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Commit b7088b74 authored by peastman's avatar peastman Committed by Robert McGibbon
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Python 2/3 compatibility in single code base, plus python 3 testing on travis.

parent 4c00b312
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wrappers/python/simtk/openmm/app/charmmpsffile.py
View file @ b7088b74
......@@ -33,11 +33,14 @@ OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
USE OR OTHER DEALINGS IN THE SOFTWARE.
"""
from __future__ import division
from __future__ import absolute_import
from __future__ import print_function
from functools import wraps
from math import pi, cos, sin, sqrt
import os
import re
import sys
import simtk.openmm as mm
from simtk.openmm.vec3 import Vec3
import simtk.unit as u
......@@ -58,7 +61,8 @@ import warnings
TINY = 1e-8
WATNAMES = ('WAT', 'HOH', 'TIP3', 'TIP4', 'TIP5', 'SPCE', 'SPC')
if sys.version_info >= (3, 0):
xrange = range
def _catchindexerror(func):
"""
......@@ -70,7 +74,7 @@ def _catchindexerror(func):
""" Catch the index error """
try:
return func(*args, **kwargs)
except IndexError, e:
except IndexError as e:
raise CharmmPSFError('Array is too short: %s' % e)
return newfunc
......@@ -386,8 +390,8 @@ class CharmmPsfFile(object):
"""
try:
return type(string)
except ValueError, e:
print e
except ValueError as e:
print(e)
raise CharmmPSFError('Could not convert %s' % message)
@staticmethod
......@@ -1251,8 +1255,8 @@ class CharmmPsfFile(object):
elif implicitSolvent is GBn2:
gb = GBSAGBn2Force(solventDielectric, soluteDielectric, None,
cutoff, kappa=implicitSolventKappa)
for i, atom in enumerate(self.atom_list):
gb.addParticle([atom.charge] + list(gb_parms[i]))
for atom, gb_parm in zip(self.atom_list, gb_parms):
gb.addParticle([atom.charge] + list(gb_parm))
# Set cutoff method
if nonbondedMethod is ff.NoCutoff:
gb.setNonbondedMethod(mm.NonbondedForce.NoCutoff)
......
wrappers/python/simtk/openmm/app/checkpointreporter.py
View file @ b7088b74
......@@ -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 absolute_import
__author__ = "Robert McGibbon"
__version__ = "1.0"
......@@ -77,7 +78,7 @@ class CheckpointReporter(object):
"""
self._reportInterval = reportInterval
if isinstance(file, basestring):
if isinstance(file, str):
self._own_handle = True
self._out = open(file, 'w+b', 0)
else:
......
wrappers/python/simtk/openmm/app/dcdfile.py
View file @ b7088b74
......@@ -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 absolute_import
__author__ = "Peter Eastman"
__version__ = "1.0"
......
wrappers/python/simtk/openmm/app/dcdreporter.py
View file @ b7088b74
......@@ -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 absolute_import
__author__ = "Peter Eastman"
__version__ = "1.0"
......
wrappers/python/simtk/openmm/app/desmonddmsfile.py
View file @ b7088b74
......@@ -24,6 +24,7 @@ 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 absolute_import
import os
import math
......
wrappers/python/simtk/openmm/app/element.py
View file @ b7088b74
......@@ -28,12 +28,18 @@ 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 absolute_import
__author__ = "Christopher M. Bruns"
__version__ = "1.0"
import sys
from collections import OrderedDict
from simtk.unit import daltons, is_quantity
import copy_reg
if sys.version_info >= (3, 0):
import copyreg
else:
import copy_reg as copyreg
class Element(object):
"""An Element represents a chemical element.
......@@ -128,7 +134,7 @@ class Element(object):
diff = mass
best_guess = None
for elemmass, element in Element._elements_by_mass.iteritems():
for elemmass, element in _iteritems(Element._elements_by_mass):
massdiff = abs(elemmass - mass)
if massdiff < diff:
best_guess = element
......@@ -172,7 +178,7 @@ def get_by_symbol(symbol):
def _pickle_element(element):
return (get_by_symbol, (element.symbol,))
copy_reg.pickle(Element, _pickle_element)
copyreg.pickle(Element, _pickle_element)
# NOTE: getElementByMass assumes all masses are Quantity instances with unit
# "daltons". All elements need to obey this assumption, or that method will
......@@ -299,3 +305,10 @@ ununhexium = Element(116, "ununhexium", "Uuh", 292*daltons)
# relational operators will work with any chosen name
sulphur = sulfur
aluminium = aluminum
if sys.version_info >= (3, 0):
def _iteritems(dict):
return dict.items()
else:
def _iteritems(dict):
return dict.iteritems()
wrappers/python/simtk/openmm/app/forcefield.py
View file @ b7088b74
......@@ -28,6 +28,8 @@ 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 absolute_import
from __future__ import print_function
__author__ = "Peter Eastman"
__version__ = "1.0"
......@@ -38,7 +40,7 @@ import math
from math import sqrt, cos
import simtk.openmm as mm
import simtk.unit as unit
import element as elem
from . import element as elem
from simtk.openmm.app import Topology
def _convertParameterToNumber(param):
......@@ -1883,7 +1885,7 @@ def countConstraint(data):
if (isConstrained):
angleCount += 1
print "Constraints bond=%d angle=%d total=%d" % (bondCount, angleCount, (bondCount+angleCount))
print("Constraints bond=%d angle=%d total=%d" % (bondCount, angleCount, (bondCount+angleCount)))
## @private
class AmoebaBondGenerator:
......
wrappers/python/simtk/openmm/app/gromacsgrofile.py
View file @ b7088b74
......@@ -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 absolute_import
__author__ = "Lee-Ping Wang"
__version__ = "1.0"
......@@ -36,7 +37,7 @@ import sys
from simtk.openmm import Vec3
from re import sub, match
from simtk.unit import nanometers, angstroms, Quantity
import element as elem
from . import element as elem
try:
import numpy
except:
......
wrappers/python/simtk/openmm/app/gromacstopfile.py
View file @ b7088b74
......@@ -28,14 +28,15 @@ 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 absolute_import
__author__ = "Peter Eastman"
__version__ = "1.0"
from simtk.openmm.app import Topology
from simtk.openmm.app import PDBFile
import forcefield as ff
import element as elem
import amberprmtopfile as prmtop
from . import forcefield as ff
from . import element as elem
from . import amberprmtopfile as prmtop
import simtk.unit as unit
import simtk.openmm as mm
import math
......@@ -601,7 +602,7 @@ class GromacsTopFile(object):
for key in self._dihedralTypes:
if key[1] == 'X' or key[2] == 'X':
wildcardDihedralTypes.append(key)
for types in dihedralTypeTable.itervalues():
for types in dihedralTypeTable.values():
types.append(key)
# Loop over molecules and create the specified number of each type.
......@@ -617,7 +618,7 @@ class GromacsTopFile(object):
try:
bondedTypes = [self._atomTypes[t][1] for t in atomTypes]
except KeyError as e:
raise ValueError('Unknown atom type: '+e.message)
raise ValueError('Unknown atom type: ' + e.message)
bondedTypes = [b if b is not None else a for a, b in zip(atomTypes, bondedTypes)]
# Add atoms.
......
wrappers/python/simtk/openmm/app/internal/amber_file_parser.py
View file @ b7088b74
......@@ -34,6 +34,8 @@ 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 absolute_import
from __future__ import print_function
#=============================================================================================
# GLOBAL IMPORTS
......@@ -54,7 +56,7 @@ import simtk.openmm
from simtk.openmm.app import element as elem
from simtk.openmm.app.internal.unitcell import computePeriodicBoxVectors
from simtk.openmm.vec3 import Vec3
import customgbforces as customgb
from . import customgbforces as customgb
#=============================================================================================
# AMBER parmtop loader (from 'zander', by Randall J. Radmer)
......@@ -713,7 +715,7 @@ def readAmberSystem(topology, prmtop_filename=None, prmtop_loader=None, shake=No
raise Exception("Cannot specify both a filename and a loader")
if prmtop_filename is not None:
# Load prmtop file.
if verbose: print "Reading prmtop file '%s'..." % prmtop_filename
if verbose: print("Reading prmtop file '%s'..." % prmtop_filename)
prmtop = PrmtopLoader(prmtop_filename)
else:
prmtop = prmtop_loader
......@@ -737,11 +739,11 @@ def readAmberSystem(topology, prmtop_filename=None, prmtop_loader=None, shake=No
mm = simtk.openmm
# Create OpenMM System.
if verbose: print "Creating OpenMM system..."
if verbose: print("Creating OpenMM system...")
system = mm.System()
# Populate system with atomic masses.
if verbose: print "Adding particles..."
if verbose: print("Adding particles...")
for mass in prmtop.getMasses():
system.addParticle(mass)
......@@ -759,7 +761,7 @@ def readAmberSystem(topology, prmtop_filename=None, prmtop_loader=None, shake=No
system.addConstraint(iAtom, jAtom, rMin)
# Add harmonic bonds.
if verbose: print "Adding bonds..."
if verbose: print("Adding bonds...")
force = mm.HarmonicBondForce()
if flexibleConstraints or (shake not in ('h-bonds', 'all-bonds', 'h-angles')):
for (iAtom, jAtom, k, rMin) in prmtop.getBondsWithH():
......@@ -771,7 +773,7 @@ def readAmberSystem(topology, prmtop_filename=None, prmtop_loader=None, shake=No
system.addForce(force)
# Add harmonic angles.
if verbose: print "Adding angles..."
if verbose: print("Adding angles...")
force = mm.HarmonicAngleForce()
if shake == 'h-angles':
numConstrainedBonds = system.getNumConstraints()
......@@ -809,14 +811,14 @@ def readAmberSystem(topology, prmtop_filename=None, prmtop_loader=None, shake=No
system.addForce(force)
# Add torsions.
if verbose: print "Adding torsions..."
if verbose: print("Adding torsions...")
force = mm.PeriodicTorsionForce()
for (iAtom, jAtom, kAtom, lAtom, forceConstant, phase, periodicity) in prmtop.getDihedrals():
force.addTorsion(iAtom, jAtom, kAtom, lAtom, periodicity, phase, forceConstant)
system.addForce(force)
# Add nonbonded interactions.
if verbose: print "Adding nonbonded interactions..."
if verbose: print("Adding nonbonded interactions...")
force = mm.NonbondedForce()
if (prmtop.getIfBox() == 0):
# System is non-periodic.
......@@ -1044,7 +1046,7 @@ def readAmberSystem(topology, prmtop_filename=None, prmtop_loader=None, shake=No
# Convert implicitSolventKappa to nanometers if it is a unit.
if units.is_quantity(implicitSolventKappa):
implicitSolventKappa = implicitSolventKappa.value_in_unit((1/units.nanometers).unit)
if verbose: print "Adding GB parameters..."
if verbose: print("Adding GB parameters...")
charges = prmtop.getCharges()
cutoff = None
if nonbondedMethod != 'NoCutoff':
......@@ -1071,14 +1073,15 @@ def readAmberSystem(topology, prmtop_filename=None, prmtop_loader=None, shake=No
gb = customgb.GBSAGBn2Force(solventDielectric, soluteDielectric, 'ACE', cutoff, implicitSolventKappa)
else:
raise Exception("Illegal value specified for implicit solvent model")
for iAtom in range(prmtop.getNumAtoms()):
for charge, gb_parm in zip(charges, gb_parms):
if gbmodel == 'OBC2' and implicitSolventKappa == 0:
gb.addParticle(charges[iAtom], gb_parms[iAtom][0], gb_parms[iAtom][1])
gb.addParticle(charge, gb_parm[0], gb_parm[1])
elif gbmodel == 'GBn2':
gb.addParticle([charges[iAtom], gb_parms[iAtom][0], gb_parms[iAtom][1],
gb_parms[iAtom][2], gb_parms[iAtom][3], gb_parms[iAtom][4]])
gb.addParticle([charge, gb_parm[0], gb_parm[1],
gb_parm[2], gb_parm[3], gb_parm[4]])
else:
gb.addParticle([charges[iAtom], gb_parms[iAtom][0], gb_parms[iAtom][1]])
gb.addParticle([charge, gb_parm[0], gb_parm[1]])
system.addForce(gb)
if nonbondedMethod == 'NoCutoff':
gb.setNonbondedMethod(mm.NonbondedForce.NoCutoff)
......
wrappers/python/simtk/openmm/app/internal/charmm/_charmmfile.py
View file @ b7088b74
......@@ -33,7 +33,12 @@ 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 absolute_import
from simtk.openmm.app.internal.charmm.exceptions import CharmmFileError
import sys
if sys.version_info < (3, 0):
from codecs import open
class CharmmFile(object):
"""
......@@ -54,8 +59,8 @@ class CharmmFile(object):
else:
self.status = 'NEW'
try:
self._handle = open(fname, mode)
except IOError, e:
self._handle = open(fname, mode, encoding='utf-8')
except IOError as e:
raise CharmmFileError(str(e))
self.closed = False
self.line_number = 0
......
wrappers/python/simtk/openmm/app/internal/charmm/topologyobjects.py
View file @ b7088b74
......@@ -32,6 +32,7 @@ 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 absolute_import
from simtk.openmm.app.internal.charmm.exceptions import (
SplitResidueWarning, BondError, ResidueError, CmapError,
MissingParameter)
......
wrappers/python/simtk/openmm/app/internal/customgbforces.py
View file @ b7088b74
......@@ -30,6 +30,7 @@ USE OR OTHER DEALINGS IN THE SOFTWARE.
