mstk.topology.Atom

class mstk.topology.Atom(name='UNK')

An atom is a particle in simulation.

It can be an real atom, a Drude particle, a virtual site or a coarse-grained bead.

Parameters:

name (str) –

id

Index of this atom in topology. -1 means information haven’t been updated by topology

Type:

int

id_in_mol

Index of this atom in molecule. -1 means information haven’t been updated by topology

Type:

int

name

Name of this atom, not necessarily unique

Type:

str

type

Atom type in force field. Required for assigning force field parameters

Type:

str

symbol

Atomic symbol. Mainly used for output topology or trajectory

Type:

str

mass

Mass assigned. Required for output simulation files

Type:

float

charge

Charge assigned. Required for output simulation files

Type:

float

alpha

Isotropic polarizability. Required for output Drude polarizable simulation files This property is set for parent atom, not Drude particle

Type:

float

thole

Thole screening for induced dipole. Required for output Drude polarizable simulation files This property is set for parent atom, not Drude particle

Type:

float

formal_charge

Formal charge calculated from valence bond theory. Optionally required by typing engine

Type:

int

is_drude

Whether or not this is a Drude particle for polarizable model

Type:

bool

virtual_site

None if this atom is not a virtual site. Otherwise the instance of subclass of VirtualSite

Type:

None or subclass of VirtualSite

has_position

Whether or not the position of this atom is set

Type:

bool

Methods

__init__([name])

Attributes

bond_partners	All the bond partners of this atom.
bonds	All the bonds involving this atom.
molecule	The molecule this atom belongs to
position	The position of this atom
rdatom	The rdkit.Chem.Atom object associated with this atom.
residue	The residue this atom belongs to

property molecule

The molecule this atom belongs to

Returns:

molecule

Return type:

Molecule

property residue

The residue this atom belongs to

Returns:

residue

Return type:

Residue

property bonds

All the bonds involving this atom.

Bonds of Drude dipoles are included if exist.

Returns:

bonds

Return type:

list of Bond

property bond_partners

All the bond partners of this atom.

Drude particles are included if exist.

Returns:

partners

Return type:

list of Atom

property position

The position of this atom

Setter:

Set the position of this atom

Returns:

position – The position is a numpy array of shape (3,)

Return type:

array_like

property rdatom

The rdkit.Chem.Atom object associated with this atom.

It exists only if this atom belongs to a molecule.

Returns:

rdbond

Return type:

rdkit.Chem.Atom