InSty: NameError: name 'Interactions' is not defined

[TangYiChing]

Which module is this Interactions class dependent on?

interactions = Interactions()
http://www.bahargroup.org/prody/tutorials/insty_tutorial/insty_tutorial.pdf

[karolamik13]

Did you install the developed version of ProDy (from GitHub: https://github.com/prody/ProDy)?
If not, you may not have this module, and that is why you have this error. InSty module works independently (it needs only ProDy).

On the GitHub version, everything is working:
Python 3.9.15 (main, Nov 24 2022, 14:31:59)
Type 'copyright', 'credits' or 'license' for more information
IPython 8.7.0 -- An enhanced Interactive Python. Type '?' for help.

In [1]: from prody import *
In [2]: PDBfile = '5kqm_all_sci.pdb'
In [3]: coords = parsePDB(PDBfile)
@> 19321 atoms and 1 coordinate set(s) were parsed in 0.17s.
In [4]: atoms = coords.select('protein')
In [5]: interactions = Interactions()
In [6]: all_interactions = interactions.calcProteinInteractions(atoms)
@> Calculating interations.
@> Calculating hydrogen bonds.
@> DONOR (res chid atom) <---> ACCEPTOR (res chid atom) Distance Angle
@> ARG101 P NH1_1516 <---> ASP98 P OD1_1463 2.0 33.1
@> HIS72 P NE2_1042 <---> ASN15 P OD1_165 2.6 34.8
@> GLN143 P NE2_2192 <---> GLU139 P OE2_2126 2.7 9.2
@> HIS66 P NE2_957 <---> GLU139 P OE1_2125 2.7 6.4
@> ARG40 P N_561 <---> LYS6 P O_37 2.7 17.1
@> ARG58 P N_813 <---> ASP56 P OD1_788 2.7 30.0
@> ALA45 P N_634 <---> ARG75 P O_1097 2.8 35.1
@> ASN53 P ND2_747 <---> GLU50 P OE1_708 2.8 18.2
@> ALA74 P N_1064 <---> ASN53 P O_751 2.8 21.3
@> ASP56 P N_780 <---> ILE16 P O_189 2.8 27.0
@> LYS110 P NZ_1667 <---> THR84 P O_1240 2.8 38.2
@> LEU116 P N_1758 <---> CYS90 P O_1342 2.8 15.0
@> SER103 P N_1546 <---> LEU99 P O_1485 2.8 29.1
@> ASN134 P N_2045 <---> ASP137 P OD2_2091 2.8 22.6
...

[jamesmkrieger]

Yes and in the released versions it is not. We have the same issue in #1924

[karolamik13]

In case someone does not know what to do:
(1) Go to Github: https://github.com/prody/ProDy and download this version of ProDy. You can do it via git or just using download.
(2) cd ProDy (unpack if needed)
(3) Use the following commands:

python setup.py build
python setup.py install

Done. Enjoy using InSty and WatFinder.

[TangYiChing]

Thank you. Re-install the developed version works for me.
However, I encountered some issue with the use case "addHydrogen":

from prody import *
from pylab import *
import matplotlib
ion()

fetchPDB('5kqm', compressed=False)
PDBname = '5kqm.pdb'
addMissingAtoms(PDBname, method='pdbfixer')
atoms = parsePDB('addH_'+str(PDBname)).select('protein')
interactions = Interactions('addH_5qkm')
all_interactions = interactions.calcProteinInteractions(atoms)

@> PDB file is found in working directory (5kqm.pdb).
@> Hydrogens were added to the structure. New structure is saved as addH_5kqm.pdb.
@> 2800 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> Calculating interations.
AttributeError Traceback (most recent call last)
Cell In[30], line 1
----> 1 all_interactions = interactions.calcProteinInteractions(atoms)

File /tools/ProDy/prody/proteins/interactions.py:2731, in Interactions.calcProteinInteractions(self, atoms, **kwargs)
2727 raise TypeError('coords must be an object '
2728 'with getCoords method')
2730 LOGGER.info('Calculating interations.')
-> 2731 HBs_calculations = calcHydrogenBonds(atoms.protein, **kwargs) #1 in scoring
2732 SBs_calculations = calcSaltBridges(atoms.protein, **kwargs) #2
2733 SameChargeResidues = calcRepulsiveIonicBonding(atoms.protein, **kwargs) #3

File /tools/ProDy/prody/proteins/interactions.py:434, in calcHydrogenBonds(atoms, **kwargs)
431 if atoms.hydrogen == None or atoms.hydrogen.numAtoms() < 10:
432 LOGGER.info("Provide structure with hydrogens or install Openbabel to add missing hydrogens using addMissingAtoms(pdb_name) first.")
--> 434 contacts = findNeighbors(atoms.heavy, distA)
435 short_contacts = cleanNumbers(contacts)
436 pairList = [] # list with Donor-Hydrogen-Acceptor(indices)-distance-Angle

