schrodinger.application.matsci.reaction_workflow_utils module¶
Utilities for reaction workflows.
Copyright Schrodinger, LLC. All rights reserved.
- 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.Site(from_idx, to_idx, hash_idx, structure_idx)¶
Bases:
tuple
- from_idx¶
Alias for field number 0
- hash_idx¶
Alias for field number 2
- structure_idx¶
Alias for field number 3
- to_idx¶
Alias for field number 1
- class schrodinger.application.matsci.reaction_workflow_utils.Source(rgroup_st, site_idxs)¶
Bases:
tuple
- rgroup_st¶
Alias for field number 0
- site_idxs¶
Alias for field number 1
- schrodinger.application.matsci.reaction_workflow_utils.get_msg(site, msg)¶
- 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 ofrelative
) 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.
- 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 chirality flipping should be prevented.
- Parameters
st (schrodinger.structure.Structure) – the structure
- Return type
list or None
- Returns
list of atom indices (1-based), whether chiral or not, which in the event of being chiral should not be allowed to flip chirality during the calculation or use None for the default MacroModel behavior
- exception schrodinger.application.matsci.reaction_workflow_utils.InvalidInput¶
Bases:
Exception
- 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 givenenergy_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 conformersffld_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), whether chiral or not, which in the event of being chiral should not be allowed to flip chirality during the calculation or use None for the default MacroModel 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 conformerjob_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.update_index_properties(st, old_to_new)¶
Update the index properties of the given structure.
- Parameters
st (
structure.Structure
) – the structureold_to_new (dict) – a map of old-to-new atom indices
- schrodinger.application.matsci.reaction_workflow_utils.get_core_idxs(st)¶
Return a set of atom indices for the core of the given structure.
- Parameters
st (schrodinger.structure.Structure) – the structure
- Return type
set
- Returns
core atom indices
- 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 givensibling_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
- 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 workflowschrodinger.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 workflowschrodinger.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 typeenergy_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 providedhas_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
- 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
- class schrodinger.application.matsci.reaction_workflow_utils.Sites¶
Bases:
object
Manage enumeration sites.
- static getSites(sites_data, n_structures=1)¶
Return a list of Site from the given sites data.
- Parameters
sites_data (list) – contains for each site a list of data [from_idx, to_idx, hash_idx] with an optional fourth item structure_idx
n_structures (int) – the number of structures, used if the given sites lack the optional fourth item
- Raises
InvalidInput – if there is an issue
- Return type
list
- Returns
contains
Site
- static validateSitesFormat(sites)¶
Validate the given sites format.
- Parameters
sites (list) – contains
Site
- Raises
InvalidInput – if there is an issue
- static delete_substitution_site_bonds(st, sites)¶
Delete bonds in the given structure that occur after the given substitution sites and return extracted core information.
- Parameters
st (
structure.Structure
) – the structuresites (list) – contains
Site
- Return type
structure.Structure
, dict- Returns
the extracted core and old-to-new atom index map
- static validateSitesData(sites, st)¶
Validate the given sites data.
- Parameters
sites (list) – contains
Site
st (
structure.Structure
) – the structure
- Raises
InvalidInput – if there is an issue
- schrodinger.application.matsci.reaction_workflow_utils.get_RGE_sources(rgroup_sts, binned_sites, old_to_new)¶
Return a list of Source that is prepared for enumeration using the R-Group Enumeration module.
- schrodinger.application.matsci.reaction_workflow_utils.substitute(st, rgroups_dict, sites_dict)¶
Return a copy of the given structure that has been substituted with the given R-groups at the given sites.
- Parameters
st (
structure.Structure
) – the structure on which the substitution is performedrgroups_dict (dict) – keys are integer hashes relating to sites, values are
structure.Structure
sites_dict (dict) – keys are integer hashes relating to R-groups, values are lists of
Site
- Raises
InvalidInput – if there is an issue
- Return type
structure.Structure
- Returns
the substituted structure
- class schrodinger.application.matsci.reaction_workflow_utils.EnumerateReactionWorkflow(rxnwf_file, rgroup_files, sites, force_hetero_substitution=False, out_rep=None, base_name='enumerate_reaction_workflow', logger=None)¶
Bases:
object
Manage enumeration of a reaction workflow.
- __init__(rxnwf_file, rgroup_files, sites, force_hetero_substitution=False, out_rep=None, base_name='enumerate_reaction_workflow', logger=None)¶
Create an instance.
