The Interactive Sketchmap Visualizer is no longer developed. We invite you to try its successor,
chemiscope. You can see it deployed as a web ap at chemiscope.org or
try it as a jupyter widget with pip install chemiscope.
The source code is available in a dedicated github repo.
The code to generate Interactive Sketchmap visualizer using bokeh.
To see an demo version try : https://interactive.sketchmap.org/
To know about sketchmap go to http://sketchmap.org/
git clone https://github.com/sandipde/Interactive-Sketchmap-Visualizer.git
cd Interactive Sketchmap Visualizer/example
sudo pip install jinja2 pyyaml argparse tornado==4.5.3 numpy bokeh==0.12.14 pandas selenium pillow ase
python ../build.py --data Arginine-Dipeptide.dat Qm7b.dat Pyrole.dat --traj traj-Arginine-Dipeptide.xyz traj-qm7b.xyz traj-Pyrole.xyz
bokeh serve Arginine-Dipeptide Qm7b Pyrole --show
Independent apps are portable and contain all resources in one folder. SO if you just need to make one or two apps this is the option you want. SRCPATH= is the directory when you have cloned the repository
python SRCPATH/build.py --data mydatafile1.dat mydatafile2.dat mydatafile3.dat --traj my-trajectory-file1 my-trajectory-file-2 my-trajectory-file-3
This will set up three apps with folder name mydatafile1, mydatafile2 and mydatafile3. If you want to specify the name of the apps by yourself you can add following option to the above script.
--app MYapp1 Myapp2 Myapp3
At the end of the build it will tell you how to view the apps. To view a specific app you can run
bokeh serve myapp1 --show --args -u 1:2:3 -ps 10 --jmol "Spin ON"
It means start bokeh server to plot using the first two columns in the COLVAR file present in example-app/data/ folder. Use 3rd column as color and pointsize set to 10. You are also supplying an additional jmol option. jmol options can be as complex as you want and allows for customzing the display, eg.
bokeh serve myapp --show --args -u 1:2:4 -ps 10 -jmol "connect 1.0 1.2 (carbon) (hydrogen) SINGLE CREATE ; connect 1.0 1.2 (nitrogen) (hydrogen) SINGLE CREATE ; connect 1.0 4.2 (carbon) (nitrogen) SINGLE CREATE ; connect 3.0 6 (phosphorus) (iodine) SINGLE CREATE ; set perspectiveDepth OFF "
The problem with independent apps are that they all need their own static resources. If you have multiple apps, this means that you end of having same javascript libraries multiple times and waste the server disk space. To tell the build.py script that you intend to make a server, you just need to supply one additional flag '--extserver'
python SRCPATH/build.py --data mydatafile1.dat mydatafile2.dat mydatafile3.dat --traj my-trajectory-file1 my-trajectory-file-2 my-trajectory-file-3 --extserver
At the end of the build it will tell you how to view the apps. In this case you will run the server with
python server.py --app myapp1 myapp2 myapp3
To get additional options run
python server.py -h
Datafile format containing the sketchmap and property data
ColumnName_1 CoulumnName_2 ... ... ...
data11 data12 ... ... ...
: :
: :
: :
We support both neumerical and Categorical data. See example/Pyrole.dat for example. The trajectory files are read through ase interface. All the formats supported by ase are naturally supported from now on. Get the full list of supported input from https://wiki.fysik.dtu.dk/ase/ase/io/io.html you can also add userdefined jmol settings by adding -jmol "jmol settings" eg.
bokeh serve MAPbI --show --args -u 1:2:4 -ps 10 -jmol "connect 1.0 1.2 (carbon) (hydrogen) SINGLE CREATE ; connect 1.0 1.2 (nitrogen) (hydrogen) SINGLE CREATE ; connect 1.0 4.2 (carbon) (nitrogen) SINGLE CREATE ; connect 3.0 6 (phosphorus) (iodine) SINGLE CREATE ; set perspectiveDepth OFF "
The data file coloumn names should not contain wild characters.
For safety only use "_" as separator eg . atomic_energy
Work with both Python 2.7 and 3.3
Building dependency
argparse
pyyaml
tornado==4.5.3
numpy
bokeh==0.12.14
pandas
jinja2
selenium
pillow
ase
Runtime Dependency
argparse
tornado==4.5.3
numpy
bokeh==0.12.14
pandas
jinja2