fep_pose_builder.py Command Help
Command: $SCHRODINGER/run fep_pose_builder.py
models.param_cli: Skipping param 'default_ref_title' in argparser - unsupported type. To silence this message, call skipParamArg() on this subparam.
models.param_cli: Skipping param 'ligand_asl' in argparser - unsupported type. To silence this message, call skipParamArg() on this subparam.
usage: fep_pose_builder.py [-h] -references REFERENCES [-receptor RECEPTOR]
[-max_lig_size MAX_LIG_SIZE]
[-skip_ligprep [SKIP_LIGPREP]]
[-ligprep_file LIGPREP_FILE | -ligprep_args LIGPREP_ARGS]
[-ligfilter_file LIGFILTER_FILE]
[-match_input_title]
[-ligand_to_ref_map LIGAND_TO_REF_MAP]
[-default_ref_title DEFAULT_REF_TITLE]
[-smarts_to_ref_map SMARTS_TO_REF_MAP]
[-auto_ref_select {SIM_2D,SIM_3D}]
[-core_definition {MCS,BM,auto,both,SMARTS}]
[-align_program {tug_align,align_ligands,confgen,auto}]
[-align_refine [ALIGN_REFINE]]
[-skip_clash_resolution [SKIP_CLASH_RESOLUTION]]
[-exclude_asl EXCLUDE_ASL] [-ofac OFAC]
[-include_h [INCLUDE_H]]
[-max_conformers MAX_CONFORMERS]
[-only_check_ring_spears [ONLY_CHECK_RING_SPEARS]]
[-receptor_mapping RECEPTOR_MAPPING]
[-ref_to_cov_settings_map REF_TO_COV_SETTINGS_MAP]
[-not_write_ref [NOT_WRITE_REF]]
[-poses_per_lig POSES_PER_LIG]
[-refine_output [REFINE_OUTPUT]]
[-filter_pseudo_chiral_amine [FILTER_PSEUDO_CHIRAL_AMINE]]
[-HOST <hostname>] [-JOBNAME JOBNAME]
ligands
FEP+ Pose Builder for 2D or 3D input ligands.
Pose builder consists of:
1) LigPrep - Generate initial conformations, including tautomeric/protonation
state assignment, optionally filter out undesired states.
2) Reference Matching - Assign a reference to each ligand.
3) Ligand Alignment - Use either the align_ligands or tug_align backend to
align ligands to its reference.
4) Clash Resolution - Resolve ligand clashes with a provided receptor,
freezing in place that ligand's core atoms.
positional arguments:
ligands Input ligands file. Can be in Maestro or SD format.
options:
-h, --help show this help message and exit
-references REFERENCES
Reference ligands file containing docked 3D poses.
-receptor RECEPTOR A structure file containing the receptor. Additional
membrane components, e.g. POPC and water can also be
provided but they need to be grouped with the receptor
structure in Maestro. This is required unless
-skip_clash_resolution is provided.
-max_lig_size MAX_LIG_SIZE
The maximum allowed ligand size in number of atoms.
This is to prevent the program from running if the
input contains large structures (e.g. protein)
Default: (500)
-not_write_ref [NOT_WRITE_REF]
Do not write the reference ligands to the
outputstructure file.
-poses_per_lig POSES_PER_LIG
The maximum number of output poses to write for each
ligand. More than 1 poses per lig only apply when
-align_program is confgen.
-refine_output [REFINE_OUTPUT]
Refine the output poses to ensure the R group pose
consistency between different states of each ligand.
This works only when -poses_per_lig is 1 and the
ligands contain multiple potential ring snappings in
alignment. This is achieved by generating multiple
ring flip poses for each ligand with Confgen and
select poses with highest shape similarity to the best
pose across states. However, it is recommended to
generate multiple poses in such cases. Note this will
not work for macrocycle and disconnected R group
alignment.
-filter_pseudo_chiral_amine [FILTER_PSEUDO_CHIRAL_AMINE]
Filter output to keep only structures with the same
pseudochiral amine chirality as the reference
structure. For each reference, detect pseudochiral
protonated amine groups and filter corresponding
ligand structures to match the reference chirality.
Ligand Preparation Settings:
-skip_ligprep [SKIP_LIGPREP]
Whether to skip the LigPrep stage. This will only skip
the LigPrep stage, if a ligfilter file is provided
ligfilter will still be run.
