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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Interface Summary Interface Description AlignmentMoleculeFactory.ProgressBarInterface MCSAlignment Align molecules using the the maximum common substructure (MCS) of the given molecules.
Usage examples:MCSAlignmentResult Result class for MCS alignment calculation.PairwiseComparison This interface designed for comparing two molecules in 3D by various overlay methodologies. -
Class Summary Class Description Alignment 3D Alignment aligns two or more 3D molecules onto each other.AlignmentMolecule AlignmentMoleculeFactory Creates anAlignmentMoleculeform aMoleculebased on the settings.AlignOnPairedAtoms Overlays two molecules using the user defined atom pairs
Example:AlignRigidEasy Aligns pairs of molecules by translating and rotating one of them and leave the one called the reference molecule intact.AtropIsomerDetector Molecular mechanics based atropisomer detection.DihedralRotator Rotates a dihedral in a 3D moleculeMCSAlignment.Factory Factory class for ConformationAlignment.MinMaxDistance Calculates the minimum or maximum intermolecular Cartesian distance between atoms by rotating flexible bonds.MMPAlignment 3D Molecular alignment that uses the maximum common substructure to align a pair of structures.MMPAlignmentProperties Input property settings for MMPAlignment.MMPAlignmentResult Results of the MMPAlignment process.PairwiseAlignment Align pairs of molecules (query and the target) using the shapeAlignmentPairwiseSimilarity3D Align pairs of molecules (query and the target) using the atom/atom matcherSimilarity3DPharmacophore3D 3D Pharmacophore representation for 3D alignments.RotatableBondDetector -
Enum Summary Enum Description AlignmentAccuracyMode Settings for the representation of a molecular shape.AlignmentProperties AlignmentProperties.ColoringScheme AlignmentProperties.ColorNotSpecifiedCase AlignmentProperties.DegreeOfFreedomType AlignmentProperties.FlexibilityMode Conformational flexibility treatment during the alignment for a pair of a molecule.AlignmentProperties.NodeType AlignmentProperties.OrientationType AtropIsomerDetector.Accuracy