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

Module xpdes

Classes for reading and writing Glide XP Descriptor (.xpdes) files.

Classes

XpDesReader
Class for parsing XP descriptor (.xpdes) files Written by Rajorshi Biswas Original version was not parsing the first line correctly (it was assuing the title is an integer).

XpDesWriter

XpParser
Class for parsing XP descriptor (.xpdes) files Written by Rajorshi Biswas Original version was not parsing the first line correctly (it was assuing the title is an integer).

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)

_find_num_rings_for_atoms(st, lig_atoms)
get the number of rings in the structure represented by this set of atoms

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 (.xpdes) files.

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',
...