def _DoubleBondCenters(molecule):
"""Treat the double bond centers."""
# . Find all double bonds between two sp2 carbons.
dcenters = []
edcenters = []
zdcenters = []
udcenters = []
for (b, bond) in enumerate(molecule.connectivity.bonds):
if bond.type is DoubleBond():
i = bond.i
j = bond.j
atomi = molecule.atoms[i]
atomj = molecule.atoms[j]
if ( atomi.atomicNumber == 6 ) and ( atomi.connections == 3 ) and \
( atomj.atomicNumber == 6 ) and ( atomj.connections == 3 ):
# . Save the bond.
dcenters.append(b)
# . Get the connected atoms.
iatoms = molecule.connectivity.bonds.GetConnectedAtoms(i)
iatoms.remove(j)
jatoms = molecule.connectivity.bonds.GetConnectedAtoms(j)
jatoms.remove(i)
# . Assign priorities.
oiatoms = _CIPPriorityOrderer(molecule, i, iatoms)
ojatoms = _CIPPriorityOrderer(molecule, j, jatoms)
if (oiatoms is not None) and (ojatoms is not None):
label = _DoubleBondCenterLabel(molecule.coordinates3, i,
oiatoms[0], j, ojatoms[0])
if label == "E": edcenters.append(b)
else: zdcenters.append(b)
# . Cannot assign priorities to the atoms.
else:
udcenters.append(b)
return (dcenters, edcenters, zdcenters, udcenters)
def Finalize(self):
"""Create a final connectivity.
To be used once all AddAtom and AddBond calls have been made.
"""
# . Define the rings and flag ring atoms.
self.FindRings()
# . Atom checks.
for atom in self.atoms:
atom.VerifyAromaticity()
atom.SetValence()
atom.AddImplicitHydrogens()
atom.VerifyChirality()
# . Bond checks - change non-aromatic to aromatic bonds between atoms.
for bond in self.bonds:
if bond.atom1.isAromatic and bond.atom2.isAromatic and (
not bond.type.isAromatic):
if bond.type is SingleBond(): bond.type = AromaticSingleBond()
elif bond.type is DoubleBond():
bond.type = AromaticDoubleBond()
else:
raise SMILESConnectivityError(
"Invalid bond type between aromatic atoms.", bond=bond)
# . Global checks.
self.VerifyAromaticity()
self.RemoveExplicitHydrogens()
self.IndexAtoms()
def _MakeDefaultVariants():
"""Make variants for the default distribution."""
# . Initialization.
variants = []
# . CTerminal.
variants.append(
PDBComponentVariant(label="C Terminal",
atomsToDelete=["HXT"],
formalCharges={"OXT": -1}))
# . NTerminal - general case and UNK.
atomsToAdd = [
PDBComponentAtom(atomicNumber=1, label="H1", pdbAlign=0, toFollow="N"),
PDBComponentAtom(atomicNumber=1, label="H2", pdbAlign=0,
toFollow="H1"),
PDBComponentAtom(atomicNumber=1, label="H3", pdbAlign=0, toFollow="H2")
]
bondsToAdd = [
PDBComponentBond(atomLabel1="H1",
atomLabel2="N",
bondType=SingleBond()),
PDBComponentBond(atomLabel1="H2",
atomLabel2="N",
bondType=SingleBond()),
PDBComponentBond(atomLabel1="H3",
atomLabel2="N",
bondType=SingleBond())
]
variants.append(
PDBComponentVariant(label="N Terminal",
atomsToAdd=atomsToAdd,
atomsToDelete=["H", "H2"],
formalCharges={"N": +1},
bondsToAdd=bondsToAdd))
variants.append(
PDBComponentVariant(componentLabel="UNK",
label="N Terminal",
atomsToAdd=atomsToAdd,
atomsToDelete=["H", "H2"],
formalCharges={"N": +1},
bondsToAdd=bondsToAdd))
# . NTerminal - PRO.
atomsToAdd = [
PDBComponentAtom(atomicNumber=1, label="H2", pdbAlign=0, toFollow="N"),
PDBComponentAtom(atomicNumber=1, label="H3", pdbAlign=0, toFollow="H2")
]
bondsToAdd = [
PDBComponentBond(atomLabel1="H2",
atomLabel2="N",
bondType=SingleBond()),
PDBComponentBond(atomLabel1="H3",
atomLabel2="N",
bondType=SingleBond())
]
variants.append(
PDBComponentVariant(componentLabel="PRO",
label="N Terminal",
atomsToAdd=atomsToAdd,
atomsToDelete=["H"],
formalCharges={"N": +1},
bondsToAdd=bondsToAdd))
# . Deprotonated ASP and GLU.
variants.append(
PDBComponentVariant(componentLabel="ASP",
label="Deprotonated",
atomsToDelete=["HD2"],
formalCharges={"OD2": -1}))
variants.append(
PDBComponentVariant(componentLabel="GLU",
label="Deprotonated",
atomsToDelete=["HE2"],
formalCharges={"OE2": -1}))
