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Merge pull request #200 from cdk/patch/cxsmiles-read
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Patch/cxsmiles read
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@egonw
egonw committed Apr 21, 2016
2 parents a07f829 + 937f107 commit 18639d9
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Showing 13 changed files with 1,994 additions and 63 deletions.
18 changes: 17 additions & 1 deletion app/depict/src/main/java/org/openscience/cdk/depict/DepictionGenerator.java
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Original file line number Diff line number Diff line change
Expand Up @@ -498,10 +498,16 @@ public Depiction depict(IReaction rxn) throws CDKException {
productTitles.add(copy.generateTitle(product));
}

final Bounds conditions = generateReactionConditions(rxn, fgcol);

return new ReactionDepiction(model,
reactantBounds, productBounds, agentBounds,
plus, rxn.getDirection(), dimensions,
reactantTitles, productTitles, title, fgcol);
reactantTitles,
productTitles,
title,
conditions,
fgcol);
}

/**
Expand Down Expand Up @@ -648,6 +654,16 @@ private Bounds generateTitle(IChemObject chemObj) {
"title"));
}

private Bounds generateReactionConditions(IReaction chemObj, Color fg) {
String title = chemObj.getProperty(CDKConstants.REACTION_CONDITIONS);
if (title == null || title.isEmpty())
return new Bounds();
final double scale = 1 / getParameterValue(BasicSceneGenerator.Scale.class);

return new Bounds(MarkedElement.markup(StandardGenerator.embedText(font, title, fg, scale),
"conditions"));
}


/**
* Automatically generate coordinates if a user has provided a molecule without them.
Expand Down
82 changes: 63 additions & 19 deletions app/depict/src/main/java/org/openscience/cdk/depict/ReactionDepiction.java
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Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,6 @@
import org.openscience.cdk.renderer.RendererModel;
import org.openscience.cdk.renderer.elements.Bounds;
import org.openscience.cdk.renderer.elements.GeneralPath;
import org.openscience.cdk.renderer.elements.IRenderingElement;
import org.openscience.cdk.renderer.elements.LineElement;
import org.openscience.cdk.renderer.elements.RectangleElement;
import org.openscience.cdk.renderer.generators.BasicSceneGenerator;
Expand Down Expand Up @@ -60,6 +59,7 @@ final class ReactionDepiction extends Depiction {
// molecule sets and titles
private final List<Bounds> mainComp = new ArrayList<>();
private final List<Bounds> sideComps = new ArrayList<>();
private final Bounds conditions;
private final Bounds title;

// arrow info
Expand All @@ -71,6 +71,8 @@ final class ReactionDepiction extends Depiction {
// dimensions and spacing of side components
private final Dimensions sideDim;
private final Dimensions mainDim;
private final Dimensions condDim;

private final double[] xOffsets, yOffsets;
private final double[] xOffsetSide, yOffsetSide;

Expand All @@ -88,6 +90,7 @@ public ReactionDepiction(RendererModel model,
List<Bounds> reactantTitles,
List<Bounds> productTitles,
Bounds title,
Bounds conditions,
Color fgcol) {
super(model);
this.model = model;
Expand Down Expand Up @@ -159,6 +162,8 @@ public ReactionDepiction(RendererModel model,
this.nCol = mainComp.size();
}

this.conditions = conditions;

// arrow params
this.arrowIdx = Math.max(reactants.size() + reactants.size() - 1, 0);
this.direction = direction;
Expand All @@ -169,19 +174,37 @@ public ReactionDepiction(RendererModel model,
yOffsets = new double[nRow + 1],
xOffsets = new double[nCol + 1]);

// avoid v. small arrows
if (prelimSideDim.w < minArrowWidth) {
double middleRequired = Math.max(prelimSideDim.w, conditions.width());

