schrodinger.application.matsci.reaction_workflow_utils module¶

Utilities for reaction workflows.

class schrodinger.application.matsci.reaction_workflow_utils.TempData(temp_start, temp_step, temp_n)¶

Bases: tuple

temp_n¶: Alias for field number 2

temp_start¶: Alias for field number 0

temp_step¶: Alias for field number 1

class schrodinger.application.matsci.reaction_workflow_utils.PressData(press_start, press_step, press_n)¶

Bases: tuple

press_n¶: Alias for field number 2

press_start¶: Alias for field number 0

press_step¶: Alias for field number 1

class schrodinger.application.matsci.reaction_workflow_utils.ReactProdTS(name, other_name)¶

Bases: tuple

name¶: Alias for field number 0

other_name¶: Alias for field number 1

class schrodinger.application.matsci.reaction_workflow_utils.SameTypeGSTS(name, other_name)¶

Bases: tuple

name¶: Alias for field number 0

other_name¶: Alias for field number 1

class schrodinger.application.matsci.reaction_workflow_utils.DfCustomRateColumns(TS_Sibling, Other_Sibling, Temperature_K, Pressure_atm, Energy_Property, Energy_Barrier_kcal_per_mol, TS_Partition_F, Other_Partition_F, Rate_Constant, Rate_Constant_Type, Rate_Constant_Units)¶

Bases: tuple

Energy_Barrier_kcal_per_mol¶: Alias for field number 5

Energy_Property¶: Alias for field number 4

Other_Partition_F¶: Alias for field number 7

Other_Sibling¶: Alias for field number 1

Pressure_atm¶: Alias for field number 3

Rate_Constant¶: Alias for field number 8

Rate_Constant_Type¶: Alias for field number 9

Rate_Constant_Units¶: Alias for field number 10

TS_Partition_F¶: Alias for field number 6

TS_Sibling¶: Alias for field number 0

Temperature_K¶: Alias for field number 2

class schrodinger.application.matsci.reaction_workflow_utils.DfCustomEqColumns(Sibling, Other_Sibling, Temperature_K, Pressure_atm, Energy_Barrier_kcal_per_mol, Energy_Property, Keq)¶

Bases: tuple

Energy_Barrier_kcal_per_mol¶: Alias for field number 4

Energy_Property¶: Alias for field number 5

Keq¶: Alias for field number 6

Other_Sibling¶: Alias for field number 1

Pressure_atm¶: Alias for field number 3

Sibling¶: Alias for field number 0

Temperature_K¶: Alias for field number 2

class schrodinger.application.matsci.reaction_workflow_utils.MmodEnergyKeys(absolute, relative)¶

Bases: tuple

absolute¶: Alias for field number 0

relative¶: Alias for field number 1

class schrodinger.application.matsci.reaction_workflow_utils.EnergyAnalysisProperty(sibling_group, conformer_groups, representative_conformers, temperature, pressure, energy_key, property_key, avg_property_key, atom_idx, ensemble, include_x_terms, only_lowest_energy)¶

Bases: tuple

atom_idx¶: Alias for field number 8

avg_property_key¶: Alias for field number 7

conformer_groups¶: Alias for field number 1

energy_key¶: Alias for field number 5

ensemble¶: Alias for field number 9

include_x_terms¶: Alias for field number 10

only_lowest_energy¶: Alias for field number 11

pressure¶: Alias for field number 4

property_key¶: Alias for field number 6

representative_conformers¶: Alias for field number 2

sibling_group¶: Alias for field number 0

temperature¶: Alias for field number 3

class schrodinger.application.matsci.reaction_workflow_utils.JaguarKeyStructPropData(jaguar_key, struct_prop, default)¶

Bases: tuple

default¶: Alias for field number 2

jaguar_key¶: Alias for field number 0

struct_prop¶: Alias for field number 1

schrodinger.application.matsci.reaction_workflow_utils.log(msg, **kwargs)¶

Add a message to the log file

Parameters: msg (str) – The message to log

Additional keyword arguments are passed to the textlogger.log_msg function

schrodinger.application.matsci.reaction_workflow_utils.get_mmod_energy_key(ffld_name=None)¶

Returns the corresponding MacroModel energy key for the given forcefield. If no forcefield is given and the license is available, it defaults to S-OPLS. If no forcefield is given and the license is NOT available, it defaults to OPLS2005.

Parameters: ffld_name (str) – The forcefield to get the energy key for. If None, defaults to the latest forcefield available given your licenses.
Return str energy_key: The MacroModel suffix key for the default forcefield. Units are in kJ/mol

schrodinger.application.matsci.reaction_workflow_utils.get_mmod_rel_energy_key(ffld_name=None)¶

Returns the corresponding MacroModel relative energy key for the given forcefield. If no forcefield is given and the license is available, it defaults to S-OPLS. If no forcefield is given and the license is NOT available, it defaults to OPLS2005.

Parameters: ffld_name (str) – The forcefield to get the energy key for. If None, defaults to the latest forcefield available given your licenses.
Return str energy_key: The MacroModel suffix key for the default forcefield.

schrodinger.application.matsci.reaction_workflow_utils.get_mmod_energy_keys(ffld_name=None)¶

Returns the corresponding MacroModel energy key for the given forcefield. If no forcefield is given and the license is available, it defaults to S-OPLS. If no forcefield is given and the license is NOT available, it defaults to OPLS2005.

Parameters: ffld_name (str) – The forcefield to get the energy key for. If None, defaults to the latest forcefield available given your licenses.
Return namedtuple energy_keys: A named two-tuple where the first element (with a key of absolute) is the MacroModel suffix for the absolute energy (in kJ/mol), and the second element (with a key of relative) is the MacroModel suffix for the relative energy.

class schrodinger.application.matsci.reaction_workflow_utils.DF_RATE_TYPE(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)¶

Bases: enum.Enum

DEFAULT = 'default'¶

LNQ = 'lnq'¶

ANH_LNQ = 'anharmonic_lnq'¶

schrodinger.application.matsci.reaction_workflow_utils.get_reactions_data(sts)¶

Given conformers dictionary return list of reactions.

Parameters: sts (list[structure.Structure]) – List of structures
Return type: list
Returns: contains ReactProdTS (TS, Int) and/or SameTypeGSTS (Int, Int) or (TS, TS)

schrodinger.application.matsci.reaction_workflow_utils.add_remove_props(sts, prop, add_props)¶

Set additional properties equal to the original property from input structures, original property will be deleted.

Parameters

sts (list[structure.Structure]) – List of structures to be modified
prop (str) – Value of this property will be used, the property will be deleted
add_props (list[str]) – List of properties to be added to the structure

schrodinger.application.matsci.reaction_workflow_utils.set_extra_energy_props(sts, extra_stages_file, press_data, temp_data)¶

Set temp/pressure dependent extra properties in the input structures based on the original properties.

Parameters

sts (list[structure.Structure]) – List of structures to be modified
extra_stages_file (str) – Extra stage file name
press_data (PressData) – Pressure data
temp_data (TempData) – Temperature data

Return type

set[str]

Returns

Set of extra energy properties

schrodinger.application.matsci.reaction_workflow_utils.get_pressures_temps(press_data, temp_data)¶

Get list of pressures and temepratures from input data.

Parameters

press_data (PressData) – Pressure data
temp_data (TempData) – Temperature data

Return type

list[float], list[float]

Returns

List of pressures, list of temperatures

schrodinger.application.matsci.reaction_workflow_utils.set_gas_phase_zpe_props(sts, press_data, temp_data, stage_idx)¶

Set temp/pressure dependent gas phase + ZPE property in the input structures based on the original property

Parameters

sts (list[structure.Structure]) – List of structures to be modified
press_data (PressData) – Pressure data
temp_data (TempData) – Temperature data
stage_idx (int) – Stage index

schrodinger.application.matsci.reaction_workflow_utils.get_eprop_data(eprop)¶

Get conversion factor to kcal/mol, temperature in K, pressure in atm, from energy property

Parameters: eprop (str) – Energy property
Return type: float, float, float
Returns: conversion factor to kcal/mol, temperature in K, pressure in atm

schrodinger.application.matsci.reaction_workflow_utils.validate_energy_property_names(energy_property_names)¶

Validate the energy property names.