- Parameters
rxnwf_file (str) – the reaction workflow file
rgroup_files (dict) – keys are hash_idx (see sites), values are file names
sites (list) – contains
Site
force_hetero_substitution (bool) – if True then for hetero-eumeration do not additionally include homo-enumeration results
out_rep – if a string then must be either module constant parserutils.CENTROID or parserutils.ETA, if None then do nothing
base_name (str) – the base name to use in naming the enumerated output files
logger (logging.Logger) – the logger
- validate()¶
Validate.
- Raises
InvalidInput – if there is an issue
- setRGroupStructures()¶
Set the R-group structures.
- setHasStructureSpecificSites()¶
Set has structure specific sites.
- getStructures()¶
Generates structure dictionaries where keys are enumeration indices and values are structures.
- Return type
dict
- Returns
keys are enumeration indices, values are
structure.Structure
- doEnumeration()¶
Do the enumeration.
- run()¶
Run it.
- schrodinger.application.matsci.reaction_workflow_utils.replace_rxnwf_file_suffix(rxnwf_file, suffix)¶
Replace the suffix in the given reaction workflow file with a new suffix.
- Parameters
rxnwf_file (str) – the reaction workflow file
suffix (str) – the new suffix
- Return type
str
- Returns
the new string
- class schrodinger.application.matsci.reaction_workflow_utils.EnumerateSwapMixin¶
Bases:
object
Manage enumeration and swapping.
- runEnumerateRXNWF(tag)¶
Run enumerate reaction workflow.
- Parameters
tag (str) – either the REFERENCE or NOVEL module constant
- Raises
ReactionWorkflowException – if there is an issue
- Return type
set
- Returns
the names of the enumerated reaction workflow files
- runSwapFragments(enumerated_novel_files, reference_rxnwf_file)¶
Run swap fragments.
- Parameters
enumerated_novel_files (set) – the names of the enumerated novel files
reference_rxnwf_file (str) – the reference reaction workflow file
- Raises
ReactionWorkflowException – if there is an issue
- Return type
set
- Returns
the names of the enumerated reaction workflow files
- getRXNWFInputFiles()¶
Return all reaction workflow input files.
- Return type
set
- Returns
all reaction workflow input files
- class schrodinger.application.matsci.reaction_workflow_utils.EnumerateSwap(reference_rxnwf_file, novel_rxnwf_file=None, rgroup_files=None, reference_sites=None, novel_sites=None, force_hetero_substitution=False, require_identical_bonds=False, logger=None)¶
Bases:
schrodinger.application.matsci.reaction_workflow_utils.EnumerateSwapMixin
Manage enumeration and swapping.
- __init__(reference_rxnwf_file, novel_rxnwf_file=None, rgroup_files=None, reference_sites=None, novel_sites=None, force_hetero_substitution=False, require_identical_bonds=False, logger=None)¶
Create an instance.
- Parameters
reference_rxnwf_file (str) – the reaction workflow file containing the reference structures
novel_rxnwf)file – the reaction workflow file containing the single novel structure
rgroup_files (dict) – keys are hash_idx (see sites), values are file names
reference_sites (list) – contains
Site
for the reference structuresnovel_sites (list) – contains
Site
for the novel structureforce_hetero_substitution (bool) – if True then for hetero-eumeration do not additionally include homo-enumeration results
require_identical_bonds (bool) – whether to require that bonds to be created must exist in both novel and reference structures and be of the same bond order
logger (logging.Logger or None) – output logger or None if there isn’t one
- run()¶
Run it.
- Return type
set
- Returns
all reaction workflow input files
- schrodinger.application.matsci.reaction_workflow_utils.enumerate_swap(reference_rxnwf_file, novel_rxnwf_file=None, rgroup_files=None, reference_sites=None, novel_sites=None, force_hetero_substitution=False)¶
Return all reaction workflow files created by R-group enumerating the given reference and novel structures and swapping reference fragments for novel fragments.
- Parameters
reference_rxnwf_file (str) – the reaction workflow file containing the reference structures
novel_rxnwf)file – the reaction workflow file containing the single novel structure
rgroup_files (dict) – keys are hash_idx (see sites), values are file names
reference_sites (list) – contains
Site
for the reference structuresnovel_sites (list) – contains
Site
for the novel structureforce_hetero_substitution (bool) – if True then for hetero-eumeration do not additionally include homo-enumeration results
- Return type
set
- Returns
all reaction workflow input files
- 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
rxnwfu.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.get_smiles(st)¶
Return the smiles of the given metal complex.
- Parameters
st (
schrodinger.structure.Structure
) – the metal complex- Raise
(
rdkit_adapter.InconsistentStructureError
,rdkit_adapter.UnsupportedStructureError
)- Return type
str
- Returns
smiles
- 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 structureseps (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 structureststart (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
- run()¶
Export the energy level diagrams
- 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
- 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
- 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 structureset_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