerGenerator(generator)
1912
1913
1914
1915
1916
1917
        generator.energy = element.attrib['energy']
        for param in element.findall('GlobalParameter'):
            generator.globalParams[param.attrib['name']] = float(param.attrib['defaultValue'])
        for param in element.findall('PerAngleParameter'):
            generator.perAngleParams.append(param.attrib['name'])
        for angle in element.findall('Angle'):
1918
            types = ff._findAtomTypes(angle.attrib, 3)
peastman's avatar
peastman committed
1919
            if None not in types:
1920
1921
1922
1923
                generator.types1.append(types[0])
                generator.types2.append(types[1])
                generator.types3.append(types[2])
                generator.paramValues.append([float(angle.attrib[param]) for param in generator.perAngleParams])
Justin MacCallum's avatar
Justin MacCallum committed
1924

1925
1926
1927
1928
1929
1930
1931
1932
1933
1934
1935
1936
1937
1938
1939
1940
1941
1942
1943
1944
1945
1946
    def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
        force = mm.CustomAngleForce(self.energy)
        sys.addForce(force)
        for param in self.globalParams:
            force.addGlobalParameter(param, self.globalParams[param])
        for param in self.perAngleParams:
            force.addPerAngleParameter(param)
        for angle in data.angles:
            type1 = data.atomType[data.atoms[angle[0]]]
            type2 = data.atomType[data.atoms[angle[1]]]
            type3 = data.atomType[data.atoms[angle[2]]]
            for i in range(len(self.types1)):
                types1 = self.types1[i]
                types2 = self.types2[i]
                types3 = self.types3[i]
                if (type1 in types1 and type2 in types2 and type3 in types3) or (type1 in types3 and type2 in types2 and type3 in types1):
                    force.addAngle(angle[0], angle[1], angle[2], self.paramValues[i])
                    break

parsers["CustomAngleForce"] = CustomAngleGenerator.parseElement


1947
## @private
1948
class CustomTorsion(object):
1949
1950
1951
1952
1953
1954
1955
1956
1957
    """A CustomTorsion records the information for a custom torsion definition."""

    def __init__(self, types, paramValues):
        self.types1 = types[0]
        self.types2 = types[1]
        self.types3 = types[2]
        self.types4 = types[3]
        self.paramValues = paramValues

1958
## @private
1959
class CustomTorsionGenerator(object):
1960
    """A CustomTorsionGenerator constructs a CustomTorsionForce."""
Justin MacCallum's avatar
Justin MacCallum committed
1961

1962
1963
    def __init__(self, forcefield):
        self.ff = forcefield
1964
1965
1966
1967
        self.proper = []
        self.improper = []
        self.globalParams = {}
        self.perTorsionParams = []
Justin MacCallum's avatar
Justin MacCallum committed
1968

1969
1970
    @staticmethod
    def parseElement(element, ff):
1971
1972
        generator = CustomTorsionGenerator(ff)
        ff.registerGenerator(generator)
1973
1974
1975
1976
1977
1978
        generator.energy = element.attrib['energy']
        for param in element.findall('GlobalParameter'):
            generator.globalParams[param.attrib['name']] = float(param.attrib['defaultValue'])
        for param in element.findall('PerTorsionParameter'):
            generator.perTorsionParams.append(param.attrib['name'])
        for torsion in element.findall('Proper'):
1979
            types = ff._findAtomTypes(torsion.attrib, 4)
peastman's avatar
peastman committed
1980
            if None not in types:
1981
1982
                generator.proper.append(CustomTorsion(types, [float(torsion.attrib[param]) for param in generator.perTorsionParams]))
        for torsion in element.findall('Improper'):
1983
            types = ff._findAtomTypes(torsion.attrib, 4)
peastman's avatar
peastman committed
1984
            if None not in types:
1985
                generator.improper.append(CustomTorsion(types, [float(torsion.attrib[param]) for param in generator.perTorsionParams]))
Justin MacCallum's avatar
Justin MacCallum committed
1986

1987
1988
1989
1990
1991
1992
1993
1994
1995
1996
1997
1998
1999
2000
2001
2002
2003
2004
2005
2006
2007
2008
2009
2010
2011
2012
2013
2014
2015
2016
2017
2018
    def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
        force = mm.CustomTorsionForce(self.energy)
        sys.addForce(force)
        for param in self.globalParams:
            force.addGlobalParameter(param, self.globalParams[param])
        for param in self.perTorsionParams:
            force.addPerTorsionParameter(param)
        wildcard = self.ff._atomClasses['']
        for torsion in data.propers:
            type1 = data.atomType[data.atoms[torsion[0]]]
            type2 = data.atomType[data.atoms[torsion[1]]]
            type3 = data.atomType[data.atoms[torsion[2]]]
            type4 = data.atomType[data.atoms[torsion[3]]]
            match = None
            for tordef in self.proper:
                types1 = tordef.types1
                types2 = tordef.types2
                types3 = tordef.types3
                types4 = tordef.types4
                if (type2 in types2 and type3 in types3 and type4 in types4 and type1 in types1) or (type2 in types3 and type3 in types2 and type4 in types1 and type1 in types4):
                    hasWildcard = (wildcard in (types1, types2, types3, types4))
                    if match is None or not hasWildcard: # Prefer specific definitions over ones with wildcards
                        match = tordef
                    if not hasWildcard:
                        break
            if match is not None:
                force.addTorsion(torsion[0], torsion[1], torsion[2], torsion[3], match.paramValues)
        for torsion in data.impropers:
            type1 = data.atomType[data.atoms[torsion[0]]]
            type2 = data.atomType[data.atoms[torsion[1]]]
            type3 = data.atomType[data.atoms[torsion[2]]]
            type4 = data.atomType[data.atoms[torsion[3]]]
2019
            match = None
2020
2021
2022
2023
2024
            for tordef in self.improper:
                types1 = tordef.types1
                types2 = tordef.types2
                types3 = tordef.types3
                types4 = tordef.types4
2025
2026
2027
2028
                hasWildcard = (wildcard in (types1, types2, types3, types4))
                if match is not None and hasWildcard:
                    # Prefer specific definitions over ones with wildcards
                    continue
2029
2030
2031
                if type1 in types1:
                    for (t2, t3, t4) in itertools.permutations(((type2, 1), (type3, 2), (type4, 3))):
                        if t2[0] in types2 and t3[0] in types3 and t4[0] in types4:
2032
                            if hasWildcard:
2033
2034
2035
2036
2037
2038
2039
2040
2041
2042
2043
                                # Workaround to be more consistent with AMBER.  It uses wildcards to define most of its
                                # impropers, which leaves the ordering ambiguous.  It then follows some bizarre rules
                                # to pick the order.
                                a1 = torsion[t2[1]]
                                a2 = torsion[t3[1]]
                                e1 = data.atoms[a1].element
                                e2 = data.atoms[a2].element
                                if e1 == e2 and a1 > a2:
                                    (a1, a2) = (a2, a1)
                                elif e1 != elem.carbon and (e2 == elem.carbon or e1.mass < e2.mass):
                                    (a1, a2) = (a2, a1)
2044
                                match = (a1, a2, torsion[0], torsion[t4[1]], tordef)
2045
2046
                            else:
                                # There are no wildcards, so the order is unambiguous.
2047
                                match = (torsion[0], torsion[t2[1]], torsion[t3[1]], torsion[t4[1]], tordef)
2048
                            break
2049
2050
2051
            if match is not None:
                (a1, a2, a3, a4, tordef) = match
                force.addTorsion(a1, a2, a3, a4, tordef.paramValues)
2052
2053
2054
2055

parsers["CustomTorsionForce"] = CustomTorsionGenerator.parseElement


2056
## @private
2057
class CustomNonbondedGenerator(object):
2058
2059
    """A CustomNonbondedGenerator constructs a CustomNonbondedForce."""

2060
2061
    def __init__(self, forcefield, energy, bondCutoff):
        self.ff = forcefield
2062
2063
2064
2065
2066
2067
2068
2069
        self.energy = energy
        self.bondCutoff = bondCutoff
        self.globalParams = {}
        self.perParticleParams = []
        self.functions = []

    @staticmethod
    def parseElement(element, ff):
2070
2071
        generator = CustomNonbondedGenerator(ff, element.attrib['energy'], int(element.attrib['bondCutoff']))
        ff.registerGenerator(generator)
2072
2073
2074
2075
        for param in element.findall('GlobalParameter'):
            generator.globalParams[param.attrib['name']] = float(param.attrib['defaultValue'])
        for param in element.findall('PerParticleParameter'):
            generator.perParticleParams.append(param.attrib['name'])
2076
2077
        generator.params = ForceField._AtomTypeParameters(ff, 'CustomNonbondedForce', 'Atom', generator.perParticleParams)
        generator.params.parseDefinitions(element)
2078
2079
2080
2081
2082
2083
2084
2085
2086
2087
2088
2089
2090
2091
2092
2093
2094
2095
2096
2097
2098
2099
2100
2101
2102
2103

    def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
        methodMap = {NoCutoff:mm.CustomNonbondedForce.NoCutoff,
                     CutoffNonPeriodic:mm.CustomNonbondedForce.CutoffNonPeriodic,
                     CutoffPeriodic:mm.CustomNonbondedForce.CutoffPeriodic}
        if nonbondedMethod not in methodMap:
            raise ValueError('Illegal nonbonded method for CustomNonbondedForce')
        force = mm.CustomNonbondedForce(self.energy)
        for param in self.globalParams:
            force.addGlobalParameter(param, self.globalParams[param])
        for param in self.perParticleParams:
            force.addPerParticleParameter(param)
        for (name, type, values, params) in self.functions:
            if type == 'Continuous1D':
                force.addTabulatedFunction(name, mm.Continuous1DFunction(values, params['min'], params['max']))
            elif type == 'Continuous2D':
                force.addTabulatedFunction(name, mm.Continuous2DFunction(params['xsize'], params['ysize'], values, params['xmin'], params['xmax'], params['ymin'], params['ymax']))
            elif type == 'Continuous3D':
                force.addTabulatedFunction(name, mm.Continuous2DFunction(params['xsize'], params['ysize'], params['zsize'], values, params['xmin'], params['xmax'], params['ymin'], params['ymax'], params['zmin'], params['zmax']))
            elif type == 'Discrete1D':
                force.addTabulatedFunction(name, mm.Discrete1DFunction(values))
            elif type == 'Discrete2D':
                force.addTabulatedFunction(name, mm.Discrete2DFunction(params['xsize'], params['ysize'], values))
            elif type == 'Discrete3D':
                force.addTabulatedFunction(name, mm.Discrete2DFunction(params['xsize'], params['ysize'], params['zsize'], values))
        for atom in data.atoms:
2104
2105
            values = self.params.getAtomParameters(atom, data)
            force.addParticle(values)
2106
2107
2108
2109
2110
        force.setNonbondedMethod(methodMap[nonbondedMethod])
        force.setCutoffDistance(nonbondedCutoff)
        sys.addForce(force)

    def postprocessSystem(self, sys, data, args):
2111
        # Create exclusions based on bonds.
2112

2113
2114
2115
        bondIndices = []
        for bond in data.bonds:
            bondIndices.append((bond.atom1, bond.atom2))
2116
2117
2118

        # If a virtual site does *not* share exclusions with another atom, add a bond between it and its first parent atom.

2119
2120
        for i in range(sys.getNumParticles()):
            if sys.isVirtualSite(i):
2121
2122
2123
                (site, atoms, excludeWith) = data.virtualSites[data.atoms[i]]
                if excludeWith is None:
                    bondIndices.append((i, site.getParticle(0)))
2124

2125
2126
        # Certain particles, such as lone pairs and Drude particles, share exclusions with a parent atom.
        # If the parent atom does not interact with an atom, the child particle does not either.
2127

2128
2129
2130
2131
2132
2133
2134
2135
2136
        for atom1, atom2 in bondIndices:
            for child1 in data.excludeAtomWith[atom1]:
                bondIndices.append((child1, atom2))
                for child2 in data.excludeAtomWith[atom2]:
                    bondIndices.append((child1, child2))
            for child2 in data.excludeAtomWith[atom2]:
                bondIndices.append((atom1, child2))

        # Create the exclusions.
2137

2138
2139
2140
2141
2142
2143
        nonbonded = [f for f in sys.getForces() if isinstance(f, mm.CustomNonbondedForce)][0]
        nonbonded.createExclusionsFromBonds(bondIndices, self.bondCutoff)

parsers["CustomNonbondedForce"] = CustomNonbondedGenerator.parseElement


2144
## @private
2145
class CustomGBGenerator(object):
2146
    """A CustomGBGenerator constructs a CustomGBForce."""
Justin MacCallum's avatar
Justin MacCallum committed
2147

2148
2149
    def __init__(self, forcefield):
        self.ff = forcefield
2150
2151
2152
2153
2154
2155
2156
2157
        self.globalParams = {}
        self.perParticleParams = []
        self.computedValues = []
        self.energyTerms = []
        self.functions = []

    @staticmethod
    def parseElement(element, ff):
2158
2159
        generator = CustomGBGenerator(ff)
        ff.registerGenerator(generator)
2160
2161
2162
2163
        for param in element.findall('GlobalParameter'):
            generator.globalParams[param.attrib['name']] = float(param.attrib['defaultValue'])
        for param in element.findall('PerParticleParameter'):
            generator.perParticleParams.append(param.attrib['name'])
2164
2165
        generator.params = ForceField._AtomTypeParameters(ff, 'CustomGBForce', 'Atom', generator.perParticleParams)
        generator.params.parseDefinitions(element)
2166
2167
2168
2169
2170
2171
2172
2173
2174
        computationMap = {"SingleParticle" : mm.CustomGBForce.SingleParticle,
                          "ParticlePair" : mm.CustomGBForce.ParticlePair,
                          "ParticlePairNoExclusions" : mm.CustomGBForce.ParticlePairNoExclusions}
        for value in element.findall('ComputedValue'):
            generator.computedValues.append((value.attrib['name'], value.text, computationMap[value.attrib['type']]))
        for term in element.findall('EnergyTerm'):
            generator.energyTerms.append((term.text, computationMap[term.attrib['type']]))
        for function in element.findall("Function"):
            values = [float(x) for x in function.text.split()]
2175
2176
2177
2178
2179
2180
2181
2182
2183
2184
2185
            if 'type' in function.attrib:
                type = function.attrib['type']
            else:
                type = 'Continuous1D'
            params = {}
            for key in function.attrib:
                if key.endswith('size'):
                    params[key] = int(function.attrib[key])
                elif key.endswith('min') or key.endswith('max'):
                    params[key] = float(function.attrib[key])
            generator.functions.append((function.attrib['name'], type, values, params))
Justin MacCallum's avatar
Justin MacCallum committed
2186

2187
2188
2189
2190
2191
    def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
        methodMap = {NoCutoff:mm.CustomGBForce.NoCutoff,
                     CutoffNonPeriodic:mm.CustomGBForce.CutoffNonPeriodic,
                     CutoffPeriodic:mm.CustomGBForce.CutoffPeriodic}
        if nonbondedMethod not in methodMap:
Justin MacCallum's avatar
Justin MacCallum committed
2192
            raise ValueError('Illegal nonbonded method for CustomGBForce')
2193
2194
2195
2196
2197
2198
2199
2200
2201
        force = mm.CustomGBForce()
        for param in self.globalParams:
            force.addGlobalParameter(param, self.globalParams[param])
        for param in self.perParticleParams:
            force.addPerParticleParameter(param)
        for value in self.computedValues:
            force.addComputedValue(value[0], value[1], value[2])
        for term in self.energyTerms:
            force.addEnergyTerm(term[0], term[1])
2202
2203
2204
2205
2206
2207
2208
2209
2210
2211
2212
2213
2214
        for (name, type, values, params) in self.functions:
            if type == 'Continuous1D':
                force.addTabulatedFunction(name, mm.Continuous1DFunction(values, params['min'], params['max']))
            elif type == 'Continuous2D':
                force.addTabulatedFunction(name, mm.Continuous2DFunction(params['xsize'], params['ysize'], values, params['xmin'], params['xmax'], params['ymin'], params['ymax']))
            elif type == 'Continuous3D':
                force.addTabulatedFunction(name, mm.Continuous2DFunction(params['xsize'], params['ysize'], params['zsize'], values, params['xmin'], params['xmax'], params['ymin'], params['ymax'], params['zmin'], params['zmax']))
            elif type == 'Discrete1D':
                force.addTabulatedFunction(name, mm.Discrete1DFunction(values))
            elif type == 'Discrete2D':
                force.addTabulatedFunction(name, mm.Discrete2DFunction(params['xsize'], params['ysize'], values))
            elif type == 'Discrete3D':
                force.addTabulatedFunction(name, mm.Discrete2DFunction(params['xsize'], params['ysize'], params['zsize'], values))
2215
        for atom in data.atoms:
2216
2217
            values = self.params.getAtomParameters(atom, data)
            force.addParticle(values)
2218
2219
2220
2221
2222
2223
        force.setNonbondedMethod(methodMap[nonbondedMethod])
        force.setCutoffDistance(nonbondedCutoff)
        sys.addForce(force)

parsers["CustomGBForce"] = CustomGBGenerator.parseElement

2224
2225

## @private
2226
class CustomManyParticleGenerator(object):
2227
2228
2229
2230
2231
2232
2233
2234
2235
2236
2237
2238
    """A CustomManyParticleGenerator constructs a CustomManyParticleForce."""

    def __init__(self, forcefield, particlesPerSet, energy, permutationMode, bondCutoff):
        self.ff = forcefield
        self.particlesPerSet = particlesPerSet
        self.energy = energy
        self.permutationMode = permutationMode
        self.bondCutoff = bondCutoff
        self.globalParams = {}
        self.perParticleParams = []
        self.functions = []
        self.typeFilters = []
2239

2240
2241
2242
2243
2244
2245
2246
2247
2248
2249
2250
2251
    @staticmethod
    def parseElement(element, ff):
        permutationMap = {"SinglePermutation" : mm.CustomManyParticleForce.SinglePermutation,
                          "UniqueCentralParticle" : mm.CustomManyParticleForce.UniqueCentralParticle}
        generator = CustomManyParticleGenerator(ff, int(element.attrib['particlesPerSet']), element.attrib['energy'], permutationMap[element.attrib['permutationMode']], int(element.attrib['bondCutoff']))
        ff.registerGenerator(generator)
        for param in element.findall('GlobalParameter'):
            generator.globalParams[param.attrib['name']] = float(param.attrib['defaultValue'])
        for param in element.findall('PerParticleParameter'):
            generator.perParticleParams.append(param.attrib['name'])
        for param in element.findall('TypeFilter'):
            generator.typeFilters.append((int(param.attrib['index']), [int(x) for x in param.attrib['types'].split(',')]))
2252
2253
        generator.params = ForceField._AtomTypeParameters(ff, 'CustomManyParticleForce', 'Atom', generator.perParticleParams)
        generator.params.parseDefinitions(element)
2254
2255
2256
2257
2258
2259
2260
2261
2262
2263
2264
2265
2266
2267
2268
2269
2270
2271
2272
2273
2274
2275
2276
2277
2278
2279
2280
2281
2282

    def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
        methodMap = {NoCutoff:mm.CustomManyParticleForce.NoCutoff,
                     CutoffNonPeriodic:mm.CustomManyParticleForce.CutoffNonPeriodic,
                     CutoffPeriodic:mm.CustomManyParticleForce.CutoffPeriodic}
        if nonbondedMethod not in methodMap:
            raise ValueError('Illegal nonbonded method for CustomManyParticleForce')
        force = mm.CustomManyParticleForce(self.particlesPerSet, self.energy)
        force.setPermutationMode(self.permutationMode)
        for param in self.globalParams:
            force.addGlobalParameter(param, self.globalParams[param])
        for param in self.perParticleParams:
            force.addPerParticleParameter(param)
        for index, types in self.typeFilters:
            force.setTypeFilter(index, types)
        for (name, type, values, params) in self.functions:
            if type == 'Continuous1D':
                force.addTabulatedFunction(name, mm.Continuous1DFunction(values, params['min'], params['max']))
            elif type == 'Continuous2D':
                force.addTabulatedFunction(name, mm.Continuous2DFunction(params['xsize'], params['ysize'], values, params['xmin'], params['xmax'], params['ymin'], params['ymax']))
            elif type == 'Continuous3D':
                force.addTabulatedFunction(name, mm.Continuous2DFunction(params['xsize'], params['ysize'], params['zsize'], values, params['xmin'], params['xmax'], params['ymin'], params['ymax'], params['zmin'], params['zmax']))
            elif type == 'Discrete1D':
                force.addTabulatedFunction(name, mm.Discrete1DFunction(values))
            elif type == 'Discrete2D':
                force.addTabulatedFunction(name, mm.Discrete2DFunction(params['xsize'], params['ysize'], values))
            elif type == 'Discrete3D':
                force.addTabulatedFunction(name, mm.Discrete2DFunction(params['xsize'], params['ysize'], params['zsize'], values))
        for atom in data.atoms:
2283
2284
2285
            values = self.params.getAtomParameters(atom, data)
            type = int(self.params.getExtraParameters(atom, data)['filterType'])
            force.addParticle(values, type)
2286
2287
2288
2289
2290
2291
        force.setNonbondedMethod(methodMap[nonbondedMethod])
        force.setCutoffDistance(nonbondedCutoff)
        sys.addForce(force)

    def postprocessSystem(self, sys, data, args):
        # Create exclusions based on bonds.
2292