Parameters: energy_property_names (list) – the energy property names to validate
Raises: ValueError – if there is an issue

schrodinger.application.matsci.reaction_workflow_utils.add_custom_eq_rows(name, other_name, energy, other_energy, eprop, dframe)¶

Add data with kEQ to the dataframe

Parameters

name (str) – Sibling name
other_name (str) – Other sibling name
energy (float) – energy for sibling name, see eprop for units
other_energy (float) – energy for other sibling name, see eprop for units
eprop (str) – Energy property
dframe (pandas.DataFrame) – Input dataframe

Return type

pandas.DataFrame

Returns

Updated dataframe

schrodinger.application.matsci.reaction_workflow_utils.add_custom_rate_rows(ts_name, name, ts_energy, energy, ts_lnq, lnq, ifreq, eprop, dframe, wigner_tunnel_corr=False)¶

Add data with custom rates to the dataframe

Parameters

ts_name (str) – the TS name
name (str) – the intermediate name
ts_energy (float) – the TS energy, see eprop for units
energy (float) – the intermediate energy, see eprop for units
ts_lnq (float) – the TS lnQ
lnq (float) – the intermediate lnQ
ifreq (float) – Lowest negative frequency to compute rate with partition function, in 1/cm
eprop (str) – Energy property
dframe (pandas.DataFrame) – Input dataframe
wigner_tunnel_corr (bool) – whether to include the Wigner tunneling correction when computing rate constant(s)

Return type

pandas.DataFrame

Returns

Updated dataframe

schrodinger.application.matsci.reaction_workflow_utils.set_temp_press_props(sts, press_data, temp_data, extra_stages_file=None)¶

Set temperature and pressure dependent properties.

Parameters

sts (list[schrodinger.structure.Structure]) – the structures on which to set the properties
press_data (PressData) – pressure data
temp_data (TempData) – temperature data
extra_stages_file (str or None) – extra stage file name or None if there isn’t one

Return type

set[str]

Returns

the property keys set

schrodinger.application.matsci.reaction_workflow_utils.get_custom_keq_rates(out_mae, press_data, temp_data, extra_stages_file=None, compute_rates=True, wigner_tunnel_corr=False, logger=None)¶

Given output mae file, write custom equilibrium constants and optionally custom rates to CSV dataframes.

Parameters

out_mae (str) – Output file name
press_data (PressData) – Pressure data
temp_data (TempData) – Temperature data
extra_stages_file (str or None) – Extra stage file name or None
compute_rates (bool) – Whether to compute rates or only equilibrium constants
wigner_tunnel_corr (bool) – whether to include the Wigner tunneling correction when computing rate constant(s)
logger (logging.Logger or None) – output logger or None if there isn’t one

Raises

ReactionWorkflowException – if there is an issue

schrodinger.application.matsci.reaction_workflow_utils.get_keq(energy, temp)¶

Get k_equilibrium given energy and temperature.

Parameters

energy (float) – energy in kcal/mol
temp (float) – Temperature in Kelvin

Return type

float

Returns

k_equilibrium

schrodinger.application.matsci.reaction_workflow_utils.get_custom_rate(energy, temp, dlnq=None, ifreq=None, wigner_tunnel_corr=False)¶

Get custom rate.

Parameters

energy (float) – Energy in kcal/mol (!)
temp – Temperature in K
lnq (None or float) – lnQ to compute rate with partition function, unitless
ifreq (None or float) – Lowest negative frequency to compute rate with partition function, in 1/cm
wigner_tunnel_corr (bool) – whether to include the Wigner tunneling correction when computing rate constant(s)

Return type

float

Returns

Rate in 1/s

schrodinger.application.matsci.reaction_workflow_utils.get_present_props(en_starter, properties, stage_idx=None)¶

Get all properties with a certain starter and optionally stage index

Parameters

en_starter (str) – Property must start with this
properties (list[str]) – List of properties
stage_idx (None or int) – Stage index

Return type

list[str]

Returns

List of matching properties

schrodinger.application.matsci.reaction_workflow_utils.get_present_props_from_sts(sts, prefix, stage_idx=None)¶

Get properties that start with prefix and end with stage index (if provided). Check if pressure/temperature is present. Ensure that all the structures have at least the same list of properties

Parameters

sts (list[structure.Structure]) – List of structures
prefix (str) – Property must start with this
stage_idx (None or int) – Stage index

Return type

set[str]

Returns

Set of properties

schrodinger.application.matsci.reaction_workflow_utils.get_lnq_key(eprop)¶

Return the lnQ key.

Parameters: e_prop (str) – Energy property
Return type: str
Returns: the lnQ key

schrodinger.application.matsci.reaction_workflow_utils.get_restrain_atom_idxs(st)¶

Return a list of indices of restrain atoms in the given structure.

Parameters: st (schrodinger.structure.Structure) – the structure
Return type: list
Returns: contains indices of restrain atoms

schrodinger.application.matsci.reaction_workflow_utils.get_prevent_chirality_flip_idxs(st)¶

Return a list of atom indices (1-based) for which to prevent chirality flipping in MacroModel.

Parameters: st (schrodinger.structure.Structure) – the structure
Return type: list
Returns: list of atom indices (1-based) for which to prevent chirality flipping in MacroModel

schrodinger.application.matsci.reaction_workflow_utils.get_idx_groups(text)¶

Get index groups from the given string.

Parameters: text (str) – the string
Raise: InvalidInput if there is a formatting issue
Return type: list
Returns: contains list of indices

schrodinger.application.matsci.reaction_workflow_utils.get_restrain_distance_idxs(st)¶

Return a list of lists of indices of restrain distances in the given structure.

Parameters: st (schrodinger.structure.Structure) – the structure
Return type: list
Returns: contains lists of restrain distances

schrodinger.application.matsci.reaction_workflow_utils.get_restrain_angle_idxs(st)¶

Return a list of lists of indices of restrain angles in the given structure.

Parameters: st (schrodinger.structure.Structure) – the structure
Return type: list
Returns: contains lists of restrain angles

schrodinger.application.matsci.reaction_workflow_utils.get_restrain_dihedral_idxs(st)¶

Return a list of lists of indices of restrain dihedrals in the given structure.

Parameters: st (schrodinger.structure.Structure) – the structure
Return type: list
Returns: contains lists of restrain dihedrals

schrodinger.application.matsci.reaction_workflow_utils.get_jaguar_keywords_list(jaguar_keywords_dict)¶

Return the Jaguar keywords list from the given dict.

Parameters: jaguar_keywords_dict (dict) – the Jaguar keywords dict
Return type: list
Returns: the Jaguar keywords list

schrodinger.application.matsci.reaction_workflow_utils.type_cast_jaguar_keywords(jaguar_keywords, reserved_keys={'ifreq', 'igeopt', 'itrvec', 'molchg', 'multip', 'nhesref', 'npress', 'ntemp', 'press', 'press_step', 'tmpini', 'tmpstp'}, exception_type=<class 'argparse.ArgumentTypeError'>)¶

Type cast the Jaguar keywords.

Parameters

jaguar_keywords (str or unicode or list) – the Jaguar keywords, a whitespace delimited string of ‘<key>=<value>’ tokens or a list of such tokens
reserved_keys (set) – contains reserved Jaguar keys
exception_type (type) – the exception type to raise if invalid

Return type

dict

Returns

the Jaguar keywords

schrodinger.application.matsci.reaction_workflow_utils.check_ff_assignment(sts, ffld_name=None)¶

Check the assignment of the given force field to the given structures.

Parameters

sts (list) – contains schrodinger.structure.Structure
ffld_name (str) – the force field name.

Raises

ValueError – if invalid

schrodinger.application.matsci.reaction_workflow_utils.get_molecular_weight(st, idxs=None, decimal=None)¶

Return the molecular weight (amu) taken over the given atom indices in the given structure.

Parameters

st (schrodinger.structure.Structure) – the structure
idxs (list) – the atom indices
decimal (None or int) – an optional number of decimal places to which to round the weight

Return type

float

Returns

the molecular weight (amu)

schrodinger.application.matsci.reaction_workflow_utils.check_centroid_rep(st)¶

Check the centroid representation of the given structure.

Parameters: st (schrodinger.structure.Structure) – the structure
Raises: ValueError – if invalid

schrodinger.application.matsci.reaction_workflow_utils.check_conformers(conformers, conformers_group_hash)¶

Check conformers. If the given structures are conformers then their atom numberings are all changed in place so that they are equivalent to that of the first of the given conformers.

Parameters

conformers (list) – contains schrodinger.structure.Structure of conformers
conformers_group_hash (str) – a group hash

Raises

ValueError – if invalid

schrodinger.application.matsci.reaction_workflow_utils.check_reaction_wf_structures(rxn_sts, ffld_name=None, mass_conserved=False, keep_atoms_only=False, out_rep=False)¶

Check the given reaction workflow structues.

