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) – Populatedargparse.Namespaceinstance.- 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