2293
2294
2295
2296
2297
2298
2299
2300
2301
2302
2303
        bondIndices = []
        for bond in data.bonds:
            bondIndices.append((bond.atom1, bond.atom2))

        # If a virtual site does *not* share exclusions with another atom, add a bond between it and its first parent atom.

        for i in range(sys.getNumParticles()):
            if sys.isVirtualSite(i):
                (site, atoms, excludeWith) = data.virtualSites[data.atoms[i]]
                if excludeWith is None:
                    bondIndices.append((i, site.getParticle(0)))
2304

2305
2306
        # Certain particles, such as lone pairs and Drude particles, share exclusions with a parent atom.
        # If the parent atom does not interact with an atom, the child particle does not either.
2307

2308
2309
2310
2311
2312
2313
2314
2315
2316
        for atom1, atom2 in bondIndices:
            for child1 in data.excludeAtomWith[atom1]:
                bondIndices.append((child1, atom2))
                for child2 in data.excludeAtomWith[atom2]:
                    bondIndices.append((child1, child2))
            for child2 in data.excludeAtomWith[atom2]:
                bondIndices.append((atom1, child2))

        # Create the exclusions.
2317

2318
2319
2320
2321
2322
        nonbonded = [f for f in sys.getForces() if isinstance(f, mm.CustomManyParticleForce)][0]
        nonbonded.createExclusionsFromBonds(bondIndices, self.bondCutoff)

parsers["CustomManyParticleForce"] = CustomManyParticleGenerator.parseElement

Peter Eastman's avatar
Peter Eastman committed
2323
def getAtomPrint(data, atomIndex):
2324

Peter Eastman's avatar
Peter Eastman committed
2325
2326
2327
    if (atomIndex < len(data.atoms)):
        atom = data.atoms[atomIndex]
        returnString = "%4s %4s %5d" % (atom.name, atom.residue.name, atom.residue.index)
2328
    else:
Peter Eastman's avatar
Peter Eastman committed
2329
        returnString = "NA"
2330
2331
2332
2333
2334

    return returnString

#=============================================================================================

Peter Eastman's avatar
Peter Eastman committed
2335
def countConstraint(data):
2336

Peter Eastman's avatar
Peter Eastman committed
2337
    bondCount = 0
2338
2339
2340
2341
2342
2343
2344
    angleCount = 0
    for bond in data.bonds:
        if bond.isConstrained:
            bondCount += 1

    angleCount = 0
    for (angle, isConstrained) in zip(data.angles, data.isAngleConstrained):
Peter Eastman's avatar
Peter Eastman committed
2345
        if (isConstrained):
2346
            angleCount += 1
Justin MacCallum's avatar
Justin MacCallum committed
2347

2348
    print("Constraints bond=%d angle=%d  total=%d" % (bondCount, angleCount, (bondCount+angleCount)))
2349

2350
## @private
2351
class AmoebaBondGenerator(object):
2352
2353
2354

    #=============================================================================================

2355
    """An AmoebaBondGenerator constructs a AmoebaBondForce."""
2356
2357

    #=============================================================================================
Justin MacCallum's avatar
Justin MacCallum committed
2358

2359
2360
    def __init__(self, cubic, quartic):

Peter Eastman's avatar
Peter Eastman committed
2361
2362
2363
2364
2365
2366
        self.cubic = cubic
        self.quartic = quartic
        self.types1 = []
        self.types2 = []
        self.length = []
        self.k = []
Justin MacCallum's avatar
Justin MacCallum committed
2367

2368
2369
2370
2371
2372
    #=============================================================================================

    @staticmethod
    def parseElement(element, forceField):

2373
        # <AmoebaBondForce bond-cubic="-25.5" bond-quartic="379.3125">
2374
        # <Bond class1="1" class2="2" length="0.1437" k="156900.0"/>
Justin MacCallum's avatar
Justin MacCallum committed
2375

2376
        generator = AmoebaBondGenerator(float(element.attrib['bond-cubic']), float(element.attrib['bond-quartic']))
2377
2378
        forceField._forces.append(generator)
        for bond in element.findall('Bond'):
2379
            types = forceField._findAtomTypes(bond.attrib, 2)
peastman's avatar
peastman committed
2380
            if None not in types:
2381
2382
2383
2384
2385
                generator.types1.append(types[0])
                generator.types2.append(types[1])
                generator.length.append(float(bond.attrib['length']))
                generator.k.append(float(bond.attrib['k']))
            else:
2386
                outputString = "AmoebaBondGenerator: error getting types: %s %s" % (
2387
                                    bond.attrib['class1'],
Peter Eastman's avatar
Peter Eastman committed
2388
                                    bond.attrib['class2'])
Justin MacCallum's avatar
Justin MacCallum committed
2389
2390
                raise ValueError(outputString)

2391
2392
    #=============================================================================================

Peter Eastman's avatar
Peter Eastman committed
2393
    def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
2394

Mark Friedrichs's avatar
Mark Friedrichs committed
2395
        #countConstraint(data)
Mark Friedrichs's avatar
Cleanup  
Mark Friedrichs committed
2396

Peter Eastman's avatar
Peter Eastman committed
2397
        existing = [sys.getForce(i) for i in range(sys.getNumForces())]
2398
        existing = [f for f in existing if type(f) == mm.AmoebaBondForce]
2399
        if len(existing) == 0:
2400
            force = mm.AmoebaBondForce()
2401
2402
2403
2404
            sys.addForce(force)
        else:
            force = existing[0]

2405
2406
        force.setAmoebaGlobalBondCubic(self.cubic)
        force.setAmoebaGlobalBondQuartic(self.quartic)
2407
2408
2409
2410
2411
2412
2413
2414
2415
2416

        for bond in data.bonds:
            type1 = data.atomType[data.atoms[bond.atom1]]
            type2 = data.atomType[data.atoms[bond.atom2]]
            for i in range(len(self.types1)):
                types1 = self.types1[i]
                types2 = self.types2[i]
                if (type1 in types1 and type2 in types2) or (type1 in types2 and type2 in types1):
                    bond.length = self.length[i]
                    if bond.isConstrained:
2417
                        data.addConstraint(sys, bond.atom1, bond.atom2, self.length[i])
2418
2419
2420
2421
                    elif self.k[i] != 0:
                        force.addBond(bond.atom1, bond.atom2, self.length[i], self.k[i])
                    break

2422
parsers["AmoebaBondForce"] = AmoebaBondGenerator.parseElement
2423
2424
2425
2426

#=============================================================================================
# Add angle constraint
#=============================================================================================
Justin MacCallum's avatar
Justin MacCallum committed
2427

Peter Eastman's avatar
Peter Eastman committed
2428
def addAngleConstraint(angle, idealAngle, data, sys):
2429
2430

    # Find the two bonds that make this angle.
Justin MacCallum's avatar
Justin MacCallum committed
2431

Peter Eastman's avatar
Peter Eastman committed
2432
2433
    bond1 = None
    bond2 = None
2434
2435
2436
2437
2438
2439
2440
    for bond in data.atomBonds[angle[1]]:
        atom1 = data.bonds[bond].atom1
        atom2 = data.bonds[bond].atom2
        if atom1 == angle[0] or atom2 == angle[0]:
            bond1 = bond
        elif atom1 == angle[2] or atom2 == angle[2]:
            bond2 = bond
Justin MacCallum's avatar
Justin MacCallum committed
2441

2442
        # Compute the distance between atoms and add a constraint
Justin MacCallum's avatar
Justin MacCallum committed
2443

2444
2445
2446
2447
        if bond1 is not None and bond2 is not None:
            l1 = data.bonds[bond1].length
            l2 = data.bonds[bond2].length
            if l1 is not None and l2 is not None:
Peter Eastman's avatar
Peter Eastman committed
2448
                length = sqrt(l1*l1 + l2*l2 - 2*l1*l2*cos(idealAngle))
2449
                data.addConstraint(sys, angle[0], angle[2], length)
2450
2451
2452
                return

#=============================================================================================
2453
## @private
2454
class AmoebaAngleGenerator(object):
2455
2456

    #=============================================================================================
2457
    """An AmoebaAngleGenerator constructs a AmoebaAngleForce."""
2458
    #=============================================================================================
Justin MacCallum's avatar
Justin MacCallum committed
2459

2460
2461
    def __init__(self, forceField, cubic, quartic, pentic, sextic):

Peter Eastman's avatar
Peter Eastman committed
2462
2463
2464
2465
2466
        self.forceField = forceField
        self.cubic = cubic
        self.quartic = quartic
        self.pentic = pentic
        self.sextic = sextic
2467

Peter Eastman's avatar
Peter Eastman committed
2468
2469
2470
        self.types1 = []
        self.types2 = []
        self.types3 = []
2471

Peter Eastman's avatar
Peter Eastman committed
2472
2473
        self.angle = []
        self.k = []
Justin MacCallum's avatar
Justin MacCallum committed
2474

2475
2476
2477
2478
2479
    #=============================================================================================

    @staticmethod
    def parseElement(element, forceField):

2480
        # <AmoebaAngleForce angle-cubic="-0.014" angle-quartic="5.6e-05" angle-pentic="-7e-07" angle-sextic="2.2e-08">
2481
2482
        #   <Angle class1="2" class2="1" class3="3" k="0.0637259642196" angle1="122.00"  />

2483
        generator = AmoebaAngleGenerator(forceField, float(element.attrib['angle-cubic']), float(element.attrib['angle-quartic']),  float(element.attrib['angle-pentic']), float(element.attrib['angle-sextic']))
2484
2485
        forceField._forces.append(generator)
        for angle in element.findall('Angle'):
2486
            types = forceField._findAtomTypes(angle.attrib, 3)
peastman's avatar
peastman committed
2487
            if None not in types:
2488
2489
2490
2491
2492
2493

                generator.types1.append(types[0])
                generator.types2.append(types[1])
                generator.types3.append(types[2])

                angleList = []
Peter Eastman's avatar
Peter Eastman committed
2494
                angleList.append(float(angle.attrib['angle1']))
2495
2496

                try:
Peter Eastman's avatar
Peter Eastman committed
2497
                    angleList.append(float(angle.attrib['angle2']))
2498
                    try:
Peter Eastman's avatar
Peter Eastman committed
2499
                        angleList.append(float(angle.attrib['angle3']))
2500
2501
2502
2503
2504
2505
2506
                    except:
                        pass
                except:
                    pass
                generator.angle.append(angleList)
                generator.k.append(float(angle.attrib['k']))
            else:
2507
                outputString = "AmoebaAngleGenerator: error getting types: %s %s %s" % (
2508
2509
                                    angle.attrib['class1'],
                                    angle.attrib['class2'],
Peter Eastman's avatar
Peter Eastman committed
2510
                                    angle.attrib['class3'])
Justin MacCallum's avatar
Justin MacCallum committed
2511
2512
                raise ValueError(outputString)

2513
2514
2515
2516
    #=============================================================================================
    # createForce is bypassed here since the AmoebaOutOfPlaneBendForce generator must first execute
    # and partition angles into in-plane and non-in-plane angles
    #=============================================================================================
Justin MacCallum's avatar
Justin MacCallum committed
2517

Peter Eastman's avatar
Peter Eastman committed
2518
    def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
2519
2520
2521
2522
2523
2524
        pass

    #=============================================================================================
    # createForcePostOpBendAngle is called by AmoebaOutOfPlaneBendForce with the list of
    # non-in-plane angles
    #=============================================================================================
Justin MacCallum's avatar
Justin MacCallum committed
2525

Peter Eastman's avatar
Peter Eastman committed
2526
    def createForcePostOpBendAngle(self, sys, data, nonbondedMethod, nonbondedCutoff, angleList, args):
2527
2528
2529
2530

        # get force

        existing = [sys.getForce(i) for i in range(sys.getNumForces())]
2531
        existing = [f for f in existing if type(f) == mm.AmoebaAngleForce]
2532
2533

        if len(existing) == 0:
2534
            force = mm.AmoebaAngleForce()
2535
2536
2537
2538
            sys.addForce(force)
        else:
            force = existing[0]

Mark Friedrichs's avatar
Cleanup  
Mark Friedrichs committed
2539
        # set scalars
2540

2541
2542
2543
2544
        force.setAmoebaGlobalAngleCubic(self.cubic)
        force.setAmoebaGlobalAngleQuartic(self.quartic)
        force.setAmoebaGlobalAnglePentic(self.pentic)
        force.setAmoebaGlobalAngleSextic(self.sextic)
2545
2546

        for angleDict in angleList:
Peter Eastman's avatar
Peter Eastman committed
2547
2548
            angle = angleDict['angle']
            isConstrained = angleDict['isConstrained']
2549

Peter Eastman's avatar
Peter Eastman committed
2550
2551
2552
            type1 = data.atomType[data.atoms[angle[0]]]
            type2 = data.atomType[data.atoms[angle[1]]]
            type3 = data.atomType[data.atoms[angle[2]]]
2553
2554
2555
2556
2557
2558
2559
            for i in range(len(self.types1)):
                types1 = self.types1[i]
                types2 = self.types2[i]
                types3 = self.types3[i]
                if (type1 in types1 and type2 in types2 and type3 in types3) or (type1 in types3 and type2 in types2 and type3 in types1):
                    if isConstrained and self.k[i] != 0.0:
                        angleDict['idealAngle'] = self.angle[i][0]
2560
                        addAngleConstraint(angle, self.angle[i][0]*math.pi/180.0, data, sys)
2561
                    elif self.k[i] != 0:
Peter Eastman's avatar
Peter Eastman committed
2562
2563
                        lenAngle = len(self.angle[i])
                        if (lenAngle > 1):
2564
2565
2566
2567
2568
2569
                            # get k-index by counting number of non-angle hydrogens on the central atom
                            # based on kangle.f
                            numberOfHydrogens = 0
                            for bond in data.atomBonds[angle[1]]:
                                atom1 = data.bonds[bond].atom1
                                atom2 = data.bonds[bond].atom2
Peter Eastman's avatar
Peter Eastman committed
2570
                                if (atom1 == angle[1] and atom2 != angle[0] and atom2 != angle[2] and (sys.getParticleMass(atom2)/unit.dalton) < 1.90):
2571
                                    numberOfHydrogens += 1
Peter Eastman's avatar
Peter Eastman committed
2572
                                if (atom2 == angle[1] and atom1 != angle[0] and atom1 != angle[2] and (sys.getParticleMass(atom1)/unit.dalton) < 1.90):
2573
                                    numberOfHydrogens += 1
Peter Eastman's avatar
Peter Eastman committed
2574
                            if (numberOfHydrogens < lenAngle):
2575
2576
                                angleValue =  self.angle[i][numberOfHydrogens]
                            else:
2577
                                outputString = "AmoebaAngleGenerator angle index=%d is out of range: [0, %5d] " % (numberOfHydrogens, lenAngle)
Justin MacCallum's avatar
Justin MacCallum committed
2578
                                raise ValueError(outputString)
2579
2580
                        else:
                            angleValue =  self.angle[i][0]
Justin MacCallum's avatar
Justin MacCallum committed
2581

2582
                        angleDict['idealAngle'] = angleValue
Peter Eastman's avatar
Peter Eastman committed
2583
                        force.addAngle(angle[0], angle[1], angle[2], angleValue, self.k[i])
2584
2585
2586
2587
2588
2589
                    break

    #=============================================================================================
    # createForcePostOpBendInPlaneAngle is called by AmoebaOutOfPlaneBendForce with the list of
    # in-plane angles
    #=============================================================================================
Justin MacCallum's avatar
Justin MacCallum committed
2590

Peter Eastman's avatar
Peter Eastman committed
2591
    def createForcePostOpBendInPlaneAngle(self, sys, data, nonbondedMethod, nonbondedCutoff, angleList, args):
2592
2593
2594
2595

        # get force

        existing = [sys.getForce(i) for i in range(sys.getNumForces())]
2596
        existing = [f for f in existing if type(f) == mm.AmoebaInPlaneAngleForce]
2597
2598

        if len(existing) == 0:
2599
            force = mm.AmoebaInPlaneAngleForce()
2600
2601
2602
2603
2604
2605
            sys.addForce(force)
        else:
            force = existing[0]

        # scalars

2606
2607
2608
2609
        force.setAmoebaGlobalInPlaneAngleCubic(self.cubic)
        force.setAmoebaGlobalInPlaneAngleQuartic(self.quartic)
        force.setAmoebaGlobalInPlaneAnglePentic(self.pentic)
        force.setAmoebaGlobalInPlaneAngleSextic(self.sextic)
2610
2611

        for angleDict in angleList:
Justin MacCallum's avatar
Justin MacCallum committed
2612

Peter Eastman's avatar
Peter Eastman committed
2613
2614
            angle = angleDict['angle']
            isConstrained = angleDict['isConstrained']
2615

Peter Eastman's avatar
Peter Eastman committed
2616
2617
2618
            type1 = data.atomType[data.atoms[angle[0]]]
            type2 = data.atomType[data.atoms[angle[1]]]
            type3 = data.atomType[data.atoms[angle[2]]]
2619
2620
2621
2622
2623
2624
2625
2626
2627

            for i in range(len(self.types1)):

                types1 = self.types1[i]
                types2 = self.types2[i]
                types3 = self.types3[i]

                if (type1 in types1 and type2 in types2 and type3 in types3) or (type1 in types3 and type2 in types2 and type3 in types1):
                    angleDict['idealAngle'] = self.angle[i][0]
Peter Eastman's avatar
Peter Eastman committed
2628
                    if (isConstrained and self.k[i] != 0.0):
2629
                        addAngleConstraint(angle, self.angle[i][0]*math.pi/180.0, data, sys)
2630
2631
2632
2633
                    else:
                        force.addAngle(angle[0], angle[1], angle[2], angle[3], self.angle[i][0], self.k[i])
                    break

2634
parsers["AmoebaAngleForce"] = AmoebaAngleGenerator.parseElement
2635
2636
2637

#=============================================================================================
# Generator for the AmoebaOutOfPlaneBend covalent force; also calls methods in the
2638
2639
# AmoebaAngleGenerator to generate the AmoebaAngleForce and
# AmoebaInPlaneAngleForce
2640
2641
#=============================================================================================

2642
## @private
2643
class AmoebaOutOfPlaneBendGenerator(object):
2644
2645
2646
2647

    #=============================================================================================

    """An AmoebaOutOfPlaneBendGenerator constructs a AmoebaOutOfPlaneBendForce."""
Justin MacCallum's avatar
Justin MacCallum committed
2648

2649
2650
2651
2652
    #=============================================================================================

    def __init__(self, forceField, type, cubic, quartic, pentic, sextic):

Peter Eastman's avatar
Peter Eastman committed
2653
2654
2655
2656
2657
2658
        self.forceField = forceField
        self.type = type
        self.cubic = cubic
        self.quartic = quartic
        self.pentic = pentic
        self.sextic = sextic
2659

Peter Eastman's avatar
Peter Eastman committed
2660
2661
2662
2663
        self.types1 = []
        self.types2 = []
        self.types3 = []
        self.types4 = []
2664

Peter Eastman's avatar
Peter Eastman committed
2665
        self.ks = []
2666
2667
2668
2669
2670

    #=============================================================================================
    # Local version of findAtomTypes needed since class indices are 0 (i.e., not recognized)
    # for types3 and 4
    #=============================================================================================
Justin MacCallum's avatar
Justin MacCallum committed
2671

2672
2673
2674
2675
2676
2677
2678
2679
2680
2681
2682
2683
2684
2685
2686
2687
2688
2689
2690
2691
2692
2693
2694
2695
2696
    def findAtomTypes(self, forceField, node, num):
        """Parse the attributes on an XML tag to find the set of atom types for each atom it involves."""
        types = []
        attrib = node.attrib
        for i in range(num):
            if num == 1:
                suffix = ''
            else:
                suffix = str(i+1)
            classAttrib = 'class'+suffix
            if classAttrib in attrib:
                if attrib[classAttrib] in forceField._atomClasses:
                    types.append(forceField._atomClasses[attrib[classAttrib]])
                else:
                    types.append(set())
        return types

