PDB_EXTRACT
Extract data from PDB files

PDB_EXTRACT is a FORTRAN90 program which extracts certain columns from certain lines of a Protein Data Bank file.

Right now, the controls for which lines are to be considered, and what data is to be extracted, are hardwired into the code. For instance, we might want to consider every line in which the fourth word is "CA", and for those lines, we would write out columns 9 and 10.

Licensing:

The computer code and data files described and made available on this web page are distributed under the GNU LGPL license.

Languages:

PDB_EXTRACT is available in a FORTRAN90 version.

Related Data and Programs:

PDB, a data directory which contains a description and examples of the PDB format.

PDB_READ, a FORTRAN90 program which can read a PDB file.

PDB_TO_XYZ, a FORTRAN90 program which reads the coordinates of atoms in a PDB file and writes them out as an XYZ file.

XYZ_TO_PDB, a FORTRAN90 program which reads an XYZ file and writes the data as coordinates of atoms in a PDB file.

Reference:

1. http://www.rcsb.org/pdb/
   The Protein Data Bank Home Page.

Source Code:

• pdb_extract.f90, the source code;
• pdb_extract.sh, commands to compile and load the source code;

Examples and Tests:

• input.txt, a sample input PDB file;
• output.txt, a sample output file;

List of Routines:

• MAIN is the main program for PDB_EXTRACT.
• CH_CAP capitalizes a single character.
• CH_EQI is a case insensitive comparison of two characters for equality.
• CH_TO_DIGIT returns the integer value of a base 10 digit.
• GET_UNIT returns a free FORTRAN unit number.
• S_TO_R8 reads an R8 from a string.
• TIMESTAMP prints the current YMDHMS date as a time stamp.
• WORD_FIND finds the word of a given index in a string.

You can go up one level to the FORTRAN90 source codes.