allpy
changeset 1055:6c7e74a75d13 1.4.2
Merge fix of typo in algorithm name Bron?Kerbosch from default into 1.4.2
| author | Boris Nagaev <bnagaev@gmail.com> |
|---|---|
| date | Tue, 03 Apr 2012 12:25:56 +0400 |
| parents | 027f0f2f5417 53690e470eff |
| children | 71e60ae2cd1a |
| files | allpy/base.py allpy/config.py allpy/graph.py allpy/structure.py blocks3d/blocks3d.py geometrical_core/geometrical-core pair_cores/pair_cores.py sequence_based_blocks_search/blocks_finder.py |
| diffstat | 5 files changed, 13 insertions(+), 13 deletions(-) [+] |
line diff
1.1 --- a/blocks3d/blocks3d.py Mon Mar 26 22:09:09 2012 +0400 1.2 +++ b/blocks3d/blocks3d.py Tue Apr 03 12:25:56 2012 +0400 1.3 @@ -22,7 +22,7 @@ 1.4 p = argparse.ArgumentParser( 1.5 description='Blocks3D', 1.6 epilog='''1) Distance spreading [angstrom] 1.7 -2) -1 timeout means running Bron-Kerbosh algorithm without timeout''', 1.8 +2) -1 timeout means running Bron-Kerbosch algorithm without timeout''', 1.9 formatter_class=argparse.ArgumentDefaultsHelpFormatter, 1.10 ) 1.11 1.12 @@ -36,8 +36,8 @@ 1.13 p.add_argument('-d',help='Distance spreading',metavar='float',type=f_nng,default=c.delta) 1.14 p.add_argument('-e',help='Ignore cores, owned by one SS element',type=bool, default=False) 1.15 p.add_argument('-m',help='Min block width',metavar='int',type=pos,default=c.min_width) 1.16 -p.add_argument('-t',help='Bron-Kerbosh (couple cores) timeout (-1 - unlimited)',metavar='int',type=timeout,default=0) 1.17 -p.add_argument('-T',help='Bron-Kerbosh (blocks) timeout (-1 - unlimited)',metavar='int',type=timeout,default=c.timeout_2) 1.18 +p.add_argument('-t',help='Bron-Kerbosch (couple cores) timeout (-1 - unlimited)',metavar='int',type=timeout,default=0) 1.19 +p.add_argument('-T',help='Bron-Kerbosch (blocks) timeout (-1 - unlimited)',metavar='int',type=timeout,default=c.timeout_2) 1.20 1.21 args = p.parse_args() 1.22
2.1 --- a/blocks3d/wt/locales/blocks3d.xml Mon Mar 26 22:09:09 2012 +0400 2.2 +++ b/blocks3d/wt/locales/blocks3d.xml Tue Apr 03 12:25:56 2012 +0400 2.3 @@ -6,10 +6,10 @@ 2.4 <message id='delta'>Distance spreading</message> 2.5 <message id='min_block_width'>Min block width</message> 2.6 <message id='timeout'> 2.7 - Bron-Kerbosh (couple cores) timeout (seconds, -1 - unlimited) 2.8 + Bron-Kerbosch (couple cores) timeout (seconds, -1 - unlimited) 2.9 </message> 2.10 <message id='timeout2'> 2.11 - Bron-Kerbosh (blocks) timeout (seconds, -1 - unlimited) 2.12 + Bron-Kerbosch (blocks) timeout (seconds, -1 - unlimited) 2.13 </message> 2.14 <message id='Run'>Run</message> 2.15 <message id='Reset'>Reset</message>
3.1 --- a/geometrical_core/geometrical-core Mon Mar 26 22:09:09 2012 +0400 3.2 +++ b/geometrical_core/geometrical-core Tue Apr 03 12:25:56 2012 +0400 3.3 @@ -22,7 +22,7 @@ 3.4 p = argparse.ArgumentParser( 3.5 description='Geometrical Core building tool.', 3.6 epilog='''1) Distance spreading [angstrom] 3.7 -2) -1 timeout means running Bron-Kerbosh algorithm without timeout 3.8 +2) -1 timeout means running Bron-Kerbosch algorithm without timeout 3.9 3) Alternative core new aa part: read documentation for more information 3.10 4) Superposition