Build example on the HTMD website doesn't work

mj-harvey commented 7 years ago

from htmd import *
m = Molecule('2HBA')
m.filter('(protein and chain A) or waters within 5 of (protein and chain A)')
pm = proteinPrepare(m)      # protonation, side chain optimization
pm = autoSegment(pm)        # set protein segments
pmsol = solvate(pm, pad=12) # solvate
bm = charmm.build(pmsol, outdir='./build', saltconc=0.15) # build topology


$ python --version
Python 3.5.2 :: Continuum Analytics, Inc.
-bash-4.2$ python3 build.py 

Please cite -- HTMD: High-Throughput Molecular Dynamics for Molecular Discovery
J. Chem. Theory Comput., 2016, 12 (4), pp 1845-1852. 
http://pubs.acs.org/doi/abs/10.1021/acs.jctc.6b00049

You are on the latest HTMD version (1.5.4).

2016-12-14 17:41:17,676 - htmd.molecule.molecule - INFO - Attempting PDB query for 2HBA
2016-12-14 17:41:18,334 - htmd.molecule.molecule - INFO - Removed 468 atoms. 462 atoms remaining in the molecule.
2016-12-14 17:41:18,383 - propka - INFO - No pdbfile provided
Traceback (most recent call last):
  File "build.py", line 5, in <module>
    pm = proteinPrepare(m)      # protonation, side chain optimization
  File "/home/mjharvey/miniconda3/lib/python3.5/site-packages/htmd/builder/preparation.py", line 268, in proteinPrepare
    holdList=hlist)
ValueError: too many values to unpack (expected 4)
´´´

1) What is wrong?

2) Why isn't this one of the CI tests?

j3mdamas commented 7 years ago

the problem is with proteinPrepare. Toni is making lots of changes. @tonigi, I updated htmd-pdb2pqr and it's still giving the same error as it's giving to Matt

In [5]: pm = proteinPrepare(m)
---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-5-c6f13288c56a> in <module>()
----> 1 pm = proteinPrepare(m)

/home/joao/miniconda3/lib/python3.5/site-packages/htmd/builder/preparation.py in proteinPrepare(mol_in, pH, verbose, returnDetails, hydrophobicThickness, holdSelection)
    266                                                              ph_calc_method="propka31",
    267                                                              ph_calc_options=propka_opts,
--> 268                                                              holdList=hlist)
    269     tmpin.close()
    270 

ValueError: too many values to unpack (expected 4)

mj-harvey commented 7 years ago

Any example that appears on the web page must also be a travis test so, at the very least!, we have warning to keep them up to date. This is with a release, not the HEAD, so it shouldn't happen. Right now HTMD's going to fail any new user at the first hurdle. Accordingly, I¡m marking this as high.

j3mdamas commented 7 years ago

Update htmd to 1.5.5. It works there.

mj-harvey commented 7 years ago

Ok, seems conda had lost my channels settings, so it was lying when it claimed it had the latest release.

Nevertheless, it should not have been possible to make 1.5.4 release. The CI should have caught this.

j3mdamas commented 7 years ago

1.5.4 is not compatible with the latest htmd-pdb2pqr

tonigi commented 7 years ago

It is an unfortunate version dependency, sorry, but I needed to change the internal API for the "repreparation" (change protonation) function.

Il 14 dic 2016 6:54 PM, "João M. Damas" notifications@github.com ha scritto:

Closed #207 https://github.com/Acellera/htmd/issues/207.

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub https://github.com/Acellera/htmd/issues/207#event-894030622, or mute the thread https://github.com/notifications/unsubscribe-auth/ACn-Cx1ivc6Q6SdMfswqtDMbcMQDtJ6sks5rIC0_gaJpZM4LNNWB .

Acellera / htmd

Build example on the HTMD website doesn't work #207