schrodinger.application.matsci.reaction_workflow_enum_utils module¶

Utilities for enumerating reaction workflows.

class schrodinger.application.matsci.reaction_workflow_enum_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_enum_utils.Source(rgroup_st, site_idxs)¶

Bases: tuple

rgroup_st¶: Alias for field number 0

site_idxs¶: Alias for field number 1

class schrodinger.application.matsci.reaction_workflow_enum_utils.PositionedRGroup(hash_idx, sites, st, permutation)¶

Bases: tuple

hash_idx¶: Alias for field number 0

permutation¶: Alias for field number 3

sites¶: Alias for field number 1

st¶: Alias for field number 2

schrodinger.application.matsci.reaction_workflow_enum_utils.get_msg(site, msg)¶

schrodinger.application.matsci.reaction_workflow_enum_utils.get_core_idxs(st)¶

Return a set of atom indices for the core of the given structure.

Parameters:: st (Structure) – the structure
Return type:: set
Returns:: core atom indices

schrodinger.application.matsci.reaction_workflow_enum_utils.get_rgroup_sts_by_n_site(rgroup_file)¶

Return R-group structures binned by the number of attachment sites on the R-group.

Parameters:: rgroup_file (str) – the R-group file
Return type:: dict[int]=list[schrodinger.structure.Structure]
Returns:: the R-group structures binned by the number of sites attachment sites on the R-group

schrodinger.application.matsci.reaction_workflow_enum_utils.get_rge_sources(st, rgroup_sts, binned_sites, old_to_new)¶

Return a list of Source that is prepared for enumeration using the R-Group Enumeration module and a copy of the input structure with potentially duplicated to-atoms.

Parameters:

st (schrodinger.structure.Structure) – the structure
rgroup_sts (list of structure.Structure) – the R-group structures
binned_sites (list of lists of Site) – the binned sites
old_to_new (dict) – a map of old-to-new atom indices

Return type:

list, schrodinger.structure.Structure

Returns:

contains Source, a copy of the input structure with potentially duplicated to-atoms

schrodinger.application.matsci.reaction_workflow_enum_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

class schrodinger.application.matsci.reaction_workflow_enum_utils.RgroupEnumerator(core_st, sources, optimize_sidechains=True, deduplicate=True, start=0, stop=None, copy_properties=False, enumerate_cistrans=True, yield_renum_maps=False, concentrations=())¶

Bases: RGroupEnumerator

See parent class.

schrodinger.application.matsci.reaction_workflow_enum_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 performed
rgroups_dict (dict) – keys are integers which are the hash_idx values relating to sites, values are structure.Structure
sites_dict (dict) – keys are integers which are the hash_idx values relating to R-groups, values are lists of Site

Raises:

InvalidInput – if there is an issue

Return type:

structure.Structure, dict, list[str]

Returns:

the substituted structure, dictionary mapping old atom indices to new atom indices, R-group titles

schrodinger.application.matsci.reaction_workflow_enum_utils.get_updated_sites_dict(sites_dict, old_to_new)¶

Return the given sites dictionary with updated indices according to the given index map.

Parameters:

sites_dict (dict) – keys are integers which are the hash_idx values relating to R-groups, values are lists of Site
old_to_new (dict) – a map of old-to-new atom indices

Return type:

dict

Returns:

keys are integers which are the hash_idx values relating to R-groups, values are lists of Site

schrodinger.application.matsci.reaction_workflow_enum_utils.substitute_or_sculpt(st, rgroups_dict, sites_dict, rgroups_perm_dict=None)¶

Return structures created by substituting or sculpting the given R-groups onto the given structure at the given sites.

