ch_ligand_driver Command Help
Command: $SCHRODINGER/utilities/ch_ligand_driver
usage: ch_ligand_driver [OPTIONS] <Template_in><Cores_in> <Cores_out> <Options>
Ligand-Based Core Hopping.
[-h] [-HOST <hostname>] [-WAIT] [-NOJOBID] [-t T] [-d D] [-g G] [-s S]
[-n N] [-r R] [-m M] [-x X] [-f F] [-c C] [-o O] [-p P] [-b B] [-a A]
[--ligand_bump LIGAND_BUMP] [--core_restrict CORE_RESTRICT]
[--core_restrict_from CORE_RESTRICT_FROM]
[--require_pharma REQUIRE_PHARMA] [--pharma_dist PHARMA_DIST]
[--min_hbonds MIN_HBONDS] [--require_hbonds REQUIRE_HBONDS]
[--hbond_dist HBOND_DIST] [--min_heavy MIN_HEAVY]
[--max_heavy MAX_HEAVY] [--min_acceptors MIN_ACCEPTORS]
[--max_acceptors MAX_ACCEPTORS] [--min_donors MIN_DONORS]
[--max_donors MAX_DONORS] [--min_no MIN_NO] [--max_no MAX_NO]
[--min_chiral MIN_CHIRAL] [--max_chiral MAX_CHIRAL]
[--min_times_found MIN_TIMES_FOUND] [--max_times_found MAX_TIMES_FOUND]
[--ignore_grow_name IGNORE_GROW_NAME] [--pareto PARETO]
[--query_cuda: QUERY_CUDA:] [--cuda CUDA] [--ngpu NGPU]
[--watermap WATERMAP] [--smiles SMILES] [--nolinkers NOLINKERS]
[--linkers LINKERS] [--linker_geom_score LINKER_GEOM_SCORE]
[--attachment_points ATTACHMENT_POINTS [ATTACHMENT_POINTS ...]]
[--time TIME] [--time_summary TIME_SUMMARY] [--max_output MAX_OUTPUT]
[--terminal_out TERMINAL_OUT] [--result_viewer_pipe RESULT_VIEWER_PIPE]
[--no_execute]
template_file cores_file output_file
positional arguments:
template_file Template input file specifying initial structure
cores_file Input file specifying candidate cores
output_file Output file name
options:
-h, --help show this help message and exit
-t T Set the computation threads (>=0, default number of
cpu's)
-d D Set the verbosity (>=1, default 1)
-g G Set the thread-dispatch verbosity (>=1, default 1)
-s S Set the density of the star vectors (>=1, default 3)
-n N Set the number of translations on each star vector
(>=1, default 3)
-r R Set the number of rotations around each star vector
(>=1, default 12)
-m M Set the minimum number in the pipeline at once (>=0,
default nthreads+1)
-x X Set the maximum number in the pipeline at once (>=1,
default 2*nthreads+2)
-f F Set maximum geometric from chord distance (>0, default
1.0)
-c C Set maximum sidechain RMSD (>0, default 1.0)
-o O Set minimum core overlap score (>0, default 0.0)
-p P Define a receptor with a pocket the original ligand
was placed in (Mae file, default None)
-b B Receptor bump check maximum distance (>=0, default
2.2)
-a A Receptor bump check maximum bumps (>=0, default 2)
--ligand_bump LIGAND_BUMP
Ligand bump check maximum distance (>=0, default 2.2)
--core_restrict CORE_RESTRICT
Name of property denoting to-atoms
--core_restrict_from CORE_RESTRICT_FROM
Name of property denoting from-atoms
--require_pharma REQUIRE_PHARMA
Respect template pharma constraints (0/1, default 0)
--pharma_dist PHARMA_DIST
Maximum distance for pharma atom match (>0, default
0.75)
--min_hbonds MIN_HBONDS
Require minimum receptor hbond interactions(>=0,
default 0)
--require_hbonds REQUIRE_HBONDS
Respect receptor hbond constraints (0/1, default 0)
--hbond_dist HBOND_DIST
Maximum distance for hbond match (>0, default 3.0)
--min_heavy MIN_HEAVY
Minimum heavy atoms on core (>=0, default 0, sqlite
input only)
--max_heavy MAX_HEAVY
Maximum heavy atoms on core (>=0, default 0, sqlite
input only)
--min_acceptors MIN_ACCEPTORS
Minimum potential acceptors on core (>=0, default 0,
sqlite input only)
--max_acceptors MAX_ACCEPTORS
Maximum potential acceptors on core (>=0, default 0,
sqlite input only)
--min_donors MIN_DONORS
Minimum potential donors on core (>=0, default 0,
sqlite input only)
--max_donors MAX_DONORS
Maximum potential donors on core (>=0, default 0,
sqlite input only)
--min_no MIN_NO Minimum Nitrogen+Oxygen atoms on core (>=0, default 0,
sqlite input only)
--max_no MAX_NO Maximum Nitrogen+Oxygen atoms on core (>=0, default 0,
sqlite input only)
--min_chiral MIN_CHIRAL
Minimum chiral centers on core (>=0, default 0, sqlite
input only)
--max_chiral MAX_CHIRAL
Maximum chiral centers on core (>=0, default 0, sqlite
input only)
--min_times_found MIN_TIMES_FOUND
Minimum times a core was found (>=0, default 0, sqlite
input only)
--max_times_found MAX_TIMES_FOUND
Maximum times a core was found (>=0, default 0, sqlite
input only)
--ignore_grow_name IGNORE_GROW_NAME
Don't skip cores with glide-linkers (0/1, default 0)
--pareto PARETO Add pareto score of 3 normal scores (0/1, default 1)
--query_cuda: QUERY_CUDA:
Query cuda devices and return
--cuda CUDA Allow cuda to be used (if available) (0/1, default 1)
--ngpu NGPU Select a single GPU to use. (>=0, Off by default)
--watermap WATERMAP Applies watermap scoring to output cores (filename)
--smiles SMILES Core-hop using only a single smiles (Smiles string)
--nolinkers NOLINKERS
Explicitly disable the use of linkers (0/1, default 0)
--linkers LINKERS Provide linkers to use in place of Schrodinger
provided linkers (filename.sqlite)
--linker_geom_score LINKER_GEOM_SCORE
--linker_geom_score arg: Select linkers purely on
their geometric fit, not order in file (0/1, default
0)
--attachment_points ATTACHMENT_POINTS [ATTACHMENT_POINTS ...]
Atom pairs denoting attachment points, such as 1,2
4,10 forattachment points between atoms 1 and 2, and 4
and 10
--time TIME Report stage times (0/1, default 0)
--time_summary TIME_SUMMARY
Report final times (0/1, default 0)
--max_output MAX_OUTPUT
Maximum number of output structures (>0, default
10,000)
--terminal_out TERMINAL_OUT
Output to stderr instead of log (only useful with
-NOJOBID)
--result_viewer_pipe RESULT_VIEWER_PIPE
(Used only by GUI)
--no_execute Don't actually call the backend, just prepare input
files
Job Control Options:
-HOST <hostname> Run job remotely on the indicated host entry.
-WAIT Do not return a prompt until the job completes.
-NOJOBID Run the job directly, without Job Control layer.