GOR IV

GOR is an algorithm for predicting secondary structure from an amino acid sequence. It is described in GOR Method for Predicting Protein Secondary Structure from Amino Acid Sequence.

The original C code

The GOR IV code in this directory is based on the C code available from http://mig.jouy.inra.fr/?q=en/node/85.

The original C code uses 1-based array offsets. I have not attempted to change that, or to otherwise clean up the code, tempting as it has been.

Python interface

I used cffi to make a Python interface to GOR IV.

Usage is as follows:

from gor4 import GOR4

gor4 = GOR4()
result = gor4.predict('DKATIPSESPFAAAEVADGAIVVDIAKMKYETP')

print('Predicted secondary structure', result['predictions'])
print('Prediction probabilities', result['probabilities'])

For detailed usage examples, see the tests in test/test_gor4.py.

Notes:

• The initialization of a GOR4 instance is very slow (due to reading large files of AA structure infomation from gor4/data), so you will likely want to make a singleton instance and just use that.

• It is possible to pass alternate known sequence and secondary structure files to GOR4.__init__ but this is not done in any of the test examples.

C interface files

The files in the src directory are as follows:

• api.c: An API library suitable for calling via Cython. This has 3 functions, initialize, predict and finalize. Initialize returns a struct containing pointers to mallocd memory that is freed in finalize. To get a secondary structure prediction, predict must be called.
• build.py: Python to tell cffi how to build the module, and what functions are available.
• gor4-base.c: A very slightly modified copy of the original gor.c file. The modification is that some #define constants have been moved into gor4-base.h so they can also be used in api.c.
• gor4-base.h: Some #define constants that used to be in gor4-base.c, plus the definition of the struct returned by initialize.
• nrutil.{c,h}: The original files from the GOR IV distribution.