schrodinger.livedesign.bbchem_endpoints module¶

Collection of functions intended as bbchem web endpoints.

schrodinger.livedesign.bbchem_endpoints.split_data_blocks(data: str, input_format: Format, options: Optional[RegistrationOptions] = None)¶

Iterates across serialized formats, yielding a single data block at a time. Supports iterating across SD, Maestro, and FASTA files; other formats are returned as a single block. NOTE: if a FASTA mapping is set on the registration options, the FASTA is parsed as a single block.

Parameters:

data – input text string
input_format – input format of the data
options – registration options

Returns:

an iterator of data blocks

schrodinger.livedesign.bbchem_endpoints.to_registration_data(data: str, input_format: Format, options: Optional[RegistrationOptions] = None) → Iterator[Union[RegistrationData, Exception]]¶: Generalizes small molecule and biologics registration processes, returning all data LiveDesign stores in it’s internal databases. This includes returning rdmol binaries directly as for each entity. Output includes properties from the input mol, computed properties, and potentially any child data of derived virtuals.

schrodinger.livedesign.bbchem_endpoints.to_format(mol_input: str, input_format: Format, output_format: Format, additional_properties: Optional[Dict] = None) → str¶

Main entrypoint for converting to a serialized text format.

Parameters:

mol_input – serialized mol
input_format – input format of the mol string
output_format – desired format for output string
additional_properties – property data to include on serialization

Returns:

converted text string

schrodinger.livedesign.bbchem_endpoints.to_image(mol_input: Optional[str], alignment_input: Optional[str] = None, substructure_options: Optional[QueryOptions] = None, highlight_input: Optional[str] = None, render_options: Optional[ImageGenOptions] = None, force_atomistic: bool = False) → bytes¶

Generates an image from a serialized input string; the request may include alignment, or substructure highlighting, or both.

Parameters:

mol_input – serialized mol
alignment_input – molecule to align to prior to image generation
substructure_options – substructure matching options
highlight_input – core to highlight in generated image
render_options – image generation options
force_atomistic – whether to force monomeric mols to be represented atomistically

Returns:

generated image SVG or PNG bytes

schrodinger.livedesign.bbchem_endpoints.to_entity_stock_image(entity_class: EntityClass, draw_options: ImageGenOptions) → bytes¶

Parameters:: entity_class – the entity class to get the stock image for
Returns:: bytes for the entity specific stock image

schrodinger.livedesign.bbchem_endpoints.requires_entity_stock_image(mol_input: str) → bool¶

Parameters:: mol_input – serialized mol
Returns:: whether the image should fall back to stock images derived from entity type

schrodinger.livedesign.bbchem_endpoints.to_fingerprint(mol_input: str, use: FingerprintUse, substructure_options: Optional[QueryOptions] = None) → ExplicitBitVect¶

Generates a substructure or similarity fingerprint for a given mol.

Parameters:

mol_input – serialized mol
use – type of fingerprint to generate
substructure_options – substructure matching options

schrodinger.livedesign.bbchem_endpoints.num_substructure_matches(*args, **kwargs) → int¶

Returns:: number of substructure/subsequence matches

schrodinger.livedesign.bbchem_endpoints.has_substructure_match(*args, **kwargs) → bool¶

Returns:: whether any substructure/subsequence match was found

schrodinger.livedesign.bbchem_endpoints.to_sequence_viewer_data(mol_binary_str: str, scheme: AntibodyCDRScheme = AntibodyCDRScheme.Kabat) → Dict[str, Dict]¶

Returns:: biologics sequence viewer data for the given mol

schrodinger.livedesign.bbchem_endpoints.get_mutated_helm(mol_binary_str: str, mut_res_by_idx: dict[tuple[str, int], str]) → str¶

Given a monomeric mol and mutations that indicate which monomers to mutate to which other monomers, returns a new monomeric mol HELM string with the mutations applied.

