| age |
author |
description |
| Mon, 14 Jan 2013 05:07:37 +0400 |
Boris Nagaev |
structure: put comment about commen 'by_block' to output pymol file |
| Mon, 14 Jan 2013 02:19:31 +0400 |
Boris Nagaev |
geometrical_cores: if ignore_one_ss, discard only for alpha-helix or beta-chain |
| Fri, 11 Jan 2013 21:25:33 +0400 |
Boris Nagaev |
structure/blocks_to_pymol: create object for each sequence |
| Fri, 11 Jan 2013 20:14:28 +0400 |
Boris Nagaev |
structure/blocks_to_pymol/pair_fit: refine columns filter |
| Fri, 21 Dec 2012 15:04:53 +0400 |
Boris Nagaev |
structure.py: add error messages to asserts |
| Sat, 02 Jun 2012 19:33:42 +0400 |
Daniil Alexeyevsky |
Added backreferences to `Seqeunce`s from `Monomer`s (closes #49) |
| Fri, 01 Jun 2012 14:32:07 +0400 |
Daniil Alexeyevsky |
Silenced all known noisy points in allpy |
| Fri, 25 May 2012 20:53:18 +0400 |
Daniil Alexeyevsky |
Hidded the misbehaved not-to-be-released-publically SequenceSecondaryStructureMarkup class into allpy.structure to postpone the problem of introducing the proper secondary structure markup to after the release while not breaking the added functionality of blocks3d; please note, this is a very dirty hack |
| Thu, 17 May 2012 01:31:26 +0400 |
Boris Nagaev |
structure: add parameter 'read_local' to auto_pdb() |
| Tue, 03 Apr 2012 12:25:56 +0400 |
Boris Nagaev |
Merge fix of typo in algorithm name Bron?Kerbosch from default into 1.4.21.4.2 |
| Tue, 03 Apr 2012 12:20:13 +0400 |
Boris Nagaev |
fix a typo in algorithm name Bron?Kerbosch in allpy library |
| Sun, 25 Mar 2012 22:54:35 +0400 |
Boris Nagaev |
allpy: do not print debugging messages, unless allpy.config.debug |
| Mon, 19 Mar 2012 13:52:56 +0400 |
Boris Nagaev |
Merged utils, pair_cores, blocks3d and geometrical-core from 9ae23 into 1.4.21.4.2 |
| Fri, 16 Mar 2012 23:43:28 +0400 |
Boris Nagaev |
blocks_to_pymol(): orient visible (cosmetic improvement) |
| Fri, 16 Mar 2012 23:41:59 +0400 |
Boris Nagaev |
blocks_to_pymol(): take alter code into account while fitting |
| Fri, 16 Mar 2012 16:45:00 +0400 |
Daniil Alexeyevsky |
Merged allpy & tests from 1.4.0 into 1.4.21.4.2 |
| Fri, 16 Mar 2012 16:06:18 +0400 |
Boris Nagaev |
blocks_to_pymol(): add pymol command by_block |
| Fri, 16 Mar 2012 15:07:14 +0400 |
Boris Nagaev |
blocks_to_pymol(): add selections for blocks |
| Fri, 16 Mar 2012 00:54:26 +0400 |
Boris Nagaev |
blocks_to_pymol(): fix the order of pair_fit arguments |
| Fri, 16 Mar 2012 00:20:00 +0400 |
Boris Nagaev |
blocks_to_pymol(): hide atoms, absent in the alignment |
| Fri, 16 Mar 2012 00:10:42 +0400 |
Boris Nagaev |
blocks_to_pymol(): show blocks with cartoon, other with transparent sticks |
| Thu, 15 Mar 2012 23:17:23 +0400 |
Boris Nagaev |
blocks_to_pymol(): use all blocks, not only the first one |
| Thu, 15 Mar 2012 23:07:25 +0400 |
Boris Nagaev |
blocks_to_pymol(): hide all except involved chains, represented as cartoon |
| Thu, 15 Mar 2012 19:50:25 +0400 |
Boris Nagaev |
allpy/structure.py: cosmetic improvements of blocks_to_pymol()'s implementation |
| Thu, 15 Mar 2012 19:47:56 +0400 |
Boris Nagaev |
