tooluniverse.chem_tool module

tooluniverse.chem_tool.quote('abc def') → 'abc%20def'

Each part of a URL, e.g. the path info, the query, etc., has a different set of reserved characters that must be quoted. The quote function offers a cautious (not minimal) way to quote a string for most of these parts.

RFC 3986 Uniform Resource Identifier (URI): Generic Syntax lists the following (un)reserved characters.

unreserved = ALPHA / DIGIT / “-” / “.” / “_” / “~” reserved = gen-delims / sub-delims gen-delims = “:” / “/” / “?” / “#” / “[” / “]” / “@” sub-delims = “!” / “$” / “&” / “’” / “(” / “)”

/ “*” / “+” / “,” / “;” / “=”

Each of the reserved characters is reserved in some component of a URL, but not necessarily in all of them.

The quote function %-escapes all characters that are neither in the unreserved chars (“always safe”) nor the additional chars set via the safe arg.

The default for the safe arg is ‘/’. The character is reserved, but in typical usage the quote function is being called on a path where the existing slash characters are to be preserved.

Python 3.7 updates from using RFC 2396 to RFC 3986 to quote URL strings. Now, “~” is included in the set of unreserved characters.

string and safe may be either str or bytes objects. encoding and errors must not be specified if string is a bytes object.

The optional encoding and errors parameters specify how to deal with non-ASCII characters, as accepted by the str.encode method. By default, encoding=’utf-8’ (characters are encoded with UTF-8), and errors=’strict’ (unsupported characters raise a UnicodeEncodeError).

class tooluniverse.chem_tool.BaseTool(tool_config)

Bases: object

__init__(tool_config)

classmethod get_default_config_file()

Get the path to the default configuration file for this tool type.

This method uses a robust path resolution strategy that works across different installation scenarios:

1. Installed packages: Uses importlib.resources for proper package resource access

2. Development mode: Falls back to file-based path resolution

3. Legacy Python: Handles importlib.resources and importlib_resources

Override this method in subclasses to specify a custom defaults file.

Returns:

Path or resource object pointing to the defaults file

classmethod load_defaults_from_file()

Load defaults from the configuration file

run(arguments=None)

Execute the tool.

The default BaseTool implementation accepts an optional arguments mapping to align with most concrete tool implementations which expect a dictionary of inputs.

check_function_call(function_call_json)

get_required_parameters()

Retrieve required parameters from the endpoint definition. Returns: list: List of required parameters for the given endpoint.

tooluniverse.chem_tool.register_tool(tool_type_name=None, config=None)

Decorator to automatically register tool classes and their configs.

Usage:

@register_tool(‘CustomToolName’, config={…}) class MyTool:

pass

class tooluniverse.chem_tool.Indigo

Bases: object

ABS = 1

OR = 2

AND = 3

EITHER = 4

UP = 5

DOWN = 6

CIS = 7

TRANS = 8

CHAIN = 9

RING = 10

ALLENE = 11

SINGLET = 101

DOUBLET = 102

TRIPLET = 103

RC_NOT_CENTER = -1

RC_UNMARKED = 0

RC_CENTER = 1

RC_UNCHANGED = 2

RC_MADE_OR_BROKEN = 4

RC_ORDER_CHANGED = 8

SG_TYPE_GEN = 0

SG_TYPE_DAT = 1

SG_TYPE_SUP = 2

SG_TYPE_SRU = 3

SG_TYPE_MUL = 4

SG_TYPE_MON = 5

SG_TYPE_MER = 6

SG_TYPE_COP = 7

SG_TYPE_CRO = 8

SG_TYPE_MOD = 9

SG_TYPE_GRA = 10

SG_TYPE_COM = 11

SG_TYPE_MIX = 12

SG_TYPE_FOR = 13

SG_TYPE_ANY = 14

getSessionId() → int

__init__()

deserialize(arr: bytes) → IndigoObject

Creates molecule or reaction object from binary serialized CMF

format

Parameters:

arr (bytes) – array of bytes

Returns:

molecule or reaction object

Return type:

IndigoObject

unserialize(arr: bytes) → IndigoObject

[DEPRECATED] Creates molecule or reaction object from binary

serialized CMF format

Parameters:

arr (list) – array of bytes

Returns:

molecule or reaction object

Return type:

IndigoObject

setOption(option, value1, value2=None, value3=None)

Sets option value

Parameters:

• option (str) – option name

• value1 (int, str, bool, float) – option value

• value2 (int, float) – option value for tuples. Optional, defaults to None.

