schrodinger.application.phase.shape_screen_reporter.task_utils module¶

Performs task-based work for generating and using shape screen report databases.

schrodinger.application.phase.shape_screen_reporter.task_utils.check_user_query(reporter, user_features, user_tol=None, user_rules=None)¶

Returns a non-empty error message if any of the supplied query data are illegal.

Parameters:

reporter (phase.PhpShapeScreenReporter) – Connection to a shape screen report database
user_features – Feature names with 1-based numbering, e.g., [‘A1’, ‘D5’, ‘H9’, ‘R12’]
user_tol (dict{str, float} or NoneType) – Dictionary of <feature>:<tol> pairs, where <feature> consists of a feature name and <tol> is the matching tolerance, e.g., {‘A1’: 1.5, ‘R12’, 2.5}.
user_rules (dict{str, str} or NoneType) – Dictionary of <feature>:<permitted> pairs, where <feature> consists of a feature name and <permitted> contains the first character of <feature>, followed by any other types <feature> is allowed to match, e.g., {‘A1’:’AN’, ‘R12’:’RH’}

Returns:

Non-empty error message if any data are invalid

Return type:

str

schrodinger.application.phase.shape_screen_reporter.task_utils.cluster_hits(args, logger=None)¶

Clusters hits in a shape screen report database according to the query features they match or the largest Bemis-Murcko scaffold they contain.

Parameters:

args (argparse.Namespace) – argparse.Namespace with command line arguments
logger (logging.Logger) – Logger for info level output

Returns:

Dictionary of cluster descripion –> cluster size, where the description is a string of matched features or the scaffold SMILES/SMARTS.

Return type:

dict{string: int}

schrodinger.application.phase.shape_screen_reporter.task_utils.cluster_hits_by_features(args, logger=None)¶

Clusters hits in a shape screen report database according to the query features they match. Any created hypotheses are copied into the archive <jobname>_hypos.zip to simplify file transfer.

Parameters:

args (argparse.Namespace) – argparse.Namespace with command line arguments
logger (logging.Logger) – Logger for info level output

Returns:

Dictionary of matched features –> cluster size

Return type:

dict{string: int}

schrodinger.application.phase.shape_screen_reporter.task_utils.cluster_hits_by_scaffold(args, logger=None)¶

Clusters hits in a shape screen report database according to the largest Bemis-Murcko scaffold they contain.

Parameters:

args (argparse.Namespace) – argparse.Namespace with command line arguments
logger (logging.Logger) – Logger for info level output

Returns:

Dictionary of scaffold SMILES/SMARTS –> cluster size

Return type:

dict{string: int}

schrodinger.application.phase.shape_screen_reporter.task_utils.create_cluster_hypo(reporter, subset=None, user_tol=None, user_rules=None)¶

Constructs a pharmacophore hypothesis from the shape query for use in the “cluster” task. All shape query sites are used to perform the initial clustering, whereas a subset of sites are used the create the hypothesis for a particular cluster. Positional tolerances and feature-matching rules in the hypothesis are modified according to dictionaries that contain any user-specified <feature>:<tol> and <feature>:<permitted> pairs, where <feature> consists of only a feature type, with no number.

Parameters:

reporter (phase.PhpShapeScreenReporter) – Connection to a shape screen report database
subset (list(int) or NoneType) – Zero-based list of query site numbers. All sites are used by default.
user_tol (dict{str, float} or NoneType) – Dictionary of <feature>:<tol> pairs, where <feature> consists of only a feature type and <tol> is the matching tolerance, e.g., {‘A’: 1.5, ‘R’, 2.5}.
user_rules (dict{str, str} or NoneType) – Dictionary of <feature>:<permitted> pairs, where <feature> consists of only a feature type and <permitted> contains <feature>, followed by any other types <feature> is allowed to match, e.g., {‘A’:’AN’, ‘H’:’HR’, ‘R’:’RH’}

Returns:

The requested pharmacophore hypothesis

Return type:

phase.PhpHypoAdaptor

schrodinger.application.phase.shape_screen_reporter.task_utils.create_database(args, logger=None)¶

Creates a new shape screen report database.

