| 1 | #!@PYTHON@
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| 2 | #
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| 3 | # if a given block from a PDB was cut out, water molecules may have been cut through. This is bad for the neighbour numbers in the TIP3 potential.
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| 4 | # Hence, this script removes all dangling atoms.
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| 5 |
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| 6 | import sys, string, re, math
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| 7 | wrerr = sys.stderr.write
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| 8 | wrout = sys.stdout.write
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| 9 |
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| 10 | # check for parameters
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| 11 | if len(sys.argv) < 3:
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| 12 | wrerr("Usage: "+sys.argv[0]+" <datafile> <offset to SeqID>\n")
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| 13 | sys.exit(1)
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| 14 |
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| 15 | input = open(sys.argv[1], "r")
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| 16 | output = open(sys.argv[1]+".new", "w")
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| 17 | offsetID=int(sys.argv[2])
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| 18 |
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| 19 | ids={}
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| 20 | for line in input:
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| 21 | if "#" in line:
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| 22 | continue
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| 23 | if "END" in line:
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| 24 | break
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| 25 | entries=line.split()
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| 26 | if "TIP3" in line:
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| 27 | id=int(entries[offsetID])
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| 28 | if ids.has_key(id):
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| 29 | ids[id]=ids[id]+1
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| 30 | else:
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| 31 | ids[id]=1
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| 32 | #wrout("for key %d: %d present\n" % (id, ids[id]))
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| 33 |
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| 34 | wrout("The following ids will be removed: ")
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| 35 | for key in ids.keys():
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| 36 | if ids[key] < 3:
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| 37 | wrout("(%d = %d) " % (key, ids[key]))
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| 38 | wrout("\n")
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| 39 |
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| 40 | input.seek(0)
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| 41 | origin=[0., 0., 0.]
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| 42 | id=1
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| 43 | for line in input:
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| 44 | if "#" in line:
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| 45 | output.write(line)
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| 46 | continue
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| 47 | if "END" in line:
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| 48 | output.write(line)
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| 49 | break
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| 50 | entries=line.split()
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| 51 | if "TIP3" in line:
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| 52 | if (ids[int(entries[offsetID])] == 3):
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| 53 | #wrout("%d present, keeping line: %s" % (ids[id], line))
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| 54 | output.write("ATOM %6d %-4s%3s%2s %4s %8.3f%8.3f%8.3f%6.2f%6.2f %4s%2s \n" % (id, entries[2], entries[3], entries[4], entries[5], float(entries[6])-origin[0], float(entries[7])-origin[1], float(entries[8])-origin[2], float(entries[9]), float(entries[10]), entries[11], entries[2][0]))
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| 55 | id+=1
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| 56 | else:
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| 57 | wrout("Only %d present, dropping line: %s" % (ids[int(entries[offsetID])], line))
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| 58 | else:
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| 59 | output.write("ATOM %6d %-4s %3s%3s%4s %8.3f%8.3f%8.3f%6.2f%6.2f %4s%2s \n" % (id, entries[2], entries[3], entries[4], entries[5], float(entries[6])-origin[0], float(entries[7])-origin[1], float(entries[8])-origin[2], float(entries[9]), float(entries[10]), entries[11], entries[2][0]))
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| 60 | id+=1
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| 61 | input.close()
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| 62 | output.close()
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