reaction_workflow_driver.py Command Help
Command: $SCHRODINGER/run reaction_workflow_gui_dir/reaction_workflow_driver.py
usage: $SCHRODINGER/run reaction_workflow_gui_dir/reaction_workflow_driver.py
[-h] [-dedup_geom_eps DEDUP_GEOM_EPS]
[-csearch_engine {Macromodel,Crest}] [-forcefield FORCE_FIELD]
[-skip_eta_rotamers] [-metal_index METAL_INDEX] [-com_fn COM_FN]
[-seed SEED] [-n_conformers N_CONFORMERS]
[-pp_rel_energy_thresh PP_REL_ENERGY_THRESH] [-return_csearch_files]
[-qm_selection] [-n_rotamers N_ROTAMERS] [-refined_energy]
[-refined_energy_jaguar_keywords [<key_1>=<value_1> [<key_2>=<value_2> ...]]]
[-refined_energy_thermo_correction]
[-refined_energy_thermo_correction_jaguar_keywords [<key_1>=<value_1> [<key_2>=<value_2> ...]]]
[-refined_energy_n_conformers REFINED_ENERGY_N_CONFORMERS]
[-refined_energy_pp_rel_energy_thresh REFINED_ENERGY_PP_REL_ENERGY_THRESH]
[-mopac] [-xtb] [-uma]
[-jaguar_keywords [<key_1>=<value_1> [<key_2>=<value_2> ...]]]
[-ts_jaguar_keywords [<key_1>=<value_1> [<key_2>=<value_2> ...]]]
[-temp_start TEMP_START] [-temp_step TEMP_STEP] [-temp_n TEMP_N]
[-press_start PRESS_START] [-press_step PRESS_STEP] [-press_n PRESS_N]
[-temp_press_props_file TEMP_PRESS_PROPS_FILE] [-return_jaguar_files]
[-solvation_entropy]
[-solvation_entropy_solvent {1,1,1-trichloroethane,1,1,2-trichloroethane,1,2,4-trimethylbenzene,1,2-dibromoethane,1,2-dichloroethane,1,2-ethanediol,1,4-dioxane,1-bromo-2-methylpropane,1-bromooctane,1-bromopentane,1-bromopropane,1-butanol,1-chlorohexane,1-chloropentane,1-chloropropane,1-decanol,1-fluorooctane,1-heptanol,1-hexanol,1-hexene,1-hexyne,1-iodobutane,1-iodohexadecane,1-iodopentane,1-iodopropane,1-nitropropane,1-nonanol,1-octanol,1-pentanol,1-pentene,1-pentyne,1-propanol,2,2,2-trifluoroethanol,2,2,4-trimethylpentane,2,4-dimethylpentane,2,4-dimethylpyridine,2,6-dimethylpyridine,2-bromopropane,2-butanol,2-chlorobutane,2-heptanone,2-hexanone,2-methoxyethanol,2-methyl-1-propanol,2-methyl-2-propanol,2-methylpentane,2-methylpyridine,2-methyltetrahydrofuran,2-nitropropane,2-octanone,2-pentanone,2-propanol,2-propen-1-ol,3-methylpyridine,3-pentanone,4-heptanone,4-methyl-2-pentanone,4-methylpyridine,5-nonanone,DMSO,E-1,2-dichloroethene,E-2-pentene,N-methylaniline,N-methylformamide,Z-1,2-dichloroethene,a-chlorotoluene,acetic acid,acetic_acid,acetone,acetonitrile,acetophenone,amyl acetate,aniline,anisole,benzaldehyde,benzene,benzonitrile,benzyl alcohol,benzyl_alcohol,bromobenzene,bromoethane,bromoform,butanal,butanenitrile,butanoic acid,butanoic_acid,butanone,butyl ethanoate,butyl_ethanoate,butylamine,carbon disulfide,carbon tetrachloride,carbon_disulfide,carbon_tet,chlorobenzene,chloroform,cis-1,2-dimethylcyclohexane,cis-decalin,cyclohexane,cyclohexanone,cyclopentane,cyclopentanol,cyclopentanone,decalin,decalin_(mixture),dibromomethane,dibutyl_ether,dibutylether,dichloroethane,dichloromethane,diethyl_ether,diethyl_sulfide,diethylamine,diethylether,diethylsulfide,diiodomethane,diisopropyl