This module reads in a Brookhaven Protein DataBase Molecule and builds a Chemistry Pyramid. This module has implemented the CONECT program from BNL to determine the bonds. If this algorithm fails to find any bonds, then a covalent algorithm is used.



Port: Filename
Type: Text
Filename of PDB file

Port: Element
Type: Text
Filename of reference chemical data. This file includes the following properties for all atoms:

atom number, covalent radius, Van Der Waals radius, maximum number of bonds.


Port: Molecule
Type: Pyramid
Constraints: n-layer
Constraints: optional-baseLat
Constraints: n-D compression
Constraints: n-compression type
The output is a Chemical-based pyramid. This pyramid has 4 layers of lattices. The levels are: molecule, residue, atom, and bonds. Each level can have an arbitrary number of data values. The current interpretation for some of the data at the bond and atom level is defined. The bond level assumes the first four data variables are: bond order, 2 atom numbers that comprise the bond and topology. The first eleven data values for the atom level are: ID, element number, vdw radius, color, covalent radius, mass, charge, valence, radical, ionization, and hybridization. If any additional variables are used in either the bond or the atom level, they are user specified.


If the residue name exists, then only the first character of the element name is used to lookup the element.


AtomicSurf, BallStick, PrintPyr.
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© The Numerical Algorithms Group Ltd, Oxford UK. 2000