def setAtomTypeForSulfurs(self, mol):
num_atoms = len(mol.atoms)
atom = Atom()
atom_linked = Atom()
index = -1
i = 0
while i < num_atoms:
atom = mol.atoms[i]
if atom.element.lower() == "S".lower():
atom_linked = mol.atoms[atom.linkage[0]]
if atom.num_linkages == 2:
# SG311: sulphur, SH, -S-
atom.atomType = "SG311"
if not atom.isRingAtom:
if atom.isThiocarbonylS:
# SG2D1: thiocarbonyl S
atom.atomType = "SG2D1"
elif atom.num_linkages == 2 and atom.numSulfurAtoms == 1 and atom.numCarbonAtoms == 1:
# SG301: sulfur C-S-S-C type
atom.atomType = "SG301"
elif atom.isDeprotonatedSulfur:
# SG302: thiolate sulfur (-1)
atom.atomType = "SG302"
elif atom.num_linkages == 3 and atom.numCarbonAtoms == 2 and atom.numOxygenAtoms == 1:
# SG3O3: neutral sulfoxide sulfur
atom.atomType = "SG3O3"
if atom.numOxygenAtoms >= 2:
charge = self.getCharge(mol, i)
if charge == -1:
# SG3O1: sulfate -1 sulfur
atom.atomType = "SG3O1"
elif charge == 0:
# SG3O2: neutral sulfone/sulfonamide sulfur
atom.atomType = "SG3O2"
else:
if atom.numOxygenAtoms >= 2 and self.getCharge(mol,
i) == 0:
# SG3O2: neutral sulfone/sulfonamide sulfur
atom.atomType = "SG3O2"
elif atom.numRingAtoms[0] == 5:
# SG2R50: THIP, thiophene
atom.atomType = "SG2R50"
i += 1
def setAtomTypeForMiscellaneousAtoms(self, mol):
num_atoms = len(mol.atoms)
atom = Atom()
atom_linked = Atom()
index = -1
i = 0
while i < num_atoms:
atom = mol.atoms[i]
if atom.element.lower() == "P".lower():
if atom.numSulfurAtoms == 0:
charge = self.getCharge(mol, i)
if charge == 0:
# PG0: neutral phosphate
atom.atomType = "PG0"
elif charge == -1:
# PG1: phosphate -1
atom.atomType = "PG1"
elif charge == -2:
# PG2: phosphate -2
atom.atomType = "PG2"
else:
j = 0
while j < atom.num_linkages:
atom_linked = mol.atoms[atom.linkage[j]]
if atom_linked.element.lower() == "O".lower(
) and atom_linked.num_linkages == 1:
# OG2S1: mono-thio S-P bond modulated oxygen; lsk
atom_linked.atomType = "OG2S1"
j += 1
elif atom.element.lower() == "LP".lower():
# LPH: Lone pair for halogens
atom.atomType = "LPH"
elif atom.element.lower() == "AL".lower():
if self.countSpecificElement(mol, i, "F") == 4:
# ALG1: Aluminum, for ALF4, AlF4-
atom.atomType = "ALG1"
elif atom.element.lower() == "S".lower():
if atom.num_linkages == 1:
atom_linked = mol.atoms[atom.linkage[0]]
if atom_linked.element.lower() == "P".lower():
if num_S == 1:
# SG2P1: mono-thio S-P bond; lsk
atom.atomType = "SG2P1"
elif num_S == 2:
# SG2P2: di-thio S-P bond; lsk
atom.atomType = "SG2P2"
i += 1
def setAtomTypeForHydrogens(self, mol):
num_atoms = len(mol.atoms)
atom = Atom()
atom_linked = Atom()
i = 0
while i < num_atoms:
atom = mol.atoms[i]
if atom.element.lower() == "H".lower():
atom_linked = mol.atoms[atom.linkage[0]]
element = atom_linked.element
atomType = atom_linked.atomType
if atom_linked.isAromatic:
# HGR61: aromatic H
atom.atomType = "HGR61"
if element.lower() == "C".lower():
if not atom_linked.isAromatic:
if atom_linked.numHydrogenAtoms == 1:
# HGA1: alphatic proton, CH
atom.atomType = "HGA1"
