4. API Reference¶
The propka3 command provides a command-line interface to
PROPKA 3’s functionality. It is built on classes and functions in the
propka
module. The API of propka
is documented here for
developers who might want to directly use the PROPKA 3 code.
Note
The API is still changing and there is currently no guarantee that it will remain stable between minor releases.
4.1. Data structures¶
Atom |
|
Bonds |
|
Data structures for groups |
|
Molecular data structures |
|
PDB molecular container |
4.2. I/O¶
Input handling |
|
Set-up of a PROPKA calculation |
|
Output |
|
Configuration file parameters |
|
Hybrid36 PDB-like file format |
|
Ligand pKa values from Marvin |
|
Script functionality |
|
Version-based configuration |
4.3. Structure processing¶
Protonate a structure |
|
Hydrogens |
|
Ligand atom typing |
4.4. Calculations¶
Calculations |
|
Coupling between groups |
|
Determinant |
|
Working with Determinants |
|
Energy calculations |
|
Working with Determinants |
|
Vector calculations |