As mentioned in #1 , I tried to construct a test script for nDOPE evaluation.
I am implementing nDOPE as a stand-alone function as get_nDOPE(). Issue get_nDOPE( filename ) will seek the PDB file specifiied by the "filename" and calculate the nDOPE score for the contained structure.
Several points worth noting:
complete_pdb() would change the PDB file itself.
The modeller dependency is very complicated. This means:
The modeller is licensed to non-academic use for free, but we need to avoid any copyright issue,
Figure out how to maintain these dependencies automatically.
Remove system-dependency preferably.
Figure out how does Modeller handle different chains.
It'd be great to allow some flexibility in "filename", so that one can specify the pdb folder and return a list as output.
Logic:
How is nDOPE defined mathematically anyway?
Test:
The test_pdb.py will check the PDB-nDOPE correspondency as stored earlier. The testing is only to 3 decimal place.
As mentioned in #1 , I tried to construct a test script for nDOPE evaluation.
I am implementing nDOPE as a stand-alone function as
get_nDOPE(). Issueget_nDOPE( filename )will seek the PDB file specifiied by the "filename" and calculate the nDOPE score for the contained structure.Several points worth noting:
Logic:
Test:
The test_pdb.py will check the PDB-nDOPE correspondency as stored earlier. The testing is only to 3 decimal place.
Any suggestion is appreciated.