This struct holds all objects used inside the MM parametrization algorithm. More...

Collaboration diagram for Scine::StructurePreparation::StructurePreparationData:

Public Attributes
Utils::AtomCollection	fullStructure
	The structure of the system to prepare.

Utils::AtomCollection	proteinStructure
	The protein substructure, i. e. all correctly identified amino acids.

Utils::AtomCollection	nonregularContainer
	The nonregular substructure.

Utils::BondOrderCollection	bondOrders
	A bond order matrix of the full system.

int	numberOfAtoms {0}
	Number of atoms in the full structure.

std::vector< int >	vectorOfProteinIndices
	Vector of indices of the full structure that belong to the protein subsystem.

std::vector< int >	vectorOfNonRegContainerIndices
	Vector of indices of the full structure that belong to the nonRegContainer subsystem.

std::vector< std::list< int > >	listsOfNeighbors
	The connectivity of the system. It is a vector of a list of neighbor atom indices for each atom.

std::vector< std::vector< int > >	atomIndexMapping
	Vector of all fragments containing a vector of indices that correspond to the indices of the atoms inside the fragment in the full system.

std::vector< std::vector< int > >	subsystemMapping
	Vector containing a vector of indices that correspond to the indices of the protein and the nonregular_container in the full system.

std::vector< ProteinAtom >	protein
	A vector of ProteinAtoms that assigns to each atom index the residue name, the atom type name and the position.

std::vector< int >	listOfBackboneAlphaCarbons
	A vector that contains the indices of all carbon atoms in the peptid bond.

Detailed Description

This struct holds all objects used inside the MM parametrization algorithm.

This struct holds all objects used inside the structure preparation algorithm.

The documentation for this struct was generated from the following file:

Public Attributes