def ExtractAtomData ( self, dataBlock, blockCode ):
"""Extract atom data from a data block."""
system = xyzC = xyzF = None
table = dataBlock.get ( "atom_site", None )
if table is not None:
# . Atom labels and symbols.
labels = table.ColumnValues ( "atom_site_label" )
symbols = table.ColumnValues ( "atom_site_type_symbol" )
# . Make the symbols from the labels if necessary.
if symbols is None:
if labels is not None:
symbols = []
for label in labels:
characters = []
for c in label:
if c.isalpha ( ): characters.append ( c )
else: break
symbols.append ( "".join ( characters ) )
# . Make the basic system.
if symbols is not None:
system = System.FromAtoms ( symbols )
system.label = blockCode
# . Use the labels in the data block.
if labels is not None:
for ( atom, label ) in zip ( system.atoms, labels ):
atom.label = label
# . Coordinates.
xyzC = self.ExtractCoordinates ( table, "atom_site_Cartn" )
xyzF = self.ExtractCoordinates ( table, "atom_site_fract" )
return ( system, xyzC, xyzF )
def ToSystem(self):
"""Generate a system from the component."""
# . Bonds.
labelIndices = {}
for (i, atom) in enumerate(self.atoms):
labelIndices[atom.label] = i
bonds = []
for bond in self.bonds:
bonds.append((labelIndices[bond.atomLabel1],
labelIndices[bond.atomLabel2], bond.bondType))
# . System from atoms and bonds.
system = System.FromAtoms(self.atoms, bonds=bonds, withSequence=True)
# . Set additional atom data.
for (pAtom, sAtom) in zip(self.atoms, system.atoms):
sAtom.formalCharge = pAtom.formalCharge
sAtom.label = pAtom.label
# . Label.
system.label = "PDB Component"
if self.label is not None: system.label += " " + self.label
# . Define component labels.
for entity in system.sequence.children:
for component in entity.children:
component.label = self.label
# . Finish up.
return system
def ToSystem(self, QBEST=True):
"""Return a system constructed from the file data."""
system = None
if self.QPARSED and len(self.atomicNumbers > 0):
system = System.FromAtoms(self.atomicNumbers)
system.coordinates3 = self.ToCoordinates3(QBEST=QBEST)
system.label = "System from Jaguar Output File"
return system
def ToSystem(self):
"""Return a system."""
system = None
if self.QPARSED and hasattr(self, "atomicNumbers"):
system = System.FromAtoms(self.atomicNumbers)
system.label = self.title
system.coordinates3 = self.ToCoordinates3()
return system
def ToSystem ( self ):
"""Return a system."""
system = None
if self.QPARSED:
system = System.FromAtoms ( self.atomicNumbers )
system.label = self.title
system.coordinates3 = self.ToCoordinates3 ( )
system.electronicState = ElectronicState ( charge = self.charge, multiplicity = self.multiplicity )
return system
def ToSystem(self):
"""Return a system."""
if self.QPARSED:
system = System.FromAtoms(self.atomicNumbers)
system.label = self.label
system.coordinates3 = self.ToCoordinates3()
return system
else:
return None
def ToSystem(self):
"""Return a system."""
system = None
if self.QPARSED and hasattr(self, "atomicNumbers"):
system = System.FromAtoms(self.atomicNumbers)
system.coordinates3 = self.ToCoordinates3()
system.electronicState = self.ToElectronicState()
if hasattr(self, "entryname"): system.label = self.entryname
return system
def ToSystem(self):
"""Return a system from the CRD data but without sequence information."""
if self.QPARSED:
atoms = []
for (aname, atomicNumber, x, y, z) in self.atoms:
atoms.append(atomicNumber)
system = System.FromAtoms(atoms)
system.coordinates3 = self.ToCoordinates3()
return system
else:
return None
def ToSystem(self, frameIndex=-1):
"""Return a system."""
system = None
if self.QPARSED:
frame = self.frames[frameIndex]
atomicNumbers = frame.GetItem("Atomic Numbers")
if atomicNumbers is not None:
(head, tail) = os.path.split(self.name)
system = System.FromAtoms(atomicNumbers)
system.label = _DefaultSystemLabel + " " + tail
system.coordinates3 = self.ToCoordinates3()
system.electronicState = self.ToElectronicState()
return system
def ToSystem(self):
"""Return a system."""
system = None
if self.QPARSED:
try:
system = System.FromAtoms(self.atomicNumbers,
bonds=getattr(self, "bonds", None))
system.label = self.label
system.coordinates3 = self.xyz
if hasattr(self, "crystalClass") and hasattr(
self, "symmetryParameters"):
definitions = self.crystalClass.GetUniqueSymmetryParameters(
self.symmetryParameters)
definitions["crystalClass"] = self.crystalClass
system.DefineSymmetry(**definitions)
except:
pass
return system
def ToSystem(self, index=0):
"""Return a system."""
if self.QPARSED:
if index in range(len(self.molrecords)):
# . Get data.
(label, atomicNumbers, bonds, charges, coordinates3, mchg,
miso, mrad) = self.molrecords[index]
# . Make atoms.
atoms = self.ToAtoms(atomicNumbers, charges, mchg, miso, mrad)
# . Make system.
system = System.FromAtoms(atoms, bonds=bonds)
system.label = label
system.coordinates3 = coordinates3
return system
else:
raise IndexError(
"MOL record index {:d} not in range [0,{:d}].".format(
index,
len(self.molrecords) - 1))
else:
return None
def ToSystem(self, **keywordArguments):
"""Return a system.
Implicit hydrogens are added unless |QOMITIMPLICITHYDROGENS| is True.
The hydrogens are placed after their host atom.
"""
# . Options.
QOMIT = keywordArguments.get("QOMITIMPLICITHYDROGENS", False)
# . Atoms.
if QOMIT:
atoms = self.atoms
else:
atoms = []
index = 0
for atom in self.atoms:
atom.index = index
atoms.append(atom)
for i in range(atom.implicithydrogens):
atoms.append(1)
index += atom.implicithydrogens + 1
# . Bonds.
bonds = []
for bond in self.bonds:
bonds.append((bond.atom1.index, bond.atom2.index, bond.type))
if not QOMIT:
for atom in self.atoms:
for i in range(atom.implicithydrogens):
bonds.append(
(atom.index, atom.index + i + 1, SingleBond()))
self.IndexAtoms()
# . Make the system.
system = System.FromAtoms(atoms, bonds=bonds)
# . Set the aromaticity and formalCharge of the new atoms.
for atom in self.atoms:
index = atom.index
system.atoms[index].formalCharge = atom.formalCharge
system.atoms[index].isAromatic = atom.isAromatic
# . Finish up.
return system