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
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attributes: 3 Atoms, spring constant (kcal/mol/rad^2), angle eq. |
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Atom Object Definition |
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AtomType per atom in gaff or amber. |
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attributes: pair of Atoms, spring constant (kcal/mol), dist. |
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attributes: 4 Atoms, spring constant (kcal/mol), periodicity, phase (rad) |