ether,diisopropyl_ether,dimethyl disulfide,dimethyl_disulfide,dimethylacetamide,dimethylformamide,dioxane,diphenyl ether,diphenylether,dipropylamine,dma,dmso,e-1,2-dichloroethene,e-2-pentene,ethanethiol,ethanol,ethyl acetate,ethyl methanoate,ethyl phenyl ether,ethyl_ethanoate,ethyl_methanoate,ethyl_phenyl_ether,ethylbenzene,fluorobenzene,formamide,formic acid,formic_acid,hexanoic acid,hexanoic_acid,iodobenzene,iodoethane,iodomethane,iso-butanol,isopropylbenzene,m-cresol,m-xylene,mesitylene,methanol,methyl acetate,methyl benzoate,methyl butanoate,methyl formate,methyl propionate,methyl_benzoate,methyl_butanoate,methyl_ethanoate,methyl_methanoate,methyl_propanoate,methylcyclohexane,n-butylbenzene,n-decane,n-dodecane,n-heptane,n-hexadecane,n-hexane,n-methylaniline,n-methylformamide_(mixture),n-nonane,n-octane,n-pentadecane,n-pentane,n-undecane,nitrobenzene,nitroethane,nitromethane,o-chlorotoluene,o-cresol,o-dichlorobenzene,o-nitrotoluene,o-xylene,p-isopropyltoluene,p-xylene,pentanal,pentanoic acid,pentanoic_acid,pentyl_ethanoate,pentylamine,perfluorobenzene,propanal,propanenitrile,propanoic acid,propanoic_acid,propyl acetate,propyl_ethanoate,propylamine,pyridine,pyrrolidine,sec-butylbenzene,tert-butanol,tert-butylbenzene,tetrachloroethene,tetrahydrofuran,tetrahydrothiophene-S,S-dioxide,tetrahydrothiophene_dioxide,tetralin,thiophene,thiophenol,toluene,trans-decalin,tributyl phosphate,tributylphosphate,trichloroethene,triethylamine,water,xylene_(mixture),z-1,2-dichloroethene}]
[-anharm] [-return_anharm_files] [-anharm_max_freq WAVENUMBERS]
[-anharm_factor_data START STEP N_POINTS START STEP N_POINTS START STEP N_POINTS]
[-rate_constants] [-return_rate_constant_files]
[-custom_rate_constants] [-wigner_tunnel_corr]
[-max_i_freq WAVENUMBERS] -reaction_wf_input_file
REACTION_WF_INPUT_FILE [-extra_stages_file EXTRA_STAGES_FILE]
[-mass_conserved] [-out_rep {centroid,eta}] [-HOST <hostname>] [-SAVE]
[-JOBNAME JOBNAME] [-n_jmswf_subjobs N_JMSWF_SUBJOBS]
[-SUBHOST SUBHOST] [-TPP TPP] [-max_retries MAX_RETRIES]
Driver for reaction workflow. Copyright Schrodinger, LLC. All rights reserved.
options:
-h, -help Show this help message and exit.
-dedup_geom_eps DEDUP_GEOM_EPS
Reduce the number of calculations by deduplicating the
input structures based on geometry, using this
threshold in Ang., and only calculating the
representatives. A value of zero means no
deduplicating. (default: 0.25)
-mopac Use this option to run Mopac geometry optimizations
and frequencies on each conformer. (default: False)
-xtb Use this option to run xTB geometry optimizations on
each conformer. (default: False)
-uma Use this option to run UMA geometry optimizations on
each conformer. (default: False)
-jaguar_keywords [<key_1>=<value_1> [<key_2>=<value_2> ...]]