elif atom_linked.numHydrogenAtoms == 2:
# HGA2: alphatic proton, CH2
atom.atomType = "HGA2"
elif atom_linked.numHydrogenAtoms == 3:
# HGA3: alphatic proton, CH3
atom.atomType = "HGA3"
if self.hasCarbonDoubleBond(mol, atom_linked):
if atom_linked.numHydrogenAtoms == 1:
# HGA4: alkene proton; RHC=
atom.atomType = "HGA4"
elif atom_linked.numHydrogenAtoms == 2:
# HGA5: alkene proton; H2C=CR
atom.atomType = "HGA5"
num_fluorides = self.countSpecificElement(
mol, atom_linked, "F")
if num_fluorides > 0:
if num_fluorides == 1:
# HGA6: aliphatic H on fluorinated C, monofluoro
atom.atomType = "HGA6"
elif num_fluorides == 2:
# HGA7: aliphatic H on fluorinated C, difluoro
atom.atomType = "HGA7"
if atom_linked.numNitrogenAtoms > 0:
index = self.getIndex(mol, atom_linked, "N")
if not mol.atoms[index].isProtonatedNitrogen:
num_methyl = self.countMethyl(
mol, mol.atoms[index])
if num_methyl == 3 and mol.atoms[
index].numHydrogenAtoms == 0:
# HGAAM0: aliphatic H, NEUTRAL trimethylamine (#)
atom.atomType = "HGAAM0"
elif num_methyl == 2 and mol.atoms[
index].numHydrogenAtoms == 1:
# HGAAM1: aliphatic H, NEUTRAL dimethylamine (#)
atom.atomType = "HGAAM1"
elif num_methyl == 1 and mol.atoms[
index].numHydrogenAtoms == 2:
# HGAAM2: aliphatic H, NEUTRAL methylamine (#)
atom.atomType = "HGAAM2"
if atom_linked.numHydrogenAtoms == 3 and atom_linked.numNitrogenAtoms == 1:
if mol.atoms[index].atomType.lower(
) == "NG3P0".lower():
# HGP5: polar H on quarternary ammonium salt (choline)
atom.atomType = "HGP5"
if atom_linked.num_linkages == 2 and self.hasTripleBond(
atom_linked):
# HGPAM1: polar H, NEUTRAL dimethylamine (#), terminal alkyne H
atom.atomType = "HGPAM1"
# HGR52: Aldehyde H, formamide H (RCOH); nonpolar H, neutral 5-mem planar ring C adjacent to heteroatom or + charge
# CG201, CG202, CG203, CG204
# CG2R51, CG2R52, CG2R53 linked to heteroatom
# CG2D1, CG2DC1 linked to protonated N
if atomType != None and (
atomType.lower() == "CG2O1".lower()
or atomType.lower() == "CG2O2".lower()
or atomType.lower() == "CG2O3".lower()
or atomType.lower() == "CG2O4".lower()):
atom.atomType = "HGR52"
elif atomType != None and (
atomType.lower() == "CG2R51".lower()
or atomType.lower() == "CG2R52".lower()
or atomType.lower()
== "CG2R53".lower()) and self.hasHeteroAtom(
mol, atom_linked):
atom.atomType = "HGR52"
elif atomType != None and (
atomType.lower() == "CG2D1".lower()
or atomType.lower() == "CG2DC1".lower()
) and self.hasProtonatedNitrogen(mol, atom_linked):
atom.atomType = "HGR52"
if atomType != None and atomType.lower() == "CG2R53".lower(
) and self.hasProtonatedNitrogen(mol, atom_linked):
# HGR53: nonpolar H, +ve charge HIS he1(+1)
atom.atomType = "HGR53"
if atom_linked.isAromatic and atom_linked.numRingAtoms[
0] == 5 and atomType.lower() == "CG2R51".lower(
) and not self.hasHeteroAtom(mol, atom_linked):
# HGR51: nonpolar H, neutral 5-mem planar ring C, LJ based on benzene
atom.atomType = "HGR51"
if atom_linked.isRingAtom:
if atom_linked.isAromatic:
