Input / Output

IO Submodule

class scine_molassembler.io.LineNotation

Generates Molecule instances from line notations of molecules

enabled = True
static from_canonical_smiles(canonical_smiles: str) → scine_molassembler.Molecule

Construct a single Molecule from a canonical SMILES string

static from_inchi(inchi: str) → scine_molassembler.Molecule

Construct a single Molecule from an InChI string

static from_isomeric_smiles(isomeric_smiles: str) → scine_molassembler.Molecule

Construct a single Molecule from an isomeric SMILES string

scine_molassembler.io.read(filename: str) → scine_molassembler.Molecule

Reads a single Molecule from a file. Interprets the file format from its extension. Supported formats: - mol: MOLFile V2000 - xyz: XYZ file - cbor/bson/json: Serialization formats of molecules

Parameters

filename – File to read.

scine_molassembler.io.split(filename: str) → List[scine_molassembler.Molecule]

Reads multiple molecules from a file. Interprets the file format from its extension just like read(). Note that serializations of molecules contain only a single Molecule. Use read() instead.

Parameters

filename – File to read.

scine_molassembler.io.write(*args, **kwargs)

Overloaded function.

  1. write(filename: str, molecule: scine_molassembler.Molecule, positions: numpy.ndarray[float64[m, 3]]) -> None

    Write a Molecule and its positions to a file

    param filename

    File to write to. File format is interpreted from this parameter’s file extension.

    param molecule

    Molecule to write to file

    param positions

    Positions of molecule’s atoms in bohr

  2. write(filename: str, molecule: scine_molassembler.Molecule) -> None

    Write a Molecule serialization with the endings json/cbor/bson or a graph representation with ending dot/svg to a file.

    param filename

    File to write to. File format is interpreted from this parameter’s file extension

    param molecule

    Molecule to write to file