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johnmayjohnmay
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New Bond display property. Will eventually drop the IBond.Stereo all together but for now we just make sure if it's set the display is updated.
1 parent 78681bb commit 166f8e8

5 files changed

Lines changed: 166 additions & 2 deletions

File tree

  • base
    • core/src/main/java/org/openscience/cdk
    • data/src/main/java/org/openscience/cdk
    • interfaces/src/main/java/org/openscience/cdk/interfaces
    • isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers
    • silent/src/main/java/org/openscience/cdk/silent

‎base/core/src/main/java/org/openscience/cdk/BondRef.java‎

Lines changed: 17 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -226,6 +226,23 @@ public void setStereo(Stereo stereo) {
226226
bond.setStereo(stereo);
227227
}
228228

229+
230+
/**
231+
* {@inheritDoc}
232+
*/
233+
@Override
234+
public Display getDisplay() {
235+
return bond.getDisplay();
236+
}
237+
238+
/**
239+
* {@inheritDoc}
240+
*/
241+
@Override
242+
public void setDisplay(Display display) {
243+
bond.setDisplay(display);
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}
245+
229246
/**
230247
* {@inheritDoc}
231248
*/

‎base/data/src/main/java/org/openscience/cdk/Bond.java‎

Lines changed: 35 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -81,6 +81,8 @@ public class Bond extends ElectronContainer implements IBond, Serializable, Clon
8181
*/
8282
protected IBond.Stereo stereo;
8383

84+
protected IBond.Display display = Display.Solid;
85+
8486
/**
8587
* Constructs an empty bond.
8688
*/
@@ -408,6 +410,39 @@ public IBond.Stereo getStereo() {
408410
@Override
409411
public void setStereo(IBond.Stereo stereo) {
410412
this.stereo = stereo;
413+
switch (stereo) {
414+
case UP:
415+
display = Display.WedgeBegin;
416+
break;
417+
case DOWN:
418+
display = Display.WedgedHashBegin;
419+
break;
420+
case UP_INVERTED:
421+
display = Display.WedgeEnd;
422+
break;
423+
case DOWN_INVERTED:
424+
display = Display.WedgedHashEnd;
425+
break;
426+
case UP_OR_DOWN:
427+
case UP_OR_DOWN_INVERTED:
428+
display = Display.Wavy;
429+
break;
430+
}
431+
notifyChanged();
432+
}
433+
434+
/**
435+
* {@inheritDoc}
436+
*/
437+
public IBond.Display getDisplay() {
438+
return display;
439+
}
440+
441+
/**
442+
* {@inheritDoc}
443+
*/
444+
public void setDisplay(IBond.Display display) {
445+
this.display = display;
411446
notifyChanged();
412447
}
413448

‎base/interfaces/src/main/java/org/openscience/cdk/interfaces/IBond.java‎

Lines changed: 64 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -44,7 +44,7 @@ enum Order {
4444

4545
private final Integer bondedElectronPairs;
4646

47-
private Order(Integer bondedElectronPairs) {
47+
Order(Integer bondedElectronPairs) {
4848
this.bondedElectronPairs = bondedElectronPairs;
4949
}
5050

