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Commit 4c00b312 authored by peastman's avatar peastman
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Merge pull request #1081 from swails/pdbx 

Add PDBxReporter class
parents 300566f3 c885f3d7
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wrappers/python/simtk/openmm/app/__init__.py
View file @ 4c00b312
"""
OpenMM Application
"""
from __future__ import absolute_import
__docformat__ = "epytext en"
__author__ = "Peter Eastman"
......@@ -10,26 +12,26 @@ __license__ = "MIT"
__maintainer__ = "Peter Eastman"
__email__ = "peastman@stanford.edu"
from topology import Topology, Chain, Residue, Atom
from pdbfile import PDBFile
from pdbxfile import PDBxFile
from forcefield import ForceField
from simulation import Simulation
from pdbreporter import PDBReporter
from amberprmtopfile import AmberPrmtopFile, HCT, OBC1, OBC2, GBn, GBn2
from amberinpcrdfile import AmberInpcrdFile
from dcdfile import DCDFile
from gromacsgrofile import GromacsGroFile
from gromacstopfile import GromacsTopFile
from dcdreporter import DCDReporter
from modeller import Modeller
from statedatareporter import StateDataReporter
from element import Element
from desmonddmsfile import DesmondDMSFile
from checkpointreporter import CheckpointReporter
from charmmcrdfiles import CharmmCrdFile, CharmmRstFile
from charmmparameterset import CharmmParameterSet
from charmmpsffile import CharmmPsfFile, CharmmPSFWarning
from .topology import Topology, Chain, Residue, Atom
from .pdbfile import PDBFile
from .pdbxfile import PDBxFile
from .forcefield import ForceField
from .simulation import Simulation
from .pdbreporter import PDBReporter, PDBxReporter
from .amberprmtopfile import AmberPrmtopFile, HCT, OBC1, OBC2, GBn, GBn2
from .amberinpcrdfile import AmberInpcrdFile
from .dcdfile import DCDFile
from .gromacsgrofile import GromacsGroFile
from .gromacstopfile import GromacsTopFile
from .dcdreporter import DCDReporter
from .modeller import Modeller
from .statedatareporter import StateDataReporter
from .element import Element
from .desmonddmsfile import DesmondDMSFile
from .checkpointreporter import CheckpointReporter
from .charmmcrdfiles import CharmmCrdFile, CharmmRstFile
from .charmmparameterset import CharmmParameterSet
from .charmmpsffile import CharmmPsfFile, CharmmPSFWarning
# Enumerated values
......
wrappers/python/simtk/openmm/app/pdbfile.py
View file @ 4c00b312
......@@ -28,6 +28,7 @@ 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.
"""
from __future__ import print_function, division, absolute_import
__author__ = "Peter Eastman"
__version__ = "1.0"
......@@ -39,12 +40,13 @@ from copy import copy
from datetime import date
from simtk.openmm import Vec3, Platform
from simtk.openmm.app.internal.pdbstructure import PdbStructure
from simtk.openmm.app.internal.unitcell import computeLengthsAndAngles
from simtk.openmm.app import Topology
from simtk.unit import nanometers, angstroms, is_quantity, norm, Quantity, dot
import element as elem
from . import element as elem
try:
import numpy
except:
except ImportError:
pass
class PDBFile(object):
......@@ -252,17 +254,13 @@ class PDBFile(object):
- topology (Topology) The Topology defining the molecular system being written
- file (file=stdout) A file to write the file to
"""
print >>file, "REMARK 1 CREATED WITH OPENMM %s, %s" % (Platform.getOpenMMVersion(), str(date.today()))