"""
from __future__ import division
from __future__ import absolute_import
from simtk.openmm import CustomGBForce, Continuous2DFunction
......@@ -369,13 +370,13 @@ def GBSAGBn2Force(solventDielectric=78.5, soluteDielectric=1, SA=None,
def convertParameters(params, gbmodel):
"""Convert the GB parameters from the file into the values expected by the appropriate CustomGBForce."""
newparams = [None]*len(params)
if gbmodel == 'GBn2':
offset = 0.0195141
else:
offset = 0.009
for i in range(len(params)):
newparams[i] = list(params[i])
newparams[i][0] -= offset
newparams[i][1] *= newparams[i][0]
return newparams
for p in params:
newParam = list(p)
newParam[0] -= offset
newParam[1] *= newParam[0]
yield newParam
wrappers/python/simtk/openmm/app/internal/pdbstructure.py
View file @ b7088b74
#!/bin/env python
"""
pdbstructure.py: Used for managing PDB formated 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) 2012-2015 Stanford University and the Authors.
Authors: Christopher M. Bruns
Contributors: Peter Eastman
Permission is hereby granted, free of charge, to any person obtaining a
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.
"""
__author__ = "Christopher M. Bruns"
__version__ = "1.0"
from simtk.openmm.vec3 import Vec3
import simtk.unit as unit
from .. import element
from unitcell import computePeriodicBoxVectors
import warnings
import sys
import math
class PdbStructure(object):
"""
PdbStructure object holds a parsed Protein Data Bank format file.
Examples:
Load a pdb structure from a file:
> pdb = PdbStructure(open("1ARJ.pdb"))
Fetch the first atom of the structure:
> print pdb.iter_atoms().next()
ATOM 1 O5' G N 17 13.768 -8.431 11.865 1.00 0.00 O
Loop over all of the atoms of the structure
> for atom in pdb.iter_atoms():
> print atom
ATOM 1 O5' G N 17 13.768 -8.431 11.865 1.00 0.00 O
...
Get a list of all atoms in the structure:
> atoms = list(pdb.iter_atoms())
also:
residues = list(pdb.iter_residues())
positions = list(pdb.iter_positions())
chains = list(pdb.iter_chains())
models = list(pdb.iter_models())
Fetch atomic coordinates of first atom:
> print pdb.iter_positions().next()
[13.768, -8.431, 11.865] A
or
> print pdb.iter_atoms().next().position
[13.768, -8.431, 11.865] A
Strip the length units from an atomic position:
> import simtk.unit
> pos = pdb.iter_positions().next()
> print pos
[13.768, -8.431, 11.865] A
> print pos / simtk.unit.angstroms
[13.768, -8.431, 11.865]
> print pos / simtk.unit.nanometers
[1.3768, -0.8431, 1.1865]
The hierarchical structure of the parsed PDB structure is as follows:
PdbStructure
Model
Chain
Residue
Atom
Location
Model - A PDB structure consists of one or more Models. Each model corresponds to one version of
an NMR structure, or to one frame of a molecular dynamics trajectory.
Chain - A Model contains one or more Chains. Each chain corresponds to one molecule, although multiple
water molecules are frequently included in the same chain.
Residue - A Chain contains one or more Residues. One Residue corresponds to one of the repeating
unit that constitutes a polymer such as protein or DNA. For non-polymeric molecules, one Residue
represents one molecule.
Atom - A Residue contains one or more Atoms. Atoms are chemical atoms.
Location - An atom can sometimes have more that one position, due to static disorder in X-ray
crystal structures. To see all of the atom positions, use the atom.iter_positions() method,
or pass the parameter "include_alt_loc=True" to one of the other iter_positions() methods.
> for pos in pdb.iter_positions(include_alt_loc=True):
> ...
Will loop over all atom positions, including multiple alternate locations for atoms that have
multiple positions. The default value of include_alt_loc is False for the iter_positions()
methods.
"""
def __init__(self, input_stream, load_all_models = False):
"""Create a PDB model from a PDB file stream.
Parameters:
- self (PdbStructure) The new object that is created.
- input_stream (stream) An input file stream, probably created with
open().
- load_all_models (bool) Whether to load every model of an NMR
structure or trajectory, or just load the first model, to save memory.
"""
# initialize models
self.load_all_models = load_all_models
self.models = []
self._current_model = None
self.default_model = None
self.models_by_number = {}
self._periodic_box_vectors = None
self.sequences = []
self.modified_residues = []
# read file
self._load(input_stream)
def _load(self, input_stream):
self._reset_atom_numbers()
self._reset_residue_numbers()
# Read one line at a time
for pdb_line in input_stream:
if not isinstance(pdb_line, str):
pdb_line = pdb_line.decode('utf-8')
# Look for atoms
if (pdb_line.find("ATOM ") == 0) or (pdb_line.find("HETATM") == 0):
self._add_atom(Atom(pdb_line, self))
# Notice MODEL punctuation, for the next level of detail
# in the structure->model->chain->residue->atom->position hierarchy
elif (pdb_line.find("MODEL") == 0):
model_number = int(pdb_line[10:14])
self._add_model(Model(model_number))
self._reset_atom_numbers()
self._reset_residue_numbers()
elif (pdb_line.find("ENDMDL") == 0):
self._current_model._finalize()
if not self.load_all_models:
break
elif (pdb_line.find("END") == 0):
self._current_model._finalize()
if not self.load_all_models:
break
elif (pdb_line.find("TER") == 0 and pdb_line.split()[0] == "TER"):
self._current_model._current_chain._add_ter_record()
self._reset_residue_numbers()
elif (pdb_line.find("CRYST1") == 0):
a_length = float(pdb_line[6:15])*0.1
b_length = float(pdb_line[15:24])*0.1
c_length = float(pdb_line[24:33])*0.1
alpha = float(pdb_line[33:40])*math.pi/180.0
beta = float(pdb_line[40:47])*math.pi/180.0
gamma = float(pdb_line[47:54])*math.pi/180.0
self._periodic_box_vectors = computePeriodicBoxVectors(a_length, b_length, c_length, alpha, beta, gamma)
elif (pdb_line.find("CONECT") == 0):
atoms = [int(pdb_line[6:11])]
for pos in (11,16,21,26):
try:
atoms.append(int(pdb_line[pos:pos+5]))
except:
pass
self._current_model.connects.append(atoms)
elif (pdb_line.find("SEQRES") == 0):
chain_id = pdb_line[11]
if len(self.sequences) == 0 or chain_id != self.sequences[-1].chain_id:
self.sequences.append(Sequence(chain_id))
self.sequences[-1].residues.extend(pdb_line[19:].split())
elif (pdb_line.find("MODRES") == 0):
self.modified_residues.append(ModifiedResidue(pdb_line[16], int(pdb_line[18:22]), pdb_line[12:15].strip(), pdb_line[24:27].strip()))
self._finalize()
def _reset_atom_numbers(self):
self._atom_numbers_are_hex = False
self._next_atom_number = 1
def _reset_residue_numbers(self):
self._residue_numbers_are_hex = False
self._next_residue_number = 1
def write(self, output_stream=sys.stdout):
"""Write out structure in PDB format"""
for model in self.models:
if len(model.chains) == 0:
continue
if len(self.models) > 1:
print >>output_stream, "MODEL %4d" % (model.number)
model.write(output_stream)
if len(self.models) > 1:
print >>output_stream, "ENDMDL"
print >>output_stream, "END"
def _add_model(self, model):
if self.default_model == None:
self.default_model = model
self.models.append(model)
self._current_model = model
if model.number not in self.models_by_number:
self.models_by_number[model.number] = model
def get_model(self, model_number):
return self.models_by_number[model_number]
def model_numbers(self):
return self.models_by_number.keys()
def __contains__(self, model_number):
return self.models_by_number.__contains__(model_number)
def __getitem__(self, model_number):
return self.models_by_number[model_number]
def __iter__(self):
for model in self.models:
yield model
def iter_models(self, use_all_models=False):
if use_all_models:
for model in self:
yield model
elif len(self.models) > 0:
yield self.models[0]
def iter_chains(self, use_all_models=False):
for model in self.iter_models(use_all_models):
for chain in model.iter_chains():
yield chain
def iter_residues(self, use_all_models=False):
for model in self.iter_models(use_all_models):
for res in model.iter_residues():
yield res
def iter_atoms(self, use_all_models=False):
for model in self.iter_models(use_all_models):
for atom in model.iter_atoms():
yield atom
def iter_positions(self, use_all_models=False, include_alt_loc=False):
"""
Iterate over atomic positions.
Parameters
- use_all_models (bool=False) Get positions from all models or just the first one.
- include_alt_loc (bool=False) Get all positions for each atom, or just the first one.
"""
for model in self.iter_models(use_all_models):
for loc in model.iter_positions(include_alt_loc):
yield loc
def __len__(self):
return len(self.models)
def _add_atom(self, atom):
"""
"""
if self._current_model == None:
self._add_model(Model(0))
atom.model_number = self._current_model.number
# Atom might be alternate position for existing atom
self._current_model._add_atom(atom)
def _finalize(self):
"""Establish first and last residues, atoms, etc."""
for model in self.models:
model._finalize()
def get_periodic_box_vectors(self):
"""Get the vectors defining the crystallographic unit cell (may be None)."""
return self._periodic_box_vectors
class Sequence(object):
"""Sequence holds the sequence of a chain, as specified by SEQRES records."""
def __init__(self, chain_id):
self.chain_id = chain_id
self.residues = []
class ModifiedResidue(object):
"""ModifiedResidue holds information about a modified residue, as specified by a MODRES record."""
def __init__(self, chain_id, number, residue_name, standard_name):
self.chain_id = chain_id
self.number = number
self.residue_name = residue_name
self.standard_name = standard_name
class Model(object):
"""Model holds one model of a PDB structure.
NMR structures usually have multiple models. This represents one
of them.