allpy/structure.py: cosmetic improvements of blocks_to_pymol()'s implementation |
| Tue, 06 Mar 2012 22:40:22 +0400 |
Boris Nagaev |
allpy/structure: remove useless import of a code from Bio.PDB.DSSP |
| Tue, 06 Mar 2012 19:23:24 +0400 |
Boris Nagaev |
structure, blocks_to_homology: sure not to add 'number' markup multiple times |
| Tue, 06 Mar 2012 19:21:59 +0400 |
Boris Nagaev |
structure, ignore_one_ss: fix a crash for alignments of >=3 sequences |
| Wed, 29 Feb 2012 22:40:54 +0400 |
Boris Nagaev |
allpy/structure: add method blocks_from_homology() |
| Wed, 29 Feb 2012 15:13:12 +0400 |
Boris Nagaev |
allpy/structure: add ``parts'' argument to blocks3d() |
| Wed, 29 Feb 2012 11:00:56 +0400 |
Boris Nagaev |
allpy/structure: add description of ignore_one_ss argument to .blocks3d() |
| Thu, 03 Nov 2011 15:40:25 +0300 |
Boris Nagaev |
remove some debugging prints from allpy library |
| Fri, 28 Oct 2011 20:40:55 +0300 |
Boris Nagaev |
remove junk code from structure.get_id_parse() |
| Fri, 21 Oct 2011 13:48:47 +0300 |
Boris Nagaev |
add pymol superimposition feature (draft) |
| Wed, 05 Oct 2011 20:42:15 +0300 |
Boris Nagaev |
structure: allow to load custom pdbs |
| Sun, 18 Sep 2011 16:32:59 +0400 |
Boris Nagaev |
Geometrical core improvement: ignore cores, owned by one SS element |
| Sun, 18 Sep 2011 12:38:10 +0400 |
Boris Nagaev |
DownloadPdb, CachedDownloadPdb: change case of pdb code to lower |
| Sun, 18 Sep 2011 12:32:38 +0400 |
Boris Nagaev |
CachedDownloadPdb: fix a bug causing most of downloaded pdb files not to save |
| Sun, 18 Sep 2011 12:23:09 +0400 |
Boris Nagaev |
CachedDownloadPdb: add an argument not to save downloaded pdb to cache_dir |
| 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 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 |
| Wed, 13 Jul 2011 01:39:16 +0400 |
boris (kodomo) |
CachedDownloadPdb: try to unlink file if writting failed |
| 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 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 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 18:27:37 +0400 |
Daniil Alexeyevsky |
Added allpy.structure.cached_download_pdb helper to speed up running extract_pfam. |
| Sat, 09 Jul 2011 14:52:42 +0200 |
boris |
fix 3D superimposition by set of columns: refresh ca_xyz afterwards |
| Fri, 08 Jul 2011 20:21:39 +0200 |
boris |
blocks3d/www: allow blocks not to be continuous |
| Fri, 08 Jul 2011 18:55:53 +0200 |
boris |
SequenceMixin.set_pdb_chain: resi_begin and resi_end can exceed pdb chain. |
| Fri, 08 Jul 2011 18:53:14 +0200 |
boris |
SequenceMixin: args resi_begin and resi_end of set_pdb_chain can be integers |
| Fri, 08 Jul 2011 00:18:42 +0200 |
boris |
fix typos in method blocks_to_homology() of structure.AlignmentMixin |
| Thu, 07 Jul 2011 22:33:21 +0200 |
boris |
structure.AlignmentMixin: add method blocks_to_homology() |
| Wed, 06 Jul 2011 20:49:31 +0200 |
boris |
structure/SequenceMixin: add resi_begin and resi_end parameters to PDB loader |
| Fri, 29 Apr 2011 16:04:51 +0400 |
boris (kodomo) |
allpy/structure.py: move superimpose(+fix) and save_pdb to AlignmentMixin |
