MCSAlignmentResult (Marvin API documentation (c) 1998-2023 Chemaxon Ltd.)

```
@Beta
@PublicAPI
public interface MCSAlignmentResult
```
Result class for MCS alignment calculation.
Please note that this class is marked with @Beta annotation, so it can be subject of incompatible changes or removal in later releases.

Since:

15.7.20

See Also:

MCSAlignment

Method Summary

All Methods Instance Methods Abstract Methods
Modifier and Type	Method	Description
`int[]`	`atomMapping()`	Array of atom - atom mapping.
`double`	`rmsd()`	Root mean square deviation from the reference molecule.
`Molecule`	`rotatedAndReferenceFused()`	Fuse the rotated and the reference molecule.
`Molecule`	`rotatedMolecule()`	The rotated molecule.

- Method Detail
  - rmsd
```
double rmsd()
```
    Root mean square deviation from the reference molecule.
    
    Returns:
    
    the rmsd value
  - rotatedMolecule
```
Molecule rotatedMolecule()
```
    The rotated molecule.
    
    Returns:
    
    rotated molecule.
  - atomMapping
```
int[] atomMapping()
```
    Array of atom - atom mapping.
    
    Returns:
    
    mapping[first mols atomseq] = second mols atomseq
  - rotatedAndReferenceFused
```
Molecule rotatedAndReferenceFused()
```
    Fuse the rotated and the reference molecule.
    
    Returns:
    
    the fused molecule