Alignment (Marvin API documentation (c) 1998-2019 ChemAxon Ltd.)

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

All Implemented Interfaces:: chemaxon.license.Licensable

@PublicAPI
public class Alignment
extends java.lang.Object

3D Alignment aligns two or more 3D molecules onto each other. The conformation of all molecules can be kept flexible so as to maximize the molecular overlap or also the input conformation of some of the molecules can be frozen. Alignment tries to maximize the overlap of atoms of the same type of different molecules.
Example source

 Molecule[] mols = new Molecule[2];
 mols[0] = MolImporter.importMol("CCCCC");
 mols[1] = MolImporter.importMol("CCCCCCC");
 mols[0].aromatize();
 mols[1].aromatize();
 mols[0].clean(3, null);
 mols[1].clean(3, null);
 Alignment aa = new Alignment();
 aa.addMolecule(mols[0], false, false); // adds a molecule no roatation / no
 // conformational flexibility
 aa.addMolecule(mols[1], true, true); // adds a molecule with roatation/ with
 // conformational flexibility
 aa.addUserConstraint(0, 3, 1, 4); // optional: add user constraint between atoms
 // of two different molecules. Any
 // constraint can be added
 aa.align();
 Molecule result = aa.getMoleculeWithAlignedCoordinates(1);
 double tanimoto = aa.tanimoto();

Since:: 5.2
Author:: Adrian Kalaszi

Constructor Summary

Constructors
Constructor and Description

Alignment()

Alignment(AlignmentProperties props)

Constructors
Constructor and Description
`Alignment()`
`Alignment(AlignmentProperties props)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method and Description
`void`	`addConstraintsFromUserMappedAtoms()` An atomMap can be added to some of the atoms in MarvinSketch using the single reaction arrow.
`void`	`addMolecule(Molecule m, boolean flexible, boolean enableTranslateAndRotate)` Add molecule to align
`void`	`addNodeColorWeight(int t1, int t2, double w)` User may define extra weights between colors defined at setColoringScheme.
`void`	`addUserConstraint(int molSeq0, int atomSeq0, int molSeq1, int atomSeq1)` Adds user constraint between two atoms of two different molecules The addMol method calls must precede this method.
`void`	`align()` 3D alignment on two or more molecules.
`Molecule`	`getAlignedMoleculesAsFragments()`
`double`	`getMaxGradLimit()`
`java.util.Collection<AlignmentMolecule>`	`getMolecules()`
`Molecule`	`getMoleculeWithAlignedCoordinates(int molID)` After the alignment result molecule can be obtained.
`chemaxon.marvin.alignment.NodeColor`	`getNodeColor()`
`AlignmentProperties.NodeType`	`getNodeType()`
`AlignmentProperties.OrientationType`	`getOrientationType()`
`double`	`getRmsd()`
`chemaxon.marvin.alignment.Status`	`getStatus()`
`int`	`getStepLimit()`
`int`	`getTimeLimit()`
`double`	`getVolumeScore()` Calculates the volume score between the current orientation and conformation of the two molecules.
`boolean`	`isLicensed()`
`static Molecule`	`randomizeRotatableDihedrals(Molecule m, java.util.Random r)` Rotates rotatable bonds by a random dihedral angle value.
`void`	`removeAllConstraints()`
`void`	`removeAllMolecules()` before every new alignment the molecules have to be removed.
`void`	`setAromatize(boolean arg0)` Deprecated.
`void`	`setColoringScheme(AlignmentProperties.ColoringScheme c)`
`void`	`setConformerCount(int conformerCount)` The the dihedral angles of every flexible molecule should be randomized before alignment.
`void`	`setDefaultNodeWeightBehavior(AlignmentProperties.ColorNotSpecifiedCase n)`
`void`	`setDehidrogenize(boolean arg0)` Deprecated.
`void`	`setFlexibleRingRotatableBondCount(int arg0)`
`void`	`setFlexibleRingSize(int arg0)`
`void`	`setLicenseEnvironment(java.lang.String arg0)`
`void`	`setMinimumCommonSize(int minimumCommonSize)` Deprecated.
`void`	`setMode(AlignmentAccuracyMode mode)`
`void`	`setMolecules(AlignmentMolecule reference, AlignmentMolecule toAlign)`
`void`	`setNodeType(AlignmentProperties.NodeType arg0)`
`void`	`setOrientationType(AlignmentProperties.OrientationType orientationType)`
`void`	`setProgressMonitor(MProgressMonitor arg0)`
`void`	`setProperty(AlignmentProperties props)`
`void`	`setProximity(chemaxon.marvin.alignment.AlignmentProperties.ProximityPotentialType arg0)`
`void`	`setStepLimit(int arg0)`
`void`	`setTimeLimit(int arg0)`
`double`	`tanimoto()` Calculates the atomic colored volume Tanimoto similarity of two 3D molecules.

