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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.

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DOI

Interactive Sketchmap Visualizer

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/

Getting Started

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

Usage Scenario 1: Build independent apps

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 "

Usage Scenario 2: Build Custom app server

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

DATA FORMATS

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 "

Known Issues

The data file coloumn names should not contain wild characters. 
For safety only use "_" as separator eg . atomic_energy

Dependencies

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