print("REMARK 1 CREATED WITH OPENMM %s, %s" % (Platform.getOpenMMVersion(), str(date.today())), file=file)
vectors = topology.getPeriodicBoxVectors()
if vectors is not None:
(a, b, c) = vectors.value_in_unit(angstroms)
a_length = norm(a)
b_length = norm(b)
c_length = norm(c)
alpha = math.acos(dot(b, c)/(b_length*c_length))*180.0/math.pi
beta = math.acos(dot(c, a)/(c_length*a_length))*180.0/math.pi
gamma = math.acos(dot(a, b)/(a_length*b_length))*180.0/math.pi
print >>file, "CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f P 1 1 " % (a_length, b_length, c_length, alpha, beta, gamma)
a, b, c, alpha, beta, gamma = computeLengthsAndAngles(vectors)
RAD_TO_DEG = 180/math.pi
print("CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f P 1 1 " % (
a*10, b*10, c*10, alpha*RAD_TO_DEG, beta*RAD_TO_DEG, gamma*RAD_TO_DEG), file=file)
@staticmethod
def writeModel(topology, positions, file=sys.stdout, modelIndex=None, keepIds=False):
......@@ -288,7 +286,7 @@ class PDBFile(object):
atomIndex = 1
posIndex = 0
if modelIndex is not None:
print >>file, "MODEL %4d" % modelIndex
print("MODEL %4d" % modelIndex, file=file)
for (chainIndex, chain) in enumerate(topology.chains()):
if keepIds:
chainName = chain.id
......@@ -320,14 +318,14 @@ class PDBFile(object):
atomIndex%100000, atomName, resName, chainName, resId, _format_83(coords[0]),
_format_83(coords[1]), _format_83(coords[2]), symbol)
assert len(line) == 80, 'Fixed width overflow detected'
print >>file, line
print(line, file=file)
posIndex += 1
atomIndex += 1
if resIndex == len(residues)-1:
print >>file, "TER %5d %3s %s%4s" % (atomIndex, resName, chainName, resId)
print("TER %5d %3s %s%4s" % (atomIndex, resName, chainName, resId), file=file)
atomIndex += 1
if modelIndex is not None:
print >>file, "ENDMDL"
print("ENDMDL", file=file)
@staticmethod
def writeFooter(topology, file=sys.stdout):
......@@ -381,13 +379,13 @@ class PDBFile(object):
for index1 in sorted(atomBonds):
bonded = atomBonds[index1]
while len(bonded) > 4:
print >>file, "CONECT%5d%5d%5d%5d" % (index1, bonded[0], bonded[1], bonded[2])
print("CONECT%5d%5d%5d%5d" % (index1, bonded[0], bonded[1], bonded[2]), file=file)
del bonded[:4]
line = "CONECT%5d" % index1
for index2 in bonded:
line = "%s%5d" % (line, index2)
print >>file, line
print >>file, "END"
print(line, file=file)
print("END", file=file)
def _format_83(f):
......
wrappers/python/simtk/openmm/app/pdbreporter.py
View file @ 4c00b312
......@@ -32,7 +32,7 @@ __author__ = "Peter Eastman"
__version__ = "1.0"
import simtk.openmm as mm
from simtk.openmm.app import PDBFile
from simtk.openmm.app import PDBFile, PDBxFile
class PDBReporter(object):
"""PDBReporter outputs a series of frames from a Simulation to a PDB file.
......@@ -77,8 +77,34 @@ class PDBReporter(object):
self._nextModel += 1
PDBFile.writeModel(simulation.topology, state.getPositions(), self._out, self._nextModel)
self._nextModel += 1
if hasattr(self._out, 'flush') and callable(self._out.flush):
self._out.flush()
def __del__(self):
if self._topology is not None:
PDBFile.writeFooter(self._topology, self._out)
self._out.close()
class PDBxReporter(PDBReporter):
"""PDBxReporter outputs a series of frames from a Simulation to a PDBx/mmCIF file.
To use it, create a PDBxReporter, then add it to the Simulation's list of reporters.
"""
def report(self, simulation, state):
"""Generate a report.
