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

• Molecule::Molecule(char *, Scene *)
  The first argument is the source of the data, it is a string indicating either a file, or some remote computer, or perhaps some other source. The second argument is the Scene to which this molecule should be added. This version of the constructor should only be used if no MoleculeList is being used.

• Molecule::Molecule(char *, Displayable *)
  Same as above, except a parent Displayable is specified instead of a Scene. This is the version that should be used mainly in VMD, with the global MoleculeList object specified as the parent Displayable for the molecule.

Internal data structures

• char *source - the source of the molecule structure data.

• ResizeArray<CoorFileData *> coorIOFiles - data on which files containing atomic coordinates are to be read in by this object. Each CoorFileData instance contains data on which file to read, what type of file it is, and which frames to read from the file. The same data is stored in the case where a file is to be written instead of read.

Nonvirtual member functions

• int read_coor_file(char *, int, int=(-1), int=(-1), int=(-1)) - request to read in the specified file. The second argument is the type, and the remaining are the beginning frame, ending frame, and frame skip values. If any are not specified or are < 0, default values are used.

• write_coor_file(char *, int, int=(-1), int=(-1), int=(-1)) - same as above, but requests to write out a file.

Virtual member functions

• virtual void prepare(DisplayDevice *) - does any preparation necessary before redrawing. If data files are being read, this will read the next frame from them.

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.