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.

close()

prepareStructure(ct)

Applies ligprep to ct.

Returns

(outcomes, failures, summary) tuple

Return type

(list(structure.Structure), list(structure.Structure), dict)

yieldStructures()

Reads consecutive entries from the input file, applies LigPrep and yields resulting structures.

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