fep_active_learning.py evaluate Command Help
Command: $SCHRODINGER/run -FROM scisol fep_active_learning.py evaluate
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usage: fep_active_learning.py evaluate [-h]
[-infile_list_file <infile_path_list>]
[-block_size <num_lig_per_block>]
[-smi_index <smiles_column_index>]
[-name_index <title_column_index>]
[-no_header]
[-result_prefix <output_file_prefix>]
[-remote_input_ligands]
[-restart_file <restart_pkl_file>]
[-avoid_splitting_csv_files]
[-infile INFILE]
[-props_filter_file <file>]
[-receptor <receptor>]
[-grid <gridfile>]
[-reference_ligand <reference_mae_file>]
[-jobname <jobname>]
[-stop_after <stop_workflow_after_stage>]
[-max_ml_eval_cpu <maximum_ml_evaluation_cpu>]
[-eval_with_mq] [-use_autoqsar]
[-fep_gpu_host <FEP_JOBS_GPU_HOST>]
[-max_fep_subjob_restarts <maximum_number_retries_fep_subjob>]
[-max_ligprep_cpu <maximum_ligprep_cpu>]
[-max_ffbuilder_cpu <maximum_ffbuilder_cpu>]
[-max_fep_subjobs <maximum_fep_subjobs>]
[-max_concurrent_fep_subjobs <maximum_concurrent_fep_subjobs>]
[-max_glide_cpu <maximum_glide_cpu>]
[-model <ml_model.qzip>]
[-random_seed <random_seed_number>]
[-overwrite_args] [-force_restart]
[-ligprep_args <ligprep_arguments>]
[-need_ligprep]
[-fep_job_batch_size <ligands_per_fep_job>]
[-opls_dir <opls_ff_dir>]
[-fep_restraints_file <fep_restraints_file>]
[-optimization_target ml_optimization_property]
[-use_graphdb]
[-graphdb_proj <graphdb_project_name>]
[-standalone_ffbuilder]
[-max_docking_cpu <maximum_docking_cpu>]
[-train_with_glide_feature]
[-feature_options <feature_apply_options>]
[-glide_mq]
[-extra_docking_inputs <input_file_of_extra_docking_inputs>]
[-need_align {mcs,fep-pose-builder,None}]
[-num_final_rescore_ligand <num_final_rescore_ligand>]
[-use_fep_mapper]
[-rescore_with_optimal_map]
[-fep_mapper_args <fep_mapper_arguments>]
[-fep_single_edge_args <fep_plus_arguments>]
[-fep_final_rescore_args <fep_plus_final_stage_rescore_arguments>]
[-al_fep_json_args_file]
[-core_smarts <fep_plus_core_smarts>]
[-complex_rest_atoms_rule <complex_rest_atoms_all_or_default>]
[-solvent_rest_atoms_rule <solvent_rest_atoms_all_or_default>]
[-receptor_rest_asl <ASL_of_receptor_rest_region>]
[-fep_groups_ph <fep_groups_ph>]
[-expand_protomers]
[-poses_per_lig <docking_poses_per_lig>]
[-minimal_mcs_similarity <glide_mcs_docking_minimal_similarity>]
[-mcs_no_accept_fla_clash]
[-mcs_docking_alignment_only]
[-mcs_mode {STATIC,STANDARD,SHAPE,FEP}]
[-edge_sim_cutoff <fep_map_edge_similarity_cutoff>]
[-exp_aff_propname EXP_AFF_PROPNAME]
[-exp_aff_unit {kcal/mol,pKi,Ki_nM,Ki_uM,Ki_mM}]
[-keep <num_returned_ligand> | -keep_fraction <fraction_of_returned_ligand>]
[-num_rescore_ligand <num_rescore_ligand> | -rescore_ligand_fraction <fraction_of_rescore_ligand>]
options:
-h, --help show this help message and exit
-random_seed <random_seed_number>
Random seed number for shuffling all the ligands
and seeding ligand_ml training.
-overwrite_args Overwrite previous arguments, Default is False.
-force_restart Force the workflow to restart when some restarting files are missing.
-ligprep_args <ligprep_arguments>
Arguments for using ligprep to prepare the ligands. Default is '-pht 1.0 -epik -s16'.
-need_ligprep Run ligprep on input ligands.
-fep_job_batch_size <ligands_per_fep_job>
Number of ligands per FEP job. Default is 100.
-opls_dir <opls_ff_dir>
Path of the OPLS force field directory.
-fep_restraints_file <fep_restraints_file>
Apply positional restraints to the receptor as specified
in the provided file. Only available for AL-FEP+ and AL-ABFEP.
The file should give the restraints in Ark format,
e.g., a file could contain: restraints={existing=ignore
new=[{atoms='asl:(protein and backbone and not a.ele H)'
force_constants=[1.0 2.0 3.0] name=posre_harm}]}
-optimization_target ml_optimization_property
Optimization target of the workflow.
Supported target:
*dG -> Optimize dG value
*LE -> Optimize ligand efficiency
*LLE -> Optimize ligand lipophilicity efficiency
*AEI -> Optimize ADME efficiency index
Default value is dG.