Parameters

rxn_sts (str or list) – the reaction workflow structures, a file name or list of schrodinger.structure.Structure
ffld_name (str) – the force field name to use when optionally checking its assignment to the given structures
mass_conserved (bool) – check that mass is conserved (see also keep_atoms_only kwarg)
keep_atoms_only (bool) – specifies that only keep atoms be considered when checking if mass is conserved (see also mass_conserved kwarg)
out_rep (bool) – check the output representation of haptic ligands

Raises

ValueError – if invalid

schrodinger.application.matsci.reaction_workflow_utils.type_cast_reaction_wf_input(reaction_wf_input, exception_type=<class 'argparse.ArgumentTypeError'>, mass_conserved=False, out_rep=False)¶

Type cast the reaction workflow input.

Parameters

reaction_wf_input (str or unicode or list) – the reaction workflow input, a file name or list of schrodinger.structure.Structure
exception_type (type) – the exception type to raise if invalid
mass_conserved (bool) – check that mass is conserved
out_rep (bool) – check the output representation of haptic ligands

Return type

str or list

Returns

the reaction workflow input, a file name or list of schrodinger.structure.Structure

schrodinger.application.matsci.reaction_workflow_utils.bin_structures_by_property(sts, key='s_matsci_Reaction_Workflow_Conformers_Group', inner_key=None)¶

Return a dictionary of structures binned by a property with the given key. If inner_key is provided then return a dictionary of dictionaries of structures with the inner dictionaries keyed by inner_key and outer dictionaries keyed by key.

Parameters

sts (list) – the structures
key (str) – the key for the property by which to bin
inner_key (str) – additionally bin by this inner_key

Return type

dict or dict of dict

Returns

dictionary where keys are properties and values are lists of structures or dictionary of dictionaries where the outer dictionary is keyed by key and inner dictionary is keyed by inner_key and values of the inner dictionary are lists of structures

schrodinger.application.matsci.reaction_workflow_utils.append_unique_conformers(sts, unique_sts, rmsd_thresh=0.1, n_conformers=None)¶

Append any unique conformers found in the given structures to the given unique structures.

Parameters

sts (list) – schrodinger.structure.Structure candidate conformers
unique_sts (list) – schrodinger.structure.Structure unique conformers
rmsd_thresh (float) – the maximum allowable RMSD (Ang.) between two structures before they can be considered different conformers
n_conformers (int or None) – number of sought conformers or None if there isn’t one

schrodinger.application.matsci.reaction_workflow_utils.get_conformers(sts, n_conformers, pp_rel_energy_thresh=None, rmsd_thresh=0.1, ffld_name=None, energy_key=None)¶

Return either (1) at most the given number of conformers or (2) all conformers with relative energies less than the given value. If (2) then an attempt is made to return at least the given number of conformers even if that means having relative energies larger than the given value.

Parameters

sts (list) – schrodinger.structure.Structure conformers
n_conformers (int) – either the maximum number of conformers if pp_rel_energy_thresh is None or a target minimum number of conformers if pp_rel_energy_thresh is given
pp_rel_energy_thresh (None or float) – relative energy threshold, if None then only the n_conformers lowest energy conformers are returned, units are in kJ/mol if there is no energy key given otherwise the same units as energy_key
rmsd_thresh (float) – the maximum allowable RMSD (Ang.) between two structures before they can be considered different conformers
ffld_name (str or None) – the name of the force field to use for the search, if None, then defaults to the latest forcefield available, not used if energy key is given
energy_key (str or None) – the energy key to use for selecting conformers, takes precedence over ffld_name

Return type

list

Returns

schrodinger.structure.Structure conformers

schrodinger.application.matsci.reaction_workflow_utils.postprocess_conformational_search(conformer, out_mae_path, ffld_name=None, csearch_engine='Macromodel')¶

Postprocess a conformational search. Rewrite the given out *mae file so that the conformers in it have properly updated properties.

Parameters

conformer (structure.Structure) – a representative conformer that seeded the search being postprocessed
out_mae_path (str) – the file path to the out *mae file containing the conformers
ffld_name (str) – the name of the force field to use for the search. If None, then defaults to the latest forcefield available.
csearch_engine (str) – the engine to use for conformational search, either module constant parserutils.MACROMODEL or parserutils.CREST

schrodinger.application.matsci.reaction_workflow_utils.write_com_file(in_mae_fn, out_mae_fn, com_fn, restrain_idxs=None, seed=1234, ffld_name=None, rel_energy_thresh=50.0, rmsd_thresh=0.1, ref_com_fn=None, prevent_chirality_flip_idxs=None, csearch_method='Monte Carlo Multiple Minimum')¶

Write a MacroModel .com file.

Parameters

in_mae_fn (str) – the input .mae file name
out_mae_fn (str) – the output .mae file name
com_fn (str) – the input .com file name
restrain_idxs (list) – indices to restrain
seed (int) – seed for random number generator
ffld_name (str) – the force field name
rel_energy_thresh (float) – relative energy threshold in kJ/mol, structures with energies (relative to that of the global minimum structure) greater than this value are not considered conformers, used in MacroModel
rmsd_thresh (float) – the maximum allowable RMSD (Ang.) between two structures before they can be considered different conformers
ref_com_fn (None or str) – if given then use the settings in this file for the search rather than the default settings
prevent_chirality_flip_idxs (list or None) – list of atom indices (1-based) for which to prevent chirality flipping in MacroModel, an empty list allows all chirality flipping, or None for MacroModel’s default behavior
csearch_method (str) – either module constant MCMM or LMCS

schrodinger.application.matsci.reaction_workflow_utils.add_macromodel_csearch(conformers, job_dj, restrain_idxs=None, seed=1234, launch_dir=None, base_name=None, ffld_name=None, rel_energy_thresh=50.0, rmsd_thresh=0.1, ref_com_fn=None, max_retries=0)¶

Perform a restrained MacroModel conformational search seeded with the given conformers.

Parameters

conformers (list) – schrodinger.structure.Structure conformers used to seed the search
job_dj (queue.JobDJ) – add the job to this queue
restrain_idxs (list) – indices to restrain
seed (int) – seed for random number generator
launch_dir (str) – a launch subdirectory to use for the job
base_name (str) – a base name to use for file and job naming
ffld_name (str) – the force field name
rel_energy_thresh (float) – relative energy threshold in kJ/mol, structures with energies (relative to that of the global minimum structure) greater than this value are not considered conformers, used in MacroModel
rmsd_thresh (float) – the maximum allowable RMSD (Ang.) between two structures before they can be considered different conformers
ref_com_fn (None or str) – if given then use the settings in this file for the search rather than the default settings
max_retries (int) – maximum number of times to try relaunching subjobs

Raises

ConformationalSearchException – if there is an issue

schrodinger.application.matsci.reaction_workflow_utils.add_crest_csearch(conformer, job_dj, restrain_idxs=None, metal_index=None, launch_dir=None, base_name=None, max_retries=0, tpp=1)¶

Perform a restrained Crest conformational search.

Parameters

conformer (schrodinger.structure.Structure) – the conformer
job_dj (queue.JobDJ) – add the job to this queue
restrain_idxs (list) – indices to restrain
metal_index (int or None) – index of the metal atom used to create restraints for complexes, if None and the structure has a single metal atom then that index will automatically be used
launch_dir (str) – a launch subdirectory to use for the job
base_name (str) – a base name to use for file and job naming
max_retries (int) – maximum number of times to try relaunching subjobs
tpp (int) – the number of threads to use for Crest subjobs, i.e. -TPP (threads-per-process)

Raises

ConformationalSearchException – if there is an issue

schrodinger.application.matsci.reaction_workflow_utils.get_int_tuples_from_str_property(st, key, separator=';')¶

Return a list of tuples of integers from the given string structure property.

Parameters

st (schrodinger.structure.Structure) – the structure
key (str) – the property key
separator (str) – the tuple separator used for the given property

Return type

list

Returns

contains tuples of integers

schrodinger.application.matsci.reaction_workflow_utils.representative_conformers(sibling_conformers_dict, specific_sibling_group=None)¶

Generator over representative conformers.

Parameters

sibling_conformers_dict (dict) – dictionary of dictionaries where the outer dictionary is keyed by sibling and inner dictionary is keyed by conformer and values of the inner dictionary are lists of structures
specific_sibling_group (str or None) – if not None then restrict conformers to be generated only over this sibling group

Return type

tuple

Returns

the sibling and conformer group names and the representative conformer or None if one doesn’t exist

class schrodinger.application.matsci.reaction_workflow_utils.RepresentativeConformersMixin¶

Bases: object

representativeConformers(sibling_conformers_dict=None, specific_sibling_group=None)¶

Generator over representative conformers.

Parameters

sibling_conformers_dict (dict or None) – dictionary of dictionaries where the outer dictionary is keyed by sibling and inner dictionary is keyed by conformer and values of the inner dictionary are lists of structures, if None then the class attr is used
specific_sibling_group (str or None) – if not None then restrict conformers to be generated only over this sibling group

Return type

tuple

Returns

the sibling and conformer group names and the representative conformer

schrodinger.application.matsci.reaction_workflow_utils.get_rxnwf_graph(file_path=None, sts=None, sibling_conformers_dict=None)¶

Return a reaction workflow graph.

