XYZ_TO_PDB
Write PDB Atom Coordinates to XYZ File

XYZ_TO_PDB is a FORTRAN90 program which reads an XYZ file containing a list of spatial coordinates, and writes a PDB file containing ATOM records with the given coordinates.

The PDB file has many fields that must be filled in. This program attempts to fill in these fields with plausible values, but really only the atomic coordinates will have any meaning.

Usage:

xyz_to_pdb

xyz_to_pdb file.xyz file.pdb

• file.xyz is the input coordinate data;
• file.pdb is the PDB file created.

Licensing:

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

Languages:

XYZ_TO_PDB 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_EXTRACT, a FORTRAN90 program which can extract certain records from a PDB file.

PDB_READ, a FORTRAN90 program which can read the information in a PDB file.

PDB_TO_XYZ, a FORTRAN90 program which reads the ATOM records from a PDB file, and writes the atomic coordinates to an XYZ file.

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

XYZ_IO, a FORTRAN90 library which reads and writes XYZ files.

Reference:

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

Source Code:

• xyz_to_pdb.f90, the source code;
• xyz_to_pdb.sh, commands to compile the source code;

Examples and Tests:

TINY is a sample XYZ file with 12 sets of 3D coordinates.

• tiny.xyz, a sample XYZ file;
• tiny.pdb, the corresponding PDB file.

MOMOMER is a sample XYZ file with 888 sets of 3D coordinates.

• monomer.xyz, a sample XYZ file;
• monomer.pdb, the corresponding PDB file.

List of Routines:

• MAIN is the main program for XYZ_TO_PDB.
• 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_EQI is a case insensitive comparison of two strings for equality.
• S_TO_R8 reads an R8 from a string.
• S_TO_R8VEC reads an R8VEC from a string.
• TIMESTAMP prints the current YMDHMS date as a time stamp.
• TIMESTRING writes the current YMDHMS date into a string.
• XYZ_TO_PDB_ATOM_TO_XYZ writes XYZ data as ATOM records in a PDB file.

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