• value3 (float) – option value for triple. Optional, defaults to None.

Raises:

IndigoException – if option does not exist

getOption(option)

Returns option value by name

Parameters:

option (str) – option name

Returns:

option value

Return type:

str

getOptionInt(option)

Returns option integer value by name

Parameters:

option (str) – option name

Returns:

option value

Return type:

int

getOptionBool(option)

Returns option boolean value by name

Parameters:

option (str) – option name

Returns:

option value

Return type:

bool

getOptionFloat(option)

Returns option float value by name

Parameters:

option (str) – option name

Returns:

option value

Return type:

float

getOptionType(option)

Returns option value type by name

Parameters:

option (str) – option name

Returns:

option type string

Return type:

str

resetOptions()

Resets options to default state

convertToArray(iterable)

Converts iterable object to array

Parameters:

iterable (IndigoObject) – iterable object

Raises:

IndigoException – if object is not iterable

Returns:

array of objects

Return type:

IndigoObject

dbgBreakpoint()

version()

Returns Indigo version

Returns:

version string

Return type:

str

versionInfo()

Returns Indigo version info

Returns:

version info string

Return type:

str

countReferences()

Returns the number of objects in pool

Returns:

number of objects

Return type:

int

writeFile(filename)

Creates file writer object

Parameters:

filename (str) – full path to the file

Returns:

file writer object

Return type:

IndigoObject

writeBuffer()

Creates buffer to write an object

Returns:

buffer object

Return type:

IndigoObject

createMolecule()

Creates molecule object

Returns:

molecule object

Return type:

IndigoObject

createQueryMolecule()

Creates query molecule object

Returns:

query molecule

Return type:

IndigoObject

loadMolecule(string)

Loads molecule from string. Format is automatically recognized.

Parameters:

string (str) – molecule format

Returns:

molecule object

Return type:

IndigoObject

Raises:

IndigoException – Exception if structure format is incorrect

loadMoleculeFromFile(filename)

Loads molecule from file. Automatically detects input format.

Parameters:

filename (str) – full path to a file

Returns:

loaded molecular structure

Return type:

IndigoObject

Raises:

IndigoException – Exception if structure format is incorrect

loadMoleculeFromBuffer(data)

Loads molecule from buffer. Automatically detects input format.

Parameters:

data (bytes) – input byte array

Returns:

loaded molecular structure

Return type:

IndigoObject

Raises:

IndigoException – Exception if structure format is incorrect

Examples

with open (..), 'rb') as f:
    m = indigo.loadMoleculeFromBuffer(f.read())

loadMoleculeWithLib(string, library)

Loads molecule from string. Format is automatically recognized.

Parameters:

• string (str) – molecule format

• library (IndigoObject) – monomer library object

Returns:

molecule object

Return type:

IndigoObject

Raises:

IndigoException – Exception if structure format is incorrect

loadMoleculeWithLibFromFile(filename, library)

Loads molecule from file. Automatically detects input format.

Parameters:

• filename (str) – full path to a file

• library (IndigoObject) – monomer library object

Returns:

loaded molecular structure

Return type:

IndigoObject

Raises:

IndigoException – Exception if structure format is incorrect

loadMoleculeWithLibFromBuffer(data, library)

Loads molecule from buffer. Automatically detects input format.

Parameters:

• data (bytes) – input byte array

• library (IndigoObject) – monomer library object

Returns:

loaded molecular structure

Return type:

IndigoObject

Raises:

IndigoException – Exception if structure format is incorrect

Examples

with open (..), 'rb') as f:
    m = indigo.loadMoleculeFromBuffer(f.read())

loadQueryMolecule(string)

Loads query molecule from string. Format will be automatically

recognized.

Parameters:

string (str) – molecule format

Returns:

query molecule object

Return type:

IndigoObject

Raises:

IndigoException – Exception if structure format is incorrect

loadQueryMoleculeFromFile(filename)

Loads query molecule from file. Automatically detects input format.

Parameters:

filename (str) – full path to a file

Returns:

loaded query molecular structure

Return type:

IndigoObject

Raises:

IndigoException – Exception if structure format is incorrect

loadQueryMoleculeWithLib(string, library)

Loads query molecule from string. Format will be automatically

recognized.

