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Chemical Data Processing Library C++ API - Version 1.4.0
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Chemical Data Processing Library C++ API - Version 1.4.0
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Declaration of functions that operate on Chem::AtomContainer instances. More...
#include <cstddef>#include "CDPL/Chem/APIPrefix.hpp"#include "CDPL/Chem/AtomPredicate.hpp"#include "CDPL/Chem/Atom3DCoordinatesFunction.hpp"#include "CDPL/Math/Matrix.hpp"#include "CDPL/Math/VectorArray.hpp"#include "CDPL/Util/BitSet.hpp"Go to the source code of this file.
Namespaces | |
| CDPL | |
| The namespace of the Chemical Data Processing Library. | |
| CDPL::Chem | |
| Contains classes and functions related to chemistry. | |
Functions | |
| CDPL_CHEM_API bool | CDPL::Chem::hasCoordinates (const AtomContainer &cntnr, std::size_t dim) |
| Tells whether all atoms of cntnr carry coordinates of the given dimensionality. More... | |
| CDPL_CHEM_API void | CDPL::Chem::get2DCoordinates (const AtomContainer &cntnr, Math::Vector2DArray &coords, bool append=false) |
| Extracts the 2D coordinates of all atoms in cntnr into coords. More... | |
| CDPL_CHEM_API void | CDPL::Chem::set2DCoordinates (AtomContainer &cntnr, const Math::Vector2DArray &coords) |
| Writes the 2D coordinates in coords back to the corresponding atoms of cntnr. More... | |
| CDPL_CHEM_API void | CDPL::Chem::transform2DCoordinates (AtomContainer &cntnr, const Math::Matrix3D &mtx) |
| Transforms the 2D coordinates of all atoms in cntnr by the affine 3×3 matrix mtx. More... | |
| CDPL_CHEM_API void | CDPL::Chem::get3DCoordinates (const AtomContainer &cntnr, Math::Vector3DArray &coords, const Atom3DCoordinatesFunction &coords_func, bool append=false) |
| Extracts the 3D coordinates of all atoms in cntnr into coords using the per-atom coordinate lookup function coords_func. More... | |
| CDPL_CHEM_API void | CDPL::Chem::clearConformations (AtomContainer &cntnr) |
| Removes all stored conformations from the atoms of cntnr. More... | |
| CDPL_CHEM_API std::size_t | CDPL::Chem::getNumConformations (const AtomContainer &cntnr) |
| Returns the number of conformations stored on the atoms of cntnr. More... | |
| CDPL_CHEM_API void | CDPL::Chem::applyConformation (AtomContainer &cntnr, std::size_t conf_idx) |
| Promotes the stored conformation at index conf_idx to the active per-atom 3D coordinates. More... | |
| CDPL_CHEM_API void | CDPL::Chem::getConformation (const AtomContainer &cntnr, std::size_t conf_idx, Math::Vector3DArray &coords, bool append=false) |
| Extracts the conformation at index conf_idx into coords. More... | |
| CDPL_CHEM_API void | CDPL::Chem::setConformation (AtomContainer &cntnr, std::size_t conf_idx, const Math::Vector3DArray &coords) |
| Overwrites the conformation at index conf_idx with the supplied 3D coordinates. More... | |
| CDPL_CHEM_API void | CDPL::Chem::addConformation (AtomContainer &cntnr, const Math::Vector3DArray &coords) |
| Appends a new conformation built from the supplied 3D coordinates to the atoms of cntnr. More... | |
| CDPL_CHEM_API void | CDPL::Chem::transformConformation (AtomContainer &cntnr, std::size_t conf_idx, const Math::Matrix4D &mtx) |
| Transforms the conformation at index conf_idx by the homogeneous 4×4 matrix mtx. More... | |
| CDPL_CHEM_API void | CDPL::Chem::transformConformations (AtomContainer &cntnr, const Math::Matrix4D &mtx) |
| Transforms every stored conformation of the atoms in cntnr by the homogeneous 4×4 matrix mtx. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::alignConformations (AtomContainer &cntnr, const Util::BitSet &ref_atoms, const Math::Vector3DArray &ref_coords) |
