auto_reaction_workflow.py Command Help
Command: $SCHRODINGER/run auto_reaction_workflow.py
usage: $SCHRODINGER/run auto_reaction_workflow.py [-h]
[-novel_rxnwf_file NOVEL_RXNWF_FILE]
[-novel_sdf_file NOVEL_SDF_FILE]
[-only_sdf_conversion]
-reference_rxnwf_file
REFERENCE_RXNWF_FILE
[-only_rxnwf_files]
[-require_identical_bonds]
[-mass_conserved]
[-out_rep {centroid,eta}]
[-rgroup_file FILE_NAME INDEX FILE_NAME INDEX]
[-site [KEEP_ATOM_INDEX REPLACE_ATOM_INDEX INDEX [STRUCTURE_INDEX]
[NOVEL or REFERENCE] ...]]
[-force_hetero_substitution]
[-dup_smiles]
[-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]
[-dedup_geom_eps DEDUP_GEOM_EPS]
[-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]
[-extra_stages_file EXTRA_STAGES_FILE]
[-max_i_freq WAVENUMBERS]
[-descriptors]
[-energy_prop PROPERTY_NAME]
[-lowest]
[-return_descriptor_files]
[-HOST <hostname>] [-SAVE]
[-JOBNAME JOBNAME]
[-n_rxnwf_subjobs N_RXNWF_SUBJOBS]
[-n_jmswf_subjobs N_JMSWF_SUBJOBS]
[-TPP TPP]
[-jmswf_host JMSWF_HOST]
[-max_retries MAX_RETRIES]
Driver for automatic reaction workflow. Copyright Schrodinger, LLC. All rights
reserved.
options:
-h, -help Show this help message and exit.
-novel_rxnwf_file NOVEL_RXNWF_FILE
Specify a reaction workflow Maestro file containing
the single novel structure. This structure must
contain atoms marked with the
"b_matsci_Reaction_Workflow_Keep_Atom" property which
specify those atoms to be kept when swapping fragments
with the structures in the given reference reaction
workflow file (see option "-reference_rxnwf_file").
This structure must also contain atoms marked with the
"i_matsci_Reaction_Workflow_Superposition_Atom"
property which specify how to superpose it onto those
reference structures. (default: None)
-novel_sdf_file NOVEL_SDF_FILE
As an alternative to providing input using
"-novel_rxnwf_file" specify a 2D *sdf file containing
the single novel structure. This file must be marked
up with the relevant reaction workflow arguments. Also
see option "-only_sdf_conversion". (default: None)
-only_sdf_conversion Use this option to exit after converting a 2D *sdf
file specified with "-novel_sdf_file" to a 3D reaction
workflow *mae file. (default: False)
-reference_rxnwf_file REFERENCE_RXNWF_FILE
Specify a reaction workflow Maestro file containing
the reference structures. Those structures that are
swapping fragments with a given novel structure (see
option "-novel_rxnwf_file" or "-novel_sdf_file") must
contain atoms marked with the
"b_matsci_Reaction_Workflow_Keep_Atom" property which
specify those atoms to be kept when swapping
fragments. These structures must also contain atoms
marked with the
"i_matsci_Reaction_Workflow_Superposition_Atom"
property which specify how to superpose them onto a
novel structure. (default: None)
-only_rxnwf_files Use this option to exit after creating all reaction
workflow files. These files include any swaps with a
given novel structure and any R-group enumerations.
(default: False)
-require_identical_bonds
This requires that bonds being created when swapping
novel and reference catalysts must exist in both
structures and be of the same bond order. When not
used all bonds being cut in the novel structure will
be created provided that there is a reference keep
atom corresponding to the novel replace atom.
