Package chemaxon.alignment

Class AlignOnPairedAtoms

java.lang.Object

chemaxon.alignment.AlignmentBase

chemaxon.alignment.AlignOnPairedAtoms

All Implemented Interfaces:

Licensable

@PublicApi
public final class AlignOnPairedAtoms
extends AlignmentBase

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.
 System.out.println("rmsd: " + p.getRmsd());
 Molecule result = p.getAlignedWithNewCoordinates();
 

Since:

marvin 5.2.3

Constructor Summary

Constructors

Constructor	Description
AlignOnPairedAtoms()

Method Summary

Modifier and Type	Method	Description
void	addAtomPair(int atom0, int atom1)	Adds an alignment constraint between the reference and aligned molecule.
void	addAtomPair(int atom0, int atom1, double weight)	Adds an alignment constraint between the reference and aligned molecule.
double	align()
void	findFirst()	Overlays the molecule to align on the reference using the predefined atom pairs.
void	findNext()	Randomizes dihedral angles of the input conformation for flexible molecules and aligns.
Molecule	getAlignedWithNewCoordinates()
double[][]	getCoordinatesOfAligned()
double[][]	getCoordinatesOfReference()
Molecule	getReferenceWithNewCoordinates()
double	getRmsd()
void	removeAllPairs()	Removes all user defined atom pairs.
void	removeMolecules()
void	setConformerCount(int count)
void	setConvergenceLimit(double converg)
void	setMolecules(AlignmentMolecule reference, AlignmentMolecule toAlign)
void	setMoleculeToAlign(Molecule m, boolean flexible)	Sets the molecule to align to the reference.
void	setReferenceMolecule(Molecule m, boolean flexible)	Sets the reference molecule to align to.

Methods inherited from class chemaxon.alignment.AlignmentBase

getMaxGradLimit, getMolecules, getNodeColor, getNodeType, getStepLimit, getTimeLimit, isLicensed, setFlexibleRingRotatableBondCount, setFlexibleRingSize, setLicenseEnvironment, setNodeType, setProgressMonitor, setProperty, setProximity, setStepLimit, setTimeLimit

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

AlignOnPairedAtoms

public AlignOnPairedAtoms()

Method Details

removeMolecules

public void removeMolecules()

setReferenceMolecule

public void setReferenceMolecule(Molecule m,
 boolean flexible)
                          throws AlignmentException

Sets the reference molecule to align to. All previously added molecules are removed.

Parameters:

m - reference molecule

flexible - if true treat this molecule flexible. If false its conformation is frozen.

Throws:

AlignmentException

setMolecules

public void setMolecules(AlignmentMolecule reference,
 AlignmentMolecule toAlign)

setConformerCount

public void setConformerCount(int count)

setMoleculeToAlign

public void setMoleculeToAlign(Molecule m,
 boolean flexible)
                        throws AlignmentException

Sets the molecule to align to the reference.

Parameters:

m - this molecule will be translated and rotated

flexible - if true treat this molecule flexible. If false its conformation is frozen.

Throws:

AlignmentException

getCoordinatesOfReference

public double[][] getCoordinatesOfReference()

getCoordinatesOfAligned

public double[][] getCoordinatesOfAligned()

getReferenceWithNewCoordinates

public Molecule getReferenceWithNewCoordinates()

getAlignedWithNewCoordinates

public Molecule getAlignedWithNewCoordinates()

addAtomPair

public void addAtomPair(int atom0,
 int atom1,
 double weight)
                 throws AlignmentException

Adds an alignment constraint between the reference and aligned molecule. Both molecules must be added beforehand.

Parameters:

atom0 - atom seq starting from 0 from the reference molecule

atom1 - atom seq starting from 0 from the other molecule

weight - weight of the constraint of this pair

Throws:

AlignmentException - if there is no such atom

addAtomPair

public void addAtomPair(int atom0,
 int atom1)
                 throws AlignmentException

Adds an alignment constraint between the reference and aligned molecule. Both molecules must be added beforehand.

Parameters:

atom0 - atom seq starting from 0 from the reference molecule

atom1 - atom seq starting from 0 from the other molecule

Throws:

AlignmentException - if there is no such atom

findFirst

public void findFirst()
               throws AlignmentException

Overlays the molecule to align on the reference using the predefined atom pairs.

Throws:

AlignmentException

findNext

public void findNext()
              throws AlignmentException

Randomizes dihedral angles of the input conformation for flexible molecules and aligns. If only rigid molecules selected does nothing.

Throws:

AlignmentException

align

public double align()

getRmsd

public double getRmsd()

Returns:

the root mean square deviation of the current orientation of the two molecules.

removeAllPairs

public void removeAllPairs()

Removes all user defined atom pairs.

setConvergenceLimit

public void setConvergenceLimit(double converg)