PETRA is a command line based program without a graphical user interface.
By default the program looks for a file CTXINP (capitals) which contains the input data. The input file must be written in Gasteiger Cleartext format (CTX). There are several tools available for creating files in CTX format or converting other standard file formats to CTX (see CSED of the CACTVS-Tools, e.g.).
The data required by PETRA are stored under the keywords /MOLECULS, /ATOMS and /BONDS which represent the connectivity table of the considered molecul(s).
In additon, PETRA uses the following keywords:
/HISTORY, /IDENT, /NAME, /STEREO, /VALENCE, /END or /ENDBLOCK
depending on the type of calculations which should be carried out.
The calculated data are written by default into a file called RESULT. This file contains all calculated descriptors in the following manner:
/ATOPROP 1 4 APOLARIZABILITY [ANGSTROM ** 3] Effective atom polarizability R /APOLARIZ 3 3 4.4935 5.1220 4.4935
Each keyword begins with a slash. PETRA calculates descriptors for properties of ensembles (sets of molecules), molecules, atoms, and bonds. Accordingly the following keywords are provided:
These keywords indicate what type of property will follow.
After each keyword two integer numbers follow. The first one specifies the number of information units that follow. The second gives the number of lines of the dataset that follows.
In the example shown one information unit with four lines follows after the keyword /ATOPROP. In this case the information unit gives the full name of the property that is following (first line), the physical unit of the data given (second line), an short description of the calculated property (third line) and the number format in which the data are written: R for real number, I for integer number and L for logical (fourth line).