Roll for Atlas Computational Solvent Mapping with Flexibility
Version 1.7.0
Performs global search of the entire protein surface for regions that bind a number of small organic probe molecules. Original software and server are at BU: http://ftmap.bu.edu/home.php
Current software (binary) distro is atlas-1.7.0-nopython.tar.bz2 recevied from D. Hall (agreement with Amaro lab). Repack the distro after fixing the bugs and removign extra files from examples/:
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src/atlas.py
- line 922: rm env={} (subprocess.call([prms.atlas_base+'/pdb2pqr/pdb2pqr.py'...)
- line 934: cast to str env_dictionary['OMP_NUM_THREADS'] = str(prms.np)
- line 1367: change '.???.sdf' to '.*.sdf' (per D. Hall email Aud 20.)
- line 1170: bug fix for flex_residue_min()
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src/run_atlas.py
- line 85: cast to str env_dictionary['OMP_NUM_THREADS'] = str(prms.np)
- line 169: add bug fix per D. Hall email Sep 2.
Roll installs :
- atlas software on all nodes in /opt/atlas-1.7.0/
- SGE parallel enviornment "threaded" with allocation rule "pe_slots" on frontend.
- python wrappers for ATLAS and FLEX opal web services and respective xml files on opal server