Recipes

Here are code snippets that demonstrate the features of cctk. Please bake responsibly.

• Reading and Writing Gaussian Files
  • Reading a Gaussian Input File
  • Reading a Gaussian Output File
  • Writing One Molecule to a Gaussian Input File
  • Multiple Link1 Sections
  • Writing Multiple Molecules to One Gaussian Input File
  • Using Custom Basis Sets from the Basis Set Exchange
  • Creating Molecules By Name
• Extracting Molecular Properties (Energies, Frequencies, Charges, etc.)
  • Example: opt freq
  • properties_dict
  • Correcting Free Energies
  • Sorting Ensembles
  • Lowest Energy Molecules
• Manipulating Molecule Objects
  • Measuring Distances and Angles
  • Setting Distances and Angles
  • Checking For Clashes
  • Generating Non-Ground States
  • Optimizing Geometries
• Bond Connectivity and Atom Selection
  • Bond Connectivity
  • Atom Selection
  • Renumbering Molecules
• Aligning Structures and Redundant Conformer Elimination
  • Calculating RMSD
  • Aligning Two Molecules
  • Redundant Conformer Elimination
• NMR Spectroscopy
  • Chemical Shifts
  • Coupling Constants
  • Shielding Tensors
• Reading and Writing Other File Formats
  • XYZ Files
  • MOL2 Files
  • Maestro Files
• Creating and Adding Groups
  • Using a Preloaded Group
  • Creating a New Group
  • Epimerization
  • Detecting Groups
• Reading and Writing ORCA Files
  • Writing a simple ORCA input file
  • Writing an ORCA input file from a SMILES string
  • Reading Output of ORCA Geometry Optimization