MolType: Topology of a single molecular type
Molecular Type is a container for storing molecular topology, i.e. atoms (and their types ) and bond-types (and bonds). It must belong to some [System]System. In addition to the topology, MolType stores the list of actual [Molecule]molecules of this type.
The molecular type instance can be read from mcm-file, otherwise an stub molecular type will be created. When the molecular type is read from file, it automatically gets one corresponding molecule assigned.
- Properties:
-
- Name
- - The molecular type name
- System
- - The system which the Molecular Type belongs to
- Molecules
- - Molecules of the Molecular Type
- BondTypes (also PairBondTypes and AngleBondTypes)
- - List of BondTypes belonging to the Molecular Type
- Bonds (also PairBonds and AngleBond)
- - List of Bonds belonging to the Molecular Type
- Atoms
- - List of atoms belonging to molecules of the molecular type
-
- Methods:
-
- AddMolecule
- - Add molecule to the MolType
- Write2MCM
- - Write the molecular file to a mcm-file
Examples:
moltype_DNA = MagicTools.MolType('DNA.CG', system) # Read molecular type from file
moltype_stub = MagicTools.MolType('stub', system) # Create a stub
