pybio package¶

Subpackages¶

pybio.tools package

Submodules¶

pybio.atom module¶

class pybio.atom.Atom(symbol, mass_number=None, charge=None)¶

Bases: object

Smallest particle still characterizing a chemical element

Parameters:	symbol (str) – Atomic symbol mass_number (int, optional) – Atomic mass number (A) charge (int, optional) – Charge number

atomic_number¶: int – Atomic number (Z)

charge_regex = '([-+]\\d*)?'¶

mass_number_regex = '(\\d+)?'¶

symbol_regex = '([A-Z][a-z]{,2})'¶

class pybio.atom.Electron¶

Bases: pybio.atom.Atom

Subatomic elementary particle with a negative elementary electric charge

References

atomic_number = 0¶

charge = -1¶

mass_number = 0¶

symbol = ''¶

pybio.formula module¶

class pybio.formula.Formula(formula=None)¶

Bases: collections.OrderedDict

Molecular formula

Parameters:	formula (str or Mapping) – formula as a string or Atom-to-count mapping

pybio.formula.formula(composition)¶

pybio.glycan module¶

class pybio.glycan.Glycan(notation=None, composition=None)¶: Bases: pybio.molecule.Molecule

pybio.molecule module¶

class pybio.molecule.Group(value)¶

Bases: pybio.tools.graph.Node

single node in a molecule

A defined linked collection of atoms or a single atom within a molecular entity.

—http://goldbook.iupac.org/html/G/G02705.html

class pybio.molecule.Molecule¶

Bases: pybio.tools.graph.Graph

Molecular entity

Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.

—http://goldbook.iupac.org/html/M/M03986.html

Node¶: alias of Group

add(group)¶

pybio.peptide module¶

class pybio.peptide.Peptide(sequence)¶: Bases: pybio.molecule.Molecule