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Gabriele Lanaro
@gabrielelanaro
thanks I was about to ask
Jaime Rodríguez-Guerra
@jaimergp
currently, it simply exposes the underneath Python implementation
but at least you can do "import chimera" now
without that, you are restricted to their own inhouse IDLE
and installing packages is a nightmare
Gabriele Lanaro
@gabrielelanaro
that's a pretty good idea to make it accessible from standard python
Jaime Rodríguez-Guerra
@jaimergp
i desperately needed that for my own research
Gabriele Lanaro
@gabrielelanaro
yes I think it's totally worth it
Jaime Rodríguez-Guerra
@jaimergp
debugging sessions were awful and any little snippet would require to launch the full GUI
I was about to drop it entirely but somehow this idea came to mind
and I'm proud to say it's working really nice
it just proves that Chimera is Python after all
it plays nice with chemview to, if you export the molecules to the topology dict and so on
i have a notebook somewhere, let me find it
there you go
the only caveat with pychimera is that you need to patch the environment before running the kernel
after installing it with conda
use "pychimera notebook"
Gabriele Lanaro
@gabrielelanaro
thanks I'll check it out
Jaime Rodríguez-Guerra
@jaimergp
it will look for Chimera in the usual locations and start it up
thanks to you! you are responsible for a lot of the knowledge I've gathered in the last few months about Python, numpy, openmm and so on
this may sound creepy, but I'll mention that in my thesis acknowledgments, for sure! ;)
Gabriele Lanaro
@gabrielelanaro
well I'm glad!
Gabriele Lanaro
@gabrielelanaro
@jaimergp Hi! I'm starting to wrap up a first version of the protein viewer. It would be helpful if you could give it a test before releasing to check installation problems.

Steps:

1) install chemview from git
2) install chemlab from git

3) Create a notebook with the following code (the file should be in the tests/data directory

from chemlab.io import datafile
system = datafile('../tests/data/pdb1g8p.ent', format='pdb').read('system')
system.display(kind='cartoon')
Gabriele Lanaro
@gabrielelanaro
@salotz I just realized you were also interested in the protein viewer, maybe you can check it out as well... Unfortunately I didn't have time to implement the viewer for the other backends (qt, povray)
Jaime Rodríguez-Guerra
@jaimergp
Hi @gabrielelanaro! It's working for me!
Captura de pantalla de 2016-02-19 10-22-11.png
I had to install several packages, though.
Jaime Rodríguez-Guerra
@jaimergp
conda create -n ribbons python=3 cython six numba numpy scipy matplotlib h5py jupyter notebook ipython
salotz
@salotz
Following installation in documentation it worked for python 3.5.1 in Anaconda 2.4.1. One thing is that I had to install dask, which isn't mentioned in the installation instructions.
I told my PI about the notebook and he seemed excited to use it so keep up the good work. The notebook will have it's place I'm sure.
Gabriele Lanaro
@gabrielelanaro
@jaimergp @salotz thank you very much guys! That's really helpful especially regarding those extra dependencies that crippled in
Hitesh
@hitech_twitter

Hi guys, wondering if you could help... I am trying to setup chemlab on my Mac and having some issues.

UnsatisfiableError: The following specifications were found to be in conflict:

  • chemlab -> cclib -> numpy 1.9 -> python 2.6 -> openssl 1.0.1*
  • chemlab -> chemview -> distribute
  • python 3.6*
    Use "conda info <package>" to see the dependencies for each package.
thanks in advance
Hitesh
@hitech_twitter
ok, i was able to partially progress. Here is what helped me
Step 1. Create a Python2.7 environment using conda
conda create --name chemlab python=2.7 anaconda
Step 2. Activate the Environment
source activate chemlab
Step 3. Install using conda
conda install -c http://conda.binstar.org/gabrielelanaro chemlab
which works
However, when i try to run a few examples like the following
from chemlab.graphics import QtViewer
v = QtViewer()

from chemlab.graphics.renderers import AtomRenderer
from chemlab.db  import ChemlabDB
water = ChemlabDB().get('molecule', 'example.water')
ar = v.add_renderer(AtomRenderer, water.r_array, water.type_array)
v.run()
i get errors
Traceback (most recent call last):
File "try.py", line 1, in <module>
from chemlab.graphics import QtViewer
ImportError: cannot import name QtViewer
Giovanni Abbadessa
@GiovanniAbbade_twitter
Hi I am having the seme problem. How did you solve it?