"""
def __init__(self, model_number=1):
self.number = model_number
self.chains = []
self._current_chain = None
self.chains_by_id = {}
self.connects = []
def _add_atom(self, atom):
"""
"""
if len(self.chains) == 0:
self._add_chain(Chain(atom.chain_id))
# Create a new chain if the chain id has changed
if self._current_chain.chain_id != atom.chain_id:
self._add_chain(Chain(atom.chain_id))
# Create a new chain after TER record, even if ID is the same
elif self._current_chain.has_ter_record:
self._add_chain(Chain(atom.chain_id))
self._current_chain._add_atom(atom)
def _add_chain(self, chain):
self.chains.append(chain)
self._current_chain = chain
if not chain.chain_id in self.chains_by_id:
self.chains_by_id[chain.chain_id] = chain
def get_chain(self, chain_id):
return self.chains_by_id[chain_id]
def chain_ids(self):
return self.chains_by_id.keys()
def __contains__(self, chain_id):
return self.chains_by_id.__contains__(chain_id)
def __getitem__(self, chain_id):
return self.chains_by_id[chain_id]
def __iter__(self):
return iter(self.chains)
def iter_chains(self):
for chain in self:
yield chain
def iter_residues(self):
for chain in self:
for res in chain.iter_residues():
yield res
def iter_atoms(self):
for chain in self:
for atom in chain.iter_atoms():
yield atom
def iter_positions(self, include_alt_loc=False):
for chain in self:
for loc in chain.iter_positions(include_alt_loc):
yield loc
def __len__(self):
return len(self.chains)
def write(self, output_stream=sys.stdout):
# Start atom serial numbers at 1
sn = Model.AtomSerialNumber(1)
for chain in self.chains:
chain.write(sn, output_stream)
def _finalize(self):
for chain in self.chains:
chain._finalize()
class AtomSerialNumber(object):
"""pdb.Model inner class for pass-by-reference incrementable serial number"""
def __init__(self, val):
self.val = val
def increment(self):
self.val += 1
class Chain(object):
def __init__(self, chain_id=' '):
self.chain_id = chain_id
self.residues = []
self.has_ter_record = False
self._current_residue = None
self.residues_by_num_icode = {}
self.residues_by_number = {}
def _add_atom(self, atom):
"""
"""
# Create a residue if none have been created
if len(self.residues) == 0:
self._add_residue(Residue(atom.residue_name_with_spaces, atom.residue_number, atom.insertion_code, atom.alternate_location_indicator))
# Create a residue if the residue information has changed
elif self._current_residue.number != atom.residue_number:
self._add_residue(Residue(atom.residue_name_with_spaces, atom.residue_number, atom.insertion_code, atom.alternate_location_indicator))
elif self._current_residue.insertion_code != atom.insertion_code:
self._add_residue(Residue(atom.residue_name_with_spaces, atom.residue_number, atom.insertion_code, atom.alternate_location_indicator))
elif self._current_residue.name_with_spaces == atom.residue_name_with_spaces:
# This is a normal case: number, name, and iCode have not changed
pass
elif atom.alternate_location_indicator != ' ':
# OK - this is a point mutation, Residue._add_atom will know what to do
pass
else: # Residue name does not match
# Only residue name does not match
warnings.warn("WARNING: two consecutive residues with same number (%s, %s)" % (atom, self._current_residue.atoms[-1]))
self._add_residue(Residue(atom.residue_name_with_spaces, atom.residue_number, atom.insertion_code, atom.alternate_location_indicator))
self._current_residue._add_atom(atom)
def _add_residue(self, residue):
if len(self.residues) == 0:
residue.is_first_in_chain = True
self.residues.append(residue)
self._current_residue = residue
key = str(residue.number) + residue.insertion_code
# only store the first residue with a particular key
if key not in self.residues_by_num_icode:
self.residues_by_num_icode[key] = residue
if residue.number not in self.residues_by_number:
self.residues_by_number[residue.number] = residue
def write(self, next_serial_number, output_stream=sys.stdout):
for residue in self.residues:
residue.write(next_serial_number, output_stream)
if self.has_ter_record:
r = self.residues[-1]
print >>output_stream, "TER %5d %3s %1s%4d%1s" % (next_serial_number.val, r.name_with_spaces, self.chain_id, r.number, r.insertion_code)
next_serial_number.increment()
def _add_ter_record(self):
self.has_ter_record = True
self._finalize()
def get_residue(self, residue_number, insertion_code=' '):
return self.residues_by_num_icode[str(residue_number) + insertion_code]
def __contains__(self, residue_number):
return self.residues_by_number.__contains__(residue_number)
def __getitem__(self, residue_number):
"""Returns the FIRST residue in this chain with a particular residue number"""
return self.residues_by_number[residue_number]
def __iter__(self):
for res in self.residues:
yield res
def iter_residues(self):
for res in self:
yield res
def iter_atoms(self):
for res in self:
for atom in res:
yield atom;
def iter_positions(self, include_alt_loc=False):
for res in self:
for loc in res.iter_positions(include_alt_loc):
yield loc
def __len__(self):
return len(self.residues)
def _finalize(self):
self.residues[0].is_first_in_chain = True
self.residues[-1].is_final_in_chain = True
for residue in self.residues:
residue._finalize()
class Residue(object):
def __init__(self, name, number, insertion_code=' ', primary_alternate_location_indicator=' '):
alt_loc = primary_alternate_location_indicator
self.primary_location_id = alt_loc
self.locations = {}
self.locations[alt_loc] = Residue.Location(alt_loc, name)
self.name_with_spaces = name
self.number = number
self.insertion_code = insertion_code
self.atoms = []
self.atoms_by_name = {}
self.is_first_in_chain = False
self.is_final_in_chain = False
self._current_atom = None
def _add_atom(self, atom):
"""
"""
alt_loc = atom.alternate_location_indicator
if not self.locations.has_key(alt_loc):
self.locations[alt_loc] = Residue.Location(alt_loc, atom.residue_name_with_spaces)
assert atom.residue_number == self.number
assert atom.insertion_code == self.insertion_code
# Check whether this is an existing atom with another position
if (atom.name_with_spaces in self.atoms_by_name):
old_atom = self.atoms_by_name[atom.name_with_spaces]
# Unless this is a duplicated atom (warn about file error)
if atom.alternate_location_indicator in old_atom.locations:
warnings.warn("WARNING: duplicate atom (%s, %s)" % (atom, old_atom._pdb_string(old_atom.serial_number, atom.alternate_location_indicator)))
else:
for alt_loc, position in atom.locations.items():
old_atom.locations[alt_loc] = position
return # no new atom added
# actually use new atom
self.atoms_by_name[atom.name] = atom
self.atoms_by_name[atom.name_with_spaces] = atom
self.atoms.append(atom)
self._current_atom = atom
def write(self, next_serial_number, output_stream=sys.stdout, alt_loc = "*"):
for atom in self.atoms:
atom.write(next_serial_number, output_stream, alt_loc)
def _finalize(self):
if len(self.atoms) > 0:
self.atoms[0].is_first_atom_in_chain = self.is_first_in_chain
self.atoms[-1].is_final_atom_in_chain = self.is_final_in_chain
for atom in self.atoms:
atom.is_first_residue_in_chain = self.is_first_in_chain
atom.is_final_residue_in_chain = self.is_final_in_chain
def set_name_with_spaces(self, name, alt_loc=None):
# Gromacs ffamber PDB files can have 4-character residue names
# assert len(name) == 3
if alt_loc == None:
alt_loc = self.primary_location_id
loc = self.locations[alt_loc]
loc.name_with_spaces = name
loc.name = name.strip()
def get_name_with_spaces(self, alt_loc=None):
if alt_loc == None:
alt_loc = self.primary_location_id
loc = self.locations[alt_loc]
return loc.name_with_spaces
name_with_spaces = property(get_name_with_spaces, set_name_with_spaces, doc='four-character residue name including spaces')
def get_name(self, alt_loc=None):
if alt_loc == None:
alt_loc = self.primary_location_id
loc = self.locations[alt_loc]
return loc.name
name = property(get_name, doc='residue name')
def get_atom(self, atom_name):
return self.atoms_by_name[atom_name]
def __contains__(self, atom_name):
return self.atoms_by_name.__contains__(atom_name)
def __getitem__(self, atom_name):
"""Returns the FIRST atom in this residue with a particular atom name"""
return self.atoms_by_name[atom_name]
def __iter__(self):
"""
>>> pdb_lines = [ \
"ATOM 188 N CYS A 42 40.714 -5.292 12.123 1.00 11.29 N",\
"ATOM 189 CA CYS A 42 39.736 -5.883 12.911 1.00 10.01 C",\
"ATOM 190 C CYS A 42 40.339 -6.654 14.087 1.00 22.28 C",\
"ATOM 191 O CYS A 42 41.181 -7.530 13.859 1.00 13.70 O",\
"ATOM 192 CB CYS A 42 38.949 -6.825 12.002 1.00 9.67 C",\
"ATOM 193 SG CYS A 42 37.557 -7.514 12.922 1.00 20.12 S"]
>>> res = Residue("CYS", 42)
>>> for l in pdb_lines:
... res._add_atom(Atom(l))
...
>>> for atom in res:
... print atom
ATOM 188 N CYS A 42 40.714 -5.292 12.123 1.00 11.29 N
ATOM 189 CA CYS A 42 39.736 -5.883 12.911 1.00 10.01 C
ATOM 190 C CYS A 42 40.339 -6.654 14.087 1.00 22.28 C
ATOM 191 O CYS A 42 41.181 -7.530 13.859 1.00 13.70 O
ATOM 192 CB CYS A 42 38.949 -6.825 12.002 1.00 9.67 C
ATOM 193 SG CYS A 42 37.557 -7.514 12.922 1.00 20.12 S
"""
for atom in self.iter_atoms():
yield atom
# Three possibilities: primary alt_loc, certain alt_loc, or all alt_locs
def iter_atoms(self, alt_loc=None):
if alt_loc == None:
locs = [self.primary_location_id]
elif alt_loc == "":
locs = [self.primary_location_id]
elif alt_loc == "*":
locs = None
else:
locs = list(alt_loc)
# If an atom has any location in alt_loc, emit the atom
for atom in self.atoms:
use_atom = False # start pessimistic
for loc2 in atom.locations.keys():
# print "#%s#%s" % (loc2,locs)
if locs == None: # means all locations
use_atom = True
elif loc2 in locs:
use_atom = True
if use_atom:
yield atom
def iter_positions(self, include_alt_loc=False):
"""
Returns one position per atom, even if an individual atom has multiple positions.
>>> pdb_lines = [ \
"ATOM 188 N CYS A 42 40.714 -5.292 12.123 1.00 11.29 N",\
"ATOM 189 CA CYS A 42 39.736 -5.883 12.911 1.00 10.01 C",\
"ATOM 190 C CYS A 42 40.339 -6.654 14.087 1.00 22.28 C",\
"ATOM 191 O CYS A 42 41.181 -7.530 13.859 1.00 13.70 O",\
"ATOM 192 CB CYS A 42 38.949 -6.825 12.002 1.00 9.67 C",\
"ATOM 193 SG CYS A 42 37.557 -7.514 12.922 1.00 20.12 S"]
>>> res = Residue("CYS", 42)
>>> for l in pdb_lines: res._add_atom(Atom(l))
>>> for c in res.iter_positions:
... print c
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
TypeError: 'instancemethod' object is not iterable
>>> for c in res.iter_positions():
... print c
[40.714, -5.292, 12.123] A
[39.736, -5.883, 12.911] A
[40.339, -6.654, 14.087] A
[41.181, -7.53, 13.859] A
[38.949, -6.825, 12.002] A
[37.557, -7.514, 12.922] A
"""
for atom in self:
if include_alt_loc:
for loc in atom.iter_positions():
yield loc
else:
yield atom.position
def __len__(self):
return len(self.atoms)
# Residues can have multiple locations, based on alt_loc indicator
class Location:
"""
Inner class of residue to allow different residue names for different alternate_locations.
"""
def __init__(self, alternate_location_indicator, residue_name_with_spaces):
self.alternate_location_indicator = alternate_location_indicator
self.residue_name_with_spaces = residue_name_with_spaces
class Atom(object):
"""Atom represents one atom in a PDB structure.
"""
def __init__(self, pdb_line, pdbstructure=None):
"""Create a new pdb.Atom from an ATOM or HETATM line.
Example line:
ATOM 2209 CB TYR A 299 6.167 22.607 20.046 1.00 8.12 C
00000000011111111112222222222333333333344444444445555555555666666666677777777778
12345678901234567890123456789012345678901234567890123456789012345678901234567890
ATOM line format description from
http://deposit.rcsb.org/adit/docs/pdb_atom_format.html:
COLUMNS DATA TYPE CONTENTS
--------------------------------------------------------------------------------
1 - 6 Record name "ATOM "
7 - 11 Integer Atom serial number.
13 - 16 Atom Atom name.
17 Character Alternate location indicator.
18 - 20 Residue name Residue name.
22 Character Chain identifier.
23 - 26 Integer Residue sequence number.
27 AChar Code for insertion of residues.
31 - 38 Real(8.3) Orthogonal coordinates for X in Angstroms.
39 - 46 Real(8.3) Orthogonal coordinates for Y in Angstroms.
47 - 54 Real(8.3) Orthogonal coordinates for Z in Angstroms.
55 - 60 Real(6.2) Occupancy (Default = 1.0).
61 - 66 Real(6.2) Temperature factor (Default = 0.0).
73 - 76 LString(4) Segment identifier, left-justified.
77 - 78 LString(2) Element symbol, right-justified.
79 - 80 LString(2) Charge on the atom.