    #=============================================================================================

    @staticmethod
    def parseElement(element, forceField):

        #  <AmoebaOutOfPlaneBendForce type="ALLINGER" opbend-cubic="-0.014" opbend-quartic="5.6e-05" opbend-pentic="-7e-07" opbend-sextic="2.2e-08">
        #   <Angle class1="2" class2="1" class3="0" class4="0" k="0.0531474541591"/>
        #   <Angle class1="3" class2="1" class3="0" class4="0" k="0.0898536095496"/>
Justin MacCallum's avatar
Justin MacCallum committed
2697

2698
2699
        # get global scalar parameters

Peter Eastman's avatar
Peter Eastman committed
2700
        generator = AmoebaOutOfPlaneBendGenerator(forceField, element.attrib['type'],
2701
2702
2703
                                                   float(element.attrib['opbend-cubic']),
                                                   float(element.attrib['opbend-quartic']),
                                                   float(element.attrib['opbend-pentic']),
Peter Eastman's avatar
Peter Eastman committed
2704
                                                   float(element.attrib['opbend-sextic']))
2705
2706
2707
2708

        forceField._forces.append(generator)

        for angle in element.findall('Angle'):
Peter Eastman's avatar
Peter Eastman committed
2709
            types = generator.findAtomTypes(forceField, angle, 4)
2710
2711
            if types is not None:

Peter Eastman's avatar
Peter Eastman committed
2712
2713
2714
2715
                generator.types1.append(types[0])
                generator.types2.append(types[1])
                generator.types3.append(types[2])
                generator.types4.append(types[3])
2716

Peter Eastman's avatar
Peter Eastman committed
2717
                generator.ks.append(float(angle.attrib['k']))
2718
2719

            else:
Mark Friedrichs's avatar
Cleanup  
Mark Friedrichs committed
2720
2721
                outputString = "AmoebaOutOfPlaneBendGenerator error getting types: %s %s %s %s." % (
                               angle.attrib['class1'], angle.attrib['class2'], angle.attrib['class3'], angle.attrib['class4'])
Justin MacCallum's avatar
Justin MacCallum committed
2722
2723
                raise ValueError(outputString)

2724
2725
2726
2727
2728
2729
    #=============================================================================================
    # Get middle atom in a angle
    # return index of middle atom or -1 if no middle is found
    # This method appears not to be needed since the angle[1] entry appears to always
    # be the middle atom. However, was unsure if this is guaranteed
    #=============================================================================================
Justin MacCallum's avatar
Justin MacCallum committed
2730

Peter Eastman's avatar
Peter Eastman committed
2731
    def getMiddleAtom(self, angle, data):
2732
2733
2734

        # find atom shared by both bonds making up the angle

Peter Eastman's avatar
Peter Eastman committed
2735
        middleAtom = -1
Justin MacCallum's avatar
Justin MacCallum committed
2736
        for atomIndex in angle:
Peter Eastman's avatar
Peter Eastman committed
2737
            isMiddle = 0
2738
2739
2740
            for bond in data.atomBonds[atomIndex]:
                atom1 = data.bonds[bond].atom1
                atom2 = data.bonds[bond].atom2
Peter Eastman's avatar
Peter Eastman committed
2741
                if (atom1 != atomIndex):
2742
2743
2744
                    partner = atom1
                else:
                    partner = atom2
Justin MacCallum's avatar
Justin MacCallum committed
2745
                if (partner == angle[0] or partner == angle[1] or partner == angle[2]):
2746
2747
                    isMiddle += 1

Peter Eastman's avatar
Peter Eastman committed
2748
            if (isMiddle == 2):
2749
2750
2751
2752
2753
                return atomIndex
        return -1

    #=============================================================================================

Peter Eastman's avatar
Peter Eastman committed
2754
    def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
2755
2756
2757
2758
2759
2760
2761
2762
2763
2764
2765
2766
2767

        # get force

        existing = [sys.getForce(i) for i in range(sys.getNumForces())]
        existing = [f for f in existing if type(f) == mm.AmoebaOutOfPlaneBendForce]
        if len(existing) == 0:
            force = mm.AmoebaOutOfPlaneBendForce()
            sys.addForce(force)
        else:
            force = existing[0]

        # set scalars

Peter Eastman's avatar
Peter Eastman committed
2768
2769
2770
2771
        force.setAmoebaGlobalOutOfPlaneBendCubic(  self.cubic)
        force.setAmoebaGlobalOutOfPlaneBendQuartic(self.quartic)
        force.setAmoebaGlobalOutOfPlaneBendPentic( self.pentic)
        force.setAmoebaGlobalOutOfPlaneBendSextic( self.sextic)
2772
2773
2774
2775

        # this hash is used to insure the out-of-plane-bend bonds
        # are only added once

Peter Eastman's avatar
Peter Eastman committed
2776
        skipAtoms = dict()
2777
2778
2779
2780

        # these lists are used in the partitioning of the angles into
        # angle and inPlane angles

Peter Eastman's avatar
Peter Eastman committed
2781
2782
        inPlaneAngles = []
        nonInPlaneAngles = []
2783
        nonInPlaneAnglesConstrained = []
Peter Eastman's avatar
Peter Eastman committed
2784
        idealAngles = []*len(data.angles)
2785
2786
2787

        for (angle, isConstrained) in zip(data.angles, data.isAngleConstrained):

Peter Eastman's avatar
Peter Eastman committed
2788
2789
2790
            middleAtom = self.getMiddleAtom(angle, data)
            if (middleAtom > -1):
                middleType = data.atomType[data.atoms[middleAtom]]
2791
2792
                middleCovalency = len(data.atomBonds[middleAtom])
            else:
Peter Eastman's avatar
Peter Eastman committed
2793
                middleType = -1
2794
2795
                middleCovalency = -1

Justin MacCallum's avatar
Justin MacCallum committed
2796
            # if middle atom has covalency of 3 and
2797
            # the types of the middle atom and the partner atom (atom bonded to
Mark Friedrichs's avatar
Cleanup  
Mark Friedrichs committed
2798
            # middle atom, but not in angle) match types1 and types2, then
Justin MacCallum's avatar
Justin MacCallum committed
2799
            # three out-of-plane bend angles are generated. Three in-plane angle
Mark Friedrichs's avatar
Cleanup  
Mark Friedrichs committed
2800
            # are also generated. If the conditions are not satisfied, the angle is marked as 'generic' angle (not a in-plane angle)
2801

Peter Eastman's avatar
Peter Eastman committed
2802
            if (middleAtom > -1 and middleCovalency == 3 and middleAtom not in skipAtoms):
2803

Peter Eastman's avatar
Peter Eastman committed
2804
2805
2806
2807
                partners = []
                partnerSet = set()
                partnerTypes = []
                partnerK = []
2808
2809
2810
2811

                for bond in data.atomBonds[middleAtom]:
                    atom1 = data.bonds[bond].atom1
                    atom2 = data.bonds[bond].atom2
Peter Eastman's avatar
Peter Eastman committed
2812
                    if (atom1 != middleAtom):
2813
2814
2815
2816
2817
2818
2819
2820
                        partner = atom1
                    else:
                        partner = atom2

                    partnerType = data.atomType[data.atoms[partner]]
                    for i in range(len(self.types1)):
                        types1 = self.types1[i]
                        types2 = self.types2[i]
Peter Eastman's avatar
Peter Eastman committed
2821
2822
2823
2824
2825
                        if (middleType in types2 and partnerType in types1):
                            partners.append(partner)
                            partnerSet.add(partner)
                            partnerTypes.append(partnerType)
                            partnerK.append(self.ks[i])
Justin MacCallum's avatar
Justin MacCallum committed
2826

Peter Eastman's avatar
Peter Eastman committed
2827
                if (len(partners) == 3):
2828

Peter Eastman's avatar
Peter Eastman committed
2829
2830
2831
                    force.addOutOfPlaneBend(partners[0], middleAtom, partners[1], partners[2], partnerK[2])
                    force.addOutOfPlaneBend(partners[0], middleAtom, partners[2], partners[1], partnerK[1])
                    force.addOutOfPlaneBend(partners[1], middleAtom, partners[2], partners[0], partnerK[0])
2832

Mark Friedrichs's avatar
Cleanup  
Mark Friedrichs committed
2833
2834
                    # skipAtoms is used to insure angles are only included once

2835
                    skipAtoms[middleAtom] = set()
Peter Eastman's avatar
Peter Eastman committed
2836
2837
2838
2839
                    skipAtoms[middleAtom].add(partners[0])
                    skipAtoms[middleAtom].add(partners[1])
                    skipAtoms[middleAtom].add(partners[2])

Mark Friedrichs's avatar
Cleanup  
Mark Friedrichs committed
2840
2841
                    # in-plane angle

Peter Eastman's avatar
Peter Eastman committed
2842
2843
2844
2845
2846
                    angleDict = {}
                    angleList = []
                    angleList.append(angle[0])
                    angleList.append(angle[1])
                    angleList.append(angle[2])
2847
2848
                    angleDict['angle'] = angleList

Peter Eastman's avatar
Peter Eastman committed
2849
                    angleDict['isConstrained'] = 0
2850

Peter Eastman's avatar
Peter Eastman committed
2851
2852
2853
2854
                    angleSet = set()
                    angleSet.add(angle[0])
                    angleSet.add(angle[1])
                    angleSet.add(angle[2])
2855
2856

                    for atomIndex in partnerSet:
Peter Eastman's avatar
Peter Eastman committed
2857
2858
                        if (atomIndex not in angleSet):
                            angleList.append(atomIndex)
2859

Peter Eastman's avatar
Peter Eastman committed
2860
                    inPlaneAngles.append(angleDict)
2861
2862

                else:
Peter Eastman's avatar
Peter Eastman committed
2863
2864
2865
2866
                    angleDict = {}
                    angleDict['angle'] = angle
                    angleDict['isConstrained'] = isConstrained
                    nonInPlaneAngles.append(angleDict)
2867
            else:
Peter Eastman's avatar
Peter Eastman committed
2868
                if (middleAtom > -1 and middleCovalency == 3 and middleAtom in skipAtoms):
2869

Peter Eastman's avatar
Peter Eastman committed
2870
                    partnerSet = skipAtoms[middleAtom]
Justin MacCallum's avatar
Justin MacCallum committed
2871

Peter Eastman's avatar
Peter Eastman committed
2872
                    angleDict = {}
2873

Peter Eastman's avatar
Peter Eastman committed
2874
2875
2876
2877
2878
                    angleList = []
                    angleList.append(angle[0])
                    angleList.append(angle[1])
                    angleList.append(angle[2])
                    angleDict['angle'] = angleList
2879

Peter Eastman's avatar
Peter Eastman committed
2880
                    angleDict['isConstrained'] = isConstrained
2881

Peter Eastman's avatar
Peter Eastman committed
2882
2883
2884
2885
                    angleSet = set()
                    angleSet.add(angle[0])
                    angleSet.add(angle[1])
                    angleSet.add(angle[2])
2886
2887

                    for atomIndex in partnerSet:
Peter Eastman's avatar
Peter Eastman committed
2888
2889
                        if (atomIndex not in angleSet):
                            angleList.append(atomIndex)
2890

Peter Eastman's avatar
Peter Eastman committed
2891
                    inPlaneAngles.append(angleDict)
2892
2893

                else:
Peter Eastman's avatar
Peter Eastman committed
2894
2895
                    angleDict = {}
                    angleDict['angle'] = angle
2896
                    angleDict['isConstrained'] = isConstrained
Peter Eastman's avatar
Peter Eastman committed
2897
                    nonInPlaneAngles.append(angleDict)
2898

2899
        # get AmoebaAngleGenerator and add AmoebaAngle and AmoebaInPlaneAngle forces
2900
2901

        for force in self.forceField._forces:
Justin MacCallum's avatar
Justin MacCallum committed
2902
            if (force.__class__.__name__ == 'AmoebaAngleGenerator'):
Peter Eastman's avatar
Peter Eastman committed
2903
2904
                force.createForcePostOpBendAngle(sys, data, nonbondedMethod, nonbondedCutoff, nonInPlaneAngles, args)
                force.createForcePostOpBendInPlaneAngle(sys, data, nonbondedMethod, nonbondedCutoff, inPlaneAngles, args)
2905
2906

        for force in self.forceField._forces:
Justin MacCallum's avatar
Justin MacCallum committed
2907
            if (force.__class__.__name__ == 'AmoebaStretchBendGenerator'):
2908
                for angleDict in inPlaneAngles:
Peter Eastman's avatar
Peter Eastman committed
2909
                    nonInPlaneAngles.append(angleDict)
2910
                force.createForcePostAmoebaBondForce(sys, data, nonbondedMethod, nonbondedCutoff, nonInPlaneAngles, args)
2911
2912
2913
2914
2915

parsers["AmoebaOutOfPlaneBendForce"] = AmoebaOutOfPlaneBendGenerator.parseElement

#=============================================================================================

2916
## @private
2917
class AmoebaTorsionGenerator(object):
2918
2919
2920
2921
2922
2923
2924

    #=============================================================================================
    """An AmoebaTorsionGenerator constructs a AmoebaTorsionForce."""
    #=============================================================================================

    def __init__(self, torsionUnit):

Peter Eastman's avatar
Peter Eastman committed
2925
        self.torsionUnit = torsionUnit
2926

Peter Eastman's avatar
Peter Eastman committed
2927
2928
2929
2930
        self.types1 = []
        self.types2 = []
        self.types3 = []
        self.types4 = []
2931

Peter Eastman's avatar
Peter Eastman committed
2932
2933
2934
        self.t1 = []
        self.t2 = []
        self.t3 = []
Justin MacCallum's avatar
Justin MacCallum committed
2935

2936
2937
2938
2939
2940
2941
2942
2943
    #=============================================================================================

    @staticmethod
    def parseElement(element, forceField):

        #  <AmoebaTorsionForce torsionUnit="0.5">
        #   <Torsion class1="3" class2="1" class3="2" class4="3"   amp1="0.0" angle1="0.0"   amp2="0.0" angle2="3.14159265359"   amp3="0.0" angle3="0.0" />
        #   <Torsion class1="3" class2="1" class3="2" class4="6"   amp1="0.0" angle1="0.0"   amp2="0.0" angle2="3.14159265359"   amp3="-0.263592" angle3="0.0" />
Justin MacCallum's avatar
Justin MacCallum committed
2944

Peter Eastman's avatar
Peter Eastman committed
2945
        generator = AmoebaTorsionGenerator(float(element.attrib['torsionUnit']))
2946
2947
2948
2949
2950
2951
        forceField._forces.append(generator)

        # collect particle classes and t1,t2,t3,
        # where ti=[amplitude_i,angle_i]

        for torsion in element.findall('Torsion'):
2952
            types = forceField._findAtomTypes(torsion.attrib, 4)
peastman's avatar
peastman committed
2953
            if None not in types:
2954
2955
2956
2957
2958
2959
2960

                generator.types1.append(types[0])
                generator.types2.append(types[1])
                generator.types3.append(types[2])
                generator.types4.append(types[3])

                for ii in range(1,4):
Peter Eastman's avatar
Peter Eastman committed
2961
2962
                    tInfo = []
                    suffix = str(ii)
2963
2964
2965
2966
2967
2968
                    ampName = 'amp' + suffix
                    tInfo.append(float(torsion.attrib[ampName]))

                    angName = 'angle' + suffix
                    tInfo.append(float(torsion.attrib[angName]))

Peter Eastman's avatar
Peter Eastman committed
2969
2970
2971
2972
2973
2974
                    if (ii == 1):
                        generator.t1.append(tInfo)
                    elif (ii == 2):
                        generator.t2.append(tInfo)
                    elif (ii == 3):
                        generator.t3.append(tInfo)
2975
2976
2977

            else:
                outputString = "AmoebaTorsionGenerator: error getting types: %s %s %s %s" % (
2978
2979
2980
2981
                                    torsion.attrib['class1'],
                                    torsion.attrib['class2'],
                                    torsion.attrib['class3'],
                                    torsion.attrib['class4'])
Justin MacCallum's avatar
Justin MacCallum committed
2982
2983
                raise ValueError(outputString)

2984
2985
2986
2987
2988
    #=============================================================================================

    def createForce(self, sys, data, nontorsionedMethod, nontorsionedCutoff, args):

        existing = [sys.getForce(i) for i in range(sys.getNumForces())]
2989
        existing = [f for f in existing if type(f) == mm.PeriodicTorsionForce]
2990
        if len(existing) == 0:
2991
            force = mm.PeriodicTorsionForce()
2992
2993
2994
            sys.addForce(force)
        else:
            force = existing[0]
Mark Friedrichs's avatar
Cleanup  
Mark Friedrichs committed
2995

2996
2997
2998
2999
3000
3001
3002
3003
3004
3005
3006
3007
3008
3009
3010
3011
        for torsion in data.propers:

            type1 = data.atomType[data.atoms[torsion[0]]]
            type2 = data.atomType[data.atoms[torsion[1]]]
            type3 = data.atomType[data.atoms[torsion[2]]]
            type4 = data.atomType[data.atoms[torsion[3]]]

            for i in range(len(self.types1)):

                types1 = self.types1[i]
                types2 = self.types2[i]
                types3 = self.types3[i]
                types4 = self.types4[i]

                # match types in forward or reverse direction

Peter Eastman's avatar
Peter Eastman committed
3012
                if (type1 in types1 and type2 in types2 and type3 in types3 and type4 in types4) or (type4 in types1 and type3 in types2 and type2 in types3 and type1 in types4):
3013
3014
3015
3016
3017
3018
                    if self.t1[i][0] != 0:
                        force.addTorsion(torsion[0], torsion[1], torsion[2], torsion[3], 1, self.t1[i][1], self.t1[i][0])
                    if self.t2[i][0] != 0:
                        force.addTorsion(torsion[0], torsion[1], torsion[2], torsion[3], 2, self.t2[i][1], self.t2[i][0])
                    if self.t3[i][0] != 0:
                        force.addTorsion(torsion[0], torsion[1], torsion[2], torsion[3], 3, self.t3[i][1], self.t3[i][0])
3019
3020
3021
3022
3023
3024
                    break

parsers["AmoebaTorsionForce"] = AmoebaTorsionGenerator.parseElement

#=============================================================================================

3025
## @private
3026
class AmoebaPiTorsionGenerator(object):
3027
3028
3029
3030
3031
3032

    #=============================================================================================

    """An AmoebaPiTorsionGenerator constructs a AmoebaPiTorsionForce."""

