schrodinger.application.hitexpander module¶
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schrodinger.application.hitexpander.
fp_types
()¶ Returns a (sorted) list of the available fingerprint type names.
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schrodinger.application.hitexpander.
make_fp_generator_from_canvas_fpfile
(filename)¶ Instantiates fingerprint generator from Canvas FP file.
Parameters: filename (string) – Canvas FP file name. Returns: Fingerprint generator. Return type: canvas.ChmFPOut32
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schrodinger.application.hitexpander.
is_phdb_path
(path)¶
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exception
schrodinger.application.hitexpander.
UnsupportedFormat
¶ Bases:
ValueError
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schrodinger.application.hitexpander.
count_ligands
(path)¶
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schrodinger.application.hitexpander.
structure_file_reader
(filename, logger=None, molids=None, keepsmiles=False)¶ Generator that yields
(mol_id, st)
tuples for the structures in the file identified byfilename
. The file can be in Maestro/SD/SMILES format.Parameters: - filename – File name.
- logger (
logging.Logger
) – Logger for warnings. - molids (iterable over integers) – IDs (1-based indices) of the desired structures.
None
means “all”. - keepsmiles (bool) – Should SMILES text be converted into
schrodinger.structure.Structure
instances?
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schrodinger.application.hitexpander.
phdb_mol_reader
(path, molids=None)¶ Generator that yields
(mol_id, st)
tuples for the ligands in the Phase DB.Parameters: - path (str) – Path to the Phase DB.
- molids (iterable over integers) – IDs of the desired structures.
None
means “all”.
Bases:
KeyError
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schrodinger.application.hitexpander.
phdb_fpreader
(path, kind, molids=None)¶ Generator yielding
(mol_id, fp)
tuples for fingerprints of the desiredkind
for the molecules selected viamolids
(in order of sortedmolids
) from Phase DB pointed to bypath
.Parameters: - path (str) – Path to Phase DB.
- kind – Name of the desired fingerprints type.
- molids (iterable over int) – Identificators of the molecules for which fingerprints are to be loaded.
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schrodinger.application.hitexpander.
multifpfile_fpreader
(path, kind, molids=None)¶ Generator yielding
(mol_id, fp)
tuples for fingerprints of the desiredkind
for the molecules selected viamolids
(in order of sortedmolids
) from multi-fingerprint file pointed to bypath
.Parameters: - path (str) – Path to the multi-fingerprint file.
- kind – Name of the desired fingerprints type.
- molids (int containment checkable or
None
) – Identificators of the molecules for which fingerprints are to be loaded.
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schrodinger.application.hitexpander.
structure_fpreader
(path, kind, molids=None, logger=None)¶ Generator yielding
(mol_id, fp)
tuples for fingerprints of the desiredkind
for the molecules selected viamolids
(in order of sortedmolids
) from multi-fingerprint file pointed to bypath
.Parameters: - path (str) – Path to the multi-fingerprint file.
- kind – Name of the desired fingerprints type.
- molids (int containment checkable or
None
) – Identificators of the molecules for which fingerprints are to be loaded.
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schrodinger.application.hitexpander.
canvasfp_fpreader
(path, molids=None, logger=None)¶ Generator yielding
(mol_id, fp)
tuples for fingerprints of the molecules selected viamolids
(in order of sortedmolids
) from Canvas FP file pointed to bypath
.Parameters: - path (str) – Path to the Canvas FP file.
- molids (iterable over int) – Identificators of the molecules for which fingerprints are to be loaded.
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schrodinger.application.hitexpander.
check_fp_availability
(path, kinds)¶ Check whether fingerprints of the desired type are available, raise exception if they are not.
Parameters: - path (str) – Name of the structure/multi-fingerprint file or Phase DB.
- kinds – Iterable over desired fingerprint kinds.
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schrodinger.application.hitexpander.
prog_for_argparse
(scriptfile)¶ Returns strings like “$SCHRODINGER/run script.py”.
Parameters: scriptfile – Name of a script file. Returns: String to be used to launch the script. Return type: str