Input / Output

IO Submodule

class scine_molassembler.io.LineNotation

Generates Molecule instances from line notations of molecules via OpenBabel, if found in the runtime path.

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

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[numpy.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

Experimental

note

Functions in this module are unstable and should be used with caution. Check your results. Upon stabilization, functions will be deprecated and move to a different module.

scine_molassembler.io.experimental.emit_smiles(molecule: scine_molassembler.Molecule) → str

Generate a smiles string for a molecule

Parameters

molecule – Molecule to generate smiles string for

Returns

A (partially) normalized openSMILES-standard compliant smiles string.

Warning

This is a lossy serialization format! The openSMILES standard does not contain stereodescriptors for shapes other than the tetrahedron, square, trigonal bipyramid and octahedron. Generated smiles containing stereocenters with other shapes will not contain stereodescriptors for these centers.

Note

Missing normalization: Aromaticity detection in kekulized graph to aromatic atom types.

>>> biphenyl = io.experimental.from_smiles("c1ccccc1-c2ccccc2")
>>> io.experimental.emit_smiles(biphenyl)
'c1ccccc1-c2ccccc2'
scine_molassembler.io.experimental.from_smiles(smiles_str: str) → scine_molassembler.Molecule

Parse a smiles string containing only a single molecule

The smiles parser is implemented according to the OpenSMILES spec. It supports the following features:

  • Isotope markers

  • Valence filling of the organic subset

  • Set local shapes from VSEPR

  • Ring closures (and concatenation between dot-separated components)

  • Stereo markers - Double bond - Tetrahedral - Square planar - Trigonal bipyramidal - Octahedral

Parameters

smiles_str – A smiles string containing a single molecule

>>> import scine_utilities as utils
>>> methane = io.experimental.from_smiles("C")
>>> methane.graph.V
5
>>> cobalt_complex = io.experimental.from_smiles("Br[Co@OH12](Cl)(I)(F)(S)C")
>>> cobalt_index = cobalt_complex.graph.atoms_of_element(utils.ElementType.Co)[0]
>>> permutator = cobalt_complex.stereopermutators.option(cobalt_index)
>>> permutator is not None
True
>>> permutator.assigned is not None
True
scine_molassembler.io.experimental.from_smiles_multiple(smiles_str: str) → List[scine_molassembler.Molecule]

Parse a smiles string containing possibly multiple molecules

The smiles parser is implemented according to the OpenSMILES spec. It supports the following features:

  • Arbitrarily many molecules in a string

  • Isotope markers

  • Valence filling of the organic subset

  • Set shapes from VSEPR

  • Ring closures

  • Stereo markers - Double bond - Tetrahedral - Square planar - Trigonal bipyramidal - Octahedral

Parameters

smiles_str – A smiles string containing possibly multiple molecules

>>> methane_and_ammonia = io.experimental.from_smiles_multiple("C.[NH4+]")
>>> len(methane_and_ammonia) == 2
True