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Commit dc4d96fa authored by Peter Eastman's avatar Peter Eastman
Browse files

Cleaning up Python wrappers

parent 65b9d0b6
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wrappers/python/MANIFEST.in
View file @ dc4d96fa
include setup.py include setup.py
include *.py include *.py
include *.txt include *.txt
include doc/*.pdf
include images/*.bmp
include images/*.png
global-include README global-include README
recursive-include simtk *.txt *.py recursive-include simtk *.txt *.py
recursive-include OpenMM *.txt *.py *.so *.dll *.lib *.dylib *.h recursive-include OpenMM *.txt *.py *.so *.dll *.lib *.dylib *.h
recursive-include examples *.txt *.py *.pdb *.top *.prmtop *.crd *.sh *.leap
recursive-include test *.txt *.py *.pdb *.top *.prmtop *.crd *.sh *.in *log
recursive-include scripts *.txt *.py
recursive-include src *.txt *.py *.i *.c *.cxx *.h *.sh Doxyfile recursive-include src *.txt *.py *.i *.c *.cxx *.h *.sh Doxyfile
prune src/swig_doxygen/doxygen/html prune src/swig_doxygen/doxygen/html
prune src/swig_doxygen/doxygen/xml prune src/swig_doxygen/doxygen/xml
......
wrappers/python/simtk/chem/element.py deleted 100644 → 0
View file @ 65b9d0b6
#!/bin/env python
"""
element.py: Used for managing elements.
"""
__author__ = "Christopher M. Bruns"
__version__ = "1.0"
from simtk.unit import daltons
class Element:
elements_by_symbol = {}
def __init__(self, number, name, symbol, mass):
self.atomic_number = number
self.name = name
self.symbol = symbol
self.mass = mass
# Index this element in a global table
s = symbol.strip().upper()
assert s not in Element.elements_by_symbol
Element.elements_by_symbol[s] = self
def get_by_symbol(symbol):
s = symbol.strip().upper()
return Element.elements_by_symbol[s]
hydrogen = Element( 1, "hydrogen", "H", 1.007947*daltons)
deuterium = Element( 1, "deuterium", "D", 2.01355321270*daltons)
helium = Element( 2, "helium", "He", 4.003*daltons)
lithium = Element( 3, "lithium", "Li", 6.9412*daltons)
beryllium = Element( 4, "beryllium", "Be", 9.0121823*daltons)
boron = Element( 5, "boron", "B", 10.8117*daltons)
carbon = Element( 6, "carbon", "C", 12.01078*daltons)
nitrogen = Element( 7, "nitrogen", "N", 14.00672*daltons)
oxygen = Element( 8, "oxygen", "O", 15.99943*daltons)
fluorine = Element( 9, "fluorine", "F", 18.99840325*daltons)
neon = Element( 10, "neon", "Ne", 20.17976*daltons)
sodium = Element( 11, "sodium", "Na", 22.989769282*daltons)
magnesium = Element( 12, "magnesium", "Mg", 24.30506*daltons)
aluminum = Element( 13, "aluminum", "Al", 26.98153868*daltons)
silicon = Element( 14, "silicon", "Si", 28.08553*daltons)
phosphorus = Element( 15, "phosphorus", "P", 30.9737622*daltons)
sulfur = Element( 16, "sulfur", "S", 32.0655*daltons)
chlorine = Element( 17, "chlorine", "Cl", 35.4532*daltons)
argon = Element( 18, "argon", "Ar", 39.9481*daltons)
potassium = Element( 19, "potassium", "K", 39.09831*daltons)
calcium = Element( 20, "calcium", "Ca", 40.0784*daltons)
scandium = Element( 21, "scandium", "Sc", 44.9559126*daltons)
titanium = Element( 22, "titanium", "Ti", 47.8671*daltons)
vanadium = Element( 23, "vanadium", "V", 50.94151*daltons)
chromium = Element( 24, "chromium", "Cr", 51.99616*daltons)
manganese = Element( 25, "manganese", "Mn", 54.9380455*daltons)
iron = Element( 26, "iron", "Fe", 55.8452*daltons)
cobalt = Element( 27, "cobalt", "Co", 58.9331955*daltons)
nickel = Element( 28, "nickel", "Ni", 58.69342*daltons)
copper = Element( 29, "copper", "Cu", 63.5463*daltons)
zinc = Element( 30, "zinc", "Zn", 65.4094*daltons)
gallium = Element( 31, "gallium", "Ga", 69.7231*daltons)
germanium = Element( 32, "germanium", "Ge", 72.641*daltons)
arsenic = Element( 33, "arsenic", "As", 74.921602*daltons)
selenium = Element( 34, "selenium", "Se", 78.963*daltons)
bromine = Element( 35, "bromine", "Br", 79.9041*daltons)
krypton = Element( 36, "krypton", "Kr", 83.7982*daltons)
rubidium = Element( 37, "rubidium", "Rb", 85.46783*daltons)
strontium = Element( 38, "strontium", "Sr", 87.621*daltons)
yttrium = Element( 39, "yttrium", "Y", 88.905852*daltons)
zirconium = Element( 40, "zirconium", "Zr", 91.2242*daltons)
niobium = Element( 41, "niobium", "Nb", 92.906382*daltons)
