| age |
author |
description |
| Wed, 13 Jul 2011 17:05:46 +0200 |
boris |
pair_cores_all: allow pass alignments, not markups, fix globs processing |
| Wed, 13 Jul 2011 20:30:45 +0400 |
Daniil Alexeyevsky |
Added utils/pool, a helper to run a large queue of small tasks in parallel |
| Wed, 13 Jul 2011 18:01:42 +0400 |
Daniil Alexeyevsky |
extract_pfam.py: command-line option parsing no longer interferes with importing of this script as a module |
| Wed, 13 Jul 2011 17:48:12 +0400 |
Daniil Alexeyevsky |
extract_pfam: added command line options for everything (closes #80) |
| Wed, 13 Jul 2011 12:14:27 +0200 |
boris |
pair_cores_all: change -l option to take list of filenames or globs |
| Wed, 13 Jul 2011 13:08:44 +0400 |
Daniil Alexeyevsky |
allpy.data: Added more codes for semi-known monomers (Leucine/Isoleucine etc) |
| Wed, 13 Jul 2011 11:22:59 +0400 |
Daniil Alexeyevsky |
Automated merge with ssh://kodomo/allpy |
| Wed, 13 Jul 2011 11:22:54 +0400 |
Daniil Alexeyevsky |
extract_pfam.SequencePdbResiMarkup.add_pdb now sets ca_xyz attribute. Untested. (closes #88) |
| Wed, 13 Jul 2011 03:31:06 +0400 |
boris (kodomo) |
pair_cores_all: upgrade to current pair_cores |
| Wed, 13 Jul 2011 02:19:40 +0400 |
boris (kodomo) |
pair_cores: change metavar for pdb cache directory from FILE to DIR |
| Wed, 13 Jul 2011 02:18:17 +0400 |
boris (kodomo) |
pair_cores: create main function and run it in try-clause |
| Wed, 13 Jul 2011 01:54:26 +0400 |
boris (kodomo) |
pair_cores: set ca_xyz attribute of monomer when markups is used |
| Wed, 13 Jul 2011 01:47:32 +0400 |
boris (kodomo) |
pair_cores: use pdb_getter when loading from markup |
| Wed, 13 Jul 2011 01:42:25 +0400 |
Daniil Alexeyevsky |
Automated merge with ssh://kodomo/allpy |
| Wed, 13 Jul 2011 01:42:21 +0400 |
Daniil Alexeyevsky |
extract_pfam.SequencePdbResiMarkup: added way to specify pdb downloader to add_pdb() method |
| Wed, 13 Jul 2011 01:39:16 +0400 |
boris (kodomo) |
CachedDownloadPdb: try to unlink file if writting failed |
| Tue, 12 Jul 2011 23:57:18 +0400 |
boris (kodomo) |
refactoring of pair_cores.py |
| Wed, 13 Jul 2011 00:41:11 +0400 |
boris (kodomo) |
change cached_download_pdb not to raise if cache_dir is read-only |
| Tue, 12 Jul 2011 23:55:28 +0400 |
boris (kodomo) |
fix typos in pdb_getter functors |
| Tue, 12 Jul 2011 23:52:54 +0400 |
Daniil Alexeyevsky |
allpy.base: when filling by_code3 tables, unmodified classes take precedence |
| Tue, 12 Jul 2011 23:38:54 +0400 |
Daniil Alexeyevsky |
allpy.data.codes: added codes for selenocysteine and pyrrolysine |
| Tue, 12 Jul 2011 23:30:29 +0400 |
Daniil Alexeyevsky |
Re-generated allpy.data.codes from newer components.cif |
| Tue, 12 Jul 2011 22:25:52 +0400 |
boris (kodomo) |
replace pdb_getter functions with functors |
| Tue, 12 Jul 2011 21:14:58 +0400 |
boris (kodomo) |
allpy/structure: replace deprecated process() method with realign() |
| Tue, 12 Jul 2011 20:12:14 +0400 |
Andrei |
Automated merge with ssh://kodomo.fbb.msu.ru/allpy |
| Tue, 12 Jul 2011 20:12:09 +0400 |
Andrei |
homology minor changes |
| Tue, 12 Jul 2011 20:11:21 +0400 |
Andrei |
utils/make_homologies.py can read a file of markup format.tested. |
| Tue, 12 Jul 2011 20:11:01 +0400 |
Andrei |
utils/make_homologies.py can read a file of markup format.corrected. |
| Tue, 12 Jul 2011 17:56:43 +0400 |
Daniil Alexeyevsky |
extract_pfam: save & reload status of skipped sequences too |
| Tue, 12 Jul 2011 17:56:42 +0400 |
Daniil Alexeyevsky |
extract_pfam: do not overwrite (skip over) existsing files |
