extract res if only 1 in extendAtoms

[jamesmkrieger]

fixes #1962

for some reason HierView getResidue gets atoms from multiple residues for GLN 357 and it's fixed in the list comprehension of _getResidue so we only have one entry in the list. So, it throws an error that there's a list when really we can extract it, which we now do.

[karolamik13]

Could you provide the PDB code and what to check?
It would be easier for me to test changes. Although the code looks ok.

[jamesmkrieger]

I'll forward you the pdb file with the problem. The code and error should be the following

Python 3.9.19 (main, May  6 2024, 19:43:03) 
Type 'copyright', 'credits' or 'license' for more information
IPython 8.15.0 -- An enhanced Interactive Python. Type '?' for help.

In [1]: from prody import *

In [2]: fex = parsePDB('comp_min.pdb')
@> 136109 atoms and 1 coordinate set(s) were parsed in 1.56s.

In [3]: fex_bb = fex.select('protein name CA C N O or resname CY1 name CA C N O')

In [4]: fex_ca = fex.select('protein name CA or resname CY1 name CA')

In [5]: y = extendAtoms(fex_ca, fex_bb)
---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
Cell In[5], line 1
----> 1 y = extendAtoms(fex_ca, fex_bb)

File ~/software/scipion3/software/em/prody-github/ProDy/prody/atomic/functions.py:349, in extendAtoms(nodes, atoms, is3d)
    347     raise ValueError('atoms must contain a residue for all atoms')
    348 if isinstance(res, list):
--> 349     raise ValueError('not enough data to get a single residue for all atoms')
    351 res_atom_indices = res._getIndices()
    352 if not fastin(res, residues):

ValueError: not enough data to get a single residue for all atoms

[karolamik13]

Old code:
In [1]: from prody import *

In [2]: fex = parsePDB('comp_min.pdb')
@> 136109 atoms and 1 coordinate set(s) were parsed in 2.23s.

In [3]: fex_bb = fex.select('protein name CA C N O or resname CY1 name CA C N O')

In [4]: fex_ca = fex.select('protein name CA or resname CY1 name CA')

In [5]: y = extendAtoms(fex_ca, fex_bb)

ValueError Traceback (most recent call last)
in
----> 1 y = extendAtoms(fex_ca, fex_bb)

~/anaconda3/lib/python3.9/site-packages/ProDy-2.5.0-py3.9-linux-x86_64.egg/prody/atomic/functions.py in extendAtoms(nodes, atoms, is3d)
347 raise ValueError('atoms must contain a residue for all atoms')
348 if isinstance(res, list):
--> 349 raise ValueError('not enough data to get a single residue for all atoms')
350
351 res_atom_indices = res._getIndices()

ValueError: not enough data to get a single residue for all atoms

New code:
In [1]: from prody import *

In [2]: x = parsePDB('comp_min.pdb')
@> 136109 atoms and 1 coordinate set(s) were parsed in 2.24s.

In [3]: x_bb = x.select('protein name CA C N O or resname CY1 name CA C N O')

In [4]: x_ca = x.select('protein name CA or resname CY1 name CA')

In [5]: y = extendAtoms(x_ca, x_bb)

In [6]: y
Out[7]:
(array([ 0, 0, 0, ..., 680, 680, 680]),
<AtomMap: comp_min from comp_min (2724 atoms)>)