| age |
author |
description |
| 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] |
| 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 |
| 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 11:22:54 +0400 |
Daniil Alexeyevsky |
extract_pfam.SequencePdbResiMarkup.add_pdb now sets ca_xyz attribute. Untested. (closes #88) |
| Wed, 13 Jul 2011 01:42:21 +0400 |
Daniil Alexeyevsky |
extract_pfam.SequencePdbResiMarkup: added way to specify pdb downloader to add_pdb() method |
| 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 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 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 |
| 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 14:36:57 +0400 |
Daniil Alexeyevsky |
extract_pfam: Added sequence case markup. (closes #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 |
| Fri, 08 Jul 2011 20:03:55 +0400 |
Daniil Alexeyevsky |
Reconfigured extract_pfam.py to convert the whole Pfam |
| Fri, 08 Jul 2011 19:49:27 +0400 |
Daniil Alexeyevsky |
extract_pfam now downloads PDB and stores PDB residue numbers in ouput |
| Fri, 08 Jul 2011 14:47:23 +0400 |
Daniil Alexeyevsky |
Restructured rewrite of extract_pfam.py |
| Sat, 26 Feb 2011 18:59:48 +0300 |
Daniil Alexeyevsky |
Chaned sequence name format in extract_pfam.py to ">PDBID_PDBCHAIN ORIGINAL_NAME ORIGINAL_DESCRIPTION LIST_OF_ASSOCIATED_PDB_FRAGMENTS" |
| Sat, 26 Feb 2011 18:52:23 +0300 |
Daniil Alexeyevsky |
Added util extract_pfam |
