2.1.1.4.1.1. wc_utils.util.chem package

2.1.1.4.1.1.1. Submodules

2.1.1.4.1.1.2. wc_utils.util.chem.core module

Chemistry utilities

Author

Jonathan Karr <jonrkarr@gmail.com>

Date

2018-02-07

Copyright

2018, Karr Lab

License

MIT

class wc_utils.util.chem.core.EmpiricalFormula(value='')[source]

Bases: attrdict.default.AttrDefault

An empirical formula

__add__(other)[source]

Add two empirical formulae

Parameters

other (EmpiricalFormula or str) – another empirical formula

Returns

sum of the empirical formulae

Return type

EmpiricalFormula

__contains__(element)[source]
Parameters

element (str) – element symbol

Returns

True if the empirical formula contains the element

Return type

bool

__div__(quantity)[source]

Subtract two empirical formulae (for Python 2)

Parameters

quantity (float) –

Returns

division of the empirical formula by quantity

Return type

EmpiricalFormula

__hash__()[source]

Generate a hash

Returns

hash

Return type

int

__mul__(quantity)[source]

Subtract two empirical formulae

Parameters

quantity (float) –

Returns

multiplication of the empirical formula by quantity

Return type

EmpiricalFormula

__setitem__(element, coefficient)[source]

Set the count of an element

Parameters

  • element (str) – element symbol

  • coefficient (float) – element coefficient

Raises

ValueError – if the coefficient is not a float

__str__()[source]

Generate a string representation of the formula

__sub__(other)[source]

Subtract two empirical formulae

Parameters

other (EmpiricalFormula or str) – another empirical formula

Returns

difference of the empirical formulae

Return type

EmpiricalFormula

__truediv__(quantity)[source]

Subtract two empirical formulae

Parameters

quantity (float) –

Returns

division of the empirical formula by quantity

Return type

EmpiricalFormula

get_molecular_weight()[source]

Get the molecular weight

Returns

molecular weight

Return type

float

class wc_utils.util.chem.core.OpenBabelUtils[source]

Bases: object

classmethod export(mol, format, options=())[source]

Export an OpenBabel molecule to format

Parameters

  • mol (openbabel.OBMol) – molecule

  • format (str) – format

  • options (list of str, optional) – export options

Returns

format representation of molecule

Return type

str

static get_formula(mol)[source]

Get the formula of an OpenBabel molecule

Parameters

mol (openbabel.OBMol) – molecule

Returns

formula

Return type

EmpiricalFormula

classmethod get_inchi(mol, options=('r', 'F'))[source]

Get the InChI-encoded structure of an OpenBabel molecule

Parameters

  • mol (openbabel.OBMol) – molecule

  • options (list of str, optional) – export options

Returns

InChI-encoded structure

Return type

str

classmethod get_smiles(mol, options=())[source]

Get the SMILES-encoded structure of an OpenBabel molecule

Parameters

  • mol (openbabel.OBMol) – molecule

  • options (list of str, optional) – export options

Returns

SMILES-encoded structure

Return type

str

2.1.1.4.1.1.3. wc_utils.util.chem.marvin module

Chemistry utilities from ChemAxon Marvin

Author

Jonathan Karr <jonrkarr@gmail.com>

Date

2020-01-07

Copyright

2018-2020, Karr Lab

License

MIT

wc_utils.util.chem.marvin.draw_molecule(structure, format, image_format='svg', atom_labels=None, atom_label_font_size=0.4, atom_sets=None, bond_sets=None, show_atom_nums=False, width=200, height=200, include_xml_header=True)[source]

Draw an image of a molecule

Parameters

  • structure (str) – chemical structure

  • format (str) – format of structure (e.g. ‘inchi’ or ‘smiles’)

  • image_format (str, optional) – format of generated image {emf, eps, jpeg, msbmp, pdf, png, or svg}

  • atom_labels (list of dict, optional) – list of atom labels (dictionaries with keys {position, element, label, color})

  • atom_label_font_size (float, optional) – font size of atom labels

  • atom_sets (list of dict, optional) – list of atom sets (dictionaries with keys {positions, elements, color})

  • bond_sets (list of dict, optional) – list of bond sets (dictionaries with keys {positions, elements, color})

  • show_atom_nums (bool, optional) – if True, show the numbers of the atoms

  • width (int, optional) – width in pixels

  • height (int, optional) – height in pixels

  • include_xml_header (bool, optional) – if True, include XML header

Returns

image of chemical structure

Return type

str

wc_utils.util.chem.marvin.get_major_micro_species(structure_or_structures, in_format, out_format, ph=7.4, major_tautomer=False, keep_hydrogens=False, dearomatize=False)[source]

Get the major protonation state of one or more compounds at a specific pH.

Parameters

  • structure_or_structures (str or list of str) – chemical structure or list of chemical structures

  • in_format (str) – format of structure_or_structures (e.g. ‘inchi’ or ‘smiles’)

  • out_format (str) – format of output (e.g. ‘inchi’ or ‘smiles’)

  • ph (float, optional) – pH at which to calculate major protonation microspecies

  • major_tautomer (bool, optional) – if True, use the major tautomeric in the calculation

  • keep_hydrogens (bool, optional) – if True, keep explicity defined hydrogens

  • dearomatize (bool, optional) – if True, dearomatize molecule

Returns

protonated chemical structure or

list of protonated chemical structures

Return type

str or list of str

2.1.1.4.1.1.4. Module contents