Parameters:

st (structure.Structure) – the structure on which the substitutions or sculpts are performed
rgroups_dict (dict) – keys are integers which are the hash_idx values relating to sites, values are structure.Structure
sites_dict (dict) – keys are integers which are the hash_idx values relating to R-groups, values are lists of Site
rgroups_perm_dict (dict or None) – for those hash indices that draw multi-site R-groups this dictionary allows for specifying which permutation of these R-group sites to use to connect it to the structure, keys are integers which are the hash_idx values relating to sites, values are 1-based permutations indices, if None all permutations are considered

Return type:

dict[schrodinger.structure.Structure]=list[str], list[str]

Returns:

keys are structures and values are lists of R-group titles added to the given structure, the list contains titles of enumerated structures that have ring-spears

schrodinger.application.matsci.reaction_workflow_enum_utils.get_smiles(st)¶

Return the smiles of the given metal complex.

Parameters:: st (schrodinger.structure.Structure) – the metal complex
Return type:: str
Returns:: smiles

schrodinger.application.matsci.reaction_workflow_enum_utils.get_st_with_valid_charge_and_multiplicity(st)¶

Return a copy of the given structure with its molecular charge and spin multiplicity properties stamped such that the pair satisfies the jaguarworkflows charge and multiplicity validator for the structure.

R-group substitution changes the electron count of the assembled structure, so the original core’s charge and multiplicity may no longer satisfy the validator’s parity constraint. When the current pair is invalid the charge is adjusted by one, first in the toward-zero direction (decremented when positive, incremented otherwise) and then in the opposite direction if that first attempt still fails; the multiplicity is left unchanged. Whether or not adjustment was needed, both properties are written explicitly onto the returned copy so downstream consumers such as the Project Table see them.

The per-atom formal-charge and unpaired-electron properties carried over from the original core and R-group atoms are also removed because they cannot be reconciled with an atom-agnostic total; leaving them would trigger consistency failures in downstream helpers that sum atomic values to derive structure totals.

Parameters:: st (schrodinger.structure.Structure) – the assembled structure
Raises:: InvalidInput – if neither charge adjustment produces a (charge, multiplicity) pair accepted by the validator
Return type:: schrodinger.structure.Structure
Returns:: a copy with valid charge and multiplicity properties set

exception schrodinger.application.matsci.reaction_workflow_enum_utils.InvalidInput¶: Bases: Exception

exception schrodinger.application.matsci.reaction_workflow_enum_utils.RingSpearsOutput¶: Bases: Exception

class schrodinger.application.matsci.reaction_workflow_enum_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 structure, potentially modified in place
sites (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

static getBinnedSites(sites)¶

Get the sites binned firstly by structure_idx and secondly by hash_idx.

Parameters:: sites (list) – contains Site
Return type:: dict
Returns:: keys are structure_idx, values are dicts whose keys are hash_idx and values are lists of Site

class schrodinger.application.matsci.reaction_workflow_enum_utils.SculptMultiRGroup(st, rgroups_dict, sites_dict, rgroups_perm_dict=None, xtb=False)¶

Bases: object

Use sculpting to enumerate using R-groups with multiple sites.

__init__(st, rgroups_dict, sites_dict, rgroups_perm_dict=None, xtb=False)¶

Parameters:

st (structure.Structure) – the structure on which the sculpts are performed
rgroups_dict (dict) – keys are integers which are the hash_idx values relating to sites, values are structure.Structure
sites_dict (dict) – keys are integers which are the hash_idx values relating to R-groups, values are lists of Site
rgroups_perm_dict (dict or None) – for those hash indices that draw multi-site R-groups this dictionary allows for specifying which permutation of these R-group sites to use to connect it to the structure, keys are integers which are the hash_idx values relating to sites, values are 1-based permutations indices, if None all permutations are considered
xtb (bool) – if True then use xtb optimization for sculpting otherwise use a classical force field

getRGroupSitesDict()¶

Return the R-group sites dictionary.

Return type:: dict
Returns:: keys are integers which are the hash_idx values relating to R-groups, values are lists of Site

prepareStructure()¶: Prepare the structure for enumeration by removing the appropriate atoms that exist after the substitution sites.

getPositionedRGroups(hash_idx)¶

Enumerate the R-group for the given hash index on the available structures sites and put it in a favorable position for sculpting.