Parameters

file_path (str or None) – the path to the reaction workflow file or None if other input is given
sts (list[schrodinger.structure.Structure] or None) – the reaction workflow structures or None if other input is given
sibling_conformers_dict (dict or None) – dictionary of dictionaries where the outer dictionary is keyed by sibling group name and the inner dictionary is keyed by conformer group name and the values of the inner dictionary are lists of schrodinger.structure.Structure or None if other input is given

Return type

RxnNetworkGraph

Returns

the reaction workflow graph

exception schrodinger.application.matsci.reaction_workflow_utils.ReactionWorkflowFileException¶: Bases: Exception

class schrodinger.application.matsci.reaction_workflow_utils.ReactionWorkflowFile(rxn_sts, ffld_name=None, mass_conserved=False, keep_atoms_only=False, out_rep=False)¶

Bases: object

Manage a reaction workflow file.

__init__(rxn_sts, ffld_name=None, mass_conserved=False, keep_atoms_only=False, out_rep=False)¶

Parameters

rxn_sts (str or list[schrodinger.structure.Structure]) – the reaction workflow structures, a reaction workflow file path or list of reaction workflow schrodinger.structure.Structure
ffld_name (str or None) – if given then check that this force field can be applied to all reaction workflow structures
mass_conserved (bool) – check that mass is conserved for each sibling group in the reaction workflow (see also keep_atoms_only)
keep_atoms_only (bool) – specifies that only keep atoms be considered when checking if mass is conserved (see also mass_conserved)
out_rep (bool) – check the output representation of haptic ligands

Raises

ReactionWorkflowFileException – if there is an issue

getReactantsConformersDict()¶

Return the reactants conformers dictionary.

Return type: dict
Returns: keys are conformer group names, values are lists of schrodinger.structure.Structure

class schrodinger.application.matsci.reaction_workflow_utils.UniqueGeomMixin¶

Bases: object

Manage uniqueifying structures by geometry.

class schrodinger.application.matsci.reaction_workflow_utils.ReactionWorkflowEnergyAnalysis(rxn_sts, energy_keys, dedup_geom_eps=0.25, ffld_name=None, mass_conserved=False, keep_atoms_only=False, out_rep=False)¶

Bases: schrodinger.application.matsci.reaction_workflow_utils.ReactionWorkflowFile, schrodinger.application.matsci.reaction_workflow_utils.UniqueGeomMixin

Manage a reaction workflow energy analysis.

__init__(rxn_sts, energy_keys, dedup_geom_eps=0.25, ffld_name=None, mass_conserved=False, keep_atoms_only=False, out_rep=False)¶

Parameters

rxn_sts (str or list[schrodinger.structure.Structure]) – the reaction workflow structures, a reaction workflow file path or list of reaction workflow schrodinger.structure.Structure
energy_keys (list) – structure property energy keys to consider, if it is temperature dependent then include the temperature (K) as a number followed by ‘K’ in the key and the corresponding energy must be in supported units (au, kcal/mol, eV, kJ/mol) and must be present in the key as ‘(<units>)’
dedup_geom_eps (float) – 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
ffld_name (str or None) – if given then check that this force field can be applied to all reaction workflow structures
mass_conserved (bool) – check that mass is conserved for each sibling group in the reaction workflow (see also keep_atoms_only)
keep_atoms_only (bool) – specifies that only keep atoms be considered when checking if mass is conserved (see also mass_conserved)
out_rep (bool) – check the output representation of haptic ligands

Raises

ReactionWorkflowException – if there is an issue

getUnitsData(prop)¶

Get conversion factor to kcal/mol, pressure and temperature from a property, saving the data into a dict.

Parameters: prop (str) – Property to use
Return type: float or None, float or None, float or None
Returns: Conversion to kcal/mol, pressure, temperature

static getHeader(energy_key)¶

Return a header for the given energy key.

Parameters: energy_key (str) – structure property energy key
Return type: str
Returns: the header

static getTemperature(energy_key)¶

Return the temperature (K) for the given energy key.

Parameters: energy_key (str) – structure property energy key
Return type: float, None
Returns: the temperature (K) if there is one

static getPressure(energy_key)¶

Return the pressure (atm) for the given energy key.

Parameters: energy_key (str) – structure property energy key
Return type: float, None
Returns: the pressure (atm) if there is one

static getUnits(energy_key)¶

Return the units for the given energy key.

Parameters: energy_key (str) – structure property energy key
Return type: str, None
Returns: the units if there is one

static getKcalPerMolConversion(energy_key)¶

Return the kcal/mol conversion factor for the given energy key.

Parameters: energy_key (str) – structure property energy key
Return type: float, None
Returns: the kcal/mol conversion factor if there is one

static getEnergyPropertyValues(sts, energy_key, include_x_terms=False, property_key=None, atom_idx=None)¶

Return energy and property value pairs for the given structures.

Parameters

sts (list[schrodinger.structure.Structure]) – a collection of conformers, if including cross terms then it is a single conformer from each structure type in the sibling group, otherwise it is all conformers for a given structure type
energy_key (str) – the energy key
include_x_terms (bool) – whether to include cross terms
property_key (str or None) – the relevant property key, if not specified it is the same as the energy key
atom_idx (int or None) – if an integer then the given property key is for an atomic property and this is the atom index, if None then the given property key is a structure property

Return type

list[tuple]

Returns

energy and property value pairs for the given structures

getPropertyEnsemble(conformers_dict, energy_key, conversion, temp, do_boltzmann, include_x_terms=False, only_lowest_energy=False, property_key=None, atom_idx=None)¶

Return an ensemble of properties for the given conformers dictionary of siblings and given energy key.

Parameters

conformers_dict (dict) – keys are conformer group names, values are lists of structure.Structure
energy_key (str) – the relevant energy key
conversion (float) – the energy conversion factor to kcal/mol
temp (float) – the temperature in K
do_boltzmann (bool) – if True perform a Boltzmann average, otherwise an algebraic average
include_x_terms (bool) – whether to include cross terms in the conformational averaging
only_lowest_energy (bool) – use only the lowest energy conformer rather than averaging over conformers
property_key (str) – the relevant property key, if not specified it is the same as the energy key
atom_idx (int or None) – if an integer then the given property key is for an atomic property and this is the atom index, if None then the given property key is a structure property

Raises

ReactionWorkflowException – if there is an issue

Return type

list

Returns

ensemble of properties

getProperties(include_x_terms=False, only_lowest_energy=False, property_key=None, atomic=False, temps=None)¶

Return the properties.

Parameters

include_x_terms (bool) – whether to include cross terms
only_lowest_energy (bool) – use only the lowest energy conformer rather than averaging over conformers
property_key (str) – the property key, if not specified energy energy keys are used
atomic (bool) – if True then the given property key is an atomic property, otherwise is a structure property
temps (list) – temperatures in K, only used for temperature independent energy and property keys

Raises

ReactionWorkflowException – if there is an issue

Return type

list[EnergyAnalysisProperty]

Returns

the properties

getConfAvgRelEnergies(include_x_terms=True, only_lowest_energy=False)¶

Return the conformationally averaged energies relative to that of the reactants.

Parameters

include_x_terms (bool) – whether to include cross terms in the conformational averaging
only_lowest_energy (bool) – use only the lowest energy conformer rather than averaging over conformers

Raises

ReactionWorkflowException – if there is an issue

Return type

dict

Returns

keys are sibling group names, values are dicts with energy keys as keys and energy values as values

setGraphEnergies()¶: Set energies on the reaction workflow graph.

writeDataFiles()¶: Write data files.

schrodinger.application.matsci.reaction_workflow_utils.get_stage_idx(astr, is_filename=False)¶

Return the stage index from the given string, can be a filename.

Parameters

astr (str) – the string
is_filename (bool) – Whether astr is filename or not

Return type

int

Returns

the stage index

schrodinger.application.matsci.reaction_workflow_utils.check_TS_vetting(out_file)¶

Return False if TS vetting failed in the given Jaguar out file.

Parameters: out_file (str) – Jaguar out file
Return type: bool
Returns: False if TS vetting failed

schrodinger.application.matsci.reaction_workflow_utils.get_sub_host_str(obj, sub_host_attr, n_procs_attr)¶

Return the command line -HOST argument for using a subhost.

