search

chadadavis / sbglib

Automatically exported from code.google.com/p/sbglib
0 stars 0 forks source link

Support common PDB paths #210

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
Use environment variables from common packages:

STAMP: $STAMPDIR/pdb.directories (already parsing this)
MATT: $MATT_PDB_PATH
Rasmol: $RASMOLPDBPATH (colon-separated list)
Modeller: $ATOM_FILES_DIRECTORY (colon-separated list)

Original issue reported on code.google.com by chad.a.davis@gmail.com on 20 May 2011 at 11:25

GoogleCodeExporter commented 9 years ago 
And determine which, if any, are writable, so that they can be used to fetch 
missing files as well (don't need WWW::PDB for this, just LWP::Simple::mirror)

Original comment by chad.a.davis@gmail.com on 21 May 2011 at 4:41

GoogleCodeExporter commented 9 years ago 
For each PDB ID:
* 'divided' or 'all' directory structure (former is faster to lookup)
* Prefix: pdb or ''
* Suffix: .ent or .pdb
* Assembly: \d*
* Compression: .gz or ''

Log name of file used

Original comment by chad.a.davis@gmail.com on 17 Jun 2011 at 2:30