Parameters:: hash_idx (int) – the hash index of the R-group
Return type:: list[PositionedRGroup]
Returns:: the positioned R-groups

addRGroups(positioned_r_groups)¶

Return a copy of the structure with the given R-groups added in their guess positions, bonded, and ready for minimization.

Parameters:: positioned_r_groups (list[PositionedRGroups]) – the positioned R-groups
Return type:: schrodinger.structure.Structure, list, dict, list
Returns:: the structure, list containing atom indices to fix, dictionary mapping R-group site from indices to a numpy array of the xyz coordinates indicating the location to which it will be sculpted, list of pair tuples of atom indices of bonds created

addDummyAtomAnchors(st, restrain_pairs)¶

Return a copy of the given structure with dummy atom anchors added at the given locations.

Parameters:

st (schrodinger.structure.Structure) – the structure
restrain_pairs (dict) – dictionary mapping R-group site from indices to a numpy array of the xyz coordinates indicating the location to which it will be sculpted

Return type:

schrodinger.structure.Structure, dict

Returns:

the structure, dictionary mapping R-group site from indices to dummy atom indices indicating the location to which it will be sculpted

sculptRGroupsWClassical(positioned_r_groups)¶

Sculpt the given R-groups onto the structure using a classical forcefield.

Parameters:: positioned_r_groups (list[PositionedRGroups]) – the positioned R-groups
Raises:: InvalidInput – if there is an issue
Return type:: schrodinger.structure.Structure
Returns:: the structure

sculptRGroupsWXtb(positioned_r_groups)¶

Sculpt the given R-groups onto the structure using xTB.

Parameters:: positioned_r_groups (list[PositionedRGroups]) – the positioned R-groups
Raises:: InvalidInput – if there is an issue
Return type:: schrodinger.structure.Structure
Returns:: the structure

sculptRGroups(positioned_r_groups)¶

Sculpt the given R-groups onto the structure.

Parameters:: positioned_r_groups (list[PositionedRGroups]) – the positioned R-groups
Return type:: schrodinger.structure.Structure
Returns:: the structure

sculptAllRGroups()¶

Sculpt all R-groups onto the structure.

Return type:: dict[schrodinger.structure.Structure]=list[str]
Returns:: keys are structures and values are lists of R-group titles added to the given structure

run()¶

Run it.

Return type:: dict[schrodinger.structure.Structure]=list[str]
Returns:: keys are structures and values are lists of R-group titles added to the given structure

class schrodinger.application.matsci.reaction_workflow_enum_utils.EnumerateReactionWorkflow(rxnwf_file, rgroup_files, sites, force_hetero_substitution=False, out_rep=None, base_name='enumerate_reaction_workflow', ext='.mae', dedup_smiles=True, post_enum_opt=True, 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', ext='.mae', dedup_smiles=True, post_enum_opt=True, 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
ext (str) – file name extension
dedup_smiles (bool) – if True then deduplicate by SMILES, needed because of multi-site R-group permutations
post_enum_opt (bool) – whether to perform geometry optimization after enumeration
logger (logging.Logger) – the logger

getNSitesByHashIdx(sites_dict, rgroup_file)¶

Return the number of attachment sites that can be drawn for from the given R-group file for each hash index in the given sites dictionary as a dictionary.

Parameters:

sites_dict (dict) – keys are integers which are the hash_idx values relating to R-groups, values are lists of Site
rgroup_file (str) – the R-group file

Raises:

InvalidInput – if there is an issue

Return type:

dict[int]=list[int]

Returns:

the number of attachment sites that can be drawn for from the given R-group file for each hash index

getNCombinations(n_site_group, rgroup_file)¶

Return the number of combinations for drawing R-groups from the given file according to the given numbers of sites for which to draw for.