// avoid v. small arrows, we take in to account the padding provided by the arrow head height/length
if (middleRequired < minArrowWidth - arrowHeight - arrowHeight) {
// adjust x-offset so side components are centered
double xAdjust = (minArrowWidth - prelimSideDim.w) / 2;
double xAdjust = (minArrowWidth - middleRequired) / 2;
for (int i = 0; i < xOffsetSide.length; i++)
xOffsetSide[i] += xAdjust;
// need to recenter agents
if (conditions.width() > prelimSideDim.w) {
for (int i = 0; i < xOffsetSide.length; i++)
xOffsetSide[i] += (conditions.width() - prelimSideDim.w) / 2;
}
// update side dims
this.sideDim = new Dimensions(minArrowWidth, prelimSideDim.h);
this.condDim = new Dimensions(minArrowWidth, conditions.height());
} else {
// arrow padding
for (int i = 0; i < xOffsetSide.length; i++)
xOffsetSide[i] += arrowHeight;
this.sideDim = new Dimensions(2*arrowHeight + prelimSideDim.w,

// need to recenter agents
if (conditions.width() > prelimSideDim.w) {
for (int i = 0; i < xOffsetSide.length; i++)
xOffsetSide[i] += (conditions.width() - prelimSideDim.w) / 2;
}

this.sideDim = new Dimensions(2 * arrowHeight + middleRequired,
prelimSideDim.h);
this.condDim = new Dimensions(2 * arrowHeight + middleRequired,
conditions.height());
}
}

Expand All @@ -201,6 +224,7 @@ public BufferedImage toImg() {

Dimensions sideRequired = sideDim.scale(scale * zoom);
Dimensions mainRequired = mainDim.scale(scale * zoom);
Dimensions condRequired = condDim.scale(scale * zoom);

Dimensions titleRequired = new Dimensions(title.width(), title.height()).scale(scale * zoom);

Expand Down Expand Up @@ -234,8 +258,8 @@ public BufferedImage toImg() {

// MAIN COMPONENTS DRAW
// x,y base coordinates include the margin and centering (only if fitting to a size)
final double totalRequiredWidth = 2 * margin + (nCol - 1) * padding + (nSideCol - 1) * padding + (rescale * xOffsets[nCol]);
final double totalRequiredHeight = 2 * margin + (nRow - 1) * padding + (!title.isEmpty() ? padding : 0) + Math.max(mainCompOffset, 0) + fitting * mainRequired.h + fitting * Math.max(0, titleRequired.h);
final double totalRequiredWidth = 2 * margin + Math.max(0, nCol - 1) * padding + Math.max(0, nSideCol - 1) * padding + (rescale * xOffsets[nCol]);
final double totalRequiredHeight = 2 * margin + Math.max(0, nRow - 1) * padding + (!title.isEmpty() ? padding : 0) + Math.max(mainCompOffset, 0) + fitting * mainRequired.h + fitting * Math.max(0, titleRequired.h);
double xBase = margin + (total.w - totalRequiredWidth) / 2;
double yBase = margin + Math.max(mainCompOffset, 0) + (total.h - totalRequiredHeight) / 2;
for (int i = 0; i < mainComp.size(); i++) {
Expand All @@ -253,7 +277,7 @@ public BufferedImage toImg() {

// intercept arrow draw and make it as big as need
if (i == arrowIdx) {
w = rescale * (xOffsets[i + 1] - xOffsets[i]) + (nSideCol - 1) * padding;
w = rescale * (xOffsets[i + 1] - xOffsets[i]) + Math.max(0, nSideCol - 1) * padding;
draw(visitor,
1, // no zoom since arrows is drawn as big as needed
createArrow(w, arrowHeight * rescale),
Expand All @@ -263,7 +287,7 @@ public BufferedImage toImg() {

// extra padding from the side components
if (i > arrowIdx)
x += (nSideCol - 1) * padding;
x += Math.max(0, nSideCol - 1) * padding;

// skip empty elements
final Bounds bounds = this.mainComp.get(i);
Expand Down Expand Up @@ -298,6 +322,15 @@ public BufferedImage toImg() {
draw(visitor, zoom, sideComps.get(i), rect(x, y, w, h));
}

// CONDITIONS DRAW
if (!conditions.isEmpty()) {
yBase += mainCompOffset; // back to top
yBase += mainRequired.h / 2; // now on center line (arrow)
yBase += padding; // now just bellow
draw(visitor, zoom, conditions, rect(xBase,
yBase,
condRequired.w, condRequired.h));
}

