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#!/usr/bin/env python
# Copyright 2008 Nanorex, Inc. See LICENSE file for details.
"""
SplitDotInFile.py
Splits an AMBER .in file containing residues with internal coordinates
into multiple .in_frag files, one for each residue.
"""
import sys
def parseInFile(fileName):
file = open(fileName)
lines = file.readlines()
file.close()
inFile = False
nextIndex = -1
line1 = line2 = line3 = line4 = line5 = line6 = ''
for line in lines:
line6 = line5
line5 = line4
line4 = line3
line3 = line2
line2 = line1
line1 = line
columns = line.strip().split()
if (len(columns) < 10):
if (inFile):
# After the last line in a residue, there's a blank
# line, which will get us here.
nextIndex = -1
inFile = False
out.close()
continue
if (columns[0] == '1' and columns[1] == 'DUMM' and columns[2] == 'DU'):
# This is the start of a new residue (dummy atoms for
# defining the internal coordinate system). Earlier lines
# (saved in lineX) contain various info about the residue.
# We extract short and long names to build the filename.
fullName = line6.strip()
fullName = fullName.replace(' ', '_')
fullName = fullName.replace('*', '_x_')
fullName = fullName.replace('/', '_s_')
fullName = fullName.replace("'", '_p_')
fullName = fullName.replace('[', '_os_')
fullName = fullName.replace(']', '_cs_')
fullName = fullName.replace('(', '_op_')
fullName = fullName.replace(')', '_cp_')
cols4 = line4.strip().split()
shortName = cols4[0]
newFileName = "%s_%s.in_frag" % (shortName, fullName)
out = open(newFileName, 'w')
nextIndex = 1
inFile = True
warned = False
if (inFile):
# Within the residue itself, column 0 is an index number
# which usually increments sequentially.
index = int(columns[0])
igraph = columns[1]
isymbl = columns[2]
itree = columns[3]
na = int(columns[4])
nb = int(columns[5])
nc = int(columns[6])
r = float(columns[7])
theta = float(columns[8])
phi = float(columns[9])
print >>out, "%3d %4s %2s %s %3d %3d %3d %10.3f %10.3f %10.3f" % (nextIndex, igraph, isymbl, itree, na, nb, nc, r, theta, phi)
if (index != nextIndex and not warned):
print "%s %s index not sequential" % (fileName, newFileName)
warned = True
nextIndex = nextIndex + 1
if (__name__ == '__main__'):
parseInFile(sys.argv[1])
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