TPRReaderDevelopment

Tyler Reddy edited this page May 5, 2015 · 2 revisions

Introduction

Gromacs combines structure and topology information into a binary tpr file. This file is used as a run file and is not user-readable; it can be printed out using 'gmxdump' command.

The aim is to be able to read a tpr just like any other structure/topology file format. No write support is intended at this stage.

Current implementation in MDAnalysis

The implementation has been discussed in Issue 2.

alfred532008's TPR reader is available as the feature branch pyTPRparser in the repository.

Anyone who wants to play with the code should be able to do so with commands such as

git fetch origin
git checkout pyTPRparser

Current limitations:

  • limited TPR file versions (as of March 2013):
    • version 58 (Gromacs releases 4.0.x)
    • version 73 (Gromacs releases 4.5.x)
  • does not read all parts of the TPR file (see source code of TPRparser.py)

For additional information see the developer thread mdnalysis-devel: Issue 2 in mdanalysis: reading Gromacs tpr files instead of psf.

Developer notes

Details

The relevant GROMACS source files are

  • src/programs/gmxdump
  • gromacs/gmxlib/tpxio.c
  • gromacs/gmxlib/gmxfio.c

The binary file can be read-in in python using xdrlib http://docs.python.org/py3k/library/xdrlib.html

Conventions

It would help not to simplify/expand gromacs variable names and data structure. It's hard enough getting ones had around what's going on in gromacs source right now. It will only introduce confusion to have two naming conventions in the future, when the gromacs devs introduce changes to the tpr format.

Example TPR reader


__author__      = "Jan Domanski"
__copyright__   = "GNU Public Licence, v2"

import xdrlib

def main():
  """
  Based on the following gromacs source files
    - gmxdump.c
    - tpxio.c (the most important one)
    - gmxfio.h
  """

  tpr = "adk_oplsaa.tpr"

  f = open(tpr).read() 

  data = xdrlib.Unpacker(f) 

  # From src/gromacs/legacyheaders/typedefs.h
  STRLEN = 4096
  BIG_STRLEN = 1048576

  number = data.unpack_int()

  version_string = data.unpack_string()

  precision = data.unpack_int()

  fver = data.unpack_int()

  gen = data.unpack_int()

  tpx_natoms = data.unpack_int()

  return

  if fver >= 28:
    tpx_ngtc = data.unpack_int()
  else:
    tpx_ngtc = 0 
    
  if fver < 62:
    idum = data.unpack_int()
    rdum = data.unpack_float()
    
  tpx_lambda0 = data.unpack_float()
  tpx_bIr =  data.unpack_int()
  tpx_bTop =  data.unpack_int()
  tpx_bX =  data.unpack_int()
  tpx_bV =  data.unpack_int()
  tpx_bF =  data.unpack_int()  
  tpx_bBox =  data.unpack_int()    
  
if __name__ == "__main__":
  main()

Project Information

About
GNU GPL v2 code license
Labels: python, molecular dynamics, analysis, DCD, CHARMM, LAMMPS, NAMD, Gromacs, computer simulation, atoms, coordinates, trajectory, XTC, Library, object-oriented
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