| Aligns each stored conformation of cntnr onto the supplied reference coordinates using the atoms flagged in ref_atoms as alignment anchors. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::alignConformations (AtomContainer &cntnr, const AtomContainer &ref_atoms, const Math::Vector3DArray &ref_coords) |
| Aligns each stored conformation of cntnr onto the supplied reference coordinates using the atoms of ref_atoms as alignment anchors. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::alignConformations (AtomContainer &cntnr, const Util::BitSet &ref_atoms) |
| Aligns each stored conformation of cntnr to the first conformation using the atoms flagged in ref_atoms as alignment anchors. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::alignConformations (AtomContainer &cntnr, const AtomContainer &ref_atoms) |
| Aligns each stored conformation of cntnr to the first conformation using the atoms of ref_atoms as alignment anchors. More... | |
| CDPL_CHEM_API std::size_t | CDPL::Chem::getMaxComponentGroupID (const AtomContainer &cntnr) |
| Returns the largest component-group ID assigned to any atom of cntnr. More... | |
| CDPL_CHEM_API std::size_t | CDPL::Chem::getMaxAtomMappingID (const AtomContainer &cntnr) |
| Returns the largest atom-mapping ID assigned to any atom of cntnr. More... | |
| CDPL_CHEM_API std::size_t | CDPL::Chem::createAtomTypeMask (const AtomContainer &cntnr, Util::BitSet &mask, unsigned int type, bool reset=true, bool strict=true) |
| Sets bits in mask corresponding to atoms of cntnr whose atom type matches type. More... | |
| CDPL_CHEM_API void | CDPL::Chem::copyAtomsIf (const AtomContainer &cntnr, Molecule &mol, const AtomPredicate &pred, bool append=false) |
| Copies every atom of cntnr that satisfies pred into the molecule mol. More... | |
| CDPL_CHEM_API void | CDPL::Chem::copyAtomsIf (const AtomContainer &cntnr, Fragment &frag, const AtomPredicate &pred, bool append=false) |
| Copies every atom of cntnr that satisfies pred into the fragment frag. More... | |
| CDPL_CHEM_API void | CDPL::Chem::copyAtomsIfNot (const AtomContainer &cntnr, Molecule &mol, const AtomPredicate &pred, bool append=false) |
| Copies every atom of cntnr that does not satisfy pred into the molecule mol. More... | |
| CDPL_CHEM_API void | CDPL::Chem::copyAtomsIfNot (const AtomContainer &cntnr, Fragment &frag, const AtomPredicate &pred, bool append=false) |
| Copies every atom of cntnr that does not satisfy pred into the fragment frag. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::calcCenterOfMass (const AtomContainer &cntnr, const Atom3DCoordinatesFunction &coords_func, Math::Vector3D &ctr) |
| Computes the mass-weighted center of mass of the atoms in cntnr. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::calcCentroid (const AtomContainer &cntnr, const Atom3DCoordinatesFunction &coords_func, Math::Vector3D &ctr) |
| Computes the unweighted centroid (arithmetic mean of atom coordinates) of cntnr. More... | |
| CDPL_CHEM_API void | CDPL::Chem::calcBoundingBox (const AtomContainer &cntnr, Math::Vector3D &min, Math::Vector3D &max, const Atom3DCoordinatesFunction &coords_func, bool reset=true) |
| Computes the axis-aligned bounding box enclosing the atoms of cntnr. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::insideBoundingBox (const AtomContainer &cntnr, const Math::Vector3D &min, const Math::Vector3D &max, const Atom3DCoordinatesFunction &coords_func) |
| Tells whether every atom of cntnr lies inside the axis-aligned bounding box defined by min and max. More... | |
| CDPL_CHEM_API bool | CDPL::Chem::intersectsBoundingBox (const AtomContainer &cntnr, const Math::Vector3D &min, const Math::Vector3D &max, const Atom3DCoordinatesFunction &coords_func) |
| Tells whether at least one atom of cntnr lies inside the axis-aligned bounding box defined by min and max. More... | |
Declaration of functions that operate on Chem::AtomContainer instances.
1.9.1