schrodinger.application.phase.packages.mmp3d_driver_utils module¶
Provides argument parsing, job setup/cleanup, and other and miscellaneous functionality for phase_mmp3d_driver.py.
Copyright Schrodinger LLC, All Rights Reserved.
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class
schrodinger.application.phase.packages.mmp3d_driver_utils.
SubjobType
¶ Bases:
enum.Enum
An enumeration.
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align_pairs
= 2¶
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smiles_to_3d
= 1¶
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schrodinger.application.phase.packages.mmp3d_driver_utils.
add_transformations
(mmp2d_path, maefile)¶ Adds MMP transformation dictionaries to each of the aligned pairs in maefile and overwrites the file with the updated structures. The transformations (see mmp2d.get_transformations) are stored in the property MMP2D_TRANSFORMATIONS as a base64-encoded string which holds a JSON-encoded representation of the underlying Python data structure. Use decode_transformations to extract the data.
Parameters: - mmp2d_path (str) – Path to MMP 2D database
- maefile (str) – Maestro file with pairs of alignments. Overwritten.
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schrodinger.application.phase.packages.mmp3d_driver_utils.
align_pairs
(project_path, id_pairs_file, out_mae, verbose=False)¶ Aligns pairs of multi-conformer ligands and writes the alignments to a Maestro file.
Parameters: - project_path (str) – Phase project containing the ligands
- id_pairs_file – CSV file with sorted pairs of ligand IDs
- out_mae (str) – Output Maestro file for alignments
- verbose (bool) – If true, a one-line summary will be printed for each pair
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schrodinger.application.phase.packages.mmp3d_driver_utils.
combine_alignments
(args, nsub)¶ Combines pairwise alignments from subjobs.
Parameters: - args (argparser.Namespace) – argparser.Namespace with command line options
- nsub (int) – Number of subjobs
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schrodinger.application.phase.packages.mmp3d_driver_utils.
convert_smiles_to_3d
(in_smiles, out_mae, verbose=False)¶ Creates 3D structures from SMILES.
Parameters: - in_smiles (str) – Input CSV file with id, public_id, smiles, and prop_value
- out_mae (str) – Output Maestro file for 3D structures
- verbose (bool) – If true, each input row from infile will be printed
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schrodinger.application.phase.packages.mmp3d_driver_utils.
create_phase_project
(project_path, maefiles)¶ Creates a multi-conformer Phase project from the supplied Maestro files.
Parameters: - project_path (str) – Path to project to be created
- maefiles (str) – List of Maestro files with one conformer per compound
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schrodinger.application.phase.packages.mmp3d_driver_utils.
decode_transformations
(st)¶ Decodes the MMP transformations in the provided structure and returns them as a list of dictionaries. Each dictionary contains the following key, value pairs, which describe a single transformation linking the provided structure to its associated MMP:
Key Value — —– TRANS_KEYS.FROM_SMILES MMP fragment SMIRKS for the first compound (str) TRANS_KEYS.TO_SMILES MMP fragment SMIRKS for the second compound (str) TRANS_KEYS.MIN The min statistic for the transformation (float) TRANS_KEYS.MAX The max statistic for the transformation (float) TRANS_KEYS.AVG The avg statistic for the transofrmation (float) TRANS_KEYS.STD The std statistic for the transformation (float) TRANS_KEYS.COUNT The count statistic for the transformation (int)
Note that TRANS_KEYS is defined in the mmp2d module.
Parameters: st (structure.Structure) – Structure containing the property MMP2D_TRANSFORMATIONS Returns: List of transformation dictionaries Return type: list[dict{str: str/str/float/float/float/float/int}]
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schrodinger.application.phase.packages.mmp3d_driver_utils.
get_compound_id_pairs
(maefile)¶ Given a Maestro file with pairs of aligned structures, this function reads pairs of compound ids from MMP3D_ID_PROP and returns the pairs in a set.
Parameters: maefile (str) – Maestro file with pairs of alignments Returns: Set containing pairs of compound ids Return type: set((int, int))
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schrodinger.application.phase.packages.mmp3d_driver_utils.
get_parser
()¶ Creates argparse.ArgumentParser with supported command line options.
Returns: Argument parser object Return type: argparser.ArgumentParser
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schrodinger.application.phase.packages.mmp3d_driver_utils.
get_ligand_id_pairs
(project_path, mmp_id_pairs)¶ Returns pairs of ligand IDs in the supplied Phase project that correspond to the provided pairs of compound IDs from the MMP 2D database. A pair will be skipped if either of the compounds in the pair failed to be imported into the project due to size or other characteristics that are unacceptable to phase_database.
Parameters: - project_path (str) – Path to Phase project
- mmp_id_pairs (list((int, int))) – Pairs of compounds IDs from MMP 2D database
Returns: Pairs of ligand IDs
Return type: list((int, int))
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schrodinger.application.phase.packages.mmp3d_driver_utils.
get_num_subjobs
(args, total_inputs, subjob_type)¶ Returns the number of subjobs to run, taking into account the requested number of CPUs and the minimum allowed inputs per subjob.
Parameters: - args (argparser.Namespace) – argparser.Namespace with command line options
- total_inputs (int) – Total number of inputs to be distributed over subjobs
- subjob_type (SubjobType) – Subjob type
Returns: Number of subjobs
Return type: int
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schrodinger.application.phase.packages.mmp3d_driver_utils.
get_parent_jobname
(args)¶ Returns parent job name of the current subjob.
Parameters: args (argparser.Namespace) – argparser.Namespace with command line options Returns: Parent job name Return type: str
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schrodinger.application.phase.packages.mmp3d_driver_utils.
setup_distributed_align_pairs
(args)¶ Does setup for distributed alignment of activity cliff pairs.
Parameters: args (argparser.Namespace) – argparser.Namespace with command line options Returns: list of subjob commands Return type: list(list(str))
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schrodinger.application.phase.packages.mmp3d_driver_utils.
setup_distributed_smiles_to_3d
(args)¶ Does setup for a distributed conversion of SMILES to 3D.
Parameters: args (argparser.Namespace) – argparser.Namespace with command line options Returns: list of subjob commands Return type: list(list(str))
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schrodinger.application.phase.packages.mmp3d_driver_utils.
split_inputs
(args, rows, subjob_type, nsub=None)¶ Divides rows of input data over subjob CSV files and returns the commands to run the subjobs.
Parameters: - args (argparser.Namespace) – argparser.Namespace with command line arguments
- rows (list(tuple)) – Rows to split
- subjob_type (SubjobType) – Subjob type
- nsub (int) – Overrides automatic determination of number of subjobs
Returns: list of subjob commands
Return type: list(list(str))
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schrodinger.application.phase.packages.mmp3d_driver_utils.
validate_args
(args)¶ Checks the validity of command line arguments.
Parameters: args (argparser.Namespace) – argparser.Namespace with command line arguments Returns: tuple of validity and non-empty error message if not valid Return type: bool, str