Metadata-Version: 2.1
Name: faerun
Version: 0.1.9
Summary: A python package for generating interactive views of chemical spaces.
Home-page: https://github.com/reymond-group/faerun-python
Author: Daniel Probst
License: UNKNOWN
Description: # Faerun (Python)
        Faerun (Python) is based on the [Lore.js](https://github.com/reymond-group/lore) 3D WebGL engine for interactive big data rendering and the [FUn](http://doc.gdb.tools/fun/) project. It facilitates the creation of interactive (2D and 3D) HTML plots of chemical data (or chemical spaces). Molecular structures are rendered using [SmilesDrawer](https://github.com/reymond-group/smilesDrawer).
         
        **Associated Publication**: https://academic.oup.com/bioinformatics/article/34/8/1433/4657075
        
        <img alt="Faerun Python" src="http://doc.gdb.tools/faerun-python/intro.png"></img>
        
        ## Installation
        ```Bash
        pip install faerun
        ```
        
        ## Examples
        - **[Drugbank 3D](http://doc.gdb.tools/faerun-python/example3d)**
        - **[Drugbank 2D](http://doc.gdb.tools/faerun-python/example2d)**
        
        The code of the examples shown above for creating interactive 2D and 3D maps from Drugbank can be found in the examples directory. Following, a simple [example](http://doc.gdb.tools/faerun-python/example) of plotting any data:
        ```Python
        import numpy as np
        from faerun import Faerun
        
        faerun = Faerun(view='free', shader='circle')
        
        t = np.linspace(0, 12.0, 326)
        s = np.sin(np.pi * t)
        c = np.cos(np.pi * t)
         
        faerun.plot({ 'x': t, 'y': s, 'z': c, 'c': t / max(t) })
        ```
        
        The code above writes two files to the current directory: `index.html` and `data.js`. These files can be used locally or be moved to a (even minimalistic) web server.
        
        ## TODO
        - [ ] Add the abilty to draw shapes as well as colours
        - [ ] Make output templatable
        
        ## Documentation
        ```Python
        Faerun(title='python-faerun', point_size=5, tree_color='#aaaaaa', clear_color='#111111', fog_intensity=2.6, coords=True, coords_color='#888888', view='free', shader='circle')
        ```
        | Parameter | Default | Description |
        |---|---|---|
        | title | `'python-faerun'` | The title of the HTML document. |
        | point_size | `5` | The size of the points. |
        | tree_color | `'#aaaaaa'` | Not yet implemented. |
        | clear_color | `'#111111'` | The clear colour,  or background colour is used to clear the canvas after each rendering step. |
        | fog_intensity | `2.6` | Fog is used to darken / lighten far away points depending on the `clear_color`. This is a visual cue helpful for depth perception in orthogonal projections. |
        | coords | `True` | Whether or not to draw the coordinate axes. |
        | coords_color | `'#888888'` | The colour used to draw the coordinate axes. |
        | view | `'free'` | The view mode. Available options: `free`, `front`, `back`, `left`, `right`, `bottom`, `top` |
        | shader | `circle` | The name of the shader used to draw the points. Available options: `circle`, `legacyCircle`, `sphere` |
        
        ```Python
        Faerun.plot(path, data, x='x', y='y', z='z', c='c', colormap='plasma', smiles='smiles', tree=None)
        ```
        | Parameter | Default | Description |
        |---|---|---|
        | data | | A `dict` or a Pandas `DataFrame` containing the data. |
        | x | `x` | The name of the column containing the x-coordinates. |
        | x | `y` | The name of the column containing the y-coordinates. |
        | x | `z` | The name of the column containing the z-coordinates. |
        | c | `c` | The name of the column containing the values by which the points are coloured. **Has to be normalized between 0.0 and 1.0** |
        | colormap | `'plasma'` | The colour map to be used. Valid values are [matplotlib colormap names](https://matplotlib.org/examples/color/colormaps_reference.html). |
        | smiles | `smiles` | The name of the column containing the SMILES strings with which the points are annotated. |
        | path | `''` | The path to which the HTML and data files will be written. |
        | tree | `None` | Not yet implemented. |
        
Platform: UNKNOWN
Description-Content-Type: text/markdown
Provides-Extra: dev
