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

__contains__

Return key in self.

__init__

Initialize self. See help(type(self)) for accurate signature.

__len__

Return len(self).

count(value) → integer -- return number of occurrences of value
index(value[, start[, stop]]) → integer -- return first index of value.

Raises ValueError if the value is not present.

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

__contains__

Return key in self.

__init__

Initialize self. See help(type(self)) for accurate signature.

__len__

Return len(self).

count(value) → integer -- return number of occurrences of value
index(value[, start[, stop]]) → integer -- return first index of value.

Raises ValueError if the value is not present.

press_n

Alias for field number 2

press_start

Alias for field number 0

press_step

Alias for field number 1

schrodinger.application.matsci.reaction_workflow_utils.get_idxs_marked_atoms(st, prop)

Return a list of indices of atoms in the given structure that have the given property defined.

Parameters:
Return type:

list
Returns:

contains indices of atoms
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
exception schrodinger.application.matsci.reaction_workflow_utils.InvalidInput

Bases: Exception

__init__

Initialize self. See help(type(self)) for accurate signature.

args
with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

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_idx_groups_str(idx_groups)

Get a string representation of the given index groups.

Parameters:idx_groups (list) – contains lists of indices
Return type:str
Returns:the string
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 (OrderedDict) – the Jaguar keywords dict
Return type:list
Returns:the Jaguar keywords list
schrodinger.application.matsci.reaction_workflow_utils.type_cast_seed(seed, exception_type=<class 'argparse.ArgumentTypeError'>)

Type cast the seed.

Parameters:
  • seed (str or unicode) – seed for random number generator
  • exception_type (type) – the exception type to raise if invalid
Return type:

int
Returns:

the seed
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:

OrderedDict
Returns:

the Jaguar keywords OrderedDict
schrodinger.application.matsci.reaction_workflow_utils.check_ff_assignment(sts, ffld_name='OPLS3e')

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)

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

Parameters:
Return type:

float
Returns:

the molecular weight (amu)
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)

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)
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)

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
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

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

Parameters:
  • conformers (list) – schrodinger.structure.Structure conformers used to seed the search
  • n_conformers (int) – number of sought conformers
  • 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
  • job_dj (queue.JobDJ) – if an instance is given then add the current job and return
  • clean (bool) – if not given a job_dj then this option controls cleaning up after the job that was run
Raises:

RuntimeError – if the MacroModel job fails
Return type:

list
Returns:

schrodinger.structure.Structure conformers, could be less than n_conformers
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 structure
  • old_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
class schrodinger.application.matsci.reaction_workflow_utils.ReactionWorkflowFile(rxnwf_file)

Bases: object

Manage a reaction workflow file.

__init__(rxnwf_file)

Create an instance.

Parameters:rxnwf_file (str) – the reaction workflow file
getReactantsSiblingGroupName()

Return the reactants sibling group name.

Return type:str
Returns:the reactants sibling group name
getReactantsConformersDict()

Return the reactants conformers dictionary.

Return type:dict
Returns:keys are conformer group names, values are lists of structure.Structure
class schrodinger.application.matsci.reaction_workflow_utils.ReactionWorkflowEnergyAnalysis(rxnwf_file, energy_keys)

Bases: schrodinger.application.matsci.reaction_workflow_utils.ReactionWorkflowFile

Manage a reaction workflow energy analysis.

__init__(rxnwf_file, energy_keys)

Create an instance.

Parameters:
  • rxnwf_file (str) – the reaction workflow file
  • 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>)’
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 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
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
getGraph()

Return a NetworkX directed graph of the reaction workflow energy level diagram.

Return type:networkx.DiGraph
Returns:nodes are sibling group names and have energy dictionary kwargs, edges are directed (parent, child) pairs
static getOrderedNodeNames(graph)

Return an ordered list of node names from the given graph.

Parameters:graph (networkx.DiGraph) – nodes are sibling group names and have energy dictionary kwargs, edges are directed (parent, child) pairs
Return type:list
Returns:contains ordered node names
writeDataFiles()

Write data files.

getReactantsConformersDict()

Return the reactants conformers dictionary.

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

Return the reactants sibling group name.

Return type:str
Returns:the reactants sibling group name
exception schrodinger.application.matsci.reaction_workflow_utils.ReactionWorkflowException

Bases: Exception

__init__

Initialize self. See help(type(self)) for accurate signature.

args
with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

class schrodinger.application.matsci.reaction_workflow_utils.ReactionWorkflow(reaction_wf_input_sts, n_conformers=5, seed=123, return_csearch_files=False, jaguar_keywords={'basis': 'LACVP**', 'dftname': 'B3LYP'}, temp_data=None, press_data=None, return_jaguar_files=False, rate_constants=False, return_rate_constant_files=False, extra_stages_file=None, n_jmswf_subjobs=1, subhost=None, tpp=1, logger=None)

Bases: object

Manage a reaction workflow.

__init__(reaction_wf_input_sts, n_conformers=5, seed=123, return_csearch_files=False, jaguar_keywords={'basis': 'LACVP**', 'dftname': 'B3LYP'}, temp_data=None, press_data=None, return_jaguar_files=False, rate_constants=False, return_rate_constant_files=False, extra_stages_file=None, n_jmswf_subjobs=1, subhost=None, tpp=1, logger=None)

Create an instance.

Parameters:
  • reaction_wf_input_sts (list) – reaction workflow input structures
  • n_conformers (int) – number of conformers to search for
  • seed (int) – seed for random number generator
  • return_csearch_files (bool) – whether to return all output files from the conformational search subjobs
  • jaguar_keywords (OrderedDict) – 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
  • 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
  • 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
  • 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
validate()

Validate.

Raises:ReactionWorkflowException – if there is an issue
createConformers()

Create the conformers.

Raises:ReactionWorkflowException – if there is an issue
runJMSWF()

Run the Jaguar multistage workflow.

Raises:ReactionWorkflowException – if there is an issue
prepareJMSWFOutput()

Prepare Jaguar multistage workflow output.

prepareRXNWFOutput()

Prepare reaction workflow output.

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
run()

Run the reaction workflow.