cheminformatics

In the folder, process_smiles https://github.com/KarimElgammal/cheminformatics/tree/main/process_smiles, you can find a notebook for generating xyz files from smiles and fetch some experimental properties using 3 libraries

Please feel free to recommend other tools or corrections to this code!

Generate xyz files from smiles and fetch some experimental properties

In the notebook: "process_smiles" [process smiles] (https://github.com/KarimElgammal/cheminformatics/blob/main/process_smiles/smiles2xyz.ipynb) , I wrote simple code with different functionalities to convert a list of smiles stored in an excel sheet to xyz while storing multiple related details in the 2nd line of each of the xyz files The scheme of the 2nd line works as follow:

molecule name
molecular formula
molecular weight (g/mol)
experimental boiling point (degC)
experimental melting point (degC)

Used dependicies:

Here, I used the awesome Leruli tool and rdkit
for more about Leruli, please check https://www.leruli.com/ installable using: pip install leruli
for more about rdkit, please check https://www.rdkit.org/ installable using: pip install rdkit for more about plams, please check https://www.scm.com/doc/plams/index.html installable using: pip install plams

ofcourse, those functionalities are implemented in so many libraries, I just find those tools handy

What I like in Leruli is that it gives so many useful information in a efficient way and free of charge

example:

Aspirin.xyz
14
Aspirin C1COCCO1 88.05 101.605 -16.565
C -0.731 1.16 0.225
C 0.732 1.16 -0.225
O 1.393 -0.0 0.236
C 0.732 -1.16 -0.223
C -0.733 -1.16 0.223
O -1.393 0.001 -0.235
H -0.774 1.202 1.324
H -1.268 2.011 -0.196
H 0.775 1.201 -1.324
H 1.27 2.01 0.196
H 1.268 -2.01 0.2
H 0.777 -1.205 -1.322
H -1.27 -2.009 -0.201
H -0.778 -1.204 1.322

Please feel free to recommend other tools or corrections to this code!

Generate smiles list from a given xyz files

A code inspired from the kaggle challenge solution (https://www.kaggle.com/code/roccomeli/easy-xyz-to-smiles-conversion/notebook by Rocco Meli) that can convert xyz to smiles in case you need such format in your calculations

###Used dependicies:

Here, I used openbabel tool (http://openbabel.org/wiki/Main_Page) which can be installed by "conda install openbabel -c openbabel -y"
I tried mybest to install it using pip but failed, maybe you should compile it locally or so
if openbabel installation is not easy to install in your environment, you can use docker
For successfully doing this notebook (and sometimes other for other libraries) I used docker to pull a conda image

I pulled an x86 image to avoid any further workarounds for the moment (https://hub.docker.com/r/continuumio/miniconda3): docker pull continuumio/miniconda3
run the docker image through: docker run --name cheminformatics -it -p 127.0.0.1:80:8080 -v ./cheminformatics_host_folder:/codes -w /codes continuumio/miniconda3:latest

ofcourse, for this simple example: you don't need port forwarding or sharing the volume by -v flag which is not as fast as using docker volumes -vol but I just needed that to share some folder I have already plus I am not so familiar yet with docker volumes at the time of writing this! note: I just add port forwarding as I may need it for other tools that I may use using the same container

Please let me know if you have other implementations or tools!

KarimElgammal / cheminformatics