Parameters:
- simulation (Simulation) The Simulation to generate a report for
- state (State) The current state of the simulation
"""
if self._nextModel == 0:
PDBxFile.writeHeader(simulation.topology, self._out)
self._nextModel += 1
PDBxFile.writeModel(simulation.topology, state.getPositions(), self._out, self._nextModel)
self._nextModel += 1
if hasattr(self._out, 'flush') and callable(self._out.flush):
self._out.flush()
def __del__(self):
self._out.close()
wrappers/python/simtk/openmm/app/pdbxfile.py
View file @ 4c00b312
"""
pdbfile.py: Used for loading PDB files.
pdbxfile.py: Used for loading PDBx/mmCIF files.
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.
Portions copyright (c) 2014-2015 Stanford University and the Authors.
Portions copyright (c) 2015 Stanford University and the Authors.
Authors: Peter Eastman
Contributors:
Contributors: Jason Swails
Permission is hereby granted, free of charge, to any person obtaining a
copy of this software and associated documentation files (the "Software"),
......@@ -28,18 +28,20 @@ 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.
"""
from __future__ import division, absolute_import, print_function
__author__ = "Peter Eastman"
__version__ = "1.0"
__version__ = "2.0"
import os
import sys
import math
from simtk.openmm import Vec3
from simtk.openmm import Vec3, Platform
from datetime import date
from simtk.openmm.app.internal.pdbx.reader.PdbxReader import PdbxReader
from simtk.openmm.app.internal.unitcell import computePeriodicBoxVectors
from simtk.openmm.app.internal.unitcell import computePeriodicBoxVectors, computeLengthsAndAngles
from simtk.openmm.app import Topology
from simtk.unit import nanometers, angstroms, is_quantity, norm, Quantity
import element as elem
from simtk.unit import nanometers, angstroms, is_quantity, norm, Quantity, dot
from . import element as elem
try:
import numpy
except:
......@@ -202,3 +204,120 @@ class PDBxFile(object):
self._numpyPositions[frame] = Quantity(numpy.array(self._positions[frame].value_in_unit(nanometers)), nanometers)
return self._numpyPositions[frame]
return self._positions[frame]
@staticmethod
def writeFile(topology, positions, file=sys.stdout, keepIds=False,
entry=None):
"""Write a PDBx/mmCIF file containing a single model.
Parameters:
- topology (Topology) The Topology defining the model to write
- positions (list) The list of atomic positions to write
- file (file=stdout) A file to write to
- keepIds (bool=False) If True, keep the residue and chain IDs specified in the Topology rather than generating
new ones. Warning: It is up to the caller to make sure these are valid IDs that satisfy the requirements of
the PDBx/mmCIF format. Otherwise, the output file will be invalid.
- entry (str=None) The entry ID to assign to the CIF file
"""
PDBxFile.writeHeader(topology, file, entry)
PDBxFile.writeModel(topology, positions, file, keepIds=keepIds)
@staticmethod
def writeHeader(topology, file=sys.stdout, entry=None):
"""Write out the header for a PDBx/mmCIF file.
