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