Package schrodinger :: Package application :: Package glide :: Module xpdes
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Module xpdes

Classes for reading and writing Glide XP Descriptor blocks from pose files.

Copyright Schrodinger LLC. All rights reserved.

Classes [hide private]
  TermKeywords
XP-descriptor term keywords.
  XpPVParser
Class for parsing a PV file with XP-descriptor information
Functions [hide private]
 
extract_Phob_pack_ligand_indices(data_row)
Returns the ligand indices of the Phob_pack indices data row.
 
get_prop(cthandle, dn)
Helper function for m_glide_XPviz_* functions
 
get_prop_idx(cthandle, dn, dim)
Helper function for m_glide_XPviz_* functions
 
m_glide_XPviz_hbonds(cthandle)
 
m_glide_XPviz_phobcon_hb(cthandle)
 
m_glide_XPviz_hexsp(cthandle)
 
m_glide_XPviz_phobpack(cthandle)
 
m_glide_XPviz_stacking(cthandle)
 
m_glide_XPviz_rotbonds(cthandle)
 
m_glide_XPviz_watmol(cthandle)
 
m_glide_XPviz_hexpairs(cthandle)
 
m_glide_XPviz_exposure(cthandle)
 
m_glide_XPviz_penal_blkpchg(cthandle)
 
m_glide_XPviz_water_ligand(cthandle)
 
m_glide_XPviz_penal_polar(cthandle)
 
m_glide_XPviz_water_protein(cthandle)
 
m_glide_XPviz_penal_ddpen(cthandle)
 
m_glide_XPviz_penal_twistam(cthandle)
 
m_glide_XPviz_penal_charge(cthandle)
 
m_glide_XPviz_penalties(cthandle)
 
m_glide_XPviz_picat(cthandle)
Variables [hide private]
  __doc__ = ...
  _GLIDE_TERM_NAMES = ['r_glide_XP_GScore', 'r_glide_XP_Lipophil...
  _ALL_BLOCKS = {'m_glide_XPviz_exposure': 'm_glide_XPviz_exposu...
  logger = log.get_output_logger("xpdes.py")
  __package__ = 'schrodinger.application.glide'
Function Details [hide private]

extract_Phob_pack_ligand_indices(data_row)

 

Returns the ligand indices of the Phob_pack indices data row.
The Phob_pack data block contains a row of indices containing
[pack value, number of ligand indices, number of protein indices,
 lig_0, lig_1, lig_2, ..., prot_0, prot_1, prot_2, ...]
Note that indices in this data block are zero based, and are incremented
here for use in ct atom index access.

@param data_row: second row in the Phob_pack data block
@type data_row: list of int

@return: ligand indices in the Phob_pack data block
@rtype: list of int


Variables Details [hide private]

__doc__

Value:
"""
Classes for reading and writing Glide XP Descriptor blocks from pose f\
iles.

Copyright Schrodinger LLC. All rights reserved.

"""

_GLIDE_TERM_NAMES

Value:
['r_glide_XP_GScore',
 'r_glide_XP_LipophilicEvdW',
 'r_glide_XP_PhobEn',
 'r_glide_XP_PhobEnHB',
 'r_glide_XP_PhobEnPairHB',
 'r_glide_XP_HBond',
 'r_glide_XP_Electro',
 'r_glide_XP_Sitemap',
...

_ALL_BLOCKS

Value:
{'m_glide_XPviz_exposure': 'm_glide_XPviz_exposure',
 'm_glide_XPviz_hbonds': 'm_glide_XPviz_hbonds',
 'm_glide_XPviz_hexpairs': 'm_glide_XPviz_hexpairs',
 'm_glide_XPviz_hexsp': 'm_glide_XPviz_hexsp',
 'm_glide_XPviz_penalties': 'm_glide_XPviz_penalties',
 'm_glide_XPviz_phobcon_hb': 'm_glide_XPviz_phobcon_hb',
 'm_glide_XPviz_phobpack': 'm_glide_XPviz_phobpack',
 'm_glide_XPviz_picat': 'm_glide_XPviz_picat',
...