Parameters:
- topology (Topology) The Topology defining the molecular system being written
- file (file=stdout) A file to write the file to
- entry (str=None) The entry ID to assign to the CIF file
"""
if entry is not None:
print('data_%s' % entry, file=file)
else:
print('data_cell', file=file)
print("# Created with OpenMM %s, %s" % (Platform.getOpenMMVersion(), str(date.today())), file=file)
print('#', file=file)
vectors = topology.getPeriodicBoxVectors()
if vectors is not None:
a, b, c, alpha, beta, gamma = computeLengthsAndAngles(vectors)
RAD_TO_DEG = 180/math.pi
print('_cell.length_a %10.4f' % (a*10), file=file)
print('_cell.length_b %10.4f' % (b*10), file=file)
print('_cell.length_c %10.4f' % (c*10), file=file)
print('_cell.angle_alpha %10.4f' % (alpha*RAD_TO_DEG), file=file)
print('_cell.angle_beta %10.4f' % (beta*RAD_TO_DEG), file=file)
print('_cell.angle_gamma %10.4f' % (gamma*RAD_TO_DEG), file=file)
print('##', file=file)
print('loop_', file=file)
print('_atom_site.group_PDB', file=file)
print('_atom_site.id', file=file)
print('_atom_site.type_symbol', file=file)
print('_atom_site.label_atom_id', file=file)
print('_atom_site.label_alt_id', file=file)
print('_atom_site.label_comp_id', file=file)
print('_atom_site.label_asym_id', file=file)
print('_atom_site.label_entity_id', file=file)
print('_atom_site.label_seq_id', file=file)
print('_atom_site.pdbx_PDB_ins_code', file=file)
print('_atom_site.Cartn_x', file=file)
print('_atom_site.Cartn_y', file=file)
print('_atom_site.Cartn_z', file=file)
print('_atom_site.occupancy', file=file)
print('_atom_site.B_iso_or_equiv', file=file)
print('_atom_site.Cartn_x_esd', file=file)
print('_atom_site.Cartn_y_esd', file=file)
print('_atom_site.Cartn_z_esd', file=file)
print('_atom_site.occupancy_esd', file=file)
print('_atom_site.B_iso_or_equiv_esd', file=file)
print('_atom_site.pdbx_formal_charge', file=file)
print('_atom_site.auth_seq_id', file=file)
print('_atom_site.auth_comp_id', file=file)
print('_atom_site.auth_asym_id', file=file)
print('_atom_site.auth_atom_id', file=file)
print('_atom_site.pdbx_PDB_model_num', file=file)
@staticmethod
def writeModel(topology, positions, file=sys.stdout, modelIndex=1, keepIds=False):
"""Write out a model to a PDBx/mmCIF file.
Parameters:
- topology (Topology) The Topology defining the model to write
- positions (list) The list of atomic positions to write
- file (file=stdout) A file to write the model to
- modelIndex (int=1) The model number of this frame
- keepIds (bool=False) If True, keep the residue and chain IDs specified in the Topology rather than generating
new ones. Warning: It is up to the caller to make sure these are valid IDs that satisfy the requirements of
the PDBx/mmCIF format. Otherwise, the output file will be invalid.
"""
if len(list(topology.atoms())) != len(positions):
raise ValueError('The number of positions must match the number of atoms')
if is_quantity(positions):
positions = positions.value_in_unit(angstroms)
if any(math.isnan(norm(pos)) for pos in positions):
raise ValueError('Particle position is NaN')
if any(math.isinf(norm(pos)) for pos in positions):
raise ValueError('Particle position is infinite')
atomIndex = 1
posIndex = 0
for (chainIndex, chain) in enumerate(topology.chains()):
if keepIds:
chainName = chain.id
else:
chainName = chr(ord('A')+chainIndex%26)
residues = list(chain.residues())
for (resIndex, res) in enumerate(residues):
if keepIds:
resId = res.id
else:
resId = resIndex + 1
for atom in res.atoms():
coords = positions[posIndex]
if atom.element is not None:
symbol = atom.element.symbol
else:
symbol = '?'
