Frequently Asked Questions

Can I use OpenStructure modules from Python?

That's definitely possible, provided you have set the proper environment variables. On Linux you need to set LD_LIBRARY_PATH to the directory containing the libraries and PYTHONPATH to the directory containing the python modules. For a 64 bit platform this would look like:

export PYTHONPATH=/path/to/bundle/lib64/openstructure
export LD_LIBRARY_PATH=/path/to/bundle/lib64

On a 32bit system, the exchange lib64 for lib.

On MacOS X, you only need to set the PYTHONPATH. No need to set DYLD_LIBRARY_PATH.

How do I load a crappy PDB file?

The easiest way is to use the fault_tolerant option of LoadPDB. If you set the value to true, it will load the structure and just skip erroneus records:

ent=io.LoadPDB('pdb_with_errors.pdb', fault_tolerant=True)

How do I load all PDB files in a directory?

The python glob module can be used to match files in a certain directory against a glob pattern. Then use LoadPDB as you normally would.

import glob
pdbs=[]
for pdb_file in glob.glob(os.path.join(dir_path, '*.pdb')):
  pdbs.append(io.LoadPDB(os.path.join(dir_path, pdb_file)))

Which licensing does Openstructure come with?

Openstructure is released under GNU-LGPL license

Which software libraries does Openstructure depend on?

Openstructure depends on the following software libraries to implement its functionality:

Why another molecular Viewer?

Openstructure is not aiming to be a Viewer, but more a molecular modelling platform, a toolkit. It features nice graphics, though!