biotite.database.pubchem.FormulaQuery

class biotite.database.pubchem.FormulaQuery(formula, allow_other_elements=False, number=None)[source]

Bases: Query

A query that searches for compounds with the given molecular formula.

The formula can also be created from an AtomArray using the from_atoms() method.

Parameters
formulastr

The molecular formula, i.e. each capitalized element with its count in the compound concatenated into a single string.

allow_other_elementsbool, optional

If set to true, compounds with additional elements, not present in the molecular formula, will also match.

numberint, optional

The maximum number of matches that this query may return. By default, the PubChem default value is used, which can be considered unlimited.

Examples

>>> print(search(FormulaQuery("C4H10", number=5)))
[7843, ..., ..., ..., ...]
>>> atom_array = residue("ALA")
>>> print(search(FormulaQuery.from_atoms(atom_array, number=5)))
[5950, ..., ..., ..., ...]
static from_atoms(atoms, allow_other_elements=False, number=None)

Create the query from an the given structure by using its molecular formula.

Parameters
atomsAtomArray or AtomArrayStack

The structure to take the molecular formula from.

allow_other_elementsbool, optional

If set to true, compounds with additional elements, not present in the molecular formula, will also match.

numberint, optional

The maximum number of matches that this query may return. By default, the PubChem default value is used, which can be considered unlimited.

get_files()

Get the POST file payload for this query.

Returns
paramsdict (str -> object)

The file payload.

get_input_url_path()

Get the input part of the request URL.

Returns
get_input_url_pathstr

The input part of the request URL. Must not contain slash characters at the beginning and end of the string.

get_params()

Get the POST payload for this query.

Returns
paramsdict (str -> object)

The payload.