MMPAlignment (JChem Base API documentation (c) 1998-2019 ChemAxon Ltd.)

java.lang.Object
- chemaxon.marvin.alignment.MMPAlignment

@PublicAPI
public final class MMPAlignment
extends java.lang.Object

3D Molecular alignment that uses the maximum common substructure to align a pair of structures. The name MMP comes from the expression of matched molecule pairs, as this kind of alignment is an extension of the traditional shape based approach for MMP cases. The coordinates of the atoms in the MCS of the "toAlign" structure will be exactly the same as in the MCS atoms of the reference structure. While the non-MCS parts of the "toAlign" are flexibly aligned to the non-MCS parts reference, to maximize the overall shape score. If multiple MCSes were found, the first 10 are examined as above and the overlay returning the best shape score is returned. If the MCS Tanimoto similarity McsSearchResult.getSimilarity() does not reach a predefined limit, shape based Alignment is applied on the molecule pair.

  Example usage:  
 
  final Molecule reference = MolImporter.importMol("CCCCOC");
  final Molecule toAlign = MolImporter.importMol("CCCCNCC");

  // Either you can generate 3D coordinates :
  // Cleaner.clean(reference, 3, "");
  // Cleaner.clean(toAlign, 3, "");
  // Molecule referenceP = reference;
  // Molecule toAlignP = toAlign;
  
  // or alternatively:
   boolean beautify = true;
   final Molecule referenceP = MMPAlignment.preprocess(reference, beautify);
   final Molecule toAlignP = MMPAlignment.preprocess(toAlign, beautify);
   
  // In this latter case the following actions are performed on Molecules:
  // 1. keep largest fragment, 2. generate 3D coordinates, if the structure is not in 3D, 
  // 3. Additionally, if the "beautify" parameter is true:
  //   - remove atom aliases
  //   - remove lone pairs
  //   - remove explicit Hydrogen atoms
  //   - fix valence errors (needs Checker license)


  final MMPAlignment mmp = new MMPAlignment(referenceP, toAlignP);
  final MMPAlignmentResult result = mmp.calculate();
  final Molecule aligned = result.getMolecule2Aligned();

  System.err.println("3D Tanimoto score: " + result.getShapeScore());
  System.err.println("Coordinate RMSD of the MCS after the alignment: " + result.getRmsd());
  
  // Call a simple utility to write Molecule object into mrv format
  MolGeom.writeMol(result.toMolecule(), "alignedResult.mrv");
 }

Since:: Marvin 6.0.0
Author:: Adrian Kalaszi

Constructor Summary

Constructors
Constructor and Description
`MMPAlignment(Molecule reference, Molecule toAlign)` Constructs an MMPAlignment object for later alignment of two structures.
`MMPAlignment(Molecule reference, Molecule toAlign, MMPAlignmentProperties props)` Constructs an MMPAlignment object for later alignment of two structures.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`MMPAlignmentResult`	`calculate()` Runs the MCS alignment calculation on the two structures of the constructor.
`void`	`cancel()` Cancel the ongoing calculation
`static Molecule`	`clean3d(Molecule m)` Utility for preprocessing structure for alignment.
`static Molecule`	`clean3d(Molecule m, int conformerCount)` Utility for preprocessing structure for alignment.
`static void`	`fixValence(Molecule mol)` Utility for preprocessing structure for alignment.
`static Molecule`	`keepLargestFragment(Molecule m)` Utility for preprocessing structure for alignment.
`static Molecule`	`preprocess(Molecule m, boolean beautify)` Utility for preprocessing structure for alignment.
`static void`	`removeAtomAliases(Molecule m)` Utility for preprocessing structure for alignment.
`static void`	`removeLonePairs(Molecule m)` Utility for preprocessing structure for alignment.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - MMPAlignment
```
public MMPAlignment(Molecule reference,
                    Molecule toAlign,
                    MMPAlignmentProperties props)
```
    Constructs an MMPAlignment object for later alignment of two structures. The conformational flexibility of the two molecules during the alignment can be adjusted using MMPAlignmentProperties.getFlexibilityMode(). The coordinates of the MCS atoms of the reference Molecule are transferred to the MCS atoms of the "toAlign" Molecule. The conformation of the non-MCS parts can be optimized to obtain the best alignment.
    
