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Subsections


Molecule

Files: Molecule.h, Molecule.C
Derived from: \bf DrawMolecule
Global instance (if any): none
Used in optional component: Part of main VMD code

Description

This is the class used generally throughout VMD to represent and access a molecule. It is derived from several base classes which provide the storage and control over the molecule's structure (BaseMolecule), animation list (Animation), and graphical display (DrawMolecule). It still does not contain the abilities to read in new molecular data from different sources, instead these are in classes derived from Molecule. This class is used as the basic class that all other parts of VMD are aware of, since once a molecule is read in from some source, it acts just like any other molecule.

The one level of extra functionality which is provided directly by the Molecule class is the ability to read in new coordinate frames from an external coordinate file, either a PDB or a DCD file.

Constructors

Internal data structures

Nonvirtual member functions

Virtual member functions

Method of use

New molecules are created in VMD in the CmdMolNew object, which is a particular Command-derived object. When a new molecule is to be created, the type of molecule source and necessary data are specified (such as filenames, remote computer names, etc) and given to the constructor of a specialized subclass of Molecule. The resulting (empty) molecule is assigned to a Molecule * pointer variable, and then the virtual create routine is called. After this, the molecule is added to the MoleculeList, and any extra actions are taken such as requesting for more coordinate files to be read, etc.


next up previous contents
Next: Timestep Up: Molecule objects Previous: DrawMolecule   Contents
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