-
BIOPZ-Johner Niklaus authoredBIOPZ-Johner Niklaus authored
Blocks
The most basic type of residue description is the BuildingBlock. It contains information on atom names and their corresponding types, charges and optionally also their masses. Interactions for all particles can also be defined even though they are optional, except the bonds giving information about the connectivity. You often need to manipulate building blocks or the residues they refer to in an automated manner. That's where the BlockModifiers come in, with the GromacsBlockModifier as a specific implementation. As a special case there also exist HydrogenConstructors.
The BuildingBlock Class
Block Modifiers
Basis class. Block modifiers are used to change building blocks or residues. See :class:`GromacsBlockModifier` for a specific example.
Hydrogen Constructors
Basis class. Hydrogen constructors are used to add hydrogens to residues.
The :class:`GromacsHydrogenConstructor` is the Gromacs way of adding hydrogens to a structure.
As soon as we leave the well defined world of Gromacs residue definitions, we have to find new ways for constructing hydrogens. The :class:`HeuristicHydrogenConstructor` takes a :class:`BuildingBlock` at initialization and builds heuristic rules to build hydrogens based on the connecticity defined in the given block.
| param block: | :class:`BuildingBlock` from which the connectivity information for hydrogen construction is extracted |
|---|