"""
# We might modify first/final status during _finalize() methods
self.is_first_atom_in_chain = False
self.is_final_atom_in_chain = False
self.is_first_residue_in_chain = False
self.is_final_residue_in_chain = False
# Start parsing fields from pdb line
self.record_name = pdb_line[0:6].strip()
if pdbstructure is not None and pdbstructure._atom_numbers_are_hex:
self.serial_number = int(pdb_line[6:11], 16)
else:
try:
self.serial_number = int(pdb_line[6:11])
except:
try:
self.serial_number = int(pdb_line[6:11], 16)
pdbstructure._atom_numbers_are_hex = True
except:
# Just give it the next number in sequence.
self.serial_number = pdbstructure._next_atom_number
self.name_with_spaces = pdb_line[12:16]
alternate_location_indicator = pdb_line[16]
self.residue_name_with_spaces = pdb_line[17:20]
# In some MD codes, notably ffamber in gromacs, residue name has a fourth character in
# column 21
possible_fourth_character = pdb_line[20:21]
if possible_fourth_character != " ":
# Fourth character should only be there if official 3 are already full
if len(self.residue_name_with_spaces.strip()) != 3:
raise ValueError('Misaligned residue name: %s' % pdb_line)
self.residue_name_with_spaces += possible_fourth_character
self.residue_name = self.residue_name_with_spaces.strip()
self.chain_id = pdb_line[21]
if pdbstructure is not None and pdbstructure._residue_numbers_are_hex:
self.residue_number = int(pdb_line[22:26], 16)
else:
try:
self.residue_number = int(pdb_line[22:26])
except:
try:
self.residue_number = int(pdb_line[22:26], 16)
pdbstructure._residue_numbers_are_hex = True
except:
# When VMD runs out of hex values it starts filling the residue ID field with ****.
# Look at the most recent atoms to figure out whether this is a new residue or not.
if pdbstructure._current_model is None or pdbstructure._current_model._current_chain is None or pdbstructure._current_model._current_chain._current_residue is None:
# This is the first residue in the model.
self.residue_number = pdbstructure._next_residue_number
else:
currentRes = pdbstructure._current_model._current_chain._current_residue
if currentRes.name_with_spaces != self.residue_name_with_spaces:
# The residue name has changed.
self.residue_number = pdbstructure._next_residue_number
elif self.name_with_spaces in currentRes.atoms_by_name:
# There is already an atom with this name.
self.residue_number = pdbstructure._next_residue_number
else:
self.residue_number = currentRes.number
self.insertion_code = pdb_line[26]
# coordinates, occupancy, and temperature factor belong in Atom.Location object
x = float(pdb_line[30:38])
y = float(pdb_line[38:46])
z = float(pdb_line[46:54])
try:
occupancy = float(pdb_line[54:60])
except:
occupancy = 1.0
try:
temperature_factor = float(pdb_line[60:66]) * unit.angstroms * unit.angstroms
except:
temperature_factor = 0.0 * unit.angstroms * unit.angstroms
self.locations = {}
loc = Atom.Location(alternate_location_indicator, Vec3(x,y,z) * unit.angstroms, occupancy, temperature_factor, self.residue_name_with_spaces)
self.locations[alternate_location_indicator] = loc
self.default_location_id = alternate_location_indicator
# segment id, element_symbol, and formal_charge are not always present
self.segment_id = pdb_line[72:76].strip()
self.element_symbol = pdb_line[76:78].strip()
try: self.formal_charge = int(pdb_line[78:80])
except ValueError: self.formal_charge = None
# figure out atom element
try:
# Try to find a sensible element symbol from columns 76-77
self.element = element.get_by_symbol(self.element_symbol)
except KeyError:
self.element = None
if pdbstructure is not None:
pdbstructure._next_atom_number = self.serial_number+1
pdbstructure._next_residue_number = self.residue_number+1
def iter_locations(self):
"""
Iterate over Atom.Location objects for this atom, including primary location.
>>> atom = Atom("ATOM 2209 CB TYR A 299 6.167 22.607 20.046 1.00 8.12 C")
>>> for c in atom.iter_locations():
... print c
...
[6.167, 22.607, 20.046] A
"""
for alt_loc in self.locations:
yield self.locations[alt_loc]
def iter_positions(self):
"""
Iterate over atomic positions. Returns Quantity(Vec3(), unit) objects, unlike
iter_locations, which returns Atom.Location objects.
"""
for loc in self.iter_locations():
yield loc.position
def iter_coordinates(self):
"""
Iterate over x, y, z values of primary atom position.
>>> atom = Atom("ATOM 2209 CB TYR A 299 6.167 22.607 20.046 1.00 8.12 C")
>>> for c in atom.iter_coordinates():
... print c
...
6.167 A
22.607 A
20.046 A
"""
for coord in self.position:
yield coord
# Hide existence of multiple alternate locations to avoid scaring casual users
def get_location(self, location_id=None):
id = location_id
if (id == None):
id = self.default_location_id
return self.locations[id]
def set_location(self, new_location, location_id=None):
id = location_id
if (id == None):
id = self.default_location_id
self.locations[id] = new_location
location = property(get_location, set_location, doc='default Atom.Location object')
def get_position(self):
return self.location.position
def set_position(self, coords):
self.location.position = coords
position = property(get_position, set_position, doc='orthogonal coordinates')
def get_alternate_location_indicator(self):
return self.location.alternate_location_indicator
alternate_location_indicator = property(get_alternate_location_indicator)
def get_occupancy(self):
return self.location.occupancy
occupancy = property(get_occupancy)
def get_temperature_factor(self):
return self.location.temperature_factor
temperature_factor = property(get_temperature_factor)
def get_x(self): return self.position[0]
x = property(get_x)
def get_y(self): return self.position[1]
y = property(get_y)
def get_z(self): return self.position[2]
z = property(get_z)
def _pdb_string(self, serial_number=None, alternate_location_indicator=None):
"""
Produce a PDB line for this atom using a particular serial number and alternate location
"""
if serial_number == None:
serial_number = self.serial_number
if alternate_location_indicator == None:
alternate_location_indicator = self.alternate_location_indicator
# produce PDB line in three parts: names, numbers, and end
# Accomodate 4-character residue names that use column 21
long_res_name = self.residue_name_with_spaces
if len(long_res_name) == 3:
long_res_name += " "
assert len(long_res_name) == 4
names = "%-6s%5d %4s%1s%4s%1s%4d%1s " % (
self.record_name, serial_number, \
self.name_with_spaces, alternate_location_indicator, \
long_res_name, self.chain_id, \
self.residue_number, self.insertion_code)
numbers = "%8.3f%8.3f%8.3f%6.2f%6.2f " % (
self.x.value_in_unit(unit.angstroms), \
self.y.value_in_unit(unit.angstroms), \
self.z.value_in_unit(unit.angstroms), \
self.occupancy, \
self.temperature_factor.value_in_unit(unit.angstroms * unit.angstroms))
end = "%-4s%2s" % (\
self.segment_id, self.element_symbol)
formal_charge = " "
if (self.formal_charge != None): formal_charge = "%+2d" % self.formal_charge
return names+numbers+end+formal_charge
def __str__(self):
return self._pdb_string(self.serial_number, self.alternate_location_indicator)
def write(self, next_serial_number, output_stream=sys.stdout, alt_loc = "*"):
"""
alt_loc = "*" means write all alternate locations
alt_loc = None means write just the primary location
alt_loc = "AB" means write locations "A" and "B"
"""
if alt_loc == None:
locs = [self.default_location_id]
elif alt_loc == "":
locs = [self.default_location_id]
elif alt_loc == "*":
locs = self.locations.keys()
locs.sort()
else:
locs = list(alt_loc)
for loc_id in locs:
print >>output_stream, self._pdb_string(next_serial_number.val, loc_id)
next_serial_number.increment()
def set_name_with_spaces(self, name):
assert len(name) == 4
self._name_with_spaces = name
self._name = name.strip()
def get_name_with_spaces(self):
return self._name_with_spaces
name_with_spaces = property(get_name_with_spaces, set_name_with_spaces, doc='four-character residue name including spaces')
def get_name(self):
return self._name
name = property(get_name, doc='residue name')
class Location(object):
"""
Inner class of Atom for holding alternate locations
"""
def __init__(self, alt_loc, position, occupancy, temperature_factor, residue_name):
self.alternate_location_indicator = alt_loc
self.position = position
self.occupancy = occupancy
self.temperature_factor = temperature_factor
self.residue_name = residue_name
def __iter__(self):
"""
Examples
>>> from simtk.openmm.vec3 import Vec3
>>> import simtk.unit as unit
>>> l = Atom.Location(' ', Vec3(1,2,3)*unit.angstroms, 1.0, 20.0*unit.angstroms**2, "XXX")
>>> for c in l:
... print c
...
1 A
2 A
3 A
"""
for coord in self.position:
yield coord
def __str__(self):
return str(self.position)
# run module directly for testing
if __name__=='__main__':
# Test the examples in the docstrings
import doctest, sys
doctest.testmod(sys.modules[__name__])
import os
import gzip
import re
import time
# Test atom line parsing
pdb_line = "ATOM 2209 CB TYR A 299 6.167 22.607 20.046 1.00 8.12 C"
a = Atom(pdb_line)
assert a.record_name == "ATOM"
assert a.serial_number == 2209
assert a.name == "CB"
assert a.name_with_spaces == " CB "
assert a.residue_name == "TYR"
assert a.residue_name_with_spaces == "TYR"
assert a.chain_id == "A"
assert a.residue_number == 299
assert a.insertion_code == " "
assert a.alternate_location_indicator == " "
assert a.x == 6.167 * unit.angstroms
assert a.y == 22.607 * unit.angstroms
assert a.z == 20.046 * unit.angstroms
assert a.occupancy == 1.00
assert a.temperature_factor == 8.12 * unit.angstroms * unit.angstroms
assert a.segment_id == ""
assert a.element_symbol == "C"
# print pdb_line
# print str(a)
assert str(a).rstrip() == pdb_line.rstrip()
a = Atom("ATOM 2209 CB TYR A 299 6.167 22.607 20.046 1.00 8.12 C")
# misaligned residue name - bad
try:
a = Atom("ATOM 2209 CB TYRA 299 6.167 22.607 20.046 1.00 8.12 C")
assert(False)
except ValueError: pass
# four character residue name -- not so bad
a = Atom("ATOM 2209 CB NTYRA 299 6.167 22.607 20.046 1.00 8.12 C")
atom_count = 0
residue_count = 0
chain_count = 0
model_count = 0
structure_count = 0
def parse_one_pdb(pdb_file_name):
global atom_count, residue_count, chain_count, model_count, structure_count
print pdb_file_name
if pdb_file_name[-3:] == ".gz":
fh = gzip.open(pdb_file_name)
else:
fh = open(pdb_file_name)
pdb = PdbStructure(fh, load_all_models=True)
# print " %d atoms found" % len(pdb.atoms)
atom_count += len(list(pdb.iter_atoms()))
residue_count += len(list(pdb.iter_residues()))
chain_count += len(list(pdb.iter_chains()))
model_count += len(list(pdb.iter_models()))
structure_count += 1
fh.close
return pdb
# Parse one file
pdb_file_name = "/home/Christopher Bruns/Desktop/1ARJ.pdb"
if os.path.exists(pdb_file_name):
parse_one_pdb(pdb_file_name)
# try parsing the entire PDB
pdb_dir = "/cygdrive/j/pdb/data/structures/divided/pdb"
if os.path.exists(pdb_dir):
parse_entire_pdb = False
parse_one_division = False
parse_one_file = False
start_time = time.time()
if parse_one_file:
pdb_id = "2aed"
middle_two = pdb_id[1:3]
full_pdb_file = os.path.join(pdb_dir, middle_two, "pdb%s.ent.gz" % pdb_id)
parse_one_pdb(full_pdb_file)
if parse_one_division:
subdir = "ae"
full_subdir = os.path.join(pdb_dir, subdir)
for pdb_file in os.listdir(full_subdir):
if not re.match("pdb.%2s.\.ent\.gz" % subdir , pdb_file):
continue
full_pdb_file = os.path.join(full_subdir, pdb_file)
parse_one_pdb(full_pdb_file)
if parse_entire_pdb:
for subdir in os.listdir(pdb_dir):
if not len(subdir) == 2: continue
full_subdir = os.path.join(pdb_dir, subdir)
if not os.path.isdir(full_subdir):
continue
for pdb_file in os.listdir(full_subdir):
if not re.match("pdb.%2s.\.ent\.gz" % subdir , pdb_file):
continue
full_pdb_file = os.path.join(full_subdir, pdb_file)
parse_one_pdb(full_pdb_file)
end_time = time.time()
elapsed = end_time - start_time
minutes = elapsed / 60
seconds = elapsed % 60
hours = minutes / 60
minutes = minutes % 60
print "%dh:%02dm:%02ds elapsed" % (hours, minutes, seconds)
print "%d atoms found" % atom_count
print "%d residues found" % residue_count
print "%d chains found" % chain_count
print "%d models found" % model_count
print "%d structures found" % structure_count
"""
pdbstructure.py: Used for managing PDB formated 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) 2012-2015 Stanford University and the Authors.