// reset shared xOffsets
if (!sideComps.isEmpty()) {
Expand Down Expand Up @@ -337,6 +370,7 @@ String toVecStr(String fmt) {

Dimensions sideRequired = sideDim.scale(scale * zoom);
Dimensions mainRequired = mainDim.scale(scale * zoom);
Dimensions condRequired = condDim.scale(scale * zoom);

Dimensions titleRequired = new Dimensions(title.width(), title.height()).scale(scale * zoom);

Expand All @@ -358,7 +392,7 @@ String toVecStr(String fmt) {
}

// background color
visitor.setTransform(AffineTransform.getScaleInstance(1,-1));
visitor.setTransform(AffineTransform.getScaleInstance(1, -1));
visitor.visit(new RectangleElement(0, -(int) Math.ceil(total.h), (int) Math.ceil(total.w), (int) Math.ceil(total.h),
true, model.get(BasicSceneGenerator.BackgroundColor.class)));

Expand All @@ -374,8 +408,8 @@ String toVecStr(String fmt) {

// MAIN COMPONENTS DRAW
// x,y base coordinates include the margin and centering (only if fitting to a size)
final double totalRequiredWidth = 2 * margin + (nCol - 1) * padding + (nSideCol - 1) * padding + (rescale * xOffsets[nCol]);
final double totalRequiredHeight = 2 * margin + (nRow - 1) * padding + (!title.isEmpty() ? padding : 0) + Math.max(mainCompOffset, 0) + fitting * mainRequired.h + fitting * Math.max(0, titleRequired.h);
final double totalRequiredWidth = 2 * margin + Math.max(0, nCol - 1) * padding + Math.max(0, nSideCol - 1) * padding + (rescale * xOffsets[nCol]);
final double totalRequiredHeight = 2 * margin + Math.max(0, nRow - 1) * padding + (!title.isEmpty() ? padding : 0) + Math.max(mainCompOffset, 0) + fitting * mainRequired.h + fitting * Math.max(0, titleRequired.h);
double xBase = margin + (total.w - totalRequiredWidth) / 2;
double yBase = margin + Math.max(mainCompOffset, 0) + (total.h - totalRequiredHeight) / 2;
for (int i = 0; i < mainComp.size(); i++) {
Expand All @@ -393,7 +427,7 @@ String toVecStr(String fmt) {

// intercept arrow draw and make it as big as need
if (i == arrowIdx) {
w = rescale * (xOffsets[i + 1] - xOffsets[i]) + (nSideCol - 1) * padding;
w = rescale * (xOffsets[i + 1] - xOffsets[i]) + Math.max(0, nSideCol - 1) * padding;
draw(visitor,
1, // no zoom since arrows is drawn as big as needed
createArrow(w, arrowHeight * rescale),
Expand All @@ -403,7 +437,7 @@ String toVecStr(String fmt) {

// extra padding from the side components
if (i > arrowIdx)
x += (nSideCol - 1) * padding;
x += Math.max(0, nSideCol - 1) * padding;

// skip empty elements
final Bounds bounds = this.mainComp.get(i);
Expand Down Expand Up @@ -438,6 +472,16 @@ String toVecStr(String fmt) {
draw(visitor, zoom, sideComps.get(i), rect(x, y, w, h));
}

// CONDITIONS DRAW
if (!conditions.isEmpty()) {
yBase += mainCompOffset; // back to top
yBase += mainRequired.h / 2; // now on center line (arrow)
yBase += padding; // now just bellow
draw(visitor, zoom, conditions, rect(xBase,
yBase,
condRequired.w, condRequired.h));
}

// reset shared xOffsets
if (!sideComps.isEmpty()) {
for (int i = arrowIdx + 1; i < xOffsets.length; i++)
Expand Down Expand Up @@ -511,11 +555,11 @@ private Dimensions calcTotalDimensions(double margin, double padding, Dimensions
titleExtra += padding;

return mainRequired.add(2 * margin, 2 * margin)
.add((nCol - 1) * padding, (nRow - 1) * padding)
.add(Math.max(0, sideRequired.w), 0) // side component extra width
.add((nSideCol - 1) * padding, 0) // side component padding
.add(0, mainCompOffset)
.add(0, titleExtra);
.add(Math.max(0, nCol - 1) * padding, (nRow - 1) * padding)
.add(Math.max(0, sideRequired.w), 0) // side component extra width
.add(Math.max(0, nSideCol - 1) * padding, 0) // side component padding
.add(0, mainCompOffset)
.add(0, titleExtra);

