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Class pmr.cml.MOLNode

java.lang.Object
   |
   +----pmr.sgml.SGMLNode
           |
           +----pmr.sgml.DrawableSGMLNode
                   |
                   +----pmr.cml.DrawableX_Node
                           |
                           +----pmr.cml.MOLNode

public class MOLNode

extends DrawableX_Node

implements SubAddressable

Author:

(C) P. Murray-Rust, 1996

MOLNode(String, SGMLTree)

normal constructor

action(Event, Object)

Reset button has to reset transformation matrix (rotMat) as well as scaling the scaler2d

addMolecularObject(MolecularObject, String)

add a MolecularObject (usually called from constructor of MolecularObject)

addSubAddress(IntRange)

addSubAddresses(IntRangeVector)

clearSubAddresses()

debug()

for debug

display()

Kicks off a ScrollableTopLevel which contains the object.

display(Graphics)

called from the display() routine of DrawableX_Node

drawBond(Graphics, int, int, int, int, int, double, double)

drawIcon(Graphics, int, int)

draw Icon

drawTruncated(Graphics, int, int, int, int, double, double)

get2DMolecule()

probably obsolete - just calculates mol2d

getAtomCount()

common get routines

getBondAtom(Choice2)

get array of all first atoms in bond or all second atoms

getBondCount()

getBondOrderCount(int)

return the number of bonds with a given (integer) order.

getBonds()

get serial numbers of bonded atoms, 2 per bond

getDoubleBondEquivalentCount()

get double bond equivalent count

getELSYM()

get the ATOMS Object public ATOMSNode getATOMS() { if (!processed) {process();} return cat; } /** get element symbols as array

getHydrogenCount()

get the hydrogen count as best as possible

getMolecularWeight()

gets molecular weight

getORDER()

get bond orders

getRingCount()

get ring count

getSimpleSMILES()

gets (unnormalised) SMILES; not yet working

getSTER()

get bond stereochemistries

getSubAddresses()

getXYZ3()

get the coordinates as a Point3Vector; this is a REFERENCE, so will change if 'this' changes its coordinates

highlight(IntSet)

general highlighting routine (for any node) assumes it is the ATOMS.

highlightAtom(int)

highlightAtoms(IntSet)

highlight atoms

highlightSubAddresses(boolean)

mayContain(SGMLNode)

can this node contain others.

mouseDown(Event, int, int)

action when mouse is clicked; if not overridden, no action

mouseDrag(Event, int, int)

action when mouse is dragged; if not overridden, no action

mouseUp(Event, int, int)

action when mouse is unclicked; if not overridden, no action

process()

complex objects may require processing; override this.

setMolecularObjectSelection(String, boolean)

select/unselect molecular object

showHelp()

display Help (includes ATOMS and BONDS)

  public MOLNode(String giName,
                 SGMLTree tree)

normal constructor

  public void showHelp()

display Help (includes ATOMS and BONDS)

Overrides:

showHelp in class DrawableX_Node

  public int getBondOrderCount(int order)

return the number of bonds with a given (integer) order. You cannot rely on anything other than 1, 2, or 3 at this stage

  public int getRingCount()

get ring count

  public int getDoubleBondEquivalentCount()

get double bond equivalent count

  public int getHydrogenCount()

get the hydrogen count as best as possible

  public double getMolecularWeight()

gets molecular weight

  public SimpleSMILES getSimpleSMILES()

gets (unnormalised) SMILES; not yet working

  public void get2DMolecule()

probably obsolete - just calculates mol2d

  public void drawBond(Graphics g,
                       int x0,
                       int y0,
                       int x1,
                       int y1,
                       int order,
                       double f0,
                       double f1)

  public void drawTruncated(Graphics g,
                            int x0,
                            int y0,
                            int x1,
                            int y1,
                            double f0,
                            double f1)

  public boolean mayContain(SGMLNode n)

can this node contain others.

Overrides:

mayContain in class DrawableX_Node

  public void process()

complex objects may require processing; override this.

Overrides:

process in class DrawableSGMLNode

  public int getAtomCount()

common get routines

  public int getBondCount()

  public Point3Vector getXYZ3()

get the coordinates as a Point3Vector; this is a REFERENCE, so will change if 'this' changes its coordinates

  public String[] getELSYM()

get the ATOMS Object public ATOMSNode getATOMS() { if (!processed) {process();} return cat; } /** get element symbols as array

  public int[] getORDER()

get bond orders

  public int[] getSTER()

get bond stereochemistries

  public Int2Vector getBonds()

get serial numbers of bonded atoms, 2 per bond

  public IntArray getBondAtom(Choice2 c)

get array of all first atoms in bond or all second atoms

  public void addMolecularObject(MolecularObject mo,
                                 String name)

add a MolecularObject (usually called from constructor of MolecularObject)

  public void setMolecularObjectSelection(String name,
                                          boolean selected)

select/unselect molecular object

  public void display()

Kicks off a ScrollableTopLevel which contains the object.

Overrides:

display in class DrawableSGMLNode

  public void display(Graphics g)

called from the display() routine of DrawableX_Node

Overrides:

display in class DrawableX_Node

  public int drawIcon(Graphics g,
                      int x,
                      int y)

draw Icon

Overrides:

drawIcon in class DrawableX_Node

  public void highlightAtoms(IntSet is)

highlight atoms

  public void highlight(IntSet is)

general highlighting routine (for any node) assumes it is the ATOMS. (for bonds you have to use BONDS)

Overrides:

highlight in class DrawableX_Node

  public void highlightAtom(int jatom)

  public boolean action(Event e,
                        Object arg)

Reset button has to reset transformation matrix (rotMat) as well as scaling the scaler2d

Overrides:

action in class DrawableX_Node

  public boolean mouseUp(Event evt,
                         int x,
                         int y)

action when mouse is unclicked; if not overridden, no action

Overrides:

mouseUp in class DrawableX_Node

  public boolean mouseDown(Event evt,
                           int x,
                           int y)

action when mouse is clicked; if not overridden, no action

Overrides:

mouseDown in class DrawableX_Node

  public boolean mouseDrag(Event evt,
                           int x,
                           int y)

action when mouse is dragged; if not overridden, no action

Overrides:

mouseDrag in class DrawableX_Node

  public void clearSubAddresses()

  public void addSubAddress(IntRange ir)

  public void addSubAddresses(IntRangeVector irv)

  public IntRangeVector getSubAddresses()

  public void highlightSubAddresses(boolean onOff)

  public void debug()

for debug

Overrides:

debug in class DrawableX_Node

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