chemaxon.marvin.alignment

Class AtropIsomerDetector

java.lang.Object

chemaxon.marvin.alignment.AtropIsomerDetector

All Implemented Interfaces:

chemaxon.license.Licensable

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

Molecular mechanics based atropisomer detection. 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 by the current implementation.

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();
 

Limitations:

• The presence of a single rotational barrier is recognized as an atrop bond. This can result false positives for simpler hindered rotatable bonds.
• Symmetries of the rotated parts are not examined. This can result in false positives for symmetric structures showing rotation barriers without differentiable conformers.

Author:

Adrian Kalaszi

See Also:

Atropisomer on wiki

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	AtropIsomerDetector.Accuracy

Field Summary

Fields

Modifier and Type	Field and Description
static int	DEFAULT_SAMPLING_ACCURACY Default for parameter setSamplingAccuracy(int).

Constructor Summary

Constructors

Constructor and Description
AtropIsomerDetector()

Method Summary

Modifier and Type	Method and Description
void	calculate(Molecule input) Run the atropisomer calculation.
void	calculate(Molecule input, SubProgressObserver progressObserver) Run the atropisomer calculation.
void	calculate(Molecule input, SubProgressObserver progressObserver, DihedralScanListener dihedralScanListener) Run the atropisomer calculation.
int[]	getAtropBonds() After the calculate method finished.
java.util.List<DihedralScanResult>	getDihedralScanResults() Get results of executed dihedral scans.
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()
void	setBarrierLimit(double barrierLimit) Set the energy barrier limit.
void	setFlexibleRingRotatableBondCount(int i)
void	setFlexibleRingSize(int size)
void	setLicenseEnvironment(java.lang.String env)
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 accuracy) Set sampling accuracy.
void	setSamplingAccuracy(int accuracy) Set sampling accuracy.
void	setTimeoutInSeconds(int timeoutInSeconds) Set time out.

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_SAMPLING_ACCURACY

public static final int DEFAULT_SAMPLING_ACCURACY

Default for parameter setSamplingAccuracy(int).

Constructor Detail

AtropIsomerDetector

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

Throws:

chemaxon.marvin.alignment.AlignmentException

Method Detail

isLicensed

public boolean isLicensed()

Specified by:

isLicensed in interface chemaxon.license.Licensable

setLicenseEnvironment

public void setLicenseEnvironment(java.lang.String env)

Specified by:

setLicenseEnvironment in interface chemaxon.license.Licensable

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)

Set sampling accuracy.

Parameters:

accuracy - Sample count for a full rotation to use

setTimeoutInSeconds

public void setTimeoutInSeconds(int timeoutInSeconds)

Set time out.

Parameters:

timeoutInSeconds - Timeout to use or 0 for no timeout.

setSamplingAccuracy

public void setSamplingAccuracy(AtropIsomerDetector.Accuracy accuracy)

Set sampling accuracy.

Parameters:

accuracy - Preset value representing sample count for a full rotation to use

setFlexibleRingRotatableBondCount

public void setFlexibleRingRotatableBondCount(int i)

setFlexibleRingSize

public void setFlexibleRingSize(int size)

calculate

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

Run the atropisomer calculation.

Parameters:

input - the input molecule

Throws:

AlignmentException - Propagated

calculate

public void calculate(Molecule input,
                      SubProgressObserver progressObserver)
               throws chemaxon.marvin.alignment.AlignmentException

Run the atropisomer calculation.

Parameters:

input - the input molecule

progressObserver - Observer to track progress of dihedral scans. Total work unit count is set to the visited rotatable bond counts. Note that dihedral scan for a rotatable bond can be skipped depending on the settings. Note that ProgressObserver.done() is invoked when execution finished.

Throws:

AlignmentException - Propagated

calculate

@Beta
public void calculate(Molecule input,
                            SubProgressObserver progressObserver,
                            DihedralScanListener dihedralScanListener)
                     throws chemaxon.marvin.alignment.AlignmentException

Run the atropisomer calculation.

Parameters:

input - the input molecule

progressObserver - Observer to track progress of dihedral scans. Total work unit count is set to the visited rotatable bond counts. Note that dihedral scan for a rotatable bond can be skipped depending on the settings. Note that ProgressObserver.done() is invoked when execution finished.

dihedralScanListener - Listener to use or null Please note that this method is marked with Beta annotation, so it can be subject of incompatible changes or removal in any of the later releases.

Throws:

AlignmentException - Propagated

java.util.concurrent.CancellationException - When a specified progressObserver is cancelled by returning true from CancelObserver.isCancelled() or when timeout occurred

getAtropBonds

public int[] getAtropBonds()

After the calculate method finished.

Returns:

the indices of the detected atrop bonds.

getDihedralScanResults

@Beta
public java.util.List<DihedralScanResult> getDihedralScanResults()

Get results of executed dihedral scans. Please note that this method is marked with Beta annotation, so it can be subject of incompatible changes or removal in any of the later releases.

Returns:

Executed dihedral scan results

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.