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
- 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.