Package chemaxon.marvin.alignment

Class AlignOnPairedAtoms

java.lang.Object
chemaxon.marvin.alignment.AlignOnPairedAtoms
All Implemented Interfaces:
chemaxon.license.Licensable
@PublicApi public final class AlignOnPairedAtoms extends 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 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)

    • setProperty

      public void setProperty(AlignmentProperties arg0)

    • getMaxGradLimit

      public double getMaxGradLimit()

    • getNodeType

      public AlignmentProperties.NodeType getNodeType()

    • getNodeColor

      public chemaxon.marvin.alignment.NodeColor getNodeColor()

    • setAromatize

      @Deprecated(forRemoval=true) @SubjectToRemoval(date=JUL_01_2025) public void setAromatize(boolean arg0)
      Deprecated, for removal: This API element is subject to removal in a future version.

    • setDehidrogenize

      @Deprecated(forRemoval=true) @SubjectToRemoval(date=JUL_01_2025) public void setDehidrogenize(boolean arg0)
      Deprecated, for removal: This API element is subject to removal in a future version.

    • setFlexibleRingSize

      public void setFlexibleRingSize(int arg0)

    • setFlexibleRingRotatableBondCount

      public void setFlexibleRingRotatableBondCount(int arg0)

    • getMolecules

      public Collection<AlignmentMolecule> getMolecules()

    • isLicensed

      public boolean isLicensed()
      Specified by:
      isLicensed in interface chemaxon.license.Licensable

    • setLicenseEnvironment

      public void setLicenseEnvironment(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)