File /tools/ProDy/prody/measure/contacts.py:306, in findNeighbors(atoms, radius, atoms2, unitcell, seqsep)
302 def findNeighbors(atoms, radius, atoms2=None, unitcell=None, seqsep=None):
303 """Returns list of neighbors that are within radius of each other and the
304 distance between them. See :func:iterNeighbors for more details."""
--> 306 return list(iterNeighbors(atoms, radius, atoms2, unitcell, seqsep))

File /tools/ProDy/prody/measure/contacts.py:217, in iterNeighbors(atoms, radius, atoms2, unitcell, seqsep)
215 yield (i, j, r)
216 else:
--> 217 for (i, j), r in zip(*kdtree(radius)):
218 a1 = _dict.get(i)
219 if a1 is None:

File /tools/ProDy/prody/kdtree/kdtree.py:179, in KDTree.call(self, radius, center)
177 self.search(radius, center)
178 if self._oncall == 'both':
--> 179 return self.getIndices(), self.getDistances()
180 elif self._oncall == 'dist':
181 return self.getDistances()

File /tools/ProDy/prody/kdtree/kdtree.py:259, in KDTree.getIndices(self)
255 def getIndices(self):
256 """Returns array of indices for points or pairs, depending on the type
257 of the most recent search."""
--> 259 if self.getCount():
260 if self._unitcell is None:
261 if self._neighbors is None:

File /tools/ProDy/prody/kdtree/kdtree.py:291, in KDTree.getCount(self)
289 return self._kdtree.get_count()
290 else:
--> 291 return self._kdtree.neighbor_get_count()
292 else:
293 return len(self._pbcdict)

AttributeError: 'C KDTree' object has no attribute 'neighbor_get_count'

[karolamik13]

That's interesting.
That is what I am receiving with this code (see below).
Hydrogens are added and atoms are parsed successfully. For some reason, interactions failed.
@jamesmkrieger any idea?

In [1]: from prody import *
...: from pylab import *
...: import matplotlib
...: ion()
...:
...: fetchPDB('5kqm', compressed=False)
...: PDBname = '5kqm.pdb'
...: addMissingAtoms(PDBname, method='pdbfixer')
...: atoms = parsePDB('addH_'+str(PDBname)).select('protein')
...: interactions = Interactions('addH_5qkm')
...: all_interactions = interactions.calcProteinInteractions(atoms)

@> Connecting wwPDB FTP server RCSB PDB (USA).
@> 5kqm downloaded (5kqm.pdb)
@> PDB download via FTP completed (1 downloaded, 0 failed).
@> Hydrogens were added to the structure. New structure is saved as addH_5kqm.pdb.
@> 2800 atoms and 1 coordinate set(s) were parsed in 0.03s.
@> Calculating interations.
@> Calculating hydrogen bonds.
@> DONOR (res chid atom) <---> ACCEPTOR (res chid atom) Distance Angle
@> ASN130 A N_2045 <---> ASP133 A OD2_2093 2.8 39.9
@> ARG23 A N_340 <---> GLU19 A O_284 2.8 36.9
@> ARG93 A N_1431 <---> GLU89 A O_1377 2.9 39.8
@> LYS60 A N_900 <---> GLN56 A O_849 2.9 12.8
@> ASN96 A N_1486 <---> LEU92 A O_1417 2.9 23.4
@> GLU150 A N_2360 <---> ARG146 A O_2292 3.0 33.0
@> ILE31 A N_478 <---> VAL26 A O_410 3.0 28.6
@> VAL142 A N_2225 <---> TYR138 A O_2164 3.0 37.2
@> ASN49 A N_738 <---> GLU46 A O_702 3.0 28.7
@> LEU25 A N_386 <---> VAL21 A O_309 3.0 27.0
@> SER43 A N_658 <---> LEU9 A O_136 3.0 27.1
@> VAL26 A N_405 <---> PHE22 A O_325 3.0 22.4
@> GLN101 A N_1571 <---> LYS98 A O_1529 3.0 38.6
@> CYS58 A N_872 <---> ARG54 A O_818 3.1 24.4
...

[jamesmkrieger]

Try this

python setup.py build_ext --inplace --force
pip install -Ue .

[jamesmkrieger]

Building the C extensions should fix kdtree and using inplace and -e should make sure python can find them

[TangYiChing]

problem solved!

[jamesmkrieger]

Great. Let’s keep it open so other people see it

[jamesmkrieger]

I believe we now have better build instructions inside prody so that this works but we need to double check

[jamesmkrieger]

This should now be solved and released