Authors: Christopher M. Bruns
Contributors: Peter Eastman
Permission is hereby granted, free of charge, to any person obtaining a
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.
"""
from __future__ import absolute_import
from __future__ import print_function
__author__ = "Christopher M. Bruns"
__version__ = "1.0"
from simtk.openmm.vec3 import Vec3
import simtk.unit as unit
from .. import element
from .unitcell import computePeriodicBoxVectors
import warnings
import sys
import math
class PdbStructure(object):
"""
PdbStructure object holds a parsed Protein Data Bank format file.
Examples:
Load a pdb structure from a file:
> pdb = PdbStructure(open("1ARJ.pdb"))
Fetch the first atom of the structure:
> print pdb.iter_atoms().next()
ATOM 1 O5' G N 17 13.768 -8.431 11.865 1.00 0.00 O
Loop over all of the atoms of the structure
> for atom in pdb.iter_atoms():
> print atom
ATOM 1 O5' G N 17 13.768 -8.431 11.865 1.00 0.00 O
...
Get a list of all atoms in the structure:
> atoms = list(pdb.iter_atoms())
also:
residues = list(pdb.iter_residues())
positions = list(pdb.iter_positions())
chains = list(pdb.iter_chains())
models = list(pdb.iter_models())
Fetch atomic coordinates of first atom:
> print pdb.iter_positions().next()
[13.768, -8.431, 11.865] A
or
> print pdb.iter_atoms().next().position
[13.768, -8.431, 11.865] A
Strip the length units from an atomic position:
> import simtk.unit
> pos = pdb.iter_positions().next()
> print pos
[13.768, -8.431, 11.865] A
> print pos / simtk.unit.angstroms
[13.768, -8.431, 11.865]
> print pos / simtk.unit.nanometers
[1.3768, -0.8431, 1.1865]
The hierarchical structure of the parsed PDB structure is as follows:
PdbStructure
Model
Chain
Residue
Atom
Location
Model - A PDB structure consists of one or more Models. Each model corresponds to one version of
an NMR structure, or to one frame of a molecular dynamics trajectory.
Chain - A Model contains one or more Chains. Each chain corresponds to one molecule, although multiple
water molecules are frequently included in the same chain.
Residue - A Chain contains one or more Residues. One Residue corresponds to one of the repeating
unit that constitutes a polymer such as protein or DNA. For non-polymeric molecules, one Residue
represents one molecule.
Atom - A Residue contains one or more Atoms. Atoms are chemical atoms.
Location - An atom can sometimes have more that one position, due to static disorder in X-ray
crystal structures. To see all of the atom positions, use the atom.iter_positions() method,
or pass the parameter "include_alt_loc=True" to one of the other iter_positions() methods.
> for pos in pdb.iter_positions(include_alt_loc=True):
> ...
Will loop over all atom positions, including multiple alternate locations for atoms that have
multiple positions. The default value of include_alt_loc is False for the iter_positions()
methods.
"""
def __init__(self, input_stream, load_all_models = False):
"""Create a PDB model from a PDB file stream.
Parameters:
- self (PdbStructure) The new object that is created.
- input_stream (stream) An input file stream, probably created with
open().
- load_all_models (bool) Whether to load every model of an NMR
structure or trajectory, or just load the first model, to save memory.
"""
# initialize models
self.load_all_models = load_all_models
self.models = []
self._current_model = None
self.default_model = None
self.models_by_number = {}
self._periodic_box_vectors = None
self.sequences = []
self.modified_residues = []
# read file
self._load(input_stream)
def _load(self, input_stream):
self._reset_atom_numbers()
self._reset_residue_numbers()
# Read one line at a time
for pdb_line in input_stream:
if not isinstance(pdb_line, str):
pdb_line = pdb_line.decode('utf-8')
# Look for atoms
if (pdb_line.find("ATOM ") == 0) or (pdb_line.find("HETATM") == 0):
self._add_atom(Atom(pdb_line, self))
# Notice MODEL punctuation, for the next level of detail
# in the structure->model->chain->residue->atom->position hierarchy
elif (pdb_line.find("MODEL") == 0):
model_number = int(pdb_line[10:14])
self._add_model(Model(model_number))
self._reset_atom_numbers()
self._reset_residue_numbers()
elif (pdb_line.find("ENDMDL") == 0):
self._current_model._finalize()
if not self.load_all_models:
break
elif (pdb_line.find("END") == 0):
self._current_model._finalize()
if not self.load_all_models:
break
elif (pdb_line.find("TER") == 0 and pdb_line.split()[0] == "TER"):
self._current_model._current_chain._add_ter_record()
self._reset_residue_numbers()
elif (pdb_line.find("CRYST1") == 0):
a_length = float(pdb_line[6:15])*0.1
b_length = float(pdb_line[15:24])*0.1
c_length = float(pdb_line[24:33])*0.1
alpha = float(pdb_line[33:40])*math.pi/180.0
beta = float(pdb_line[40:47])*math.pi/180.0
gamma = float(pdb_line[47:54])*math.pi/180.0
self._periodic_box_vectors = computePeriodicBoxVectors(a_length, b_length, c_length, alpha, beta, gamma)
elif (pdb_line.find("CONECT") == 0):
atoms = [int(pdb_line[6:11])]
for pos in (11,16,21,26):
try:
atoms.append(int(pdb_line[pos:pos+5]))
except:
pass
self._current_model.connects.append(atoms)
elif (pdb_line.find("SEQRES") == 0):
chain_id = pdb_line[11]
if len(self.sequences) == 0 or chain_id != self.sequences[-1].chain_id:
self.sequences.append(Sequence(chain_id))
self.sequences[-1].residues.extend(pdb_line[19:].split())
elif (pdb_line.find("MODRES") == 0):
self.modified_residues.append(ModifiedResidue(pdb_line[16], int(pdb_line[18:22]), pdb_line[12:15].strip(), pdb_line[24:27].strip()))
self._finalize()
def _reset_atom_numbers(self):
self._atom_numbers_are_hex = False
self._next_atom_number = 1
def _reset_residue_numbers(self):
self._residue_numbers_are_hex = False
self._next_residue_number = 1
def write(self, output_stream=sys.stdout):
"""Write out structure in PDB format"""
for model in self.models:
if len(model.chains) == 0:
continue
if len(self.models) > 1:
print("MODEL %4d" % (model.number), file=output_stream)
model.write(output_stream)
if len(self.models) > 1:
print("ENDMDL", file=output_stream)
print("END", file=output_stream)
def _add_model(self, model):
if self.default_model == None:
self.default_model = model
self.models.append(model)
self._current_model = model
if model.number not in self.models_by_number:
self.models_by_number[model.number] = model
def get_model(self, model_number):
return self.models_by_number[model_number]
def model_numbers(self):
return self.models_by_number.keys()
def __contains__(self, model_number):
return self.models_by_number.__contains__(model_number)
def __getitem__(self, model_number):
return self.models_by_number[model_number]
def __iter__(self):
for model in self.models:
yield model
def iter_models(self, use_all_models=False):
if use_all_models:
for model in self:
yield model
elif len(self.models) > 0:
yield self.models[0]
def iter_chains(self, use_all_models=False):
for model in self.iter_models(use_all_models):
for chain in model.iter_chains():
yield chain
def iter_residues(self, use_all_models=False):
for model in self.iter_models(use_all_models):
for res in model.iter_residues():
yield res
def iter_atoms(self, use_all_models=False):
for model in self.iter_models(use_all_models):
for atom in model.iter_atoms():
yield atom
def iter_positions(self, use_all_models=False, include_alt_loc=False):
"""
Iterate over atomic positions.
Parameters
- use_all_models (bool=False) Get positions from all models or just the first one.
- include_alt_loc (bool=False) Get all positions for each atom, or just the first one.
"""
for model in self.iter_models(use_all_models):
for loc in model.iter_positions(include_alt_loc):
yield loc
def __len__(self):
return len(self.models)
def _add_atom(self, atom):
"""
"""
if self._current_model == None:
self._add_model(Model(0))
atom.model_number = self._current_model.number
# Atom might be alternate position for existing atom
self._current_model._add_atom(atom)
def _finalize(self):
"""Establish first and last residues, atoms, etc."""
for model in self.models:
model._finalize()
def get_periodic_box_vectors(self):
"""Get the vectors defining the crystallographic unit cell (may be None)."""
return self._periodic_box_vectors
class Sequence(object):
"""Sequence holds the sequence of a chain, as specified by SEQRES records."""
def __init__(self, chain_id):
self.chain_id = chain_id
self.residues = []
class ModifiedResidue(object):
"""ModifiedResidue holds information about a modified residue, as specified by a MODRES record."""
def __init__(self, chain_id, number, residue_name, standard_name):
self.chain_id = chain_id
self.number = number
self.residue_name = residue_name
self.standard_name = standard_name
class Model(object):
"""Model holds one model of a PDB structure.
NMR structures usually have multiple models. This represents one
of them.