Specify Jaguar &gen section key-value pairs. 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**'])
-ts_jaguar_keywords [<key_1>=<value_1> [<key_2>=<value_2> ...]]
Specify Jaguar &gen section key-value pairs for
transition state searches. Each key-value pair should
be separated from the next by whitespace and each
should be represented in terms of a '<key>=<value>'
pair. If not given then the Jaguar keywords given
using the flag -jaguar_keywords will be used for
transition state searches. (default: None)
-temp_start TEMP_START
Specify the starting temperature (K) at which
thermochemical properties will be calculated.
(default: 298.15)
-temp_step TEMP_STEP Specify the step size of the temperature (K) (see
option -temp_start). (default: 10.0)
-temp_n TEMP_N Specify the number of temperatures (see options
-temp_start and -temp_step). (default: 1)
-press_start PRESS_START
Specify the starting pressure (atm) at which
thermochemical properties will be calculated.
(default: 1.0)
-press_step PRESS_STEP
Specify the step size of the pressure (atm) (see
option -press_start). (default: 1.0)
-press_n PRESS_N Specify the number of pressures (see options
-press_start and -press_step). (default: 1)
-temp_press_props_file TEMP_PRESS_PROPS_FILE
Specify a csv file of temperature and/or pressure
dependent properties. Temperature and/or pressure
values therein must be among those generated using the
start, step, and number of points flags: -temp_start,
-temp_step, -temp_n, -press_start, -press_step, and
-press_n. The columns of the csv must be named
temperature_K, pressure_atm, and
solvent_density_g_cm3. (default: None)
-return_jaguar_files Use this option to return all output files from any
Jaguar subjobs. (default: False)
-solvation_entropy Use this option to correct thermochemical properties,
and rate constants, by accounting for the entropy of
solvation using the model proposed by Garza. (default:
False)
-solvation_entropy_solvent {1,1,1-trichloroethane,1,1,2-trichloroethane,1,2,4-trimethylbenzene,1,2-dibromoethane,1,2-dichloroethane,1,2-ethanediol,1,4-dioxane,1-bromo-2-methylpropane,1-bromooctane,1-bromopentane,1-bromopropane,1-butanol,1-chlorohexane,1-chloropentane,1-chloropropane,1-decanol,1-fluorooctane,1-heptanol,1-hexanol,1-hexene,1-hexyne,1-iodobutane,1-iodohexadecane,1-iodopentane,1-iodopropane,1-nitropropane,1-nonanol,1-octanol,1-pentanol,1-pentene,1-pentyne,1-propanol,2,2,2-trifluoroethanol,2,2,4-trimethylpentane,2,4-dimethylpentane,2,4-dimethylpyridine,2,6-dimethylpyridine,2-bromopropane,2-butanol,2-chlorobutane,2-heptanone,2-hexanone,2-methoxyethanol,2-methyl-1-propanol,2-methyl-2-propanol,2-methylpentane,2-methylpyridine,2-methyltetrahydrofuran,2-nitropropane,2-octanone,2-pentanone,2-propanol,2-propen-1-ol,3-methylpyridine,3-pentanone,4-heptanone,4-methyl-2-pentanone,4-methylpyridine,5-nonanone,DMSO,E-1,2-dichloroethene,E-2-pentene,N-methylaniline,N-methylformamide,Z-1,2-dichloroethene,a-chlorotoluene,acetic acid,acetic_acid,acetone,acetonitrile,acetophenone,amyl acetate,aniline,anisole,benzaldehyde,benzene,benzonitrile,benzyl alcohol,benzyl_alcohol,bromobenzene,bromoethane,bromoform,butanal,butanenitrile,butanoic acid,butanoic_acid,butanone,butyl ethanoate,butyl_ethanoate,butylamine,carbon disulfide,carbon tetrachloride,carbon_disulfide,carbon_tet,chlorobenzene,chloroform,cis-1,2-dimethylcyclohexane,cis-decalin,cyclohexane,cyclohexanone,cyclopentane,cyclopentanol,cyclopentanone,decalin,decalin_(mixture),dibromomethane,dibutyl_ether,dibutylether,dichloroethane,dichloromethane,diethyl_ether,diethyl_sulfide,diethylamine,diethylether,diethylsulfide,diiodomethane,diisopropyl ether,diisopropyl_ether,dimethyl disulfide,dimethyl_disulfide,dimethylacetamide,dimethylformamide,dioxane,diphenyl ether,diphenylether,dipropylamine,dma,dmso,e-1,2-dichloroethene,e-2-pentene,ethanethiol,ethanol,ethyl