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Virtual Chemical Reactor and scripts for automated quantum chemistry calculations

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# AutoChem

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Chemical Reaction Network Calculator

This program generates all the products coming from the combination of a starting pool of compounds 
 and a set of reactions. 
 The program can also download modules and pathways from KEGG database. 
 Moreover, input files for ORCA, Gaussian, CREST and xTB can be produced for further calculations of free energies.
 For this aim, bash scripts present in the scripts directory help the automation process 
 for the submission of jobs, their checking and automatic restarting in order to have optimized 
 structures with no imaginary frequencies. 
 Scripts permit to calculate the reactions deltaG and to prepare a chemical network for 
 subsequent analysis. 
 In addition, calculations can be saved and iterated, giving the possibility to mix calculations 
 on KEGG downloaded reactions and generated reactions or to make subsequent calculations with different
 reactions and/or reactants. 
 AutoChem was published on the SoftwareX Journal https://doi.org/10.1016/j.softx.2024.101851 
 
 IMPORTANT:
 The starting conditions (reactants and reactions) are defined in the plain text files starting_reactants.txt and starting_reactions.txt. 
 Anyway, a basic editor is present in the program for inserting, enabling and disabling both reagents 
 and reactions.

The program creates some supplementary files: 
 COMPOUNDS.csv: A list of the compound number, its molecular formula and MW. Energy at the RDKit level is also added if the optimization flag is enabled 
 FREQUENCY.csv: A frequency distribution of molecular weights (aka: number of compounds having the same 
 molecular weight) 
 REACTIONS.txt: A list of all reactions calculated or downloaded from KEGG (useful for the determination of reactions 
 free energies) 
 SUMMARY.txt: A file containing summary informations for the calculations made. This is an important log
 file. 
 reactions.html: A html file containing the visual representation of reactions considered and calculated. 
 smarts_reactions.txt: A text file containing all the reactions inserted by user in SMARTS format together with 
 auxiliary reagents and products
 
 ## Note
 AutoChem is divided in two programs: 
 AutoChem, written in Python, is managing the reaction generation 
 check, written in BASH, is managing the job submission with the automatic calculation of free energies 
 
# Installation
 
AutoChem: Download and install RdKit library in the proper Conda environment (follow instructions on RdKit website/anaconda installation) 
Copy the whole directory of AutoChem in your PC. 
Launch Autochem.py from your favourite IDE (we suggest Spyder) 
 
 
check: 
You should have awk, bc available on your Linux environment together with a task spooler like tsp or slurm 
If you use Windows for Autochem you should also install dos2unix 
To activate check for the first time you should: 
1) Copy the whole content of the folder scripts in your Linux working environment for calculations. 
2) Render the scripts runnable: 
chmod +x chmodme 
and then launch chmodme 
./chmodme 
 
After doing this, you can put in the same folder the inputs to be calculated. 
Then launch check: 
./check 
and follow instructions. 
After some time launch check again and again up to the calculations of all inputs. 
Check will take care the resubmission of jobs in the case of negative frequencies. 
(if you are expert, you can add launch to chron or to some automatic running of check)

# QUICKSTART
 Watch the video: (AutoChem program with SMARTS reactions) 
https://raw.githubusercontent.com/Daniele-Dondi/AutoChem/main/videos/AutoChem_example.mp4

https://github.com/user-attachments/assets/3b95d033-b533-40df-97f6-128ca5fede92

Watch the video: (check program with crest) 
https://raw.githubusercontent.com/Daniele-Dondi/AutoChem/main/videos/check.mp4

https://github.com/user-attachments/assets/cb7bd15c-823a-44bd-8b3b-2234a6f599dc

Watch the video: (check program with xtb and deltaG calculations) 
https://raw.githubusercontent.com/Daniele-Dondi/AutoChem/main/videos/xtb_+_deltaG.mp4

https://github.com/user-attachments/assets/003b1c4b-01f4-4b33-b956-cf628a6a7b8d

# SLURM setup 
In order to have the slurm queue manager working, you have to edit some files. 
 
1) slurm_settings. Edit the file inserting you username and accountname: 
user=your username 
account=your account 
 
2) Ask system administrators to have an example of slurm script for the program you are going to use 
as an example, we are going to use gaussian, so we create the file slurm_gaussian. 
In the file, substitute your username with $user and your accountname with $account. 
Substitute also the file name with $file, the memory allocation with $mem and the number of processors with $proc. 
These variables will be substituted when a file is submitted to the queue. 
 
3) Check if the slurm script is properly setup. 
To do this, edit the file run 
and locate the following code (locate the section related to the program you are going to use) 
 sbatch $file.tmp #2>/dev/null 
 #cat $file.tmp 
 rm $file.tmp 
modify as follows: 
 #sbatch $file.tmp #2>/dev/null 
 cat $file.tmp 
 #rm $file.tmp 
get ready with a simple example file to launch and write the command: 
./run yourtestfile 
(note that you should have prepared previously files like SLURM and GAUSSIAN too) 
check if the slurm header is well prepared: 
cat yourtestfile.tmp 
If it is OK, submit to the queue to check: 
sbatch yourtestfile.tmp 
 
4) If everything works, revert back to the previous version of run. 
 
5) Start your calculations with ./check and... good luck

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