schrodinger.application.phase.packages.hypo_refine.project_utils module¶
Module with phase_hypo_refine project-related functionality.
Copyright Schrodinger LLC, All Rights Reserved.
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schrodinger.application.phase.packages.hypo_refine.project_utils.
create_project
(infile, fd, conf_options, dest_dir=None)¶ Creates a multi-conformer zipped Phase project from a Maestro/SD file.
Parameters: - infile (str) – Input Maestro/SD file
- fd (list of phase.PhpFeatureDefinition) – Feature definitions
- conf_options (phase.PhpConfOptions) – Conformer generation options
- dest_dir (str) – Directory in which to create the project (default: cwd).
Returns: Zipped project name including any leading path
Return type: str
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schrodinger.application.phase.packages.hypo_refine.project_utils.
create_projects
(args, dest_dir=None)¶ Creates any required zipped projects from Maestro/SD files in args. No action is taken for an argument which already corresponds to a zipped project. args.actives and args.decoys are replaced with the zipped project names if zipped projects are created. If args.valid is set, the actives2 and/or decoys2 values are similarly replaced.
Parameters: - args (argparser.Namespace) – argparser.Namespace with command line arguments
- dest_dir (str) – Directory in which to create projects (default: cwd).
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schrodinger.application.phase.packages.hypo_refine.project_utils.
derive_project_name
(file_path, zipped=False)¶ Determines the name of the Phase project to associate with the supplied Maestro file, SD file, or zipped project name. For example, if file_path is “/home/jsmith/actives.maegz”, the returned value would be “actives.phprj”. If zipped is True, the returned value would be “actives.phzip”.
Parameters: file_path (str) – Name of Maestro/SD file or zipped project Returns: Project name derived from file_path Return type: str
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schrodinger.application.phase.packages.hypo_refine.project_utils.
get_ligand_titles
(zipped_project, unique=False)¶ Extracts ligand titles from a zipped project. If unique is True, only unique titles will be returned.
Parameters: - zipped_project (str) – Name of zipped project
- unique (bool) – Whether to return only unique titles
Returns: Ligand titles
Return type: list(str)
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schrodinger.application.phase.packages.hypo_refine.project_utils.
get_project_file_names
(project_path, file_name)¶ Returns the appropriate file name to use, zip_file_path, to extract the indicated file from the provided zipped Phase project, and the file name to use, disk_file_path, to access the extracted file on disk. Use forward slashes in file_name if it’s located in a subdirectory of the project, e.g., hypotheses/AADRR_1.phypo. The returned zip_file_path always contains forward slashes, whereas disk_file_path contains the appropriate platform-dependent separators.
Parameters: - project_path (str) – Path to zipped project
- file_name (str) – Name of file in archive
Returns: tuple of zip_file_path, disk_file_path
Return type: str, str
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schrodinger.application.phase.packages.hypo_refine.project_utils.
get_screen_dict
(args)¶ Creates a dictionary from the active/decoy files to screen:
“actives” –> args.actives “decoys” –> args.decoys “actives2” –> actives2 file extracted from args.valid, if provided “decoys2” –> decoys2 file extracted from args.valid, if provided
Parameters: args (argparse.Namespace) – Command line arguments Returns: Dictionary of active/decoy files keyed as described above Return type: dict of str:str
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schrodinger.application.phase.packages.hypo_refine.project_utils.
zip_project
(project_path, dest_dir=None)¶ Zips a Phase project, removes the project directory, and returns the name of the zipped project.
Parameters: - project_path (str) – Path to project (.phprj)
- dest_dir (str) – Destination directory for zipped project (default: cwd).
Returns: Zipped project name (.phzip) including any leading path
Return type: str