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

- Constructor Detail
  - Alignment
```
public Alignment()
```
  - Alignment
```
public Alignment(AlignmentProperties props)
```
- Method Detail
  - getMoleculeWithAlignedCoordinates
```
public Molecule getMoleculeWithAlignedCoordinates(int molID)
```
    After the alignment result molecule can be obtained.
    
    Parameters:
    
    molID - input sequence / Which molecule to return.
    
    Returns:
    
    the result molecule
  - setMode
```
public void setMode(AlignmentAccuracyMode mode)
```
  - getAlignedMoleculesAsFragments
```
public Molecule getAlignedMoleculesAsFragments()
```
  - getOrientationType
```
public AlignmentProperties.OrientationType getOrientationType()
```
  - setProperty
```
public final void setProperty(AlignmentProperties props)
```
  - setConformerCount
```
public void setConformerCount(int conformerCount)
```
    The the dihedral angles of every flexible molecule should be randomized before alignment.
    
    Parameters:
    
    conformerCount - number of randomized conformations to try to align
  - randomizeRotatableDihedrals
```
public static Molecule randomizeRotatableDihedrals(Molecule m,
                                                   java.util.Random r)
```
    Rotates rotatable bonds by a random dihedral angle value. The resulting conformation is optimized, to avoid steric clashes.
    
    Parameters:
    
    m - this Molecule object will be cloned and the coordinates will remain intact.
    
    r - parameterized Random object
    
    Returns:
    
    the Molecule in changed conformation
  - setColoringScheme
```
public void setColoringScheme(AlignmentProperties.ColoringScheme c)
```
  - addNodeColorWeight
```
public void addNodeColorWeight(int t1,
                               int t2,
                               double w)
```
    User may define extra weights between colors defined at setColoringScheme. The default weights are 1 for the same and 0 for the dissimilar types.
    
    Parameters:
    
    t1 - color 1 (Atomtype)
    
    t2 - color 2 (Atomtype)
    
    w - weight
  - setDefaultNodeWeightBehavior
```
public void setDefaultNodeWeightBehavior(AlignmentProperties.ColorNotSpecifiedCase n)
```
  - setOrientationType
```
public void setOrientationType(AlignmentProperties.OrientationType orientationType)
```
  - removeAllConstraints
```
public void removeAllConstraints()
```
  - removeAllMolecules
```
public void removeAllMolecules()
```
    before every new alignment the molecules have to be removed.
  - addMolecule
```
public void addMolecule(Molecule m,
                        boolean flexible,
                        boolean enableTranslateAndRotate)
                 throws chemaxon.marvin.alignment.AlignmentException
```
    Add molecule to align
    
    Parameters:
    
    m - Molecule to align
    
    flexible - if "false" the molecule kept rigid. If "true" the rotatable bonds are rotated to achieve the best alignment.
    
    enableTranslateAndRotate - Turn translation and rotation on if true. If false molecule is frozen.
    
    Throws:
    
    AlignmentException
  - addUserConstraint
```
public void addUserConstraint(int molSeq0,
                              int atomSeq0,
                              int molSeq1,
                              int atomSeq1)
                       throws chemaxon.marvin.alignment.AlignmentException
```
    Adds user constraint between two atoms of two different molecules The addMol method calls must precede this method.
    
    Parameters:
    
    molSeq0 -
    
    atomSeq0 -
    
    molSeq1 -
    
    atomSeq1 -
    
    Throws:
    
    chemaxon.marvin.alignment.AlignmentException - if there is no such atom or molecule.
  - tanimoto
```
public double tanimoto()
                throws chemaxon.marvin.alignment.AlignmentException
```
    Calculates the atomic colored volume Tanimoto similarity of two 3D molecules.
    