# . Histidine variants.
# . Doubly protonated - leave as is but shift charge to Nepsilon.
bondTypes = [
PDBComponentBond(atomLabel1="CE1",
atomLabel2="ND1",
bondType=SingleBond()),
PDBComponentBond(atomLabel1="CE1",
atomLabel2="NE2",
bondType=DoubleBond())
]
variants.append(
PDBComponentVariant(componentLabel="HIS",
label="Doubly Protonated",
formalCharges={
"ND1": 0,
"NE2": +1
},
bondTypes=bondTypes))
# . Delta protonated.
bondTypes = [
PDBComponentBond(atomLabel1="CE1",
atomLabel2="ND1",
bondType=SingleBond()),
PDBComponentBond(atomLabel1="CE1",
atomLabel2="NE2",
bondType=DoubleBond())
]
variants.append(
PDBComponentVariant(componentLabel="HIS",
label="Delta Protonated",
atomsToDelete=["HE2"],
formalCharges={
"ND1": 0,
"NE2": 0
},
bondTypes=bondTypes))
# . Epsilon protonated.
variants.append(
PDBComponentVariant(componentLabel="HIS",
label="Epsilon Protonated",
atomsToDelete=["HD1"],
formalCharges={
"ND1": 0,
"NE2": 0
}))
# . Fully deprotonated.
variants.append(
PDBComponentVariant(componentLabel="HIS",
label="Fully Deprotonated",
atomsToDelete=["HD1", "HE2"],
formalCharges={
"ND1": 0,
"NE2": -1
}))
# . Finish up.
return variants
#===================================================================================================================================
# . Classes and functions to read MOL2 files.
#===================================================================================================================================
from pCore import Coordinates3, logFile, LogFileActive, Real1DArray, TextFileReader
from ExportImport import _Importer
from pMolecule import CrystalClass_FromSpaceGroupNumber, PeriodicTable, System, SymmetryParameters, \
AromaticSingleBond, DoubleBond, SingleBond, TripleBond, UndefinedBond
#===================================================================================================================================
# . Definitions.
#===================================================================================================================================
# . Bond type definitions.
_MOL2BONDTYPES = {
"1": SingleBond(),
"2": DoubleBond(),
"3": TripleBond(),
"am": SingleBond(),
"ar": AromaticSingleBond(),
"du": UndefinedBond(),
"un": UndefinedBond(),
"nc": None
}
# . Generic (non-element) atom types.
_GENERICATOMTYPES = ("Any", "Du", "Hal", "Het", "Hev", "LP")
# . Section header.
_RTISTRING = "@<TRIPOS>"
"""PDB Components."""
import os, os.path
from pCore import logFile, LogFileActive
from pMolecule import AromaticSingleBond, DoubleBond, SingleBond, TripleBond, UndefinedBond, \
MMSequenceAtom, MMSequenceComponent, MMSequenceLink, MMSequenceVariant, \
Sequence, System
#===================================================================================================================================
# . Parameters.
#===================================================================================================================================
# . Bond label/object mappings.
_BondLabelObjectMapping = {
"Aromatic Single": AromaticSingleBond(),
"Double": DoubleBond(),
"Single": SingleBond(),
"Triple": TripleBond(),
"Undefined": UndefinedBond()
}
_BondObjectLabelMapping = {
AromaticSingleBond(): "Aromatic Single",
DoubleBond(): "Double",
SingleBond(): "Single",
TripleBond(): "Triple",
UndefinedBond(): "Undefined"
}
# . Key separators.
_KeyTokenSeparator = "_"
from pMolecule import DoubleBond, NullBond, SingleBond, TripleBond, PeriodicTable
from SMILESUtilities import ELEMENTSAROMATIC, ELEMENTSORGANIC, SMILESAtom, SMILESBond, SMILESConnectivity, SMILESConnectivityError
#===============================================================================
# . Parameters.
#===============================================================================
# . Tokens used for parsing Smiles strings.
# . Bonds - no aromaticity distinction is made here.
_BONDTOKENS = {
".": NullBond(),
"-": SingleBond(),
"/": SingleBond(),
"\\": SingleBond(),
":": SingleBond(),
"=": DoubleBond(),
"#": TripleBond()
}
# . Charge.
_CHARGETOKENS = {
"+": 1,
"++": 2,
"+++": 3,
"++++": 4,
"-": -1,
"--": -2,
"---": -3,
"----": -4
}
# . License : CeCILL French Free Software License (http://www.cecill.info)
#-------------------------------------------------------------------------------
"""Classes and functions for reading PDB chemical component files in mmCIF format."""
