Metadata-Version: 2.1
Name: PESViewer
Version: 1.1
Summary: Depiction of Potential Energy Surfaces.
Home-page: https://github.com/rubenvdvijver/PESViewer.git
Author: Ruben Van de Vijver
Author-email: vandevijver.ruben@gmail.com
License: MIT
Description: # PESViewer
        Visualize a potential energy surface
        
        ## Developer: Ruben Van de Vijver, Laboratory for Chemical Technology, Ghent University
        
        The PESViewer is a code to depict and analyze a potential energy surface 
        characterized by wells, bimolecular products, transition states and barrierless reactions.
        Their energy is needed to plot the potential energy surface. 
        Written values of the energies and 2D plots (structural formulas) of the wells and products can be added to the figure 
        
        To run this code, you need python version 2.7, matplotlib, numpy and optionally OpenBabel or RDKit to create 2D plots
        
        ## INSTALL
        
        Clone the project onto your machine and go to the PESViewer directory. Type:
        
            python setup.py build
            python setup.py install 
        
        ## INPUT
        
        A text file containing the stationary points, energies, names identifiers and options, see the input.txt as example.
        
        For wells, write each well on a separate line as follows (smiles are optional to depict the molecule, if no xyz's are available):
        
            name energy smiles
        
        For bimolecular products (again smiles are optional):
        
            name energy smiles
        
        For reactions (colors are optional, and if available the line of the reaction will be given that color):
        
            name energy reactant product color
        
        For bimolecular products (again colors are optional)
        
            name reactant product color
        
        
        The plotting options (to be written in the input file) are:
        
        
        | option | default | Description |
        | ------- | ------- | ------- |
        | title | 0 | print a title (1) or not (0) |
        | units | kcal/mol | energy units |
        | use_xyz | 1 |use xyz, put 0  to switch off |
        | rescale | 0 | no rescale , put the well or bimolecular name here to rescale to that value |
        | fh | 9. | figure height |
        | fw | 18. | figure width |
        | margin | 0.2 | margin fraction on the x and y axis |
        | dpi | 120 | dpi of the molecule figures |
        | save | 0 | does the plot need to be saved (1) or displayed (0) |
        | write_ts_values | 1 | booleans tell if the ts energy values should be written |
        | write_well_values | 1 | booleans tell if the well and bimolecular energy values should be written |
        | bimol_color | red | color of the energy values for the bimolecular products |
        | well_color | blue | color of the energy values of the wells |
        | ts_color | green | color or the energy values of the ts, put to 'none' to use same color as line |
        | show_images | 1 | boolean tells whether the molecule images should be shown on the graph |
        | rdkit4depict | 1 | boolean that specifies which code to use for the 2D depiction |
        | axes_size | 10 | font size of the axes |
        | text_size | 10 | font size of the energy values on the graph |
        
        Optionally a folder xyz/ containing the xyz coordinates of the stationary points ($name.xyz)
        (for bimolecular products, use several xyz coordinates files ($name$index.xyz) )
        
        
        ## RUN
        
        With the input file input.inp, type:
        
            pesviewer input.inp
        
        ## OUTPUT
        
        The output is a modifiable matplotlib figure.
        
        2 modifications are possible
        - modifing the x-position of a stationary point by a 'drag and drop' of the energy value
        - modifing the position of 2D structure images by a 'drag and drop' of the image
        
        
Platform: UNKNOWN
Description-Content-Type: text/markdown