Parameters:

• string (str) – molecule format

• library (IndigoObject) – monomer library object

Returns:

query molecule object

Return type:

IndigoObject

Raises:

IndigoException – Exception if structure format is incorrect

loadQueryMoleculeWithLibFromFile(filename, library)

Loads query molecule from file. Automatically detects input format.

Parameters:

• filename (str) – full path to a file

• library (IndigoObject) – monomer library object

Returns:

loaded query molecular structure

Return type:

IndigoObject

Raises:

IndigoException – Exception if structure format is incorrect

loadSmarts(string)

Loads query molecule from string in SMARTS format

Parameters:

string (str) – smarts string

Returns:

loaded query molecular structure

Return type:

IndigoObject

Raises:

IndigoException – Exception if structure format is incorrect

loadSmartsFromFile(filename)

Loads query molecule from file in SMARTS format

Parameters:

filename (str) – full path to the file with smarts strings

Returns:

loaded query molecular structure

Return type:

IndigoObject

Raises:

IndigoException – Exception if structure format is incorrect

loadMonomerLibrary(string)

Loads monomer library from ket string

Parameters:

string (str) – ket

Returns:

loaded monomer library

Return type:

IndigoObject

Raises:

IndigoException – Exception if structure format is incorrect

loadMonomerLibraryFromFile(filename)

Loads monomer library from from file in ket format

Parameters:

string (str) – full path to the file with ket

Returns:

loaded monomer library

Return type:

IndigoObject

Raises:

IndigoException – Exception if structure format is incorrect

loadKetDocument(string)

Loads ket document from ket string

Parameters:

string (str) – ket

Returns:

loaded ket document

Return type:

IndigoObject

Raises:

IndigoException – Exception if structure format is incorrect

loadKetDocumentFromFile(filename)

Loads ket document from from file in ket format

Parameters:

string (str) – full path to the file with ket

Returns:

loaded ket document

Return type:

IndigoObject

Raises:

IndigoException – Exception if structure format is incorrect

loadSequence(string, seq_type, library)

Loads molecule from DNA/RNA/PEPTIDE sequence string

Parameters:

• string (str) – sequence string

• seq_type (str) – sequence type (RNA/DNA/PEPTIDE)

• library (IndigoObject) – monomer library object

Returns:

loaded query molecular structure

Return type:

IndigoObject

Raises:

IndigoException – Exception if structure format is incorrect

loadSequenceFromFile(filename, seq_type, library)

Loads query molecule from file in sequence format

Parameters:

• filename (str) – full path to the file with sequence string

• seq_type (str) – sequence type (RNA/DNA/PEPTIDE)

• library (IndigoObject) – monomer library object

Returns:

loaded query molecular structure

Return type:

IndigoObject

Raises:

IndigoException – Exception if structure format is incorrect

loadFasta(string, seq_type, library)

Loads molecule from DNA/RNA/PEPTIDE sequence string

Parameters:

• string (str) – sequence string

• seq_type (str) – sequence type (RNA/DNA/PEPTIDE)

• library (IndigoObject) – monomer library object

Returns:

loaded query molecular structure

Return type:

IndigoObject

Raises:

IndigoException – Exception if structure format is incorrect

loadFastaFromFile(filename, seq_type, library)

Loads query molecule from file in sequence format

Parameters:

• filename (str) – full path to the file with sequence string

• seq_type (str) – sequence type (RNA/DNA/PEPTIDE)

• library (IndigoObject) – monomer library object

Returns:

loaded query molecular structure

Return type:

IndigoObject

Raises:

IndigoException – Exception if structure format is incorrect

loadIdt(string, library)

Loads molecule from IDT string

Parameters:

• string (str) – sequence string

• library (IndigoObject) – monomer library object

Returns:

loaded query molecular structure

Return type:

IndigoObject

Raises:

IndigoException – Exception if structure format is incorrect

loadIdtFromFile(filename, library)

Loads query molecule from file in IDT sequence format

Parameters:

• filename (str) – full path to the file with sequence string

• library (IndigoObject) – monomer library object

Returns:

loaded query molecular structure

Return type:

IndigoObject

Raises:

IndigoException – Exception if structure format is incorrect

loadHelm(string, library)

Loads molecule from HELM string

Parameters:

• string (str) – sequence string

• library (IndigoObject) – monomer library object

Returns:

loaded query molecular structure

Return type:

IndigoObject

Raises:

IndigoException – Exception if structure format is incorrect

loadHelmFromFile(filename, library)

Loads query molecule from file in HELM sequence format

Parameters:

• filename (str) – full path to the file with sequence string

• library (IndigoObject) – monomer library object

Returns:

loaded query molecular structure

Return type:

IndigoObject

Raises:

IndigoException – Exception if structure format is incorrect

loadReaction(string)

Loads reaction from string. Format will be automatically recognized.