"""
def __init__(self, model_number=1):
self.number = model_number
self.chains = []
self._current_chain = None
self.chains_by_id = {}
self.connects = []
def _add_atom(self, atom):
"""
"""
if len(self.chains) == 0:
self._add_chain(Chain(atom.chain_id))
# Create a new chain if the chain id has changed
if self._current_chain.chain_id != atom.chain_id:
self._add_chain(Chain(atom.chain_id))
# Create a new chain after TER record, even if ID is the same
elif self._current_chain.has_ter_record:
self._add_chain(Chain(atom.chain_id))
self._current_chain._add_atom(atom)
def _add_chain(self, chain):
self.chains.append(chain)
self._current_chain = chain
if not chain.chain_id in self.chains_by_id:
self.chains_by_id[chain.chain_id] = chain
def get_chain(self, chain_id):
return self.chains_by_id[chain_id]
def chain_ids(self):
return self.chains_by_id.keys()
def __contains__(self, chain_id):
return self.chains_by_id.__contains__(chain_id)
def __getitem__(self, chain_id):
return self.chains_by_id[chain_id]
def __iter__(self):
return iter(self.chains)
def iter_chains(self):
for chain in self:
yield chain
def iter_residues(self):
for chain in self:
for res in chain.iter_residues():
yield res
def iter_atoms(self):
for chain in self:
for atom in chain.iter_atoms():
yield atom
def iter_positions(self, include_alt_loc=False):
for chain in self:
for loc in chain.iter_positions(include_alt_loc):
yield loc
def __len__(self):
return len(self.chains)
def write(self, output_stream=sys.stdout):
# Start atom serial numbers at 1
sn = Model.AtomSerialNumber(1)
for chain in self.chains:
chain.write(sn, output_stream)
def _finalize(self):
for chain in self.chains:
chain._finalize()
class AtomSerialNumber(object):
"""pdb.Model inner class for pass-by-reference incrementable serial number"""
def __init__(self, val):
self.val = val
def increment(self):
self.val += 1
class Chain(object):
def __init__(self, chain_id=' '):
self.chain_id = chain_id
self.residues = []
self.has_ter_record = False
self._current_residue = None
self.residues_by_num_icode = {}
self.residues_by_number = {}
def _add_atom(self, atom):
"""
"""
# Create a residue if none have been created
if len(self.residues) == 0:
self._add_residue(Residue(atom.residue_name_with_spaces, atom.residue_number, atom.insertion_code, atom.alternate_location_indicator))
# Create a residue if the residue information has changed
elif self._current_residue.number != atom.residue_number:
self._add_residue(Residue(atom.residue_name_with_spaces, atom.residue_number, atom.insertion_code, atom.alternate_location_indicator))
elif self._current_residue.insertion_code != atom.insertion_code:
self._add_residue(Residue(atom.residue_name_with_spaces, atom.residue_number, atom.insertion_code, atom.alternate_location_indicator))
elif self._current_residue.name_with_spaces == atom.residue_name_with_spaces:
# This is a normal case: number, name, and iCode have not changed
pass
elif atom.alternate_location_indicator != ' ':
# OK - this is a point mutation, Residue._add_atom will know what to do
pass
else: # Residue name does not match
# Only residue name does not match
warnings.warn("WARNING: two consecutive residues with same number (%s, %s)" % (atom, self._current_residue.atoms[-1]))
self._add_residue(Residue(atom.residue_name_with_spaces, atom.residue_number, atom.insertion_code, atom.alternate_location_indicator))
self._current_residue._add_atom(atom)
def _add_residue(self, residue):
if len(self.residues) == 0:
residue.is_first_in_chain = True
self.residues.append(residue)
self._current_residue = residue
key = str(residue.number) + residue.insertion_code
# only store the first residue with a particular key
if key not in self.residues_by_num_icode:
self.residues_by_num_icode[key] = residue
if residue.number not in self.residues_by_number:
self.residues_by_number[residue.number] = residue
def write(self, next_serial_number, output_stream=sys.stdout):
for residue in self.residues:
residue.write(next_serial_number, output_stream)
if self.has_ter_record:
r = self.residues[-1]
print("TER %5d %3s %1s%4d%1s" % (next_serial_number.val, r.name_with_spaces, self.chain_id, r.number, r.insertion_code), file=output_stream)
next_serial_number.increment()
def _add_ter_record(self):
self.has_ter_record = True
self._finalize()
def get_residue(self, residue_number, insertion_code=' '):
return self.residues_by_num_icode[str(residue_number) + insertion_code]
def __contains__(self, residue_number):
return self.residues_by_number.__contains__(residue_number)
def __getitem__(self, residue_number):
"""Returns the FIRST residue in this chain with a particular residue number"""
return self.residues_by_number[residue_number]
def __iter__(self):
for res in self.residues:
yield res
def iter_residues(self):
for res in self:
yield res
def iter_atoms(self):
for res in self:
for atom in res:
yield atom;
def iter_positions(self, include_alt_loc=False):
for res in self:
for loc in res.iter_positions(include_alt_loc):
yield loc
def __len__(self):
return len(self.residues)
def _finalize(self):
self.residues[0].is_first_in_chain = True
self.residues[-1].is_final_in_chain = True
for residue in self.residues:
residue._finalize()
class Residue(object):
def __init__(self, name, number, insertion_code=' ', primary_alternate_location_indicator=' '):
alt_loc = primary_alternate_location_indicator
self.primary_location_id = alt_loc
self.locations = {}
self.locations[alt_loc] = Residue.Location(alt_loc, name)
self.name_with_spaces = name
self.number = number
self.insertion_code = insertion_code
self.atoms = []
self.atoms_by_name = {}
self.is_first_in_chain = False
self.is_final_in_chain = False
self._current_atom = None
def _add_atom(self, atom):
"""
"""
alt_loc = atom.alternate_location_indicator
if alt_loc not in self.locations:
self.locations[alt_loc] = Residue.Location(alt_loc, atom.residue_name_with_spaces)
assert atom.residue_number == self.number
assert atom.insertion_code == self.insertion_code
# Check whether this is an existing atom with another position
if (atom.name_with_spaces in self.atoms_by_name):
old_atom = self.atoms_by_name[atom.name_with_spaces]
# Unless this is a duplicated atom (warn about file error)
if atom.alternate_location_indicator in old_atom.locations:
warnings.warn("WARNING: duplicate atom (%s, %s)" % (atom, old_atom._pdb_string(old_atom.serial_number, atom.alternate_location_indicator)))
else:
for alt_loc, position in atom.locations.items():
old_atom.locations[alt_loc] = position
return # no new atom added
# actually use new atom
self.atoms_by_name[atom.name] = atom
self.atoms_by_name[atom.name_with_spaces] = atom
self.atoms.append(atom)
self._current_atom = atom
def write(self, next_serial_number, output_stream=sys.stdout, alt_loc = "*"):
for atom in self.atoms:
atom.write(next_serial_number, output_stream, alt_loc)
def _finalize(self):
if len(self.atoms) > 0:
self.atoms[0].is_first_atom_in_chain = self.is_first_in_chain
self.atoms[-1].is_final_atom_in_chain = self.is_final_in_chain
for atom in self.atoms:
atom.is_first_residue_in_chain = self.is_first_in_chain
atom.is_final_residue_in_chain = self.is_final_in_chain
def set_name_with_spaces(self, name, alt_loc=None):
# Gromacs ffamber PDB files can have 4-character residue names
# assert len(name) == 3
if alt_loc == None:
alt_loc = self.primary_location_id
loc = self.locations[alt_loc]
loc.name_with_spaces = name
loc.name = name.strip()
def get_name_with_spaces(self, alt_loc=None):
if alt_loc == None:
alt_loc = self.primary_location_id
loc = self.locations[alt_loc]
return loc.name_with_spaces
name_with_spaces = property(get_name_with_spaces, set_name_with_spaces, doc='four-character residue name including spaces')
def get_name(self, alt_loc=None):
if alt_loc == None:
alt_loc = self.primary_location_id
loc = self.locations[alt_loc]
return loc.name
name = property(get_name, doc='residue name')
def get_atom(self, atom_name):
return self.atoms_by_name[atom_name]
def __contains__(self, atom_name):
return self.atoms_by_name.__contains__(atom_name)
def __getitem__(self, atom_name):
"""Returns the FIRST atom in this residue with a particular atom name"""
return self.atoms_by_name[atom_name]
def __iter__(self):
"""
>>> pdb_lines = [ \
"ATOM 188 N CYS A 42 40.714 -5.292 12.123 1.00 11.29 N",\
"ATOM 189 CA CYS A 42 39.736 -5.883 12.911 1.00 10.01 C",\
"ATOM 190 C CYS A 42 40.339 -6.654 14.087 1.00 22.28 C",\
"ATOM 191 O CYS A 42 41.181 -7.530 13.859 1.00 13.70 O",\
"ATOM 192 CB CYS A 42 38.949 -6.825 12.002 1.00 9.67 C",\
"ATOM 193 SG CYS A 42 37.557 -7.514 12.922 1.00 20.12 S"]
>>> res = Residue("CYS", 42)
>>> for l in pdb_lines:
... res._add_atom(Atom(l))
...
>>> for atom in res:
... print atom
ATOM 188 N CYS A 42 40.714 -5.292 12.123 1.00 11.29 N
ATOM 189 CA CYS A 42 39.736 -5.883 12.911 1.00 10.01 C
ATOM 190 C CYS A 42 40.339 -6.654 14.087 1.00 22.28 C
ATOM 191 O CYS A 42 41.181 -7.530 13.859 1.00 13.70 O
ATOM 192 CB CYS A 42 38.949 -6.825 12.002 1.00 9.67 C
ATOM 193 SG CYS A 42 37.557 -7.514 12.922 1.00 20.12 S
"""
for atom in self.iter_atoms():
yield atom
# Three possibilities: primary alt_loc, certain alt_loc, or all alt_locs
def iter_atoms(self, alt_loc=None):
if alt_loc == None:
locs = [self.primary_location_id]
elif alt_loc == "":
locs = [self.primary_location_id]
elif alt_loc == "*":
locs = None
else:
locs = list(alt_loc)
# If an atom has any location in alt_loc, emit the atom
for atom in self.atoms:
use_atom = False # start pessimistic
for loc2 in atom.locations.keys():
# print "#%s#%s" % (loc2,locs)
if locs == None: # means all locations
use_atom = True
elif loc2 in locs:
use_atom = True
if use_atom:
yield atom
def iter_positions(self, include_alt_loc=False):
"""
Returns one position per atom, even if an individual atom has multiple positions.
>>> pdb_lines = [ \
"ATOM 188 N CYS A 42 40.714 -5.292 12.123 1.00 11.29 N",\
"ATOM 189 CA CYS A 42 39.736 -5.883 12.911 1.00 10.01 C",\
"ATOM 190 C CYS A 42 40.339 -6.654 14.087 1.00 22.28 C",\
"ATOM 191 O CYS A 42 41.181 -7.530 13.859 1.00 13.70 O",\
"ATOM 192 CB CYS A 42 38.949 -6.825 12.002 1.00 9.67 C",\
"ATOM 193 SG CYS A 42 37.557 -7.514 12.922 1.00 20.12 S"]
>>> res = Residue("CYS", 42)
>>> for l in pdb_lines: res._add_atom(Atom(l))
>>> for c in res.iter_positions:
... print c
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
TypeError: 'instancemethod' object is not iterable
>>> for c in res.iter_positions():
... print c
[40.714, -5.292, 12.123] A
[39.736, -5.883, 12.911] A
[40.339, -6.654, 14.087] A
[41.181, -7.53, 13.859] A
[38.949, -6.825, 12.002] A
[37.557, -7.514, 12.922] A
"""
for atom in self:
if include_alt_loc:
for loc in atom.iter_positions():
yield loc
else:
yield atom.position
def __len__(self):
return len(self.atoms)
# Residues can have multiple locations, based on alt_loc indicator
class Location:
"""
Inner class of residue to allow different residue names for different alternate_locations.
"""
def __init__(self, alternate_location_indicator, residue_name_with_spaces):
self.alternate_location_indicator = alternate_location_indicator
self.residue_name_with_spaces = residue_name_with_spaces
class Atom(object):
"""Atom represents one atom in a PDB structure.
"""
def __init__(self, pdb_line, pdbstructure=None):
"""Create a new pdb.Atom from an ATOM or HETATM line.
Example line:
ATOM 2209 CB TYR A 299 6.167 22.607 20.046 1.00 8.12 C
00000000011111111112222222222333333333344444444445555555555666666666677777777778
12345678901234567890123456789012345678901234567890123456789012345678901234567890
ATOM line format description from
http://deposit.rcsb.org/adit/docs/pdb_atom_format.html:
COLUMNS DATA TYPE CONTENTS
--------------------------------------------------------------------------------
1 - 6 Record name "ATOM "
7 - 11 Integer Atom serial number.
13 - 16 Atom Atom name.
17 Character Alternate location indicator.
18 - 20 Residue name Residue name.
22 Character Chain identifier.
23 - 26 Integer Residue sequence number.
27 AChar Code for insertion of residues.
31 - 38 Real(8.3) Orthogonal coordinates for X in Angstroms.
39 - 46 Real(8.3) Orthogonal coordinates for Y in Angstroms.
47 - 54 Real(8.3) Orthogonal coordinates for Z in Angstroms.
55 - 60 Real(6.2) Occupancy (Default = 1.0).
61 - 66 Real(6.2) Temperature factor (Default = 0.0).
73 - 76 LString(4) Segment identifier, left-justified.
77 - 78 LString(2) Element symbol, right-justified.
79 - 80 LString(2) Charge on the atom.
"""
# We might modify first/final status during _finalize() methods
self.is_first_atom_in_chain = False
self.is_final_atom_in_chain = False
self.is_first_residue_in_chain = False
self.is_final_residue_in_chain = False
# Start parsing fields from pdb line
self.record_name = pdb_line[0:6].strip()
if pdbstructure is not None and pdbstructure._atom_numbers_are_hex:
self.serial_number = int(pdb_line[6:11], 16)
else:
try:
self.serial_number = int(pdb_line[6:11])
except:
try:
self.serial_number = int(pdb_line[6:11], 16)
pdbstructure._atom_numbers_are_hex = True
except:
# Just give it the next number in sequence.
self.serial_number = pdbstructure._next_atom_number
self.name_with_spaces = pdb_line[12:16]
alternate_location_indicator = pdb_line[16]
self.residue_name_with_spaces = pdb_line[17:20]
# In some MD codes, notably ffamber in gromacs, residue name has a fourth character in
# column 21
possible_fourth_character = pdb_line[20:21]
if possible_fourth_character != " ":
# Fourth character should only be there if official 3 are already full
if len(self.residue_name_with_spaces.strip()) != 3:
raise ValueError('Misaligned residue name: %s' % pdb_line)
self.residue_name_with_spaces += possible_fourth_character
self.residue_name = self.residue_name_with_spaces.strip()
self.chain_id = pdb_line[21]
if pdbstructure is not None and pdbstructure._residue_numbers_are_hex:
self.residue_number = int(pdb_line[22:26], 16)
else:
try:
self.residue_number = int(pdb_line[22:26])
except:
try:
self.residue_number = int(pdb_line[22:26], 16)
pdbstructure._residue_numbers_are_hex = True
except:
# When VMD runs out of hex values it starts filling the residue ID field with ****.
# Look at the most recent atoms to figure out whether this is a new residue or not.
if pdbstructure._current_model is None or pdbstructure._current_model._current_chain is None or pdbstructure._current_model._current_chain._current_residue is None:
# This is the first residue in the model.
self.residue_number = pdbstructure._next_residue_number
else:
currentRes = pdbstructure._current_model._current_chain._current_residue
if currentRes.name_with_spaces != self.residue_name_with_spaces:
# The residue name has changed.
self.residue_number = pdbstructure._next_residue_number
elif self.name_with_spaces in currentRes.atoms_by_name:
# There is already an atom with this name.
self.residue_number = pdbstructure._next_residue_number
else:
self.residue_number = currentRes.number
self.insertion_code = pdb_line[26]
# coordinates, occupancy, and temperature factor belong in Atom.Location object
x = float(pdb_line[30:38])
y = float(pdb_line[38:46])
z = float(pdb_line[46:54])
try:
occupancy = float(pdb_line[54:60])
except:
occupancy = 1.0
try:
temperature_factor = float(pdb_line[60:66]) * unit.angstroms * unit.angstroms
except:
temperature_factor = 0.0 * unit.angstroms * unit.angstroms
self.locations = {}
loc = Atom.Location(alternate_location_indicator, Vec3(x,y,z) * unit.angstroms, occupancy, temperature_factor, self.residue_name_with_spaces)
self.locations[alternate_location_indicator] = loc
self.default_location_id = alternate_location_indicator
# segment id, element_symbol, and formal_charge are not always present
self.segment_id = pdb_line[72:76].strip()
self.element_symbol = pdb_line[76:78].strip()
try: self.formal_charge = int(pdb_line[78:80])
except ValueError: self.formal_charge = None
# figure out atom element
try:
# Try to find a sensible element symbol from columns 76-77
self.element = element.get_by_symbol(self.element_symbol)
except KeyError:
self.element = None
if pdbstructure is not None:
pdbstructure._next_atom_number = self.serial_number+1
pdbstructure._next_residue_number = self.residue_number+1
def iter_locations(self):
"""
Iterate over Atom.Location objects for this atom, including primary location.
>>> atom = Atom("ATOM 2209 CB TYR A 299 6.167 22.607 20.046 1.00 8.12 C")
>>> for c in atom.iter_locations():
... print c
...
[6.167, 22.607, 20.046] A
"""
for alt_loc in self.locations:
yield self.locations[alt_loc]
def iter_positions(self):
"""
Iterate over atomic positions. Returns Quantity(Vec3(), unit) objects, unlike
iter_locations, which returns Atom.Location objects.
"""
for loc in self.iter_locations():
yield loc.position
def iter_coordinates(self):
"""
Iterate over x, y, z values of primary atom position.
>>> atom = Atom("ATOM 2209 CB TYR A 299 6.167 22.607 20.046 1.00 8.12 C")
>>> for c in atom.iter_coordinates():
... print c
...
6.167 A
22.607 A
20.046 A
"""
for coord in self.position:
yield coord
# Hide existence of multiple alternate locations to avoid scaring casual users
def get_location(self, location_id=None):
id = location_id
if (id == None):
id = self.default_location_id
return self.locations[id]
def set_location(self, new_location, location_id=None):
id = location_id
if (id == None):
id = self.default_location_id
self.locations[id] = new_location
location = property(get_location, set_location, doc='default Atom.Location object')
def get_position(self):
return self.location.position
def set_position(self, coords):
self.location.position = coords
position = property(get_position, set_position, doc='orthogonal coordinates')
def get_alternate_location_indicator(self):
return self.location.alternate_location_indicator
alternate_location_indicator = property(get_alternate_location_indicator)
def get_occupancy(self):
return self.location.occupancy
occupancy = property(get_occupancy)
def get_temperature_factor(self):
return self.location.temperature_factor
temperature_factor = property(get_temperature_factor)
def get_x(self): return self.position[0]
x = property(get_x)
def get_y(self): return self.position[1]
y = property(get_y)
def get_z(self): return self.position[2]
z = property(get_z)
def _pdb_string(self, serial_number=None, alternate_location_indicator=None):
"""
Produce a PDB line for this atom using a particular serial number and alternate location
"""
if serial_number == None:
serial_number = self.serial_number
if alternate_location_indicator == None:
alternate_location_indicator = self.alternate_location_indicator
# produce PDB line in three parts: names, numbers, and end
# Accomodate 4-character residue names that use column 21
long_res_name = self.residue_name_with_spaces
if len(long_res_name) == 3:
long_res_name += " "
assert len(long_res_name) == 4
names = "%-6s%5d %4s%1s%4s%1s%4d%1s " % (
self.record_name, serial_number, \
self.name_with_spaces, alternate_location_indicator, \
long_res_name, self.chain_id, \
self.residue_number, self.insertion_code)
numbers = "%8.3f%8.3f%8.3f%6.2f%6.2f " % (
self.x.value_in_unit(unit.angstroms), \
self.y.value_in_unit(unit.angstroms), \
self.z.value_in_unit(unit.angstroms), \
self.occupancy, \
self.temperature_factor.value_in_unit(unit.angstroms * unit.angstroms))
end = "%-4s%2s" % (\
self.segment_id, self.element_symbol)
formal_charge = " "
if (self.formal_charge != None): formal_charge = "%+2d" % self.formal_charge
return names+numbers+end+formal_charge
def __str__(self):
return self._pdb_string(self.serial_number, self.alternate_location_indicator)
def write(self, next_serial_number, output_stream=sys.stdout, alt_loc = "*"):
"""
alt_loc = "*" means write all alternate locations
alt_loc = None means write just the primary location
alt_loc = "AB" means write locations "A" and "B"
"""
if alt_loc == None:
locs = [self.default_location_id]
elif alt_loc == "":
locs = [self.default_location_id]
elif alt_loc == "*":
locs = self.locations.keys()
locs.sort()
else:
locs = list(alt_loc)
for loc_id in locs:
print(self._pdb_string(next_serial_number.val, loc_id), file=output_stream)
next_serial_number.increment()
def set_name_with_spaces(self, name):
assert len(name) == 4
self._name_with_spaces = name
self._name = name.strip()
def get_name_with_spaces(self):
return self._name_with_spaces
name_with_spaces = property(get_name_with_spaces, set_name_with_spaces, doc='four-character residue name including spaces')
def get_name(self):
return self._name
name = property(get_name, doc='residue name')
class Location(object):
"""
Inner class of Atom for holding alternate locations
"""
def __init__(self, alt_loc, position, occupancy, temperature_factor, residue_name):
self.alternate_location_indicator = alt_loc
self.position = position
self.occupancy = occupancy
self.temperature_factor = temperature_factor
self.residue_name = residue_name
def __iter__(self):
"""
Examples
>>> from simtk.openmm.vec3 import Vec3
>>> import simtk.unit as unit
>>> l = Atom.Location(' ', Vec3(1,2,3)*unit.angstroms, 1.0, 20.0*unit.angstroms**2, "XXX")
>>> for c in l:
... print c
...
1 A
2 A
3 A
"""
for coord in self.position:
yield coord
def __str__(self):
return str(self.position)
# run module directly for testing
if __name__=='__main__':
# Test the examples in the docstrings
import doctest, sys
doctest.testmod(sys.modules[__name__])
import os
import gzip
import re
import time
# Test atom line parsing
pdb_line = "ATOM 2209 CB TYR A 299 6.167 22.607 20.046 1.00 8.12 C"
a = Atom(pdb_line)
assert a.record_name == "ATOM"
assert a.serial_number == 2209
assert a.name == "CB"
assert a.name_with_spaces == " CB "
assert a.residue_name == "TYR"
assert a.residue_name_with_spaces == "TYR"
assert a.chain_id == "A"
assert a.residue_number == 299
assert a.insertion_code == " "
assert a.alternate_location_indicator == " "
assert a.x == 6.167 * unit.angstroms
assert a.y == 22.607 * unit.angstroms
assert a.z == 20.046 * unit.angstroms
assert a.occupancy == 1.00
assert a.temperature_factor == 8.12 * unit.angstroms * unit.angstroms
assert a.segment_id == ""
assert a.element_symbol == "C"
# print pdb_line
# print str(a)
assert str(a).rstrip() == pdb_line.rstrip()
a = Atom("ATOM 2209 CB TYR A 299 6.167 22.607 20.046 1.00 8.12 C")
# misaligned residue name - bad
try:
a = Atom("ATOM 2209 CB TYRA 299 6.167 22.607 20.046 1.00 8.12 C")
assert(False)
except ValueError: pass
# four character residue name -- not so bad
a = Atom("ATOM 2209 CB NTYRA 299 6.167 22.607 20.046 1.00 8.12 C")
atom_count = 0
residue_count = 0
chain_count = 0
model_count = 0
structure_count = 0
def parse_one_pdb(pdb_file_name):
global atom_count, residue_count, chain_count, model_count, structure_count
print(pdb_file_name)
if pdb_file_name[-3:] == ".gz":
fh = gzip.open(pdb_file_name)
else:
fh = open(pdb_file_name)
pdb = PdbStructure(fh, load_all_models=True)
# print " %d atoms found" % len(pdb.atoms)
atom_count += len(list(pdb.iter_atoms()))
residue_count += len(list(pdb.iter_residues()))
chain_count += len(list(pdb.iter_chains()))
model_count += len(list(pdb.iter_models()))
structure_count += 1
fh.close
return pdb
# Parse one file
pdb_file_name = "/home/Christopher Bruns/Desktop/1ARJ.pdb"
if os.path.exists(pdb_file_name):
parse_one_pdb(pdb_file_name)
# try parsing the entire PDB
pdb_dir = "/cygdrive/j/pdb/data/structures/divided/pdb"
if os.path.exists(pdb_dir):
parse_entire_pdb = False
parse_one_division = False
parse_one_file = False
start_time = time.time()
if parse_one_file:
pdb_id = "2aed"
middle_two = pdb_id[1:3]
full_pdb_file = os.path.join(pdb_dir, middle_two, "pdb%s.ent.gz" % pdb_id)
parse_one_pdb(full_pdb_file)
if parse_one_division:
subdir = "ae"
full_subdir = os.path.join(pdb_dir, subdir)
for pdb_file in os.listdir(full_subdir):
if not re.match("pdb.%2s.\.ent\.gz" % subdir , pdb_file):
continue
full_pdb_file = os.path.join(full_subdir, pdb_file)
parse_one_pdb(full_pdb_file)
if parse_entire_pdb:
for subdir in os.listdir(pdb_dir):
if not len(subdir) == 2: continue
full_subdir = os.path.join(pdb_dir, subdir)
if not os.path.isdir(full_subdir):
continue
for pdb_file in os.listdir(full_subdir):
if not re.match("pdb.%2s.\.ent\.gz" % subdir , pdb_file):
continue
full_pdb_file = os.path.join(full_subdir, pdb_file)
parse_one_pdb(full_pdb_file)
end_time = time.time()
elapsed = end_time - start_time
minutes = elapsed / 60
seconds = elapsed % 60
hours = minutes / 60
minutes = minutes % 60
print("%dh:%02dm:%02ds elapsed" % (hours, minutes, seconds))
print("%d atoms found" % atom_count)
print("%d residues found" % residue_count)
print("%d chains found" % chain_count)
print("%d models found" % model_count)
print("%d structures found" % structure_count)
wrappers/python/simtk/openmm/app/internal/pdbx/reader/PdbxContainers.py
View file @ b7088b74
......@@ -36,6 +36,7 @@ The DataCategory class provides base storage container for instance
data and definition meta data.
"""
from __future__ import absolute_import
__docformat__ = "restructuredtext en"
__author__ = "John Westbrook"
......@@ -99,13 +100,13 @@ class ContainerBase(object):
self.__name=name
def exists(self,name):
if self.__objCatalog.has_key(name):
if name in self.__objCatalog:
return True
else:
return False
def getObj(self,name):
if self.__objCatalog.has_key(name):
if name in self.__objCatalog:
return self.__objCatalog[name]
else:
return None
......@@ -118,7 +119,7 @@ class ContainerBase(object):
of the same name will be overwritten.
"""
if obj.getName() is not None:
if not self.__objCatalog.has_key(obj.getName()):
if obj.getName() not in self.__objCatalog:
# self.__objNameList is keeping track of object order here --
self.__objNameList.append(obj.getName())
self.__objCatalog[obj.getName()]=obj
......@@ -126,7 +127,7 @@ class ContainerBase(object):
def replace(self,obj):
""" Replace an existing object with the input object
"""
if ((obj.getName() is not None) and (self.__objCatalog.has_key(obj.getName())) ):
if ((obj.getName() is not None) and (obj.getName() in self.__objCatalog) ):
self.__objCatalog[obj.getName()]=obj
......@@ -158,7 +159,7 @@ class ContainerBase(object):
""" Revmove object by name. Return True on success or False otherwise.