@@ -131,6 +131,54 @@ enum Stereo {
131131
E_Z_BY_COORDINATES
132132
}
133133

134+
/**
135+
* Bond display style, controlling how bonds appear in a 2D depiction.
136+
*/
137+
enum Display {
138+
/** Display as a solid line (default). */
139+
Solid,
140+
/** Display as a dashed line. */
141+
Dash,
142+
/** Display as a hashed line. */
143+
Hash,
144+
/** Display as a bold line. */
145+
Bold,
146+
/** Display as a wavy line. */
147+
Wavy,
148+
/** Display as a dotted line. */
149+
Dot,
150+
/**
151+
* Display as a hashed wedge, with the narrow end
152+
* towards the begin atom of the bond ({@link IBond#getBegin()}).
153+
*/
154+
WedgedHashBegin,
155+
/**
156+
* Display as a hashed wedge, with the narrow end
157+
* towards the end atom of the bond ({@link IBond#getEnd()}).
158+
*/
159+
WedgedHashEnd,
160+
/**
161+
* Display as a bold wedge, with the narrow end
162+
* towards the begin atom of the bond ({@link IBond#getBegin()}).
163+
*/
164+
WedgeBegin,
165+
/**
166+
* Display as a bold wedge, with the narrow end
167+
* towards the end atom of the bond ({@link IBond#getEnd()}).
168+
*/
169+
WedgeEnd,
170+
/**
171+
* Display as an arrow (e.g. coordination bond), the arrow points
172+
* to the begin ({@link IBond#getBegin()}) atom.
173+
*/
174+
ArrowBeg,
175+
/**
176+
* Display as an arrow (e.g. coordination bond), the arrow points
177+
* to the end ({@link IBond#getEnd()}) atom.
178+
*/
179+
ArrowEnd
180+
}
181+
134182
/**
135183
* Returns the Iterable to atoms making up this bond.
136184
*
@@ -270,13 +318,27 @@ enum Stereo {
270318
IBond.Stereo getStereo();
271319

272320
/**
273-
* Sets the stereo descriptor for this bond.
321+
* Sets the stereo descriptor for this bond. Note this function will
322+
* also modify the bond display style.
274323
*
275324
* @param stereo The stereo descriptor to be assigned to this bond.
276325
* @see #getStereo
326+
* @see #setDisplay(Display)
277327
*/
278328
void setStereo(IBond.Stereo stereo);
279329

330+
/**
331+
* Access the bond display style.
332+
* @return the bond display
333+
*/
334+
IBond.Display getDisplay();
335+
336+
/**
337+
* Set the bond display style.
338+
* @param display the display
339+
*/
340+
void setDisplay(IBond.Display display);
341+
280342
/**
281343
* Returns the geometric 2D center of the bond.
282344
*

‎base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/QueryBond.java‎

Lines changed: 16 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -417,6 +417,22 @@ public void setStereo(IQueryBond.Stereo stereo) {
417417
notifyChanged();
418418
}
419419

420+
/**
421+
* Not used for query bonds. {@inheritDoc}
422+
*/
423+
@Override
424+
public Display getDisplay() {
425+
return null;
426+
}
427+
428+
/**
429+
* Not used for query bonds. {@inheritDoc}
430+
*/
431+
@Override
432+
public void setDisplay(Display display) {
433+
434+
}
435+
420436
/**
421437
* Returns the geometric 2D center of the query bond.
422438
*

‎base/silent/src/main/java/org/openscience/cdk/silent/Bond.java‎

Lines changed: 34 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -84,6 +84,8 @@ public class Bond extends ElectronContainer implements IBond, Serializable, Clon
8484
*/
8585
protected IBond.Stereo stereo;
8686

87+
protected IBond.Display display = Display.Solid;
88+
8789
/**
8890
* Constructs an empty bond.
8991
*/
@@ -402,6 +404,38 @@ public IBond.Stereo getStereo() {
402404
@Override
403405
public void setStereo(IBond.Stereo stereo) {
404406
this.stereo = stereo;
407+
switch (stereo) {
408+
case UP:
409+
display = Display.WedgeBegin;
410+
break;
411+
case DOWN:
412+
display = Display.WedgedHashBegin;
413+
break;
414+
case UP_INVERTED:
415+
display = Display.WedgeEnd;
416+
break;
417+
case DOWN_INVERTED:
418+
display = Display.WedgedHashEnd;
419+
break;
420+
case UP_OR_DOWN:
421+
case UP_OR_DOWN_INVERTED:
422+
display = Display.Wavy;
423+
break;
424+
}
425+
}
426+
427+
/**
428+
* {@inheritDoc}
429+
*/
430+
public IBond.Display getDisplay() {
431+
return display;
432+
}
433+
434+
/**
435+
* {@inheritDoc}
436+
*/
437+
public void setDisplay(IBond.Display display) {
438+
this.display = display;
405439
}
406440

407441
/**

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