-use_graphdb Run FEP on GraphDB.
-graphdb_proj <graphdb_project_name>
Name of the GraphDB project for running FEP plus job.
-standalone_ffbuilder
Do not use graphdb's ffbuilder to run forcefield calculations.
Uses standalone ffbuilder. Default is False.
-max_docking_cpu <maximum_docking_cpu>
Maximum number of CPUs for Glide SIP jobs.
-train_with_glide_feature
Include Glide per residual score as additional features in ML model building.
Ligands supplied by -known_fep_dg will not be included in the initial training
if this flag is on. Residue interactions are obtained using Glide's score-in-place method.
-feature_options <feature_apply_options>
A space-separated string that configures the set of features used during training.
Trains separate models for each specified option and selects the best
performing model based on R2 score,
no_feature -> Train using only default ligand features.
additionally derived features will not be used.
only_feature -> Train using only additionally derived features.
ligand features will not be used.
with_feature -> Train using both additionally derived features and
ligand features.
Example:
-feature_options with_feature no_feature only_feature
Default value is no_feature.
-glide_mq Turn on Glide execution with ZMQ.
-extra_docking_inputs <input_file_of_extra_docking_inputs>
a file with additional Glide keywords and values for generating input poses.
-need_align {mcs,fep-pose-builder,None}
Select alignment tool for generating ligand poses.
Default is None.
-num_final_rescore_ligand <num_final_rescore_ligand>
Number of the best ligands determined by single edge map
FEP+ to run FEP+ with either full cycle closure map or optimal map.
Default is 100.
-use_fep_mapper Run fep_mapper.py to generate FEP+ input map.
Default is False.
-rescore_with_optimal_map
Run the final FEP+ rescore with optimal map instead of full cycle closure map.
Default is False.
-fep_mapper_args <fep_mapper_arguments>
Extra arguments for generating FEP mapper with fep_mapper.py.
-fep_single_edge_args <fep_plus_arguments>
Arguments string for single edge map FEP+ jobs.
Default is '-time 2000'
-fep_final_rescore_args <fep_plus_final_stage_rescore_arguments>
Arguments string for final full cycle closure or optimal map
FEP+ rescore jobs.
Default is '-time 10000'
-al_fep_json_args_file
.json file containing arguments for fep_mapper, single edge fep jobs
,and final rescore fep jobs. The format should be parsable by json.load() as:
{
"fep_mapper_args": { "arg": value, ... },
"fep_single_edge_args": { "arg": value, ... },
"fep_final_rescore_args": { "arg": value, ... }
}
-core_smarts <fep_plus_core_smarts>
SMARTS of customized core atoms when -use_fep_mapper is not used.
-complex_rest_atoms_rule <complex_rest_atoms_all_or_default>
Rule for setting the ligand REST atoms in complex leg.
Default is default
-solvent_rest_atoms_rule <solvent_rest_atoms_all_or_default>
Rule for setting the ligand REST atoms in solvent leg.
Default is default
-receptor_rest_asl <ASL_of_receptor_rest_region>
ASL for setting the REST atoms of the receptor.
-fep_groups_ph <fep_groups_ph>
pH for FEP Groups population calculations.
Requires -expand_protomers. Default is 7.4.
-expand_protomers Expand selected ligands to include protomers for FEP Groups.
-poses_per_lig <docking_poses_per_lig>
Number of poses generated per ligand from Glide MCS
docking or from fep-pose-builder. Default value is 1.
-minimal_mcs_similarity <glide_mcs_docking_minimal_similarity>
Minimal similarity in MSC docking for pose generation.
Default value is 0.3.
-mcs_no_accept_fla_clash
Align the pose from a failed docked ligand to the reference ligand.
Default value is True.
-mcs_docking_alignment_only
Force docking job to find a pose.
Default value is False.
-mcs_mode {STATIC,STANDARD,SHAPE,FEP}
STATIC mode runs in parallel one ligand per subjob.
STANDARD mode runs serially (regular MCS docking setup).
SHAPE mode applies Shape constraint on all ref atoms.
FEP applies SMARTS constraints on ref MCS atoms.
SHAPE and FEP mode set input ref ligand as the docking ref ligand.
Default value is FEP.
-edge_sim_cutoff <fep_map_edge_similarity_cutoff>
Minimal similarity required to connect two nodes when building a FEP+ map.
Default value is 0.0.
-exp_aff_propname EXP_AFF_PROPNAME
Property name of reference ligands' experimental affinity.
Required if not 'r_fepmapper_exp_dG'.
-exp_aff_unit {kcal/mol,pKi,Ki_nM,Ki_uM,Ki_mM}
Unit of reference ligands' experimental affinity.
Valid options are: kcal/mol, pKi, Ki_nM, Ki_uM, Ki_mM.
Default is kcal/mol.
-keep <num_returned_ligand>
Number of best ligands to be returned. Default is 100000.
