fix adp matrix

[jamesmkrieger]

Fixes this error, picked up building the website

In [1]:        from prody import *
   ...:        protein = parsePDB('1ejg')
   ...:        calphas = protein.select('calpha')
   ...:        adp_matrix = buildADPMatrix(calphas)
@> Connecting wwPDB FTP server RCSB PDB (USA).
@> 1ejg downloaded (1ejg.pdb.gz)
@> PDB download via FTP completed (1 downloaded, 0 failed).
@> 637 atoms and 1 coordinate set(s) were parsed in 0.01s.
---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
Cell In[1], line 4
      2 protein = parsePDB('1ejg')
      3 calphas = protein.select('calpha')
----> 4 adp_matrix = buildADPMatrix(calphas)

File ~/code/ProDy/prody/measure/measure.py:814, in buildADPMatrix(atoms)
    812     element[0, 2] = element[2, 0] = anisou[4]
    813     element[1, 2] = element[2, 1] = anisou[5]
--> 814     adp[i*3:i*3, i*3:i*3] = element
    815 return adp

ValueError: could not broadcast input array from shape (3,3) into shape (0,0)

[jamesmkrieger]

I guess this isn't essential as people don't use this function much as far as I'm aware, but if we can check it and merge it before the release that would be good.

[atbogetti]

@jamesmkrieger I can confirm this works. Somehow, the code giving the error runs just fine on 2.4.0 (the most recent conda release version), but not on the most recent Git version. In any case, your fix solves the issue.

What could have caused this to stop working in the first place?

[jamesmkrieger]

I don’t know, but I’m glad it works.

Maybe it’s something to do with dimensions of one of the arrays in the input or one of the intermediate steps?