KinBot file structure

KinBot file structure

KinBot contains 4 files in the root directory and 5 sub-directories

Root: kinbot/

• init.py Empty file, necessary for python to recognize the directory as a part of the project
  • bfgs.py BFGS algorithm used to optimize a geometry with one or more updated coordinates
  • bond_combinations.py Files to enumerate all possible bond forming and bond breaking steps (not operational yet)
  • cheminfo.py Methods to link the KinBot species representation to the cheminformatics packages RDKit and OpenBabel.
  • conformers.py Methods to generate and run conformer searches for cyclic and open-chain molecules and transition states
  • constants.py List of constants necessary for KinBot
  • find_motif.py Algorithm to find a structural motif in a species
  • frequencies.py Algorithm to get the frequencies from a full hessian matrix by projecting out translation, external rotation and internal rotation.
  • geometry.py List of methods to calculate key values based on a geometry and to perform geometry transformations
  • hindered_rotors.py Methods to generate the geometries along a scan and run them.
  • homolytic_scissions.py Method to search for all homolytic bond scission products of a species
  • irc.py Methods to run the Intrinsic Reaction Coordinate calculations starting from a transition state and to identify the products and verify the connectivity to the original well
  • kb.py General script to run KinBot (only one well, see pes.py for a full PES search)
  • license_message.py License message that is printed when running KinBot and in the output and log files
  • mesmer.py Methods to build MESMER input files and automatically run them
  • mess.py Methods to build MESS input files and automatically run them
  • modify_geom.py Method to update a geometry based on a list of coordinates that need to change
  • molpro.py Method to build MolPro input files
  • optimize.py Collection of methods to, starting from a geometry (either a well or saddle point), goes through the list of conformer searches, high-level optimizations and hindered rotor calculations
  • parameters.py Parameters and options of the KinBot calculations
  • pes.py General script to run a full PES search
  • postprocess.py Scripts to postprocess KinBot and write the appropriate output files and figures
  • qc.py Methods to couple KinBot to quantum chemistry software packages through ASE
  • reac_family.py Generic method for a reaction family
  • reac_*.py There is a separate file per reaction family (replacing the asterisk with the family name) which contains the necessary data and recipe for the reaction family
  • reaction_finder.py Methods to find the candidate reactions of a species
  • reaction_generator.py Methods to go through each candidate reaction, generate a transition state structure, optimize that structure, do IRC calculations and optimize the products
  • stationary_pt.py Class for a stationary point on the PES, holding all the data of that stationary point, and providing algorithm to analyze the stationary point (find cycles, calculate aID’s, etc.)
  • symmetry.py Algorithm to calculate the external and internal symmetry numbers and numbers of optical isomers
  • thread_kinbot.py Algorithm to thread many KinBot runs, used by the pes.py script.
  • zmatrix.py Algorithms to convert a geometry in cartesian coordinates to a zmatrix representation and vice versa
• tpl/ This directory contains the templates for KinBot, these are simple text files that are read by KinBot and converted to useful files by formatting them appropriately.
• tests/ This directory contains a collection of tests for KinBot
• examples/
• gvl_reactions/ Directory with input files for an example of the exploration of the reactions for gamma valerolactone
• pentyl_pes/ Directory with input files for an example of the full exploration of a PES for the n-pentyl radical
• propanol_homolytic_scissions/ Directory with input files for an example of the search for all homolytic scission reactions in propanol
• propanol_radical_ME/ Directory with input files for an example of the full exploration of a well, including conformation searches, high-level optimizations and hindered rotor calculations, of which the results are collected in an input file for MESS. The rate coefficients are subsequently calculated with MESS.
• docs/ This directory contains the manual of KinBot
• init.py to Empty file, necessary for python to recognize the directory as a part of the project
• LICENSE License message
• README.md README file for KinBot
• setup.py Setup file used to build and install KinBot