PDB to graphic relational format converter

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The graphic relational format (grf) is the format for the aocr Utility. The converter pdb2grf allows you to use the aocr Utility with your molecules in pdb format.

It takes an argument consisting of a list of files with (organic) compounds in pdb format and writes to stdout a file in grf format containing the compounds in the files. Use the redirection > to save the output to a file.

The obtained file is ready to be edited (viewed and modified) with the Graphic Composer of the aocr Utility and to be used as start or searched compounds for the Computation Tool.

The converter arranges the formulas of the compounds from the argument list in a grid:
and multiplies the coordinates by a factor mf. The parameters vertical border vb, horizontal origin ho, vertical origin vo, horizontal distance hd, vertical distance vd, multiplicator mf can be passed to the converter through the file .grf in the same directory of the executable pdb2grf. The file has the following form:

# As many lines with comments
# beginning with #
# as wished. No empty lines.
Vertical border: 100
Horizontal origin: 200
Vertical origin: 200
Horizontal distance: 400
Vertical distance: 200
Multiplicator: 50

If .grf does not exist or the parameter can not be read from it, the default values are used which are:

Vertical border: 50
Horizontal origin: 100
Vertical origin: 100
Horizontal distance: 200
Vertical distance: 200
Multiplicator: 30

Once the file has been opened with the Graphic Composer the redraw feature can be used to obtain a better graphical representation of the formulas. Some manual corrections might be necessary, too.

This release of the converter disregards the charges and the radicals in the pdb files. They have to be added manually when the file is edited.

The accepted pdb format is described in the pdbguide 2.2 of the rscb web site. The "CONECT" records are mandatory to obtain the bonds.

Free download of the PDB to graphic relational converter:

Binary executable for Microsoft Windows.
Binary executable for Sun Solaris Sparc (gzip compressed).
The files of C source code, scanAtom-2.c, symbolValue-1.c, setParam-2.c, that can be compiled with the options -o pdb2grf -lm.