from pCore import logFile, LogFileActive, TextFileReader
from pMolecule import AromaticSingleBond, DoubleBond, SingleBond, TripleBond, UndefinedBond, \
PeriodicTable
from PDBComponent import PDBComponent, PDBComponentAtom, PDBComponentBond
#===================================================================================================================================
# . Parameters.
#===================================================================================================================================
# . Bond strings.
_BondStrings = {
"AROM": AromaticSingleBond(),
"DOUB": DoubleBond(),
"SING": SingleBond(),
"TRIP": TripleBond()
}
#===================================================================================================================================
# . Class.
#===================================================================================================================================
class PDBComponentCIFFileReader(TextFileReader):
"""PDBComponentCIFFileReader is the class for PDB chemical component files in mmCIF format that are to be read."""
# . Some simplicity is assumed in the parsing as all data entries are of the form:
# . data_XXX followed by "#".
# . general info. followed by "#".
# . atom info. followed by "#".
#===================================================================================================================================
# . Parameters.
#===================================================================================================================================
# . Atom type.
_ATOMTYPE = "Any"
# . The charge type.
_CHARGETYPE = "NO_CHARGES"
# . The maximum line length.
_MAXIMUMLINELENGTH = 80
# . Bond type definitions.
_MOL2BONDTYPES = { SingleBond ( ) : "1" , \
DoubleBond ( ) : "2" , \
TripleBond ( ) : "3" , \
AromaticSingleBond ( ) : "ar", \
AromaticDoubleBond ( ) : "ar", \
UndefinedBond ( ) : "un" }
# . The molecule type.
_MOLECULETYPE = "SMALL"
# . Section header.
_RTISTRING = "@<TRIPOS>"
#===================================================================================================================================
# . MOL2 file writer class.
#===================================================================================================================================
#-------------------------------------------------------------------------------
#===================================================================================================================================
# . Classes and functions to read MOL and SDF files.
#===================================================================================================================================
from pCore import Coordinates3, logFile, LogFileActive, TextFileReader
from ExportImport import _Importer
from pMolecule import Atom, PeriodicTable, System, \
AromaticSingleBond, DoubleBond, SingleBond, TripleBond, UndefinedBond
#===================================================================================================================================
# . Definitions.
#===================================================================================================================================
# . Bond type definitions.
_MOLBONDTYPES = { 1 : SingleBond ( ), \
2 : DoubleBond ( ), \
3 : TripleBond ( ), \
4 : AromaticSingleBond ( ) }
# . Charge definitions.
_CHARGECODES = {1: 3, 2: 2, 3: 1, 4: 0, 5: -1, 6: -2, 7: -3}
#===================================================================================================================================
# . MOL file reader class.
#===================================================================================================================================
class MOLFileReader(TextFileReader):
"""MOLFileReader is the class for MOL or SDF files that are to be read."""
def Parse(self, log=logFile):
"""Parsing."""
if not self.QPARSED:
"""Classes and functions for writing MOL files."""
from pCore import Coordinates3, TextFileWriter, TextFileWriterError
from ExportImport import _Exporter
from pMolecule import PeriodicTable, System, \
AromaticSingleBond, DoubleBond, SingleBond, TripleBond
#===================================================================================================================================
# . Parameters.
#===================================================================================================================================
# . The maximum line length.
_MAXIMUMLINELENGTH = 80
# . Bond type definitions.
_MOLBONDTYPES = { SingleBond ( ) : 1, \
DoubleBond ( ) : 2, \
TripleBond ( ) : 3, \
AromaticSingleBond ( ) : 4 }
#===================================================================================================================================
# . MOL file writer class.
#===================================================================================================================================
class MOLFileWriter(TextFileWriter):
"""MOLFileWriter is the class for MOL files that are to be written."""
def WriteFrame(self, system, label=None, xyz=None):
"""Write a single frame."""
# . Check the data.
if xyz == None: xyz = system.coordinates3
if (xyz is None) or (not isinstance(
xyz, Coordinates3)) or (xyz.rows != len(system.atoms)):