| 1 | #!@PYTHON@
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| 2 | #
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| 3 | # Re-creates neighbours in .data file for water molecules OH2, H1, H2 being consecutive
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| 4 |
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| 5 | import sys, math
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| 6 |
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| 7 | if len(sys.argv) < 3:
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| 8 | print "Usage: "+sys.argv[0]+" <file> <output>"
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| 9 | sys.exit(1)
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| 10 |
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| 11 | input=open(sys.argv[1],"r")
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| 12 | output=open(sys.argv[2],"w")
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| 13 | outputXYZ=open(sys.argv[2]+".xyz","w")
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| 14 | outputXYZ.write("1734\n # test\n")
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| 15 | x=[0,0,0]
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| 16 | for line in input:
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| 17 | if "#" in line:
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| 18 | output.write(line)
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| 19 | continue
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| 20 | if " OH2" in line:
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| 21 | entries=line.split()
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| 22 | entries[0]=str(int(entries[0])-1)
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| 23 | entries[5]=str(int(entries[5])+0)
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| 24 | entries[6]=str(int(entries[6])+1)
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| 25 | output.write("%s\tOT\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % (entries[0], entries[2], entries[3], entries[4], entries[5], entries[6], entries[7], entries[8]))
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| 26 | outputXYZ.write("O\t%s\t%s\t%s\n" % (entries[2], entries[3], entries[4]))
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| 27 | continue
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| 28 | if " H1" in line:
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| 29 | entries=line.split()
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| 30 | entries[0]=str(int(entries[0])-1)
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| 31 | entries[5]=str(int(entries[5])-2)
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| 32 | output.write("%s\tHT\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % (entries[0], entries[2], entries[3], entries[4], entries[5], entries[6], entries[7], entries[8]))
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| 33 | outputXYZ.write("H\t%s\t%s\t%s\n" % (entries[2], entries[3], entries[4]))
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| 34 | continue
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| 35 | if " H2" in line:
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| 36 | entries=line.split()
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| 37 | entries[0]=str(int(entries[0])-1)
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| 38 | entries[5]=str(int(entries[5])-3)
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| 39 | output.write("%s\tHT\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % (entries[0], entries[2], entries[3], entries[4], entries[5], entries[6], entries[7], entries[8]))
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| 40 | outputXYZ.write("H\t%s\t%s\t%s\n" % (entries[2], entries[3], entries[4]))
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| 41 | continue
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| 42 | entries=line.split()
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| 43 | x[2]=str(float(entries[2]))
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| 44 | x[1]=str(float(entries[3]))
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| 45 | x[0]=str(float(entries[4]))
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| 46 | for n in range(3):
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| 47 | entries[2+n]=x[n]
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| 48 | output.write("%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % (entries[0], entries[1], entries[2], entries[3], entries[4], entries[5], entries[6], entries[7], entries[8]))
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| 49 | outputXYZ.write("%s\t%s\t%s\t%s\n" % (entries[1], entries[2], entries[3], entries[4]))
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| 50 |
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| 51 | sys.exit(0)
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