MoleculeType

Description

The MoleculeType is the data type that carry molecular information between modules. It uses another sub type (MoleculeDataType) to describe data associated to atoms, bonds or to the whole structure.

group MoleculeDataType {
    int num_components;		// How many components are described
    int num_values;		// How many values
    group data[num_components] {
	byte len;           		// 1 for scalar, 3 for vector
	float values[num_values][len];  // data values
	string name;        		// optional variable name
    };
};

The MoleculeType is composed by the following objects:

group MoleculeType {

    //
    // Global data
    //
    int step[4];    // If the structure is part of an animation step contains:
		    // [0] start, [1] end, [2] increment, [3] curr step. (values start from 1)
		    // otherwise it contains {1,1,1,1}
    int info_set;   // InfoSet used for subsequent bonds computation etc. (superceded in DrawStructure)

    //
    // Data associated to the structure as a whole
    //
    MoleculeDataType global_data;

    //
    // Base structure
    //
    int    natoms;              // number of atoms
    float  xyz[natoms][3];      // coordinates of those atoms
    int    Z[natoms];           // Z value of the atoms
    string name[];              // size: 0 or natoms. if 0 compute the name from Z
    byte   render[natoms];      // if the atom should be rendered or not
				// or the rendering method for the atom
				// (described by RenderType enum)

    //
    // Fragment naming and grouping (eg. Residues)
    //
    int fragment[];             // size: 0 or natoms. Contains the indices into the
				// fragment_table of the fragments each atom pertains
    group fragment_table {      // the arrays in fragment_table should have the same size
	    int id[];           // id is one of the idx in fragment_id
	    string name[];      // the name of the particular fragment
				// optionally another int table could carry the code
				// that identify known fragment types (like residues)
    };

    //
    // Data associated to atoms
    //
    MoleculeDataType atoms_data;

    //
    // Bonds
    //
    int  nbonds;		// Total number of bonds
    int  bonds[nbonds][2];	// Pair of indices of the bonded atoms
    byte bonds_type[nbonds];	// Content described by BondType enum

    //
    // Data associated to bonds
    //
    MoleculeDataType bonds_data;

    //
    // Unit cell
    //
    float unit_cell[][];    // unit_cell[0][0..2] a
			    // unit_cell[1][0..2] b
			    // unit_cell[2][0..2] c
			    // unit_cell[3][0..2] origin
			    // unit_cell[0..2][3] <zero>
			    // unit_cell[3][3]    <one>
			    // if size [0][0] no unit cell associated, otherwise [4][4]

    //
    // Symmetries
    //
    string space_group;	    // the Hermann-Mauguin space group symmetry code (eg. P 21 21 21)
};