Parameters:

args (argparser.Namespace) – argparser.Namespace with command line arguments
logger (logging.Logger) – Logger for info level output

schrodinger.application.phase.shape_screen_reporter.task_utils.create_user_hypo(reporter, user_features, user_tol=None, user_rules=None)¶

Constructs a pharmacophore hypothesis from the shape query based on a list of feature names supplied by the user. Positional tolerances and feature-matching rules in the hypothesis are modified according to dictionaries that contain any user-specified <feature>:<tol> and <feature>:<permitted> pairs, where <feature> consists of a feature type followed by a 1-based feature number.

Parameters:

reporter (phase.PhpShapeScreenReporter) – Connection to a shape screen report database
user_features (list(str)) – Feature names with 1-based numbering, e.g., [‘A1’, ‘D5’, ‘H9’, ‘R12’]
user_tol (dict{str, float} or NoneType) – Dictionary of <feature>:<tol> pairs, where <feature> consists of a feature name and <tol> is the matching tolerance, e.g., {‘A1’: 1.5, ‘R12’, 2.5}.
user_rules (dict{str, str} or NoneType) – Dictionary of <feature>:<permitted> pairs, where <feature> consists of a feature name and <permitted> contains the first character of <feature>, followed by any other types <feature> is allowed to match, e.g., {‘A1’:’AN’, ‘R12’:’RH’}

Returns:

The requested pharmacophore hypothesis

Return type:

phase.PhpHypoAdaptor

Raise:

ValueError if any of the supplied feature names is illegal or not found in the shape query, or if any of the tolerances or permitted feature strings is illegal.

schrodinger.application.phase.shape_screen_reporter.task_utils.export_hits_or_hypo(args, logger=None)¶

Exports hits and/or hypothesis for a subset of query features.

Parameters:

args (argparser.Namespace) – argparser.Namespace with command line arguments
logger (logging.Logger) – Logger for info level output

Raise:

ValueError if any of the feature names, feature tolerances or feature rules are illegal.

schrodinger.application.phase.shape_screen_reporter.task_utils.filter_hits(args, logger=None)¶

Filters hits according to property and/or SMARTS filters.

Parameters:

args (argparser.Namespace) – argparser.Namespace with command line arguments
logger (logging.Logger) – Logger for info level output

schrodinger.application.phase.shape_screen_reporter.task_utils.get_feature_overlap_mappings(base_features_hit, base_features_query, result)¶

Constructs a list of FeatureOverlapMapping objects from the base features of the hit, the base features of the query and the PhpShapeScreenResult from screening the hit against the query.

Parameters:

base_features_hit (list(phase.PhpBaseFeature)) – All base features in the hit
base_features_query (list(phase.PhpBaseFeature)) – All base features in the query
result (phase.PhpShapeScreenResult) – The result from screening the hit against the query

Returns:

List of FeatureOverlapMapping objects

Return type:

list(canvas2d.FeatureOverlapMapping)

schrodinger.application.phase.shape_screen_reporter.task_utils.get_jobname(dbfile, task)¶

Determines the job name from SCHRODINGER_JOBNAME or from the base name of the shape screen report database and the task.

Parameters:

dbfile (str) – Shape screen report database file
task (str) – The task being performed

Returns:

Job name

Return type:

str

schrodinger.application.phase.shape_screen_reporter.task_utils.get_structures(reporter, rows, max_in_memory=1000)¶

Generator that yields structures from a shape screen report database while limiting the number of structures held in memory.

Parameters:

reporter (phase.PhpShapeScreenReporter) – Connection to a shape screen report database
rows (list(int)) – The rows to read. Row 0 corresponds to the shape query, while rows 1, 2, etc. correspond to the hits. Rows may be in any order.
max_in_memory (int) – The maximum number of structures that will be held in memory while reading

Yield:

The next structure in the list of rows

Ytype:

structure.Structure

schrodinger.application.phase.shape_screen_reporter.task_utils.print_images(images, ncols, pdf_file, page_size=PageSize.Letter)¶

Prints a list of images to a table in PDF format.

Parameters:

images (list(report2d.StructInfo)) – List of images.
ncols (int) – Number of columns in table
pdf_file (str) – Name of PDF file
page_size (option_utils.PageSize) – Page size

schrodinger.application.phase.shape_screen_reporter.task_utils.print_report(args, logger=None)¶

Generates a PDF file containing a table of annotated 2D hits that match a set of features in the shape query. Must construct a QApplication before calling this function.

