Molecule

class molecule.Molecule(chain, sites)

Molecule with more than one titrable sites

getArrayPosition(atom_id)

Returns the index of the atom in DelPhi position array

Disclamer: used only in testing

getAtomsList()

Returns a list of atoms details

Atoms details = (id, instance, atom index in DelPhi data structures) sorted by atom id number

getNAtoms()

Return number of atoms of the Site.

getTautNAtoms(taut_name)

Return number of atoms of the tautomer named taut_name

Disclamer: it was used for testing

getTautomerInstance(tautname, site_resnum)

Return the tautomer instance named tautname

Tautomer instance must exist in the site of the residue number site_resnum

iterAtoms()

Generator that iterates through all atoms details (name, id, position) in the Site.

iterNonRefSitesTautomers()

Generator that iterates through all Tautomer instances except the reference ones.

printAllSites()

Prints all Site names.

printAllTautomers()

Prints all Tautomer details