molybdenum = Element( 42, "molybdenum", "Mo", 95.942*daltons)
technetium = Element( 43, "technetium", "Tc", 98*daltons)
ruthenium = Element( 44, "ruthenium", "Ru", 101.072*daltons)
rhodium = Element( 45, "rhodium", "Rh", 102.905502*daltons)
palladium = Element( 46, "palladium", "Pd", 106.421*daltons)
silver = Element( 47, "silver", "Ag", 107.86822*daltons)
cadmium = Element( 48, "cadmium", "Cd", 112.4118*daltons)
indium = Element( 49, "indium", "In", 114.8183*daltons)
tin = Element( 50, "tin", "Sn", 118.7107*daltons)
antimony = Element( 51, "antimony", "Sb", 121.7601*daltons)
tellurium = Element( 52, "tellurium", "Te", 127.603*daltons)
iodine = Element( 53, "iodine", "I", 126.904473*daltons)
xenon = Element( 54, "xenon", "Xe", 131.2936*daltons)
cesium = Element( 55, "cesium", "Cs", 132.90545192*daltons)
barium = Element( 56, "barium", "Ba", 137.3277*daltons)
lanthanum = Element( 57, "lanthanum", "La", 138.905477*daltons)
cerium = Element( 58, "cerium", "Ce", 140.1161*daltons)
praseodymium = Element( 59, "praseodymium", "Pr", 140.907652*daltons)
neodymium = Element( 60, "neodymium", "Nd", 144.2423*daltons)
promethium = Element( 61, "promethium", "Pm", 145*daltons)
samarium = Element( 62, "samarium", "Sm", 150.362*daltons)
europium = Element( 63, "europium", "Eu", 151.9641*daltons)
gadolinium = Element( 64, "gadolinium", "Gd", 157.253*daltons)
terbium = Element( 65, "terbium", "Tb", 158.925352*daltons)
dysprosium = Element( 66, "dysprosium", "Dy", 162.5001*daltons)
holmium = Element( 67, "holmium", "Ho", 164.930322*daltons)
erbium = Element( 68, "erbium", "Er", 167.2593*daltons)
thulium = Element( 69, "thulium", "Tm", 168.934212*daltons)
ytterbium = Element( 70, "ytterbium", "Yb", 173.043*daltons)
lutetium = Element( 71, "lutetium", "Lu", 174.9671*daltons)
hafnium = Element( 72, "hafnium", "Hf", 178.492*daltons)
tantalum = Element( 73, "tantalum", "Ta", 180.947882*daltons)
tungsten = Element( 74, "tungsten", "W", 183.841*daltons)
rhenium = Element( 75, "rhenium", "Re", 186.2071*daltons)
osmium = Element( 76, "osmium", "Os", 190.233*daltons)
iridium = Element( 77, "iridium", "Ir", 192.2173*daltons)
platinum = Element( 78, "platinum", "Pt", 195.0849*daltons)
gold = Element( 79, "gold", "Au", 196.9665694*daltons)
mercury = Element( 80, "mercury", "Hg", 200.592*daltons)
thallium = Element( 81, "thallium", "Tl", 204.38332*daltons)
lead = Element( 82, "lead", "Pb", 207.21*daltons)
bismuth = Element( 83, "bismuth", "Bi", 208.980401*daltons)
polonium = Element( 84, "polonium", "Po", 209*daltons)
astatine = Element( 85, "astatine", "At", 210*daltons)
radon = Element( 86, "radon", "Rn", 222.018*daltons)
francium = Element( 87, "francium", "Fr", 223*daltons)
radium = Element( 88, "radium", "Ra", 226*daltons)
actinium = Element( 89, "actinium", "Ac", 227*daltons)
thorium = Element( 90, "thorium", "Th", 232.038062*daltons)
protactinium = Element( 91, "protactinium", "Pa", 231.035882*daltons)
uranium = Element( 92, "uranium", "U", 238.028913*daltons)
neptunium = Element( 93, "neptunium", "Np", 237*daltons)
plutonium = Element( 94, "plutonium", "Pu", 244*daltons)
americium = Element( 95, "americium", "Am", 243*daltons)
curium = Element( 96, "curium", "Cm", 247*daltons)
berkelium = Element( 97, "berkelium", "Bk", 247*daltons)
californium = Element( 98, "californium", "Cf", 251*daltons)
einsteinium = Element( 99, "einsteinium", "Es", 252*daltons)
fermium = Element(100, "fermium", "Fm", 257*daltons)
mendelevium = Element(101, "mendelevium", "Md", 258*daltons)
nobelium = Element(102, "nobelium", "No", 259*daltons)
lawrencium = Element(103, "lawrencium", "Lr", 262*daltons)
rutherfordium = Element(104, "rutherfordium", "Rf", 261*daltons)
dubnium = Element(105, "dubnium", "Db", 262*daltons)
seaborgium = Element(106, "seaborgium", "Sg", 266*daltons)
bohrium = Element(107, "bohrium", "Bh", 264*daltons)
hassium = Element(108, "hassium", "Hs", 269*daltons)
meitnerium = Element(109, "meitnerium", "Mt", 268*daltons)
darmstadtium = Element(110, "darmstadtium", "Ds", 281*daltons)
roentgenium = Element(111, "roentgenium", "Rg", 272*daltons)
ununbium = Element(112, "ununbium", "Uub", 285*daltons)
ununtrium = Element(113, "ununtrium", "Uut", 284*daltons)
ununquadium = Element(114, "ununquadium", "Uuq", 289*daltons)
