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Commit 818db2b2 authored by jchodera's avatar jchodera
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Also return residue templates; add docs.

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docs-source/usersguide/application.rst
View file @ 818db2b2
......@@ -723,7 +723,7 @@ For the main force field, OpenMM provides the following options:
.. tabularcolumns:: |l|L|
============================= ================================================================================
File Force Field
File Force Field
============================= ================================================================================
:code:`amber96.xml` Amber96\ :cite:`Kollman1997`
:code:`amber99sb.xml` Amber99\ :cite:`Wang2000` with modified backbone torsions\ :cite:`Hornak2006`
......@@ -731,7 +731,7 @@ File Force Field
:code:`amber99sbnmr.xml` Amber99SB with modifications to fit NMR data\ :cite:`Li2010`
:code:`amber03.xml` Amber03\ :cite:`Duan2003`
:code:`amber10.xml` Amber10 (documented in the AmberTools_ manual as `ff10`)
:code:`amoeba2009.xml` AMOEBA 2009\ :cite:`Ren2002`. This force field is deprecated. It is
:code:`amoeba2009.xml` AMOEBA 2009\ :cite:`Ren2002`. This force field is deprecated. It is
recommended to use AMOEBA 2013 instead.
:code:`amoeba2013.xml` AMOEBA 2013\ :cite:`Shi2013`
:code:`charmm_polar_2013.xml` CHARMM 2013 polarizable force field\ :cite:`Lopes2013`
......@@ -746,14 +746,14 @@ files:
.. tabularcolumns:: |l|L|
=================== ============================================
File Water Model
File Water Model
=================== ============================================
:code:`tip3p.xml` TIP3P water model\ :cite:`Jorgensen1983`
:code:`tip3pfb.xml` TIP3P-FB water model\ :cite:`Wang2014`
:code:`tip4pew.xml` TIP4P-Ew water model\ :cite:`Horn2004`
:code:`tip4pfb.xml` TIP4P-FB water model\ :cite:`Wang2014`
:code:`tip5p.xml` TIP5P water model\ :cite:`Mahoney2000`
:code:`spce.xml` SPC/E water model\ :cite:`Berendsen1987`
:code:`tip3p.xml` TIP3P water model\ :cite:`Jorgensen1983`
:code:`tip3pfb.xml` TIP3P-FB water model\ :cite:`Wang2014`
:code:`tip4pew.xml` TIP4P-Ew water model\ :cite:`Horn2004`
:code:`tip4pfb.xml` TIP4P-FB water model\ :cite:`Wang2014`
:code:`tip5p.xml` TIP5P water model\ :cite:`Mahoney2000`
:code:`spce.xml` SPC/E water model\ :cite:`Berendsen1987`
:code:`swm4ndp.xml` SWM4-NDP water model\ :cite:`Lamoureux2006`
=================== ============================================
......@@ -769,7 +769,7 @@ the following files:
.. tabularcolumns:: |l|L|
========================= =================================================================================================
File Implicit Solvation Model
File Implicit Solvation Model
========================= =================================================================================================
:code:`amber96_obc.xml` GBSA-OBC solvation model\ :cite:`Onufriev2004` for use with Amber96 force field
:code:`amber99_obc.xml` GBSA-OBC solvation model for use with Amber99 force fields
......@@ -821,15 +821,15 @@ allowed values for :code:`implicitSolvent`\ :
.. tabularcolumns:: |l|L|
============= ==================================================================================================================================
Value Meaning
Value Meaning
============= ==================================================================================================================================
:code:`None` No implicit solvent is used.
:code:`HCT` Hawkins-Cramer-Truhlar GBSA model\ :cite:`Hawkins1995` (corresponds to igb=1 in AMBER)
:code:`OBC1` Onufriev-Bashford-Case GBSA model\ :cite:`Onufriev2004` using the GB\ :sup:`OBC`\ I parameters (corresponds to igb=2 in AMBER).
:code:`None` No implicit solvent is used.
:code:`HCT` Hawkins-Cramer-Truhlar GBSA model\ :cite:`Hawkins1995` (corresponds to igb=1 in AMBER)
:code:`OBC1` Onufriev-Bashford-Case GBSA model\ :cite:`Onufriev2004` using the GB\ :sup:`OBC`\ I parameters (corresponds to igb=2 in AMBER).
:code:`OBC2` Onufriev-Bashford-Case GBSA model\ :cite:`Onufriev2004` using the GB\ :sup:`OBC`\ II parameters (corresponds to igb=5 in AMBER).
