QMzymeAtom

class QMzyme.QMzymeAtom.QMzymeAtom(name, element, position, resid, resname, id=1, region=None, **kwargs)

QMzymeAtom represents a single atom in the molecular system and is the most fundamental object within QMzyme. A QMzymeAtom instance inherits all its attributes from its MDAnalysis Atom counterpart.

Required Parameters

param name:

Atom name: ex., 'C1'

type name:

str

param element:

Element one-letter name: ex., 'C'

type element:

str

param position:

Array of cartesian coordinates.

type position:

List[float] or np.array

param resid:

Integer residue number.

type resid:

int

param resname:

Three letter residue name: ex., 'VAL'

type resname:

str

Pararmeters with defaults

param id:

Atom id. If the atom is generated from an MDAnalysis AtomGroup (probably the case) the id will be the universe atom ID.

type id:

int, default=1

param region:

Region the atom exists within (if any).

type region:

QMzymeRegion, default=None

Note

User may add any number of additional attributes as keyword arguments (kwargs).

property region

Returns:

Region this atom belongs to. If it does not belong to a region, returns None.

Return type:

:class`~QMzyme.QMzymeRegion.QMzymeRegion`

property atomic_number

Returns:

Atomic number corresponding to QMzymeAtom.element.

Return type:

integer

set_neighbor(value: bool = True)

Sets is_neighbor=True for QMzymeAtom instance, unless 'value=False' is passed.

Note

The DistanceCutoff class calls this method. This might be useful if you want to further evaluate why what residues were included in a QMzymeRegion that was selected based on the distance cutoff scheme.

set_fixed(value: bool = True)

Sets is_fixed=True for QMzymeAtom instance, unless 'value=False' is passed.

Note

The :module:`~QMzyme.CalculateModel` module will read what atoms have set_fixed=True and use that information to communicate to :module:`~QMzyme.Writers` what atoms to constrain in the calculation input file.

set_point_charge(value: bool = True)

Sets is_point_charge=True for QMzymeAtom instance, unless 'value=False' is passed. This will eventually be used for calculations with charge embedding.

Raises:

UserWarning if the atom does not have the attribute 'charge'.

get_chain()

Searches possible attribute names chain can live under (chainID, chain_ID, chain,id) and returns value if found.

is_within(region)

Parameters:

region (QMzymeRegion, required) -- Region to search for atom in.

Returns:

True if the same atom is found in region. Used to avoid duplication.

Return type:

bool