def write(self, object, configuration = None, tag = None):
"""
Write an object to the file
:param object: the object to be written
:type object: :class:~MMTK.Collections.GroupOfAtoms
:param configuration: the configuration from which the coordinates
are taken (default: current configuration)
:type configuration: :class:~MMTK.ParticleProperties.Configuration
"""
if not ChemicalObjects.isChemicalObject(object):
for o in object:
self.write(o, configuration)
else:
toplevel = tag is None
if toplevel:
tag = Utility.uniqueAttribute()
if hasattr(object, 'pdbmap'):
for residue in object.pdbmap:
self.file.nextResidue(residue[0], )
sorted_atoms = residue[1].items()
sorted_atoms.sort(lambda x, y:
cmp(x[1].number, y[1].number))
for atom_name, atom in sorted_atoms:
atom = object.getAtom(atom)
p = atom.position(configuration)
if Utility.isDefinedPosition(p):
try: occ = atom.occupancy
except AttributeError: occ = 0.
try: temp = atom.temperature_factor
except AttributeError: temp = 0.
self.file.writeAtom(atom_name, p/Units.Ang,
occ, temp, atom.type.symbol)
self.atom_sequence.append(atom)
else:
self.warning = True
setattr(atom, tag, None)
else:
if hasattr(object, 'is_protein'):
for chain in object:
self.write(chain, configuration, tag)
elif hasattr(object, 'is_chain'):
self.file.nextChain(None, object.name)
for residue in object:
self.write(residue, configuration, tag)
self.file.terminateChain()
elif hasattr(object, 'molecules'):
for m in object.molecules:
self.write(m, configuration, tag)
elif hasattr(object, 'groups'):
for g in object.groups:
self.write(g, configuration, tag)
if toplevel:
for a in object.atomList():
if not hasattr(a, tag):
self.write(a, configuration, tag)
delattr(a, tag)
def write(self, object, configuration = None, tag = None):
"""
Write an object to the file
:param object: the object to be written
:type object: :class:`~MMTK.Collections.GroupOfAtoms`
:param configuration: the configuration from which the coordinates
are taken (default: current configuration)
:type configuration: :class:`~MMTK.ParticleProperties.Configuration`
"""
if not ChemicalObjects.isChemicalObject(object):
for o in object:
self.write(o, configuration)
else:
toplevel = tag is None
if toplevel:
tag = Utility.uniqueAttribute()
if hasattr(object, 'pdbmap'):
for residue in object.pdbmap:
self.file.nextResidue(residue[0], )
sorted_atoms = residue[1].items()
sorted_atoms.sort(lambda x, y:
cmp(x[1].number, y[1].number))
for atom_name, atom in sorted_atoms:
atom = object.getAtom(atom)
p = atom.position(configuration)
if Utility.isDefinedPosition(p):
try: occ = atom.occupancy
except AttributeError: occ = 0.
try: temp = atom.temperature_factor
except AttributeError: temp = 0.
self.file.writeAtom(atom_name, p/Units.Ang,
occ, temp, atom.type.symbol)
self.atom_sequence.append(atom)
else:
self.warning = True
setattr(atom, tag, None)
else:
if hasattr(object, 'is_protein'):
for chain in object:
self.write(chain, configuration, tag)
elif hasattr(object, 'is_chain'):
self.file.nextChain(None, object.name)
for residue in object:
self.write(residue, configuration, tag)
self.file.terminateChain()
elif hasattr(object, 'molecules'):
for m in object.molecules:
self.write(m, configuration, tag)
elif hasattr(object, 'groups'):
for g in object.groups:
self.write(g, configuration, tag)
if toplevel:
for a in object.atomList():
if not hasattr(a, tag):
self.write(a, configuration, tag)
delattr(a, tag)
def __init__(self, *items, **properties):
"""
:param items: either a sequence of peptide chain objects, or
a string, which is interpreted as the name of a
database definition for a protein.
If that definition does not exist, the string
is taken to be the name of a PDB file, from which
all peptide chains are constructed and
assembled into a protein.
:keyword model: one of "all" (all-atom), "no_hydrogens" or "none"
(no hydrogens),"polar_hydrogens" or "polar"
(united-atom with only polar hydrogens),
"polar_charmm" (like "polar", but defining
polar hydrogens like in the CHARMM force field),
"polar_opls" (like "polar", but defining
polar hydrogens like in the latest OPLS force field),
"calpha" (only the |C_alpha| atom of each residue).
Default is "all".
