Package chemaxon.marvin.alignment
package chemaxon.marvin.alignment
The 3D molecular alignment package that can be used to align two or more 3D molecules onto each other.
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ClassDescription3D Alignment aligns two or more 3D molecules onto each other.Settings for the representation of a molecular shape.Creates an
AlignmentMoleculeform aMoleculebased on the settings.Conformational flexibility treatment during the alignment for a pair of a molecule.Overlays two molecules using the user defined atom pairs
Example: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.Rotates a dihedral in a 3D moleculeAlign molecules using the the maximum common substructure (MCS) of the given molecules.
Usage examples: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.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.