1.1 --- /dev/null	Thu Jan 01 00:00:00 1970 +0000
     1.2 +++ b/geometrical_core/geometrical_core.py	Sun Oct 24 16:30:44 2010 +0400
     1.3 @@ -0,0 +1,40 @@
     1.4 +"""
     1.5 +Geometrical Core building tool
     1.6 +version 2.0
     1.7 +"""
     1.8 +
     1.9 +from allpy.lib import config, project, block
    1.10 +Block = block.Block
    1.11 +Project = project.Project
    1.12 +import argparse
    1.13 +
    1.14 +r = argparse.FileType('r')
    1.15 +w = argparse.FileType('w')
    1.16 +c = config
    1.17 +
    1.18 +p = argparse.ArgumentParser(
    1.19 +description='Geometrical Core building tool.',
    1.20 +epilog='''1) Distance spreading [angstrom]
    1.21 +2) -1 timeout means running Bron-Kerbosh algorithm without timeout
    1.22 +3) Alternative core new aa part: read documentation for more information
    1.23 +4) Superposition core identifier: main core is 0, first alternative is 1 etc. ''',
    1.24 +formatter_class=argparse.ArgumentDefaultsHelpFormatter, 
    1.25 +#~ argument_default=argparse.SUPPRESS,
    1.26 +)
    1.27 +
    1.28 +p.add_argument('-v','--version',action='version',version='%(prog)s 2.0')
    1.29 +p.add_argument('-i',help='Input alignment file',metavar='FILE',type=r,required=True)
    1.30 +p.add_argument('-c',help='PDB names conformity file',metavar='FILE',type=r)
    1.31 +p.add_argument('-l',help='Output list file',metavar='FILE',type=w)
    1.32 +p.add_argument('-f',help='Output fasta file',metavar='FILE',type=w)
    1.33 +p.add_argument('-g',help='Output msf file',metavar='FILE',type=w)
    1.34 +p.add_argument('-p',help='Output pdb file',metavar='FILE',type=w)
    1.35 +p.add_argument('-s',help='Output spt file',metavar='FILE',type=w)
    1.36 +p.add_argument('-d',help='Distance spreading',metavar='DELTA',type=float,default=c.delta)
    1.37 +p.add_argument('-m',help='Min core size',metavar='MIN_SIZE',type=int,default=c.minsize)
    1.38 +p.add_argument('-t',help='Bron-Kerbosh algorithm timeout',type=int,default=c.timeout)
    1.39 +p.add_argument('-n',help='Alternative core new aa part',type=float,default=c.ac_new_atoms)
    1.40 +p.add_argument('-a',help='Cores count',metavar='NEW_ATOMS',type=int,default=c.ac_count)
    1.41 +p.add_argument('-x',help='Superposition core identifier',metavar='SUPER',type=int,default=0)
    1.42 +
    1.43 +args = p.parse_args()