:type model: str
:keyword position: the center-of-mass position of the protein
:type position: Scientific.Geometry.Vector
:keyword name: a name for the protein
:type name: str
"""
if items == (None,):
return
self.name = ''
if len(items) == 1 and type(items[0]) == type(''):
try:
filename = Database.databasePath(items[0], 'Proteins')
found = 1
except IOError:
found = 0
if found:
blueprint = Database.BlueprintProtein(items[0])
items = blueprint.chains
for attr, value in vars(blueprint).items():
if attr not in ['type', 'chains']:
setattr(self, attr, value)
else:
import PDB
conf = PDB.PDBConfiguration(items[0])
model = properties.get('model', 'all')
items = conf.createPeptideChains(model)
molecules = []
for i in items:
if ChemicalObjects.isChemicalObject(i):
molecules.append(i)
else:
molecules = molecules + list(i)
for m, i in zip(molecules, range(len(molecules))):
m._numbers = [i]
if not m.name:
m.name = 'chain'+`i`
ss = self._findSSBridges(molecules)
new_mol = {}
for m in molecules:
new_mol[m] = ([m],[])
for bond in ss:
m1 = new_mol[bond[0].topLevelChemicalObject()]
m2 = new_mol[bond[1].topLevelChemicalObject()]
if m1 == m2:
m1[1].append(bond)
else:
combined = (m1[0] + m2[0], m1[1] + m2[1] + [bond])
for m in combined[0]:
new_mol[m] = combined
self.molecules = []
while new_mol:
m = new_mol.values()[0]
for i in m[0]:
del new_mol[i]
bonds = m[1]
if len(m[0]) == 1:
m = m[0][0]
m._addSSBridges(bonds)
else:
numbers = sum((i._numbers for i in m[0]), [])
m = ConnectedChains(m[0])
m._numbers = numbers
m._addSSBridges(bonds)
m._finalize()
for c in m:
c.parent = self
m.parent = self
self.molecules.append(m)
self.atoms = []
self.chains = []
for m in self.molecules:
self.atoms.extend(m.atoms)
if hasattr(m, 'is_connected_chains'):
for c, name, i in zip(range(len(m)),
m.chain_names, m._numbers):
self.chains.append((m, c, name, i))
else:
try: name = m.name
except AttributeError: name = ''
self.chains.append((m, None, name, m._numbers[0]))
self.chains.sort(lambda c1, c2: cmp(c1[3], c2[3]))
self.chains = map(lambda c: c[:3], self.chains)
self.parent = None
self.type = None
self.configurations = {}
try:
self.name = properties['name']
del properties['name']
except KeyError: pass
if properties.has_key('position'):
self.translateTo(properties['position'])
del properties['position']
self.addProperties(properties)
undefined = 0
for a in self.atoms:
if a.position() is None:
undefined += 1
if undefined > 0 and undefined != len(self.atoms):
Utility.warning('Some atoms in a protein ' +
'have undefined positions.')
def __init__(self, *items, **properties):
"""
:param items: either a sequence of peptide chain objects, or
a string, which is interpreted as the name of a
database definition for a protein.
If that definition does not exist, the string
is taken to be the name of a PDB file, from which
all peptide chains are constructed and
assembled into a protein.
:keyword model: one of "all" (all-atom), "no_hydrogens" or "none"
(no hydrogens),"polar_hydrogens" or "polar"
(united-atom with only polar hydrogens),
"polar_charmm" (like "polar", but defining
polar hydrogens like in the CHARMM force field),
"polar_opls" (like "polar", but defining
polar hydrogens like in the latest OPLS force field),
"calpha" (only the |C_alpha| atom of each residue).
Default is "all".
:type model: str
:keyword position: the center-of-mass position of the protein
:type position: Scientific.Geometry.Vector
:keyword name: a name for the protein
:type name: str
"""
if items == (None,):
return
self.name = ''
if len(items) == 1 and type(items[0]) == type(''):
try:
filename = Database.databasePath(items[0], 'Proteins')
found = 1
except IOError:
found = 0
if found:
blueprint = Database.BlueprintProtein(items[0])
items = blueprint.chains
for attr, value in vars(blueprint).items():
if attr not in ['type', 'chains']:
setattr(self, attr, value)
else:
import PDB
conf = PDB.PDBConfiguration(items[0])
model = properties.get('model', 'all')
items = conf.createPeptideChains(model)
molecules = []
for i in items:
if ChemicalObjects.isChemicalObject(i):
molecules.append(i)
else:
molecules = molecules + list(i)
for m, i in zip(molecules, range(len(molecules))):
m._numbers = [i]
if not m.name:
m.name = 'chain'+`i`
ss = self._findSSBridges(molecules)
new_mol = {}
for m in molecules:
new_mol[m] = ([m],[])
for bond in ss:
m1 = new_mol[bond[0].topLevelChemicalObject()]
m2 = new_mol[bond[1].topLevelChemicalObject()]
if m1 == m2:
m1[1].append(bond)
else:
combined = (m1[0] + m2[0], m1[1] + m2[1] + [bond])
for m in combined[0]:
new_mol[m] = combined
self.molecules = []
while new_mol:
m = new_mol.values()[0]
for i in m[0]:
del new_mol[i]
bonds = m[1]
if len(m[0]) == 1:
m = m[0][0]
m._addSSBridges(bonds)
else:
numbers = sum((i._numbers for i in m[0]), [])
m = ConnectedChains(m[0])
m._numbers = numbers
m._addSSBridges(bonds)
m._finalize()
for c in m:
c.parent = self
m.parent = self
self.molecules.append(m)
self.atoms = []
self.chains = []
for m in self.molecules:
self.atoms.extend(m.atoms)
if hasattr(m, 'is_connected_chains'):
for c, name, i in zip(range(len(m)),
m.chain_names, m._numbers):
self.chains.append((m, c, name, i))
else:
try: name = m.name
except AttributeError: name = ''
self.chains.append((m, None, name, m._numbers[0]))
self.chains.sort(lambda c1, c2: cmp(c1[3], c2[3]))
self.chains = map(lambda c: c[:3], self.chains)
self.parent = None
self.type = None
self.configurations = {}
try:
self.name = properties['name']
del properties['name']
except KeyError: pass
if properties.has_key('position'):
self.translateTo(properties['position'])
del properties['position']
self.addProperties(properties)
undefined = 0
for a in self.atoms:
if a.position() is None:
undefined += 1
if undefined > 0 and undefined != len(self.atoms):
Utility.warning('Some atoms in a protein ' +
'have undefined positions.')