Package jme
Class JMEmol
java.lang.Object
jme.JMEmol
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Field Summary
FieldsModifier and TypeFieldDescriptionint
int
boolean
static final int
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Constructor Summary
ConstructorsConstructorDescriptionJMEmol
(JME jme, JmolAdapterAtomIterator atomIterator, JmolAdapterBondIterator bondIterator) -
Method Summary
Modifier and TypeMethodDescriptionvoid
center()
void
void
static String
findSeparator
(String molFile) int
int
int[]
getBondProperties
(int i) int
getCharge
(int i) int
getHydrogenCount
(int i) protected void
double
getX
(int i) double
getY
(int i) void
mark()
static String
nextData
(StringTokenizer st, String separator) void
int
void
restoreXY
(double[][] xy) double[][]
saveXY()
void
setAtomColoring
(int atom, int n) void
setAtomProperties
(double xx, double yy, int ahc, int aq) void
setBondProperties
(int bp0, int bp1, int bp2, int bp3) void
shiftToXY
(double marginPixelsX, double marginPixelsY) shift to an origin and return a dimension
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Field Details
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natoms
public int natoms -
nbonds
public int nbonds -
needRecentering
public boolean needRecentering -
RBOND
public static final int RBOND- See Also:
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Constructor Details
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JMEmol
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Method Details
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nextData
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findSeparator
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getAtomCount
public int getAtomCount() -
getBondCount
public int getBondCount() -
getX
public double getX(int i) -
getY
public double getY(int i) -
setAtomProperties
public void setAtomProperties(double xx, double yy, int ahc, int aq) -
getHydrogenCount
public int getHydrogenCount(int i) -
getCharge
public int getCharge(int i) -
getBondProperties
public int[] getBondProperties(int i) -
setBondProperties
public void setBondProperties(int bp0, int bp1, int bp2, int bp3) -
completeMolecule
public void completeMolecule() -
center
public void center() -
draw
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getMinMax
protected void getMinMax() -
shiftToXY
shift to an origin and return a dimension- Parameters:
marginPixelsX
-marginPixelsY
-- Returns:
- pixel dimension of framed model
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setAtomColoring
public void setAtomColoring(int atom, int n) -
mark
public void mark() -
numberAtoms
public void numberAtoms() -
setLabel
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reactionPart
public int reactionPart() -
saveXY
public double[][] saveXY() -
restoreXY
public void restoreXY(double[][] xy)
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