What is meant by structural cleanup?
The term "structure cleaning" refers to the process of correcting, standardizing, and optimizing molecular structures to ensure they meet the required chemical and formal standards. This cleaning is often necessary to correct flawed or incomplete structures to allow precise and reliable analyses, simulations, or other chemical calculations.
Typical software functions in the area of "structure cleaning":
- Error Detection and Correction: Identification and correction of invalid bonds, missing atoms, or unphysical geometries.
- Normalization of Chemical Structures: Adjusting structures to standard conventions, such as the correct representation of aromatic compounds or tautomers.
- Geometry Optimization: Enhancing the three-dimensional geometry of the molecule to achieve energetically favorable conformations.
- Electron Count Verification: Ensuring that all atoms have the correct number of electrons according to their valency.
- Completion of Missing Atoms or Bonds: Automatically adding missing hydrogen atoms or other bonds to complete the structure.
- Configuration Validation: Reviewing and correcting stereochemical configurations (e.g., chirality).
- Format Conversion: Converting the structure into various file formats or notations, e.g., from 2D to 3D.