chemaxon.marvin.alignment
Class AtropIsomerDetector

java.lang.Object
  chemaxon.marvin.alignment.AtropIsomerDetector

All Implemented Interfaces:

chemaxon.license.Licensable

public class AtropIsomerDetector
extends java.lang.Object
implements chemaxon.license.Licensable

If the full rotation around a rotatable bond is blocked a steric proximity usually two isomers occurs. The algorithm rotates all rotatable bonds stepwise and optimizes the conformation id the domain of the remaining dihedrals. The energy values are obtained from MMFF dihedral potential and MMFF long range. If the conformational energy barrier is higher than a user defined limit that bond defined as atrop bond.
Usage:

  Molecule m = MolImporter.importMol("CC(C)[C@@](C)(N(C(=O)C=C)C1=C(I)C=CC=C1)C(O)=O");
  AtropIsomerDetector atp = new AtropIsomerDetector();
  atp.calculate(m);
  int[] found = atp.getAtropBonds();
 

Author:

Adrian

See Also:

Atropisomer on wiki

Nested Class Summary

static class

AtropIsomerDetector.Accuracy

Constructor Summary

AtropIsomerDetector()

Method Summary

void	calculate(Molecule m) Run the atropisomer calculation.
int[]	getAtropBonds() After the calculate method finished.
int	getPossibleRotatableBondCount() Rotatable bond count before the atrop isomer calculation.
int	getRealRotatableBondCount() Rotatable bond count (atrop bonds excluded)
Molecule	getResultMolecule() The result molecule will be 3D and aromatized version of the input molecules.
boolean	isLicensed() Returns information about the licensing of the product.
void	setBarrierLimit(double barrierLimit) Set the energy barrier limit.
void	setFlexibleRingRotatableBondCount(int i)
void	setFlexibleRingSize(int size)
void	setLicenseEnvironment(java.lang.String env) Every license can have a modifier environment that's typically an integration environment.
void	setMethylsRotatable(boolean methylsRotatable) This is a speedup heuristics.
void	setNumberOfAtomsAcceptToRotate(int numberOfAtomsAcceptToRotate) If only a given number of atoms (or less) can be found at one of the side of the dihedral skip this.
void	setSamplingAccuracy(AtropIsomerDetector.Accuracy a)
void	setSamplingAccuracy(int accuracy)

Methods inherited from class java.lang.Object

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

Constructor Detail

AtropIsomerDetector

public AtropIsomerDetector()
                    throws chemaxon.marvin.alignment.AlignmentException

Throws:

chemaxon.marvin.alignment.AlignmentException

Method Detail

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

setMethylsRotatable

public void setMethylsRotatable(boolean methylsRotatable)

This is a speedup heuristics. Rotating the three hydrogens of a methyl group rarely results in atrop bonds.

Parameters:

methylsRotatable - if true rotate methyl groups too. Default is false.

setNumberOfAtomsAcceptToRotate

public void setNumberOfAtomsAcceptToRotate(int numberOfAtomsAcceptToRotate)

If only a given number of atoms (or less) can be found at one of the side of the dihedral skip this.

Parameters:

numberOfAtomsAcceptToRotate - default is 1.

setBarrierLimit

public void setBarrierLimit(double barrierLimit)

Set the energy barrier limit.

Parameters:

barrierLimit - New energy barrier limit in kcal/mol. default is 200

setSamplingAccuracy

public void setSamplingAccuracy(int accuracy)

setSamplingAccuracy

public void setSamplingAccuracy(AtropIsomerDetector.Accuracy a)

setFlexibleRingRotatableBondCount

public void setFlexibleRingRotatableBondCount(int i)

setFlexibleRingSize

public void setFlexibleRingSize(int size)

calculate

public void calculate(Molecule m)
               throws chemaxon.marvin.alignment.AlignmentException

Run the atropisomer calculation.

Parameters:

m - input molecule

Throws:

chemaxon.marvin.alignment.AlignmentException

getAtropBonds

public int[] getAtropBonds()

After the calculate method finished.

Returns:

the indices of the atrop bonds.

getRealRotatableBondCount

public int getRealRotatableBondCount()

Rotatable bond count (atrop bonds excluded)

Returns:

Rotatable bond count

getPossibleRotatableBondCount

public int getPossibleRotatableBondCount()

Rotatable bond count before the atrop isomer calculation.

Returns:

All rotatable bond count

getResultMolecule

public Molecule getResultMolecule()

The result molecule will be 3D and aromatized version of the input molecules. Hydrogens are also added.

Returns:

the result molecule.