Parameters:

string (str) – reaction format

Returns:

reaction object

Return type:

IndigoObject

Raises:

IndigoException – Exception if structure format is incorrect

loadReactionFromFile(filename)

Loads reaction from file

Parameters:

filename (str) – full path to a file

Returns:

loaded reaction

Return type:

IndigoObject

Raises:

IndigoException – Exception if structure format is incorrect

loadQueryReaction(string)

Loads query reaction from string. Format will be automatically

recognized.

Parameters:

string (str) – reaction format

Returns:

query reaction object

Return type:

IndigoObject

loadQueryReactionFromFile(filename)

Loads query reaction from file. Automatically detects input format.

Parameters:

filename (str) – full path to a file

Returns:

loaded query reaction object

Return type:

IndigoObject

Raises:

IndigoException – Exception if structure format is incorrect

loadReactionWithLib(string, library)

Loads reaction from string. Format will be automatically recognized.

Parameters:

• string (str) – reaction format

• library (IndigoObject) – monomer library object

Returns:

reaction object

Return type:

IndigoObject

Raises:

IndigoException – Exception if structure format is incorrect

loadReactionFromFileWithLib(filename, library)

Loads reaction from file

Parameters:

• filename (str) – full path to a file

• library (IndigoObject) – monomer library object

Returns:

loaded reaction

Return type:

IndigoObject

Raises:

IndigoException – Exception if structure format is incorrect

loadQueryReactionWithLib(string, library)

Loads query reaction from string. Format will be automatically

recognized.

Parameters:

• string (str) – reaction format

• library (IndigoObject) – monomer library object

Returns:

query reaction object

Return type:

IndigoObject

loadQueryReactionFromFileWithLib(filename, library)

Loads query reaction from file. Automatically detects input format.

Parameters:

• filename (str) – full path to a file

• library (IndigoObject) – monomer library object

Returns:

loaded query reaction object

Return type:

IndigoObject

Raises:

IndigoException – Exception if structure format is incorrect

loadReactionSmarts(string)

Loads query reaction from string in SMARTS format

Parameters:

string (str) – smarts string

Returns:

loaded query reaction

Return type:

IndigoObject

Raises:

IndigoException – Exception if structure format is incorrect

loadReactionSmartsFromFile(filename)

Loads query reaction from file in SMARTS format

Parameters:

filename (str) – full path to the file with smarts strings

Returns:

loaded query reaction

Return type:

IndigoObject

Raises:

IndigoException – Exception if structure format is incorrect

loadStructure(structure_str, parameter=None)

Loads structure from string

Parameters:

• structure_str (str) – string with structure format

• parameter (str) – parameters for loading. Optional, defaults to None.

Returns:

loaded object

Return type:

IndigoObject

loadStructureFromBuffer(structure_data, parameter=None)

Loads structure object from buffer

Parameters:

• structure_data (list) – array of bytes

• parameter (str) – parameters for loading. Optional, defaults to None.

Returns:

loaded object

Return type:

IndigoObject

loadStructureFromFile(filename, parameter=None)

Loads structure object from file

Parameters:

• filename (str) – full path with structure information

• parameter (str) – parameters to load. Optional, defaults to None.

Returns:

loaded object

Return type:

IndigoObject

checkStructure(structure, props='')

Runs validation for the given structure

Parameters:

• structure (str) – structure object

• props (str) – Parameters for validation. Optional, defaults to “”.

