def calculateCyclicSymmetryNumber(molecule):
"""
Get the symmetry number correction for cyclic regions of a molecule.
For complicated fused rings the smallest set of smallest rings is used.
"""
from rdkit.Chem.rdmolops import SanitizeMol
from rdkit.Chem.rdchem import Mol
symmetryNumber = 1
rings = molecule.getSmallestSetOfSmallestRings()
# Get symmetry number for each ring in structure
for ring0 in rings:
# Make another copy structure
structure = molecule.copy(True)
ring = [structure.atoms[molecule.atoms.index(atom)] for atom in ring0]
# Remove bonds of ring from structure
for i, atom1 in enumerate(ring):
for atom2 in ring[i + 1 :]:
if structure.hasBond(atom1, atom2):
structure.removeBond(atom1.edges[atom2])
structures = structure.split()
groups = []
for struct in structures:
for atom in ring:
if struct.hasAtom(atom):
struct.removeAtom(atom)
groups.append(struct.split())
# Find equivalent functional groups on ring
equivalentGroups = []
equivalentGroupCount = []
for group in groups:
found = False
for i, eqGroup in enumerate(equivalentGroups):
if not found and len(group) == len(eqGroup):
for g, eg in zip(group, eqGroup):
if not g.isIsomorphic(eg):
# The groups do not match
break
else:
# The groups match
found = True
if found:
# We've found a matching group, so increment its count
equivalentGroupCount[i] += 1
break
else:
# No matching group found, so add it as a new group
equivalentGroups.append(group)
equivalentGroupCount.append(1)
# Find equivalent bonds on ring
equivalentBonds = []
for i, atom1 in enumerate(ring0):
for atom2 in ring0[i + 1 :]:
if molecule.hasBond(atom1, atom2):
bond = molecule.getBond(atom1, atom2)
found = False
for eqBond in equivalentBonds:
if not found:
if bond.equivalent(eqBond[0]):
eqBond.append(group)
found = True
if not found:
equivalentBonds.append([bond])
# Find maximum number of equivalent groups and bonds
minEquivalentGroups = min(equivalentGroupCount)
maxEquivalentGroups = max(equivalentGroupCount)
minEquivalentBonds = None
maxEquivalentBonds = 0
for bonds in equivalentBonds:
N = len(bonds)
if minEquivalentBonds is None or N < minEquivalentBonds:
minEquivalentBonds = N
if N > maxEquivalentBonds:
maxEquivalentBonds = N
if maxEquivalentGroups == maxEquivalentBonds == len(ring):
symmetryNumber *= len(ring) * 2
else:
symmetryNumber *= min(minEquivalentGroups, minEquivalentBonds)
return symmetryNumber
def calculateCyclicSymmetryNumber(molecule):
"""
Get the symmetry number correction for cyclic regions of a molecule.
For complicated fused rings the smallest set of smallest rings is used.
"""
from rdkit.Chem.rdmolops import SanitizeMol
from rdkit.Chem.rdchem import Mol
mcopy = molecule.toRDKitMol(removeHs=True, returnMapping=False)
SanitizeMol(mcopy)
symmetryNumber = 1
# Get symmetry number for each ring in structure
rings = molecule.getSmallestSetOfSmallestRings()
for ring0 in rings:
# Make copy of structure
structure = molecule.copy(True)
ring = [structure.atoms[molecule.atoms.index(atom)] for atom in ring0]
# Figure out which atoms and bonds are aromatic and reassign appropriately:
for i, atom1 in enumerate(ring0):
for atom2 in ring0[i + 1:]:
if molecule.hasBond(atom1, atom2):
if mcopy.GetBondBetweenAtoms(i, i + 1) is not None:
if str(
mcopy.GetBondBetweenAtoms(
i, i + 1).GetBondType()) == 'AROMATIC':
bond = molecule.getBond(atom1, atom2)
bond.applyAction(
['CHANGE_BOND', atom1, 'B', atom2])
atom1.atomType = atom2.atomType = rmgpy.molecule.atomTypes[
'Cb']
else:
pass
# Remove bonds of ring from structure
for i, atom1 in enumerate(ring):
for atom2 in ring[i + 1:]:
if structure.hasBond(atom1, atom2):