Parameters

obj (object) – the object, possibly having the given attributes defined
sub_host_attr (str) – the attribute for the subhost
n_procs_attr (str) – the attribute for the number of processors

exception schrodinger.application.matsci.reaction_workflow_utils.ConformationalSearchException¶: Bases: Exception

class schrodinger.application.matsci.reaction_workflow_utils.ConformationalSearchMixin¶

Bases: object

Manage a MacroModel conformational search.

static genEtaRotamers(sibling_conformers_dict, only_rings=True, metal_index=None)¶

Generate eta-rotamers.

Parameters

sibling_conformers_dict (dict) – dictionary of dictionaries where the outer dictionary is keyed by sibling and inner dictionary is keyed by conformer and values of the inner dictionary are lists of structures
only_rings (bool) – if True then only allow rotation of eta-bound rings, if False then also allow rotation of ligands where the eta-bound motif is acyclic, for example ethene, etc.
metal_index (int or None) – index of the metal atom around which to generate eta-rotamers, if None and the structure has a single metal atom then that index will automatically be used

Return type

dict, dict

Returns

dictionary of dictionaries where the outer dictionary is keyed by sibling and inner dictionary is keyed by conformer and values of the inner dictionary are lists of structures, for eta-complexes incoming conformers have been replaced with all possible rotamers, another dictionary mapping the structure titles of generated rotamers to the structure title of the structure from which they were generated

createConformers(sts)¶

Create the conformers.

Parameters: sts (list) – contains schrodinger.structure.Structure, the structures for which to create conformers, each unique type of structure should have a unique conformer group structure property keyed by CONFORMERS_GROUP_KEY, structures sharing the same CONFORMERS_GROUP_KEY should be conformers of the same structure and are used to seed the conformational search, an additional optional SIBLING_GROUP_KEY can be used to distinguish related groups of conformers, atoms marked with the property RESTRAINED_ATOM_KEY will be restrained
Raises: ConformationalSearchException – if there is an issue

exception schrodinger.application.matsci.reaction_workflow_utils.JMSWFException¶: Bases: Exception

class schrodinger.application.matsci.reaction_workflow_utils.JMSWFMixin¶

Bases: schrodinger.application.matsci.reaction_workflow_utils.RepresentativeConformersMixin

Manage a Jaguar multistage workflow.

runJMSWF(restrain_atoms=True, restrain_internals=True)¶

Run the Jaguar multistage workflow.

Parameters

restrain_atoms (bool) – whether to restrain the cartesian coordinates of atoms marked with the RESTRAINED_ATOM_KEY atom property
restrain_internals (bool) – whether to restrain the internal coordinates of structures marked with the RESTRAINED_DISTANCES_KEY, RESTRAINED_ANGLES_KEY, and/or RESTRAINED_DIHEDRALS_KEY structure properties

Raises

JMSWFException – if there is an issue

prepareJMSWFOutput()¶: Prepare Jaguar multistage workflow output.

checkJMSWFOutputs(out_files)¶

Raises JMSWFException if any of the given Jaguar out files should be treated as a failure.

Parameters: out_files (list) – contains Jaguar output files
Raises: JMSWFException – if any of the given Jaguar out files should be treated as a failure

setRepresentatives()¶

Associated with each structure is output data from potentially multiple Jaguar multistage workflow stages. Pick representative structures to carry the data for all stages.

Raises: JMSWFException – if there is an issue

finalizeJMSWFOutput()¶

Finalize the Jaguar multistage workflow output.

Return type: str
Returns: the Jaguar multistage workflow output file

getFreqStageIdxs()¶

Return the stage indices of frequency stages.

Return type: tuple[int]
Returns: the stage indices

class schrodinger.application.matsci.reaction_workflow_utils.DescriptorsMixin¶

Bases: object

Manage running descriptors.

DEFAULT_JOB_NAME = 'automatic_reaction_workflow'¶

getJaguarFlags(jaguar)¶

Return Jaguar flags.

Parameters: jaguar (bool) – whether to run Jaguar descriptors
Return type: list
Returns: the Jaguar flags

getMoldesFlags(mopac)¶

Return moldescriptors flags.

Parameters: mopac (bool) – whether to run Mopac descriptors
Return type: list
Returns: the moldescriptors flags

runDescriptors(files, jaguar=True, mopac=False)¶

Run descriptors.

Parameters

files (list) – the files on which to run descriptors
jaguar (bool) – whether to run Jaguar descriptors
mopac (bool) – whether to run Mopac descriptors

Return type

list

Returns

The output file paths. The returned list will be the same length as the input files list.

schrodinger.application.matsci.reaction_workflow_utils.has_transition_state(rxnwf_file_path=None, rxnwf_sts=None)¶

Return True if the reaction workflow features a transition state, False otherwise.

Return type: bool
Returns: True if the reaction workflow features a transition state, False otherwise

schrodinger.application.matsci.reaction_workflow_utils.get_rep_stage_idx(rxnwf_file_path=None, rxnwf_sts=None, has_ts=None)¶

Return the representative stage index.

Parameters

rxnwf_file_path (str or None) – the path to a reaction workflow file or None if other input has been provided
rxnwf_sts (list[schrodinger.structure.Structure] or None) – reaction workflow structures or None if other input has been provided
has_ts (bool or None) – True if it is known that there is at least a single transition state, False if it is known that there is no transition state, if None it will be determined from the other input

Return type

int

Returns

the representative stage index

exception schrodinger.application.matsci.reaction_workflow_utils.ReactionWorkflowException¶: Bases: Exception

class schrodinger.application.matsci.reaction_workflow_utils.ReactionWorkflow(reaction_wf_input_sts, dedup_geom_eps=0.25, csearch_engine='Macromodel', skip_eta_rotamers=False, metal_index=None, ffld_name=None, com_fn=None, seed=1234, n_conformers=5, pp_rel_energy_thresh=None, return_csearch_files=False, qm_selection=False, only_rings=True, mopac=False, xtb=False, jaguar_keywords={'basis': 'LACVP**', 'dftname': 'B3LYP'}, temp_data=None, press_data=None, return_jaguar_files=False, anharm=False, return_anharm_files=False, anharm_max_freq=300, anharm_factor_data=None, rate_constants=False, return_rate_constant_files=False, custom_rate_constants=False, wigner_tunnel_corr=False, extra_stages_file=None, max_i_freq=0, out_rep=None, n_jmswf_subjobs=1, subhost=None, tpp=1, logger=None, max_retries=0)¶

Bases: schrodinger.application.matsci.reaction_workflow_utils.ConformationalSearchMixin, schrodinger.application.matsci.reaction_workflow_utils.JMSWFMixin, schrodinger.application.matsci.reaction_workflow_utils.UniqueGeomMixin

Manage a reaction workflow.

__init__(reaction_wf_input_sts, dedup_geom_eps=0.25, csearch_engine='Macromodel', skip_eta_rotamers=False, metal_index=None, ffld_name=None, com_fn=None, seed=1234, n_conformers=5, pp_rel_energy_thresh=None, return_csearch_files=False, qm_selection=False, only_rings=True, mopac=False, xtb=False, jaguar_keywords={'basis': 'LACVP**', 'dftname': 'B3LYP'}, temp_data=None, press_data=None, return_jaguar_files=False, anharm=False, return_anharm_files=False, anharm_max_freq=300, anharm_factor_data=None, rate_constants=False, return_rate_constant_files=False, custom_rate_constants=False, wigner_tunnel_corr=False, extra_stages_file=None, max_i_freq=0, out_rep=None, n_jmswf_subjobs=1, subhost=None, tpp=1, logger=None, max_retries=0)¶

Create an instance.

