schrodinger.application.glide.xpdes module

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

Copyright Schrodinger LLC. All rights reserved.

schrodinger.application.glide.xpdes.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.

Parameters

data_row (list of int) – second row in the Phob_pack data block

Returns

ligand indices in the Phob_pack data block

Return type

list of int

schrodinger.application.glide.xpdes.get_prop(cthandle, dn)

Helper function for m_glide_XPviz_* functions

schrodinger.application.glide.xpdes.get_prop_idx(cthandle, dn, dim)

Helper function for m_glide_XPviz_* functions

schrodinger.application.glide.xpdes.m_glide_XPviz_hbonds(cthandle)

schrodinger.application.glide.xpdes.m_glide_XPviz_phobcon_hb(cthandle)

schrodinger.application.glide.xpdes.m_glide_XPviz_hexsp(cthandle)

schrodinger.application.glide.xpdes.m_glide_XPviz_phobpack(cthandle)

schrodinger.application.glide.xpdes.m_glide_XPviz_stacking(cthandle)

schrodinger.application.glide.xpdes.m_glide_XPviz_rotbonds(cthandle)

schrodinger.application.glide.xpdes.m_glide_XPviz_watmol(cthandle)

schrodinger.application.glide.xpdes.m_glide_XPviz_hexpairs(cthandle)

schrodinger.application.glide.xpdes.m_glide_XPviz_exposure(cthandle)

schrodinger.application.glide.xpdes.m_glide_XPviz_penal_blkpchg(cthandle)

schrodinger.application.glide.xpdes.m_glide_XPviz_water_ligand(cthandle)

schrodinger.application.glide.xpdes.m_glide_XPviz_penal_polar(cthandle)

schrodinger.application.glide.xpdes.m_glide_XPviz_water_protein(cthandle)

schrodinger.application.glide.xpdes.m_glide_XPviz_penal_ddpen(cthandle)

schrodinger.application.glide.xpdes.m_glide_XPviz_penal_twistam(cthandle)

schrodinger.application.glide.xpdes.m_glide_XPviz_penal_charge(cthandle)

schrodinger.application.glide.xpdes.m_glide_XPviz_penalties(cthandle)

schrodinger.application.glide.xpdes.m_glide_XPviz_picat(cthandle)

class schrodinger.application.glide.xpdes.TermKeywords(value)

Bases: schrodinger.StrEnum

XP-descriptor term keywords. Note that members of this enum may be compared to bare strings.

Molecule = 'Molecule'

H_bonds = 'H_bonds'

Phob_pack = 'Phob_pack'

Hex_pairs = 'Hex_pairs'

Penalties = 'Penalties'

Phobcon_HB = 'Phobcon_HB'

Picat = 'Picat'

Exposure = 'Exposure'

Rot_bonds = 'Rot_bonds'

Hex_sp = 'Hex_sp'

class schrodinger.application.glide.xpdes.XpPVParser(filename)

Bases: object

Class for parsing a PV file with XP-descriptor information

__init__(filename)

Read PV file and create a table of XP Descriptor terms

parseBlock_SL(ctnum)

XP parsing for single-ligand scoring. Given ctnum, get and parse XP block return an array of tuples. tuple[0] is an atom number and tuple[1] is the corresponding XP score for that atom Added: tuple[2] the energy type e.g. r_xpdes_HBond which will be later set as an atom-level property.

parseBlock_F(ctnum, st)

XP parsing for fragment scoring. Use st argument to determine the number of rings associated with a set of atoms. Given ctnum, get and parse XP block return an array of tuples containing energy type e.g. r_xpdes_HBond which will be later set as an atom-level property.

Each entry = (atom number, XP score, energy type property)