| Tue, 12 Jul 2011 17:12:05 +0400 |
Daniil Alexeyevsky |
Automated merge with ssh://kodomo/allpy |
| Tue, 12 Jul 2011 16:20:31 +0400 |
Daniil Alexeyevsky |
extract_pfam: fixed paths for Pfam |
| Tue, 12 Jul 2011 16:20:24 +0400 |
Daniil Alexeyevsky |
extract_pfam: tested & fixed SequencePdbIdMarkup.add_pdb method |
| Tue, 12 Jul 2011 16:19:58 +0400 |
Daniil Alexeyevsky |
extract_pfam: remove all markups (and all data) from "Gap" monomers (that have no PDB data) |
| Tue, 12 Jul 2011 16:16:08 +0400 |
Daniil Alexeyevsky |
allpy.processors: made Muscle() silent |
| Tue, 12 Jul 2011 15:00:37 +0400 |
Daniil Alexeyevsky |
Fixed markup fileIO for cases when gaps or subformat is specified. Updated tests. |
| Tue, 12 Jul 2011 14:37:05 +0400 |
Daniil Alexeyevsky |
allpy.fileio: switched to using iterator-based read methods everywhere. |
| Tue, 12 Jul 2011 01:50:56 +0400 |
Daniil Alexeyevsky |
Cleanup in extract_pfam.py |
| Tue, 12 Jul 2011 01:48:06 +0400 |
Daniil Alexeyevsky |
extract_pfam: Added assertion for parse error in stockholm PDB IDs |
| Tue, 12 Jul 2011 16:05:28 +0400 |
Andrei |
Automated merge with ssh://kodomo.fbb.msu.ru/allpy |
| Tue, 12 Jul 2011 16:05:21 +0400 |
Andrei |
utils/make_homologies.py can read a file of markup format |
| Tue, 12 Jul 2011 16:05:07 +0400 |
Andrei |
utils/make_homology.py can read a file of markup format |
| Tue, 12 Jul 2011 16:04:12 +0400 |
Andrei |
homology.case_homology can read a file of markup format |
| Tue, 12 Jul 2011 14:00:17 +0400 |
boris (kodomo) |
auto_pdb(): fix regular expression to distinguish resi_start from model |
| Tue, 12 Jul 2011 00:48:56 +0200 |
boris |
auto_pdb(): recover resi_start and resi_end args for backwards-compatibility |
| Mon, 11 Jul 2011 21:51:49 +0200 |
boris |
auto_pdb(): get resi_start and resi_end from sequence name, not as arguments |
| Mon, 11 Jul 2011 22:15:50 +0400 |
Boris Burkov |
merge |
| Mon, 11 Jul 2011 22:12:50 +0400 |
Boris Burkov |
realtive paths in sbbs_2009 are made relative to programs, not to working directory |
| Mon, 11 Jul 2011 21:55:41 +0400 |
Andrei |
Methods to construct homology (without writing) added |
| Mon, 11 Jul 2011 18:27:37 +0400 |
Daniil Alexeyevsky |
Added allpy.structure.cached_download_pdb helper to speed up running extract_pfam. |
| Mon, 11 Jul 2011 18:26:56 +0400 |
Daniil Alexeyevsky |
extract_pfam: Replace monomers without PDB structure with '.' gap sign. |
| Mon, 11 Jul 2011 17:24:30 +0400 |
Daniil Alexeyevsky |
allpy.base cleanup: removed excess empty lines. |
| Mon, 11 Jul 2011 14:36:57 +0400 |
Daniil Alexeyevsky |
extract_pfam: Added sequence case markup. (closes #76) |
| Mon, 11 Jul 2011 14:32:06 +0400 |
Daniil Alexeyevsky |
Added the ability to save/load SequenceCaseMarkup. (see #76) |
| Mon, 11 Jul 2011 14:29:54 +0400 |
Daniil Alexeyevsky |
Roll-back a bug introduces by dirty hand-merge in [723]. (closes #74) (see #76) |
| Mon, 11 Jul 2011 13:55:53 +0400 |
Daniil Alexeyevsky |
extract_pfam: Add PDB residue number information to output sequence names (closes #77) |
| Mon, 11 Jul 2011 13:47:57 +0400 |
Daniil Alexeyevsky |
extract_pfam: Removed extra data from output sequence description, only leave original sequence ID now |
| Mon, 11 Jul 2011 13:42:21 +0400 |
Daniil Alexeyevsky |
extract_pfam: Remove gap columns AFTER removing too short sequences |
| Sat, 09 Jul 2011 21:20:20 +0400 |
Andrei |
Automated merge with ssh://kodomo.fbb.msu.ru/allpy |
| Sat, 09 Jul 2011 21:20:14 +0400 |
Andrei |
Return lost part of homology.py :( |
