 |
 |
 |
Loading...
Searching...
No Matches
| |
|
|
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 > ¢eredpositions, Vector ¢er_positions, 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 > ¢eredpositions, std::vector< Vector > ¢eredreference, 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 View< Vector > positions, std::vector< Vector > &derivatives, bool squared=false) const | 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() const | PLMD::RMSD | |
| getReference() const | PLMD::RMSD | |
| OPTIMAL enum value | PLMD::RMSD | private |
| OPTIMAL_FAST enum value | PLMD::RMSD | private |
| optimalAlignment(const std::vector< double > &alignTo, const std::vector< double > &displaceFrom, const View< Vector > positions, const std::vector< Vector > &ref, std::vector< Vector > &DDistDPos, bool squared=false) const | PLMD::RMSD | |
| optimalAlignment_DDistDRef(const std::vector< double > &alignTo, const std::vector< double > &displaceFrom, const View< Vector > positions, const std::vector< Vector > &ref, std::vector< Vector > &DDistDPos, std::vector< Vector > &DDistDRef, bool squared=false) const | PLMD::RMSD | |
| optimalAlignment_DDistDRef_Rot_DRotDPos(const std::vector< double > &alignTo, const std::vector< double > &displaceFrom, const View< Vector > positions, const std::vector< Vector > &ref, 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 > &alignTo, const std::vector< double > &displaceFrom, const View< Vector > positions, const std::vector< Vector > &ref, 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 > &alignTo, const std::vector< double > &displaceFrom, const View< Vector > positions, const std::vector< Vector > &ref, Tensor &Rotation, Matrix< std::vector< Vector > > &DRotDPos, std::vector< Vector > ¢eredpositions, Vector ¢er_positions, bool squared=false) | PLMD::RMSD | |
| optimalAlignment_PCA(const std::vector< double > &alignTo, const std::vector< double > &displaceFrom, const View< Vector > positions, const std::vector< Vector > &ref, std::vector< Vector > &alignedpositions, std::vector< Vector > ¢eredpositions, std::vector< Vector > ¢eredreference, Tensor &Rotation, std::vector< Vector > &DDistDPos, Matrix< std::vector< Vector > > &DRotDPos, bool squared=false) const | PLMD::RMSD | |
| optimalAlignment_Rot(const std::vector< double > &alignTo, const std::vector< double > &displaceFrom, const View< Vector > positions, const std::vector< Vector > &ref, std::vector< Vector > &derivatives, Tensor &Rotation, bool squared=false) const | PLMD::RMSD | |
| optimalAlignment_Rot_DRotDRr01(const std::vector< double > &alignTo, const std::vector< double > &displaceFrom, const View< Vector > positions, const std::vector< Vector > &ref, Tensor &Rotation, std::array< std::array< Tensor, 3 >, 3 > &drotationPosCloseDrr01, bool squared=false) const | PLMD::RMSD | |
| optimalAlignment_SOMA(const std::vector< double > &alignTo, const std::vector< double > &displaceFrom, const View< Vector > positions, const std::vector< Vector > &ref, std::vector< Vector > &DDistDPos, std::vector< Vector > &DDistDRef, bool squared=false) const | PLMD::RMSD | |
| optimalAlignmentWithCloseStructure(const std::vector< double > &alignTo, const std::vector< double > &displaceFrom, const View< Vector > positions, const std::vector< Vector > &ref, 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 > &alignTo, const std::vector< double > &displaceFrom, const std::vector< Vector > &ref, const std::string &mytype, bool remove_center=true, bool normalize_weights=true) | PLMD::RMSD | |
| setAlign(const std::vector< double > &alignTo, bool normalize_weights=true, bool remove_center=true) | PLMD::RMSD | |
| setDisplace(const std::vector< double > &displaceFrom, bool normalize_weights=true) | PLMD::RMSD | |
| setReference(const std::vector< Vector > &ref) | PLMD::RMSD | |
| setType(const std::string &mytype) | PLMD::RMSD | |
| SIMPLE enum value | PLMD::RMSD | private |
| simpleAlignment(const std::vector< double > &alignTo, const std::vector< double > &displaceFrom, const View< Vector > positions, const std::vector< Vector > &ref, std::vector< Vector > &derivatives, std::vector< Vector > &displacement, bool squared=false) const | PLMD::RMSD |
Hosted by GitHub
|
1.13.2
|