Fix AttributeError in calcHydrophobic from nested select() call

[Copilot]

calcHydrophobic() crashes with AttributeError: Selection object has no attribute 'strip' when a Selection object is passed to .select() instead of a string.

Root Cause

Line 1508 contains a nested .select() call that passes a Selection object as an argument:

sele2_filter = sele2_filter.select(sele2.select('all and not (resid '+str(i[0])+' and chain '+i[1]+')'))

The inner sele2.select() returns a Selection object, but .select() expects a string argument.

Changes

• Remove redundant inner .select() call on line 1508 to pass the string directly, matching the pattern on line 1505:

sele2_filter = sele2_filter.select('all and not (resid '+str(i[0])+' and chain '+i[1]+')')

• Add *.npy to .gitignore to prevent test artifacts from being committed

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Original prompt

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This section details on the original issue you should resolve

<issue_title>AttributeError: Selection object has no attribute strip and 'strip' is not a valid selection string</issue_title>
<issue_description>

Description of the bug.

When I tried to calculate the protein interaction for the pdb file 4i77 in the following way, I encountered the following error: "AttributeError: Selection object has no attribute strip and 'strip' is not a valid selection string."

After checking the logs, I found that there seems to be a duplicate select operation, and the select method is expected to receive a string type. I suspect this might be an accidental coding mistake, and removing the redundant select step allows the process to complete normally. Since this is my first time using ProDy, I am not very sure if this modification is correct.

ProDy/prody/proteins/interactions.py

Line 1508 in 79c6641

sele2_filter = sele2_filter.select(sele2.select('all and not (resid '+str(i[0])+' and chain '+i[1]+')'))

Do you have any error messages or logs?

@> Number of detected cation-pi interactions: 5.
@> Please provide hpb.so file to obtain additional data.
@> Calculating hydrophobic interactions.
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
Cell In[9], line 1
----> 1 result = ia.calcProteinInteractions(atoms.select('protein'))

File ~/Documents/project/protools/.venv/lib/python3.10/site-packages/prody/proteins/interactions.py:4299, in Interactions.calcProteinInteractions(self, atoms, **kwargs)
   4297 Pi_stacking = calcPiStacking(atoms.protein, **kwargs)                       prody/ProDy#4
   4298 Pi_cation = calcPiCation(atoms.protein, **kwargs)                           prody/ProDy#5
-> 4299 Hydroph_calculations = calcHydrophobic(atoms.protein, **kwargs)             prody/ProDy#6
   4300 Disulfide_Bonds = calcDisulfideBonds(atoms.protein, **kwargs)               prody/ProDy#7
   4301 AllInteractions = [HBs_calculations, SBs_calculations, SameChargeResidues, Pi_stacking, 
   4302                     Pi_cation, Hydroph_calculations, Disulfide_Bonds]   

File ~/Documents/project/protools/.venv/lib/python3.10/site-packages/prody/proteins/interactions.py:1508, in calcHydrophobic(atoms, **kwargs)
   1505     sele2_filter = sele2_filter.select('all and not (resname TYR PHE TRP or resid '+str(i[0])+' and chain '+i[1]+')')
   1506 elif sele1_name[0] not in aromatic and i in sele2_nr:
   1507     # don't include same residue interactions but don't worry about double counting pi stacking
-> 1508     sele2_filter = sele2_filter.select('all and not (resid '+str(i[0])+' and chain '+i[1]+')')
   1510 if sele2_filter != None:
   1511     listOfAtomToCompare = cleanNumbers(findNeighbors(sele1, distA, sele2_filter))

File ~/Documents/project/protools/.venv/lib/python3.10/site-packages/prody/atomic/atomic.py:244, in Atomic.select(self, selstr, **kwargs)
    240 def select(self, selstr, **kwargs):
    241     """Returns atoms matching *selstr* criteria.  See :mod:`~.select` module
    242     documentation for details and usage examples."""
--> 244     return SELECT.select(self, selstr, **kwargs)

File ~/Documents/project/protools/.venv/lib/python3.10/site-packages/prody/atomic/select.py:895, in Select.select(self, atoms, selstr, **kwargs)
    892 self._replace = False
    894 self._selstr = selstr
--> 895 indices = self.getIndices(atoms, selstr, **kwargs)
    897 self._kwargs = None
    899 if len(indices) == 0:

File ~/Documents/project/protools/.venv/lib/python3.10/site-packages/prody/atomic/select.py:937, in Select.getIndices(self, atoms, selstr, **kwargs)
    931 def getIndices(self, atoms, selstr, **kwargs):
    932     """Returns indices of atoms matching *selstr*.  Indices correspond to
    933     the order in *atoms* argument.  If *atoms* is a subset of atoms, they
    934     should not be used for indexing the corresponding :class:`.AtomGroup`
    935     instance."""
--> 937     ss = selstr.strip()
    938     if (len(ss.split()) == 1 and ss.isalnum() and ss not in MACROS):
    939         self._evalAtoms(atoms)

File ~/Documents/project/protools/.venv/lib/python3.10/site-packages/prody/atomic/atomic.py:136, in Atomic.__getattribute__(self, name)
    133                 selstr = ' '.join(items)
    134                 return SELECT.select(self, selstr)
--> 136 raise AttributeError('{0} object has no attribute `{1}` and {2} '
    137                      'is not a valid selection string'
    138                      .format(self.__class__.__name__, name,
    139                              repr(selstr)))

AttributeError: Selection object has no attribute `strip` and 'strip' is not a valid selection string

What is your setup?

First test at My MacBook

• MacOS 15.7.1
• python: 3.10.17

Then test at My Ubuntu Server

• Ubuntu 22.04 LTS
• python: 3.10.16

How did you install ProDy?

Installed by uv add prody with version 2.6.1.

What ...

• Fixes AttributeError: Selection object has no attribute strip and 'strip' is not a valid selection string #2188

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