| age |
author |
description |
| Tue, 19 Jul 2011 20:01:36 +0400 |
Daniil Alexeyevsky |
allpy.base.default_gaps is now list instead of set, with first item being the preferred output gap symbol |
| Tue, 19 Jul 2011 19:57:34 +0400 |
Daniil Alexeyevsky |
allpy.util.lazy_import: added all the arguments that __import__ has |
| Tue, 19 Jul 2011 19:39:59 +0400 |
Daniil Alexeyevsky |
Added allpy.utils.lazy_import: a helper to break import loops less pervasively |
| Tue, 19 Jul 2011 14:40:22 +0400 |
Daniil Alexeyevsky |
Added deprecation warnings to the deprecated functions. |
| Mon, 18 Jul 2011 19:53:06 +0400 |
Daniil Alexeyevsky |
convert_homology: mapping of column numbers was totally wrong; fixed |
| Mon, 18 Jul 2011 19:26:21 +0400 |
Daniil Alexeyevsky |
Automated merge with ssh://kodomo/allpy |
| Mon, 18 Jul 2011 19:26:03 +0400 |
Daniil Alexeyevsky |
Added script utils/convert_homology.py to convert homology files for similar alignments. |
| Mon, 18 Jul 2011 18:12:03 +0400 |
Daniil Alexeyevsky |
allpy.base.MarkupContainerMixin: fix add_markup to always return the newly created markup |
| Sat, 16 Jul 2011 19:59:16 +0400 |
boris (kodomo) |
apply changes of rasmol_output to rasmol_homology |
| Sat, 16 Jul 2011 17:07:19 +0400 |
Andrei |
Minor changes of output rasmol script |
| Fri, 15 Jul 2011 19:06:47 +0400 |
Daniil Alexeyevsky |
Enhanced allpy.base.Markup.sorted_values: it now accepts `map` and `default` arugments. Somewhat tested. (closes #67) |
| Fri, 15 Jul 2011 18:45:04 +0400 |
Andrei |
Automated merge with ssh://kodomo.fbb.msu.ru/allpy |
| Fri, 15 Jul 2011 18:29:55 +0400 |
Andrei |
Minor revision of rasmol output script |
| Fri, 15 Jul 2011 18:38:01 +0400 |
Daniil Alexeyevsky |
Bug: alignment IO recorded incorrect value to sequence's source attribute -- fixed |
| Fri, 15 Jul 2011 18:01:31 +0400 |
Daniil Alexeyevsky |
allpy.fileio. markup filetype now allows either - or _ to be used in headers interchangeably [closes #89] |
| Fri, 15 Jul 2011 17:13:01 +0400 |
Daniil Alexeyevsky |
Updated markup creation (and removal) in all scripts in the repository. There may still be some uses outside the repository, so watch out! [closes #95] |
| Fri, 15 Jul 2011 17:02:09 +0400 |
Daniil Alexeyevsky |
allpy.base: added parameter use_existing to *.add_markup() to allow same markup to be added multiple times explicitly [see #95] |
| Fri, 15 Jul 2011 16:43:03 +0400 |
Daniil Alexeyevsky |
Implemented & tested new markup API. See #95 |
| Fri, 15 Jul 2011 13:57:56 +0400 |
Daniil Alexeyevsky |
Added markups.by_name dictionary and markups.update() function to fill it. |
| Fri, 15 Jul 2011 12:27:21 +0400 |
boris (kodomo) |
pair_cores: more information in exceptions when reading input and loading pdb |
| Fri, 15 Jul 2011 12:23:35 +0400 |
Daniil Alexeyevsky |
Removed references to extract_pfam from utils/make_homolog* |
| Fri, 15 Jul 2011 12:03:46 +0400 |
Daniil Alexeyevsky |
Added utils/case_to_fasta for converting markup file with case markup to fasta file with letter case significant |
| Fri, 15 Jul 2011 02:23:27 +0400 |
boris (kodomo) |
optimization of rasmol_homology: keep structure loaded of two sequences only |
| Fri, 15 Jul 2011 02:06:23 +0400 |
boris (kodomo) |
structure: create method superimpose of SequenceMixin |
| Fri, 15 Jul 2011 03:03:39 +0400 |
boris (kodomo) |
structure: fix model saving (workaround) |
| Fri, 15 Jul 2011 02:56:28 +0400 |
boris (kodomo) |
structure: fix filtering by model in save_pdb method of SequenceMixin |
| Thu, 14 Jul 2011 18:15:45 +0400 |
Daniil Alexeyevsky |
utils/rasmol_homology: added options -d and -w for removing too thin / too narrow blocks |
| Thu, 14 Jul 2011 18:03:55 +0400 |
Daniil Alexeyevsky |
Added utils/rasmol_homology.py |
| Thu, 14 Jul 2011 17:30:18 +0400 |
Daniil Alexeyevsky |
Removed some dead code from pair_cores/rasmol_output (there is more dead code left) |
| Thu, 14 Jul 2011 17:07:07 +0400 |
Daniil Alexeyevsky |
pair_cores: no need to import extract_pfam for SequencePdbRsiMarkup anymore |
| Thu, 14 Jul 2011 16:19:07 +0400 |
Daniil Alexeyevsky |
Added option --pdb-cache to extract_pfam.py |
| Thu, 14 Jul 2011 16:15:21 +0400 |
Daniil Alexeyevsky |
Moved SequencePdbResiMarkup to allpy.markups, since it is used frequently |
| Thu, 14 Jul 2011 14:44:58 +0400 |
Daniil Alexeyevsky |
utils/make_homologies: added option -g to give input files as a glob expression |
| Thu, 14 Jul 2011 14:28:32 +0400 |
Daniil Alexeyevsky |
WARNING! Changed EOL formatting to UNIX everywhere! WARNING! |
| Thu, 14 Jul 2011 14:05:39 +0400 |
Daniil Alexeyevsky |
Removed executable permission from allpy.data modules with actual data tables (there is no sense in executing them and they do not have hash-bang header) |
| Thu, 14 Jul 2011 14:04:39 +0400 |
Daniil Alexeyevsky |
Added hash-bang to executable python files in utils/ |
| Thu, 14 Jul 2011 13:55:13 +0400 |
Daniil Alexeyevsky |
Added executable permissions to all programs in utils/ |
| Wed, 13 Jul 2011 17:29:52 +0200 |
boris |
pair_cores_all: add documentation and improve help of program |
| Wed, 13 Jul 2011 17:14:42 +0200 |
boris |
pair_cores: pass xyz_only parameter to markup_loader |
| 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 |