"""
try:
if self.__objCatalog.has_key(curName):
if curName in self.__objCatalog:
del self.__objCatalog[curName]
i=self.__objNameList.index(curName)
del self.__objNameList[i]
......@@ -217,7 +218,7 @@ class DataContainer(ContainerBase):
def invokeDataBlockMethod(self,type,method,db):
self.__currentRow = 1
exec method.getInline()
exec(method.getInline())
def setGlobal(self):
self.__globalFlag=True
......@@ -328,7 +329,7 @@ class DataCategory(DataCategoryBase):
return self._rowList[0][ii]
except (IndexError, KeyError):
raise KeyError
raise TypeError, x
raise TypeError(x)
def getCurrentAttribute(self):
......@@ -464,7 +465,7 @@ class DataCategory(DataCategoryBase):
return self._rowList[rowI][self._attributeNameList.index(attribute)]
except (IndexError):
raise IndexError
raise IndexError, attribute
raise IndexError(attribute)
def setValue(self,value,attributeName=None,rowIndex=None):
if attributeName is None:
......@@ -544,13 +545,13 @@ class DataCategory(DataCategoryBase):
if (ind >= ll):
row.extend([None for ii in xrange(2*ind-ll)])
row[ind]=None
exec method.getInline()
exec(method.getInline())
self.__currentRowIndex+=1
currentRowIndex=self.__currentRowIndex
def invokeCategoryMethod(self,type,method,db):
self.__currentRowIndex = 0
exec method.getInline()
exec(method.getInline())
def getAttributeLengthMaximumList(self):
mList=[0 for i in len(self._attributeNameList)]
......@@ -750,7 +751,7 @@ class DataCategory(DataCategoryBase):
except (IndexError):
self.__lfh.write("attributeName %s rowI %r rowdata %r\n" % (attributeName,rowI,self._rowList[rowI]))
raise IndexError
raise TypeError, attribute
raise TypeError(attribute)
def getValueFormattedByIndex(self,attributeIndex,rowIndex):
......
wrappers/python/simtk/openmm/app/internal/pdbx/reader/PdbxParser.py
View file @ b7088b74
......@@ -27,6 +27,7 @@ Acknowledgements:
See: http://pymmlib.sourceforge.net/
"""
from __future__ import absolute_import
__docformat__ = "restructuredtext en"
__author__ = "John Westbrook"
......@@ -137,7 +138,7 @@ class PdbxReader(object):
# Find the first reserved word and begin capturing data.
#
while True:
curCatName, curAttName, curQuotedString, curWord = tokenizer.next()
curCatName, curAttName, curQuotedString, curWord = next(tokenizer)
if curWord is None:
continue
reservedWord, state = self.__getState(curWord)
......@@ -194,7 +195,7 @@ class PdbxReader(object):
# Get the data for this attribute from the next token
tCat, tAtt, curQuotedString, curWord = tokenizer.next()
tCat, tAtt, curQuotedString, curWord = next(tokenizer)
if tCat is not None or (curQuotedString is None and curWord is None):
self.__syntaxError("Missing data for item _%s.%s" % (curCatName,curAttName))
......@@ -215,7 +216,7 @@ class PdbxReader(object):
else:
self.__syntaxError("Missing value in item-value pair")
curCatName, curAttName, curQuotedString, curWord = tokenizer.next()
curCatName, curAttName, curQuotedString, curWord = next(tokenizer)
continue
#
......@@ -225,14 +226,14 @@ class PdbxReader(object):
# The category name in the next curCatName,curAttName pair
# defines the name of the category container.
curCatName,curAttName,curQuotedString,curWord = tokenizer.next()
curCatName,curAttName,curQuotedString,curWord = next(tokenizer)
if curCatName is None or curAttName is None:
self.__syntaxError("Unexpected token in loop_ declaration")
return
# Check for a previous category declaration.
if categoryIndex.has_key(curCatName):
if curCatName in categoryIndex:
self.__syntaxError("Duplicate category declaration in loop_")
return
......@@ -248,7 +249,7 @@ class PdbxReader(object):
# Read the rest of the loop_ declaration
while True:
curCatName, curAttName, curQuotedString, curWord = tokenizer.next()
curCatName, curAttName, curQuotedString, curWord = next(tokenizer)
if curCatName is None:
break
......@@ -280,7 +281,7 @@ class PdbxReader(object):
elif curQuotedString is not None:
curRow.append(curQuotedString)
curCatName,curAttName,curQuotedString,curWord = tokenizer.next()
curCatName,curAttName,curQuotedString,curWord = next(tokenizer)
# loop_ data processing ends if -
......@@ -306,7 +307,7 @@ class PdbxReader(object):
categoryIndex = {}
curCategory = None
curCatName,curAttName,curQuotedString,curWord = tokenizer.next()
curCatName,curAttName,curQuotedString,curWord = next(tokenizer)
elif state == "ST_DATA_CONTAINER":
#
......@@ -317,7 +318,7 @@ class PdbxReader(object):
containerList.append(curContainer)
categoryIndex = {}
curCategory = None
curCatName,curAttName,curQuotedString,curWord = tokenizer.next()
curCatName,curAttName,curQuotedString,curWord = next(tokenizer)
elif state == "ST_STOP":
return
......@@ -327,7 +328,7 @@ class PdbxReader(object):
containerList.append(curContainer)
categoryIndex = {}
curCategory = None
curCatName,curAttName,curQuotedString,curWord = tokenizer.next()
curCatName,curAttName,curQuotedString,curWord = next(tokenizer)
elif state == "ST_UNKNOWN":
self.__syntaxError("Unrecogized syntax element: " + str(curWord))
......@@ -366,7 +367,7 @@ class PdbxReader(object):
## Tokenizer loop begins here ---
while True:
line = fileIter.next()
line = next(fileIter)
self.__curLineNumber += 1
# Dump comments
......@@ -379,7 +380,7 @@ class PdbxReader(object):
if line.startswith(";"):
mlString = [line[1:]]
while True:
line = fileIter.next()
line = next(fileIter)
self.__curLineNumber += 1
if line.startswith(";"):
break
......@@ -451,7 +452,7 @@ class PdbxReader(object):
## Tokenizer loop begins here ---
while True:
line = fileIter.next()
line = next(fileIter)
self.__curLineNumber += 1
# Dump comments
......@@ -464,7 +465,7 @@ class PdbxReader(object):
if line.startswith(";"):
mlString = [line[1:]]
while True:
line = fileIter.next()
line = next(fileIter)
self.__curLineNumber += 1
if line.startswith(";"):
break
......
wrappers/python/simtk/openmm/app/internal/pdbx/reader/PdbxReadWriteTests.py
View file @ b7088b74
......@@ -10,6 +10,7 @@
##
""" Various tests caess for PDBx/mmCIF data file and dictionary reader and writer.
"""
from __future__ import absolute_import
__docformat__ = "restructuredtext en"
__author__ = "John Westbrook"
......
wrappers/python/simtk/openmm/app/internal/pdbx/reader/PdbxReader.py
View file @ b7088b74
......@@ -22,6 +22,7 @@ Acknowledgements:
See: http://pymmlib.sourceforge.net/
"""
from __future__ import absolute_import
import re,sys
from simtk.openmm.app.internal.pdbx.reader.PdbxContainers import *
......@@ -126,7 +127,7 @@ class PdbxReader(object):
# Find the first reserved word and begin capturing data.
#
while True:
curCatName, curAttName, curQuotedString, curWord = tokenizer.next()
curCatName, curAttName, curQuotedString, curWord = next(tokenizer)
if curWord is None:
continue
reservedWord, state = self.__getState(curWord)
......@@ -183,7 +184,7 @@ class PdbxReader(object):
# Get the data for this attribute from the next token
tCat, tAtt, curQuotedString, curWord = tokenizer.next()
tCat, tAtt, curQuotedString, curWord = next(tokenizer)
if tCat is not None or (curQuotedString is None and curWord is None):
self.__syntaxError("Missing data for item _%s.%s" % (curCatName,curAttName))
......@@ -204,7 +205,7 @@ class PdbxReader(object):
else:
self.__syntaxError("Missing value in item-value pair")
curCatName, curAttName, curQuotedString, curWord = tokenizer.next()
curCatName, curAttName, curQuotedString, curWord = next(tokenizer)
continue
#
......@@ -214,14 +215,14 @@ class PdbxReader(object):
# The category name in the next curCatName,curAttName pair
# defines the name of the category container.
curCatName,curAttName,curQuotedString,curWord = tokenizer.next()
curCatName,curAttName,curQuotedString,curWord = next(tokenizer)
if curCatName is None or curAttName is None:
self.__syntaxError("Unexpected token in loop_ declaration")
return
# Check for a previous category declaration.
if categoryIndex.has_key(curCatName):
if curCatName in categoryIndex:
self.__syntaxError("Duplicate category declaration in loop_")
return
......@@ -237,7 +238,7 @@ class PdbxReader(object):
# Read the rest of the loop_ declaration
while True:
curCatName, curAttName, curQuotedString, curWord = tokenizer.next()
curCatName, curAttName, curQuotedString, curWord = next(tokenizer)
if curCatName is None:
break
......@@ -269,7 +270,7 @@ class PdbxReader(object):
elif curQuotedString is not None:
curRow.append(curQuotedString)
curCatName,curAttName,curQuotedString,curWord = tokenizer.next()
curCatName,curAttName,curQuotedString,curWord = next(tokenizer)
# loop_ data processing ends if -
......@@ -295,7 +296,7 @@ class PdbxReader(object):
categoryIndex = {}
curCategory = None
curCatName,curAttName,curQuotedString,curWord = tokenizer.next()
curCatName,curAttName,curQuotedString,curWord = next(tokenizer)
elif state == "ST_DATA_CONTAINER":
#
......@@ -306,7 +307,7 @@ class PdbxReader(object):
containerList.append(curContainer)
categoryIndex = {}
curCategory = None
curCatName,curAttName,curQuotedString,curWord = tokenizer.next()
curCatName,curAttName,curQuotedString,curWord = next(tokenizer)
elif state == "ST_STOP":
return
......@@ -316,7 +317,7 @@ class PdbxReader(object):
containerList.append(curContainer)
categoryIndex = {}
curCategory = None
curCatName,curAttName,curQuotedString,curWord = tokenizer.next()
curCatName,curAttName,curQuotedString,curWord = next(tokenizer)
elif state == "ST_UNKNOWN":
self.__syntaxError("Unrecogized syntax element: " + str(curWord))
......@@ -355,7 +356,7 @@ class PdbxReader(object):
## Tokenizer loop begins here ---
while True:
line = fileIter.next()
line = next(fileIter)
self.__curLineNumber += 1
# Dump comments
......@@ -368,7 +369,7 @@ class PdbxReader(object):
if line.startswith(";"):
mlString = [line[1:]]
while True:
line = fileIter.next()
line = next(fileIter)
self.__curLineNumber += 1
if line.startswith(";"):
break
......@@ -426,7 +427,7 @@ class PdbxReader(object):
## Tokenizer loop begins here ---
while True:
line = fileIter.next()
line = next(fileIter)
self.__curLineNumber += 1
# Dump comments
......@@ -439,7 +440,7 @@ class PdbxReader(object):
if line.startswith(";"):
mlString = [line[1:]]
while True:
line = fileIter.next()
line = next(fileIter)
self.__curLineNumber += 1
if line.startswith(";"):
break
......
wrappers/python/simtk/openmm/app/internal/pdbx/reader/PdbxReaderTests.py
View file @ b7088b74
......@@ -12,6 +12,7 @@
Test cases for reading PDBx/mmCIF data files PdbxReader class -
"""
from __future__ import absolute_import
import sys, unittest, traceback
import sys, time, os, os.path, shutil
......
wrappers/python/simtk/openmm/app/internal/pdbx/writer/PdbxWriter.py
View file @ b7088b74
......@@ -11,6 +11,7 @@
Classes for writing data and dictionary containers in PDBx/mmCIF format.
"""
from __future__ import absolute_import
__docformat__ = "restructuredtext en"
__author__ = "John Westbrook"
__email__ = "jwest@rcsb.rutgers.edu"
......
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