fix alignBioPairwise for updated biopython

[jamesmkrieger]

The output of Biopython PairwiseAligner align has changed drastically in the latest versions, so the new code has an if block and handles the output depending on whether it matches the new version.

[jamesmkrieger]

I think this should be the last thing to be able to use the latest biopython

[jamesmkrieger]

oh, Biopython is also not including the biomolecular transformations for assemblies so ProDy can't parse the MMTF files that it writes

[jamesmkrieger]

We'll still need checks here too, which can be done using 3enl and 3p3w

[jamesmkrieger]

oh, Biopython is also not including the biomolecular transformations for assemblies so ProDy can't parse the MMTF files that it writes

This was actually due to a bug that is now fixed here

[jamesmkrieger]

It looks like biotite now works with the output of ProDy. We're still missing the biomoltrans and bonds because biopython doesn't handle those, but then we just get 0 bonds and empty records and it's probably ok.

Python 3.10.13 (main, Sep 11 2023, 13:44:35) [GCC 11.2.0]
Type 'copyright', 'credits' or 'license' for more information
IPython 8.20.0 -- An enhanced Interactive Python. Type '?' for help.

In [1]: from biotite.structure.io.mmtf import MMTFFile

In [2]: from prody import *

In [3]: ag, header = parsePDB('prody/tests/datafiles/pdb2k39_ca.pdb', header=True)
@> 76 atoms and 116 coordinate set(s) were parsed in 0.13s.
@> Secondary structures were assigned to 37 residues.

In [4]: writeMMTF('prody/tests/datafiles/mmtf2k39_ca', ag, header=header)
Out[4]: 'prody/tests/datafiles/mmtf2k39_ca.mmtf'

In [5]: mmtf_file = MMTFFile.read('prody/tests/datafiles/mmtf2k39_ca.mmtf')

In [6]: mmtf_file['numGroups']
Out[6]: 8816

In [7]: ag.numResidues()*ag.numCoordsets()
Out[7]: 8816

In [8]: mmtf_file['numAtoms']
Out[8]: 8816

In [9]: ag.numAtoms()*ag.numCoordsets()
Out[9]: 8816

In [10]: ag, header = parsePDB('prody/tests/datafiles/pdb6flr.pdb', header=True)
@> 6073 atoms and 1 coordinate set(s) were parsed in 0.19s.
@> Secondary structures were assigned to 484 residues.

In [11]: writeMMTF('prody/tests/datafiles/mmtf6flr', ag, header=header)
/home/jkrieger/software/miniconda/envs/biotite/lib/python3.10/site-packages/Bio/PDB/StructureBuilder.py:89: PDBConstructionWarning: WARNING: Chain A is discontinuous at line 0.
  warnings.warn(
/home/jkrieger/software/miniconda/envs/biotite/lib/python3.10/site-packages/Bio/PDB/StructureBuilder.py:89: PDBConstructionWarning: WARNING: Chain B is discontinuous at line 0.
  warnings.warn(
Out[11]: 'prody/tests/datafiles/mmtf6flr.mmtf'

In [12]: mmtf_file = MMTFFile.read('prody/tests/datafiles/mmtf6flr.mmtf')

In [13]: mmtf_file['numGroups']
Out[13]: 791

In [14]: ag.numResidues()*ag.numCoordsets()
Out[14]: 791

In [15]: ag.numResidues()
Out[15]: 791

In [16]: mmtf_file['numAtoms']
Out[16]: 6073

In [17]: ag.numAtoms()
Out[17]: 6073

In [18]: ag.getCoords()[0]
Out[18]: array([18.18 , 51.053, 34.125])

In [19]: mmtf_file['xCoordList'][0], mmtf_file['yCoordList'][0], mmtf_file['zCoordList'][0]
Out[19]: (18.18, 51.053, 34.125)

This was done in a fresh environment