Program Structure

Description: This section details the structure of all files currently in the ChemArchItect package.

Making Many Gaussian Input Files From a List of SMILES.

Order of Operations

 1. SmileToMol.py (SmileTo Mol_tester.txt for testing example)

 2. Use open babel to convert .mol files to .gjf

 3. FileCreator.py

Related Utilities

Select a random subset of smiles from the list you have

 RandInputSelect.py

Make train and test set files from a single dataset

 Separate_Train_Test.py

Change the Route Card details for already made Gaussian input files

 BasisChanger_FileCreator.py

Create files with shifted atomic cartesian coordinates from existing atomic coordinates

 ShiftedInputCreator.py

Utilities to Speed Up Gaussian Job Submission and Fixing

Make new input files for files that underwent a TIMEOUT failure.

 TimeOutRestarter.py

Make new input files for files that failed due to a bad angle.

 AngleRestarter.py

Making Input for Machine Learning

Making Encoding Dictionaries For Machine Learning Input

Encoding Dictionaries detail what each feature column refers to.

Spherical Radii Dictionary

 DictionaryMaker_SR.py

Diherdral Arcs Dictionary

 DictionaryMaker_DA.py

Angular Arcs Dictionary

 DictionaryMaker_AA.py

Extracting Encoded Interactions for Machine Learning Input

 ExtractInteractions_SepPt1.py
 ExtractAnglesAndInts_SepPt1_Portion.py
 ExtractAnglesAndInts_Sep5Deg_SepPt1.py
 ExtractAnglesAndInts_Sep5Deg_SepPt1_Portion.py
 ExtractAnglesAndInts_Sep5Deg_Portion_SepPt1_Portion.py

Extraction of Energies and Computed Properties

 ExtractProperties.py

Analysis Tools for Already Trained Models

Predict the energies for a new dataset on a trained model

 Predictor.py