structure.removeBond(atom1.edges[atom2])
structures = structure.split()
groups = []
for struct in structures:
for atom in ring:
if struct.hasAtom(atom): struct.removeAtom(atom)
groups.append(struct.split())
# Find equivalent functional groups on ring
equivalentGroups = []
equivalentGroupCount = []
for group in groups:
found = False
for i, eqGroup in enumerate(equivalentGroups):
if not found and len(group) == len(eqGroup):
for g, eg in zip(group, eqGroup):
if not g.isIsomorphic(eg):
# The groups do not match
break
else:
# The groups match
found = True
if found:
# We've found a matching group, so increment its count
equivalentGroupCount[i] += 1
break
else:
# No matching group found, so add it as a new group
equivalentGroups.append(group)
equivalentGroupCount.append(1)
# Find equivalent bonds on ring
equivalentBonds = []
for i, atom1 in enumerate(ring0):
for atom2 in ring0[i + 1:]:
if molecule.hasBond(atom1, atom2):
bond = molecule.getBond(atom1, atom2)
found = False
for eqBond in equivalentBonds:
if not found:
if bond.equivalent(eqBond[0]):
eqBond.append(group)
found = True
if not found:
equivalentBonds.append([bond])
# Find maximum number of equivalent groups and bonds
minEquivalentGroups = min(equivalentGroupCount)
maxEquivalentGroups = max(equivalentGroupCount)
minEquivalentBonds = None
maxEquivalentBonds = 0
for bonds in equivalentBonds:
N = len(bonds)
if minEquivalentBonds is None or N < minEquivalentBonds:
minEquivalentBonds = N
if N > maxEquivalentBonds:
maxEquivalentBonds = N
if maxEquivalentGroups == maxEquivalentBonds == len(ring):
symmetryNumber *= len(ring) * 2
else:
symmetryNumber *= min(minEquivalentGroups, minEquivalentBonds)
#print len(ring), minEquivalentGroups, maxEquivalentGroups, minEquivalentBonds, maxEquivalentBonds, symmetryNumber
return symmetryNumber
def calculateCyclicSymmetryNumber(molecule):
"""
Get the symmetry number correction for cyclic regions of a molecule.
For complicated fused rings the smallest set of smallest rings is used.
"""
from rdkit.Chem.rdmolops import SanitizeMol
from rdkit.Chem.rdchem import Mol
mcopy = molecule.toRDKitMol(removeHs=True, returnMapping=False)
SanitizeMol(mcopy)
symmetryNumber = 1
# Get symmetry number for each ring in structure
rings = molecule.getSmallestSetOfSmallestRings()
for ring0 in rings:
# Make copy of structure
structure = molecule.copy(True)
ring = [structure.atoms[molecule.atoms.index(atom)] for atom in ring0]
# Figure out which atoms and bonds are aromatic and reassign appropriately:
for i, atom1 in enumerate(ring0):
for atom2 in ring0[i+1:]:
if molecule.hasBond(atom1, atom2):
if mcopy.GetBondBetweenAtoms(i,i+1) is not None:
if str(mcopy.GetBondBetweenAtoms(i,i+1).GetBondType()) == 'AROMATIC':
bond = molecule.getBond(atom1, atom2)
bond.applyAction(['CHANGE_BOND', atom1, 'B', atom2])
atom1.atomType = atom2.atomType = rmgpy.molecule.atomTypes['Cb']
else:
pass
# Remove bonds of ring from structure
for i, atom1 in enumerate(ring):
for atom2 in ring[i+1:]:
if structure.hasBond(atom1, atom2):
structure.removeBond(atom1.edges[atom2])
structures = structure.split()
groups = []
for struct in structures:
for atom in ring:
if struct.hasAtom(atom): struct.removeAtom(atom)
groups.append(struct.split())
# Find equivalent functional groups on ring
equivalentGroups = []; equivalentGroupCount = []
for group in groups:
found = False
for i, eqGroup in enumerate(equivalentGroups):
if not found and len(group) == len(eqGroup):
for g, eg in zip(group, eqGroup):
if not g.isIsomorphic(eg):
# The groups do not match
break
else:
# The groups match
found = True
if found:
# We've found a matching group, so increment its count
equivalentGroupCount[i] += 1
break
else:
# No matching group found, so add it as a new group
equivalentGroups.append(group)
equivalentGroupCount.append(1)
# Find equivalent bonds on ring
equivalentBonds = []
for i, atom1 in enumerate(ring0):
for atom2 in ring0[i+1:]:
if molecule.hasBond(atom1, atom2):
bond = molecule.getBond(atom1, atom2)
found = False
for eqBond in equivalentBonds:
if not found:
if bond.equivalent(eqBond[0]):
eqBond.append(group)
found = True
if not found:
equivalentBonds.append([bond])
# Find maximum number of equivalent groups and bonds
minEquivalentGroups = min(equivalentGroupCount)
maxEquivalentGroups = max(equivalentGroupCount)
minEquivalentBonds = None
maxEquivalentBonds = 0
for bonds in equivalentBonds:
N = len(bonds)
if minEquivalentBonds is None or N < minEquivalentBonds:
minEquivalentBonds = N
if N > maxEquivalentBonds:
maxEquivalentBonds = N
if maxEquivalentGroups == maxEquivalentBonds == len(ring):
symmetryNumber *= len(ring) * 2
else:
symmetryNumber *= min(minEquivalentGroups, minEquivalentBonds)
#print len(ring), minEquivalentGroups, maxEquivalentGroups, minEquivalentBonds, maxEquivalentBonds, symmetryNumber
return symmetryNumber
def calculateCyclicSymmetryNumber(molecule):
"""
Get the symmetry number correction for cyclic regions of a molecule.
For complicated fused rings the smallest set of smallest rings is used.
"""
from rdkit.Chem.rdmolops import SanitizeMol
from rdkit.Chem.rdchem import Mol
symmetryNumber = 1
rings = molecule.getSmallestSetOfSmallestRings()
# Get symmetry number for each ring in structure
for ring0 in rings:
# Make another copy structure
structure = molecule.copy(True)
ring = [structure.atoms[molecule.atoms.index(atom)] for atom in ring0]
# Remove bonds of ring from structure
for i, atom1 in enumerate(ring):
for atom2 in ring[i + 1:]:
if structure.hasBond(atom1, atom2):
structure.removeBond(atom1.edges[atom2])
structures = structure.split()
groups = []
for struct in structures:
for atom in ring:
if struct.hasAtom(atom): struct.removeAtom(atom)
groups.append(struct.split())
# Find equivalent functional groups on ring
equivalentGroups = []
equivalentGroupCount = []
for group in groups:
found = False
for i, eqGroup in enumerate(equivalentGroups):
if not found and len(group) == len(eqGroup):
for g, eg in zip(group, eqGroup):
if not g.isIsomorphic(eg):
# The groups do not match
break
else:
# The groups match
found = True
if found:
# We've found a matching group, so increment its count
equivalentGroupCount[i] += 1
break
else:
# No matching group found, so add it as a new group
equivalentGroups.append(group)
equivalentGroupCount.append(1)
# Find equivalent bonds on ring
equivalentBonds = []
for i, atom1 in enumerate(ring0):
for atom2 in ring0[i + 1:]:
if molecule.hasBond(atom1, atom2):
bond = molecule.getBond(atom1, atom2)
found = False
for eqBond in equivalentBonds:
if not found:
if bond.equivalent(eqBond[0]):
eqBond.append(group)
found = True
if not found:
equivalentBonds.append([bond])
# Find maximum number of equivalent groups and bonds
minEquivalentGroups = min(equivalentGroupCount)
maxEquivalentGroups = max(equivalentGroupCount)
minEquivalentBonds = None
maxEquivalentBonds = 0
for bonds in equivalentBonds:
N = len(bonds)
if minEquivalentBonds is None or N < minEquivalentBonds:
minEquivalentBonds = N
if N > maxEquivalentBonds:
maxEquivalentBonds = N
if maxEquivalentGroups == maxEquivalentBonds == len(ring):
symmetryNumber *= len(ring) * 2
else:
symmetryNumber *= min(minEquivalentGroups, minEquivalentBonds)
return symmetryNumber