acetate,ethyl methanoate,ethyl phenyl ether,ethyl_ethanoate,ethyl_methanoate,ethyl_phenyl_ether,ethylbenzene,fluorobenzene,formamide,formic acid,formic_acid,hexanoic acid,hexanoic_acid,iodobenzene,iodoethane,iodomethane,iso-butanol,isopropylbenzene,m-cresol,m-xylene,mesitylene,methanol,methyl acetate,methyl benzoate,methyl butanoate,methyl formate,methyl propionate,methyl_benzoate,methyl_butanoate,methyl_ethanoate,methyl_methanoate,methyl_propanoate,methylcyclohexane,n-butylbenzene,n-decane,n-dodecane,n-heptane,n-hexadecane,n-hexane,n-methylaniline,n-methylformamide_(mixture),n-nonane,n-octane,n-pentadecane,n-pentane,n-undecane,nitrobenzene,nitroethane,nitromethane,o-chlorotoluene,o-cresol,o-dichlorobenzene,o-nitrotoluene,o-xylene,p-isopropyltoluene,p-xylene,pentanal,pentanoic acid,pentanoic_acid,pentyl_ethanoate,pentylamine,perfluorobenzene,propanal,propanenitrile,propanoic acid,propanoic_acid,propyl acetate,propyl_ethanoate,propylamine,pyridine,pyrrolidine,sec-butylbenzene,tert-butanol,tert-butylbenzene,tetrachloroethene,tetrahydrofuran,tetrahydrothiophene-S,S-dioxide,tetrahydrothiophene_dioxide,tetralin,thiophene,thiophenol,toluene,trans-decalin,tributyl phosphate,tributylphosphate,trichloroethene,triethylamine,water,xylene_(mixture),z-1,2-dichloroethene}
Specify the solvent to use when calculating the
solvation entropy. The choice of solvent defines
various parameters needed to calculate the solvation
entropy. Supported solvents are those available in
Jaguar. (default: water)
-anharm Use this option to run a workflow that corrects
thermochemical properties, and potentially rate
constants, by accounting for anharmonicities in the
low frequency normal modes. (default: False)
-return_anharm_files Use this option to return all output files from any
anharmonic workflow subjobs. (default: False)
-anharm_max_freq WAVENUMBERS
Normal modes with harmonic frequencies less than this
value in wavenumbers (cm^-1) will be treated
anharmonically. (default: 300)
-anharm_factor_data START STEP N_POINTS START STEP N_POINTS START STEP N_POINTS
Unitless data for factors that multiply normal mode
displacements. Specify whitespace separated values for
the start, step, and number of points, which should be
for the positive direction only. (default: [0.5, 1.0,
4])
-rate_constants Use this option to report rate constant(s) for the
rate determining step of the reaction using canonical
transition state theory. (default: False)
-return_rate_constant_files
Use this option to return all output files from any
rate constant subjobs. (default: False)
-custom_rate_constants
When computing rate constants with -rate_constants use
custom equations. (default: False)
-wigner_tunnel_corr Use this option to include the Wigner tunneling
correction when computing rate constant(s). (default:
False)
-max_i_freq WAVENUMBERS
Check the number of imaginary frequencies using this
tolerance in wavenumbers (cm^-1). (default: 0)
-reaction_wf_input_file REACTION_WF_INPUT_FILE
Specify an input reaction workflow Maestro file whose
base name ends in _rxnwf. (default: None)
-extra_stages_file EXTRA_STAGES_FILE
Specify extra stages for a Jaguar Multistage Workflow
subjob that will be performed using all of the output
structures from the reaction workflow. The first of
these extra stages will be skipped so that analysis
can potentially be the first extra stage. (default:
None)
-mass_conserved Use this option to early exit if mass is not conserved
in the given reaction workflow input file. (default:
False)
-out_rep {centroid,eta}
Force a specific output representation. If not
provided it will be the opposite of the input
representation. (default: None)
Conformational search and selection:
-csearch_engine {Macromodel,Crest}
The engine to use for the conformational search.