Returns:

validation results string

Return type:

str

loadFingerprintFromBuffer(buffer)

Creates a fingerprint from the supplied binary data

Parameters:

buffer (list) – array of bytes

Returns:

fingerprint object

Return type:

IndigoObject

loadFingerprintFromDescriptors(descriptors, size, density)

Packs a list of molecule descriptors into a fingerprint object

Parameters:

• descriptors (list) – list of normalized numbers (roughly) between 0.0 and 1.0

• size (int) – size of the fingerprint in bytes

• density (float) – approximate density of ‘1’s vs ‘0’s in the fingerprint

Returns:

fingerprint object

Return type:

IndigoObject

createReaction()

Creates reaction object

Returns:

reaction object

Return type:

IndigoObject

createQueryReaction()

Creates query reaction object

Returns:

query reaction object

Return type:

IndigoObject

exactMatch(item1, item2, flags='')

Creates match object for the given structures

Parameters:

• item1 (IndigoObject) – first target structure (molecule or reaction)

• item2 (IndigoObject) – second target structure (molecule or reaction)

• flags (str) – exact match options. Optional, defaults to “”.

Returns:

match object

Return type:

IndigoObject

setTautomerRule(index, beg, end)

Sets tautomer rules

Parameters:

• index (int) – tau rule index

• beg (str) – begin value

• end (str) – end value

Returns:

1 if there are no errors

Return type:

int

removeTautomerRule(index)

Removes tautomer rule

Parameters:

index (int) – tau rule index

Returns:

1 if there are no errors

Return type:

int

clearTautomerRules()

Clears all tautomer rules

Returns:

1 if there are no errors

Return type:

int

commonBits(fingerprint1, fingerprint2)

Returns the number of common 1 bits for the given fingerprints

Parameters:

• fingerprint1 (IndigoObject) – first fingerprint object

• fingerprint2 (IndigoObject) – second fingerprint object

Returns:

number of common bits

Return type:

int

similarity(item1, item2, metrics='')

Returns the similarity measure between two structures. Accepts two molecules, two reactions, or two fingerprints.

Parameters:

• item1 (IndigoObject) – molecule, reaction or fingerprint object

• item2 (IndigoObject) – molecule, reaction or fingerprint object

• metrics (str) – “tanimoto”, “tversky”, “tversky <alpha> <beta>”, “euclid-sub” or “normalized-edit”. Optional, defaults to “tanimoto”.

Returns:

[description]

Return type:

float

iterateSDFile(filename)

Returns iterator for SDF files

Parameters:

filename (str) – full file path

Returns:

SD iterator object

Return type:

IndigoObject

iterateRDFile(filename)

Returns iterator for RDF files

Parameters:

filename (str) – full file path

Returns:

RD iterator object

Return type:

IndigoObject

iterateSmilesFile(filename)

Returns iterator for smiles files

Parameters:

filename (str) – full file path

Returns:

smiles iterator object

Return type:

IndigoObject

iterateCMLFile(filename)

Returns iterator for CML files

Parameters:

filename (str) – full file path

Returns:

CML iterator object

Return type:

IndigoObject

iterateCDXFile(filename)

Returns iterator for CDX files

Parameters:

filename (str) – full file path

Returns:

CDX iterator object

Return type:

IndigoObject

createFileSaver(filename, format_)

Creates file saver object

Parameters:

• filename (str) – full file path

• format (str) – file format

Returns:

file saver object

Return type:

IndigoObject

createSaver(obj, format_)

Creates saver object

Parameters:

• obj (IndigoObject) – output object

• format (str) – format settings

Returns:

saver object

Return type:

IndigoObject

createArray()

Creates array object

Returns:

array object

Return type:

IndigoObject

substructureMatcher(target, mode='')

Creates substructure matcher

Parameters:

• target (IndigoObject) – target molecule or reaction

• mode (str) – substructure mode. Optional, defaults to “”.

Returns:

substructure matcher

Return type:

IndigoObject

extractCommonScaffold(structures, options='')

Extracts common scaffold for the given structures

Parameters:

• structures (IndigoObject) – array object of molecule structures

• options (str) – extraction options. Optional, defaults to “”.

Returns:

scaffold object

Return type:

IndigoObject

decomposeMolecules(scaffold, structures)

Creates deconvolution object for the given structures

Parameters:

• scaffold (IndigoObject) – query molecule object

• structures (IndigoObject) – array of molecule structures

Returns:

deconvolution object

Return type:

IndigoObject

rgroupComposition(molecule, options='')

Creates composition iterator

Parameters:

• molecule (IndigoObject) – target molecule object

• options (str) – rgroup composition options. Optional, defaults to “”.

Returns:

composition iterator

Return type:

IndigoObject

getFragmentedMolecule(elem, options='')

Returns fragmented molecule for the given composition element

Parameters:

• elem (IndigoObject) – composition element object

• options (str) – Fragmentation options. Optional, defaults to “”.

