Package chemaxon.marvin.alignment
Class AtropIsomerDetector
- java.lang.Object
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- chemaxon.marvin.alignment.AtropIsomerDetector
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- All Implemented Interfaces:
chemaxon.license.Licensable
@PublicAPI public class AtropIsomerDetector extends 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)[[email protected]@](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.
- See Also:
- Atropisomer on wiki
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
AtropIsomerDetector.Accuracy
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Field Summary
Fields Modifier and Type Field Description static int
DEFAULT_SAMPLING_ACCURACY
Default for parametersetSamplingAccuracy(int)
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Constructor Summary
Constructors Constructor Description AtropIsomerDetector()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method 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.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(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(int accuracy)
Set sampling accuracy.void
setSamplingAccuracy(AtropIsomerDetector.Accuracy accuracy)
Set sampling accuracy.void
setTimeoutInSeconds(int timeoutInSeconds)
Set time out.
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Field Detail
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DEFAULT_SAMPLING_ACCURACY
public static final int DEFAULT_SAMPLING_ACCURACY
Default for parametersetSamplingAccuracy(int)
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Method Detail
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isLicensed
public boolean isLicensed()
- Specified by:
isLicensed
in interfacechemaxon.license.Licensable
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setLicenseEnvironment
public void setLicenseEnvironment(String env)
- Specified by:
setLicenseEnvironment
in interfacechemaxon.license.Licensable
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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.
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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.
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setBarrierLimit
public void setBarrierLimit(double barrierLimit)
Set the energy barrier limit.- Parameters:
barrierLimit
- New energy barrier limit in kcal/mol. default is 200
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setSamplingAccuracy
public void setSamplingAccuracy(int accuracy)
Set sampling accuracy.- Parameters:
accuracy
- Sample count for a full rotation to use
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setTimeoutInSeconds
public void setTimeoutInSeconds(int timeoutInSeconds)
Set time out.- Parameters:
timeoutInSeconds
- Timeout to use or0
for no timeout.
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setSamplingAccuracy
public void setSamplingAccuracy(AtropIsomerDetector.Accuracy accuracy)
Set sampling accuracy.- Parameters:
accuracy
- Preset value representing sample count for a full rotation to use
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setFlexibleRingRotatableBondCount
public void setFlexibleRingRotatableBondCount(int i)
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setFlexibleRingSize
public void setFlexibleRingSize(int size)
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calculate
public void calculate(Molecule input) throws chemaxon.marvin.alignment.AlignmentException
Run the atropisomer calculation.- Parameters:
input
- the input molecule- Throws:
chemaxon.marvin.alignment.AlignmentException
- Propagated
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calculate
public void calculate(Molecule input, SubProgressObserver progressObserver) throws chemaxon.marvin.alignment.AlignmentException
Run the atropisomer calculation.- Parameters:
input
- the input moleculeprogressObserver
- 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 thatProgressObserver.done()
is invoked when execution finished.- Throws:
chemaxon.marvin.alignment.AlignmentException
- Propagated
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calculate
@Beta public void calculate(Molecule input, SubProgressObserver progressObserver, DihedralScanListener dihedralScanListener) throws chemaxon.marvin.alignment.AlignmentException
Run the atropisomer calculation.- Parameters:
input
- the input moleculeprogressObserver
- 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 thatProgressObserver.done()
is invoked when execution finished.dihedralScanListener
- Listener to use ornull
Please note that this method is marked withBeta
annotation, so it can be subject of incompatible changes or removal in any of the later releases.- Throws:
chemaxon.marvin.alignment.AlignmentException
- PropagatedCancellationException
- When a specifiedprogressObserver
is cancelled by returningtrue
fromCancelObserver.isCancelled()
or when timeout occurred
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getAtropBonds
public int[] getAtropBonds()
After the calculate method finished.- Returns:
- the indices of the detected atrop bonds.
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getDihedralScanResults
@Beta public List<DihedralScanResult> getDihedralScanResults()
Get results of executed dihedral scans. Please note that this method is marked withBeta
annotation, so it can be subject of incompatible changes or removal in any of the later releases.- Returns:
- Executed dihedral scan results
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getRealRotatableBondCount
public int getRealRotatableBondCount()
Rotatable bond count (atrop bonds excluded)- Returns:
- Rotatable bond count
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getPossibleRotatableBondCount
public int getPossibleRotatableBondCount()
Rotatable bond count before the atrop isomer calculation.- Returns:
- All rotatable bond count
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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.
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