    #=============================================================================================
Justin MacCallum's avatar
Justin MacCallum committed
3033

3034
    def __init__(self, piTorsionUnit):
Justin MacCallum's avatar
Justin MacCallum committed
3035
        self.piTorsionUnit = piTorsionUnit
Peter Eastman's avatar
Peter Eastman committed
3036
3037
3038
        self.types1 = []
        self.types2 = []
        self.k = []
Justin MacCallum's avatar
Justin MacCallum committed
3039

3040
3041
3042
3043
3044
3045
3046
3047
    #=============================================================================================

    @staticmethod
    def parseElement(element, forceField):

        #  <AmoebaPiTorsionForce piTorsionUnit="1.0">
        #   <PiTorsion class1="1" class2="3" k="28.6604" />

Peter Eastman's avatar
Peter Eastman committed
3048
        generator = AmoebaPiTorsionGenerator(float(element.attrib['piTorsionUnit']))
3049
3050
3051
        forceField._forces.append(generator)

        for piTorsion in element.findall('PiTorsion'):
3052
            types = forceField._findAtomTypes(piTorsion.attrib, 2)
peastman's avatar
peastman committed
3053
            if None not in types:
3054
3055
3056
3057
3058
3059
                generator.types1.append(types[0])
                generator.types2.append(types[1])
                generator.k.append(float(piTorsion.attrib['k']))
            else:
                outputString = "AmoebaPiTorsionGenerator: error getting types: %s %s " % (
                                    piTorsion.attrib['class1'],
Peter Eastman's avatar
Peter Eastman committed
3060
                                    piTorsion.attrib['class2'])
Justin MacCallum's avatar
Justin MacCallum committed
3061
3062
                raise ValueError(outputString)

3063
3064
3065
3066
3067
3068
3069
3070
3071
3072
3073
3074
3075
3076
3077
3078
    #=============================================================================================

    def createForce(self, sys, data, nonpiTorsionedMethod, nonpiTorsionedCutoff, args):

        existing = [sys.getForce(i) for i in range(sys.getNumForces())]
        existing = [f for f in existing if type(f) == mm.AmoebaPiTorsionForce]

        if len(existing) == 0:
            force = mm.AmoebaPiTorsionForce()
            sys.addForce(force)
        else:
            force = existing[0]

        for bond in data.bonds:

            # search for bonds with both atoms in bond having covalency == 3
Justin MacCallum's avatar
Justin MacCallum committed
3079

3080
3081
            atom1 = bond.atom1
            atom2 = bond.atom2
Justin MacCallum's avatar
Justin MacCallum committed
3082

3083
            if (len(data.atomBonds[atom1]) == 3 and len(data.atomBonds[atom2]) == 3):
3084
3085
3086
3087
3088
3089
3090
3091
3092
3093
3094

                type1 = data.atomType[data.atoms[atom1]]
                type2 = data.atomType[data.atoms[atom2]]

                for i in range(len(self.types1)):

                   types1 = self.types1[i]
                   types2 = self.types2[i]

                   if (type1 in types1 and type2 in types2) or (type1 in types2 and type2 in types1):

Justin MacCallum's avatar
Justin MacCallum committed
3095
3096
                       # piTorsionAtom1, piTorsionAtom2 are the atoms bonded to atom1, excluding atom2
                       # piTorsionAtom5, piTorsionAtom6 are the atoms bonded to atom2, excluding atom1
3097
3098
3099
3100
3101
3102
3103
3104
3105
3106
3107
3108

                       piTorsionAtom1 = -1
                       piTorsionAtom2 = -1
                       piTorsionAtom3 = atom1

                       piTorsionAtom4 = atom2
                       piTorsionAtom5 = -1
                       piTorsionAtom6 = -1

                       for bond in data.atomBonds[atom1]:
                           bondedAtom1 = data.bonds[bond].atom1
                           bondedAtom2 = data.bonds[bond].atom2
Peter Eastman's avatar
Peter Eastman committed
3109
                           if (bondedAtom1 != atom1):
3110
3111
3112
                               b1 = bondedAtom1
                           else:
                               b1 = bondedAtom2
Peter Eastman's avatar
Peter Eastman committed
3113
3114
                           if (b1 != atom2):
                               if (piTorsionAtom1 == -1):
Justin MacCallum's avatar
Justin MacCallum committed
3115
                                   piTorsionAtom1 = b1
3116
3117
3118
3119
3120
3121
                               else:
                                   piTorsionAtom2 = b1

                       for bond in data.atomBonds[atom2]:
                           bondedAtom1 = data.bonds[bond].atom1
                           bondedAtom2 = data.bonds[bond].atom2
Peter Eastman's avatar
Peter Eastman committed
3122
                           if (bondedAtom1 != atom2):
3123
3124
3125
3126
                               b1 = bondedAtom1
                           else:
                               b1 = bondedAtom2

Peter Eastman's avatar
Peter Eastman committed
3127
3128
                           if (b1 != atom1):
                               if (piTorsionAtom5 == -1):
Justin MacCallum's avatar
Justin MacCallum committed
3129
                                   piTorsionAtom5 = b1
3130
3131
                               else:
                                   piTorsionAtom6 = b1
Justin MacCallum's avatar
Justin MacCallum committed
3132

Peter Eastman's avatar
Peter Eastman committed
3133
                       force.addPiTorsion(piTorsionAtom1, piTorsionAtom2, piTorsionAtom3, piTorsionAtom4, piTorsionAtom5, piTorsionAtom6, self.k[i])
3134
3135
3136
3137
3138

parsers["AmoebaPiTorsionForce"] = AmoebaPiTorsionGenerator.parseElement

#=============================================================================================

3139
## @private
3140
class AmoebaTorsionTorsionGenerator(object):
3141
3142
3143
3144
3145

    #=============================================================================================
    """An AmoebaTorsionTorsionGenerator constructs a AmoebaTorsionTorsionForce."""
    #=============================================================================================

Peter Eastman's avatar
Peter Eastman committed
3146
    def __init__(self):
3147

Peter Eastman's avatar
Peter Eastman committed
3148
3149
3150
3151
3152
        self.types1 = []
        self.types2 = []
        self.types3 = []
        self.types4 = []
        self.types5 = []
3153

Peter Eastman's avatar
Peter Eastman committed
3154
        self.gridIndex = []
3155

Peter Eastman's avatar
Peter Eastman committed
3156
        self.grids = []
Justin MacCallum's avatar
Justin MacCallum committed
3157

3158
3159
3160
3161
3162
    #=============================================================================================

    @staticmethod
    def parseElement(element, forceField):

Peter Eastman's avatar
Peter Eastman committed
3163
        generator = AmoebaTorsionTorsionGenerator()
3164
3165
3166
3167
3168
3169
3170
        forceField._forces.append(generator)
        maxGridIndex = -1

        # <AmoebaTorsionTorsionForce >
        # <TorsionTorsion class1="3" class2="1" class3="2" class4="3" class5="1" grid="0" nx="25" ny="25" />

        for torsionTorsion in element.findall('TorsionTorsion'):
3171
            types = forceField._findAtomTypes(torsionTorsion.attrib, 5)
peastman's avatar
peastman committed
3172
            if None not in types:
3173
3174
3175
3176
3177
3178
3179

                generator.types1.append(types[0])
                generator.types2.append(types[1])
                generator.types3.append(types[2])
                generator.types4.append(types[3])
                generator.types5.append(types[4])

Peter Eastman's avatar
Peter Eastman committed
3180
3181
                gridIndex = int(torsionTorsion.attrib['grid'])
                if (gridIndex > maxGridIndex):
3182
3183
3184
3185
3186
3187
3188
3189
3190
                    maxGridIndex = gridIndex

                generator.gridIndex.append(gridIndex)
            else:
                outputString = "AmoebaTorsionTorsionGenerator: error getting types: %s %s %s %s %s" % (
                                    torsionTorsion.attrib['class1'],
                                    torsionTorsion.attrib['class2'],
                                    torsionTorsion.attrib['class3'],
                                    torsionTorsion.attrib['class4'],
Peter Eastman's avatar
Peter Eastman committed
3191
                                    torsionTorsion.attrib['class5'] )
Justin MacCallum's avatar
Justin MacCallum committed
3192
3193
                raise ValueError(outputString)

3194
3195
3196
3197
3198
3199
3200
3201
3202
3203
        # load grid

        # xml source

        # <TorsionTorsionGrid grid="0" nx="25" ny="25" >
        # <Grid angle1="-180.00" angle2="-180.00" f="0.0" fx="2.31064374824e-05" fy="0.0" fxy="-0.0052801799672" />
        # <Grid angle1="-165.00" angle2="-180.00" f="-0.66600912" fx="-0.06983370052" fy="-0.075058725744" fxy="-0.0044462732032" />

        # output grid:

Justin MacCallum's avatar
Justin MacCallum committed
3204
3205
3206
3207
3208
3209
        #     grid[x][y][0] = x value
        #     grid[x][y][1] = y value
        #     grid[x][y][2] = function value
        #     grid[x][y][3] = dfdx value
        #     grid[x][y][4] = dfdy value
        #     grid[x][y][5] = dfd(xy) value
3210
3211

        maxGridIndex    += 1
Peter Eastman's avatar
Peter Eastman committed
3212
        generator.grids = maxGridIndex*[]
3213
3214
        for torsionTorsionGrid in element.findall('TorsionTorsionGrid'):

Peter Eastman's avatar
Peter Eastman committed
3215
3216
3217
            gridIndex = int(torsionTorsionGrid.attrib[ "grid"])
            nx = int(torsionTorsionGrid.attrib[ "nx"])
            ny = int(torsionTorsionGrid.attrib[ "ny"])
3218

Peter Eastman's avatar
Peter Eastman committed
3219
3220
            grid = []
            gridCol = []
3221
3222
3223
3224
3225

            gridColIndex = 0

            for gridEntry in torsionTorsionGrid.findall('Grid'):

Peter Eastman's avatar
Peter Eastman committed
3226
3227
3228
3229
                gridRow = []
                gridRow.append(float(gridEntry.attrib['angle1']))
                gridRow.append(float(gridEntry.attrib['angle2']))
                gridRow.append(float(gridEntry.attrib['f']))
3230
                if 'fx' in gridEntry.attrib:
3231
3232
3233
                    gridRow.append(float(gridEntry.attrib['fx']))
                    gridRow.append(float(gridEntry.attrib['fy']))
                    gridRow.append(float(gridEntry.attrib['fxy']))
Peter Eastman's avatar
Peter Eastman committed
3234
                gridCol.append(gridRow)
3235
3236

                gridColIndex  += 1
Peter Eastman's avatar
Peter Eastman committed
3237
3238
3239
                if (gridColIndex == nx):
                    grid.append(gridCol)
                    gridCol = []
3240
3241
                    gridColIndex = 0

Justin MacCallum's avatar
Justin MacCallum committed
3242

Peter Eastman's avatar
Peter Eastman committed
3243
3244
            if (gridIndex == len(generator.grids)):
                generator.grids.append(grid)
3245
            else:
Peter Eastman's avatar
Peter Eastman committed
3246
3247
                while(len(generator.grids) < gridIndex):
                    generator.grids.append([])
3248
3249
3250
3251
                generator.grids[gridIndex] = grid

    #=============================================================================================

Peter Eastman's avatar
Peter Eastman committed
3252
    def getChiralAtomIndex(self, data, sys, atomB, atomC, atomD):
3253
3254
3255
3256
3257
3258
3259
3260

        chiralAtomIndex = -1

        # if atomC has four bonds, find the
        # two bonds that do not include atomB and atomD
        # set chiralAtomIndex to one of these, if they are
        # not the same atom(type/mass)

Peter Eastman's avatar
Peter Eastman committed
3261
        if (len(data.atomBonds[atomC]) == 4):
3262
3263
3264
3265
3266
            atomE = -1
            atomF = -1
            for bond in data.atomBonds[atomC]:
                bondedAtom1 = data.bonds[bond].atom1
                bondedAtom2 = data.bonds[bond].atom2
Peter Eastman's avatar
Peter Eastman committed
3267
3268
                hit = -1
                if (  bondedAtom1 == atomC and bondedAtom2 != atomB and bondedAtom2 != atomD):
3269
                    hit = bondedAtom2
Peter Eastman's avatar
Peter Eastman committed
3270
                elif (bondedAtom2 == atomC and bondedAtom1 != atomB and bondedAtom1 != atomD):
3271
3272
                    hit = bondedAtom1

Peter Eastman's avatar
Peter Eastman committed
3273
3274
                if (hit > -1):
                    if (atomE == -1):
3275
3276
3277
                        atomE = hit
                    else:
                        atomF = hit
Justin MacCallum's avatar
Justin MacCallum committed
3278

3279
3280
            # raise error if atoms E or F not found

Peter Eastman's avatar
Peter Eastman committed
3281
3282
            if (atomE == -1 or atomF == -1):
                outputString = "getChiralAtomIndex: error getting bonded partners of atomC=%s %d %s" % (atomC.name, atomC.resiude.index, atomC.resiude.name,)
Justin MacCallum's avatar
Justin MacCallum committed
3283
                raise ValueError(outputString)
3284
3285
3286
3287
3288

            # check for different type/mass between atoms E & F

            typeE = int(data.atomType[data.atoms[atomE]])
            typeF = int(data.atomType[data.atoms[atomF]])
Peter Eastman's avatar
Peter Eastman committed
3289
            if (typeE > typeF):
Justin MacCallum's avatar
Justin MacCallum committed
3290
                chiralAtomIndex = atomE
Peter Eastman's avatar
Peter Eastman committed
3291
            if (typeF > typeE):
Justin MacCallum's avatar
Justin MacCallum committed
3292
                chiralAtomIndex = atomF
3293

Peter Eastman's avatar
Peter Eastman committed
3294
3295
3296
            massE = sys.getParticleMass(atomE)/unit.dalton
            massF = sys.getParticleMass(atomE)/unit.dalton
            if (massE > massF):
Justin MacCallum's avatar
Justin MacCallum committed
3297
                chiralAtomIndex = massE
Peter Eastman's avatar
Peter Eastman committed
3298
            if (massF > massE):
Justin MacCallum's avatar
Justin MacCallum committed
3299
                chiralAtomIndex = massF
3300
3301
3302
3303

        return chiralAtomIndex

    #=============================================================================================
Justin MacCallum's avatar
Justin MacCallum committed
3304

3305
3306
3307
3308
3309
3310
3311
3312
3313
3314
3315
3316
3317
    def createForce(self, sys, data, nonpiTorsionedMethod, nonpiTorsionedCutoff, args):

        existing = [sys.getForce(i) for i in range(sys.getNumForces())]
        existing = [f for f in existing if type(f) == mm.AmoebaTorsionTorsionForce]

        if len(existing) == 0:
            force = mm.AmoebaTorsionTorsionForce()
            sys.addForce(force)
        else:
            force = existing[0]

        for angle in data.angles:

Justin MacCallum's avatar
Justin MacCallum committed
3318
3319
            # search for bitorsions; based on TINKER subroutine bitors()

3320
3321
3322
3323
3324
3325
3326
            ib = angle[0]
            ic = angle[1]
            id = angle[2]

            for bondIndex in data.atomBonds[ib]:
                bondedAtom1 = data.bonds[bondIndex].atom1
                bondedAtom2 = data.bonds[bondIndex].atom2
Peter Eastman's avatar
Peter Eastman committed
3327
                if (bondedAtom1 != ib):
3328
3329
3330
3331
                    ia = bondedAtom1
                else:
                    ia = bondedAtom2

Peter Eastman's avatar
Peter Eastman committed
3332
                if (ia != ic and ia != id):
3333
3334
3335
                    for bondIndex in data.atomBonds[id]:
                        bondedAtom1 = data.bonds[bondIndex].atom1
                        bondedAtom2 = data.bonds[bondIndex].atom2
Peter Eastman's avatar
Peter Eastman committed
3336
                        if (bondedAtom1 != id):
3337
3338
3339
3340
                            ie = bondedAtom1
                        else:
                            ie = bondedAtom2

Peter Eastman's avatar
Peter Eastman committed
3341
                        if (ie != ic and ie != ib and ie != ia):
3342
3343
3344
3345
3346
3347
3348
3349
3350
3351
3352
3353
3354
3355
3356
3357
3358
3359
3360
3361

                            # found candidate set of atoms
                            # check if types match in order or reverse order

                            type1 = data.atomType[data.atoms[ia]]
                            type2 = data.atomType[data.atoms[ib]]
                            type3 = data.atomType[data.atoms[ic]]
                            type4 = data.atomType[data.atoms[id]]
                            type5 = data.atomType[data.atoms[ie]]

                            for i in range(len(self.types1)):

                                types1 = self.types1[i]
                                types2 = self.types2[i]
                                types3 = self.types3[i]
                                types4 = self.types4[i]
                                types5 = self.types5[i]

                                # match in order

Peter Eastman's avatar
Peter Eastman committed
3362
3363
3364
                                if (type1 in types1 and type2 in types2 and type3 in types3 and type4 in types4 and type5 in types5):
                                    chiralAtomIndex = self.getChiralAtomIndex(data, sys, ib, ic, id)
                                    force.addTorsionTorsion(ia, ib, ic, id, ie, chiralAtomIndex, self.gridIndex[i])
3365
3366
3367

                                # match in reverse order

3368
                                elif (type5 in types1 and type4 in types2 and type3 in types3 and type2 in types4 and type1 in types5):
Peter Eastman's avatar
Peter Eastman committed
3369
3370
                                    chiralAtomIndex = self.getChiralAtomIndex(data, sys, ib, ic, id)
                                    force.addTorsionTorsion(ie, id, ic, ib, ia, chiralAtomIndex, self.gridIndex[i])
3371
3372
3373
3374

        # set grids

        for (index, grid) in enumerate(self.grids):
Peter Eastman's avatar
Peter Eastman committed
3375
            force.setTorsionTorsionGrid(index, grid)
Justin MacCallum's avatar
Justin MacCallum committed
3376

3377
3378
3379
3380
parsers["AmoebaTorsionTorsionForce"] = AmoebaTorsionTorsionGenerator.parseElement

#=============================================================================================

3381
## @private
3382
class AmoebaStretchBendGenerator(object):
Mark Friedrichs's avatar
Cleanup  
Mark Friedrichs committed
3383
3384

    #=============================================================================================
3385
3386
3387
3388
3389
    """An AmoebaStretchBendGenerator constructs a AmoebaStretchBendForce."""
    #=============================================================================================

    def __init__(self):

Peter Eastman's avatar
Peter Eastman committed
3390
3391
3392
        self.types1 = []
        self.types2 = []
        self.types3 = []
3393

Peter Eastman's avatar
Peter Eastman committed
3394
3395
        self.k1 = []
        self.k2 = []
Justin MacCallum's avatar
Justin MacCallum committed
3396

3397
3398
3399
3400
    #=============================================================================================

    @staticmethod
    def parseElement(element, forceField):
Peter Eastman's avatar
Peter Eastman committed
3401
        generator = AmoebaStretchBendGenerator()
3402
3403
3404
3405
3406
3407
3408
        forceField._forces.append(generator)

        # <AmoebaStretchBendForce stretchBendUnit="1.0">
        # <StretchBend class1="2" class2="1" class3="3" k1="5.25776946506" k2="5.25776946506" />
        # <StretchBend class1="2" class2="1" class3="4" k1="3.14005676385" k2="3.14005676385" />

        for stretchBend in element.findall('StretchBend'):
3409
            types = forceField._findAtomTypes(stretchBend.attrib, 3)
peastman's avatar
peastman committed
3410
            if None not in types:
3411
3412
3413
3414
3415
3416
3417
3418
3419
3420
3421
3422

                generator.types1.append(types[0])
                generator.types2.append(types[1])
                generator.types3.append(types[2])

                generator.k1.append(float(stretchBend.attrib['k1']))
                generator.k2.append(float(stretchBend.attrib['k2']))

            else:
                outputString = "AmoebaStretchBendGenerator : error getting types: %s %s %s" % (
                                    stretchBend.attrib['class1'],
                                    stretchBend.attrib['class2'],
Peter Eastman's avatar
Peter Eastman committed
3423
                                    stretchBend.attrib['class3'])
Justin MacCallum's avatar
Justin MacCallum committed
3424
3425
                raise ValueError(outputString)

3426
3427
    #=============================================================================================

Justin MacCallum's avatar
Justin MacCallum committed
3428
    # The setup of this force is dependent on AmoebaBondForce and AmoebaAngleForce
3429
3430
    # having been called since the ideal bond lengths and angle are needed here.
    # As a conseqeunce, createForce() is not implemented since it is not guaranteed that the generator for
Justin MacCallum's avatar
Justin MacCallum committed
3431
3432
    # AmoebaBondForce and AmoebaAngleForce have been called prior to AmoebaStretchBendGenerator().
    # Instead, createForcePostAmoebaBondForce() is called
3433
    # after the generators for AmoebaBondForce and AmoebaAngleForce have been called
3434
3435
3436

    #=============================================================================================

Peter Eastman's avatar
Peter Eastman committed
3437
    def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
3438
3439
3440
3441
3442
3443
3444
3445
        pass

    #=============================================================================================

    # Note: request for constrained bonds is ignored.

    #=============================================================================================

3446
    def createForcePostAmoebaBondForce(self, sys, data, nonbondedMethod, nonbondedCutoff, angleList, args):
3447
3448
3449
3450
3451
3452
3453
3454
3455
3456
3457
3458

        existing = [sys.getForce(i) for i in range(sys.getNumForces())]
        existing = [f for f in existing if type(f) == mm.AmoebaStretchBendForce]
        if len(existing) == 0:
            force = mm.AmoebaStretchBendForce()
            sys.addForce(force)
        else:
            force = existing[0]

        for angleDict in angleList:

            angle = angleDict['angle']
Peter Eastman's avatar
Peter Eastman committed
3459
            if ('isConstrained' in angleDict):
3460
3461
3462
3463
3464
3465
3466
3467
                isConstrained = angleDict['isConstrained']
            else:
                isConstrained = 0

            type1 = data.atomType[data.atoms[angle[0]]]
            type2 = data.atomType[data.atoms[angle[1]]]
            type3 = data.atomType[data.atoms[angle[2]]]

Peter Eastman's avatar
Peter Eastman committed
3468
            radian = 57.2957795130
3469
3470
3471
3472
3473
3474
3475
3476
3477
3478
            for i in range(len(self.types1)):

                types1 = self.types1[i]
                types2 = self.types2[i]
                types3 = self.types3[i]