if atom_linked.numRingAtoms[0] == 6:
if self.isTypeHGR62(mol, atom_linked):
# HGR62: nonpolar H, neutral 6-mem planar ring C adjacent to heteroatom
atom.atomType = "HGR62"
if atom_linked.isProtonatedPyridine or atom_linked.isProtonatedPyrimidine:
# HGR63: nonpolar H, NAD+ nicotineamide all ring CH hydrogens
atom.atomType = "HGR63"
elif atom_linked.numRingAtoms[0] == 7:
# HGR71: nonpolar H, neutral 7-mem arom ring, AZUL, azulene, kevo
atom.atomType = "HGR71"
elif element.lower() == "N".lower():
if not atom_linked.isAromatic:
if not atom_linked.isProtonatedNitrogen:
num_methyl = self.countMethyl(mol, atom_linked)
if num_methyl == 2:
# HGAAM1: aliphatic H, NEUTRAL dimethylamine (#)
atom.atomType = "HGAAM1"
elif num_methyl == 1:
# HGAAM2: aliphatic H, NEUTRAL methylamine (#)
atom.atomType = "HGAAM2"
if atomType != None and atomType.lower() == "NG311".lower(
):
if atom_linked.numCarbonAtoms == 2:
# HGPAM1: polar H, NEUTRAL dimethylamine (#), terminal alkyne H
atom.atomType = "HGPAM1"
elif atom_linked.numCarbonAtoms == 1 and (
atom_linked.numSulfurAtoms == 1
or atom_linked.numOxygenAtoms == 1):
# HGP1: polar H
atom.atomType = "HGP1"
elif atomType != None and atomType.lower(
) == "NG321".lower():
if atom_linked.numCarbonAtoms == 1:
# HGPAM2: polar H, NEUTRAL methylamine (#)
atom.atomType = "HGPAM2"
elif atom_linked.numSulfurAtoms == 1:
# HGP1: polar H
atom.atomType = "HGP1"
elif atom_linked.num_linkages == 3 and not atom_linked.isProtonatedNitrogen and atom_linked.numHydrogenAtoms == 3:
# HGPAM3: polar H, NEUTRAL ammonia (#)
atom.atomType = "HGPAM3"
if atomType != None and (
atomType.lower() == "NG2P1".lower()
or atomType.lower() == "NG3P3".lower()
or atomType.lower() == "NG2R52".lower()
or atomType.lower() == "NG3P2".lower()
or atomType.lower() == "NG3P1".lower()):
# HGP2: polar H, +ve charge
# NG2P1, NG3P3, NG2R52, NG3P2, NG3P1
atom.atomType = "HGP2"
elif atomType != None and atomType.lower(
) == "NG2P1".lower():
# HGP3: polar H, thiol
atom.atomType = "HGP3"
elif element.lower() == "S".lower():
if atomType != None and atomType.lower() == "SG311".lower(
):
# HGP3: polar H, thiol
atom.atomType = "HGP3"
if atomType != None and (
atomType.lower() == "OG311".lower()
or atomType.lower() == "NG2S2".lower()
or atomType.lower() == "NG2S1".lower()
or atomType.lower() == "NG2R51".lower()
or atomType.lower() == "NG2S3".lower()
or atomType.lower() == "NG2R61".lower()
or atomType.lower() == "NG2D1".lower()
or atomType.lower() == "NG3C51".lower()
or atomType.lower() == "NG2R53".lower()
or atomType.lower() == "NG3N1".lower()
or atomType.lower() == "NG2R43".lower()):
# HGP1: polar H
# OG311, NG2S2, NG2S1, NG2R51, NG2S3,
# NG2R61, NG2D1, NG3C51, NG2R53, NG3N1,
# NG2R43
atom.atomType = "HGP1"
if atomType.lower() == "NG321".lower(
) and atom_linked.numSulfurAtoms == 1:
atom.atomType = "HGP1"
if atom_linked.isProtonatedNitrogen and atomType.lower(
) == "NG2R61".lower():
# HGP2: polar H, +ve charge
atom.atomType = "HGP2"
if atom_linked.element.lower() == "N".lower(