Parameters:

args (argparser.Namespace) – argparser.Namespace with command line arguments
logger (logging.Logger) – Logger for info level output

Raise:

ValueError if any of the feature names, feature tolerances or feature rules are illegal.

schrodinger.application.phase.shape_screen_reporter.task_utils.run_diversity_filter(reporter, diverse_fraction, rows=None, logger=None)¶

Returns row numbers for a diverse fraction of structures in a shape screen report database.

Parameters:

reporter (phase.PhpShapeScreenReporter) – Connection to a shape screen report database
diverse_fraction (float) – Fraction on the interval (0.0, 0.2].
rows (list(int)) – The rows to screen. Row 0 corresponds to the shape query, while rows 1, 2, etc. correspond to the hits. Rows may be in any order. If omitted, rows for all hits are screened.
logger (logging.Logger) – Logger for info level output

Returns:

Row numbers for the diverse structures

Return type:

list(int)

schrodinger.application.phase.shape_screen_reporter.task_utils.run_filters(reporter, property_filter=None, smarts_filter=None, diverse_fraction=None, logger=None)¶

Returns row numbers of structures in a shape screen report database which satisfy the provided property, SMARTS and diversity filters.

Parameters:

reporter (phase.PhpShapeScreenReporter) – Connection to a shape screen report database
property_filter (phase.PhpDbPropertyQuery or NoneType) – Property filter to be satisfied
smarts_filter (filter.SmartsFilter or NoneType) – SMARTS filter to be satisfied
diverse_fraction (float or NoneType) – Optional diverse fraction of rows to retain after applying other filters. Must lie on (0.0, 0.2].
logger (logging.Logger or NoneType) – Logger for info level output

Returns:

Row numbers that satisfy the filter

Return type:

list(int)

schrodinger.application.phase.shape_screen_reporter.task_utils.run_property_filter(reporter, property_filter, logger=None)¶

Returns row numbers of structures in a shape screen report database which satisfy the provided property filter.

Parameters:

reporter (phase.PhpShapeScreenReporter) – Connection to a shape screen report database
property_filter (phase.PhpDbPropertyQuery) – Property filter to be satisfied
logger (logging.Logger) – Logger for info level output

Returns:

Row numbers that satisfy the filter

Return type:

list(int)

schrodinger.application.phase.shape_screen_reporter.task_utils.run_smarts_filter(reporter, smarts_filter, rows=None, logger=None)¶

Returns row numbers of structures in a shape screen report database which satisfy the provided SMARTS filter.

Parameters:

reporter (phase.PhpShapeScreenReporter) – Connection to a shape screen report database
smarts_filter (filter.SmartsFilter) – SMARTS filter to be satisfied
rows (list(int)) – The rows to screen. Row 0 corresponds to the shape query, while rows 1, 2, etc. correspond to the hits. Rows may be in any order. If omitted, rows for all hits are screened.
logger (logging.Logger) – Logger for info level output

Returns:

Row numbers that satisfy the filter

Return type:

list(int)

schrodinger.application.phase.shape_screen_reporter.task_utils.setup_screen(reporter, features, tol, rules)¶

Creates a pharmacophore hypothesis from user-supplied strings of features, tolerances and feature-matching rules.

Parameters:

reporter (phase.PhpShapeScreenReporter) – Connection to a shape screen report database
features (str or NoneType) – String containing a comma-delimited list of query features to match. If None, all features in the query will be used.
tol (str) – String containing a dictionary-like specification of matching tolerances
rules (str) – String containing a dictionary-like specification of feature type matching rules

Returns:

The pharmacophore hypothesis with which to perform the screen

Return type:

phase.PhpHypoAdaptor

Raise:

ValueError if any of the supplied feature names is illegal or not found in the shape query, or if any of the tolerances or permitted feature strings is illegal.

schrodinger.application.phase.shape_screen_reporter.task_utils.truncate_hits(args: Namespace, logger: Optional[Logger] = None) → None¶: Writes a truncated hits file if args.max_hits is smaller than the number of hits in arg.hits. If the query isn’t supplied in a separate file, it’s assumed that the first structure in args.hits is the query, in which case the number of hits is assumed to be the total number of structures - 1. If truncation is done, the file <jobname>_truncated.<ext> is created, where <ext> is .maegz or .sdfgz, and arg.hits is reset to to that file name.