def fix_pdb(inpath, outpath):
with open(inpath) as fd:
data = fd.readlines()
i = 1
while True:
if not len(pdbformat.getAtomStr(data, i + 1)):
break
atomStr0 = pdbformat.getAtomStr(data, i - 1)
atomStr1 = pdbformat.getAtomStr(data, i)
atomStr2 = pdbformat.getAtomStr(data, i + 1)
if (
atomStr1[0] == "H"
and atomStr1[-1] == "2"
and not atomStr0[0] == "H"
and atomStr2[0] == "H"
and atomStr2[-1] == "3"
):
newStr1 = atomStr1[:-1] + "1"
newStr2 = atomStr2[:-1] + "2"
pdbformat.setAtomStr(data, i, newStr1)
pdbformat.setAtomStr(data, i + 1, newStr2)
i += 2
print "Atom", pdbformat.getAtomNum(data, i), "Residue", pdbformat.getResidueNum(
data, i
), pdbformat.getResidueName(data, i), atomStr1, "->", newStr1
print "Atom", pdbformat.getAtomNum(data, i + 1), "Residue", pdbformat.getResidueNum(
data, i + 1
), pdbformat.getResidueName(data, i), atomStr2, "->", newStr2
else:
i += 1
with open(outpath, "w") as fd:
fd.write("".join(data))
def remove_hydrogens(data):
"""
data :: [[str]]
-> [[str]]
"""
newdata = []
i = 0
while i < len(data):
atomStr = pdbformat.getAtomStr(data, i)
if not atomStr: break
if 'H' not in atomStr:
newdata.append( data[i] )
else:
print 'Discarding line', repr(data[i])
i += 1
return newdata