Parameters

reaction_wf_input_sts (list) – reaction workflow input structures
dedup_geom_eps (float) – 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
csearch_engine (str) – the engine to use for conformational search, either module constant parserutils.MACROMODEL or parserutils.CREST
skip_eta_rotamers (bool) – skip eta rotamers generation if true
metal_index (int or None) – index of the metal atom around which to generate eta-rotamers, if None and the structure has a single metal atom then that index will automatically be used
ffld_name (str) – the name of the force field to use (e.g., OPLS2005 or S-OPLS)
com_fn (None or str) – if given then use the settings in this file for the search rather than the default settings
seed (int) – seed for random number generator
n_conformers (int) – number of conformers to search for
pp_rel_energy_thresh (None or float) – relative energy threshold in kJ/mol, if None then only the n_conformers lowest energy conformers are returned
return_csearch_files (bool) – whether to return all output files from the conformational search subjobs
qm_selection (bool) – if True then the selection of conformers uses quantum energies as opposed to classical energies
only_rings (bool) – if True then only allow rotation of eta-bound rings, if False then also allow rotation of ligands where the eta-bound motif is acyclic, for example ethene, etc.
mopac (bool) – run Mopac geometry optimizations and frequencies on each conformer
xtb (bool) – run xTB geometry optimizations on each conformer
jaguar_keywords (dict) – Jaguar keywords
temp_data (TempData) – the temperature data for thermochemical properties
press_data (PressData) – the pressure data for thermochemical properties
return_jaguar_files (bool) – whether to return all output files from the Jaguar subjobs
anharm (bool) – whether to run the anharmonic workflow
return_anharm_files (bool) – whether to return all output files from the anharmonic workflow
anharm_max_freq (float) – anharmonic potentials are created for normal modes with harmonic frequencies less than this value in wavenumbers (cm^-1)
anharm_factor_data (anharmonic.SeqData or None) – unitless factor data for factors that multiply a normal mode displacement, if None then the defaults are used, the number of points is in the positive direction only, excluding zero and the negative direction, for example using a value of 4 in turn means 2 * 4 + 1 = 9 points total
rate_constants (bool) – whether to report rate constant(s) for the rate determining step of the reaction using canonical transition state theory
return_rate_constant_files (bool) – whether to return all output files from the rate constant subjobs
custom_rate_constants (bool) – whether to compute custom rate constants
wigner_tunnel_corr (bool) – whether to include the Wigner tunneling correction when computing rate constant(s)
extra_stages_file (str) – the name of a file containing extra stages for a Jaguar Multistage Workflow subjob that will be performed on all output structures from the reaction workflow, the first of these extra stages is always skipped so as to allow analysis to potentially be the first extra stage
max_i_freq (float) – tolerate small imaginary frequencies less than this value in wavenumbers (cm^-1)
out_rep – if a string then must be either module constant parserutils.CENTROID or parserutils.ETA, if None then do nothing
n_jmswf_subjobs (int) – the maximum number of simultaneous Jaguar multistage workflow subjobs
subhost (str) – the host to use for subjobs
tpp (int) – the number of threads to use for Jaguar subjobs, i.e. -TPP (threads-per-process)
logger (logging.Logger or None) – output logger or None if there isn’t one
max_retries (int) – maximum number of times to try relaunching subjobs

validateAnharmonic()¶

Validate anharmonic.

Raises: ReactionWorkflowException – if there is an issue

validateSubhost()¶

Validate subhost.

Raises: ReactionWorkflowException – if there is an issue

validate()¶

Validate.

Raises: ReactionWorkflowException – if there is an issue

runQMConformerSelection()¶

Run the QM conformer selection.

Raises: ReactionWorkflowException – if there is an issue

runAnharmonic()¶: Run the anharmonic workflow.

processAnharmonic()¶

Process the anharmonic workflow.

Raises: ReactionWorkflowException – if there is an issue

runCTST()¶: Run canonical transition state theory calculations to determine rate constant(s) for the rate determining step of the reaction.

prepareCTSTOutput()¶

Prepare CTST output.

Raises: ReactionWorkflowException – if there is an issue

exportEnergyDiagrams()¶

Export the energy diagrams if the parents file exists.

Return type: (str, str) or None
Returns: the energy level diagrams in pdf format, the total free energy at STP energy level diagram in png format or None otherwise

static writeTOFFile(rxnwfea, logger=None)¶

Write a file containing the turn over frequencies.

Parameters

rxnwfea (ReactionWorkflowEnergyAnalysis) – the reaction workflow energy analysis instance that manages all computed energies of all sibling and conformer groups
logger (logging.Logger or None) – the logger if there is one

run()¶

Run the reaction workflow.

Raises: ReactionWorkflowException – if there is an issue

schrodinger.application.matsci.reaction_workflow_utils.get_sites(sites)¶

Return the reference and novel sites.

Parameters: sites (list) – contains for each site a list of data [from_idx, to_idx, hash_idx] with an optional fourth item structure_idx and an optional fifth item reaction_workflow_utils.REFERENCE or reaction_workflow_utils.NOVEL module constants
Raises: ReactionWorkflowException – if there is an issue
Return type: list, list
Returns: the reference and novel sites, each containing rxnwfeu.Site

schrodinger.application.matsci.reaction_workflow_utils.validate_auto_reaction_workflow_files(reaction_wf_input, novel_rxnwf_file=None, mass_conserved=False, sites=None, out_rep=False)¶

Validate auto reaction workflow input files.

Parameters

reaction_wf_input (str) – reference reaction workflow file name
novel_rxnwf_file (str or None) – if there is one the novel reaction workflow file name
mass_conserved (bool) – check that mass is conserved
sites (list) – contains for each site a list of data [from_idx, to_idx, hash_idx] with an optional fourth item structure_idx and an optional fifth item reaction_workflow_utils.REFERENCE or reaction_workflow_utils.NOVEL module constants
out_rep (bool) – check the output representation of haptic ligands

Raises

ReactionWorkflowException – if there is an issue

schrodinger.application.matsci.reaction_workflow_utils.validate_custom_rate_with_extra_stages(options)¶

Validate that if custom rates are requested and extra stages file is present, custom property has one of the known energy units

Parameters: options (SimpleNamespace) – Options
Raises: ReactionWorkflowException – if custom property has no known unit

schrodinger.application.matsci.reaction_workflow_utils.validate_crest_options(csearch_engine, skip_eta_rotamers, reaction_wf_input_sts, validate_platform=True)¶

Validate Crest options.

Parameters

csearch_engine (str) – the engine to use for conformational search, either module constant parserutils.MACROMODEL or parserutils.CREST
skip_eta_rotamers (bool) – skip eta rotamers generation if true
reaction_wf_input_sts (list) – reaction workflow input structures
validate_platform (bool) – if True then validate the platform

Raises

ReactionWorkflowException – if there is an issue

schrodinger.application.matsci.reaction_workflow_utils.has_keep_and_superpose_atoms(input_st)¶

Return True if the given structure has at least a single keep atom and a single superpose atom.

Parameters: input_st (structure.Structure) – the structure
Return type: bool
Returns: True if the structure has at least a single keep atom and a single superpose atom

schrodinger.application.matsci.reaction_workflow_utils.validate_auto_reaction_workflow_options(reaction_wf_input, novel_rxnwf_file=None, n_conformers=5, jaguar_keywords=None, ffld_name='S-OPLS')¶

Validate auto reaction workflow options.

Parameters

reaction_wf_input (str) – reference reaction workflow file name
novel_rxnwf_file (str or None) – if there is one the novel reaction workflow file name
n_conformers (int) – number of conformers to search for
jaguar_keywords (str or None) – whitespace separated Jaguar <key>=<value> tokens, if None then use the defaults
ffld_name (str) – the name of the force field to use (e.g., OPLS2005 or S-OPLS)

Raises

ReactionWorkflowException – if there is an issue

schrodinger.application.matsci.reaction_workflow_utils.validate_all_auto_reaction_workflow_options(reaction_wf_input, novel_rxnwf_file=None, mass_conserved=False, sites=None, n_conformers=5, jaguar_keywords=None, ffld_name='S-OPLS')¶

Validate all auto reaction workflow options or raise ReactionWorkflowException error.

Parameters

reaction_wf_input (str) – reference reaction workflow file name
novel_rxnwf_file (str) – the reaction workflow file containing the single novel structure
mass_conserved (bool) – True if mass is conserved else false
sites (list) – contains for each site a list of data [from_idx, to_idx, hash_idx] with an optional fourth item structure_idx and an optional fifth item reaction_workflow_utils.REFERENCE or reaction_workflow_utils.NOVEL module constants
n_conformers (int) – number of conformers to search for
jaguar_keywords (str) – whitespace separated Jaguar <key>=<value> tokens, if None then use the defaults
ffld_name (str) – the name of the force field to use (e.g., OPLS2005 or S-OPLS)

Raises

rxnwfu.ReactionWorkflowException – if there is an issue

schrodinger.application.matsci.reaction_workflow_utils.validate_options(options)¶

Validate options.

Parameters: options (SimpleNamespace) – the options
Raises: rxnwfu.ReactionWorkflowException – if there is an issue

schrodinger.application.matsci.reaction_workflow_utils.get_sibling_ownership_information(file_path=None, sts=None)¶

Get the parents and children information of sibling groups from a structure file or a list of structures

Parameters

file_path (str) – The path to the structure file to read
sts (iterable) – The structures to get information from, if file_path is not provided

Raises

ReactionWorkflowException – if there is an issue with the inputs

Return type

dict, dict

Returns

first dict maps each sibling group to its parents, second dict maps each sibling group to its children

schrodinger.application.matsci.reaction_workflow_utils.bin_by_geometry(sts, eps=0.25)¶

Return a dictionary of structures binned by common geometry.

Parameters

sts (list[schrodinger.structure.Structure]) – the structures
eps (float) – the RMSD precision in Angstrom that controls the size of the clusters, see sklearn.cluster.DBSCAN documentation for more details

Return type

dict

Returns

keys are representative structures from each geometry bin, values are lists of other structures in the same geometry bin

schrodinger.application.matsci.reaction_workflow_utils.get_orig_title(title, unique_geom_dict)¶

Return the original title of the given title.