Parameters:

mol_binary_str – input monomeric mol as RDMOL_BINARY_BASE64 string
mut_res_by_idx – dictionary mapping (chain_id, residue_index) tuples to new monomer names

Returns:

mutated monomeric mol as HELM string

schrodinger.livedesign.bbchem_endpoints.get_mutated_helms(mol_binary_str: str, mut_res_by_idx_list: list[dict[tuple[str, int], str]]) → Generator[str, None, None]¶

Given a monomeric mol and a list of mutations that indicate which monomers to mutate to which other monomers, yields new monomeric mol HELM strings with the mutations applied.

Parameters:

mol_binary_str – input monomeric mol as RDMOL_BINARY_BASE64 string
mut_res_by_idx_list – list of dictionaries mapping (chain_id, residue_index) tuples to new monomer names

Yield:

mutated monomeric mols as HELM strings

schrodinger.livedesign.bbchem_endpoints.generate_image(mol: Mol, alignment_mol: Optional[Mol] = None, substructure_options: Optional[QueryOptions] = None, highlight_mol: Optional[Mol] = None, draw_options: Optional[ImageGenOptions] = None) → bytes¶: DEPRECATED: Remove once bbchem is updated

schrodinger.livedesign.bbchem_endpoints.generate_sar_analysis_image(match_mol: Mol, scaffold_mol: Mol, substructure_options: Optional[QueryOptions] = None, draw_options: Optional[ImageGenOptions] = None) → bytes¶

Generates an image used in LiveDesign that is specifically from SAR analysis output, highlighting the core and all r-groups from the decomposition.

Parameters:

match_mol – source molecule for R-group decomposition to highlight and generate image of
scaffold_mol – scaffold molecule on which to find R-groups
substructure_options – substructure matching options
draw_options – image generation options

Returns:

generated image as a string

schrodinger.livedesign.bbchem_endpoints.pop_properties(mol: Mol) → dict¶

Parameters:: mol – molecule to extract, then clear all properties from
Returns:: map of all removed properties as strings

schrodinger.livedesign.bbchem_endpoints.set_properties(mol: Mol, new_props: dict)¶

Parameters:

mol – molecule to clear, then set given properties on
new_props – map of properties to add onto the molecule

schrodinger.livedesign.bbchem_endpoints.split_fragments(mol: Mol)¶

Param:: input molecule
Returns:: iterable containing each fragment mol

schrodinger.livedesign.bbchem_endpoints.enumerate_stereoisomers(mol: Mol, max_stereoisomers: int = 512) → Iterator[Mol]¶

Generates stereoisomers from a specified SDF structure string.

Parameters:

structure – structure from which to generate stereoisomers
max_stereoisomers – maximum number of stereoisomers to generate

Returns:

generated stereoisomers

schrodinger.livedesign.bbchem_endpoints.rgroup_decompose(scaffold_mol: Mol, match_mol: Mol, options: Optional[QueryOptions] = None) → Optional[List[dict]]¶

Decomposes a molecule into its core and R-groups given a scaffold

Parameters:

scaffold_mol – scaffold molecule on which to find R-groups
match_mol – source molecule for R-group decomposition
stereospecific – whether to consider bond stereochemistry and atom chirality of scaffold

Returns:

list of dicts of R-group matches

schrodinger.livedesign.bbchem_endpoints.get_rgroup_labels(scaffold_mol: Mol) → List[str]¶

Parameters:: scaffold_mol – scaffold molecule
Returns:: R-group labels present on the scaffold

schrodinger.livedesign.bbchem_endpoints.check_reaction(rxn_input: str) → RxnCheckResult¶

schrodinger.livedesign.bbchem_endpoints.setup_reaction(rxn_input: str) → str¶

Tidy up and convert user sketched reactions into a format that can be used for reaction enumeration.

Parameters:: rxn_input – a RXNBlock or RXNSMARTS describing the user’s reaction.
Returns:: a SMARTS string describing the cleaned up reaction

schrodinger.livedesign.bbchem_endpoints.run_reaction(rxn_input: str, reactant_lists: List[List[str]], reactant_id_lists: Optional[List[List[str]]] = None, max_products: Optional[int] = None, property_filters: Optional[Dict] = None) → Iterator[Tuple[str, List[str]]]¶

Execute a reaction on one or more sets of reagents

Basically, each “reaction” can have one or more than reagents, and could be run on one or more sets of reagents.