core: main core is 0, first alternative is 1 etc. ''', 3.11 formatter_class=argparse.ArgumentDefaultsHelpFormatter, 3.12 @@ -43,7 +43,7 @@ 3.13 p.add_argument('-e',help='Ignore cores, owned by one SS element',type=bool, default=False) 3.14 p.add_argument('-m',help='Min core size', 3.15 metavar='int',type=pos,default=c.minsize) 3.16 -p.add_argument('-t',help='Bron-Kerbosh algorithm timeout', 3.17 +p.add_argument('-t',help='Bron-Kerbosch algorithm timeout', 3.18 metavar='int',type=timeout,default=c.timeout) 3.19 p.add_argument('-n',help='Alternative core new aa part', 3.20 metavar='float',type=part,default=c.ac_new_atoms)
4.1 --- a/pair_cores/pair_cores.py Mon Mar 26 22:09:09 2012 +0400 4.2 +++ b/pair_cores/pair_cores.py Tue Apr 03 12:25:56 2012 +0400 4.3 @@ -40,8 +40,8 @@ 4.4 * out_high_blocks_html_file -- output HTML file with blocks of multiple sequences 4.5 * out_high_blocks_pymol_file -- output PyMol file with blocks of multiple sequences 4.6 * blocks3d -- if old (graph-based) blocks algorithm is used 4.7 - * blocks3d_timeout -- Bron-Kerbosh (blocks3d) timeout (-1 - unlimited) 4.8 - * pair_timeout -- Bron-Kerbosh (pair cores) timeout (-1 - unlimited) 4.9 + * blocks3d_timeout -- Bron-Kerbosch (blocks3d) timeout (-1 - unlimited) 4.10 + * pair_timeout -- Bron-Kerbosch (pair cores) timeout (-1 - unlimited) 4.11 """ 4.12 if markup_file: 4.13 input_file = markup_file 4.14 @@ -128,9 +128,9 @@ 4.15 p.add_argument('--high-blocks-html',help='Output HTML file with high blocks',metavar='FILE',type=w) 4.16 p.add_argument('--high-blocks-pymol',help='Output PyMol file with high blocks',metavar='FILE',type=w) 4.17 p.add_argument('--blocks3d',help='Use blocks3d algorithm for high blocks',action='store_true') 4.18 - p.add_argument('--blocks3d-timeout',help='Bron-Kerbosh (blocks3d) timeout (-1 - unlimited)', 4.19 + p.add_argument('--blocks3d-timeout',help='Bron-Kerbosch (blocks3d) timeout (-1 - unlimited)', 4.20 metavar='int',type=timeout,default=config.timeout_2) 4.21 - p.add_argument('--pair-timeout',help='Bron-Kerbosh (pair cores) timeout (-1 - unlimited)', 4.22 + p.add_argument('--pair-timeout',help='Bron-Kerbosch (pair cores) timeout (-1 - unlimited)', 4.23 metavar='int',type=timeout,default=0) 4.24 args = p.parse_args() 4.25 homology_from_3d(markup_file=args.m, homology_file=args.y, max_delta=args.d, ignore_one_ss=args.e,
5.1 --- a/pair_cores/web/approot/locales/pair-cores-web.xml Mon Mar 26 22:09:09 2012 +0400 5.2 +++ b/pair_cores/web/approot/locales/pair-cores-web.xml Tue Apr 03 12:25:56 2012 +0400 5.3 @@ -10,13 +10,13 @@ 5.4 Use blocks3d algorithm for high blocks 5.5 </message> 5.6 <message id='pair.in.Blocks3D_timeout'> 5.7 - Bron-Kerbosh (blocks3d) timeout (-1 - unlimited) 5.8 + Bron-Kerbosch (blocks3d) timeout (-1 - unlimited) 5.9 </message> 5.10 <message id='pair.in.Error_one_input'> 5.11 Input alignment or input markup must be specified 5.12 </message> 5.13 <message id='pair.in.Pair_timeout'> 5.14 - Bron-Kerbosh (pair cores) timeout (-1 - unlimited) 5.15 + Bron-Kerbosch (pair cores) timeout (-1 - unlimited) 5.16 </message> 5.17 5.18 <message id='pair.main.Header'><h1>PairCores</h1></message>