Dependencies

• bertrand-caron/biopython: Fork of Biopython (only used for its Vector class).
• ATB-UQ/chemical_equivalence: Predicting chemical equivalence of atoms in molecules using graph automorphisms (nauty) and chemical symmetry constraints.
• bertrand-caron/atb_outputs: Automated Topology Builder (ATB) molecule data object and output modules (PDB, YML, PICKLE, LGF, GRAPH)
• bertrand-caron/chemistry_helpers: Various chemistry related helpers.
• GNU Make: Included with most Linux distributions.

Installation

• Run make install to automatically download all dependencies. Note that chemical_equivalence, atb_outputs and chemistry_helpers will be cloned in the parent directory of Blind_RMSD. Please add the parent directory to your shell's PYTHONPATH variable. If you are using bash (Bourne Again Shell), run the following line: export PYTHONPATH=$(dirname $PWD):$PYTHONPATH

Usage

The test.py script contains code to run the Blind RMSD algorithm on a series of test cases found in the data/ directory. You can run it by running: make test (once you have successfully set up your PYTHONPATH variable).

Troubleshooting

• If you get a ModuleNotFoundError, this most likely mean there is a problem with your PYTHONPATH. Consider what happens in the following example when setting the PYTHONPATH variable to an empty string:

bertrand-caron@iMac Blind_RMSD  [11:13:47] $ PYTHONPATH="" make test
echo 'Installed'
Installed
PYTHONPATH="" python3 test.py
Traceback (most recent call last):
  File "test.py", line 3, in <module>
    from Blind_RMSD.pdb import pdb_data_for, align_pdb_on_pdb, ALL_EXCEPTION_SEARCHING_KEYWORDS
ModuleNotFoundError: No module named 'Blind_RMSD'
make: *** [test] Error 1

Citation / Attribution

To cite this work, please use the following Zenodo DOI.