) and not atom_linked.isProtonatedNitrogen and atom_linked.numHydrogenAtoms == 2 and self.hasAromaticBond(
mol, atom_linked):
# HGP4: polar H, neutral conjugated -NH2 group (NA bases)
atom.atomType = "HGP4"
i += 1
def setAtomTypeForOxygens(self, mol):
num_atoms = len(mol.atoms)
atom = Atom()
atom_linked = Atom()
index = -1
i = 0
while i < num_atoms:
atom = mol.atoms[i]
if atom.element.lower() == "O".lower():
atom_linked = mol.atoms[atom.linkage[0]]
if not atom.isRingAtom:
if atom_linked.isCarbonyl:
if atom_linked.numRingAtoms[
0] == 6 and atom_linked.isAromatic:
# OG2D4: 6-mem aromatic carbonyl oxygen (nucleic bases)
atom.atomType = "OG2D4"
elif atom_linked.numRingAtoms[0] == 5:
if not atom_linked.isKetone and (
atom_linked.isAmide
or atom_linked.isEster):
if not atom.isDeprotonatedOxygen:
# OG2D1: carbonyl O: amides, esters, [neutral] carboxylic acids, aldehydes, uera
atom.atomType = "OG2D1"
elif atom.num_linkages == 2 and atom.numHydrogenAtoms == 1:
# OG311: hydroxyl oxygen
atom.atomType = "OG311"
else:
if not atom_linked.isKetone and (
atom_linked.isAmide
or atom_linked.isEster):
if not atom.isDeprotonatedOxygen:
# OG2D1: carbonyl O: amides, esters, [neutral] carboxylic acids, aldehydes, uera
atom.atomType = "OG2D1"
else:
# OG2D2: carbonyl O: negative groups: carboxylates, carbonate
atom.atomType = "OG2D2"
else:
# OG2D3: carbonyl O: ketones
atom.atomType = "OG2D3"
elif self.isTypeOG2D5(mol, i):
# OG2D5: CO2 oxygen
atom.atomType = "OG2D5"
elif atom_linked.atomType != None and atom_linked.atomType.lower(
) == "NG2O1".lower():
# OG2N1: NITB, nitrobenzene
atom.atomType = "OG2N1"
elif atom.isPOxide or atom.isSOxide:
if atom.num_linkages == 1:
# OG2P1: =O in phosphate or sulfate
atom.atomType = "OG2P1"
elif atom.num_linkages == 2 and atom.numHydrogenAtoms == 0:
# OG303: phosphate/sulfate ester oxygen
atom.atomType = "OG303"
elif atom.num_linkages == 2 and atom.numHydrogenAtoms == 1:
# OG311: hydroxyl oxygen
atom.atomType = "OG311"
elif atom.num_linkages == 2 and atom.numHydrogenAtoms == 1:
# OG311: hydroxyl oxygen
atom.atomType = "OG311"
elif atom.num_linkages == 2 and atom.numCarbonAtoms == 2:
# OG301: ether -O- !SHOULD WE HAVE A SEPARATE ENOL ETHER??? IF YES, SHOULD WE MERGE IT WITH OG3R60???
atom.atomType = "OG301"
if atom.isEster and atom.num_linkages == 2 and atom.numCarbonAtoms == 2:
# OG302: ester -O-
atom.atomType = "OG302"
elif self.isTypeOG304(mol, i):
# OG304: linkage oxygen in pyrophosphate/pyrosulphate
atom.atomType = "OG304"
elif not atom.isEster and atom.isDeprotonatedOxygen and (
atom.numCarbonAtoms == 1
or atom.numNitrogenAtoms == 1):
# OG312: ionized alcohol oxygen
atom.atomType = "OG312"
else:
if atom.isFuran:
# OG2R50: FURA, furan
atom.atomType = "OG2R50"
elif atom.isFuranose:
# OG3C51: 5-mem furanose ring oxygen (ether)
atom.atomType = "OG3C51"
elif atom.numRingAtoms[0] == 6:
# OG3R60: O in 6-mem cyclic enol ether (PY01, PY02) or ester
atom.atomType = "OG3R60"
if not self.linkedCarbonHasDoundBond(mol, i):
