mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-03 21:44:30 +08:00
24f1737839
* remove all of the "from __future__" imports * remove the first batch of rdkit.six imports/uses * next step of rdkit.six removal * removing xrange, range, and some maps * next round of removals * next round of cleanups * fix inchi test * last bits of "from rdkit.six" are gone * and the last of the six stuff is gone * strange importlib problem
73 lines
1.6 KiB
Python
Executable File
73 lines
1.6 KiB
Python
Executable File
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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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