Package schrodinger :: Package application :: Package glide :: Module xp6classes

Module xp6classes

Classes (and top-level logging function) to generate and store data for the Glide "New XP" protocol, for a single protein-ligand complex.

Classes

[hide private]

Complex
Class to generate and store experimental and newXP information for a single protein-ligand complex

NewxpJobdata

EnsembleLigand
Store information about test-set ligands, as derived from Glide ensemble docking.

Functions

[hide private]

logwrapper(level, msg)

Variables

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newxp_steps = ('WMAP_SETUP', 'WMAP_RUN', 'REORG_SETUP', 'REORG...

debug = False

WCUT = -2.5

KW = 0.25

KH = 0.6

WOFF = 0.0

newxpdicetemplate = '\nwrite file "GLIDENAME.out" -\ntitle "GL...

fitrefligdice = '\nCREATE\n load ct reflig -\n maestro file...

spdicetemplate = '\nwrite file -\n"GLIDENAME.out" -\n tit...

htvsdicetemplate = '\nwrite file -\n"GLIDENAME.out" -\n t...
Top-level function to write info/warning/error messages.

__package__ = 'schrodinger.application.glide'

Variables Details

[hide private]

newxp_steps

Value:

('WMAP_SETUP',
 'WMAP_RUN',
 'REORG_SETUP',
 'REORG_RUN',
 'REORG_FIT',
 'ENSEMBLE_SETUP',
 'ENSEMBLE_RUN',
 'ENSEMBLE_SORT',
...

newxpdicetemplate

Value:

'''
write file "GLIDENAME.out" -
title "GLIDENAME" *

PUT 0 INTO \'buildcheck\' 
PUT 1 INTO \'startlig\' 
PUT 0 INTO \'endlig\' 
PUT -1 INTO \'strucseq\' 
...

fitrefligdice

Value:

'''
CREATE
  load ct reflig -
   maestro file -
"REFLIGNAME" -
   gotostruct 1
QUIT

...

spdicetemplate

Value:

'''
write file -
"GLIDENAME.out" -
      title -
"GLIDENAME" *

PUT 0 INTO \'buildcheck\' 
PUT START_SPEC INTO \'startlig\' 
...

htvsdicetemplate

Top-level function to write info/warning/error messages. Here "level" is an arbitrary string passed by the caller.

Value:

'''
write file -
"GLIDENAME.out" -
      title -
"GLIDENAME" *

PUT 0 INTO \'buildcheck\' 
PUT START_SPEC INTO \'startlig\' 
...