| age |
author |
description |
| 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 :( |
| Sat, 09 Jul 2011 15:48:27 +0200 |
boris |
prevent graph.cliques() from dropping vertex by mistake |
| Sat, 09 Jul 2011 14:52:42 +0200 |
boris |
fix 3D superimposition by set of columns: refresh ca_xyz afterwards |
| Sat, 09 Jul 2011 16:31:36 +0400 |
Boris Burkov |
Merge with Nagaev |
| Sat, 09 Jul 2011 16:30:28 +0400 |
Boris Burkov |
sbbs_2009 created. test_homology.py contains function that writes classes of homology to file. |
| Fri, 08 Jul 2011 21:13:54 +0200 |
boris |
html viewer of blocks: now compatible with jquery-1.4.2 |
| 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 20:52:06 +0400 |
Boris Burkov |
test_homology added |
| Fri, 08 Jul 2011 20:44:11 +0400 |
Boris Burkov |
Merge with Dendik |
| Fri, 08 Jul 2011 20:42:57 +0400 |
Boris Burkov |
create_file_with_monomer_homology once tested |
| Fri, 08 Jul 2011 20:03:55 +0400 |
Daniil Alexeyevsky |
Reconfigured extract_pfam.py to convert the whole Pfam |
| Fri, 08 Jul 2011 19:49:29 +0400 |
Daniil Alexeyevsky |
Automated merge with ssh://kodomo/allpy |
| Fri, 08 Jul 2011 19:49:27 +0400 |
Daniil Alexeyevsky |
extract_pfam now downloads PDB and stores PDB residue numbers in ouput |
| Fri, 08 Jul 2011 18:38:31 +0400 |
Boris Burkov |
Merge |
| Fri, 08 Jul 2011 18:30:04 +0400 |
Boris Burkov |
create_monomer_homology once tested to return (not sure, whether the answer is perfect). allpy.base is essentially like dendik's one now (Column now doesn't know its alignment). |
| Fri, 08 Jul 2011 16:20:20 +0400 |
Boris Burkov |
Merge between Burkov and others. |
| Fri, 08 Jul 2011 16:06:59 +0400 |
Boris Burkov |
create_monomer_homology function is implemented in blocks_finder. |
| Wed, 06 Jul 2011 22:28:11 +0400 |
Boris Burkov |
Merge between Burkov and others, I've saved self.alignment for Column. |
| Wed, 06 Jul 2011 21:16:41 +0400 |
Boris Burkov |
Mostly meaningless commit |
| Fri, 08 Jul 2011 17:51:39 +0400 |
Daniil Alexeyevsky |
Added Makefile to test directory |
| Fri, 08 Jul 2011 17:47:40 +0400 |
Daniil Alexeyevsky |
Updated Sphinx docs |
| Fri, 08 Jul 2011 14:47:23 +0400 |
Daniil Alexeyevsky |
Restructured rewrite of extract_pfam.py |
| Fri, 08 Jul 2011 12:09:39 +0400 |
Daniil Alexeyevsky |
Added NEWS entry for markup file format |
| Fri, 08 Jul 2011 12:03:43 +0400 |
Daniil Alexeyevsky |
Added docstrings to base markup classes |
| Fri, 08 Jul 2011 00:23:51 +0200 |
boris |
pair_cores: add required option for output file with classes of homology |
| 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() |
| Thu, 07 Jul 2011 22:32:30 +0400 |
Daniil Alexeyevsky |
Automated merge with ssh://kodomo/allpy |
| Thu, 07 Jul 2011 22:32:21 +0400 |
Daniil Alexeyevsky |
Implemented markup fileIO (closes #56) |
| Thu, 07 Jul 2011 22:27:14 +0400 |
Daniil Alexeyevsky |
Renamed Markup.as_list() to Markup.sorted_values() and added Markup.sorted_keys() |
| Thu, 07 Jul 2011 21:22:53 +0400 |
Andrei |
Automated merge with ssh://kodomo.fbb.msu.ru/allpy |
| Thu, 07 Jul 2011 21:22:45 +0400 |
Andrei |
Static method .case_homology added |
| Thu, 07 Jul 2011 21:21:29 +0400 |
Andrei |
Makes (case sensitive by request) homology classes for a number of input fasta alignments |
| Thu, 07 Jul 2011 21:19:30 +0400 |
Andrei |
Function case_homology moved to allpy.homology |
| Thu, 07 Jul 2011 19:32:44 +0400 |
Daniil Alexeyevsky |
API cleanup: alignment.to_file() now returns self |
| Thu, 07 Jul 2011 19:21:12 +0400 |
Daniil Alexeyevsky |
Added fileio.File.read_alignment and fileio.File.write_alignment [closes #57] |
| Thu, 07 Jul 2011 12:53:53 +0400 |
Andrei |
Automated merge with ssh://kodomo.fbb.msu.ru/allpy |
| Thu, 07 Jul 2011 12:53:42 +0400 |
Andrei |
alignment_blocks method added to homology and tested. Blocks found in monomer homology file can be now returned to alignment blocks |
| Wed, 06 Jul 2011 20:49:31 +0200 |
boris |
structure/SequenceMixin: add resi_begin and resi_end parameters to PDB loader |
| Wed, 06 Jul 2011 18:05:51 +0400 |
Andrei |
In homology 'residue' changed to 'monomer' everywhere |
| Wed, 06 Jul 2011 18:04:58 +0400 |
Andrei |
In homology 'residue' changed to 'monomer' everywhere |
| Wed, 06 Jul 2011 14:08:46 +0400 |
Daniil Alexeyevsky |
Automated merge with ssh://kodomo/allpy |
| Tue, 05 Jul 2011 19:33:22 +0400 |
Daniil Alexeyevsky |
Added NEWS entry about Markups |
| Wed, 06 Jul 2011 11:42:41 +0400 |
Andrei |
The util makes residue holomogy file from fasta alignment. May take in account case of letters |
| Tue, 05 Jul 2011 21:54:21 +0400 |
Andrei |
Automated merge with ssh://kodomo.fbb.msu.ru/allpy |
| Tue, 05 Jul 2011 21:54:10 +0400 |
Andrei |
homology endowed with column_number in all methods and passed through tests |
| Tue, 05 Jul 2011 19:19:10 +0400 |
Daniil Alexeyevsky |
Added test for SequenceCaseMarkup and SequenceMarkup.as_list() |
