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2.13 General Glossary

data structure
A collection of arrays, scalars, and possibly other data structures which are related by part of a larger entity. For example, a coordinate set is a data structure which hold the three dimensional positions of atoms. This data structure consists of 1 scalar and three arrays. The scalar is the number of coordinates; the three arrays are the X, Y, and Z components of the coordinates.

Internal Coordinates
Bonds, angles, torsions, improper torsions. Also, a data structure used for constructing coordinates.

Iupac Names
The name of an atom with a residue. This name should be within a residue and should conform to the IUPAC nomenclature. See Biochemistry 9:3471 (1970).
Hydrogen bonds.

Constants in the energy expression (force constants, minima of energy surfaces, charges, Lennard-Jones parameters, van der Waals radii, etc.)

Protein Structure File a list of the internal coordinates and related information

Residue Identifier
A string of four characters or less which uniquely specifies residue with in a segment. This value is currently set by CONGEN to be the character representation of the residue number in the segment starting from the first real monomer unit in it. Special terminating residues gets their names as identifiers. For example, if we build a tri-peptide LYS ARG ASP using an explicit hydrogen topology file, we get five residues in the segment, NTER LYS ARG ASP CTER, and the residue identifiers are then `NTER', `1', `2', `3', and `CTER'.

residue topology file : a list of standard internal coordinates, atom charges, atom types, excluded non-bonded interactions, etc.

Segment Identifier
A string of up to four characters uniquely designating a segment. Specified in the GENErate command, see Generate Command.
list of residues.