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
¶ Bases:
str
,enum.Enum
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)
-