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 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
    • setMolecules

      public void setMolecules(AlignmentMolecule reference, AlignmentMolecule toAlign)
    • setConformerCount

      public void setConformerCount(int count)
    • 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
    • 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)