Package chemaxon.alignment
package chemaxon.alignment
Provides algorithms and tools to align molecules onto each other in 2D and 3D.
-
ClassDescription3D Alignment aligns two or more 3D molecules onto each other.Settings for the representation of a molecular shape.Base class for the alignment algorithms.Exception thrown when an error occurs during molecular alignment operations.Represents a molecule in the context of 3D molecular alignment with its coordinates and transformation state.Creates an
AlignmentMoleculeform aMoleculebased on the settings.Interface for providing progress feedback during alignment operations.Predefined configurations for 3D molecular alignment.Enumeration of degree of freedom types defining how molecules can move and flex during alignment operations.Conformational flexibility treatment during the alignment for a pair of a molecule.Represents the result of a molecular alignment operation.Overlays two molecules using the user defined atom pairs.Aligns pairs of molecules by translating and rotating one of them and leave the one called the reference molecule intact.Molecular mechanics based atropisomer detection.Sampling accuracy levels used in atrop bond detection, controlling the number of dihedral rotation steps.Rotates a dihedral in a 3D moleculeResults of a dihedral scan.Encapsulates bond info.One step in a dihedral scan.Align molecules using the maximum common substructure (MCS) of the given molecules.Factory class for ConformationAlignment.Result class for MCS alignment calculation.Calculates the minimum or maximum intermolecular Cartesian distance between atoms by rotating flexible bonds.3D Molecular alignment that uses the maximum common substructure to align a pair of structures.Input property settings for MMPAlignment.Results of the MMPAlignment process.Tool for aligning a target molecule to a pattern molecule.Defines the coloring of the nodes in the alignment graph.Align pairs of molecules (query and the target) using the shapeAlignmentThis interface designed for comparing two molecules in 3D by various overlay methodologies.Align pairs of molecules (query and the target) using the atom/atom matcherSimilarity3D3D Pharmacophore representation for 3D alignments.Detects rotatable bonds in a molecule, used for conformer generation and flexible alignment.Holds the shape representation data of a molecule used for shape-based alignment and similarity calculations.