chemaxon.marvin.alignment
Class AlignOnPairedAtoms

java.lang.Object
  chemaxon.marvin.alignment.AlignOnPairedAtoms

All Implemented Interfaces:

chemaxon.license.Licensable

public class AlignOnPairedAtoms
extends java.lang.Object

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

AlignOnPairedAtoms()

Method Summary

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.
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()
java.util.Collection<AlignmentMolecule>	getMolecules()
chemaxon.marvin.alignment.NodeColor	getNodeColor()
AlignmentProperties.NodeType	getNodeType()
Molecule	getReferenceWithNewCoordinates()
double	getRmsd()
int	getStepLimit()
int	getTimeLimit()
boolean	isLicensed() Returns information about the licensing of the product.
void	removeAllPairs() Removes all user defined atom pairs.
void	removeMolecules()
void	setAromatize(boolean aromatize)
void	setDehidrogenize(boolean hy)
void	setFlexibleRingRotatableBondCount(int b)
void	setFlexibleRingSize(int s)
void	setLicenseEnvironment(java.lang.String env) Every license can have a modifier environment that's typically an integration environment.
void	setMoleculeToAlign(Molecule m, boolean flexible) Sets the molecule to align to the reference.
void	setNodeType(AlignmentProperties.NodeType t)
void	setProgressMonitor(chemaxon.common.util.MProgressMonitor progressMonitor)
void	setProperty(AlignmentProperties props)
void	setProximity(chemaxon.marvin.alignment.AlignmentProperties.ProximityPotentialType pot)
void	setReferenceMolecule(Molecule m, boolean flexible) Sets the reference molecule to align to.
void	setStepLimit(int stepLimit)
void	setTimeLimit(int timeLimit) Sets the maximum time used for the alignment.

Methods inherited from class java.lang.Object

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

Constructor Detail

AlignOnPairedAtoms

public AlignOnPairedAtoms()

Method Detail

removeMolecules

public void removeMolecules()

setReferenceMolecule

public void setReferenceMolecule(Molecule m,
                                 boolean flexible)
                          throws chemaxon.marvin.alignment.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:

chemaxon.marvin.alignment.AlignmentException

setMoleculeToAlign

public void setMoleculeToAlign(Molecule m,
                               boolean flexible)
                        throws chemaxon.marvin.alignment.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:

chemaxon.marvin.alignment.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 chemaxon.marvin.alignment.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:

chemaxon.marvin.alignment.AlignmentException - if there is no such atom

addAtomPair

public void addAtomPair(int atom0,
                        int atom1)
                 throws chemaxon.marvin.alignment.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:

chemaxon.marvin.alignment.AlignmentException - if there is no such atom

findFirst

public void findFirst()
               throws chemaxon.marvin.alignment.AlignmentException

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

Throws:

chemaxon.marvin.alignment.AlignmentException

findNext

public void findNext()
              throws chemaxon.marvin.alignment.AlignmentException

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

Throws:

chemaxon.marvin.alignment.AlignmentException

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.

setProperty

public void setProperty(AlignmentProperties props)

getNodeType

public AlignmentProperties.NodeType getNodeType()

getNodeColor

public chemaxon.marvin.alignment.NodeColor getNodeColor()

setAromatize

public void setAromatize(boolean aromatize)

setDehidrogenize

public void setDehidrogenize(boolean hy)

setFlexibleRingSize

public void setFlexibleRingSize(int s)

setFlexibleRingRotatableBondCount

public void setFlexibleRingRotatableBondCount(int b)

getMolecules

public java.util.Collection<AlignmentMolecule> getMolecules()

isLicensed

public boolean isLicensed()

Description copied from interface: chemaxon.license.Licensable

Returns information about the licensing of the product. Example implementation: return LicenseHandler.isLicensed( LicenseHandler.MY_IDENTIFIER, licenseEnvironment );

Specified by:

isLicensed in interface chemaxon.license.Licensable

Returns:

true if the product is correctly licensed

setLicenseEnvironment

public void setLicenseEnvironment(java.lang.String env)

Description copied from interface: chemaxon.license.Licensable

Every license can have a modifier environment that's typically an integration environment. All being Licensable should be prepared to store and show a set environment to the LicenseHandler. Example implementation:

 private String licenseEnvironment = "";
 public void setLicenseEnvironment(String env) {
     licenseEnvironment = env;
 }
 

Specified by:

setLicenseEnvironment in interface chemaxon.license.Licensable

Parameters:

env - environment String to be stored and passed to the LicenseHandler in the isLicensed method

getStepLimit

public int getStepLimit()

setStepLimit

public void setStepLimit(int stepLimit)

getTimeLimit

public int getTimeLimit()

setNodeType

public void setNodeType(AlignmentProperties.NodeType t)

setTimeLimit

public void setTimeLimit(int timeLimit)

Sets the maximum time used for the alignment. If reached returns the partly aligned structures.

Parameters:

timeLimit - time limit in millisecond. if -1 then disabled.

setProgressMonitor

public void setProgressMonitor(chemaxon.common.util.MProgressMonitor progressMonitor)

setProximity

public void setProximity(chemaxon.marvin.alignment.AlignmentProperties.ProximityPotentialType pot)