Package chemaxon.marvin.alignment

The 3D molecular alignment package that can be used to align two or more 3D molecules onto each other.

See:
Description

Interface Summary

AlignmentMoleculeFactory.ProgressBarInterface
PairwiseComparison	This is an interface designed for comparing two molecules in 3D by various overlay methodologies.

Class Summary

Alignment	3D Alignment aligns two or more 3D molecules onto each other.
AlignmentMolecule
AlignmentMoleculeFactory	Creates an AlignmentMolecule form a Molecule based on the settings.
AlignOnPairedAtoms	Overlays two molecules using the user defined atom pairs Example: Molecule mRef = null; Molecule m = null; AlignOnPairedAtoms ap = new AlignOnPairedAtoms(); ap.setReferenceMolecule(mRef, false); // reference will be kept rigid ap.setMoleculeToAlign(m, true); // this will be kept flexible //add pairs where you want for (int i = 0; i < m.getAtomCount(); i++) { p.addAtomPair(i, i); } ap.findFirst(); // aligns in the input conformation ap.findNext(); // randomizes the flexible molecules if flexible alignment selected and aligns.
AlignRigidEasy	Aligns pairs of molecules by translating and rotating one of them and leave the one called the reference molecule intact.
AtropIsomerDetector	If the full rotation around a rotatable bond is blocked a steric proximity usually two isomers occurs.
DihedralRotator	Rotates a dihedral in a 3D molecule
MinMaxDistance	Calculates the minimum or maximum intermolecular Cartesian distance between atoms by rotating flexible bonds.
PairwiseAlignment	Align pairs of molecules (query and the target) using the shape Alignment
PairwiseSimilarity3D	Align pairs of molecules (query and the target) using the atom/atom matcher Similarity3D
Pharmacophore3D	3D Pharmacophore creation and representation for 3D alignments.
RotatableBondDetector

Enum Summary

AlignmentAccuracyMode
AlignmentProperties
AlignmentProperties.ColoringScheme
AlignmentProperties.ColorNotSpecifiedCase
AlignmentProperties.NodeType
AlignmentProperties.OrientationType
AtropIsomerDetector.Accuracy

Package chemaxon.marvin.alignment Description

The 3D molecular alignment package that can be used to align two or more 3D molecules onto each other.