# OG3C61: DIOX, dioxane, ether in 6-membered ring !SHOULD WE MERGE THIS WITH OG3R60???
atom.atomType = "OG3C61"
elif atom.numRingAtoms[
0] == 3 and atom.num_linkages == 2 and atom.numCarbonAtoms == 2:
# OG3C31: epoxide oxygen, 1EOX, 1BOX, sc
atom.atomType = "OG3C31"
i += 1
def setAtomTypingNitrogen(self, mol):
num_atoms = len(mol.atoms)
atom = Atom()
iminCarbonIndex = -1
i = 0
while i < num_atoms:
atom = mol.atoms[i]
if atom.element.lower() == "N".lower():
# NG1T1: N for cyano group
if self.getIndexAtomType(mol, i, "CG1N1") != -1:
atom.atomType = "NG1T1"
# NG2D1: N for neutral imine/Schiff's base (C=N-R, acyclic amidine, gunaidine)
# NG2P1: N for protonated imine/Schiff's base (C=N(+)H-R, acyclic amidinium, guanidinium)
iminCarbonIndex = self.getIndexOfImineCarbon(mol, i)
if iminCarbonIndex != -1:
if not mol.atoms[iminCarbonIndex].isProtonatedImineGroup:
atom.atomType = "NG2D1"
else:
atom.atomType = "NG2P1"
if atom.isAmide:
if atom.num_linkages == 3:
if atom.numHydrogenAtoms == 0:
# NG2S0: N,N-disubstituted amide, proline N (CO=NRR')
atom.atomType = "NG2S0"
elif atom.numHydrogenAtoms == 1:
# NG2S1: peptide nitrogen (CO=NHR)
atom.atomType = "NG2S1"
elif atom.numHydrogenAtoms == 2:
# NG2S2: terminal amide nitrogen (CO=NH2)
atom.atomType = "NG2S2"
if atom.isRingAtom:
if not atom.isBridgingAtom:
if atom.isAmide and atom.numRingAtoms[0] == 4:
# NG2R43: amide in 4-memebered ring (planar), AZDO, lsk
atom.atomType = "NG2R43"
elif atom.numRingAtoms[0] == 5:
if not atom.isProtonatedNitrogen and atom.num_linkages == 2 and atom.numHydrogenAtoms == 0:
# NG2R50: double bound neutral 5-mem planar ring, purine N7
atom.atomType = "NG2R50"
elif not atom.isProtonatedNitrogen and atom.num_linkages == 3:
if atom.isAromatic:
# NG2R51: single bound neutral 5-mem planar (all atom types sp2) ring, his, trp pyrrole (fused)
atom.atomType = "NG2R51"
if self.isTypeNG2R53(mol, i):
# NG2R53: amide in 5-memebered NON-SP2 ring (slightly pyramidized), 2PDO, kevo
atom.atomType = "NG2R53"
if self.isBipyrroleNitrogen(mol, i):
# NG2R57: 5-mem ring, bipyrroles
atom.atomType = "NG2R57"
if not atom.isAromatic and (
atom.numHydrogenAtoms == 0
or atom.numHydrogenAtoms
== 1) and not atom.isAmide:
# NG3C51: secondary sp3 amine in 5-membered ring
atom.atomType = "NG3C51"
elif iminCarbonIndex != -1 and mol.atoms[
iminCarbonIndex].isProtonatedImineGroup:
# NG2R52: protonated schiff base, amidinium, guanidinium in 5-membered ring, HIS, 2HPP, kevo
atom.atomType = "NG2R52"
elif atom.isAromatic and atom.num_linkages == 3 and not self.hasDoubleBond(
mol, i):
# NG2R51: single bound neutral 5-mem planar (all atom types sp2) ring, his, trp pyrrole (fused)
atom.atomType = "NG2R51"
elif atom.numRingAtoms[0] == 6:
if atom.isAromatic and atom.numHydrogenAtoms == 0:
# NG2R60: double bound neutral 6-mem planar ring, pyr1, pyzn
atom.atomType = "NG2R60"
if atom.isAromatic and (self.hasCarbonyl(mol, i) or
atom.isProtonatedNitrogen):
# NG2R61: single bound neutral 6-mem planar ring imino nitrogen; glycosyl linkage
atom.atomType = "NG2R61"
if self.isTypeNG2R62(mol, i):
# NG2R62: double bound 6-mem planar ring with heteroatoms in o or m, pyrd, pyrm
atom.atomType = "NG2R62"
if self.isTypeNG2R67(mol, i):
