Class InventorFragment
- java.lang.Object
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- com.actelion.research.chem.coords.InventorFragment
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public class InventorFragment extends java.lang.Object
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Field Summary
Fields Modifier and Type Field Description protected double[]
mAtomX
protected double[]
mAtomY
protected int[]
mGlobalAtom
protected int[]
mGlobalBond
protected int[]
mGlobalToLocalAtom
protected boolean
mKeepMarkedAtoms
protected int[]
mPriority
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Constructor Summary
Constructors Modifier Constructor Description protected
InventorFragment(InventorFragment f)
protected
InventorFragment(StereoMolecule mol, int atoms, boolean keepMarkedAtoms)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected void
arrangeWith(InventorFragment f)
protected double
calculatePreferredAttachmentAngle(double x, double y, int neighbourAtomCount, double padding)
protected boolean
equals(InventorFragment f)
protected void
flip(double x, double y, double mirrorAngle)
protected void
flipOneSide(int bond)
protected double
getAtomX(int index)
protected double
getAtomY(int index)
protected java.util.ArrayList<int[]>
getCollisionList()
protected double
getCollisionPanalty()
protected int
getGlobalAtom(int localAtom)
protected double
getHeight()
protected int
getLocalAtom(int globalAtom)
protected double
getWidth()
protected boolean
isMember(int globalAtom)
protected void
locateBonds()
protected void
optimizeAtomCoordinates(int atom)
protected void
rotate(double x, double y, double angleDif)
protected int
size()
protected void
translate(double dx, double dy)
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Field Detail
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mGlobalAtom
protected int[] mGlobalAtom
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mGlobalBond
protected int[] mGlobalBond
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mGlobalToLocalAtom
protected int[] mGlobalToLocalAtom
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mPriority
protected int[] mPriority
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mAtomX
protected double[] mAtomX
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mAtomY
protected double[] mAtomY
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mKeepMarkedAtoms
protected boolean mKeepMarkedAtoms
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Constructor Detail
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InventorFragment
protected InventorFragment(StereoMolecule mol, int atoms, boolean keepMarkedAtoms)
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InventorFragment
protected InventorFragment(InventorFragment f)
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Method Detail
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size
protected int size()
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equals
protected boolean equals(InventorFragment f)
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getAtomX
protected double getAtomX(int index)
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getAtomY
protected double getAtomY(int index)
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getWidth
protected double getWidth()
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getHeight
protected double getHeight()
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isMember
protected boolean isMember(int globalAtom)
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getGlobalAtom
protected int getGlobalAtom(int localAtom)
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getLocalAtom
protected int getLocalAtom(int globalAtom)
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translate
protected void translate(double dx, double dy)
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rotate
protected void rotate(double x, double y, double angleDif)
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flip
protected void flip(double x, double y, double mirrorAngle)
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flipOneSide
protected void flipOneSide(int bond)
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arrangeWith
protected void arrangeWith(InventorFragment f)
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getCollisionList
protected java.util.ArrayList<int[]> getCollisionList()
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getCollisionPanalty
protected double getCollisionPanalty()
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locateBonds
protected void locateBonds()
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optimizeAtomCoordinates
protected void optimizeAtomCoordinates(int atom)
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calculatePreferredAttachmentAngle
protected double calculatePreferredAttachmentAngle(double x, double y, int neighbourAtomCount, double padding)
- Parameters:
x
-y
-- Returns:
- angle
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