Ecosyste.ms: Awesome

An open API service indexing awesome lists of open source software.

Awesome Lists | Featured Topics | Projects

https://github.com/prheenan/mol_from_text

Turn text into molecular images!
https://github.com/prheenan/mol_from_text

chemistry fun molecule python rdkit

Last synced: 24 days ago
JSON representation

Turn text into molecular images!

Awesome Lists containing this project

README 

        
# Motivation

!['4fun' text with letters as molecular structures](Docs/4fun.gif)



We all love rdkit, but hasn't it always been missing a 'MolFromText' function to turn text into structures?



Wouldn't that be cool? Anybody think so? Bueller? No?



Well, here is one anyway!



# Nuts and bolts



`mol_from_text` is a python module which enables representing text as molecules and includes:



- optional fun colors

- optional (even more) fun animations

- compatability with ASCII codes 32-126 (uppercase only; lowercase TBD)



Below are the supported characters and their representation:



    ~|}{`_^][\@?=><;:/.-,+*)('"'"'&%$#"!9876543210ZYXWVUTSRQPONMLKJIHGFEDCBA



![listing of all available characters](Docs/all_chars.svg)



# Installation



    git clone https://github.com/prheenan/mol_from_text.git

    cd mol_from_text

    conda env create --force --yes -f env.yaml

    conda activate mol_ransom



# Testing



    conda activate mol_ransom

    python test.py



# Usage



## Making images



Images can be created as follows:



`python mol_from_text.py image  --string 'helloworld'`



This yields the image below as `helloworld.svg`:



![hello world image with letters as molecular structures](Docs/helloworld.svg)



There are many options for modifying the image as given below:



    Usage: mol_from_text.py image [OPTIONS]



    Options:

      --string TEXT                   What string to convert to molecules

                                      [required]

      --output_file PATH              Name of output file (only png and svg

                                      supported)

      --black_and_white Choice([TRUE/True/FALSE/False])

                                      If true, use black and white instead of

                                      colors

      --comic_mode Choice([TRUE/True/FALSE/False])

                                      If true, use comic-drawing mode (xkcd style)

      --letters_per_row INTEGER       How many letters per row (i.e., line

                                      character limit)

      --one_word_per_line Choice([TRUE/True/FALSE/False])

                                      If true, have one word per row/line

                                      (equivalent to setting  to

                                      the longest word length)

      --dots_per_angstrom FLOAT       See rdkit.Draw.MolDrawOptions

      --font_size INTEGER             See rdkit.Draw.MolDrawOptions

      --bond_width FLOAT              See rdkit.Draw.MolDrawOptions

      --scale FLOAT                   See rdkit.Draw.MolDrawOptions

      --letter_size_pixels INTEGER    Individual size of letters

      --help                          Show this message and exit.



## Making animations



Images can be created as follows:



`python mol_from_text.py animate  --string 'helloworld'`



This yields the image below as `helloworld.gif`:



![animated hello world image with letters as molecular structures](Docs/helloworld.gif)



There are many animations options as follows:



    Usage: mol_from_text.py animate [OPTIONS]



    Options:

      --output_file PATH              Name of output file (only gif supported)

      --string TEXT                   What string to convert to molecules

                                      [required]

      --black_and_white Choice([TRUE/True/FALSE/False])

                                      If true, use black and white instead of

                                      colors

      --comic_mode Choice([TRUE/True/FALSE/False])

                                      If true, use comic-drawing mode (xkcd style)

      --letters_per_row INTEGER       How many letters per row (i.e., line

                                      character limit)

      --one_word_per_line Choice([TRUE/True/FALSE/False])

                                      If true, have one word per row/line

                                      (equivalent to setting  to

                                      the longest word length)

      --loop_forever Choice([TRUE/True/FALSE/False])

                                      If true, loop for forever, otherwise just

                                      will run once

      --and_reverse Choice([TRUE/True/FALSE/False])

                                      If true, animation will run in forward

                                      direction then in the reverse direction

      --total_time_s FLOAT            How long for total animation

      --rotation_degrees FLOAT        Total rotation in degrees

      --frames_per_second FLOAT       How many frames per second

      --start_degrees FLOAT           Where to start animation (0 = 12 o clock,

                                      -90 would be 9 o clock, +90 would be 3 o

                                      clock, etc)

      --dots_per_angstrom FLOAT       See rdkit.Draw.MolDrawOptions

      --font_size INTEGER             See rdkit.Draw.MolDrawOptions

      --bond_width FLOAT              See rdkit.Draw.MolDrawOptions

      --scale FLOAT                   See rdkit.Draw.MolDrawOptions

      --letter_size_pixels INTEGER    Individual size of letters

      --help                          Show this message and exit.



##  Getting a molfile



If you just want a molfile of all the letters and their structures, that is easy enough:



`python mol_from_text.py export-structures --output_file "mols.sdf"`



This will export an SDF which as a `ascii_character` property for each molecule containing its text



## Future directions



- Support for lowercase? (ASCII 97-122)

- Incorporate [NanoPutian](https://en.wikipedia.org/wiki/NanoPutian)?

- Randomly change atoms during animations