YARP: Yet Another Reaction Program for Automated Reaction Exploration

This is an object-oriented refactoring of yarp methodology to be compatible with general reaction-discovery workflows. YARP is a repository that explore the reaction network for a given set of molecules (reactants). YARP consists of construction of bond-electron matrix, product enumeration, reaction conformational sampling, transition state (TS) localization by growing string method (GSM), and TS characterization by Berny optimzation and IRC calculation. More details could be found on:

1. https://www.nature.com/articles/s43588-021-00101-3
2. https://pubs.acs.org/doi/full/10.1021/acs.jctc.2c00081

1. Installation:

• 1.1 Anaconda is recommended and you can get YARP repository by:

git clone https://github.com/Savoie-Research-Group/yarp.git

• 1.2 Build the YARP environment and install required packages by:

cd yarp
conda env create -f env_linux.yaml

• 1.3 Install yarp package by:

conda activate classy-yarp
pip install .

• 1.4 Create pysis cmd by:

vi ~/.pysisyphusrc

and in .pysisyphusrc file add:

[xtb]
cmd=xtb

Finally, save and quit this file.

2. Test Your Installation

• 2.1 First install pytest via:

pip install pytest

• 2.2 Do a simple test (few seconds) that reads the structure of Fe(CO)₅ and returns the bond-electron matrix:

cd examples/
pytest -s

• 2.3 Then do a more complicated test (10 mins) that runs YARP-xTB that includes geometry optimization, conformational sampling, joint optimization, Grow-String Method (GSM), Berny optimization, and IRC

cd pyTEST_Example/
pytest -s

3. How YARP Works:

• 3.1 YARP class:

  • In yarp/yarp folder, several functions are shown
  • the bond-electron matrix and reaction enumeration are generated via these functions. More details are shown in yarp/examples/reaction.py

• 3.2 Reaction class:

  • All calculations, including conformational sampling, GSM, and TS characterization, are In yarp/reaction folder.
  • In yarp/reaction/main_xtb.py, the workflow are shown. To run main_xtb.py we need a parameters.yaml file.
  • To build a parameters.yaml file, we will need:

    input: [reaction folder or reaction file] # it could be a folder (store several xyz, mol, or smiles files) or a xyz, mol, or smiles file.
    scratch: [a path you want to store result]
    reaction_data: [a pickle file] # a pickle to store and load the result
    n_break: [an integer, n] # define a break-n-bonds-form-n-bonds reaction
    form_all: [True/False] # If true, it means you will try all break-n-bonds-form-infinity-bonds reactions.
    lewis_criteria: [a float] # the criteria to remove unfavorable products by its Lewis structure (0.0 is recommended).
    ff: [force field name] # the force field to initialize geometry (uff/mmff94 are all available)
    crest: [cmd for crest] # the command for CREST. (usually it would be crest)
    lot: [gfn2, gfn1, gfn-ff] # the level of theory in xTB.
    method: [crest/rdkit] # for conformational sampling, CREST and rdkit (by uff) are available options.
    enumeration: [True/False] # If it's true, it means that product enumeration will be applied.
    n_conf: [an integer, n] # define n conformers would be considered for further calculations.
    nconf_dft: [an integer, n] # define n conformers for DFT calculations.
    c_nprocs: [an integer] # define how many cpus you are going to use for CREST. (if you run on pc, set this as 1)
    mem: [integer] # in GB
    opt_level: [tight, vtight, and etc.] # define the convergence for xTB.
    crest_quick: [True/False] # if true, the crest with quick mode will be performed.
    low_solvation: [gbsa, alpb, False] # define the solvation models in xTB.
    solvent: [solvent name] # define the solvent.
    pysis_wt: [integer] # the walltime for xTB calculation (in second).
    charge: [integer] # charge of your system.
    multiplicity: [integer] # multiplicity for your system.
    model_path: [your yarp path/reaction/bin] # models we need for yarp.
    gsm_inp: [your yarp path/reaction/bin/inpfileq] # growing string method bin file.

More details could be found in parameters.yaml.

• 3.3 As the parameter.yaml file is created, you can run yarp by:

python main_xtb.py [your parameter yaml file]