Parameters

title (str) – the title
unique_geom_dict (dict) – keys are original titles, values are structures in the same geometry bin, with the representative structure at index 0

Return type

str, str

Returns

the original title and the extension

schrodinger.application.matsci.reaction_workflow_utils.get_unique_geom_title(title, unique_geom_dict)¶

Return the title of the unique geometry representative for the given title.

Parameters

title (str) – the title
unique_geom_dict (dict) – keys are original titles, values are structures in the same geometry bin, with the representative structure at index 0

Return type

str

Returns

the title of the representative

schrodinger.application.matsci.reaction_workflow_utils.get_titles_of_duplicates(title, unique_geom_dict)¶

Return the structure titles of structures represented by a unique structure with the given structure title.

Parameters

title (str) – the structure title of the unique representative structure
unique_geom_dict (dict) – keys are original titles, values are structures in the same geometry bin, with the representative structure at index 0

Return type

list[str]

Returns

the titles of the duplicate structures

schrodinger.application.matsci.reaction_workflow_utils.get_file_names_of_duplicates(file_name, unique_geom_dict)¶

Return duplicate file names from the given representative file name. Files are named by structure title.

Parameters

file_name (str) – the representative file name
unique_geom_dict (dict) – keys are original titles, values are structures in the same geometry bin, with the representative structure at index 0

Return type

list[str]

Returns

the duplicate file names

schrodinger.application.matsci.reaction_workflow_utils.get_energy_db_term(rxnwf_file_path=None, rxnwf_sts=None, tstart=298.15, tstep=10.0, ntemp=1, pstart=1.0, pstep=1.0, npress=1, anharm=False, extra_stages_file=False, **kwargs)¶

Get a dict containing all the energy term generated by reaction workflow

Parameters

rxnwf_file_path (str or None) – the path to a reaction workflow file
rxnwf_sts (list[schrodinger.structure.Structure] or None) – reaction workflow structures
tstart (float) – the starting temperature (K)
tstep (float) – the step size of the temperature (K)
ntemp (int) – the number of temperature points
pstart (float) – the starting pressure (atm)
pstep (float) – the step size of the pressure (atm)
npress (int) – the number of pressure points
anharm (bool) – True if anharmonic calculation is performed else False
extra_stages_file (string) – name of stage file

Rtype energy_term_dict

dict

Returns

dictionary of energy keys.

class schrodinger.application.matsci.reaction_workflow_utils.SiblingNode(name, axes)¶

Bases: object

Contains parent-child information for a sibling group as well as features for creating an energy diagram

LINE_LENGTH = 1¶

X_GAP = 0.5¶

__init__(name, axes)¶

Parameters

name (str) – The name of the sibling group
axes (matplotlib.axes.Axes) – The plot’s axes object

addToPlot(y_val, energy, text_offset)¶

Add this sibling group to the plot

Parameters

y_val (float) – The y-value of the sibling on the plot
energy (float) – The energy to show on the label
text_offset (float) – The offset for showing the label above horizontal lines

class schrodinger.application.matsci.reaction_workflow_utils.EnergyDiagramPlotter(json_path, csv_path, logger=None)¶

Bases: object

Class for exporting energy level diagrams

TOTAL_FREE_ENERGY = 'Total_Free_Energy'¶

TEXT_OFFSET_DIVISOR = 50¶

VERTICAL_SPACING_DIVISOR = 23¶

PDF_FILE_ENDING = '_e_diagrams.pdf'¶

PNG_FILE_ENDING = '_std_e_diagram.png'¶

__init__(json_path, csv_path, logger=None)¶

Parameters

json_path (str) – Path to _conf_avg_wo_x_rel_parents.json file
csv_path (str) – Path to _conf_avg_wo_x_rel_reactants.csv file

static exportEnergyDiagrams(logger=None)¶

Export the energy diagrams if the parents file exists.

Parameters: logger (logging.Logger or None) – output logger or None if there isn’t one
Return type: (str, str) or None
Returns: the energy level diagrams in pdf format, the total free energy at STP energy level diagram in png format or None otherwise

run()¶

Export the energy level diagrams.

Return type: str, str
Returns: the energy level diagrams in pdf format, the total free energy at STP energy level diagram in png format

findTotalEnergyProp()¶: Find the Total Free Energy property with temperature and pressure closest to 298.15 K and 1.0 atm

getSibling(name)¶

Get an existing sibling or create a new one and return it

Parameters: name (str) – The name of the sibling
Return type: SiblingNode
Returns: A SiblingNode object

parseSiblings()¶: Read the siblings and parent child info from json file and find the generation of each sibling

setColors()¶: Set colors for paths that have one parent and one child for all nodes, excluding the reactant

findGenerations()¶

Determine the generations of the siblings

Each child’s generation is the largest generation of its parents, plus 1 which means that if we have the following ownerships: 1 -> 2 -> 3 -> 4 1 -> 5 -> 4 “4” will be a 4th generation and “5” will be a 2nd generation, so the plot will look like this: 1 – 2 – 3 – 4 1 – 5 ——- 4 as opposed to 1 ——- 5 – 4

findSameGenerationIndices()¶: Find groups of csv indices that belong to the same generation

plotDiagram(prop)¶: Plot the energy diagram for the passed property

adjustLabels()¶: Adjust the size of labels. If a label’s width is large enough to overlap with a neighbour’s label, reduce the font and redraw

getAdjustedYValues(prop)¶

Adjust the y values so that there is enough gap between all consecutive values in the same generation so there is no overlap.

Parameters: prop (str) – The property to adjust values for
Return type: numpy.array
Returns: The adjusted Y values as a numpy array

schrodinger.application.matsci.reaction_workflow_utils.flatten_sibling_conformers(sibling_conformers_dict)¶

Return a list of structures from the given sibling conformers dictionary.

Parameters: sibling_conformers_dict (dict) – dictionary of dictionaries where the outer dictionary is keyed by sibling and inner dictionary is keyed by conformer and values of the inner dictionary are lists of structures
Return type: list[schrodinger.structure.Structure]
Returns: the structures

schrodinger.application.matsci.reaction_workflow_utils.get_out_rep(sts)¶

Return the output representation of haptic ligands.

Parameters: sts (list[schrodinger.structure.Structure]) – the structures to search
Raises: ValueError – if there are conflicting output representations, if the output representation is unknown
Return type: str or None
Returns: the output representation, either module constant parserutils.CENTROID or parserutils.ETA, if None then none was found

schrodinger.application.matsci.reaction_workflow_utils.get_check_min_jaguar_keywords(st, set_freq=True, jaguar_keywords=None)¶

Return the check minimum Jaguar keywords.

Parameters

st (schrodinger.structure.Structure) – the structure
set_freq (bool) – if True then this is a frequency job
jaguar_keywords (dict) – Jaguar keywords

Return type

dict

Returns

the check minimum Jaguar keywords

exception schrodinger.application.matsci.reaction_workflow_utils.QMConformerSelectionException¶: Bases: Exception

class schrodinger.application.matsci.reaction_workflow_utils.QMConformerSelection(sibling_conformers_dict, qm_selection=True, n_conformers=5, pp_rel_energy_thresh=None, rmsd_thresh=0.1, base_name='qm_conformer_selection', host=None, tpp=1, return_files=False, logger=None, max_retries=0)¶

Bases: object

Manage selecting conformers from QM geometry optimizations.

__init__(sibling_conformers_dict, qm_selection=True, n_conformers=5, pp_rel_energy_thresh=None, rmsd_thresh=0.1, base_name='qm_conformer_selection', host=None, tpp=1, return_files=False, logger=None, max_retries=0)¶

Parameters

sibling_conformers_dict (dict) – dictionary of dictionaries where the outer dictionary is keyed by sibling and inner dictionary is keyed by conformer and values of the inner dictionary are lists of structures
qm_selection (bool) – if True then select conformers from all geometry optimized structures using the selection criteria specified using n_conformers, pp_rel_energy_thresh, and rmsd_thresh, otherwise select all geometry optimized structures as conformers
n_conformers (int) – either the maximum number of conformers if pp_rel_energy_thresh is None or a target minimum number of conformers if pp_rel_energy_thresh is given
pp_rel_energy_thresh (None or float) – relative energy threshold, if None then only the n_conformers lowest energy conformers are returned, units are in kJ/mol
rmsd_thresh (float) – the maximum allowable RMSD (Ang.) between two structures before they can be considered different conformers
base_name (str) – the base name used to name the launch directory as well as input and output files
host (str or None) – the host string to use to create the queue, for example ‘<host>:<n>’, where <host> is the host and <n> is the number of simultaneous subjobs, if None then it will be determined automatically by job control from the toplevel -HOST
tpp (int) – the number of threads to use for subjobs, i.e. -TPP (threads-per-process)
return_files (bool) – whether to zip and return all output files
logger (logging.Logger or None) – output logger or None if there isn’t one
max_retries (int) – maximum number of times to try relaunching subjobs

writeInput(launch_dir, in_mae_file)¶

Write the input.

