comparison spring_cross.py @ 38:80a4b98121b6 draft

"planemo upload commit 22cd6b0fa88ce0ddc4052beab306f5ba10754f12"
author guerler
date Wed, 25 Nov 2020 17:38:24 +0000
parents 0be0af9e695d
children 172398348efd
comparison
equal deleted inserted replaced
37:0be0af9e695d 38:80a4b98121b6
5 from spring_package.DBKit import createFile 5 from spring_package.DBKit import createFile
6 from spring_package.Molecule import Molecule 6 from spring_package.Molecule import Molecule
7 7
8 8
9 def getId(line): 9 def getId(line):
10 line = line.split()[0] 10 line = line.strip()
11 if len(line) != 6 or line[4:5] != "_":
12 raise Exception("Invalid list entry (`PDB_CHAIN`): %s." % line)
11 return line[:4].upper() + line[4:6] 13 return line[:4].upper() + line[4:6]
12 14
13 15
14 def main(args): 16 def main(args):
15 logFile = open(args.log, "w") 17 logFile = open(args.log, "w")
59 61
60 62
61 if __name__ == "__main__": 63 if __name__ == "__main__":
62 parser = argparse.ArgumentParser(description='List filtering.') 64 parser = argparse.ArgumentParser(description='List filtering.')
63 parser.add_argument('-l', '--list', help='List of PDB chains [PDB_CHAIN]', required=True) 65 parser.add_argument('-l', '--list', help='List of PDB chains [PDB_CHAIN]', required=True)
64 parser.add_argument('-i', '--index', help='PDB Database Index file (dbkit_index)', required=True) 66 parser.add_argument('-i', '--index', help='PDB Database Index file (ffindex)', required=True)
65 parser.add_argument('-d', '--database', help='PDB Database files (dbkit)', required=True) 67 parser.add_argument('-d', '--database', help='PDB Database files (ffdata)', required=True)
66 parser.add_argument('-o', '--output', help='Output file', required=True) 68 parser.add_argument('-o', '--output', help='Output file', required=True)
67 parser.add_argument('-t', '--temp', help='Temporary Directory', required=True) 69 parser.add_argument('-t', '--temp', help='Temporary Directory', required=True)
68 parser.add_argument('-g', '--log', help='Log File', required=True) 70 parser.add_argument('-g', '--log', help='Log File', required=True)
69 args = parser.parse_args() 71 args = parser.parse_args()
70 main(args) 72 main(args)