QMzymeResidue

class QMzyme.QMzymeRegion.QMzymeResidue(resname, resid, atoms, region, chain=None)

Bases: QMzymeRegion

QMzymeResidue is a subclass of QMzymeRegion representing a molecular unit of the system as defined in the starting topology file.

Required Parameters

param resname:

Three letter residue name: ex., 'VAL'

type resname:

str

param resid:

Integer residue number.

type resid:

int

param atoms:

Atom name: ex., 'C1'

type name:

QMzymeAtom

param region:

type name:

QMzymeResidue

get_atom(atom_name)

Selects QmzymeAtom with specific atom name within the region.

Parameters:

atom_name -- The name of the atom (e.g. "CA")

set_chain(value: str)

Sets chain attribute to QMzymeAtom objects within QMzymeRgion.

Parameters:

segid (str) -- Chain name of the QMzymeAtom

guess_charge(verbose=True)

Guesses charge based on the residue_charges information in QMzymeconfiguration__init__.py. QMzyme contains charge information of standard AMBER amino acid residues. If non-AMBER residues are present, it will raise an error. To update the charge of the unknown residue, the user can use QMzyme.data.residue_charges.update({'unknown residue name': int})

Parameters:

verbose (bool) -- Returns print statements including warning and estimated charge.

read_charges(verbose=True)

Calculates total charge of QMzymeResidue by using tolopogy attribute 'charge'.

Parameters:

verbose (bool) -- Returns print statements including warning and estimated charge.

get_backbone_atoms(backbone_atoms={'C': 'C', 'CA': 'CA', 'H': 'H', 'HA': 'HA', 'N': 'N', 'O': 'O'})

Selects group of QMzymeAtom objects within QMzymeResidue that contains atom name within backbone_atoms dictionary.

Parameters:

backbone_atoms (dict, default {'C': 'C', 'CA': 'CA', 'H': 'H', 'HA': 'HA', 'N': 'N', 'O': 'O'}.) -- Sets of QMzymeAtom names that corresponds to the backbone atoms.

remove_atom(atom)

Parameters:

atom (QMzymeAtom, required) -- The atom you want to remove from the QMzymeResidue.

Warning

Ths will modify the QMzymeResidue directly.

property removed_atoms

List of atoms removed from the QMzymeResidue. Often, this is done with remove_atom() method or truncate() method.