Документ взят из кэша поисковой машины. Адрес оригинального документа : http://kodomo.fbb.msu.ru/hg/allpy/raw-rev/8565652a4019 Дата изменения: Unknown Дата индексирования: Tue Oct 2 07:37:26 2012 Кодировка:

# HG changeset patch
# User boris
# Date 1287923444 -14400
# Node ID 8565652a4019ebc967ca35e71664dcb1f7451e74
# Parent d2b53635be05718fe40cb2340ffc3f270e4530cc
geometrical_core: parser completed

diff -r d2b53635be05 -r 8565652a4019 geometrical_core/geometrical_core.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/geometrical_core/geometrical_core.py Sun Oct 24 16:30:44 2010 +0400
@@ -0,0 +1,40 @@
+"""
+Geometrical Core building tool
+version 2.0
+"""
+
+from allpy.lib import config, project, block
+Block = block.Block
+Project = project.Project
+import argparse
+
+r = argparse.FileType('r')
+w = argparse.FileType('w')
+c = config
+
+p = argparse.ArgumentParser(
+description='Geometrical Core building tool.',
+epilog='''1) Distance spreading [angstrom]
+2) -1 timeout means running Bron-Kerbosh algorithm without timeout
+3) Alternative core new aa part: read documentation for more information
+4) Superposition core identifier: main core is 0, first alternative is 1 etc. ''',
+formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+#~ argument_default=argparse.SUPPRESS,
+)
+
+p.add_argument('-v','--version',action='version',version='%(prog)s 2.0')
+p.add_argument('-i',help='Input alignment file',metavar='FILE',type=r,required=True)
+p.add_argument('-c',help='PDB names conformity file',metavar='FILE',type=r)
+p.add_argument('-l',help='Output list file',metavar='FILE',type=w)
+p.add_argument('-f',help='Output fasta file',metavar='FILE',type=w)
+p.add_argument('-g',help='Output msf file',metavar='FILE',type=w)
+p.add_argument('-p',help='Output pdb file',metavar='FILE',type=w)
+p.add_argument('-s',help='Output spt file',metavar='FILE',type=w)
+p.add_argument('-d',help='Distance spreading',metavar='DELTA',type=float,default=c.delta)
+p.add_argument('-m',help='Min core size',metavar='MIN_SIZE',type=int,default=c.minsize)
+p.add_argument('-t',help='Bron-Kerbosh algorithm timeout',type=int,default=c.timeout)
+p.add_argument('-n',help='Alternative core new aa part',type=float,default=c.ac_new_atoms)
+p.add_argument('-a',help='Cores count',metavar='NEW_ATOMS',type=int,default=c.ac_count)
+p.add_argument('-x',help='Superposition core identifier',metavar='SUPER',type=int,default=0)
+
+args = p.parse_args()