                # match types
                # get ideal bond lengths, bondAB, bondCB
                # get ideal angle

Justin MacCallum's avatar
Justin MacCallum committed
3479
                if (type2 in types2 and ((type1 in types1 and type3 in types3) or (type3 in types1 and type1 in types3))):
Mark Friedrichs's avatar
Cleanup  
Mark Friedrichs committed
3480
3481
3482
3483
3484
3485
3486
3487
3488
3489
3490
3491
3492
3493
3494
                    bondAB = -1.0
                    bondCB = -1.0
                    swap = 0
                    for bond in data.atomBonds[angle[1]]:
                        atom1 = data.bonds[bond].atom1
                        atom2 = data.bonds[bond].atom2
                        length = data.bonds[bond].length
                        if (atom1 == angle[0]):
                            bondAB = length
                        if (atom1 == angle[2]):
                            bondCB = length
                        if (atom2 == angle[2]):
                            bondCB = length
                        if (atom2 == angle[0]):
                            bondAB = length
Justin MacCallum's avatar
Justin MacCallum committed
3495

Mark Friedrichs's avatar
Cleanup  
Mark Friedrichs committed
3496
                    # check that ideal angle and bonds are set
3497

Mark Friedrichs's avatar
Cleanup  
Mark Friedrichs committed
3498
                    if ('idealAngle' not in angleDict):
3499

Mark Friedrichs's avatar
Cleanup  
Mark Friedrichs committed
3500
3501
3502
3503
3504
                       outputString = "AmoebaStretchBendGenerator: ideal angle is not set for following entry:\n"
                       outputString += "   types: %5s %5s %5s atoms: " % (type1, type2, type3)
                       outputString += getAtomPrint( data, angle[0] ) + ' '
                       outputString += getAtomPrint( data, angle[1] ) + ' '
                       outputString += getAtomPrint( data, angle[2] )
Justin MacCallum's avatar
Justin MacCallum committed
3505
                       raise ValueError(outputString)
3506

Mark Friedrichs's avatar
Cleanup  
Mark Friedrichs committed
3507
3508
3509
3510
3511
3512
3513
                    elif (bondAB < 0 or bondCB < 0):

                       outputString = "AmoebaStretchBendGenerator: bonds not set: %15.7e %15.7e. for following entry:" % (bondAB, bondCB)
                       outputString += "     types: [%5s %5s %5s] atoms: " % (type1, type2, type3)
                       outputString += getAtomPrint( data, angle[0] ) + ' '
                       outputString += getAtomPrint( data, angle[1] ) + ' '
                       outputString += getAtomPrint( data, angle[2] )
Justin MacCallum's avatar
Justin MacCallum committed
3514
                       raise ValueError(outputString)
3515

Mark Friedrichs's avatar
Cleanup  
Mark Friedrichs committed
3516
                    else:
3517
                        force.addStretchBend(angle[0], angle[1], angle[2], bondAB, bondCB, angleDict['idealAngle']/radian, self.k1[i], self.k2[i])
3518

Mark Friedrichs's avatar
Cleanup  
Mark Friedrichs committed
3519
                    break
3520
3521
3522
3523
3524

parsers["AmoebaStretchBendForce"] = AmoebaStretchBendGenerator.parseElement

#=============================================================================================

3525
## @private
3526
class AmoebaVdwGenerator(object):
3527
3528

    """A AmoebaVdwGenerator constructs a AmoebaVdwForce."""
Justin MacCallum's avatar
Justin MacCallum committed
3529

3530
3531
    #=============================================================================================

Peter Eastman's avatar
Peter Eastman committed
3532
    def __init__(self, type, radiusrule, radiustype, radiussize, epsilonrule, vdw13Scale, vdw14Scale, vdw15Scale):
3533

Justin MacCallum's avatar
Justin MacCallum committed
3534
        self.type = type
3535

Peter Eastman's avatar
Peter Eastman committed
3536
3537
3538
        self.radiusrule = radiusrule
        self.radiustype = radiustype
        self.radiussize = radiussize
3539

Peter Eastman's avatar
Peter Eastman committed
3540
        self.epsilonrule = epsilonrule
3541

Peter Eastman's avatar
Peter Eastman committed
3542
3543
3544
        self.vdw13Scale = vdw13Scale
        self.vdw14Scale = vdw14Scale
        self.vdw15Scale = vdw15Scale
3545
3546
3547
3548
3549
3550
3551

    #=============================================================================================

    @staticmethod
    def parseElement(element, forceField):

        # <AmoebaVdwForce type="BUFFERED-14-7" radiusrule="CUBIC-MEAN" radiustype="R-MIN" radiussize="DIAMETER" epsilonrule="HHG" vdw-13-scale="0.0" vdw-14-scale="1.0" vdw-15-scale="1.0" >
Justin MacCallum's avatar
Justin MacCallum committed
3552
3553
3554
3555
3556
        #   <Vdw class="1" sigma="0.371" epsilon="0.46024" reduction="1.0" />
        #   <Vdw class="2" sigma="0.382" epsilon="0.422584" reduction="1.0" />

        generator = AmoebaVdwGenerator(element.attrib['type'], element.attrib['radiusrule'], element.attrib['radiustype'], element.attrib['radiussize'], element.attrib['epsilonrule'],
                                        float(element.attrib['vdw-13-scale']), float(element.attrib['vdw-14-scale']), float(element.attrib['vdw-15-scale']))
3557
        forceField._forces.append(generator)
3558
3559
        generator.params = ForceField._AtomTypeParameters(forceField, 'AmoebaVdwForce', 'Vdw', ('sigma', 'epsilon', 'reduction'))
        generator.params.parseDefinitions(element)
3560
3561
3562
3563
3564
3565
3566
3567
3568
        two_six = 1.122462048309372

    #=============================================================================================

    # Return a set containing the indices of particles bonded to particle with index=particleIndex

    #=============================================================================================

    @staticmethod
Peter Eastman's avatar
Peter Eastman committed
3569
    def getBondedParticleSet(particleIndex, data):
3570
3571
3572
3573
3574
3575

        bondedParticleSet = set()

        for bond in data.atomBonds[particleIndex]:
            atom1 = data.bonds[bond].atom1
            atom2 = data.bonds[bond].atom2
Peter Eastman's avatar
Peter Eastman committed
3576
3577
            if (atom1 != particleIndex):
                bondedParticleSet.add(atom1)
3578
            else:
Peter Eastman's avatar
Peter Eastman committed
3579
                bondedParticleSet.add(atom2)
3580
3581

        return bondedParticleSet
Justin MacCallum's avatar
Justin MacCallum committed
3582

3583
3584
    #=============================================================================================

Peter Eastman's avatar
Peter Eastman committed
3585
    def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
3586

Peter Eastman's avatar
Peter Eastman committed
3587
        sigmaMap = {'ARITHMETIC':1, 'GEOMETRIC':1, 'CUBIC-MEAN':1}
3588
3589
3590
3591
3592
3593
3594
3595
3596
3597
3598
3599
        epsilonMap = {'ARITHMETIC':1, 'GEOMETRIC':1, 'HARMONIC':1, 'HHG':1}

        # get or create force depending on whether it has already been added to the system

        existing = [sys.getForce(i) for i in range(sys.getNumForces())]
        existing = [f for f in existing if type(f) == mm.AmoebaVdwForce]
        if len(existing) == 0:
            force = mm.AmoebaVdwForce()
            sys.addForce(force)

            # sigma and epsilon combining rules

Peter Eastman's avatar
Peter Eastman committed
3600
            if ('sigmaCombiningRule' in args):
3601
                sigmaRule = args['sigmaCombiningRule'].upper()
Peter Eastman's avatar
Peter Eastman committed
3602
3603
                if (sigmaRule.upper() in sigmaMap):
                    force.setSigmaCombiningRule(sigmaRule.upper())
3604
                else:
Peter Eastman's avatar
Peter Eastman committed
3605
                    stringList = ' ' . join(str(x) for x in sigmaMap.keys())
Mark Friedrichs's avatar
Cleanup  
Mark Friedrichs committed
3606
                    raise ValueError( "AmoebaVdwGenerator: sigma combining rule %s not recognized; valid values are %s; using default." % (sigmaRule, stringList) )
3607
            else:
Peter Eastman's avatar
Peter Eastman committed
3608
                force.setSigmaCombiningRule(self.radiusrule)
3609

Peter Eastman's avatar
Peter Eastman committed
3610
            if ('epsilonCombiningRule' in args):
3611
                epsilonRule = args['epsilonCombiningRule'].upper()
Peter Eastman's avatar
Peter Eastman committed
3612
3613
                if (epsilonRule.upper() in epsilonMap):
                    force.setEpsilonCombiningRule(epsilonRule.upper())
3614
                else:
Peter Eastman's avatar
Peter Eastman committed
3615
                    stringList = ' ' . join(str(x) for x in epsilonMap.keys())
Justin MacCallum's avatar
Justin MacCallum committed
3616
                    raise ValueError( "AmoebaVdwGenerator: epsilon combining rule %s not recognized; valid values are %s; using default." % (epsilonRule, stringList) )
3617
            else:
Peter Eastman's avatar
Peter Eastman committed
3618
                force.setEpsilonCombiningRule(self.epsilonrule)
Justin MacCallum's avatar
Justin MacCallum committed
3619

3620
3621
            # cutoff

Peter Eastman's avatar
Peter Eastman committed
3622
            if ('vdwCutoff' in args):
3623
                force.setCutoff(args['vdwCutoff'])
3624
            else:
Peter Eastman's avatar
Peter Eastman committed
3625
                force.setCutoff(nonbondedCutoff)
Mark Friedrichs's avatar
Cleanup  
Mark Friedrichs committed
3626

3627
3628
3629
            # dispersion correction

            if ('useDispersionCorrection' in args):
3630
                force.setUseDispersionCorrection(bool(args['useDispersionCorrection']))
3631

Peter Eastman's avatar
Peter Eastman committed
3632
            if (nonbondedMethod == PME):
3633
                force.setNonbondedMethod(mm.AmoebaVdwForce.CutoffPeriodic)
Justin MacCallum's avatar
Justin MacCallum committed
3634

3635
3636
3637
3638
3639
        else:
            force = existing[0]

        # add particles to force

3640
3641
3642
3643
3644
        sigmaScale = 1
        if self.radiustype == 'SIGMA':
            sigmaScale = 1.122462048309372
        if self.radiussize == 'DIAMETER':
            sigmaScale = 0.5
3645
        for (i, atom) in enumerate(data.atoms):
3646
3647
3648
3649
3650
3651
3652
3653
3654
3655
            values = self.params.getAtomParameters(atom, data)
            # ivIndex = index of bonded partner for hydrogens; otherwise ivIndex = particle index

            ivIndex = i
            if atom.element == elem.hydrogen and len(data.atomBonds[i]) == 1:
                bondIndex = data.atomBonds[i][0]
                if (data.bonds[bondIndex].atom1 == i):
                    ivIndex = data.bonds[bondIndex].atom2
                else:
                    ivIndex = data.bonds[bondIndex].atom1
3656

3657
            force.addParticle(ivIndex, values[0]*sigmaScale, values[1], values[2])
3658
3659
3660
3661
3662
3663
3664
3665
3666

        # set combining rules

        # set particle exclusions: self, 1-2 and 1-3 bonds
        # (1) collect in bondedParticleSets[i], 1-2 indices for all bonded partners of particle i
        # (2) add 1-2,1-3 and self to exclusion set

        bondedParticleSets = []
        for i in range(len(data.atoms)):
Peter Eastman's avatar
Peter Eastman committed
3667
            bondedParticleSets.append(AmoebaVdwGenerator.getBondedParticleSet(i, data))
3668
3669

        for (i,atom) in enumerate(data.atoms):
Justin MacCallum's avatar
Justin MacCallum committed
3670

3671
3672
3673
3674
3675
3676
            # 1-2 partners

            exclusionSet = bondedParticleSets[i].copy()

            # 1-3 partners

Peter Eastman's avatar
Peter Eastman committed
3677
            if (self.vdw13Scale == 0.0):
3678
                for bondedParticle in bondedParticleSets[i]:
Peter Eastman's avatar
Peter Eastman committed
3679
                    exclusionSet = exclusionSet.union(bondedParticleSets[bondedParticle])
3680
3681
3682
3683
3684

            # self

            exclusionSet.add(i)

3685
            force.setParticleExclusions(i, tuple(exclusionSet))
3686
3687
3688
3689
3690

parsers["AmoebaVdwForce"] = AmoebaVdwGenerator.parseElement

#=============================================================================================

3691
## @private
3692
class AmoebaMultipoleGenerator(object):
3693
3694
3695
3696

    #=============================================================================================

    """A AmoebaMultipoleGenerator constructs a AmoebaMultipoleForce."""
Justin MacCallum's avatar
Justin MacCallum committed
3697

3698
3699
3700
3701
3702
3703
    #=============================================================================================

    def __init__(self, forceField,
                       direct11Scale, direct12Scale, direct13Scale, direct14Scale,
                       mpole12Scale,  mpole13Scale,  mpole14Scale,  mpole15Scale,
                       mutual11Scale, mutual12Scale, mutual13Scale, mutual14Scale,
Peter Eastman's avatar
Peter Eastman committed
3704
                       polar12Scale,  polar13Scale,  polar14Scale,  polar15Scale):
3705

Peter Eastman's avatar
Peter Eastman committed
3706
        self.forceField = forceField
3707

Justin MacCallum's avatar
Justin MacCallum committed
3708
3709
3710
3711
        self.direct11Scale = direct11Scale
        self.direct12Scale = direct12Scale
        self.direct13Scale = direct13Scale
        self.direct14Scale = direct14Scale
3712

Justin MacCallum's avatar
Justin MacCallum committed
3713
3714
3715
3716
        self.mpole12Scale = mpole12Scale
        self.mpole13Scale = mpole13Scale
        self.mpole14Scale = mpole14Scale
        self.mpole15Scale = mpole15Scale
3717

Justin MacCallum's avatar
Justin MacCallum committed
3718
3719
3720
3721
        self.mutual11Scale = mutual11Scale
        self.mutual12Scale = mutual12Scale
        self.mutual13Scale = mutual13Scale
        self.mutual14Scale = mutual14Scale
3722

Justin MacCallum's avatar
Justin MacCallum committed
3723
3724
3725
3726
        self.polar12Scale = polar12Scale
        self.polar13Scale = polar13Scale
        self.polar14Scale = polar14Scale
        self.polar15Scale = polar15Scale
3727

Peter Eastman's avatar
Peter Eastman committed
3728
        self.typeMap = {}
3729
3730
3731
3732
3733
3734

    #=============================================================================================
    # Set axis type
    #=============================================================================================

    @staticmethod
Peter Eastman's avatar
Peter Eastman committed
3735
    def setAxisType(kIndices):
3736
3737
3738

                # set axis type

Peter Eastman's avatar
Peter Eastman committed
3739
3740
3741
                kIndicesLen = len(kIndices)
                if (kIndicesLen > 3):
                    ky = kIndices[3]
3742
                else:
Peter Eastman's avatar
Peter Eastman committed
3743
                    ky = 0
Justin MacCallum's avatar
Justin MacCallum committed
3744

Peter Eastman's avatar
Peter Eastman committed
3745
3746
                if (kIndicesLen > 2):
                    kx = kIndices[2]
3747
                else:
Peter Eastman's avatar
Peter Eastman committed
3748
                    kx = 0
Justin MacCallum's avatar
Justin MacCallum committed
3749

Peter Eastman's avatar
Peter Eastman committed
3750
3751
                if (kIndicesLen > 1):
                    kz = kIndices[1]
3752
                else:
Peter Eastman's avatar
Peter Eastman committed
3753
                    kz = 0
3754

Peter Eastman's avatar
Peter Eastman committed
3755
3756
                while(len(kIndices) < 4):
                    kIndices.append(0)
3757
3758

                axisType = mm.AmoebaMultipoleForce.ZThenX
Peter Eastman's avatar
Peter Eastman committed
3759
                if (kz == 0):
3760
                    axisType = mm.AmoebaMultipoleForce.NoAxisType
Peter Eastman's avatar
Peter Eastman committed
3761
                if (kz != 0 and kx == 0):
3762
                    axisType = mm.AmoebaMultipoleForce.ZOnly
Peter Eastman's avatar
Peter Eastman committed
3763
                if (kz < 0 or kx < 0):
3764
                    axisType = mm.AmoebaMultipoleForce.Bisector
Peter Eastman's avatar
Peter Eastman committed
3765
                if (kx < 0 and ky < 0):
3766
                    axisType = mm.AmoebaMultipoleForce.ZBisect
Peter Eastman's avatar
Peter Eastman committed
3767
                if (kz < 0 and kx < 0 and ky  < 0):
3768
3769
                    axisType = mm.AmoebaMultipoleForce.ThreeFold

Justin MacCallum's avatar
Justin MacCallum committed
3770
3771
3772
                kIndices[1] = abs(kz)
                kIndices[2] = abs(kx)
                kIndices[3] = abs(ky)
3773
3774
3775
3776
3777
3778
3779
3780

                return axisType

    #=============================================================================================

    @staticmethod
    def parseElement(element, forceField):

Justin MacCallum's avatar
Justin MacCallum committed
3781
        #   <AmoebaMultipoleForce  direct11Scale="0.0"  direct12Scale="1.0"  direct13Scale="1.0"  direct14Scale="1.0"  mpole12Scale="0.0"  mpole13Scale="0.0"  mpole14Scale="0.4"  mpole15Scale="0.8"  mutual11Scale="1.0"  mutual12Scale="1.0"  mutual13Scale="1.0"  mutual14Scale="1.0"  polar12Scale="0.0"  polar13Scale="0.0"  polar14Intra="0.5"  polar14Scale="1.0"  polar15Scale="1.0"  >
3782
3783
3784
        # <Multipole class="1"    kz="2"    kx="4"    c0="-0.22620" d1="0.08214" d2="0.00000" d3="0.34883" q11="0.11775" q21="0.00000" q22="-1.02185" q31="-0.17555" q32="0.00000" q33="0.90410"  />
        # <Multipole class="2"    kz="1"    kx="3"    c0="-0.15245" d1="0.19517" d2="0.00000" d3="0.19687" q11="-0.20677" q21="0.00000" q22="-0.48084" q31="-0.01672" q32="0.00000" q33="0.68761"  />

Peter Eastman's avatar
Peter Eastman committed
3785
        generator = AmoebaMultipoleGenerator(forceField,
3786
3787
3788
3789
3790
3791
3792
3793
3794
3795
3796
3797
3798
3799
3800
3801
3802
3803
                                              element.attrib['direct11Scale'],
                                              element.attrib['direct12Scale'],
                                              element.attrib['direct13Scale'],
                                              element.attrib['direct14Scale'],

                                              element.attrib['mpole12Scale'],
                                              element.attrib['mpole13Scale'],
                                              element.attrib['mpole14Scale'],
                                              element.attrib['mpole15Scale'],

                                              element.attrib['mutual11Scale'],
                                              element.attrib['mutual12Scale'],
                                              element.attrib['mutual13Scale'],
                                              element.attrib['mutual14Scale'],

                                              element.attrib['polar12Scale'],
                                              element.attrib['polar13Scale'],
                                              element.attrib['polar14Scale'],
Peter Eastman's avatar
Peter Eastman committed
3804
                                              element.attrib['polar15Scale'])
3805
3806
3807
3808
3809
3810
3811
3812



        forceField._forces.append(generator)

        # set type map: [ kIndices, multipoles, AMOEBA/OpenMM axis type]

        for atom in element.findall('Multipole'):
3813
            types = forceField._findAtomTypes(atom.attrib, 1)
peastman's avatar
peastman committed
3814
            if None not in types:
3815
3816
3817
3818
3819
3820
3821
3822

                # k-indices not provided default to 0

                kIndices = [int(atom.attrib['type'])]

                kStrings = [ 'kz', 'kx', 'ky' ]
                for kString in kStrings:
                    try:
Peter Eastman's avatar
Peter Eastman committed
3823
3824
                        if (atom.attrib[kString]):
                             kIndices.append(int(atom.attrib[kString]))
Justin MacCallum's avatar
Justin MacCallum committed
3825
                    except:
3826
3827
                        pass

Justin MacCallum's avatar
Justin MacCallum committed
3828
                # set axis type based on k-Indices
3829

Peter Eastman's avatar
Peter Eastman committed
3830
                axisType = AmoebaMultipoleGenerator.setAxisType(kIndices)
3831
3832
3833

