acpype.mol

Constructors to define and store the system’s topology

It will create instances for Atoms, AtomTypes, Bonds, Angles and Dihedrals where the topology (the relationships between atoms) is defined and paramenters are stored.

Example

>>> atom = acpype.mol.Atom(...) # to be improved
acpype.mol.Atom

define Atom

acpype.mol.AtomType

define AtomType

Classes

Angle(atoms, kTheta, thetaEq)

attributes: 3 Atoms, spring constant (kcal/mol/rad^2), angle eq.

Atom(atomName, atomType, id_, resid, mass, ...)

Atom Object Definition

AtomType(atomTypeName, mass, ACOEF, BCOEF)

AtomType per atom in gaff or amber.

Bond(atoms, kBond, rEq)

attributes: pair of Atoms, spring constant (kcal/mol), dist.

Dihedral(atoms, kPhi, period, phase)

attributes: 4 Atoms, spring constant (kcal/mol), periodicity, phase (rad)