This is the same model used by the GBSA-OBC files described in Section :ref:`force-fields`.
:code:`GBn` GBn solvation model\ :cite:`Mongan2007` (corresponds to igb=7 in AMBER).
:code:`GBn2` GBn2 solvation model\ :cite:`Nguyen2013` (corresponds to igb=8 in AMBER).
:code:`GBn` GBn solvation model\ :cite:`Mongan2007` (corresponds to igb=7 in AMBER).
:code:`GBn2` GBn2 solvation model\ :cite:`Nguyen2013` (corresponds to igb=8 in AMBER).
============= ==================================================================================================================================
......@@ -867,13 +867,13 @@ The :code:`nonbondedMethod` parameter can have any of the following values:
.. tabularcolumns:: |l|L|
========================= ===========================================================================================================================================================================================================================================
Value Meaning
Value Meaning
========================= ===========================================================================================================================================================================================================================================
:code:`NoCutoff` No cutoff is applied.
:code:`CutoffNonPeriodic` The reaction field method is used to eliminate all interactions beyond a cutoff distance. Not valid for AMOEBA.
:code:`NoCutoff` No cutoff is applied.
:code:`CutoffNonPeriodic` The reaction field method is used to eliminate all interactions beyond a cutoff distance. Not valid for AMOEBA.
:code:`CutoffPeriodic` The reaction field method is used to eliminate all interactions beyond a cutoff distance. Periodic boundary conditions are applied, so each atom interacts only with the nearest periodic copy of every other atom. Not valid for AMOEBA.
:code:`Ewald` Periodic boundary conditions are applied. Ewald summation is used to compute long range interactions. (This option is rarely used, since PME is much faster for all but the smallest systems.) Not valid for AMOEBA.
:code:`PME` Periodic boundary conditions are applied. The Particle Mesh Ewald method is used to compute long range interactions.
:code:`Ewald` Periodic boundary conditions are applied. Ewald summation is used to compute long range interactions. (This option is rarely used, since PME is much faster for all but the smallest systems.) Not valid for AMOEBA.
:code:`PME` Periodic boundary conditions are applied. The Particle Mesh Ewald method is used to compute long range interactions.
========================= ===========================================================================================================================================================================================================================================
......@@ -988,11 +988,11 @@ The :code:`constraints` parameter can have any of the following values:
.. tabularcolumns:: |l|L|
================ =============================================================================================================================================
Value Meaning
Value Meaning
================ =============================================================================================================================================
:code:`None` No constraints are applied. This is the default value.
:code:`HBonds` The lengths of all bonds that involve a hydrogen atom are constrained.
:code:`AllBonds` The lengths of all bonds are constrained.
:code:`None` No constraints are applied. This is the default value.
:code:`HBonds` The lengths of all bonds that involve a hydrogen atom are constrained.
:code:`AllBonds` The lengths of all bonds are constrained.
:code:`HAngles` The lengths of all bonds are constrained. In addition, all angles of the form H-X-H or H-O-X (where X is an arbitrary atom) are constrained.
================ =============================================================================================================================================
......@@ -1678,19 +1678,19 @@ Here is the definition of the :class:`ForceReporter` class:
.. samepage::
::
class ForceReporter(object):
def __init__(self, file, reportInterval):
self._out = open(file, 'w')
self._reportInterval = reportInterval
def __del__(self):
self._out.close()
def describeNextReport(self, simulation):
steps = self._reportInterval - simulation.currentStep%self._reportInterval
return (steps, False, False, True, False)
def report(self, simulation, state):
forces = state.getForces().value_in_unit(kilojoules/mole/nanometer)
for f in forces:
......@@ -1961,6 +1961,32 @@ are :code:`wo1`\ , :code:`wo2`\ , :code:`wo3`\ , :code:`wx1`\ , :code:`wx2`\ ,
:code:`wx3`\ , :code:`wy1`\ , :code:`wy2`\ , :code:`wy3`\ , :code:`p1`\ ,
:code:`p2`\ , and :code:`p3`\ .
Missing residue templates
=========================
.. CAUTION::
This feature is experimental, and its API is subject to change.
You can use the :method:`getUnmatchedResidues()` method to get a list of residues
in the provided :code:`topology` object that do not currently have a matching
residue template defined in the :class:`ForceField`.
