schrodinger.pipeline.stages.pull module¶

A stage for extracting a subset of ligands/compounds.

The Pull stage identifies a subset of compounds from one set of ligand structures, and extracts all variants of those compounds from a second set of ligand structures.

class schrodinger.pipeline.stages.pull.PullStage(*args, **kwargs)¶

Bases: schrodinger.pipeline.stage.Stage

Stage for extracting a subset of ligands/compounds (and their variants) from a second set of ligand files, given the number or percent to keep from a first set of ligand files. The first set must be ordered; i.e., the ligands to keep appear earliest in the set. Compounds in the second set that don’t appear in the first set are ignored.

The keywords specific to this stage are…

UNIQUEFIELD The ligand property that identifies a compound.
Multiple ligands with the same UNIQUEFIELD value are considered variants of the compound. The default is the structure title (‘s_m_title’).

NUM_TO_KEEP The number of compounds from the first set to
extract from the second set. The compounds kept are those that appear earliest in the first set.

PERCENT_TO_KEEP The percentage of compounds from the first set to
extract from the second set. The compounds kept are those that appear earliest in the first set. Ignored if NUM_TO_KEEP is used.

KEEP_CHARGES If set to True, then after the ligand is pulled from
the original file, the partial charges are set to what they were in the second file. NOTE: If set, only ONE ligand with specified field should be in the first file set. NOTE: solvation_charge property is assummed to be equal to the partial_charge.

CHARGE_PROPERTY If KEEP_CHARGES is True, the charges are taken from
this atom-level property. Default is ‘r_m_charge1’. These charges from the first set are placed in the ‘r_m_charge1’ (partial_charge) and ‘r_m_charge2’ (solvation_charge) properties of the pulled set, not the CHARGE_PROPERTY in the pulled set.

If neither NUM_TO_KEEP or PERCENT_TO_KEEP are present, all compounds in the first set are extracted from the second set. In all cases, every variant of a kept compound from the second set is extracted.

This stage takes one ordered input structure set that identifies the ligands to extract, a second input structure set from which those ligands are extracted, and it generates one output structure file set, each containing about 100,000 structures.

Issues: Keeping the first N compounds may not choose compounds from Glide results in the proper manner. If the variants of a compound are chemically distinct, it’s appropriate to choose the top compounds based on GlideScore. However, if the variants differ only in their conformations (such as when saving multiple poses per ligand), Emodel (not GlideScore) should be used to determine the representative variant of the compound for GlideScore comparison with other compounds. Hopefully, this doesn’t come up often, because it would be very tricky to reflect the proper ordering in the input files if there are both Ligprep-type variants and conformation-variants.

__init__(*args, **kwargs)¶: See class docstring.

operate()¶: Extract a subset of the first set compounds from the second set of ligand input structure files. Makes a list of compounds (identified by UNIQUEFIELD) from the first set, pares down the list according to the NUM_TO_KEEP or PERCENT_TO_KEEP setting, and extract all variants of those compounds from the second set. Raises a RuntimeError if any input file cannot be read, if there is a problem accessing the UNIQUEFIELD property of any ligand, if there is a problem writing any output file, or if no ligands are extracted.

pullCompounds()¶