complex_descriptors.py Command Help
Command: $SCHRODINGER/run complex_descriptors.py
usage: $SCHRODINGER/run complex_descriptors.py [-h] -input_file INPUT_FILE
[-stprops OUTPUT_STRUCTURE_FILE]
[-out_rep {centroid,eta}]
[-jaguar]
[-jaguar_keywords [<key_1>=<value_1> [<key_2>=<value_2> ...]]]
[-jaguar_out_files [JAGUAR_OUT_FILES ...]]
[-ligfilter]
[-no_organometallic]
[-nonmetallic_centers NONMETALLIC_CENTERS]
[-canvas] [-moldescriptors]
[-moldes_flags FLAG [FLAG ...]]
[-include_vectorized]
[-fingerprints] [-savefiles]
[-HOST <hostname>] [-SAVE]
[-JOBNAME JOBNAME] [-TPP TPP]
Driver for reporting machine learning descriptors for metal complexes.
Copyright Schrodinger, LLC. All rights reserved.
options:
-h, -help Show this help message and exit.
-input_file INPUT_FILE
Specify an input Maestro file. (default: None)
-stprops OUTPUT_STRUCTURE_FILE
Specify an output Maestro file for structures with
each descriptor stored as a structure or atom
property. (default: None)
-out_rep {centroid,eta}
Force a specific output representation. If not
provided it will be the opposite of the input
representation. (default: None)
-jaguar Specify to calculate Jaguar descriptors. (default:
False)
-jaguar_keywords [<key_1>=<value_1> [<key_2>=<value_2> ...]]
If Jaguar jobs need to be run to calculate the Jaguar
descriptors (see flag -jaguar) then specify the Jaguar
&gen section key-value pairs here. Each key-value pair
should be separated from the next by whitespace and
each should be represented in terms of a
"<key>=<value>" pair. (default: ['dftname=B3LYP',
'basis=LACVP**'])
-jaguar_out_files [JAGUAR_OUT_FILES ...]
To calculate the Jaguar descriptors (see flag -jaguar)
using existing Jaguar *.out files then specify the
files here. Files should be given in the same order as
the structures specified with the flag -input_file.
(default: None)
-ligfilter Specify to calculate Ligfilter descriptors. (default:
False)
-no_organometallic Whether organometallic descriptors should be skipped.
(default: False)
-nonmetallic_centers NONMETALLIC_CENTERS
Nonmetal elements to also consider when finding center
atoms for organometallic descriptors. (default: None)
-canvas Specify to calculate Canvas descriptors. (default:
False)
-moldescriptors Specify to calculate Molecular Descriptors
descriptors. (default: False)
-moldes_flags FLAG [FLAG ...]
Flags for the moldescriptors utility used to generate
the Molecular Descriptors. These should be a space-
separated list of flags *without* the leading "-". The
use of a YAML file is not supported, and the flags
should not contain the input structure file name,
-jobname, -omae or -ocsv flags, or any job control
options. If Mopac keywords are specified they must be
specified last. Example: -moldes_flags topo qikprop
mopac method am1 plotMO 3 mopac_keywords mullik bonds
super (default: ['topo'])
-include_vectorized Specify whether to include instance specific
descriptors that are vectorized, for example depending
on the molecule's geometric orientation, atom
indexing, etc. (default: False)
-fingerprints Create fingerprint files. (default: False)
-savefiles Save files created by subjobs (default: False)
Job Control Options:
-HOST <hostname> Run job remotely on the indicated host entry.
(default: localhost)
-SAVE Return zip archive of job directory at job completion.
(default: False)
-JOBNAME JOBNAME Provide an explicit name for the job. (default: None)
-TPP TPP Specify the number of threads to use for parallelizing
any Jaguar subjobs. (default: 1)