def addSolvent(universe, solvent, density, scale_factor=4.):
"""
Scales up the universe and adds as many solvent molecules
as are necessary to obtain the specified solvent density,
taking account of the solute molecules that are already present
in the universe. The molecules are placed at random positions
in the scaled-up universe, but without overlaps between
any two molecules.
:param universe: a finite universe
:type universe: :class:~MMTK.Universe.Universe
:param solvent: a molecule, or the name of a molecule in the database
:type solvent: :class:~MMTK.ChemicalObjects.Molecule or str
:param density: the density of the solvent (amu/nm**3)
:type density: float
:param scale_factor: the factor by which the initial universe is
expanded before adding the solvent molecules
:type scale_factor: float
"""
# Calculate number of solvent molecules and universe size
if isinstance(solvent, basestring):
solvent = ChemicalObjects.Molecule(solvent)
cell_volume = universe.cellVolume()
if cell_volume is None:
raise TypeError("universe volume is undefined")
solute = copy.copy(universe._objects)
solute_volume = 0.
excluded_regions = []
for o in solute:
solute_volume = solute_volume + surfaceAndVolume(o)[1]
excluded_regions.append(o.boundingSphere())
n_solvent = int(
round(density * (cell_volume - solute_volume) / solvent.mass()))
solvent_volume = n_solvent * solvent.mass() / density
cell_volume = solvent_volume + solute_volume
universe.translateBy(-solute.position())
universe.scaleSize((cell_volume / universe.cellVolume())**(1. / 3.))
# Scale up the universe and add solvent molecules at random positions
universe.scaleSize(scale_factor)
universe.scale_factor = scale_factor
for i in range(n_solvent):
m = copy.copy(solvent)
m.translateTo(universe.randomPoint())
while True:
s = m.boundingSphere()
collision = False
for region in excluded_regions:
if (s.center -
region.center).length() < s.radius + region.radius:
collision = True
break
if not collision:
break
m.translateTo(universe.randomPoint())
universe.addObject(m)
excluded_regions.append(s)
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 createGroups(self, mapping):
groups = []
for name in self.molecules.keys():
full_name = mapping.get(name, None)
if full_name is not None:
for molecule in self.molecules[name]:
g = ChemicalObjects.Group(full_name)
setConfiguration(g, [molecule], toplevel=0)
groups.append(g)
return groups
def makeChemicalObjects(self, template, top_level):
self.groups[template.name].locked = True
if top_level:
if template.attributes.has_key('sequence'):
object = ChemicalObjects.ChainMolecule(None)
else:
object = ChemicalObjects.Molecule(None)
else:
object = ChemicalObjects.Group(None)
object.atoms = []
object.bonds = Bonds.BondList([])
object.groups = []
object.type = self.groups[template.name]
object.parent = None
child_objects = []
for child in template.children:
if isinstance(child, GroupTemplate):
group = self.makeChemicalObjects(child, False)
object.groups.append(group)
object.atoms.extend(group.atoms)
object.bonds.extend(group.bonds)
group.parent = object
child_objects.append(group)
else:
atom = ChemicalObjects.Atom(child.element)
object.atoms.append(atom)
atom.parent = object
child_objects.append(atom)
for name, index in template.names.items():
setattr(object, name, child_objects[index])
child_objects[index].name = name
for name, value in template.attributes.items():
path = name.split('.')
setattr(self.namePath(object, path[:-1]), path[-1], value)
for atom1, atom2 in template.bonds:
atom1 = self.namePath(object, atom1)
atom2 = self.namePath(object, atom2)
object.bonds.append(Bonds.Bond((atom1, atom2)))
for name, vector in template.positions.items():
path = name.split('.')
self.namePath(object, path).setPosition(vector)
return object
def createMolecule(self, name=None):
"""
:returns: a :class:~MMTK.ChemicalObjects.Molecule object corresponding
to the molecule in the PDB file. The parameter name
specifies the molecule name as defined in the chemical database.
It can be left out for known molecules (currently
only water).
:rtype: :class:~MMTK.ChemicalObjects.Molecule
"""
if name is None:
name = molecule_names[self.name]
m = ChemicalObjects.Molecule(name)
setConfiguration(m, [self])
return m
def numberOfSolventMolecules(universe, solvent, density):
"""
:param universe: a finite universe
:type universe: :class:`~MMTK.Universe.Universe`
:param solvent: a molecule, or the name of a molecule in the database
:type solvent: :class:`~MMTK.ChemicalObjects.Molecule` or str
:param density: the density of the solvent (amu/nm**3)
:type density: float
:returns: the number of solvent molecules that must be added to the
universe, in addition to whatever it already contains,
to obtain the given solvent density.
:rtype: int
"""
if isinstance(solvent, basestring):
solvent = ChemicalObjects.Molecule(solvent)
cell_volume = universe.cellVolume()
if cell_volume is None:
raise TypeError("universe volume is undefined")
solute_volume = 0.
for o in universe._objects:
solute_volume = solute_volume + surfaceAndVolume(o)[1]
return int(round(density*(cell_volume-solute_volume)/solvent.mass()))
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 createMolecules(self, names = None, permit_undefined=True):
"""
:param names: If a list of molecule names (as defined in the
chemical database) and/or PDB residue names,
only molecules mentioned in this list will be
constructed. If a dictionary, it is used to map
PDB residue names to molecule names. With the
default (None), only water molecules are
built.
:type names: list
:param permit_undefined: If False, an exception is raised
when a PDB residue is encountered for
which no molecule name is supplied
in names. If True, an AtomCluster
object is constructed for each unknown
molecule.
:returns: a collection of :class:~MMTK.ChemicalObjects.Molecule objects,
one for each molecule in the PDB file. Each PDB residue not
describing an amino acid or nucleotide residue is considered a
molecule.
:rtype: :class:~MMTK.Collections.Collection
"""
collection = Collections.Collection()
mol_dicts = [molecule_names]
if type(names) == type({}):
mol_dicts.append(names)
names = None
for name in self.molecules.keys():
full_name = None
for dict in mol_dicts:
full_name = dict.get(name, None)
if names is None or name in names or full_name in names:
if full_name is None and not permit_undefined:
raise ValueError("no definition for molecule " + name)
for molecule in self.molecules[name]:
if full_name:
m = ChemicalObjects.Molecule(full_name)
setConfiguration(m, [molecule])
else:
pdbdict = {}
atoms = []
i = 0
for atom in molecule:
aname = atom.name
while aname[0] in string.digits:
aname = aname[1:] + aname[0]
try:
element = atom['element'].strip()
a = ChemicalObjects.Atom(element, name = aname)
except KeyError:
try:
a = ChemicalObjects.Atom(aname[:2].strip(),
name = aname)
except IOError:
a = ChemicalObjects.Atom(aname[:1],
name = aname)
a.setPosition(atom.position)
atoms.append(a)
pdbdict[atom.name] = Database.AtomReference(i)
i += 1
m = ChemicalObjects.AtomCluster(atoms, name = name)
if len(pdbdict) == len(molecule):
# pdbmap is correct only if the AtomCluster has
# unique atom names
m.pdbmap = [(name, pdbdict)]
setConfiguration(m, [molecule])
collection.addObject(m)
return collection
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.')