ununpentium = Element(115, "ununpentium", "Uup", 288*daltons)
ununhexium = Element(116, "ununhexium", "Uuh", 292*daltons)
wrappers/python/simtk/chem/openmm/__init__.py
View file @ dc4d96fa
...@@ -32,33 +32,6 @@ else: ...@@ -32,33 +32,6 @@ else:
flags = sys.getdlopenflags() flags = sys.getdlopenflags()
sys.setdlopenflags(flags | ctypes.RTLD_GLOBAL) sys.setdlopenflags(flags | ctypes.RTLD_GLOBAL)
import simtk.chem
from simtk.chem.openmm.openmm import *
skipPluginFilenames=["OpenMMFreeEnergy"]
if len(simtk.chem.__path__) > 1:
raise Exception("more than one item in simtk.chem.openmm.__path__")
pluginPath = os.path.join(simtk.chem.__path__[0],
'openmm',
'OpenMM',
'plugins')
pluginLoadingErrors={}
pluginLoadedLibNames=[]
libFilenames=glob.glob(os.path.join(pluginPath, "*.%s" % (libExt)))
# Load plugins
for filename in libFilenames:
skipPlugin=False
for pFilename in skipPluginFilenames:
fullFilename = "%s%s.%s" % (libPrefix, pFilename, libExt)
if os.path.split(filename)[-1] == fullFilename:
skipPlugin=True
break
if skipPlugin: continue
try:
Platform.loadPluginLibrary(os.path.join(pluginPath, filename))
pluginLoadedLibNames.append(filename)
except:
pluginLoadingErrors[filename]=sys.exc_info()
from simtk.chem.openmm.openmm import Platform
pluginLoadedLibNames = Platform.loadPluginsFromDirectory(Platform.getDefaultPluginsDirectory())
\ No newline at end of file
wrappers/python/simtk/chem/pdbstructure.py deleted 100644 → 0
View file @ 65b9d0b6
#!/bin/env python
"""
pdbstructure.py: Used for managing PDB formated files.
"""
__author__ = "Christopher M. Bruns"
__version__ = "1.0"
from simtk.vec3 import Vec3
import simtk.unit as unit
import simtk.chem.element as element
import warnings
import sys
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 = {}
# read file
self._load(input_stream)
def _load(self, input_stream):
# Read one line at a time
for pdb_line in input_stream:
# Look for atoms
if (pdb_line.find("ATOM ") == 0) or (pdb_line.find("HETATM") == 0):
self._add_atom(Atom(pdb_line))
# 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))
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):
self._current_model._current_chain._add_ter_record()
self._finalize()
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()
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 = {}
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 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):
"""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.
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()
self.serial_number = int(pdb_line[6:11])
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]
self.residue_number = int(pdb_line[22:26])
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])
occupancy = float(pdb_line[54:60])
temperature_factor = float(pdb_line[60:66]) * 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:
# First try to find a sensible element symbol from columns 76-77
self.element = element.get_by_symbol(self.element_symbol)
except KeyError:
# otherwise, deduce element from first two characters of atom name
# remove digits found in some hydrogen atom names
symbol = self.name_with_spaces[0:2].strip().lstrip("0123456789")
try:
# Some molecular dynamics PDB files, such as gromacs with ffamber force
# field, include 4-character hydrogen atom names beginning with "H".
# Hopefully elements like holmium (Ho) and mercury (Hg) will have fewer than four
# characters in the atom name. This problem is the fault of molecular
# dynamics code authors who feel the need to make up their own atom
# nomenclature because it is too tedious to read that provided by the PDB.
# These are the same folks who invent their own meanings for biochemical terms
# like "dipeptide". Clowntards.
if len(self.name) == 4 and self.name[0:1] == "H":
self.element = element.hydrogen
else:
self.element = element.get_by_symbol(symbol)
except KeyError:
# OK, I give up
self.element = None
warnings.warn("WARNING: Unknown element '%s': %s" % (symbol, pdb_line))
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.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 sys
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
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