buildingblock.rst

Blocks

The most basic type of a residue description is the BuildingBlock. It contains information of 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.

Automated modification of :class:`BuildingBlock` and :class:`ResidueHandle`

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.