(default: Macromodel)
-forcefield FORCE_FIELD
Force field to use. Valid force fields are OPLS_2005
and S-OPLS (default: S-OPLS)
-skip_eta_rotamers Specify that eta rotamers generation will be skipped.
(default: False)
-metal_index METAL_INDEX
Index of the metal atom around which to generate eta-
rotamers. If not provided and the structure has a
single metal atom then that index will automatically
be used. (default: None)
-com_fn COM_FN Use the settings in this example MacroModel .com file
for the conformational search rather than the default
settings. (default: None)
-seed SEED Specify a seed for the random number generator used
for any conformational searches. (default: 1234)
-n_conformers N_CONFORMERS
Specify the number of conformers to search for.
(default: 5)
-pp_rel_energy_thresh PP_REL_ENERGY_THRESH
If given, specifies to instead search for all
conformers with relative energies <= this value in
kJ/mol. (default: None)
-return_csearch_files
Use this option to return all output files from any
conformational search subjobs. (default: False)
-qm_selection Use this option to select conformers from quantum
energies rather than from classical energies.
(default: False)
-n_rotamers N_ROTAMERS
Specifies the number of guess rotamers for eta-bound
ligands prior to MacroModel conformational search. If
not given then it will be twice the number of ring
atoms in the haptic ring. (default: None)
-refined_energy Specifies a second stage of conformer selection using
refined energies. (default: False)
-refined_energy_jaguar_keywords [<key_1>=<value_1> [<key_2>=<value_2> ...]]
Specify Jaguar &gen section key-value pairs for single
point energy calculations used for refinement. 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=M06-L',
'basis=LACV3P++**'))
-refined_energy_thermo_correction
Include thermochemical corrections in the refined
energies. (default: False)
-refined_energy_thermo_correction_jaguar_keywords [<key_1>=<value_1> [<key_2>=<value_2> ...]]
Specify Jaguar &gen section key-value pairs for
optimized energy calculations used for the
thermochemical corrections to the refinement. 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: ('xtb=1',))
-refined_energy_n_conformers REFINED_ENERGY_N_CONFORMERS
The number of conformers to select after refinement.
(default: 5)
-refined_energy_pp_rel_energy_thresh REFINED_ENERGY_PP_REL_ENERGY_THRESH
If given, specifies to instead select all conformers
after refinement with relative energies <= this value
in kJ/mol. (default: None)
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)
-n_jmswf_subjobs N_JMSWF_SUBJOBS
Specify the maximum number of simultaneous Jaguar
multistage workflow subjobs. (default: 1)
-SUBHOST SUBHOST Specify the host to use for any subjobs. The driver
host is specified using -HOST. If -SUBHOST is not
specified then the value for -HOST is used. If -HOST
is not specified then localhost is used for both.
(default: None)
-TPP TPP Specify the number of threads to use for parallelizing
any Jaguar subjobs. MacroModel conformational search
subjobs use a value of 1. (default: 1)
-max_retries MAX_RETRIES
Maximum number of times to try relaunching subjobs.
(default: 0)