Parameters:

rxn_input – reaction definition in any supported format, such as RXN or reaction SMARTS.
reactant_lists – lists of reactants in any supported format, such as MOL or SMILES. Each list has to have the correct length, matching the number of reactant templates used by the reaction.
reactant_lists – lists of IDs of the reactants. Each list should have exactly the same size as the corresponding list in reactant_lists. For reactants with no ID, an empty string should be used.
max_products – yield at most this many unique products. If not provided, all products are returned without limit or deduplication. (The canonical SMILES is used as the key.)
property_filters – dictionary with JSON data describing the property filters, with the schema expected by schrodinger.ui.qt.filter_dialog_dir.filter_core.Filter.

Returns:

generator of tuples products in SDF format and their IDs.

schrodinger.livedesign.bbchem_endpoints.get_entity_properties(mol_input: str, input_format: Format = Format.AUTO_DETECT) → MolecularProperties¶

Computes and returns molecular properties for a given molecule.

Parameters:

mol_input – serialized mol string
input_format – input format of the mol string

Returns:

NamedTuple of computed properties

Raises:

ValueError – if molecule is monomeric (biologics not supported)

schrodinger.livedesign.bbchem_endpoints.get_json_formatted_structure_hierarchy(mol_input: str, input_format: Format, structure_schemes: Optional[List[str]] = None) → str¶

Returns a JSON string representing the structure hierarchy of the molecule.

Parameters:

mol_input – serialized mol string
input_format – input format of the mol string
structure_scheme – scheme to use for annotation.

Returns:

JSON string representing the structure hierarchy in specified scheme in a way of a dictionary.

{ “output_response”:[{“scheme”:”<requested_scheme>”, “output”:”<output_structure_hierarchy>”}]}

schrodinger.livedesign.bbchem_endpoints.get_sequence_to_structure_mapping(sequence_annotations: dict, structure_hierarchy_json: str) → str¶

Get the mapping of sequences to their chain names.

Parameters:

sequence_annotations – dictionary of sequences to their chain names
structure_hierarchy_json – structure hierarchy json string

Returns:

json string mapping sequence keys to their chain ids

schrodinger.livedesign.bbchem_endpoints.has_subregion_match(target_input: str, query_input: str, regions: List[str], scheme: AntibodyCDRScheme = AntibodyCDRScheme.Kabat) → bool¶

Checks for subsequence matches within specified subregions of monomeric molecules. E.g., CDRs of antibodies. If any of the specified regions have a match, returns true.

Parameters:

target_input – serialized mol of what to search
query_input – serialized mol on query molecule to search with
regions – list of subregions to search within the target
scheme – numbering scheme to use for subregion matching

Returns:

whether any subsequence match was found within the given subregions

schrodinger.livedesign.bbchem_endpoints.get_3dviz_data(mol_input: str, input_format: Format, structure_schemes: Optional[List[str]] = None) → VizData¶

Returns JSON strings for structure hierarchy and stereo labels for the given molecule input.

Parameters:

mol_input – serialized mol
input_format – input format of the mol string
structure_schemes – List of antibody structure schemes to generate structure hierarchy for.

Returns:

VizData object containing the JSON strings detailing the structure hierarchy and the chirality labels.

schrodinger.livedesign.bbchem_endpoints.get_sequence_logo_data(aligned_seqs: list[str]) → tuple[float, list[tuple[str, float]]]¶

Returns data for generating logo plots for each residue in a sequence alignment.

Parameters:

aligned_seqs – List of sequences in the alignment.

Returns:

List of conservation scores and residue data for each alignment position. The residue data details the residue codes and their respective frequencies (ratio of occurence in the position), ordered from highest to lowest frequency. Example:

[
    (4.3219..., [("A", 1.0)]),
    (3.3219..., [("E", 0.5), ("D", 0.5)]),
    ...
]