schrodinger.pipeline.stages.glide module¶
Glide Docking & Gridgen stages.
DockingStage - stage for running Glide docking jobs
- GridgenStage - stage for generating Glide grids (not functional)
- HBOND_CONSTRAINTS: List of constraints in format: “label <atomnum>” METAL_CONSTRAINTS: List of constraints in format: “label <atomnum>” POSIT_CONSTRAINTS: List of constraints in format: “label <x> <y> <z> <radius>” NOE_CONSTRAINTS: List of constraints in format: “label <x> <y> <z> <min> <max>”
Copyright Schrodinger, LLC. All rights reserved.
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class
schrodinger.pipeline.stages.glide.
DockingStage
(*args, **kwargs)¶ Bases:
schrodinger.pipeline.stage.Stage
VSW stage for performing Glide docking
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buildDockedLigandsMap
()¶ Builds up a dict of self.docked_ligands from the job names in self.glide_jobnames.
If self._force_jobs is False, the job fails in the event of subjob failure. Otherwise, the errors are logged and the job continues.
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checkInputs
()¶
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check_subjob_output
(glide_jobname)¶ Will return the output file for the specified subjob. If no valid poses were produced, None is returned. Raises a descriptive RuntimeError if logfile and/or output file is incomplete.
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generateCsvFile
(pre_csv_file, csv_props)¶
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mergeGlideOutputs
(input_files, num_comps_to_keep, best_by_compound)¶ Takes in a list of _lib.mae or _pv.mae files, and merges them together based on glidescore. Assumes that the files have already been sorted with glide_sort (default in Glide).
Parameters: - input_files (list of str) – List of docked pose files (PV or LIB).
- num_comps_to_keep (int) – Stop merging when this number of compounds have been reached.
- best_by_compound – whether to keep only the best scoring pose per compound (based on unique ID property).
Returns: Merged file path and number of structures in it (including rec). If none of the structures docked (SIP mode), will return (None, 0).
Return type: (str, int)
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operate
()¶ Perform an operation on the input files.
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processJobOutputs
()¶
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recombineInputLigands
()¶
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setupJobs
()¶ Docks the structures in ligfiles to the grid <gridprefix>.
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write_glide_input_file
(ligfile, gridfile, nreport, glide_jobname)¶ Write Glide docking job input file
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class
schrodinger.pipeline.stages.glide.
GlideSortStage
(*args, **kwargs)¶ Bases:
schrodinger.pipeline.stage.Stage
Stage for sorting Glide _pv/lib.mae files. Currently, a sorted file is produced for each input file; that is, the input files are merged and sorted together.
The keywords specific to this stage are…
- BLOCK_SORT_BY_TITLE Whether to block-sort the poses by title. If
- True (the default), all poses with the same title are grouped and sorted by the INTRATITLE_SORT_KEYS keys. The blocks themselves are sorted by applying the SORT_KEYS to just the top pose in each block.
- INTRATITLE_SORT_KEYS The sort key(s) within a title block. The
- default is ‘r_i_glide_emodel’ (appropriate for Glide HTVS/SP results). Multiple sort keys must be whitespace-separated.
- SORT_KEYS The key(s) for sorting the pose file. If
- BLOCK_SORT_BY_TITLE is True, the blocks are sorted by the values of their top pose’s SORT_KEYS properties. Multiple sort keys must be whitespace-separated.
- OUTPUT_POSES_PER_TITLE The number of top poses per title to keep.
- Applies only if BLOCK_SORT_BY_TITLE is true. The default is 0, which means retain all poses.
- INPUT_TYPE Specify whether the receptor is (‘pv’) or is
- not (‘lib’) in the file. By default, the type will be determined from the file name (i.e., _pv/lib.mae).
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operate
()¶ Sort each input pose file using the application.glide.glideanalysis module. Generates a sorted output pose file for each input pose file.
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class
schrodinger.pipeline.stages.glide.
GridgenStage
(*args, **kwargs)¶ Bases:
schrodinger.pipeline.stage.Stage
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operate
()¶ Perform an operation on the input files.
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setupJobs
()¶
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class
schrodinger.pipeline.stages.glide.
MergeStage
(*args, **kwargs)¶ Bases:
schrodinger.pipeline.stage.Stage
Stage for merging up to 999 Glide output files with ‘glide_ensemble_merge’. The input files can be either PV or LIB, and have to be sorted by GlideScoreglide. The output file will also be sorted, and the GlideScores can be offset by a specified value for each input file.
The keywords specific to this stage are…
- NREPORT Save only the top NREPORT poses. The default is 0, which
- retains all poses.
- MAXPERLIG Retain at most MAXPERLIG poses for each ligand
- (determined by the structure title). The default is 1. Use 0 to retain all poses.
UNIQUEFIELD Property to uniquely identify compounds by. Default is title.
- OFFSETS List of GlideScore offsets (float) to be applied to the
- input structures. First item in the list is the offset for the first input, second is for second input, etc. If not specified, all are defaulted to 0.0.
- MARKERS List of string lables for each receptor. Each ligand will
- be marked by this value depending on which input set it originated from.
The stage takes up to 100 input structure file sets (PV or LIB) and generates a single output pose file.
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operate
()¶ Run the ‘glide_ensemble_merge’ script on all the input files from all sets, optionally applying GlideScore offsets to some sets. Generates a single output pose file.
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schrodinger.pipeline.stages.glide.
compress
(origFile)¶ Compresses the specified file and removes the original