schrodinger.application.combinatorial_screen.fingerprint_utils module¶

This module provides Canvas fingerprint-related functionality needed for combinatorial similarity and diversity applications.

schrodinger.application.combinatorial_screen.fingerprint_utils.combine_fingerprints(subjob_names, outfile)¶

Combines fingerprints from subjobs to the indicated output file.

Parameters

subjob_names (list(str)) – Subjob names.
outfile (str) – Output fingerprint file.

schrodinger.application.combinatorial_screen.fingerprint_utils.create_reactant_fp_file(reactants_file, fp_file)¶

Creates a Canvas dendritic fingerprint file for a set of reactants in a .csv file or a .pfx zip archive.

Parameters

reactants_file (str) – Input .csv file with SMILES and titles, or .pfx archive
fp_file (str) – Output fingerprint file. Will contain titles as the structure ids and SMILES as the lone extra data column.

Returns

The number of fingerprints written

Return type

int

Raises

FileNotFoundError – If reactants_file cannot be found
canvas.ChmException – If a Canvas-related error occurs

schrodinger.application.combinatorial_screen.fingerprint_utils.get_reactant_combo_sim(query_fp, reactant_fp_lists, reactant_combo)¶

Returns the Tanimoto simliarity between the provided query fingerprint and the logical OR fingerprint of a particular reactant combination.

Parameters

query_fp (canvas.ChmSparseBitset) – Query fingerprint
reactant_fp_lists (list(list(canvas.ChmSparseBitset))) – Lists of reactant fingerprints
reactant_combo (list(int)) – A list of 0-based positions into reactant_fp_lists which define the combination of reactants

Returns

Tanimoto similarity

Return type

float

schrodinger.application.combinatorial_screen.fingerprint_utils.rank_reactants(fp_file, query_fp, max_reactants, alpha=1.0, beta=0.0)¶

Reads a file of reactant fingerprints, scores them against a query fingerprint, and returns titles, SMILES, reactant indices and bitsets sorted by decreasing score and capped at max_reactants. Scores are computed as the Tversky similarity between reactant and query:

ON(R & Q) / (ON(R & Q) + alpha * ON(R - Q) + beta * ON(Q - R))

where:

ON(R & Q) = Number of ‘on’ bits shared by reactant and query ON(R - Q) = Number of ‘on’ bits that are unique to reactant ON(Q - R) = Number of ‘on’ bits that are unique to query

Parameters

fp_file (str) – Input file of reactant fingerprints
query_fp (canvas.ChmSparseBitset) – Query fingerprint for scoring reactants
max_reactants (int) – Cap on the number of rows in each returned list
alpha (float) – Reactant weight
beta (float) – Query weight (use 1.0 for Tanimoto similarity)

Returns

Lists of titles, SMILES, zero-based indices and bitsets

Return type

list(str), list(str), list(int), list(canvas.ChmSparseBitset)

Raises

FileNotFoundError – If fp_file cannot be found
canvas.ChmException – If a Canvas-related error occurs

schrodinger.application.combinatorial_screen.fingerprint_utils.read_reactant_fps(fp_file)¶

Reads a file of reactant fingerprints and returns titles, SMILES and bitsets for all rows in the file.

Parameters

fp_file (str) – Input file of reactant fingerprints

Returns

Lists of bitsets, titles and SMILES

Return type

list(canvas.ChmSparseBitset), list(str), list(str)

Raises

FileNotFoundError – If fp_file cannot be found
canvas.ChmException – If a Canvas-related error occurs

schrodinger.application.combinatorial_screen.fingerprint_utils.smiles_to_fingerprint(smiles)¶

Returns a dendritic fingerprint for the provided SMILES string.

Parameters: smiles (str) – SMILES string
Returns: Bitset that represents the fingerprint
Return type: canvas.ChmSparseBitset
Raises: RuntimeError – If a Canvas-related error occurs

schrodinger.application.combinatorial_screen.fingerprint_utils.smiles_to_fingerprints(smiles_list)¶

Returns dendritic fingerprints for a list of SMILES strings.

Parameters: smiles_list (list(str)) – List of SMILES strings
Returns: Fingerprints for the provided SMILES strings
Return type: list(canvas.ChmSparseBitset)
Raises: RuntimeError – If a Canvas-related error occurs