                # set multipole

Peter Eastman's avatar
Peter Eastman committed
3834
                charge = float(atom.attrib['c0'])
Justin MacCallum's avatar
Justin MacCallum committed
3835

Peter Eastman's avatar
Peter Eastman committed
3836
3837
3838
3839
3840
3841
3842
3843
3844
3845
3846
3847
3848
                conversion = 1.0
                dipole = [ conversion*float(atom.attrib['d1']), conversion*float(atom.attrib['d2']), conversion*float(atom.attrib['d3'])]

                quadrupole = []
                quadrupole.append(conversion*float(atom.attrib['q11']))
                quadrupole.append(conversion*float(atom.attrib['q21']))
                quadrupole.append(conversion*float(atom.attrib['q31']))
                quadrupole.append(conversion*float(atom.attrib['q21']))
                quadrupole.append(conversion*float(atom.attrib['q22']))
                quadrupole.append(conversion*float(atom.attrib['q32']))
                quadrupole.append(conversion*float(atom.attrib['q31']))
                quadrupole.append(conversion*float(atom.attrib['q32']))
                quadrupole.append(conversion*float(atom.attrib['q33']))
3849
3850

                for t in types[0]:
Peter Eastman's avatar
Peter Eastman committed
3851
                    if (t not in generator.typeMap):
3852
3853
                        generator.typeMap[t] = []

Peter Eastman's avatar
Peter Eastman committed
3854
3855
3856
                    valueMap = dict()
                    valueMap['classIndex'] = atom.attrib['type']
                    valueMap['kIndices'] = kIndices
Justin MacCallum's avatar
Justin MacCallum committed
3857
                    valueMap['charge'] = charge
Peter Eastman's avatar
Peter Eastman committed
3858
3859
3860
3861
                    valueMap['dipole'] = dipole
                    valueMap['quadrupole'] = quadrupole
                    valueMap['axisType'] = axisType
                    generator.typeMap[t].append(valueMap)
Justin MacCallum's avatar
Justin MacCallum committed
3862

3863
            else:
Peter Eastman's avatar
Peter Eastman committed
3864
                outputString = "AmoebaMultipoleGenerator: error getting type for multipole: %s" % (atom.attrib['class'])
Justin MacCallum's avatar
Justin MacCallum committed
3865
3866
                raise ValueError(outputString)

3867
        # polarization parameters
Justin MacCallum's avatar
Justin MacCallum committed
3868

3869
        for atom in element.findall('Polarize'):
3870
            types = forceField._findAtomTypes(atom.attrib, 1)
peastman's avatar
peastman committed
3871
            if None not in types:
3872

Peter Eastman's avatar
Peter Eastman committed
3873
3874
3875
3876
                classIndex = atom.attrib['type']
                polarizability = float(atom.attrib['polarizability'])
                thole = float(atom.attrib['thole'])
                if (thole == 0):
3877
3878
                    pdamp = 0
                else:
Peter Eastman's avatar
Peter Eastman committed
3879
                    pdamp = pow(polarizability, 1.0/6.0)
3880

Peter Eastman's avatar
Peter Eastman committed
3881
3882
                pgrpMap = dict()
                for index in range(1, 7):
3883
                    pgrp = 'pgrp' + str(index)
Peter Eastman's avatar
Peter Eastman committed
3884
                    if (pgrp in atom.attrib):
3885
3886
3887
                        pgrpMap[int(atom.attrib[pgrp])] = -1

                for t in types[0]:
Peter Eastman's avatar
Peter Eastman committed
3888
3889
                    if (t not in generator.typeMap):
                        outputString = "AmoebaMultipoleGenerator: polarize type not present: %s" % (atom.attrib['type'])
Justin MacCallum's avatar
Justin MacCallum committed
3890
                        raise ValueError(outputString)
3891
3892
                    else:
                        typeMapList = generator.typeMap[t]
Peter Eastman's avatar
Peter Eastman committed
3893
3894
3895
3896
3897
3898
3899
                        hit = 0
                        for (ii, typeMap) in enumerate(typeMapList):

                            if (typeMap['classIndex'] == classIndex):
                                typeMap['polarizability'] = polarizability
                                typeMap['thole'] = thole
                                typeMap['pdamp'] = pdamp
Justin MacCallum's avatar
Justin MacCallum committed
3900
                                typeMap['pgrpMap'] = pgrpMap
Peter Eastman's avatar
Peter Eastman committed
3901
3902
3903
3904
3905
                                typeMapList[ii] = typeMap
                                hit = 1

                        if (hit == 0):
                            outputString = "AmoebaMultipoleGenerator: error getting type for polarize: class index=%s not in multipole list?" % (atom.attrib['class'])
Justin MacCallum's avatar
Justin MacCallum committed
3906
3907
                            raise ValueError(outputString)

3908
            else:
Peter Eastman's avatar
Peter Eastman committed
3909
                outputString = "AmoebaMultipoleGenerator: error getting type for polarize: %s" % (atom.attrib['class'])
Justin MacCallum's avatar
Justin MacCallum committed
3910
3911
                raise ValueError(outputString)

3912
3913
    #=============================================================================================

Peter Eastman's avatar
Peter Eastman committed
3914
    def setPolarGroups(self, data, bonded12ParticleSets, force):
3915
3916
3917
3918
3919

        for (atomIndex, atom) in enumerate(data.atoms):

            # assign multipole parameters via only 1-2 connected atoms

Peter Eastman's avatar
Peter Eastman committed
3920
3921
3922
3923
            multipoleDict = atom.multipoleDict
            pgrpMap = multipoleDict['pgrpMap']
            bondedAtomIndices = bonded12ParticleSets[atomIndex]
            atom.stage = -1
3924
3925
3926
3927
            atom.polarizationGroupSet = list()
            atom.polarizationGroups[atomIndex] = 1
            for bondedAtomIndex in bondedAtomIndices:
                bondedAtomType = int(data.atomType[data.atoms[bondedAtomIndex]])
Peter Eastman's avatar
Peter Eastman committed
3928
3929
                bondedAtom = data.atoms[bondedAtomIndex]
                if (bondedAtomType in pgrpMap):
3930
3931
                    atom.polarizationGroups[bondedAtomIndex] = 1
                    bondedAtom.polarizationGroups[atomIndex] = 1
Justin MacCallum's avatar
Justin MacCallum committed
3932

3933
3934
3935
3936
        # pgrp11

        for (atomIndex, atom) in enumerate(data.atoms):

Peter Eastman's avatar
Peter Eastman committed
3937
            if (len( data.atoms[atomIndex].polarizationGroupSet) > 0):
3938
3939
                continue

Peter Eastman's avatar
Peter Eastman committed
3940
3941
            group = set()
            visited = set()
3942
3943
            notVisited = set()
            for pgrpAtomIndex in atom.polarizationGroups:
Peter Eastman's avatar
Peter Eastman committed
3944
3945
3946
3947
                group.add(pgrpAtomIndex)
                notVisited.add(pgrpAtomIndex)
            visited.add(atomIndex)
            while(len(notVisited) > 0):
3948
                nextAtom = notVisited.pop()
Peter Eastman's avatar
Peter Eastman committed
3949
3950
                if (nextAtom not in visited):
                   visited.add(nextAtom)
3951
                   for ii in data.atoms[nextAtom].polarizationGroups:
Peter Eastman's avatar
Peter Eastman committed
3952
3953
3954
                       group.add(ii)
                       if (ii not in visited):
                           notVisited.add(ii)
3955
3956
3957

            pGroup = group
            for pgrpAtomIndex in group:
Peter Eastman's avatar
Peter Eastman committed
3958
                data.atoms[pgrpAtomIndex].polarizationGroupSet.append(pGroup)
3959
3960

        for (atomIndex, atom) in enumerate(data.atoms):
Peter Eastman's avatar
Peter Eastman committed
3961
3962
            atom.polarizationGroupSet[0] = sorted(atom.polarizationGroupSet[0])
            force.setCovalentMap(atomIndex, mm.AmoebaMultipoleForce.PolarizationCovalent11, atom.polarizationGroupSet[0])
3963
3964
3965
3966
3967

        # pgrp12

        for (atomIndex, atom) in enumerate(data.atoms):

Peter Eastman's avatar
Peter Eastman committed
3968
            if (len( data.atoms[atomIndex].polarizationGroupSet) > 1):
3969
3970
                continue

Peter Eastman's avatar
Peter Eastman committed
3971
            pgrp11 = set(atom.polarizationGroupSet[0])
3972
3973
3974
            pgrp12 = set()
            for pgrpAtomIndex in pgrp11:
                for bonded12 in bonded12ParticleSets[pgrpAtomIndex]:
Peter Eastman's avatar
Peter Eastman committed
3975
                    pgrp12 = pgrp12.union(data.atoms[bonded12].polarizationGroupSet[0])
3976
3977
            pgrp12 = pgrp12 - pgrp11
            for pgrpAtomIndex in pgrp11:
Peter Eastman's avatar
Peter Eastman committed
3978
                data.atoms[pgrpAtomIndex].polarizationGroupSet.append(pgrp12)
Justin MacCallum's avatar
Justin MacCallum committed
3979

3980
        for (atomIndex, atom) in enumerate(data.atoms):
Peter Eastman's avatar
Peter Eastman committed
3981
3982
            atom.polarizationGroupSet[1] = sorted(atom.polarizationGroupSet[1])
            force.setCovalentMap(atomIndex, mm.AmoebaMultipoleForce.PolarizationCovalent12, atom.polarizationGroupSet[1])
3983
3984
3985
3986
3987

        # pgrp13

        for (atomIndex, atom) in enumerate(data.atoms):

Peter Eastman's avatar
Peter Eastman committed
3988
            if (len(data.atoms[atomIndex].polarizationGroupSet) > 2):
3989
3990
                continue

Peter Eastman's avatar
Peter Eastman committed
3991
3992
            pgrp11 = set(atom.polarizationGroupSet[0])
            pgrp12 = set(atom.polarizationGroupSet[1])
3993
3994
3995
            pgrp13 = set()
            for pgrpAtomIndex in pgrp12:
                for bonded12 in bonded12ParticleSets[pgrpAtomIndex]:
Peter Eastman's avatar
Peter Eastman committed
3996
                    pgrp13 = pgrp13.union(data.atoms[bonded12].polarizationGroupSet[0])
3997
            pgrp13 = pgrp13 - pgrp12
Peter Eastman's avatar
Peter Eastman committed
3998
            pgrp13 = pgrp13 - set(pgrp11)
3999
            for pgrpAtomIndex in pgrp11:
Peter Eastman's avatar
Peter Eastman committed
4000
                data.atoms[pgrpAtomIndex].polarizationGroupSet.append(pgrp13)
Justin MacCallum's avatar
Justin MacCallum committed
4001

4002
        for (atomIndex, atom) in enumerate(data.atoms):
Peter Eastman's avatar
Peter Eastman committed
4003
4004
            atom.polarizationGroupSet[2] = sorted(atom.polarizationGroupSet[2])
            force.setCovalentMap(atomIndex, mm.AmoebaMultipoleForce.PolarizationCovalent13, atom.polarizationGroupSet[2])
4005
4006
4007
4008
4009

        # pgrp14

        for (atomIndex, atom) in enumerate(data.atoms):

Peter Eastman's avatar
Peter Eastman committed
4010
            if (len(data.atoms[atomIndex].polarizationGroupSet) > 3):
4011
4012
                continue

Peter Eastman's avatar
Peter Eastman committed
4013
4014
4015
            pgrp11 = set(atom.polarizationGroupSet[0])
            pgrp12 = set(atom.polarizationGroupSet[1])
            pgrp13 = set(atom.polarizationGroupSet[2])
4016
4017
4018
            pgrp14 = set()
            for pgrpAtomIndex in pgrp13:
                for bonded12 in bonded12ParticleSets[pgrpAtomIndex]:
Peter Eastman's avatar
Peter Eastman committed
4019
                    pgrp14 = pgrp14.union(data.atoms[bonded12].polarizationGroupSet[0])
4020
4021
4022

            pgrp14 = pgrp14 - pgrp13
            pgrp14 = pgrp14 - pgrp12
Peter Eastman's avatar
Peter Eastman committed
4023
            pgrp14 = pgrp14 - set(pgrp11)
4024
4025

            for pgrpAtomIndex in pgrp11:
Peter Eastman's avatar
Peter Eastman committed
4026
                data.atoms[pgrpAtomIndex].polarizationGroupSet.append(pgrp14)
Justin MacCallum's avatar
Justin MacCallum committed
4027

4028
        for (atomIndex, atom) in enumerate(data.atoms):
Peter Eastman's avatar
Peter Eastman committed
4029
4030
            atom.polarizationGroupSet[3] = sorted(atom.polarizationGroupSet[3])
            force.setCovalentMap(atomIndex, mm.AmoebaMultipoleForce.PolarizationCovalent14, atom.polarizationGroupSet[3])
4031
4032
4033

    #=============================================================================================

Peter Eastman's avatar
Peter Eastman committed
4034
    def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
4035
4036
4037
4038
4039
4040
4041
4042
4043
4044
4045

        methodMap = {NoCutoff:mm.AmoebaMultipoleForce.NoCutoff,
                     PME:mm.AmoebaMultipoleForce.PME}

        # get or create force depending on whether it has already been added to the system

        existing = [sys.getForce(i) for i in range(sys.getNumForces())]
        existing = [f for f in existing if type(f) == mm.AmoebaMultipoleForce]
        if len(existing) == 0:
            force = mm.AmoebaMultipoleForce()
            sys.addForce(force)
Justin MacCallum's avatar
Justin MacCallum committed
4046
            if (nonbondedMethod not in methodMap):
Mark Friedrichs's avatar
Cleanup  
Mark Friedrichs committed
4047
                raise ValueError( "AmoebaMultipoleForce: input cutoff method not available." )
4048
            else:
Peter Eastman's avatar
Peter Eastman committed
4049
                force.setNonbondedMethod(methodMap[nonbondedMethod])
4050
4051
            force.setCutoffDistance(nonbondedCutoff)

Peter Eastman's avatar
Peter Eastman committed
4052
            if ('ewaldErrorTolerance' in args):
4053
4054
                force.setEwaldErrorTolerance(float(args['ewaldErrorTolerance']))

Peter Eastman's avatar
Peter Eastman committed
4055
            if ('polarization' in args):
4056
                polarizationType = args['polarization']
Peter Eastman's avatar
Peter Eastman committed
4057
                if (polarizationType.lower() == 'direct'):
4058
                    force.setPolarizationType(mm.AmoebaMultipoleForce.Direct)
4059
4060
                elif (polarizationType.lower() == 'extrapolated'):
                    force.setPolarizationType(mm.AmoebaMultipoleForce.Extrapolated)
4061
4062
4063
                else:
                    force.setPolarizationType(mm.AmoebaMultipoleForce.Mutual)

Peter Eastman's avatar
Peter Eastman committed
4064
4065
            if ('aEwald' in args):
                force.setAEwald(float(args['aEwald']))
4066

Peter Eastman's avatar
Peter Eastman committed
4067
            if ('pmeGridDimensions' in args):
4068
4069
                force.setPmeGridDimensions(args['pmeGridDimensions'])

Peter Eastman's avatar
Peter Eastman committed
4070
4071
            if ('mutualInducedMaxIterations' in args):
                force.setMutualInducedMaxIterations(int(args['mutualInducedMaxIterations']))
4072

Peter Eastman's avatar
Peter Eastman committed
4073
            if ('mutualInducedTargetEpsilon' in args):
4074
4075
4076
4077
4078
4079
                force.setMutualInducedTargetEpsilon(float(args['mutualInducedTargetEpsilon']))

        else:
            force = existing[0]

        # add particles to force
Justin MacCallum's avatar
Justin MacCallum committed
4080
        # throw error if particle type not available
4081
4082
4083
4084
4085
4086
4087

        # get 1-2, 1-3, 1-4, 1-5 bonded sets

        # 1-2

        bonded12ParticleSets = []
        for i in range(len(data.atoms)):
Peter Eastman's avatar
Peter Eastman committed
4088
4089
4090
            bonded12ParticleSet = AmoebaVdwGenerator.getBondedParticleSet(i, data)
            bonded12ParticleSet = set(sorted(bonded12ParticleSet))
            bonded12ParticleSets.append(bonded12ParticleSet)
4091
4092
4093
4094
4095

        # 1-3

        bonded13ParticleSets = []
        for i in range(len(data.atoms)):
Peter Eastman's avatar
Peter Eastman committed
4096
            bonded13Set = set()
4097
            bonded12ParticleSet = bonded12ParticleSets[i]
Justin MacCallum's avatar
Justin MacCallum committed
4098
            for j in bonded12ParticleSet:
Peter Eastman's avatar
Peter Eastman committed
4099
                bonded13Set = bonded13Set.union(bonded12ParticleSets[j])
4100
4101
4102
4103

            # remove 1-2 and self from set

            bonded13Set = bonded13Set - bonded12ParticleSet
Peter Eastman's avatar
Peter Eastman committed
4104
            selfSet = set()
4105
4106
            selfSet.add(i)
            bonded13Set = bonded13Set - selfSet
Peter Eastman's avatar
Peter Eastman committed
4107
4108
            bonded13Set = set(sorted(bonded13Set))
            bonded13ParticleSets.append(bonded13Set)
4109
4110
4111
4112
4113

        # 1-4

        bonded14ParticleSets = []
        for i in range(len(data.atoms)):
Peter Eastman's avatar
Peter Eastman committed
4114
4115
            bonded14Set = set()
            bonded13ParticleSet = bonded13ParticleSets[i]
Justin MacCallum's avatar
Justin MacCallum committed
4116
            for j in bonded13ParticleSet:
Peter Eastman's avatar
Peter Eastman committed
4117
                bonded14Set = bonded14Set.union(bonded12ParticleSets[j])
Justin MacCallum's avatar
Justin MacCallum committed
4118

4119
4120
4121
4122
            # remove 1-3, 1-2 and self from set

            bonded14Set = bonded14Set - bonded12ParticleSets[i]
            bonded14Set = bonded14Set - bonded13ParticleSet
Peter Eastman's avatar
Peter Eastman committed
4123
            selfSet = set()
4124
4125
            selfSet.add(i)
            bonded14Set = bonded14Set - selfSet
Peter Eastman's avatar
Peter Eastman committed
4126
4127
            bonded14Set = set(sorted(bonded14Set))
            bonded14ParticleSets.append(bonded14Set)
4128
4129
4130
4131
4132

        # 1-5

        bonded15ParticleSets = []
        for i in range(len(data.atoms)):
Peter Eastman's avatar
Peter Eastman committed
4133
4134
            bonded15Set = set()
            bonded14ParticleSet = bonded14ParticleSets[i]
Justin MacCallum's avatar
Justin MacCallum committed
4135
            for j in bonded14ParticleSet:
Peter Eastman's avatar
Peter Eastman committed
4136
                bonded15Set = bonded15Set.union(bonded12ParticleSets[j])
4137
4138
4139
4140
4141
4142

            # remove 1-4, 1-3, 1-2 and self from set

            bonded15Set = bonded15Set - bonded12ParticleSets[i]
            bonded15Set = bonded15Set - bonded13ParticleSets[i]
            bonded15Set = bonded15Set - bonded14ParticleSet
Peter Eastman's avatar
Peter Eastman committed
4143
            selfSet = set()
4144
4145
            selfSet.add(i)
            bonded15Set = bonded15Set - selfSet
Peter Eastman's avatar
Peter Eastman committed
4146
4147
            bonded15Set = set(sorted(bonded15Set))
            bonded15ParticleSets.append(bonded15Set)
4148
4149
4150
4151
4152

        for (atomIndex, atom) in enumerate(data.atoms):
            t = data.atomType[atom]
            if t in self.typeMap:

Peter Eastman's avatar
Peter Eastman committed
4153
4154
                multipoleList = self.typeMap[t]
                hit = 0
4155
4156
4157
4158
4159
4160
                savedMultipoleDict = 0

                # assign multipole parameters via only 1-2 connected atoms

                for multipoleDict in multipoleList:

Peter Eastman's avatar
Peter Eastman committed
4161
                    if (hit != 0):
4162
4163
                        break

Peter Eastman's avatar
Peter Eastman committed
4164
                    kIndices = multipoleDict['kIndices']
Justin MacCallum's avatar
Justin MacCallum committed
4165
4166

                    kz = kIndices[1]
Peter Eastman's avatar
Peter Eastman committed
4167
4168
                    kx = kIndices[2]
                    ky = kIndices[3]
4169
4170
4171
4172

                    # assign multipole parameters
                    #    (1) get bonded partners
                    #    (2) match parameter types
Justin MacCallum's avatar
Justin MacCallum committed
4173

