schrodinger.application.phase.packages.shape_ligprep module¶

Thin LigPrep wrapper and related subroutines (for PHASE-2070).

schrodinger.application.phase.packages.shape_ligprep.get_structure_file_format(filename)¶: Much like fileutils.get_structure_file_format() except also allows for compressed SMILES and SMILESCSV.

class schrodinger.application.phase.packages.shape_ligprep.LigPrep(input_file, options='[]')¶

Bases: object

__init__(input_file, options='[]')¶

Parameters:	input_file (str) – Input file name. options (str) – Ligprep command line options (in JSON format).
Raises:	RuntimeError – If something goes wrong.

prepareStructure(ct)¶

Applies ligprep to ct.

Returns:	(outcomes, failures, summary) tuple
Return type:	(list(structure.Structure), list(structure.Structure), dict)

yieldStructures(text=False)¶: Reads consecutive entries from the input file, applies LigPrep and yields resulting structures. Optionally also yields input text from which the structures were obtained. TODO: support “strip” – minimize text size, like keep only the SMILES itself.

schrodinger.application.phase.packages.shape_ligprep.add_ligprep_arguments(parser)¶

Registers ligprep-specific options.

Parameters:	parser (`argparse.ArgumentParser`) – Command line argument parser.

schrodinger.application.phase.packages.shape_ligprep.validate_ligprep_arguments(args)¶

Validates ligprep-specific command line options.

Parameters:	args (`argparse.Namespace`) – Populated `argparse.Namespace` instance.
Returns:	Tuple of validation success, and error message.
Return type:	bool, str

schrodinger.application.phase.packages.shape_ligprep.validate_ligprep_options(text)¶

Validates ligprep-specific command-line arguments.

Parameters:	text (str) – Ligprep options as list of strings in JSON format.
Returns:	Tuple of validation success, and error message.
Return type:	bool, str