line = "ATOM %5d %-3s %-4s . %-4s %s ? %5s . %10.4f %10.4f %10.4f 0.0 0.0 ? ? ? ? ? . %5s %4s %s %4s %5d"
print(line % (atomIndex, symbol, atom.name, res.name, chainName, resId, coords[0], coords[1], coords[2],
resId, res.name, chainName, atom.name, modelIndex), file=file)
posIndex += 1
atomIndex += 1
wrappers/python/tests/TestPdbxFile.py
View file @ 4c00b312
......@@ -3,6 +3,7 @@ from simtk.openmm.app import *
from simtk.openmm import *
from simtk.unit import *
import simtk.openmm.app.element as elem
import os
class TestPdbxFile(unittest.TestCase):
"""Test the PDBx/mmCIF file parser"""
......@@ -48,6 +49,69 @@ class TestPdbxFile(unittest.TestCase):
diff = abs(p1[i]-p2[i])/scale
self.assertTrue(diff < tol)
def testReporterImplicit(self):
""" Tests the PDBxReporter without PBC """
parm = AmberPrmtopFile('systems/alanine-dipeptide-implicit.prmtop')
system = parm.createSystem()
sim = Simulation(parm.topology, system, VerletIntegrator(1*femtoseconds),
Platform.getPlatformByName('Reference'))
sim.context.setPositions(PDBFile('systems/alanine-dipeptide-implicit.pdb').getPositions())
sim.reporters.append(PDBxReporter('test.cif', 1))
sim.step(10)
pdb = PDBxFile('test.cif')
self.assertEqual(len(list(pdb.topology.atoms())), len(list(parm.topology.atoms())))
self.assertEqual(len(list(pdb.topology.residues())), len(list(parm.topology.residues())))
for res1, res2 in zip(pdb.topology.residues(), parm.topology.residues()):
self.assertEqual(res1.name, res2.name)
for atom1, atom2 in zip(res1.atoms(), res2.atoms()):
self.assertEqual(atom1.name, atom2.name)
positions = pdb.getPositions(frame=9)
self.assertFalse(all(x1 == x2 for x1, x2 in zip(positions, pdb.getPositions(frame=0))))
# There should only be 10 frames (0 through 9)
self.assertRaises(IndexError, lambda: pdb.getPositions(frame=10))
self.assertIs(pdb.topology.getPeriodicBoxVectors(), None)
os.unlink('test.cif')
def assertAlmostEqualVec(self, vec1, vec2, *args, **kwargs):
if is_quantity(vec1):
vec1 = vec1.value_in_unit_system(md_unit_system)
if is_quantity(vec2):
vec2 = vec2.value_in_unit_system(md_unit_system)
for x, y in zip(vec1, vec2):
self.assertAlmostEqual(x, y, *args, **kwargs)
def testReporterExplicit(self):
""" Tests the PDBxReporter with PBC """
parm = AmberPrmtopFile('systems/alanine-dipeptide-explicit.prmtop')
system = parm.createSystem(nonbondedCutoff=1.0, nonbondedMethod=PME)
sim = Simulation(parm.topology, system, VerletIntegrator(1*femtoseconds),
Platform.getPlatformByName('Reference'))
orig_pdb = PDBFile('systems/alanine-dipeptide-explicit.pdb')
sim.context.setPositions(orig_pdb.getPositions())
sim.context.setPeriodicBoxVectors(*parm.topology.getPeriodicBoxVectors())
sim.reporters.append(PDBxReporter('test.cif', 1))
sim.step(10)
pdb = PDBxFile('test.cif')
self.assertEqual(len(list(pdb.topology.atoms())), len(list(parm.topology.atoms())))
self.assertEqual(len(list(pdb.topology.residues())), len(list(parm.topology.residues())))
for res1, res2 in zip(pdb.topology.residues(), parm.topology.residues()):
self.assertEqual(res1.name, res2.name)
for atom1, atom2 in zip(res1.atoms(), res2.atoms()):
self.assertEqual(atom1.name, atom2.name)
positions = pdb.getPositions(frame=9)
self.assertFalse(all(x1 == x2 for x1, x2 in zip(positions, pdb.getPositions(frame=0))))
# There should only be 10 frames (0 through 9)
self.assertRaises(IndexError, lambda: pdb.getPositions(frame=10))
self.assertAlmostEqualVec(parm.topology.getPeriodicBoxVectors()[0],
pdb.topology.getPeriodicBoxVectors()[0],
places=5)
self.assertAlmostEqualVec(parm.topology.getPeriodicBoxVectors()[1],
pdb.topology.getPeriodicBoxVectors()[1],
places=5)
self.assertAlmostEqualVec(parm.topology.getPeriodicBoxVectors()[2],
pdb.topology.getPeriodicBoxVectors()[2],
places=5)
os.unlink('test.cif')
if __name__ == '__main__':
unittest.main()
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