4174
                    bondedAtomIndices = bonded12ParticleSets[atomIndex]
Peter Eastman's avatar
Peter Eastman committed
4175
4176
4177
                    zaxis = -1
                    xaxis = -1
                    yaxis = -1
4178
4179
                    for bondedAtomZIndex in bondedAtomIndices:

Peter Eastman's avatar
Peter Eastman committed
4180
                       if (hit != 0):
4181
4182
4183
                           break

                       bondedAtomZType = int(data.atomType[data.atoms[bondedAtomZIndex]])
Peter Eastman's avatar
Peter Eastman committed
4184
4185
                       bondedAtomZ = data.atoms[bondedAtomZIndex]
                       if (bondedAtomZType == kz):
4186
                          for bondedAtomXIndex in bondedAtomIndices:
Peter Eastman's avatar
Peter Eastman committed
4187
                              if (bondedAtomXIndex == bondedAtomZIndex or hit != 0):
4188
4189
                                  continue
                              bondedAtomXType = int(data.atomType[data.atoms[bondedAtomXIndex]])
Peter Eastman's avatar
Peter Eastman committed
4190
4191
4192
4193
                              if (bondedAtomXType == kx):
                                  if (ky == 0):
                                      zaxis = bondedAtomZIndex
                                      xaxis = bondedAtomXIndex
4194
4195
4196
4197
4198
4199
4200
4201
4202
4203
                                      if( bondedAtomXType == bondedAtomZType and xaxis < zaxis ):
                                          swapI = zaxis
                                          zaxis = xaxis
                                          xaxis = swapI
                                      else:
                                          for bondedAtomXIndex in bondedAtomIndices:
                                              bondedAtomX1Type = int(data.atomType[data.atoms[bondedAtomXIndex]])
                                              if( bondedAtomX1Type == kx and bondedAtomXIndex != bondedAtomZIndex and bondedAtomXIndex < xaxis ):
                                                  xaxis = bondedAtomXIndex

4204
                                      savedMultipoleDict = multipoleDict
Peter Eastman's avatar
Peter Eastman committed
4205
                                      hit = 1
4206
4207
                                  else:
                                      for bondedAtomYIndex in bondedAtomIndices:
Peter Eastman's avatar
Peter Eastman committed
4208
                                          if (bondedAtomYIndex == bondedAtomZIndex or bondedAtomYIndex == bondedAtomXIndex or hit != 0):
4209
4210
                                              continue
                                          bondedAtomYType = int(data.atomType[data.atoms[bondedAtomYIndex]])
Peter Eastman's avatar
Peter Eastman committed
4211
4212
4213
4214
                                          if (bondedAtomYType == ky):
                                              zaxis = bondedAtomZIndex
                                              xaxis = bondedAtomXIndex
                                              yaxis = bondedAtomYIndex
4215
                                              savedMultipoleDict = multipoleDict
Peter Eastman's avatar
Peter Eastman committed
4216
                                              hit = 2
Justin MacCallum's avatar
Justin MacCallum committed
4217

4218
4219
4220
4221
                # assign multipole parameters via 1-2 and 1-3 connected atoms

                for multipoleDict in multipoleList:

Peter Eastman's avatar
Peter Eastman committed
4222
                    if (hit != 0):
4223
4224
                        break

Peter Eastman's avatar
Peter Eastman committed
4225
                    kIndices = multipoleDict['kIndices']
Justin MacCallum's avatar
Justin MacCallum committed
4226
4227

                    kz = kIndices[1]
Peter Eastman's avatar
Peter Eastman committed
4228
4229
                    kx = kIndices[2]
                    ky = kIndices[3]
Justin MacCallum's avatar
Justin MacCallum committed
4230

4231
4232
4233
                    # assign multipole parameters
                    #    (1) get bonded partners
                    #    (2) match parameter types
Justin MacCallum's avatar
Justin MacCallum committed
4234

4235
4236
4237
                    bondedAtom12Indices = bonded12ParticleSets[atomIndex]
                    bondedAtom13Indices = bonded13ParticleSets[atomIndex]

Peter Eastman's avatar
Peter Eastman committed
4238
4239
4240
                    zaxis = -1
                    xaxis = -1
                    yaxis = -1
4241
4242
4243

                    for bondedAtomZIndex in bondedAtom12Indices:

Peter Eastman's avatar
Peter Eastman committed
4244
                       if (hit != 0):
4245
4246
4247
                           break

                       bondedAtomZType = int(data.atomType[data.atoms[bondedAtomZIndex]])
Peter Eastman's avatar
Peter Eastman committed
4248
                       bondedAtomZ = data.atoms[bondedAtomZIndex]
4249

Peter Eastman's avatar
Peter Eastman committed
4250
                       if (bondedAtomZType == kz):
4251
4252
                          for bondedAtomXIndex in bondedAtom13Indices:

Peter Eastman's avatar
Peter Eastman committed
4253
                              if (bondedAtomXIndex == bondedAtomZIndex or hit != 0):
4254
4255
                                  continue
                              bondedAtomXType = int(data.atomType[data.atoms[bondedAtomXIndex]])
Peter Eastman's avatar
Peter Eastman committed
4256
4257
4258
4259
                              if (bondedAtomXType == kx and bondedAtomZIndex in bonded12ParticleSets[bondedAtomXIndex]):
                                  if (ky == 0):
                                      zaxis = bondedAtomZIndex
                                      xaxis = bondedAtomXIndex
4260
4261
4262
4263
4264
4265
4266
4267

                                      # select xaxis w/ smallest index

                                      for bondedAtomXIndex in bondedAtom13Indices:
                                          bondedAtomX1Type = int(data.atomType[data.atoms[bondedAtomXIndex]])
                                          if( bondedAtomX1Type == kx and bondedAtomXIndex != bondedAtomZIndex and bondedAtomZIndex in bonded12ParticleSets[bondedAtomXIndex] and bondedAtomXIndex < xaxis ):
                                              xaxis = bondedAtomXIndex

4268
                                      savedMultipoleDict = multipoleDict
Peter Eastman's avatar
Peter Eastman committed
4269
                                      hit = 3
4270
4271
                                  else:
                                      for bondedAtomYIndex in bondedAtom13Indices:
Peter Eastman's avatar
Peter Eastman committed
4272
                                          if (bondedAtomYIndex == bondedAtomZIndex or bondedAtomYIndex == bondedAtomXIndex or hit != 0):
4273
4274
                                              continue
                                          bondedAtomYType = int(data.atomType[data.atoms[bondedAtomYIndex]])
Peter Eastman's avatar
Peter Eastman committed
4275
4276
4277
4278
                                          if (bondedAtomYType == ky and bondedAtomZIndex in bonded12ParticleSets[bondedAtomYIndex]):
                                              zaxis = bondedAtomZIndex
                                              xaxis = bondedAtomXIndex
                                              yaxis = bondedAtomYIndex
4279
                                              savedMultipoleDict = multipoleDict
Peter Eastman's avatar
Peter Eastman committed
4280
                                              hit = 4
Justin MacCallum's avatar
Justin MacCallum committed
4281

4282
4283
4284
4285
                # assign multipole parameters via only a z-defining atom

                for multipoleDict in multipoleList:

Peter Eastman's avatar
Peter Eastman committed
4286
                    if (hit != 0):
4287
4288
                        break

Peter Eastman's avatar
Peter Eastman committed
4289
                    kIndices = multipoleDict['kIndices']
Justin MacCallum's avatar
Justin MacCallum committed
4290
4291
4292
4293

                    kz = kIndices[1]
                    kx = kIndices[2]

Peter Eastman's avatar
Peter Eastman committed
4294
4295
4296
                    zaxis = -1
                    xaxis = -1
                    yaxis = -1
4297
4298
4299

                    for bondedAtomZIndex in bondedAtom12Indices:

Peter Eastman's avatar
Peter Eastman committed
4300
                        if (hit != 0):
4301
4302
4303
                            break

                        bondedAtomZType = int(data.atomType[data.atoms[bondedAtomZIndex]])
Peter Eastman's avatar
Peter Eastman committed
4304
                        bondedAtomZ = data.atoms[bondedAtomZIndex]
4305

Peter Eastman's avatar
Peter Eastman committed
4306
4307
                        if (kx == 0 and kz == bondedAtomZType):
                            kz = bondedAtomZIndex
4308
                            savedMultipoleDict = multipoleDict
Peter Eastman's avatar
Peter Eastman committed
4309
                            hit = 5
4310
4311
4312
4313
4314

                # assign multipole parameters via no connected atoms

                for multipoleDict in multipoleList:

Peter Eastman's avatar
Peter Eastman committed
4315
                    if (hit != 0):
4316
4317
                        break

Peter Eastman's avatar
Peter Eastman committed
4318
                    kIndices = multipoleDict['kIndices']
Justin MacCallum's avatar
Justin MacCallum committed
4319
4320
4321

                    kz = kIndices[1]

Peter Eastman's avatar
Peter Eastman committed
4322
4323
4324
                    zaxis = -1
                    xaxis = -1
                    yaxis = -1
4325

Peter Eastman's avatar
Peter Eastman committed
4326
                    if (kz == 0):
4327
                        savedMultipoleDict = multipoleDict
Peter Eastman's avatar
Peter Eastman committed
4328
                        hit = 6
Justin MacCallum's avatar
Justin MacCallum committed
4329

4330
4331
                # add particle if there was a hit

Peter Eastman's avatar
Peter Eastman committed
4332
                if (hit != 0):
4333

Peter Eastman's avatar
Peter Eastman committed
4334
                    atom.multipoleDict = savedMultipoleDict
4335
                    atom.polarizationGroups = dict()
4336
                    newIndex = force.addMultipole(savedMultipoleDict['charge'], savedMultipoleDict['dipole'], savedMultipoleDict['quadrupole'], savedMultipoleDict['axisType'],
4337
                                                                 zaxis, xaxis, yaxis, savedMultipoleDict['thole'], savedMultipoleDict['pdamp'], savedMultipoleDict['polarizability'])
Peter Eastman's avatar
Peter Eastman committed
4338
                    if (atomIndex == newIndex):
4339
4340
4341
4342
                        force.setCovalentMap(atomIndex, mm.AmoebaMultipoleForce.Covalent12, tuple(bonded12ParticleSets[atomIndex]))
                        force.setCovalentMap(atomIndex, mm.AmoebaMultipoleForce.Covalent13, tuple(bonded13ParticleSets[atomIndex]))
                        force.setCovalentMap(atomIndex, mm.AmoebaMultipoleForce.Covalent14, tuple(bonded14ParticleSets[atomIndex]))
                        force.setCovalentMap(atomIndex, mm.AmoebaMultipoleForce.Covalent15, tuple(bonded15ParticleSets[atomIndex]))
4343
                    else:
4344
                        raise ValueError("Atom %s of %s %d is out of sync!." %(atom.name, atom.residue.name, atom.residue.index))
4345
                else:
Peter Eastman's avatar
Peter Eastman committed
4346
                    raise ValueError("Atom %s of %s %d was not assigned." %(atom.name, atom.residue.name, atom.residue.index))
4347
            else:
Peter Eastman's avatar
Peter Eastman committed
4348
                raise ValueError('No multipole type for atom %s %s %d' % (atom.name, atom.residue.name, atom.residue.index))
4349
4350
4351

        # set polar groups

Peter Eastman's avatar
Peter Eastman committed
4352
        self.setPolarGroups(data, bonded12ParticleSets, force)
4353
4354
4355
4356
4357

parsers["AmoebaMultipoleForce"] = AmoebaMultipoleGenerator.parseElement

#=============================================================================================

4358
## @private
4359
class AmoebaWcaDispersionGenerator(object):
4360
4361

    """A AmoebaWcaDispersionGenerator constructs a AmoebaWcaDispersionForce."""
Justin MacCallum's avatar
Justin MacCallum committed
4362

4363
4364
    #=========================================================================================

Peter Eastman's avatar
Peter Eastman committed
4365
    def __init__(self, epso, epsh, rmino, rminh, awater, slevy, dispoff, shctd):
4366

Justin MacCallum's avatar
Justin MacCallum committed
4367
4368
        self.epso = epso
        self.epsh = epsh
Peter Eastman's avatar
Peter Eastman committed
4369
4370
4371
4372
4373
        self.rmino = rmino
        self.rminh = rminh
        self.awater = awater
        self.slevy = slevy
        self.dispoff = dispoff
Justin MacCallum's avatar
Justin MacCallum committed
4374
        self.shctd = shctd
4375
4376
4377
4378
4379
4380
4381
4382
4383

    #=========================================================================================

    @staticmethod
    def parseElement(element, forceField):

        #  <AmoebaWcaDispersionForce epso="0.46024" epsh="0.056484" rmino="0.17025" rminh="0.13275" awater="33.428" slevy="1.0"  dispoff="0.026" shctd="0.81" >
        #   <WcaDispersion class="1" radius="0.1855" epsilon="0.46024" />
        #   <WcaDispersion class="2" radius="0.191" epsilon="0.422584" />
Justin MacCallum's avatar
Justin MacCallum committed
4384

Peter Eastman's avatar
Peter Eastman committed
4385
        generator = AmoebaWcaDispersionGenerator(element.attrib['epso'],
4386
4387
4388
                                                  element.attrib['epsh'],
                                                  element.attrib['rmino'],
                                                  element.attrib['rminh'],
Justin MacCallum's avatar
Justin MacCallum committed
4389
                                                  element.attrib['awater'],
4390
4391
                                                  element.attrib['slevy'],
                                                  element.attrib['dispoff'],
Justin MacCallum's avatar
Justin MacCallum committed
4392
                                                  element.attrib['shctd'])
4393
        forceField._forces.append(generator)
4394
4395
        generator.params = ForceField._AtomTypeParameters(forceField, 'AmoebaWcaDispersionForce', 'WcaDispersion', ('radius', 'epsilon'))
        generator.params.parseDefinitions(element)
Justin MacCallum's avatar
Justin MacCallum committed
4396

4397
    #=========================================================================================
Justin MacCallum's avatar
Justin MacCallum committed
4398

Peter Eastman's avatar
Peter Eastman committed
4399
    def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
4400
4401
4402
4403
4404
4405
4406
4407
4408
4409
4410
4411

        # get or create force depending on whether it has already been added to the system

        existing = [sys.getForce(i) for i in range(sys.getNumForces())]
        existing = [f for f in existing if type(f) == mm.AmoebaWcaDispersionForce]
        if len(existing) == 0:
            force = mm.AmoebaWcaDispersionForce()
            sys.addForce(force)
        else:
            force = existing[0]

        # add particles to force
Justin MacCallum's avatar
Justin MacCallum committed
4412
        # throw error if particle type not available
4413

Peter Eastman's avatar
Peter Eastman committed
4414
4415
4416
4417
4418
4419
4420
4421
        force.setEpso(   float(self.epso   ))
        force.setEpsh(   float(self.epsh   ))
        force.setRmino(  float(self.rmino  ))
        force.setRminh(  float(self.rminh  ))
        force.setDispoff(float(self.dispoff))
        force.setSlevy(  float(self.slevy  ))
        force.setAwater( float(self.awater ))
        force.setShctd(  float(self.shctd  ))
4422

4423
4424
4425
        for atom in data.atoms:
            values = self.params.getAtomParameters(atom, data)
            force.addParticle(values[0], values[1])
4426
4427
4428
4429
4430

parsers["AmoebaWcaDispersionForce"] = AmoebaWcaDispersionGenerator.parseElement

#=============================================================================================

4431
## @private
4432
class AmoebaGeneralizedKirkwoodGenerator(object):
4433
4434

    """A AmoebaGeneralizedKirkwoodGenerator constructs a AmoebaGeneralizedKirkwoodForce."""
Justin MacCallum's avatar
Justin MacCallum committed
4435

4436
4437
    #=========================================================================================

Peter Eastman's avatar
Peter Eastman committed
4438
4439
4440
4441
4442
4443
4444
4445
4446
4447
4448
    def __init__(self, forceField, solventDielectric, soluteDielectric, includeCavityTerm, probeRadius, surfaceAreaFactor):

        self.forceField = forceField
        self.solventDielectric = solventDielectric
        self.soluteDielectric = soluteDielectric
        self.includeCavityTerm = includeCavityTerm
        self.probeRadius = probeRadius
        self.surfaceAreaFactor = surfaceAreaFactor

        self.radiusTypeMap = {}
        self.radiusTypeMap['Bondi'] = {}
Justin MacCallum's avatar
Justin MacCallum committed
4449
        bondiMap = self.radiusTypeMap['Bondi']
Peter Eastman's avatar
Peter Eastman committed
4450
4451
4452
4453
4454
4455
4456
4457
4458
4459
4460
4461
4462
4463
4464
4465
4466
4467
4468
4469
4470
4471
4472
4473
4474
        rscale = 1.03

        bondiMap[0] = 0.00
        bondiMap[1] = 0.12*rscale
        bondiMap[2] = 0.14*rscale
        bondiMap[5] = 0.18*rscale

        bondiMap[6] = 0.170*rscale
        bondiMap[7] = 0.155*rscale
        bondiMap[8] = 0.152*rscale
        bondiMap[9] = 0.147*rscale

        bondiMap[10] = 0.154*rscale
        bondiMap[14] = 0.210*rscale
        bondiMap[15] = 0.180*rscale
        bondiMap[16] = 0.180*rscale

        bondiMap[17] = 0.175 *rscale
        bondiMap[18] = 0.188*rscale
        bondiMap[34] = 0.190*rscale
        bondiMap[35] = 0.185*rscale

        bondiMap[36] = 0.202*rscale
        bondiMap[53] = 0.198*rscale
        bondiMap[54] = 0.216*rscale
4475
4476
4477

    #=========================================================================================

Peter Eastman's avatar
Peter Eastman committed
4478
    def getObcShct(self, data, atomIndex):
4479

Peter Eastman's avatar
Peter Eastman committed
4480
        atom = data.atoms[atomIndex]
4481
        atomicNumber = atom.element.atomic_number
Peter Eastman's avatar
Peter Eastman committed
4482
        shct = -1.0
4483
4484

        # shct
Justin MacCallum's avatar
Justin MacCallum committed
4485

Peter Eastman's avatar
Peter Eastman committed
4486
        if (atomicNumber == 1):                 # H(1)
Justin MacCallum's avatar
Justin MacCallum committed
4487
            shct = 0.85
Peter Eastman's avatar
Peter Eastman committed
4488
        elif (atomicNumber == 6):               # C(6)
Justin MacCallum's avatar
Justin MacCallum committed
4489
            shct = 0.72
Peter Eastman's avatar
Peter Eastman committed
4490
        elif (atomicNumber == 7):               # N(7)
Justin MacCallum's avatar
Justin MacCallum committed
4491
            shct = 0.79
Peter Eastman's avatar
Peter Eastman committed
4492
        elif (atomicNumber == 8):               # O(8)
Justin MacCallum's avatar
Justin MacCallum committed
4493
            shct = 0.85
Peter Eastman's avatar
Peter Eastman committed
4494
        elif (atomicNumber == 9):               # F(9)
Justin MacCallum's avatar
Justin MacCallum committed
4495
4496
4497
            shct = 0.88
        elif (atomicNumber == 15):              # P(15)
            shct = 0.86
Peter Eastman's avatar
Peter Eastman committed
4498
        elif (atomicNumber == 16):              # S(16)
4499
            shct = 0.96
Peter Eastman's avatar
Peter Eastman committed
4500
        elif (atomicNumber == 26):              # Fe(26)
4501
4502
            shct = 0.88

Justin MacCallum's avatar
Justin MacCallum committed
4503
        if (shct < 0.0):
Mark Friedrichs's avatar
Cleanup  
Mark Friedrichs committed
4504
            raise ValueError( "getObcShct: no GK overlap scale factor for atom %s of %s %d" % (atom.name, atom.residue.name, atom.residue.index) )
Justin MacCallum's avatar
Justin MacCallum committed
4505
4506

        return shct
4507
4508
4509

    #=========================================================================================

Peter Eastman's avatar
Peter Eastman committed
4510
    def getAmoebaTypeRadius(self, data, bondedAtomIndices, atomIndex):
4511

Peter Eastman's avatar
Peter Eastman committed
4512
        atom = data.atoms[atomIndex]
4513
        atomicNumber = atom.element.atomic_number
Peter Eastman's avatar
Peter Eastman committed
4514
        radius = -1.0
4515

Peter Eastman's avatar
Peter Eastman committed
4516
        if (atomicNumber == 1):                  # H(1)
Justin MacCallum's avatar
Justin MacCallum committed
4517