Parameters

launch_dir (str) – the launch directory
in_mae_file (str) – the input file name

checkJob(launch_dir, out_mae_file)¶

Check the job.

Parameters

launch_dir (str) – the launch directory
out_mae_file (str) – the output file name

Raises

QMConformerSelectionException – if there is an issue

selectConformers(sts)¶

Select representative conformers from the given geometry optimized structures.

Parameters: sts (list[schrodinger.structure.Structure]) – all conformers
Return type: list
Returns: representative conformers

run()¶: Run the QM conformer selection.

class schrodinger.application.matsci.reaction_workflow_utils.MopacConformerSelection(*args, method='PM6', **kwargs)¶

Bases: schrodinger.application.matsci.reaction_workflow_utils.QMConformerSelection

ENERGY_KEY = 'r_mopac_MOPAC_Total_Energy_EV'¶

CONVERSION = 96.48533212331012¶

NAME = 'Mopac'¶

__init__(*args, method='PM6', **kwargs)¶

See parent class.

Parameters: method (str) – the Mopac method

runJob(launch_dir, in_mae_file)¶

Run the Mopac geometry optimization.

Parameters

launch_dir (str) – the Mopac launch directory
in_mae_file (str) – the Mopac input file name

Return type

str

Returns

the Mopac output file name

class schrodinger.application.matsci.reaction_workflow_utils.JMSWFConformerSelection(*args, jaguar_keywords={'basis': 'LACVP**', 'dftname': 'B3LYP'}, max_i_freq=0, write_output_files=True, **kwargs)¶

Bases: schrodinger.application.matsci.reaction_workflow_utils.QMConformerSelection, schrodinger.application.matsci.reaction_workflow_utils.JMSWFMixin

ENERGY_KEY = 'r_j_Gas_Phase_Energy_stage_1'¶

CONVERSION = 2625.499639479825¶

NAME = 'JMSWF'¶

__init__(*args, jaguar_keywords={'basis': 'LACVP**', 'dftname': 'B3LYP'}, max_i_freq=0, write_output_files=True, **kwargs)¶

See parent class.

Parameters

jaguar_keywords (dict) – Jaguar keywords
max_i_freq (float) – tolerate small imaginary frequencies less than this value in wavenumbers (cm^-1)
write_output_files (bool) – whether to write output files

runJob(launch_dir, in_mae_file)¶

Run the JMSWF geometry optimization.

Parameters

launch_dir (str) – the JMSWF launch directory
in_mae_file (str) – the JMSWF input file name

Raises

QMConformerSelectionException – if there is an issue

Return type

str

Returns

the JMSWF output file name

class schrodinger.application.matsci.reaction_workflow_utils.XtbConformerSelection(*args, **kwargs)¶

Bases: schrodinger.application.matsci.reaction_workflow_utils.JMSWFConformerSelection

NAME = 'xTB'¶

__init__(*args, **kwargs)¶: See parent class.

exception schrodinger.application.matsci.reaction_workflow_utils.RxnNetworkGraphException¶: Bases: Exception

class schrodinger.application.matsci.reaction_workflow_utils.RxnNetworkGraph(graph, transition_state_names=None)¶

Bases: object

Manage a reaction network graph.

__init__(graph, transition_state_names=None)¶

Parameters

graph (networkx.DiGraph) – a graph of the reaction network which is a collection of named nodes and their connectivity
transition_state_names (list[str] or None) – the names of the graph nodes that are transition states or None if there aren’t any

validate()¶

Validate the graph.

Raises: RxnNetworkGraphException – if there is an issue

validateRateConstants()¶

Check if rate constants can be calculated.

Raises: RxnNetworkGraphException – if there is an issue

validateTOFs()¶

Check if turn over frequencies can be calculated.

Raises: RxnNetworkGraphException – if there is an issue

getReactantNames()¶

Return the names of the graph nodes that are reactants.

Return type: list[str]
Returns: the names of the graph nodes that are reactants

getProductNames()¶

Return the names of the graph nodes that are products.

Return type: list[str]
Returns: the names of the graph nodes that are products

getConnectedTransitionStateTriples()¶

Return a list of connected transition state triples.

Return type: list[tuple]
Returns: connected transition state triples, where each tuple is a triple of node names, the second name is the name of a transition state while the first and third names are those of preceeding and succeeding nodes, if either of those doesn’t exist then the value will be None

getBranchDivergentNames()¶

Return the names of the graph nodes that start a branch.

Return type: list[str]
Returns: the names of the graph nodes that start a branch

getBranchConvergentNames()¶

Return the names of the graph nodes that end a branch.

Return type: list[str]
Returns: the names of the graph nodes that end a branch

getIntermediateNames()¶

Return the names of the graph nodes that are intermediates.

Return type: list[str]
Returns: the names of the graph nodes that are intermediates

getTransitionStateNames()¶

Return the names of the graph nodes that are transition states.

Return type: list[str]
Returns: the names of the graph nodes that are transition states

isForward(initial_name, final_name)¶

Return True if the given node names are ordered in the forward direction of the reaction network and False otherwise as is the case if they are ordered in the reverse direction or if it is unknown due to branching.

Parameters

initial_name (str) – the name of the initial node
final_name (str) – the name of the final node

Return type

bool

Returns

True if the given node names are ordered in the forward direction of the reaction network and False otherwise as is the case if they are ordered in the reverse direction or if it is unknown due to branching

getOrderedNodeNames()¶

Return an ordered list of node names.

Return type: list[str]
Returns: an ordered list of node names

exception schrodinger.application.matsci.reaction_workflow_utils.EnergeticSpanException¶: Bases: Exception

class schrodinger.application.matsci.reaction_workflow_utils.EnergeticSpan(graph)¶

Bases: object

Manage application of the energetic span model.

__init__(graph)¶

Parameters: graph (RxnNetworkGraph) – the reaction network graph

validate()¶

Validate.

Raises: EnergeticSpanException – if there is an issue

getDeltaE(initial_name, final_name, energies)¶

Return the difference in energy between two nodes.

Parameters

initial_name (str) – the name of the initial node
final_name (str) – the name of the final node
energies (dict[str]=float) – keys are node names and values are energies in kcal/mol

Return type

float

Returns

the energy difference in kcal/mol

getDeltaERxn(energies)¶

Return the reaction energy.

Parameters: energies (dict[str]=float) – keys are node names and values are energies in kcal/mol
Raises: EnergeticSpanException – if there is an issue
Return type: float
Returns: the reaction energy in kcal/mol

getResistance(temperature, energies)¶

Return the resistance.

Parameters

temperature (float) – the temperature in K
energies (dict[str]=float) – keys are node names and values are energies in kcal/mol

Return type

float

Returns

the resistance, which is unitless

getVoltage(temperature, energies)¶

Return the voltage.

Parameters

temperature (float) – the temperature in K
energies (dict[str]=float) – keys are node names and values are energies in kcal/mol

Return type

float

Returns

the voltage in 1/s

getSOSTOF(energies, temperature)¶

Return the turn over frequency using the full sum-over-states.

Parameters

energies (dict[str]=float) – keys are node names and values are energies in kcal/mol
temperature (float) – the temperature in K

Return type

float

Returns

the turn over frequency in 1/s

getEnergeticSpans(energies)¶

Return the energetic spans.

Parameters: energies (dict[str]=float) – keys are node names and values are energies in kcal/mol
Return type: list[tuple]
Returns: the energetic spans as a list of triples, the first item is the intermediate name, the second item is the transition state name, and the third item is the energetic span in kcal/mol

getDeterminingStates(energies)¶

Return the determining states and their energetic span.

Parameters: energies (dict[str]=float) – keys are node names and values are energies in kcal/mol
Return type: str, str, float
Returns: the determining intermediate, determining transition state, and their energetic span in kcal/mol

getDeterminingStatesTOF(energetic_span, temperature)¶

Return the turn over frequency using the determining states.

Parameters

energetic_span (float) – the energetic span in kcal/mol
temperature (float) – the temperature in K

Return type

float

Returns

the turn over frequency in 1/s

schrodinger.application.matsci.reaction_workflow_utils.copy_to_autorxnwf_file(ofname)¶

Create an auto-rxnwf compatible copy of the file with the given file name.

Parameters: ofname (str) – the original file name
Return type: str
Returns: the auto-rxnwf compatible file name