-keep_fraction <fraction_of_returned_ligand>
Fraction of the ligands to be returned.
-num_rescore_ligand <num_rescore_ligand>
Number of the best ligands predicted by the last
ML model to run rescore with FEP+ single edge or
AB-FEP. Default is 1000
-rescore_ligand_fraction <fraction_of_rescore_ligand>
Fraction of the best ligands to run FEP rescore (single edge for small molecule FEP).
file options:
-infile_list_file <infile_path_list>
A file that contains a list of infile paths.
-block_size <num_lig_per_block>
Number of ligands in each sub input ligands file. Default is
15000 for AL-FEP+/AL-ABFEP and 100,000 for AL-Glide.
-smi_index <smiles_column_index>
1-based column index of ligand's SMILES.
Default is 1.
-name_index <title_column_index>
1-based column index of ligand's title.
Default is 2.
-no_header Whether the input file(s) has header in the first line.
-result_prefix <output_file_prefix>
prefix of the .csv result files. Default is -jobname.
-remote_input_ligands
Whether input ligand files are located at remote. Absolute
paths of input ligand files are required if this flag is
provided.
-restart_file <restart_pkl_file>
.pkl file for restarting or continuing the active learning
workflow.
-avoid_splitting_csv_files
Enable this option to use pre-split ligand CSV files, avoiding redundancy.
Requirements:
- Reorder columns: 'SMILES' first, 'Title' second.
- Each split CSV must have the same header: 'SMILES, Title'.
- Remove any additional columns.
- Optionally gzip compress each split CSV file.
- Archive all pre-split CSV files into one directory and zip compress it.
Pass the zipped directory to '-infile'.
-infile INFILE .csv, .smi or .mae file(s) that contains all the ligand
SMILES. Multiple files can be included by specifying
multiple -infile options.
-props_filter_file <file>
Path to a file containing property and / or smarts filters.
Each line defines a filter a hit must satisfy. Filters are specified as:
<property>,<operator>,<value1>,<value2>...
<property>: Name of a property. Available properties include:
• Physicochemical: ALOGP, MW, PSA, HBA, HBD
• Structural: TOTAL_RINGS, STEREO_CENTERS, FORMAL_CHARGE
• Classification: PROPERTY_CLASS
• Substructure: SMARTS (for substructure matching)
<operator>: SQL logical operator: =, <, >, <=, >=, <>, BETWEEN, LIKE, IN.
<value(s)>: Target value(s). Use exactly 2 values for BETWEEN,
1 or more for IN, and 1 for all other operators.
Examples:
AlogP,BETWEEN,2.0,5.0 # Lipophilicity range
MW,<,500 # Molecular weight limit
HBD,<=,5 # Hydrogen bond donors
STEREO_CENTERS,<,3 # Stereochemical complexity
SMARTS,IN,c1[nX2][nX3]cc1 # Substructure matching
Note: Physicochemical properties are computed and stored automatically.
-receptor <receptor> Protein receptor .mae file.
-grid <gridfile> Glide grid file for docking.
-reference_ligand <reference_mae_file>
Maestro file that contains the reference ligand(s).
job options:
-jobname <jobname> Job name of the active learning workflow run.
-stop_after <stop_workflow_after_stage>
Terminate the workflow after the specified stage finished.
Specify FinishAll (case-insensitive) to run all the remaining stages.
For convenience, you can also specify 'iter_X' to stop after
iteration X (e.g., 'iter_1', 'iter_2', etc.).
-max_ml_eval_cpu <maximum_ml_evaluation_cpu>
Allowed maximum number of CPU for
machine learning evaluation subjobs.
-eval_with_mq Enables ligand_ml evaluation using zeroMQ.
Specify the number of evaluation jobs with -max_ml_eval_cpu.
If running a screen or pilot, the -chosen_models flag will
automatically set to TorchGraphConv models.
-use_autoqsar Use AutoQSAR instead of DeepAutoQSAR for ML model building and evaluation. Only supports AL-FEP+ and AL-ABFEP+
-fep_gpu_host <FEP_JOBS_GPU_HOST>
GPU host name for running FEP jobs. Default is the same as -train_host.
-max_fep_subjob_restarts <maximum_number_retries_fep_subjob>
Maximum number of restart attempts for per FEP job.
Default is 1estart. This option does not impact the
graphdb or FEP+ web service runs which are restarted automatically.
-max_ligprep_cpu <maximum_ligprep_cpu>
Allowed maximum number of CPUs for ligprep subjobs.
-max_ffbuilder_cpu <maximum_ffbuilder_cpu>
Allowed maximum number of CPUs for force field builder subjobs.
-max_fep_subjobs <maximum_fep_subjobs>
Allowed maximum number of FEP jobs.
-max_concurrent_fep_subjobs <maximum_concurrent_fep_subjobs>
Allowed maximum number of concurrently running FEP jobs.
-max_glide_cpu <maximum_glide_cpu>
Allowed maximum number of CPUs for Glide subjobs.
evaluate options:
-model <ml_model.qzip>
Generated ligand_ml .qzip model.