PLMD::RMSD Member List

This is the complete list of members for PLMD::RMSD, including all inherited members.

addCenter(std::vector< Vector > &p, const Vector &c)	PLMD::RMSD	inlineprivate
align	PLMD::RMSD	private
AlignmentMethod enum name	PLMD::RMSD	private
alignmentMethod	PLMD::RMSD	private
calc_DDistDRef(const std::vector< Vector > &positions, std::vector< Vector > &DDistDPos, std::vector< Vector > &DDistDRef, const bool squared=false)	PLMD::RMSD
calc_DDistDRef_Rot_DRotDPos(const std::vector< Vector > &positions, std::vector< Vector > &DDistDPos, std::vector< Vector > &DDistDRef, Tensor &Rotation, Matrix< std::vector< Vector > > &DRotDPos, const bool squared=false)	PLMD::RMSD
calc_DDistDRef_Rot_DRotDPos_DRotDRef(const std::vector< Vector > &positions, std::vector< Vector > &DDistDPos, std::vector< Vector > &DDistDRef, Tensor &Rotation, Matrix< std::vector< Vector > > &DRotDPos, Matrix< std::vector< Vector > > &DRotDRef, const bool squared=false)	PLMD::RMSD
calc_FitElements(const std::vector< Vector > &pos, Tensor &Rotation, Matrix< std::vector< Vector > > &DRotDPos, std::vector< Vector > &centeredpositions, Vector &center_positions, const bool &squared=false)	PLMD::RMSD
calc_PCAelements(const std::vector< Vector > &pos, std::vector< Vector > &DDistDPos, Tensor &Rotation, Matrix< std::vector< Vector > > &DRotDPos, std::vector< Vector > &alignedpositions, std::vector< Vector > &centeredpositions, std::vector< Vector > &centeredreference, const bool &squared=false) const	PLMD::RMSD
calc_Rot(const std::vector< Vector > &positions, std::vector< Vector > &DDistDPos, Tensor &Rotation, const bool squared=false)	PLMD::RMSD
calc_Rot_DRotDRr01(const std::vector< Vector > &positions, Tensor &Rotation, std::array< std::array< Tensor, 3 >, 3 > &DRotDRr01, const bool squared=false)	PLMD::RMSD
calc_SOMA(const std::vector< Vector > &positions, std::vector< Vector > &DDistDPos, std::vector< Vector > &DDistDRef, const bool squared=false)	PLMD::RMSD
calculate(const std::vector< Vector > &positions, std::vector< Vector > &derivatives, bool squared=false) const	PLMD::RMSD
calculateCenter(const std::vector< Vector > &p, const std::vector< double > &w)	PLMD::RMSD	inlineprivate
calculateWithCloseStructure(const std::vector< Vector > &positions, std::vector< Vector > &DDistDPos, const Tensor &rotationPosClose, const Tensor &rotationRefClose, std::array< std::array< Tensor, 3 >, 3 > &drotationPosCloseDrr01, const bool squared=false)	PLMD::RMSD
clear()	PLMD::RMSD
displace	PLMD::RMSD	private
getAlign()	PLMD::RMSD
getDisplace()	PLMD::RMSD
getMatrixFromDRot(const Matrix< std::vector< Vector > > &drotdpos, const unsigned &i, const unsigned &a)	PLMD::RMSD	inlinestatic
getMethod()	PLMD::RMSD
getReference()	PLMD::RMSD
OPTIMAL enum value	PLMD::RMSD	private
OPTIMAL_FAST enum value	PLMD::RMSD	private
optimalAlignment(const std::vector< double > &align, const std::vector< double > &displace, const std::vector< Vector > &positions, const std::vector< Vector > &reference, std::vector< Vector > &DDistDPos, bool squared=false) const	PLMD::RMSD
optimalAlignment_DDistDRef(const std::vector< double > &align, const std::vector< double > &displace, const std::vector< Vector > &positions, const std::vector< Vector > &reference, std::vector< Vector > &DDistDPos, std::vector< Vector > &DDistDRef, bool squared=false) const	PLMD::RMSD
optimalAlignment_DDistDRef_Rot_DRotDPos(const std::vector< double > &align, const std::vector< double > &displace, const std::vector< Vector > &positions, const std::vector< Vector > &reference, std::vector< Vector > &DDistDPos, std::vector< Vector > &DDistDRef, Tensor &Rotation, Matrix< std::vector< Vector > > &DRotDPos, bool squared=false) const	PLMD::RMSD