    Returns:
    
    the 3D volume Tanimoto between 0..1 If more than two molecules are added returns -1.
    
    Throws:
    
    AlignmentException
  - getStatus
```
public chemaxon.marvin.alignment.Status getStatus()
```
  - align
```
public void align()
           throws chemaxon.marvin.alignment.AlignmentException
```
    3D alignment on two or more molecules. WARNING! The new coordinates are written back to the input molecules.
    
    Throws:
    
    AlignmentException - if there is an error with the molecule: not 3d or multi-fragment.
  - getVolumeScore
```
public double getVolumeScore()
```
    Calculates the volume score between the current orientation and conformation of the two molecules.
    
    Returns:
    
    the volume intersection score.
  - getRmsd
```
public double getRmsd()
```
  - addConstraintsFromUserMappedAtoms
```
public void addConstraintsFromUserMappedAtoms()
                                       throws chemaxon.marvin.alignment.AlignmentException
```
    An atomMap can be added to some of the atoms in MarvinSketch using the single reaction arrow. These maps are imported as user pairs.
    
    Throws:
    
    chemaxon.marvin.alignment.AlignmentException
  - setMolecules
```
public void setMolecules(AlignmentMolecule reference,
                         AlignmentMolecule toAlign)
```
  - setMinimumCommonSize
```
@Deprecated
public void setMinimumCommonSize(int minimumCommonSize)
```
    Deprecated.
    
    No effect. Will be removed in a future release.
  - getMaxGradLimit
```
public double getMaxGradLimit()
```
  - getNodeType
```
public AlignmentProperties.NodeType getNodeType()
```
  - getNodeColor
```
public chemaxon.marvin.alignment.NodeColor getNodeColor()
```
  - setAromatize
```
@Deprecated
public void setAromatize(boolean arg0)
```
    Deprecated.
  - setDehidrogenize
```
@Deprecated
public void setDehidrogenize(boolean arg0)
```
    Deprecated.
  - setFlexibleRingSize
```
public void setFlexibleRingSize(int arg0)
```
  - setFlexibleRingRotatableBondCount
```
public void setFlexibleRingRotatableBondCount(int arg0)
```
  - getMolecules
```
public java.util.Collection<AlignmentMolecule> getMolecules()
```
  - isLicensed
```
public boolean isLicensed()
```
    Specified by:
    
    isLicensed in interface chemaxon.license.Licensable
  - setLicenseEnvironment
```
public void setLicenseEnvironment(java.lang.String arg0)
```
    Specified by:
    
    setLicenseEnvironment in interface chemaxon.license.Licensable
  - getStepLimit
```
public int getStepLimit()
```
  - setStepLimit
```
public void setStepLimit(int arg0)
```
  - getTimeLimit
```
public int getTimeLimit()
```
  - setNodeType
```
public void setNodeType(AlignmentProperties.NodeType arg0)
```
  - setTimeLimit
```
public void setTimeLimit(int arg0)
```
  - setProgressMonitor
```
public void setProgressMonitor(MProgressMonitor arg0)
```
  - setProximity
```
public void setProximity(chemaxon.marvin.alignment.AlignmentProperties.ProximityPotentialType arg0)
```

Class Alignment

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

Alignment

Alignment

Method Detail

getMoleculeWithAlignedCoordinates

setMode

getAlignedMoleculesAsFragments

getOrientationType

setProperty

setConformerCount

randomizeRotatableDihedrals

setColoringScheme

addNodeColorWeight

setDefaultNodeWeightBehavior

setOrientationType

removeAllConstraints

removeAllMolecules

addMolecule

addUserConstraint

tanimoto

getStatus

align

getVolumeScore

getRmsd

addConstraintsFromUserMappedAtoms

setMolecules

setMinimumCommonSize

getMaxGradLimit

getNodeType

getNodeColor

setAromatize

setDehidrogenize

setFlexibleRingSize

setFlexibleRingRotatableBondCount

getMolecules

isLicensed

setLicenseEnvironment

getStepLimit

setStepLimit

getTimeLimit

setNodeType

setTimeLimit

setProgressMonitor

setProximity