allpy
changeset 1039:447c048047b2 1.4.2
Merge pair-cores new option for pymol high blocks from default into 1.4.2
author | Boris Nagaev <bnagaev@gmail.com> |
---|---|
date | Tue, 20 Mar 2012 01:39:28 +0400 |
parents | b551ded1420a ec921ac2b553 |
children | 73579ca7c1b5 |
files | pair_cores/pair_cores.py |
diffstat | 4 files changed, 14 insertions(+), 2 deletions(-) [+] |
line diff
1.1 --- a/pair_cores/pair_cores.py Mon Mar 19 15:22:32 2012 +0400 1.2 +++ b/pair_cores/pair_cores.py Tue Mar 20 01:39:28 2012 +0400 1.3 @@ -21,7 +21,8 @@ 1.4 def homology_from_3d(markup_file, homology_file, max_delta, ignore_one_ss=False, alignment_file=None, 1.5 out_alignment_file=None, out_pair_cores_file=None, out_html_file=None, 1.6 pdb_getter=cached_download_pdb, out_pymol_file=None, min_width=4, 1.7 - out_high_blocks_file=None, out_high_blocks_html_file=None, blocks3d=False, 1.8 + out_high_blocks_file=None, out_high_blocks_html_file=None, 1.9 + out_high_blocks_pymol_file=None, blocks3d=False, 1.10 blocks3d_timeout=-1,pair_timeout=0): 1.11 """ Turn pdb markup into homology_file 1.12 1.13 @@ -37,6 +38,7 @@ 1.14 * min_width -- min width of each core 1.15 * out_high_blocks_file -- output file with blocks of multiple sequences 1.16 * out_high_blocks_html_file -- output HTML file with blocks of multiple sequences 1.17 + * out_high_blocks_pymol_file -- output PyMol file with blocks of multiple sequences 1.18 * blocks3d -- if old (graph-based) blocks algorithm is used 1.19 * blocks3d_timeout -- Bron-Kerbosh (blocks3d) timeout (-1 - unlimited) 1.20 * pair_timeout -- Bron-Kerbosh (pair cores) timeout (-1 - unlimited) 1.21 @@ -81,7 +83,7 @@ 1.22 block.blocks_to_html(out_html_file, blocks, open(html_template).read()) 1.23 if out_pymol_file: 1.24 block.blocks_to_pymol(out_pymol_file, blocks) 1.25 - if out_high_blocks_file or out_high_blocks_html_file: 1.26 + if out_high_blocks_file or out_high_blocks_html_file or out_high_blocks_pymol_file: 1.27 high_blocks = [] 1.28 if blocks3d: 1.29 high_blocks = list(block.blocks3d(parts=blocks, 1.30 @@ -101,6 +103,8 @@ 1.31 if out_high_blocks_html_file: 1.32 block.blocks_to_html(out_high_blocks_html_file, high_blocks, 1.33 open(html_template).read()) 1.34 + if out_high_blocks_pymol_file: 1.35 + block.blocks_to_pymol(out_high_blocks_pymol_file, high_blocks) 1.36 1.37 def main(): 1.38 r = argparse.FileType('r') 1.39 @@ -122,6 +126,7 @@ 1.40 1.41 p.add_argument('--high-blocks',help='Output text file with high blocks',metavar='FILE',type=w) 1.42 p.add_argument('--high-blocks-html',help='Output HTML file with high blocks',metavar='FILE',type=w) 1.43 + p.add_argument('--high-blocks-pymol',help='Output PyMol file with high blocks',metavar='FILE',type=w) 1.44 p.add_argument('--blocks3d',help='Use blocks3d algorithm for high blocks',action='store_true') 1.45 p.add_argument('--blocks3d-timeout',help='Bron-Kerbosh (blocks3d) timeout (-1 - unlimited)', 1.46 metavar='int',type=timeout,default=config.timeout_2) 1.47 @@ -134,6 +139,7 @@ 1.48 out_pymol_file=args.p,min_width=args.w, 1.49 out_high_blocks_file=args.high_blocks, 1.50 out_high_blocks_html_file=args.high_blocks_html, 1.51 + out_high_blocks_pymol_file=args.high_blocks_pymol, 1.52 blocks3d=args.blocks3d, blocks3d_timeout=args.blocks3d_timeout, 1.53 pair_timeout=args.pair_timeout) 1.54
2.1 --- a/pair_cores/web/approot/locales/pair-cores-web.xml Mon Mar 19 15:22:32 2012 +0400 2.2 +++ b/pair_cores/web/approot/locales/pair-cores-web.xml Tue Mar 20 01:39:28 2012 +0400 2.3 @@ -48,6 +48,7 @@ 2.4 2.5 <message id='pair.out.High_blocks'>Text file with high blocks</message> 2.6 <message id='pair.out.High_html'>HTML file with high blocks</message> 2.7 + <message id='pair.out.High_pymol'>PyMol file with high blocks</message> 2.8 <message id='pair.out.Homology'>Homology file</message> 2.9 <message id='pair.out.Pair_blocks'>Pair cores file</message> 2.10 <message id='pair.out.Pair_html'>Pair cores HTML file</message>
3.1 --- a/pair_cores/web/approot/locales/pair-cores-web_ru.xml Mon Mar 19 15:22:32 2012 +0400 3.2 +++ b/pair_cores/web/approot/locales/pair-cores-web_ru.xml Tue Mar 20 01:39:28 2012 +0400 3.3 @@ -38,6 +38,7 @@ 3.4 3.5 <message id='pair.out.High_blocks'>Вертикальные блоки (текст)</message> 3.6 <message id='pair.out.High_html'>Вертикальные блоки (HTML)</message> 3.7 + <message id='pair.out.High_pymol'>Вертикальные блоки (PyMol)</message> 3.8 <message id='pair.out.Homology'>Файл гомологии</message> 3.9 <message id='pair.out.Pair_blocks'>Парные блоки (текст)</message> 3.10 <message id='pair.out.Pair_html'>Парные блоки (HTML)</message>
4.1 --- a/pair_cores/web/pair-cores.cpp Mon Mar 19 15:22:32 2012 +0400 4.2 +++ b/pair_cores/web/pair-cores.cpp Tue Mar 20 01:39:28 2012 +0400 4.3 @@ -147,6 +147,10 @@ 4.4 pymol->set_suggested_gen(boost::bind(name_gen2, "pml")); 4.5 task->add_output(pymol, tr("pair.out.Pymol")); 4.6 // 4.7 + ViewFileOutput* high_pymol = new ViewFileOutput("--high-blocks-pymol"); 4.8 + high_pymol->set_suggested_gen(boost::bind(name_gen2, "pml")); 4.9 + task->add_output(high_pymol, tr("pair.out.High_pymol")); 4.10 + // 4.11 ViewFileOutput* high_blocks = new ViewFileOutput("--high-blocks"); 4.12 high_blocks->set_suggested_gen(boost::bind(name_gen2, "blocks")); 4.13 task->add_output(high_blocks, tr("pair.out.High_blocks"));