optimalAlignment_DDistDRef_Rot_DRotDPos_DRotDRef(const std::vector< double > &align, const std::vector< double > &displace, const std::vector< Vector > &positions, const std::vector< Vector > &reference, std::vector< Vector > &DDistDPos, std::vector< Vector > &DDistDRef, Tensor &Rotation, Matrix< std::vector< Vector > > &DRotDPos, Matrix< std::vector< Vector > > &DRotDRef, bool squared=false) const	PLMD::RMSD
optimalAlignment_Fit(const std::vector< double > &align, const std::vector< double > &displace, const std::vector< Vector > &positions, const std::vector< Vector > &reference, Tensor &Rotation, Matrix< std::vector< Vector > > &DRotDPos, std::vector< Vector > &centeredpositions, Vector &center_positions, bool squared=false)	PLMD::RMSD
optimalAlignment_PCA(const std::vector< double > &align, const std::vector< double > &displace, const std::vector< Vector > &positions, const std::vector< Vector > &reference, std::vector< Vector > &alignedpositions, std::vector< Vector > &centeredpositions, std::vector< Vector > &centeredreference, Tensor &Rotation, std::vector< Vector > &DDistDPos, Matrix< std::vector< Vector > > &DRotDPos, bool squared=false) const	PLMD::RMSD
optimalAlignment_Rot(const std::vector< double > &align, const std::vector< double > &displace, const std::vector< Vector > &positions, const std::vector< Vector > &reference, std::vector< Vector > &derivatives, Tensor &Rotation, bool squared=false) const	PLMD::RMSD
optimalAlignment_Rot_DRotDRr01(const std::vector< double > &align, const std::vector< double > &displace, const std::vector< Vector > &positions, const std::vector< Vector > &reference, Tensor &Rotation, std::array< std::array< Tensor, 3 >, 3 > &drotationPosCloseDrr01, bool squared=false) const	PLMD::RMSD
optimalAlignment_SOMA(const std::vector< double > &align, const std::vector< double > &displace, const std::vector< Vector > &positions, const std::vector< Vector > &reference, std::vector< Vector > &DDistDPos, std::vector< Vector > &DDistDRef, bool squared=false) const	PLMD::RMSD
optimalAlignmentWithCloseStructure(const std::vector< double > &align, const std::vector< double > &displace, const std::vector< Vector > &positions, const std::vector< Vector > &reference, std::vector< Vector > &derivatives, const Tensor &rotationPosClose, const Tensor &rotationRefClose, std::array< std::array< Tensor, 3 >, 3 > &drotationPosCloseDrr01, bool squared=false) const	PLMD::RMSD
positions_center	PLMD::RMSD	private
positions_center_is_calculated	PLMD::RMSD	private
positions_center_is_removed	PLMD::RMSD	private
reference	PLMD::RMSD	private
reference_center	PLMD::RMSD	private
reference_center_is_calculated	PLMD::RMSD	private
reference_center_is_removed	PLMD::RMSD	private
removeCenter(std::vector< Vector > &p, const Vector &c)	PLMD::RMSD	inlineprivate
RMSD()	PLMD::RMSD
set(const PDB &, const std::string &mytype, bool remove_center=true, bool normalize_weights=true)	PLMD::RMSD
set(const std::vector< double > &align, const std::vector< double > &displace, const std::vector< Vector > &reference, const std::string &mytype, bool remove_center=true, bool normalize_weights=true)	PLMD::RMSD
setAlign(const std::vector< double > &align, bool normalize_weights=true, bool remove_center=true)	PLMD::RMSD
setDisplace(const std::vector< double > &displace, bool normalize_weights=true)	PLMD::RMSD
setReference(const std::vector< Vector > &reference)	PLMD::RMSD
setType(const std::string &mytype)	PLMD::RMSD
SIMPLE enum value	PLMD::RMSD	private
simpleAlignment(const std::vector< double > &align, const std::vector< double > &displace, const std::vector< Vector > &positions, const std::vector< Vector > &reference, std::vector< Vector > &derivatives, std::vector< Vector > &displacement, bool squared=false) const	PLMD::RMSD