(default: False)
-mass_conserved Use this option to early exit if mass is not conserved
in the given reference 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)
Enumerate Reaction Workflow:
-rgroup_file FILE_NAME INDEX FILE_NAME INDEX
Specify any R-group files using this option. Define
each file using (1) the file name and (2) an
enumeration index which maps the file to sites (see
"-site" below). Files should be Maestro files
containing R-groups prepared with the R-Group Creator
GUI. This option may be specified multiple times. For
example, "-rgroup_file alkyl.mae 1 -rgroup_file
aryl.mae 2 -rgroup_file alkyl.mae 3" means that for
sites with enumeration indices 1 and 3 the alkyl.mae
file will be used while for sites with enumeration
index 2 the aryl.mae file will be used. Note that when
multiple sites use the same file there is an
additional option "-force_hetero_substitution" which
controls whether to return only the hetero-substituted
results or both hetero- and homo-substituted results.
(default: [])
-site [KEEP_ATOM_INDEX REPLACE_ATOM_INDEX INDEX [STRUCTURE_INDEX] [NOVEL or REFERENCE] ...]
Specify any enumeration sites using this option.
Define each site using three integers, (1) an atom
index which specifies the direction of the
substitution relative to (2), (2) an atom index which
specifies the substitution site, and (3) an
enumeration index which maps the site to an R-group
file (see "-rgroup_file" above). Atom indices for (1)
(a "from" atom) and (2) (a "to" atom) should be bonded
with a single acyclic bond and on substitution are
kept and replaced, respectively. This option may be
specified multiple times. For example, "-site 4 3 1
-site 23 17 2 -site 9 10 1" means that atoms 3 and 10
will be substituted with some R-group (indexed with
the 1 mapping to some file) such that atoms 4 and 9
respectively are kept, while atom 17 will be
substituted with a potentially different R-group
(indexed with the 2 potentially mapping to a different
file) such that atom 23 is kept. An optional fourth
integer item could be specified that indexes in a
given input reaction workflow file the structure to
which this site applies to (see the following optional
fifth string item). If not provided then it is assumed
to be for the single novel structure. An optional
fifth string item could be specified to indicate
whether the site applies to the "novel" structure or
"reference" structures. If not provided then it is
assumed to be for the novel structure. (default: [])
-force_hetero_substitution
By default when sites with different enumeration
indices use the same R-group file both hetero- and
homo-enumerated results are returned. Use this option
to return only hetero-enumerated results in such
cases. (default: False)
-dup_smiles When doing multi-site R-group enumeration all
possiblepermutations of R-group sites onto structure
sites are considered and by default the resulting
structures are deduplicated using SMILES. Use this
option to instead skip the SMILES deduplication and
return all structures. (default: False)
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)
Reaction Workflow Driver:
-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**', 'maxitg=200'])
-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)
-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)
-max_i_freq WAVENUMBERS
Check the number of imaginary frequencies using this
tolerance in wavenumbers (cm^-1). (default: 0)
Descriptors:
-descriptors Use this option to report cheminformatics descriptors
for all output reaction workflow files. (default:
False)
-energy_prop PROPERTY_NAME
Specify the energy property to use for Boltzmann
averaging. If temperature dependent then the
temperature must be reported in K and this temperature
will be used for averaging. Otherwise the input
temperatures in K will be used. This energy property
key must be of known units. Valid keys are for example
r_j_Gas_Phase_Energy,
r_j_Total_Free_Energy_(au)_298.15K_1.00E+00atm,
r_matsci_my_energy_(kcal/mol), etc. (default: None)
-lowest Specify whether to return the lowest energy conformer
instead of averaging properties over conformers.
(default: False)
-return_descriptor_files
Use this option to return all output files from any
cheminformatics descriptor 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)
-n_rxnwf_subjobs N_RXNWF_SUBJOBS
Specify the maximum number of simultaneous reaction
workflow subjobs. (default: 1)
-n_jmswf_subjobs N_JMSWF_SUBJOBS
Specify the maximum number of simultaneous Jaguar
multistage workflow subjobs. (default: 1)
-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)
-jmswf_host JMSWF_HOST
Specify the host to use for any Jaguar Multistage
Workflow subjobs. The driver host is specified using
-HOST. If -jmswf_host is not specified then the value
for -HOST is used. If -HOST is not specified then
localhost is used for both. (default: None)
-max_retries MAX_RETRIES
Maximum number of times to try relaunching subjobs.
(default: 0)