    Parameters:
    
    reference - The reference structure in the alignment. The coordinates of this structure remains intact during the alignment, if MMPAlignmentProperties.getFlexibilityMode() is set to AlignmentProperties.FlexibilityMode.KEEP_BOTH_RIGID, AlignmentProperties.FlexibilityMode.KEEP_FIRST_RIGID_SECOND_FLEXIBLE or AlignmentProperties.FlexibilityMode.KEEP_FIRST_RIGID_SECOND_FLEXIBLE_EXTRA
    
    toAlign - The structure to align. The coordinates of this structure changes: rotates, translates as a rigid body, and also the rotatable bonds are tweaked in order to align to the reference structure.
    
    props - Properties to control the alignment process.
  - MMPAlignment
```
public MMPAlignment(Molecule reference,
                    Molecule toAlign)
```
    Constructs an MMPAlignment object for later alignment of two structures. The conformational flexibility of the two molecules during the alignment can be adjusted using MMPAlignmentProperties.getFlexibilityMode(). The coordinates of the MCS atoms of the reference Molecule are transferred to the MCS atoms of the "toAlign" Molecule. The conformation of the non-MCS parts can be optimized to obtain the best alignment.
    
    Parameters:
    
    reference - The reference structure in the alignment. The coordinates of this structure remains intact during the alignment, if MMPAlignmentProperties.getFlexibilityMode() is set to AlignmentProperties.FlexibilityMode.KEEP_BOTH_RIGID, AlignmentProperties.FlexibilityMode.KEEP_FIRST_RIGID_SECOND_FLEXIBLE or AlignmentProperties.FlexibilityMode.KEEP_FIRST_RIGID_SECOND_FLEXIBLE_EXTRA
    
    toAlign - The structure to align. The coordinates of this structure changes: rotates, translates as a rigid body, and also the rotatable bonds are tweaked in order to align to the reference structure.
- Method Detail
  - cancel
```
public void cancel()
```
    Cancel the ongoing calculation
  - calculate
```
public MMPAlignmentResult calculate()
```
    Runs the MCS alignment calculation on the two structures of the constructor.
    
    Returns:
    
    the calculation result object.
  - clean3d
```
public static Molecule clean3d(Molecule m)
```
    Utility for preprocessing structure for alignment. Generates 3D coordinates for a 2D structure. The lowest energy conformer will be selected from maximum 50 diverse conformations.
    
    Parameters:
    
    m - The 2D input structure.
    
    Returns:
    
    the lowest energy conformer found
  - clean3d
```
public static Molecule clean3d(Molecule m,
                               int conformerCount)
```
    Utility for preprocessing structure for alignment. Generates 3D coordinates for a 2D structure.
    
    Parameters:
    
    m - The 2D input structure
    
    conformerCount - The lowest energy conformer will be selected from maximum conformerCount diverse conformations.
    
    Returns:
    
    the lowest energy conformer found
  - removeAtomAliases
```
public static void removeAtomAliases(Molecule m)
```
    Utility for preprocessing structure for alignment. Removes atom aliases that usually exist on molecules if read from pdb.
    
    Parameters:
    
    m - removes aliases on this instance.
  - removeLonePairs
```
public static void removeLonePairs(Molecule m)
```
    Utility for preprocessing structure for alignment. Removes lone pair atoms that usually exist on molecules if read from pdb.
    
    Parameters:
    
    m - removes LP atoms on this instance.
  - keepLargestFragment
```
public static Molecule keepLargestFragment(Molecule m)
```
    Utility for preprocessing structure for alignment. Keeps the largest fragment of the moleculegraph.
    
    Parameters:
    
    m - finds the largest fragment of this Molecule
    
    Returns:
    
    a new clone of the largest fragment.
  - fixValence
```
public static void fixValence(Molecule mol)
```
    Utility for preprocessing structure for alignment. Fix valence errors if there is any. Launches ValenceErrorChecker.
    
    Parameters:
    
    mol - modifies this reference molecule
  - preprocess
```
public static Molecule preprocess(Molecule m,
                                  boolean beautify)
```
    Utility for preprocessing structure for alignment. Performs the following actions on the Molecule required by the alignment:
    1. keepLargestFragment(Molecule)
    2. Generates 3D coordinates, if the structure is not in 3D
    Optionally performs the following actions if boolean parameter is set.
    1. removeAtomAliases(Molecule)
    2. removeLonePairs(Molecule)
    3. remove explicit Hydrogen atoms
    4. Fix valence errors
    Parameters:
    
    m -
    
    Returns:
    
    the clone of the input molecule preprocessed.

Class MMPAlignment

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

MMPAlignment

MMPAlignment

Method Detail

cancel

calculate

clean3d

clean3d

removeAtomAliases

removeLonePairs

keepLargestFragment

fixValence

preprocess