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from __future__ import print_function
from Chem import rdmol
from Chem.rdmol import Atom, Bond, Mol
def ParseAtomBlock(lines, mol, nAtoms):
for i in range(nAtoms):
line = lines[i]
pX = float(line[0:10])
pY = float(line[10:20])
pZ = float(line[20:30])
symb = line[31:34].strip()
newAt = rdmol.Atom(symb)
newAt.setPos(pX, pY, pZ)
chg = int(line[36:39])
if chg in [1, 2, 3, 5, 6, 7]:
newAt.setFormalCharge(4 - chg)
# parse valence
# parse rxn component
mol.addAtom(newAt)
bondMap = {1: Bond.SINGLE, 2: Bond.DOUBLE, 3: Bond.TRIPLE, 4: Bond.AROMATIC}
def ParseBondBlock(lines, mol, nBonds):
for i in range(nBonds):
line = lines[i]
id1 = int(line[0:3]) - 1
id2 = int(line[3:6]) - 1
order = int(line[6:9])
order = bondMap.get(order, Bond.OTHER)
b = Bond(order)
b.setOwningMol(mol)
b.setBeginAtomIdx(id1)
b.setEndAtomIdx(id2)
mol.addBond(b)
def ParseMolBlock(lines, mol):
header = lines[0:3]
counts = lines[3]
nAtoms = int(counts[0:3])
nBonds = int(counts[3:6])
nLists = int(counts[6:9])
chiralFlag = int(counts[12:15])
nsText = int(counts[15:18])
nRxnComponents = int(counts[18:21])
nReactants = int(counts[21:24])
nProducts = int(counts[24:27])
nIntermediates = int(counts[27:30])
ParseAtomBlock(lines[4:], mol, nAtoms)
ParseBondBlock(lines[4 + nAtoms:], mol, nBonds)
if __name__ == '__main__':
import sys
fName = sys.argv[1]
inF = open(fName, 'r')
lines = inF.readlines()
m = rdmol.Mol()
ParseMolBlock(lines, m)
print(m.getNumAtoms())
m.debugMol()
print(rdmol.MolToCDXML(m))
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