chemlab/chemlab

The chemistry library you were waiting for

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

https://www.dropbox.com/s/szbu5w3q0wzmph0/Chimera%20%2B%20Chemview.ipynb?dl=0

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.

conda.env

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?

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