schrodinger.application.glide.xpdes module¶

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

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, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)¶

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)