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.
-
class
schrodinger.application.phase.packages.mmp3d_driver_utils.
SubjobType
(value)¶ Bases:
enum.Enum
An enumeration.
-
smiles_to_3d
= 1¶
-
align_pairs
= 2¶
-
-
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.
-
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
-
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
-
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
-
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
-
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}]
-
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))
-
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
-
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))
-
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
-
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
-
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))
-
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))
-
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))
-
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