Документ взят из кэша поисковой машины. Адрес оригинального документа : http://kodomo.fbb.msu.ru/hg/allpy/raw-rev/6c7e74a75d13
Дата изменения: Unknown
Дата индексирования: Fri Feb 28 02:52:34 2014
Кодировка:

# HG changeset patch
# User Boris Nagaev
# Date 1333441556 -14400
# Node ID 6c7e74a75d1351794b01b86bdbe018428e501694
# Parent 027f0f2f541705640e993039c61c1e86dc3556cd# Parent 53690e470effc82933aeca2aef31844eb180ad79
Merge fix of typo in algorithm name Bron?Kerbosch from default into 1.4.2

diff -r 027f0f2f5417 -r 6c7e74a75d13 blocks3d/blocks3d.py
--- a/blocks3d/blocks3d.py Mon Mar 26 22:09:09 2012 +0400
+++ b/blocks3d/blocks3d.py Tue Apr 03 12:25:56 2012 +0400
@@ -22,7 +22,7 @@
p = argparse.ArgumentParser(
description='Blocks3D',
epilog='''1) Distance spreading [angstrom]
-2) -1 timeout means running Bron-Kerbosh algorithm without timeout''',
+2) -1 timeout means running Bron-Kerbosch algorithm without timeout''',
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
)

@@ -36,8 +36,8 @@
p.add_argument('-d',help='Distance spreading',metavar='float',type=f_nng,default=c.delta)
p.add_argument('-e',help='Ignore cores, owned by one SS element',type=bool, default=False)
p.add_argument('-m',help='Min block width',metavar='int',type=pos,default=c.min_width)
-p.add_argument('-t',help='Bron-Kerbosh (couple cores) timeout (-1 - unlimited)',metavar='int',type=timeout,default=0)
-p.add_argument('-T',help='Bron-Kerbosh (blocks) timeout (-1 - unlimited)',metavar='int',type=timeout,default=c.timeout_2)
+p.add_argument('-t',help='Bron-Kerbosch (couple cores) timeout (-1 - unlimited)',metavar='int',type=timeout,default=0)
+p.add_argument('-T',help='Bron-Kerbosch (blocks) timeout (-1 - unlimited)',metavar='int',type=timeout,default=c.timeout_2)

args = p.parse_args()

diff -r 027f0f2f5417 -r 6c7e74a75d13 blocks3d/wt/locales/blocks3d.xml
--- a/blocks3d/wt/locales/blocks3d.xml Mon Mar 26 22:09:09 2012 +0400
+++ b/blocks3d/wt/locales/blocks3d.xml Tue Apr 03 12:25:56 2012 +0400
@@ -6,10 +6,10 @@
Distance spreading
Min block width

- Bron-Kerbosh (couple cores) timeout (seconds, -1 - unlimited)
+ Bron-Kerbosch (couple cores) timeout (seconds, -1 - unlimited)

- Bron-Kerbosh (blocks) timeout (seconds, -1 - unlimited)
+ Bron-Kerbosch (blocks) timeout (seconds, -1 - unlimited)

Run
Reset
diff -r 027f0f2f5417 -r 6c7e74a75d13 geometrical_core/geometrical-core
--- a/geometrical_core/geometrical-core Mon Mar 26 22:09:09 2012 +0400
+++ b/geometrical_core/geometrical-core Tue Apr 03 12:25:56 2012 +0400
@@ -22,7 +22,7 @@
p = argparse.ArgumentParser(
description='Geometrical Core building tool.',
epilog='''1) Distance spreading [angstrom]
-2) -1 timeout means running Bron-Kerbosh algorithm without timeout
+2) -1 timeout means running Bron-Kerbosch algorithm without timeout
3) Alternative core new aa part: read documentation for more information
4) Superposition core: main core is 0, first alternative is 1 etc. ''',
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
@@ -43,7 +43,7 @@
p.add_argument('-e',help='Ignore cores, owned by one SS element',type=bool, default=False)
p.add_argument('-m',help='Min core size',
metavar='int',type=pos,default=c.minsize)
-p.add_argument('-t',help='Bron-Kerbosh algorithm timeout',
+p.add_argument('-t',help='Bron-Kerbosch algorithm timeout',
metavar='int',type=timeout,default=c.timeout)
p.add_argument('-n',help='Alternative core new aa part',
metavar='float',type=part,default=c.ac_new_atoms)
diff -r 027f0f2f5417 -r 6c7e74a75d13 pair_cores/pair_cores.py
--- a/pair_cores/pair_cores.py Mon Mar 26 22:09:09 2012 +0400
+++ b/pair_cores/pair_cores.py Tue Apr 03 12:25:56 2012 +0400
@@ -40,8 +40,8 @@
* out_high_blocks_html_file -- output HTML file with blocks of multiple sequences
* out_high_blocks_pymol_file -- output PyMol file with blocks of multiple sequences
* blocks3d -- if old (graph-based) blocks algorithm is used
- * blocks3d_timeout -- Bron-Kerbosh (blocks3d) timeout (-1 - unlimited)
- * pair_timeout -- Bron-Kerbosh (pair cores) timeout (-1 - unlimited)
+ * blocks3d_timeout -- Bron-Kerbosch (blocks3d) timeout (-1 - unlimited)
+ * pair_timeout -- Bron-Kerbosch (pair cores) timeout (-1 - unlimited)
"""
if markup_file:
input_file = markup_file
@@ -128,9 +128,9 @@
p.add_argument('--high-blocks-html',help='Output HTML file with high blocks',metavar='FILE',type=w)
p.add_argument('--high-blocks-pymol',help='Output PyMol file with high blocks',metavar='FILE',type=w)
p.add_argument('--blocks3d',help='Use blocks3d algorithm for high blocks',action='store_true')
- p.add_argument('--blocks3d-timeout',help='Bron-Kerbosh (blocks3d) timeout (-1 - unlimited)',
+ p.add_argument('--blocks3d-timeout',help='Bron-Kerbosch (blocks3d) timeout (-1 - unlimited)',
metavar='int',type=timeout,default=config.timeout_2)
- p.add_argument('--pair-timeout',help='Bron-Kerbosh (pair cores) timeout (-1 - unlimited)',
+ p.add_argument('--pair-timeout',help='Bron-Kerbosch (pair cores) timeout (-1 - unlimited)',
metavar='int',type=timeout,default=0)
args = p.parse_args()
homology_from_3d(markup_file=args.m, homology_file=args.y, max_delta=args.d, ignore_one_ss=args.e,
diff -r 027f0f2f5417 -r 6c7e74a75d13 pair_cores/web/approot/locales/pair-cores-web.xml
--- a/pair_cores/web/approot/locales/pair-cores-web.xml Mon Mar 26 22:09:09 2012 +0400
+++ b/pair_cores/web/approot/locales/pair-cores-web.xml Tue Apr 03 12:25:56 2012 +0400
@@ -10,13 +10,13 @@
Use blocks3d algorithm for high blocks

- Bron-Kerbosh (blocks3d) timeout (-1 - unlimited)
+ Bron-Kerbosch (blocks3d) timeout (-1 - unlimited)

Input alignment or input markup must be specified

- Bron-Kerbosh (pair cores) timeout (-1 - unlimited)
+ Bron-Kerbosch (pair cores) timeout (-1 - unlimited)

PairCores