-ligprep_file LIGPREP_FILE
The input file containing settings that can optionally
be provided to LigPrep. (Equivalent to the file
provided via -inp to the ligprep backend
-ligprep_args LIGPREP_ARGS
Input arguments that can optionally be provided to the
LigPrep backend. Default: -epikx -ph 7.4 -pht 2.0 -m 4
-ligfilter_file LIGFILTER_FILE
An optional filter file to pass to the LigFilter
backend. This uses the same format as ligfilter.
-match_input_title When used, this option will try to find the ligprep
output structures that match the input ligand
structure and keep them the original input title while
adding the suffixes for other states. If no output
structure matches the input structure, all output
structures will have suffixes. Only works when
-skip_ligprep is not set.
Reference Matching Settings:
Match ligands to references using a hierarchical approach. 1) ligand_to_ref_map 2) smarts_to_ref_map 3) default_ref_title 4) 3D similarity
-ligand_to_ref_map LIGAND_TO_REF_MAP
A csv file containing an explicit mapping between
ligand titles and the reference titles that they
should be matched to. The csv should have two columns:
title, ref_title.
-default_ref_title DEFAULT_REF_TITLE
An optional reference title to assign to all ligands
not matched by -ref_csv.
-smarts_to_ref_map SMARTS_TO_REF_MAP
An optional csv mapping SMARTS patterns to the
references that ligands which match a pattern should
be matched to, and a column indicating whether
align_ligands or tug_align to use. The csv should have
three columns: smarts,ref_title,align_program.
-auto_ref_select {SIM_2D,SIM_3D}
What automatic reference matching algorithm to use
when multiple reference ligands are provided and no
reference mapping: -ligand_to_ref_map
-default_ref_title or -smarts_to_ref_map are supplied.
Options are scaffold based 2D similarity or FEP 3D
similarity. 2D scaffold based similarity is faster.
Ligand Alignment Settings:
-core_definition {MCS,BM,auto,both,SMARTS}
Whether to use MCS, Bemis-Murcko (BM) scaffolds or
SMARTS as the common core during alignment with
align_ligands. With SMARTS, the -smarts_to_ref_map
argument must be provided, and the provided SMARTS
patterns will be used directly as the core. Otherwise,
if -smarts_to_ref_map is provided, the MCS/BM core
containing the SMARTS patterns will be used. With auto
the larger core definition between MCS and BM will be
used. With 'both', both MCS and BM core will be used
and the better alignment will be kept. This option has
no effect when using '-align_program tug_align'.
Default auto.
-align_program {tug_align,align_ligands,confgen,auto}
Program to use for ligand alignment. With auto,
alignment program will be determined by the input
ligand type or SMARTS pattern type. Tug_align will be
used if the input ligand contains macrocycle or the
SMARTS pattern is a disconnected SMARTS. Confgen will
be used if poses_per_lig is greater than 1. Otherwise
align_ligands will be used. Default auto.
-align_refine [ALIGN_REFINE]
Whether to use the -refine argument with align_ligands
backend. This generates additional conformers with
core atoms held fixed, increasing the average in-place
shape similarity between all pairs of ligands. This
will increase the alignment time significantly.
Clash Resolution Settings:
-skip_clash_resolution [SKIP_CLASH_RESOLUTION]
Whether to skip the clash resolution stage.
-exclude_asl EXCLUDE_ASL
An ASL specifying atoms in the receptor to ignore
during clash resolution (default: water or
atom.element H)
-ofac OFAC The cutoff ratio of the distance between two atoms to
their van der waals radius to consider a clash.
-include_h [INCLUDE_H]
Whether to include hydrogen atoms in the clash
resolution logic.
-max_conformers MAX_CONFORMERS
How many conformers to generate during clash
resolution. The conformer with the fewest clashes is
returned as the best conformer.
-only_check_ring_spears [ONLY_CHECK_RING_SPEARS]
Whether to only check for ring spears between ligand
and receptor initially in clash resolution.
-receptor_mapping RECEPTOR_MAPPING
A csv file containing an explicit mapping between the
reference titles and receptor titles that they should
be matched to. The csv should have two columns:
ref_title, receptor_title
Covalent Settings:
-ref_to_cov_settings_map REF_TO_COV_SETTINGS_MAP
A csv file mapping reference titles to covalent
docking settings. The csv should have columns:
ref_title,rxn_type,rxn_file,attachment_residue
Job Control Options:
-HOST <hostname> Run job remotely on the indicated host entry.
-JOBNAME JOBNAME Provide an explicit name for the job.