# NG2R67: 6-mem planar ring substituted with 6-mem planar ring (N-phenyl pyridinones etc.)
atom.atomType = "NG2R67"
else:
if self.isTypeNG2RC0(mol, i):
# NG2RC0: 6/5-mem ring bridging N, indolizine, INDZ, kevo
atom.atomType = "NG2RC0"
if not atom.isAmide and not atom.isProtonatedNitrogen and iminCarbonIndex == -1:
if self.isTypeNG301(mol, i):
# NG301: neutral trimethylamine nitrogen
atom.atomType = "NG301"
elif atom.numRingAtoms[0] != 5 and self.isTypeNG311(
mol, i):
# NG311: neutral dimethylamine nitrogen
atom.atomType = "NG311"
elif self.isTypeNG321(mol, i):
# NG321: neutral methylamine nitrogen
atom.atomType = "NG321"
elif atom.num_linkages == 3 and atom.numHydrogenAtoms == 3:
# NG331: neutral ammonia nitrogen
atom.atomType = "NG331"
elif self.isTypeNG3N1(mol, i):
# NG3N1: N in hydrazine, HDZN
atom.atomType = "NG3N1"
# NG2S3: external amine ring nitrogen (planar/aniline), phosphoramidate (PO3-NR2), sulfamate (SO3-NR2)
if self.isTypeNG2S3(mol, i):
atom.atomType = "NG2S3"
# NG2O1: NITB, nitrobenzene
if atom.num_linkages == 3 and atom.numOxygenAtoms == 2 and atom.numCarbonAtoms == 1:
atom.atomType = "NG2O1"
if not atom.isRingAtom and atom.isProtonatedNitrogen and atom.numHydrogenAtoms == 0:
# NG3P0: quarternary N+, choline
atom.atomType = "NG3P0"
elif atom.isRingAtom and not atom.isAromatic and atom.isProtonatedNitrogen and atom.numHydrogenAtoms == 1:
# NG3P1: tertiary NH+ (PIP)
atom.atomType = "NG3P1"
elif atom.isRingAtom and not atom.isAromatic and atom.isProtonatedNitrogen and atom.numHydrogenAtoms == 2:
# NG3P2: secondary NH2+ (proline)
atom.atomType = "NG3P2"
elif not atom.isRingAtom and atom.isProtonatedNitrogen and atom.numHydrogenAtoms == 3:
# NG3P3: primary NH3+, phosphatidylethanolamine
atom.atomType = "NG3P3"
i += 1
def setAtomTypeForHalogens(self, mol):
num_atoms = len(mol.atoms)
atom = Atom()
atom_linked = Atom()
index = -1
num_element = 0
i = 0
while i < num_atoms:
atom = mol.atoms[i]
if atom.element.lower() == "CL".lower():
atom_linked = mol.atoms[atom.linkage[0]]
if atom_linked.isAromatic and atom_linked.numRingAtoms[0] == 6:
# CLGR1: CHLB, chlorobenzene
atom.atomType = "CLGR1"
else:
num_element = self.countSpecificElement(
mol, atom.linkage[0], "CL")
if num_element == 1 or num_element == 2:
# CLGA1: CLET, DCLE, chloroethane, 1,1-dichloroethane
atom.atomType = "CLGA1"
elif num_element == 3:
# CLGA3: TCLE, 1,1,1-trichloroethane
atom.atomType = "CLGA3"
elif atom.element.lower() == "BR".lower():
atom_linked = mol.atoms[atom.linkage[0]]
if atom_linked.isAromatic and atom_linked.numRingAtoms[0] == 6:
# BRGR1: BROB, bromobenzene
atom.atomType = "BRGR1"
else:
num_element = self.countSpecificElement(
mol, atom.linkage[0], "BR")
if num_element == 1:
# BRGA1: BRET, bromoethane
atom.atomType = "BRGA1"
elif num_element == 2:
# BRGA2: DBRE, 1,1-dibromoethane
atom.atomType = "BRGA2"
elif num_element == 3:
# BRGA3: TBRE, 1,1,1-dibromoethane
atom.atomType = "BRGA3"
elif atom.element.lower() == "I".lower():
atom_linked = mol.atoms[atom.linkage[0]]
if atom_linked.isAromatic and atom_linked.numRingAtoms[0] == 6:
# IGR1: IODB, iodobenzene
atom.atomType = "IGR1"
elif atom.element.lower() == "F".lower():
atom_linked = mol.atoms[atom.linkage[0]]
if atom_linked.isAromatic:
# FGR1: aromatic flourine
atom.atomType = "FGR1"
else:
num_element = self.countSpecificElement(
mol, atom.linkage[0], "F")
if num_element == 1:
# FGA1: aliphatic fluorine, monofluoro
atom.atomType = "FGA1"
elif num_element == 2:
# FGA2: aliphatic fluorine, difluoro
atom.atomType = "FGA2"
elif num_element == 3:
# FGA3: aliphatic fluorine, trifluoro
atom.atomType = "FGA3"
elif num_element == 4:
# FGP1: anionic F, for ALF4 AlF4-
atom.atomType = "FGP1"
i += 1
