parmed.topologyobjects.AtomType

class parmed.topologyobjects.AtomType(name, number, mass, atomic_number=- 1, bond_type=None, charge=0.0)

Atom types can either be compared by indexes or names. Can be assigned with a string, integer, (string is not automatically cast) or with both.

Parameters

namestr

The name of the atom type

numberint

The serial index of the atom type

massfloat

The mass of the atom type

atomic_numberint, optional

The atomic number of the element of the atom type. Default -1

bond_typestr, optional

If defined, this is the type name used to look up bonded parameters. Default is None (which falls back to name)

chargefloat, optional

If defined, this is the partial atomic charge in elementary charge units. Default is None

Notes

This object is primarily used to build parameter databases from parameter files. Also, sigma is related to Rmin, but rmin is Rmin/2, so there is an extra factor of 2 in the sigma for this reason.

Examples

>>> at = AtomType('HA', 1, 1.008, 1)
>>> at.name, at.number
('HA', 1)
>>> at2 = AtomType('CA', 2, 12.01, 6)
>>> at2.name, at2.number
('CA', 2)
>>> print("%s: %d" % (str(at), int(at)))
HA: 1

Attributes

bond_type

sigma

Sigma is Rmin / 2^(1/6)

sigma_14

Sigma is Rmin / 2^(1/6)

uepsilon

uepsilon_14

urmin

urmin_14

usigma

usigma_14

Methods

add_nbfix(typename, rmin, epsilon[, rmin14, …])	Adds a new NBFIX exclusion for this atom type
set_lj_params(eps, rmin[, eps14, rmin14])	Sets Lennard-Jones parameters on this atom type

__init__(name, number, mass, atomic_number=- 1, bond_type=None, charge=0.0)

Initialize self. See help(type(self)) for accurate signature.

Methods

__init__(name, number, mass[, …])	Initialize self.
add_nbfix(typename, rmin, epsilon[, rmin14, …])	Adds a new NBFIX exclusion for this atom type
set_lj_params(eps, rmin[, eps14, rmin14])	Sets Lennard-Jones parameters on this atom type

Attributes

bond_type
sigma	Sigma is Rmin / 2^(1/6)
sigma_14	Sigma is Rmin / 2^(1/6)
uepsilon
uepsilon_14
urmin
urmin_14
usigma
usigma_14