Python wrapper for small open-source C GNU tool

Completed Posted Nov 11, 2014 Paid on delivery
Completed Paid on delivery

Hello,

I have a simple, well-defined job that I need done very quickly.

I want an easy to use python wrapper for the GNU C library available by following the link below.

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The header files are *very* well documented and there is an example in the src/python directory that demonstrates how to write a python wrapper to read the binary ".trr" format (double precision). This library also supports a reduced precision ".xtc" format but I do not need support for this format.

I want a python script that demonstrates how to read/write numpy data (cartesian coordinates, cartesian forces, box-size, etc) from/to a trr file. trr files store a specific series of variables (a "frame") repeatedly to form a "trajectory." These trajectories can get very large so there needs to be some means to append to the end of the file or read-in a subset of the file only. To be specific, common tasks I need your code to handle include:

1.) write numpy data to a single frame trr

2.) read a single frame trr into numpy arrays

3.) read the last frame of a large trr into numpy arrays

4.) append numpy data to end of a large trr

I am very comfortable with simple python scripting and numpy/scipy usage but I know little about C and the means to interface C with python (SWIG, ctypes, cython, etc). For the right programmer this should be a nearly trivial task. Speed and code quality (small, clear, efficient, fast) are important.

Please indicate how long you expect the task to take. If we are satisfied with your service there may be more jobs of the same type available.

C Programming Linux Python

Project ID: #6718418

About the project

4 proposals Remote project Active Nov 15, 2014

Awarded to:

nnemkin

Updated proposal: I'll update xdrlib included with MDAnalysis (with SWIG binding) to handle double data instead of float.

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