Package chemaxon.marvin.alignment
Class AlignmentMolecule
- java.lang.Object
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- chemaxon.marvin.alignment.AlignmentMolecule
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@PublicAPI public class AlignmentMolecule extends Object
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Deprecated Methods Modifier and Type Method Description void
clearAssigned()
AlignmentMolecule
cloneMolecule()
void
crdMolRefresh()
void
crdSafeRefresh()
static AlignmentMolecule
create(byte[] bytes)
Deprecated.chemaxon.marvin.alignment.DistanceRangeStore
distanceRangeStore()
int
getAtomCount()
AlignmentProperties.ColoringScheme
getColoringScheme()
chemaxon.marvin.alignment.NodeColor
getColors()
double[][]
getMolCrd()
Molecule
getMoleculeOrig()
Gets back a clone of the unmodified input structure.int
getMolID()
int
getNodeCount()
chemaxon.marvin.alignment.NodeSum
getNodes()
int
getRotBondCount()
chemaxon.marvin.alignment.Visualizable
getVisualizable()
double
getVolume()
void
initVariables(boolean enableTranslateAndRotate)
boolean
isEnableTranslateAndRotate()
double
ownOverlap(AlignmentAccuracyMode mode)
void
setAssigned(int i, boolean b)
void
setEnableTranslateAndRotate(boolean enableTranslateAndRotate)
void
setMolID(int molID)
Molecule
showSelectedNodes()
byte[]
toData()
Deprecated.String
toString()
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Method Detail
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setMolID
public void setMolID(int molID)
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getNodes
public chemaxon.marvin.alignment.NodeSum getNodes()
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initVariables
public void initVariables(boolean enableTranslateAndRotate)
- Parameters:
enableTranslateAndRotate
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getColoringScheme
public AlignmentProperties.ColoringScheme getColoringScheme()
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getColors
public chemaxon.marvin.alignment.NodeColor getColors()
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getVisualizable
public chemaxon.marvin.alignment.Visualizable getVisualizable()
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getRotBondCount
public int getRotBondCount()
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create
@Deprecated public static AlignmentMolecule create(byte[] bytes)
Deprecated.
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cloneMolecule
public AlignmentMolecule cloneMolecule()
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toData
@Deprecated public byte[] toData()
Deprecated.
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distanceRangeStore
public chemaxon.marvin.alignment.DistanceRangeStore distanceRangeStore()
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getVolume
public double getVolume()
- Returns:
- the volume of the molecule in A^3
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getAtomCount
public int getAtomCount()
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crdSafeRefresh
public void crdSafeRefresh()
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crdMolRefresh
public void crdMolRefresh()
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getMolID
public int getMolID()
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getNodeCount
public int getNodeCount()
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getMolCrd
public double[][] getMolCrd()
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getMoleculeOrig
public Molecule getMoleculeOrig()
Gets back a clone of the unmodified input structure.- Returns:
- clone of the unmodified input structure
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setAssigned
public void setAssigned(int i, boolean b)
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clearAssigned
public void clearAssigned()
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isEnableTranslateAndRotate
public boolean isEnableTranslateAndRotate()
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setEnableTranslateAndRotate
public void setEnableTranslateAndRotate(boolean enableTranslateAndRotate) throws chemaxon.marvin.alignment.AlignmentException
- Throws:
chemaxon.marvin.alignment.AlignmentException
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showSelectedNodes
public Molecule showSelectedNodes()
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ownOverlap
public double ownOverlap(AlignmentAccuracyMode mode)
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