schrodinger.application.phase.packages.shape_creation_logic module¶
Creation of “binary shape files” from several kind of sources (PHASE-2070).
- schrodinger.application.phase.packages.shape_creation_logic.add_arguments(p)¶
Adds shape-creation-specific arguments to the parser.
- Parameters
p (argparser.ArgumentParser) – Parser-like instance.
- schrodinger.application.phase.packages.shape_creation_logic.validate_args(args)¶
Validates command-line arguments added by
add_arguments.- Parameters
args (argparse.Namespace) – Namespace holding command line options.
- Returns
Tuple of validation success and error message.
- Return type
(bool, str)
- schrodinger.application.phase.packages.shape_creation_logic.runtimize_paths(args)¶
Runtimizes input file paths for the command line arguments.
- Parameters
args (argparse.Namespace) – Namespace populated with command line arguments.
- schrodinger.application.phase.packages.shape_creation_logic.get_input_files(args)¶
Identifies input files among arguments (for job control purposes).
- Parameters
args (argparse.Namespace) – Namespace populated with command line arguments.
- schrodinger.application.phase.packages.shape_creation_logic.get_jobname_and_outfile(args)¶
Returns the job name and job name-derived output file name. If job name is not provided it gets derived from the input file name.
- Parameters
args (argparse.Namespace) – Namespace populated with command line arguments.
- Returns
job name, output file name
- Return type
str, str
- class schrodinger.application.phase.packages.shape_creation_logic.ShapeCreator(args)¶
Bases:
object- __init__(args)¶
Expects validated and runtimized command line arguments.
- Parameters
args (argparse.Namespace) – Namespace populated with command line arguments.
- getMetadata()¶
Returns JSON-able representation of the
self.
- schrodinger.application.phase.packages.shape_creation_logic.validate_shape_data_file_metadata(meta)¶
Validates shape data file metadata.
- Parameters
meta (dict) – Shape data file metadata.
- Returns
Validation outcome and complain (if any).
- Return type
(bool, str)
- schrodinger.application.phase.packages.shape_creation_logic.validate_shape_data_file_metadata_compatibility(meta1, meta2)¶
Validates shape data file metadata compatibility.
- Parameters
meta1 (dict) – Validated shape data file metadata #1.
meta2 (dict) – Validated shape data file metadata #2.
- Returns
Validation outcome and complain (if any).
- Return type
(bool, str)
- schrodinger.application.phase.packages.shape_creation_logic.estimate_shape_data_size(shape_type, num_conformers, compress, conformer_format=None)¶
Estimates number of bytes needed to store the shape data for a single molecule. Based on observations for 10,000 molecules picked from Enamine REAL.
- Parameters
shape_type (str) – Shape assignment scheme name (“pharm”, “atom_color” or “atom_no_color”).
num_conformers (int) – Number of conformers per molecule.
compress (bool) – File-level compression.
conformer_format (
conformer_storage.Formator NoneType) – Format used to store conformer structures (Nonefor structureless shape data).
- Returns
Estimated shape data size for a single molecule (in bytes).
- Return type
int
- schrodinger.application.phase.packages.shape_creation_logic.execute(args)¶
The “main” subroutine for the “create” task.
- Parameters
args (argparse.Namespace) – Namespace populated with command line arguments.