Peter Eastman's avatar
Peter Eastman committed
4518
            radius = 0.132
Justin MacCallum's avatar
Justin MacCallum committed
4519

Peter Eastman's avatar
Peter Eastman committed
4520
            if (len(bondedAtomIndices) < 1):
Mark Friedrichs's avatar
Cleanup  
Mark Friedrichs committed
4521
                 raise ValueError( "AmoebaGeneralizedKirkwoodGenerator: error getting atom bonded to %s of %s %d " % (atom.name, atom.residue.name, atom.residue.index) )
Justin MacCallum's avatar
Justin MacCallum committed
4522

4523
            for bondedAtomIndex in bondedAtomIndices:
Peter Eastman's avatar
Peter Eastman committed
4524
                bondedAtomAtomicNumber = data.atoms[bondedAtomIndex].element.atomic_number
4525

Peter Eastman's avatar
Peter Eastman committed
4526
            if (bondedAtomAtomicNumber == 7):
4527
                radius = 0.11
Peter Eastman's avatar
Peter Eastman committed
4528
            if (bondedAtomAtomicNumber == 8):
4529
                radius = 0.105
Justin MacCallum's avatar
Justin MacCallum committed
4530

Peter Eastman's avatar
Peter Eastman committed
4531
        elif (atomicNumber == 3):               # Li(3)
4532
            radius = 0.15
Peter Eastman's avatar
Peter Eastman committed
4533
        elif (atomicNumber == 6):               # C(6)
Justin MacCallum's avatar
Justin MacCallum committed
4534

4535
            radius = 0.20
Peter Eastman's avatar
Peter Eastman committed
4536
            if (len(bondedAtomIndices) == 3):
4537
4538
                radius = 0.205

Peter Eastman's avatar
Peter Eastman committed
4539
            elif (len(bondedAtomIndices) == 4):
4540
4541
                for bondedAtomIndex in bondedAtomIndices:
                   bondedAtomAtomicNumber = data.atoms[bondedAtomIndex].element.atomic_number
Peter Eastman's avatar
Peter Eastman committed
4542
                   if (bondedAtomAtomicNumber == 7 or bondedAtomAtomicNumber == 8):
4543
4544
                       radius = 0.175

Peter Eastman's avatar
Peter Eastman committed
4545
        elif (atomicNumber == 7):               # N(7)
4546
            radius = 0.16
Peter Eastman's avatar
Peter Eastman committed
4547
        elif (atomicNumber == 8):               # O(8)
4548
            radius = 0.155
Peter Eastman's avatar
Peter Eastman committed
4549
            if (len(bondedAtomIndices) == 2):
4550
                radius = 0.145
Peter Eastman's avatar
Peter Eastman committed
4551
        elif (atomicNumber == 9):               # F(9)
4552
            radius = 0.154
Justin MacCallum's avatar
Justin MacCallum committed
4553
        elif (atomicNumber == 10):
4554
            radius = 0.146
Justin MacCallum's avatar
Justin MacCallum committed
4555
        elif (atomicNumber == 11):
4556
            radius = 0.209
Justin MacCallum's avatar
Justin MacCallum committed
4557
        elif (atomicNumber == 12):
4558
            radius = 0.179
Justin MacCallum's avatar
Justin MacCallum committed
4559
        elif (atomicNumber == 14):
4560
            radius = 0.189
Justin MacCallum's avatar
Justin MacCallum committed
4561
        elif (atomicNumber == 15):              # P(15)
4562
            radius = 0.196
Peter Eastman's avatar
Peter Eastman committed
4563
        elif (atomicNumber == 16):              # S(16)
4564
            radius = 0.186
Justin MacCallum's avatar
Justin MacCallum committed
4565
        elif (atomicNumber == 17):
4566
            radius = 0.182
Justin MacCallum's avatar
Justin MacCallum committed
4567
        elif (atomicNumber == 18):
4568
            radius = 0.179
Justin MacCallum's avatar
Justin MacCallum committed
4569
        elif (atomicNumber == 19):
4570
            radius = 0.223
Justin MacCallum's avatar
Justin MacCallum committed
4571
        elif (atomicNumber == 20):
4572
            radius = 0.191
Justin MacCallum's avatar
Justin MacCallum committed
4573
        elif (atomicNumber == 35):
4574
            radius = 2.00
Justin MacCallum's avatar
Justin MacCallum committed
4575
        elif (atomicNumber == 36):
4576
            radius = 0.190
Justin MacCallum's avatar
Justin MacCallum committed
4577
        elif (atomicNumber == 37):
4578
            radius = 0.226
Justin MacCallum's avatar
Justin MacCallum committed
4579
        elif (atomicNumber == 53):
4580
            radius = 0.237
Justin MacCallum's avatar
Justin MacCallum committed
4581
        elif (atomicNumber == 54):
4582
            radius = 0.207
Justin MacCallum's avatar
Justin MacCallum committed
4583
        elif (atomicNumber == 55):
4584
            radius = 0.263
Justin MacCallum's avatar
Justin MacCallum committed
4585
        elif (atomicNumber == 56):
4586
4587
            radius = 0.230

Justin MacCallum's avatar
Justin MacCallum committed
4588
        if (radius < 0.0):
Mark Friedrichs's avatar
Cleanup  
Mark Friedrichs committed
4589
4590
            outputString = "No GK radius for atom %s of %s %d" % (atom.name, atom.residue.name, atom.residue.index)
            raise ValueError( outputString )
Justin MacCallum's avatar
Justin MacCallum committed
4591

4592
4593
4594
4595
        return radius

    #=========================================================================================

Peter Eastman's avatar
Peter Eastman committed
4596
    def getBondiTypeRadius(self, data, bondedAtomIndices, atomIndex):
4597

Justin MacCallum's avatar
Justin MacCallum committed
4598
        bondiMap = self.radiusTypeMap['Bondi']
Peter Eastman's avatar
Peter Eastman committed
4599
        atom = data.atoms[atomIndex]
4600
        atomicNumber = atom.element.atomic_number
Justin MacCallum's avatar
Justin MacCallum committed
4601
        if (atomicNumber in bondiMap):
4602
4603
            radius = bondiMap[atomicNumber]
        else:
Mark Friedrichs's avatar
Cleanup  
Mark Friedrichs committed
4604
4605
            outputString = "Warning no Bondi radius for atom %s of %s %d using default value=%f" % (atom.name, atom.residue.name, atom.residue.index, radius)
            raise ValueError( outputString )
Justin MacCallum's avatar
Justin MacCallum committed
4606

4607
4608
4609
4610
4611
4612
4613
4614
4615
4616
        return radius

    #=========================================================================================

    @staticmethod
    def parseElement(element, forceField):

        #  <AmoebaGeneralizedKirkwoodForce solventDielectric="78.3" soluteDielectric="1.0" includeCavityTerm="1" probeRadius="0.14" surfaceAreaFactor="-170.351730663">
        #   <GeneralizedKirkwood type="1" charge="-0.22620" shct="0.79"  />
        #   <GeneralizedKirkwood type="2" charge="-0.15245" shct="0.72"  />
Justin MacCallum's avatar
Justin MacCallum committed
4617

Peter Eastman's avatar
Peter Eastman committed
4618
        generator = AmoebaGeneralizedKirkwoodGenerator(forceField, element.attrib['solventDielectric'], element.attrib['soluteDielectric'],
Justin MacCallum's avatar
Justin MacCallum committed
4619
4620
                                                        element.attrib['includeCavityTerm'],
                                                        element.attrib['probeRadius'], element.attrib['surfaceAreaFactor'])
4621
4622
4623
        forceField._forces.append(generator)

    #=========================================================================================
Justin MacCallum's avatar
Justin MacCallum committed
4624

Peter Eastman's avatar
Peter Eastman committed
4625
    def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
4626

Mark Friedrichs's avatar
Cleanup  
Mark Friedrichs committed
4627
4628
4629
        if( nonbondedMethod != NoCutoff ):
            raise ValueError( "Only the nonbondedMethod=NoCutoff option is available for implicit solvent simulations." )

4630
4631
4632
        # check if AmoebaMultipoleForce exists since charges needed
        # if it has not been created, raise an error

Peter Eastman's avatar
Peter Eastman committed
4633
        existing = [sys.getForce(i) for i in range(sys.getNumForces())]
4634
        amoebaMultipoleForceList = [f for f in existing if type(f) == mm.AmoebaMultipoleForce]
Peter Eastman's avatar
Peter Eastman committed
4635
        if (len(amoebaMultipoleForceList) > 0):
4636
4637
4638
4639
4640
            amoebaMultipoleForce = amoebaMultipoleForceList[0]
        else:
            # call AmoebaMultipoleForceGenerator.createForce() to ensure charges have been set

            for force in self.forceField._forces:
Justin MacCallum's avatar
Justin MacCallum committed
4641
                if (force.__class__.__name__ == 'AmoebaMultipoleGenerator'):
Peter Eastman's avatar
Peter Eastman committed
4642
                    force.createForce(sys, data, nonbondedMethod, nonbondedCutoff, args)
Justin MacCallum's avatar
Justin MacCallum committed
4643

4644
4645
4646
4647
4648
4649
4650
        # get or create force depending on whether it has already been added to the system

        existing = [f for f in existing if type(f) == mm.AmoebaGeneralizedKirkwoodForce]
        if len(existing) == 0:

            force = mm.AmoebaGeneralizedKirkwoodForce()
            sys.addForce(force)
Justin MacCallum's avatar
Justin MacCallum committed
4651

Peter Eastman's avatar
Peter Eastman committed
4652
4653
            if ('solventDielectric' in args):
                force.setSolventDielectric(float(args['solventDielectric']))
4654
            else:
Peter Eastman's avatar
Peter Eastman committed
4655
                force.setSolventDielectric(   float(self.solventDielectric))
4656

Peter Eastman's avatar
Peter Eastman committed
4657
4658
            if ('soluteDielectric' in args):
                force.setSoluteDielectric(float(args['soluteDielectric']))
4659
            else:
Peter Eastman's avatar
Peter Eastman committed
4660
                force.setSoluteDielectric(    float(self.soluteDielectric))
4661

Peter Eastman's avatar
Peter Eastman committed
4662
4663
            if ('includeCavityTerm' in args):
                force.setIncludeCavityTerm(int(args['includeCavityTerm']))
4664
            else:
Peter Eastman's avatar
Peter Eastman committed
4665
               force.setIncludeCavityTerm(   int(self.includeCavityTerm))
4666
4667
4668
4669
4670

        else:
            force = existing[0]

        # add particles to force
Justin MacCallum's avatar
Justin MacCallum committed
4671
        # throw error if particle type not available
4672

Peter Eastman's avatar
Peter Eastman committed
4673
4674
        force.setProbeRadius(         float(self.probeRadius))
        force.setSurfaceAreaFactor(   float(self.surfaceAreaFactor))
4675
4676
4677
4678
4679

        # 1-2

        bonded12ParticleSets = []
        for i in range(len(data.atoms)):
Peter Eastman's avatar
Peter Eastman committed
4680
4681
4682
            bonded12ParticleSet = AmoebaVdwGenerator.getBondedParticleSet(i, data)
            bonded12ParticleSet = set(sorted(bonded12ParticleSet))
            bonded12ParticleSets.append(bonded12ParticleSet)
4683
4684

        radiusType = 'Bondi'
Peter Eastman's avatar
Peter Eastman committed
4685
4686
4687
4688
        for atomIndex in range(0, amoebaMultipoleForce.getNumMultipoles()):
            multipoleParameters = amoebaMultipoleForce.getMultipoleParameters(atomIndex)
            if (radiusType == 'Amoeba'):
                radius = self.getAmoebaTypeRadius(data, bonded12ParticleSets[atomIndex], atomIndex)
4689
            else:
Peter Eastman's avatar
Peter Eastman committed
4690
                radius = self.getBondiTypeRadius(data, bonded12ParticleSets[atomIndex], atomIndex)
4691
4692
            #shct = self.getObcShct(data, atomIndex)
            shct = 0.69
Peter Eastman's avatar
Peter Eastman committed
4693
            force.addParticle(multipoleParameters[0], radius, shct)
4694
4695
4696
4697
4698

parsers["AmoebaGeneralizedKirkwoodForce"] = AmoebaGeneralizedKirkwoodGenerator.parseElement

#=============================================================================================

4699
## @private
4700
class AmoebaUreyBradleyGenerator(object):
4701
4702
4703
4704

    #=============================================================================================
    """An AmoebaUreyBradleyGenerator constructs a AmoebaUreyBradleyForce."""
    #=============================================================================================
Justin MacCallum's avatar
Justin MacCallum committed
4705

4706
    def __init__(self):
4707

Peter Eastman's avatar
Peter Eastman committed
4708
4709
4710
        self.types1 = []
        self.types2 = []
        self.types3 = []
4711

Peter Eastman's avatar
Peter Eastman committed
4712
4713
        self.length = []
        self.k = []
4714
4715
4716
4717
4718
4719

    #=============================================================================================

    @staticmethod
    def parseElement(element, forceField):

4720
        #  <AmoebaUreyBradleyForce>
Justin MacCallum's avatar
Justin MacCallum committed
4721
        #   <UreyBradley class1="74" class2="73" class3="74" k="16003.8" d="0.15537" />
4722

4723
        generator = AmoebaUreyBradleyGenerator()
4724
4725
        forceField._forces.append(generator)
        for bond in element.findall('UreyBradley'):
4726
            types = forceField._findAtomTypes(bond.attrib, 3)
peastman's avatar
peastman committed
4727
            if None not in types:
4728
4729
4730
4731
4732
4733
4734
4735
4736
4737

                generator.types1.append(types[0])
                generator.types2.append(types[1])
                generator.types3.append(types[2])

                generator.length.append(float(bond.attrib['d']))
                generator.k.append(float(bond.attrib['k']))

            else:
                outputString = "AmoebaUreyBradleyGenerator: error getting types: %s %s %s" % (
Peter Eastman's avatar
Peter Eastman committed
4738
                                    bond.attrib['class1'], bond.attrib['class2'], bond.attrib['class3'])
Justin MacCallum's avatar
Justin MacCallum committed
4739
4740
                raise ValueError(outputString)

4741
4742
    #=============================================================================================

Peter Eastman's avatar
Peter Eastman committed
4743
    def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
4744

Peter Eastman's avatar
Peter Eastman committed
4745
        existing = [sys.getForce(i) for i in range(sys.getNumForces())]
4746
        existing = [f for f in existing if type(f) == mm.HarmonicBondForce]
4747
4748

        if len(existing) == 0:
4749
            force = mm.HarmonicBondForce()
4750
4751
4752
4753
4754
            sys.addForce(force)
        else:
            force = existing[0]

        for (angle, isConstrained) in zip(data.angles, data.isAngleConstrained):
Peter Eastman's avatar
Peter Eastman committed
4755
            if (isConstrained):
4756
4757
4758
4759
4760
4761
4762
4763
                continue
            type1 = data.atomType[data.atoms[angle[0]]]
            type2 = data.atomType[data.atoms[angle[1]]]
            type3 = data.atomType[data.atoms[angle[2]]]
            for i in range(len(self.types1)):
                types1 = self.types1[i]
                types2 = self.types2[i]
                types3 = self.types3[i]
Peter Eastman's avatar
Peter Eastman committed
4764
                if ((type1 in types1 and type2 in types2 and type3 in types3) or (type3 in types1 and type2 in types2 and type1 in types3)):
4765
                    force.addBond(angle[0], angle[2], self.length[i], 2*self.k[i])
4766
4767
4768
4769
4770
                    break

parsers["AmoebaUreyBradleyForce"] = AmoebaUreyBradleyGenerator.parseElement

#=============================================================================================
peastman's avatar
peastman committed
4771
4772
4773


## @private
4774
class DrudeGenerator(object):
peastman's avatar
peastman committed
4775
    """A DrudeGenerator constructs a DrudeForce."""
Justin MacCallum's avatar
Justin MacCallum committed
4776

4777
4778
    def __init__(self, forcefield):
        self.ff = forcefield
peastman's avatar
peastman committed
4779
4780
4781
4782
4783
4784
        self.typeMap = {}

    @staticmethod
    def parseElement(element, ff):
        existing = [f for f in ff._forces if isinstance(f, DrudeGenerator)]
        if len(existing) == 0:
4785
4786
            generator = DrudeGenerator(ff)
            ff.registerGenerator(generator)
peastman's avatar
peastman committed
4787
4788
4789
4790
        else:
            # Multiple <DrudeForce> tags were found, probably in different files.  Simply add more types to the existing one.
            generator = existing[0]
        for particle in element.findall('Particle'):
4791
            types = ff._findAtomTypes(particle.attrib, 5)
peastman's avatar
peastman committed
4792
4793
4794
4795
4796
4797
4798
4799
4800
4801
            if None not in types[:2]:
                aniso12 = 0.0
                aniso34 = 0.0
                if 'aniso12' in particle.attrib:
                    aniso12 = float(particle.attrib['aniso12'])
                if 'aniso34' in particle.attrib:
                    aniso34 = float(particle.attrib['aniso34'])
                values = (types[1], types[2], types[3], types[4], float(particle.attrib['charge']), float(particle.attrib['polarizability']), aniso12, aniso34, float(particle.attrib['thole']))
                for t in types[0]:
                    generator.typeMap[t] = values
Justin MacCallum's avatar
Justin MacCallum committed
4802

peastman's avatar
peastman committed
4803
4804
4805
4806
    def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
        force = mm.DrudeForce()
        if not any(isinstance(f, mm.NonbondedForce) for f in sys.getForces()):
            raise ValueError('<DrudeForce> must come after <NonbondedForce> in XML file')
Justin MacCallum's avatar
Justin MacCallum committed
4807

peastman's avatar
peastman committed
4808
        # Add Drude particles.
Justin MacCallum's avatar
Justin MacCallum committed
4809

peastman's avatar
peastman committed
4810
4811
4812
4813
4814
4815
4816
4817
4818
4819
4820
4821
4822
4823
4824
4825
        for atom in data.atoms:
            t = data.atomType[atom]
            if t in self.typeMap:
                # Find other atoms in the residue that affect the Drude particle.
                p = [-1, -1, -1, -1]
                values = self.typeMap[t]
                for atom2 in atom.residue.atoms():
                    type2 = data.atomType[atom2]
                    if type2 in values[0]:
                        p[0] = atom2.index
                    elif values[1] is not None and type2 in values[1]:
                        p[1] = atom2.index
                    elif values[2] is not None and type2 in values[2]:
                        p[2] = atom2.index
                    elif values[3] is not None and type2 in values[3]:
                        p[3] = atom2.index
4826
4827
                force.addParticle(atom.index, p[0], p[1], p[2], p[3], values[4], values[5], values[6], values[7])
                data.excludeAtomWith[p[0]].append(atom.index)
peastman's avatar
peastman committed
4828
        sys.addForce(force)
Justin MacCallum's avatar
Justin MacCallum committed
4829

peastman's avatar
peastman committed
4830
4831
    def postprocessSystem(self, sys, data, args):
        # For every nonbonded exclusion between Drude particles, add a screened pair.
Justin MacCallum's avatar
Justin MacCallum committed
4832

peastman's avatar
peastman committed
4833
4834
4835
4836
4837
4838
4839
        drude = [f for f in sys.getForces() if isinstance(f, mm.DrudeForce)][0]
        nonbonded = [f for f in sys.getForces() if isinstance(f, mm.NonbondedForce)][0]
        particleMap = {}
        for i in range(drude.getNumParticles()):
            particleMap[drude.getParticleParameters(i)[0]] = i
        for i in range(nonbonded.getNumExceptions()):
            (particle1, particle2, charge, sigma, epsilon) = nonbonded.getExceptionParameters(i)
4840
            if charge._value == 0 and epsilon._value == 0:
peastman's avatar
peastman committed
4841
4842
4843
4844
4845
                # This is an exclusion.
                if particle1 in particleMap and particle2 in particleMap:
                    # It connects two Drude particles, so add a screened pair.
                    drude1 = particleMap[particle1]
                    drude2 = particleMap[particle2]
4846
4847
                    type1 = data.atomType[data.atoms[particle1]]
                    type2 = data.atomType[data.atoms[particle2]]
peastman's avatar
peastman committed
4848
4849
4850
4851
                    thole1 = self.typeMap[type1][8]
                    thole2 = self.typeMap[type2][8]
                    drude.addScreenedPair(drude1, drude2, thole1+thole2)

Justin MacCallum's avatar
Justin MacCallum committed
4852
parsers["DrudeForce"] = DrudeGenerator.parseElement
John Chodera (MSKCC)'s avatar
John Chodera (MSKCC) committed
4853
4854

#=============================================================================================