::
pdb = PDBFile('input.pdb')
forcefield = ForceField('amber99sb.xml', 'tip3p.xml')
unmatched_residues = forcefield.getUnmatchedResidues(topology)
This is useful for idenfitying issues with prepared systems, debugging issues
with residue template definitions, or identifying which additional residues need
to be parameterized.
As a convenience for parameterizing new residues, you can also get a list of
residues and empty residue templates using :method:`getUniqueUnmatchedResidues`
::
pdb = PDBFile('input.pdb')
forcefield = ForceField('amber99sb.xml', 'tip3p.xml')
[residues, templates] = forcefield.getUniqueUnmatchedResidues(topology)
<HarmonicBondForce>
===================
......
wrappers/python/simtk/openmm/app/forcefield.py
View file @ 818db2b2
......@@ -640,24 +640,15 @@ class ForceField(object):
unmatched_residues = self.getUnmatchedResidues(topology)
# Generate a unique list of unmatched residues by comparing fingerprints.
bondedToAtom = self._buildBondedToAtomList(topology)
unique_unmatched_residues = list()
unique_unmatched_residues = list() # list of unique unmatched Residue objects from topology
templates = list() # corresponding _TemplateData templates
signatures = set()
for residue in unmatched_residues:
signature = _createResidueSignature([ atom.element for atom in residue.atoms() ])
template = _createResidueTemplate(residue)
is_unique = True
if signature in signatures:
# Signature is the same as an existing residue; check connectivity.
template = ForceField._TemplateData(residue.name)
for atom in residue.atoms():
template.atoms.append(ForceField._TemplateAtomData(atom.name, 'X', atom.element))
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)
for check_residue in unique_unmatched_residues:
matches = _matchResidue(check_residue, template, bondedToAtom)
if matches is not None:
......@@ -667,7 +658,7 @@ class ForceField(object):
unique_unmatched_residues.append(residue)
signatures.add(signature)
return unique_unmatched_residues
return [unique_unmatched_residues, templates]
def createSystem(self, topology, nonbondedMethod=NoCutoff, nonbondedCutoff=1.0*unit.nanometer,
constraints=None, rigidWater=True, removeCMMotion=True, hydrogenMass=None, **args):
......@@ -949,7 +940,6 @@ def _createResidueSignature(elements):
s += element.symbol+str(count)
return s
def _matchResidue(res, template, bondedToAtom):
"""Determine whether a residue matches a template and return a list of corresponding atoms.
......@@ -1094,6 +1084,34 @@ def _findMatchErrors(forcefield, res):
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.'
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():
template.atoms.append(ForceField._TemplateAtomData(atom.name, 'X', atom.element))
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
# 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,
......
wrappers/python/tests/TestForceField.py
View file @ 818db2b2
......@@ -261,19 +261,10 @@ class TestForceField(unittest.TestCase):
from uuid import uuid4
template_name = uuid4()
# Create residue template.
template = ForceField._TemplateData(template_name)
for atom in residue.atoms():
typename = 'XXX'
atom_template = ForceField._TemplateAtomData(atom.name, typename, atom.element)
template.atoms.append(atom_template)
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)
template = ForceField._createResidueTemplate(residue)
template.name = template_name
for (template_atom, residue_atom) in zip(template.atoms, residue.atoms()):
template_atom.type = 'XXX'
# Register the template.
forcefield.registerResidueTemplate(template)
......@@ -385,13 +376,18 @@ class TestForceField(unittest.TestCase):
forcefield = ForceField('tip3p.xml')
# Get list of unmatched residues.
unmatched_residues = forcefield.getUnmatchedResidues(pdb.topology)
unique_unmatched_residues = forcefield.getUniqueUnmatchedResidues(pdb.topology)
[unique_unmatched_residues, templates] = forcefield.getUniqueUnmatchedResidues(pdb.topology)
# Check results.
self.assertEqual(len(unmatched_residues), 24)
self.assertEqual(len(unique_unmatched_residues), 2)
unique_names = set([ residue.name for residue in unique_unmatched_residues ])
self.assertTrue('HOH' not in unique_names)
self.assertTrue('NA' in unique_names)
self.assertTrue('CL' in unique_names)
template_names = set([ template.name for template in templates ])
self.assertTrue('HOH' not in template_names)
self.assertTrue('NA' in template_names)
self.assertTrue('CL' in template_names)
class AmoebaTestForceField(unittest.TestCase):
"""Test the ForceField.createSystem() method with the AMOEBA forcefield."""
......
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