Returns:

fragmented structure object

Return type:

IndigoObject

createDecomposer(scaffold)

Creates deconvolution object for the given scaffold

Parameters:

scaffold (IndigoObject) – scaffold molecular structure

Returns:

deconvolution object

Return type:

IndigoObject

reactionProductEnumerate(replaced_action, monomers)

Creates reaction product enumeration iterator

Parameters:

• replaced_action (IndigoObject) – query reaction for the enumeration

• monomers (IndigoObject) – array of objects to enumerate

Returns:

result products iterator

Return type:

IndigoObject

transform(reaction, monomers)

Transforms the given monomers by reaction

Parameters:

• reaction (IndigoObject) – query reaction

• monomers (IndigoObject) – array of objects to transform

Returns:

mapping object

Return type:

IndigoObject

loadBuffer(buf)

Creates scanner object from buffer

Parameters:

buf (list) – array of bytes

Returns:

scanner object

Return type:

IndigoObject

loadString(string)

Creates scanner object from string

Parameters:

string (str) – string with information

Returns:

scanner object

Return type:

IndigoObject

iterateSDF(reader)

Creates SDF iterator from scanner object

Parameters:

reader (IndigoObject) – scanner object

Returns:

SD iterator object

Return type:

IndigoObject

iterateSmiles(reader)

Creates smiles iterator from scanner object

Parameters:

reader (IndigoObject) – scanner object

Returns:

smiles iterator object

Return type:

IndigoObject

iterateCML(reader)

Creates CML iterator from scanner object

Parameters:

reader (IndigoObject) – scanner object

Returns:

CML iterator object

Return type:

IndigoObject

iterateCDX(reader)

Creates CDX iterator from scanner object

Parameters:

reader (IndigoObject) – scanner object

Returns:

CDX iterator object

Return type:

IndigoObject

iterateRDF(reader)

Creates RDF iterator from scanner object

Parameters:

reader (IndigoObject) – scanner object

Returns:

RD iterator object

Return type:

IndigoObject

iterateTautomers(molecule, params)

Iterates tautomers for the given molecule

Parameters:

• molecule (IndigoObject) – molecule to find tautomers from

• params (str) – tau iteration parameters. “INCHI” or “RSMARTS”. Defaults to “RSMARTS”

Returns:

molecule iterator object

Return type:

IndigoObject

nameToStructure(name, params=None)

Converts a chemical name into a corresponding structure

Parameters:

• name (str) – a name to parse

• params (str) – a string (optional) containing parsing options or None if no options are changed

Raises:

IndigoException – if parsing fails or no structure is found

buildPkaModel(level, threshold, filename)

Builds pKa model into file

Parameters:

• level (int) – max level

• threshold (float) – threshold value

• filename (str) – full path to the file

Returns:

1 if level > 0, 0 otherwise

Return type:

int

transformHELMtoSCSR(item)

Transforms HELM to SCSR object

Parameters:

item (IndigoObject) – object with HELM information

Returns:

molecule with SCSR object

Return type:

IndigoObject

check(mol_str, check_flags='', props='')

Validates the given structure

Parameters:

• mol_str (str) – input structure string

• check_flags (str) – validation flags. Optional, defaults to “”.

• props (str) – validation properties. Optional, defaults to “”.

Returns:

validation string

Return type:

str

class tooluniverse.chem_tool.ChEMBLTool(tool_config, base_url='https://www.ebi.ac.uk/chembl/api/data')

Bases: BaseTool

Tool to search for molecules similar to a given compound name or SMILES using the ChEMBL Web Services API.

__init__(tool_config, base_url='https://www.ebi.ac.uk/chembl/api/data')

run(arguments)

Execute the tool.

The default BaseTool implementation accepts an optional arguments mapping to align with most concrete tool implementations which expect a dictionary of inputs.

get_chembl_id_by_name(compound_name)

Search ChEMBL for a compound by name and return the ChEMBL ID of the first match.

get_smiles_pref_name_by_chembl_id(query)

Given a ChEMBL ID, return a dict with canonical SMILES and preferred name.

get_chembl_smiles_pref_name_id_by_name(compound_name)

Search ChEMBL for a compound by name and return a list of dicts with ChEMBL ID, canonical SMILES, and preferred name for the top 5 matches.