distruct 0.0.5

a package to generate 3d molecular structures from distance constraints

diSTruct

python package name: distruct Implementation of Maxent-stress Optimization of Biomolecular systems.

diSTruct is in essence an implementation of the MaxEnt-Stress graph drawing algorithm (Gansner, E.; Hu, Y. and North, S. C.: "A Maxent-Stress Model for Graph Layout" in IEE Trans. Vis. Comput. Graph. 2013) for generating biomolecular structures from distance constraints.

Requirements

The actual structure generation in diSTruct is build on the MaxEnt-stress graph drawing implementation in NetworKit.

It aims to conveniently combine this with the PDB module in Biopython.

It also depends on lxml and requires cython.

Installation Instructions

First install NetworKit following the instructions in their homepage. Make sure you can import networkit without error. Sometimes there are issues with automatically installing all dependenicies. Simply install missing packages manually.

Install cython, Biopython and lxml. Install diSTruct with

pip install distruct

To run diSTruct it may be necessary to set your LD_LIBRARY_PATH to find the NetworKit extension. diSTruct gives further instructions on importing.

Publications

Tests

To run the python tests run "make test".