Parameters:

n_site_group (tuple(int)) – contains the number of sites being drawn for for each hash index
rgroup_file (str) – the R-group file

Return type:

int, str

Returns:

the number of combinations, the error message if there is one

getTotalNCombinations(sites_dict)¶

For the given sites dictionary return the total number of ways of enumerating the R-groups in the corresponding R-group files among the available sites.

Parameters:: sites_dict (dict) – keys are integers which are the hash_idx values relating to R-groups, values are lists of Site
Raises:: InvalidInput – if there is an issue
Return type:: int
Returns:: the number of combinations

getNumberRXNWFFiles()¶

Return the maximum number of rxnwf files that will be enumerated.

Return type:: int
Returns:: the maximum number of rxnwf files that will be enumerated

validate()¶

Validate.

Raises:: InvalidInput – if there is an issue

setRGroupStructures()¶: Set the R-group structures.

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

isCompatible(rgroups_dict)¶

Return True if the given R-group structures are compatible with the reaction workflow.

Parameters:: rgroups_dict (dict) – keys are integers which are the hash_idx values relating to sites, values are structure.Structure
Return type:: bool
Returns:: True if the given R-group structures are compatible

getPermutationIdxDict(rgroups_dict)¶

For each hash index create a list of 1-based permutation indices that specify how to connect the given R-group to the structure and return it as a dictionary.

Parameters:: rgroups_dict (dict) – keys are integers which are the hash_idx values relating to sites, values are structure.Structure
Return type:: dict[int]=list[int]
Returns:: keys are integers which are the hash_idx values relating to sites, values are lists of 1-based permutation indices

getEnumeratedRXNWFSts(rgroups_dict, rgroups_perm_dict)¶

Return enumerated rxnwf structures.

Parameters:

rgroups_dict (dict) – keys are integers which are the hash_idx values relating to sites, values are structure.Structure
rgroups_perm_dict (dict) – for those hash indices that draw multi-site R-groups this dictionary allows for specifying which permutation of these R-group sites to use to connect it to the structure, keys are integers which are the hash_idx values relating to sites, values are 1-based permutations indices

Return type:

dict[schrodinger.structure.Structure]=list[str], list[str]

Returns:

keys are the enumerated rxnwf structures and values lists of their R-group titles, the list contains titles of enumerated structures that have ring-spears

doEnumeration()¶

Do the enumeration.

Raises:: InvalidInput – if there is an issue
Return type:: int
Returns:: the number of SMILES unique files written

run()¶

Run it.

Raises:: RingSpearsOutput – if ring-spears are present in the output

schrodinger.application.matsci.reaction_workflow_enum_utils.get_post_enum_optimized(st, xtb=False, logger=None)¶

Return a geometry optimized copy of the given enumerated structure.

Parameters:

st (schrodinger.structure.Structure) – the structure
xtb (bool) – if True then use xtb optimization otherwise use a classical force field
logger (logging.Logger) – the logger

Raises:

InvalidInput – if there is an issue

Return type:

schrodinger.structure.Structure

Returns:

the geometry optimized structure

class schrodinger.application.matsci.reaction_workflow_enum_utils.EnumerateSwapMixin¶

Bases: object

Manage enumeration and swapping.

runEnumerateRXNWF(tag)¶

Run enumerate reaction workflow.

Parameters:: tag (str) – either the REFERENCE or NOVEL module constant
Return type:: set, dict[str]=list[str]
Returns:: the names of the enumerated reaction workflow files R-group titles, the dict keys are names of enumerated reaction workflow files and values are lists of structure titles for structures that have ring-spears

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:

InvalidInput – if there is an issue

Return type:

set

Returns:

the names of the enumerated reaction workflow files

getRXNWFInputFiles(job_name)¶

Return all reaction workflow input files.

Parameters:: job_name (str) – the job name
Return type:: set, dict[str]=list[str]
Returns:: all reaction workflow input files, the dict keys are names of enumerated reaction workflow files and values are lists of structure titles for structures that have ring-spears