InSty - changes in calcStatisticsInteractions #1948
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I added a new function - checkNonstandardResidues(), which checks whether we have some non-standard names in PDB. Tomorrow, I will add checks with this function in different places. When we will have non-standard residues the user will be informed. It might be useful to detect multiple side chain conformation ALYS/BLYS in protein structure as well. Except that I modified get_energy() and included a dictionary with non-standard names typical for NAMD, AMBER and GROMACS. |
I don’t think the gromacs ones make sense and I left a comment about that |
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still a few suggestions but I think it looks good
I still think it would be better to have the nonstandard residue handling in a different file like prody/atomic/atomic.py where the is AAMAP and MODAAMAP or maybe somewhere in prody/utilities, but I guess it's ok for now
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If that is all, James, can you approve the code so we can merge it? |
I believe so. I just want to check through it once more |
| 'HID': 'HIS', # AMBER name, protonated at ND1 | ||
| 'HIE': 'HIS', # AMBER name, protonated at NE2 | ||
| 'HIP': 'HIS', # AMBER name, doubly protonated | ||
| 'HISD': 'HIS', # GROMACS: protonated at ND1 |
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we can get these with long_resname=True:
In [6]: ag = parsePDB('nvt1_nojump_end.pdb', long_resname=True)
In [8]: np.unique(ag.getResnames())
Out[8]:
array(['ALA', 'ARG', 'ASN', 'ASP', 'CLA', 'CU2P', 'CYS', 'GLN', 'GLU',
'GLY', 'HISD', 'HISE', 'ILE', 'LEU', 'LYS', 'MET', 'PHE', 'PRO',
'SER', 'SOD', 'THR', 'TRP', 'TYR', 'VAL'], dtype='<U6')
| 'PTR': 'TYR', # Phosphorylated tyrosine (GROMACS/AMBER) | ||
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| # Non-standard names for aspartic and glutamic acids in low pH environments | ||
| 'ASH': 'ASP', # Protonated Asp |
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I also confirm that I've seen one of these recently too
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ok, now I approve merging it |
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oh, I actually broke something in the utilities |
actually never mind. I didn't include that in a commit anyway |
prody/proteins/interactions.py
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| 'GLUP': 'GLU', # Protonated Glu | ||
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| # Lysine (Lys) | ||
| 'LYN': 'LYS', # Deprotonated lysine (nautral) |
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actually here's another typo that I'll fix
I added try/except for the energy parameter because I had a problem analyzing a system with two chains and selecting interactions between them. I think it might be an empty list when there is no interaction at all, and that is the reason.
New changes: