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. In addition to the topology, MolType stores the list of actual 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