} else {
// we want all vector graphics dims in MM
Expand Down
6 changes: 6 additions & 0 deletions base/core/src/main/java/org/openscience/cdk/CDKConstants.java
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Original file line number Diff line number Diff line change
Expand Up @@ -343,6 +343,12 @@ public class CDKConstants {
public static final String CTAB_SGROUPS = "cdk:CtabSgroups";


/**
* Property for reaction objects where the conditions of reactions can be placed.
*/
public static final String REACTION_CONDITIONS = "cdk:ReactionConditions";


/* **************************************
* Some predefined property names for * AtomTypes *
* **************************************
Expand Down
4 changes: 2 additions & 2 deletions ...src/main/java/org/openscience/cdk/renderer/generators/standard/StandardBondGenerator.java
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Original file line number Diff line number Diff line change
Expand Up @@ -645,9 +645,9 @@ private IRenderingElement generateDoubleBond(IBond bond) {
} else {
return generateCenteredDoubleBond(bond, atom1, atom2, atom1Bonds, atom2Bonds);
}
} else if (atom1Bonds.size() == 1 && !hasDisplayedSymbol(atom1)) {
} else if (atom1Bonds.size() == 1 && !hasDisplayedSymbol(atom1) && (!hasDisplayedSymbol(atom2) || atom2Bonds.isEmpty())) {
return generateOffsetDoubleBond(bond, atom1, atom2, atom1Bonds.get(0), atom2Bonds);
} else if (atom2Bonds.size() == 1 && !hasDisplayedSymbol(atom2)) {
} else if (atom2Bonds.size() == 1 && !hasDisplayedSymbol(atom2) && (!hasDisplayedSymbol(atom1) || atom1Bonds.isEmpty())) {
return generateOffsetDoubleBond(bond, atom2, atom1, atom2Bonds.get(0), atom1Bonds);
} else if (specialOffsetBondNextToWedge(atom1, atom1Bonds) && !hasDisplayedSymbol(atom1)) {
return generateOffsetDoubleBond(bond, atom1, atom2, selectPlainSingleBond(atom1Bonds), atom2Bonds);
Expand Down
32 changes: 23 additions & 9 deletions ...sic/src/main/java/org/openscience/cdk/renderer/generators/standard/StandardGenerator.java
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Original file line number Diff line number Diff line change
Expand Up @@ -439,23 +439,37 @@ static TextOutline generateAnnotation(Point2d basePoint, String label, Vector2d


/**
* Make an embedded text label for display in a CDK renderer.
* Make an embedded text label for display in a CDK renderer. If a piece of text contains newlines
* they are centred aligned below each other with a line height of 1.4.
*
* @param font the font to embedded
* @param text the text label
* @param font the font to embedded
* @param text the text label
* @param color the color
* @param scale the resize, should include the model scale
* @return pre-rendered element
*/
public static IRenderingElement embedText(Font font, String text, Color color, double scale) {

final TextOutline outline = new TextOutline(text, font).resize(scale, -scale);
final String[] lines = text.split("\n");

ElementGroup group = new ElementGroup();
group.add(GeneralPath.shapeOf(outline.getOutline(), color));
Rectangle2D logicalBounds = outline.getLogicalBounds();
group.add(new Bounds(logicalBounds.getMinX(), logicalBounds.getMinY(),
logicalBounds.getMaxX(), logicalBounds.getMaxY()));

double yOffset = 0;
double lineHeight = 1.4d;

for (String line : lines) {
TextOutline outline = new TextOutline(line, font).resize(scale, -scale);
Point2D center = outline.getCenter();
outline = outline.translate(-center.getX(), -(center.getY() + yOffset));

yOffset += lineHeight * outline.getBounds().getHeight();

group.add(GeneralPath.shapeOf(outline.getOutline(), color));
Rectangle2D logicalBounds = outline.getLogicalBounds();
group.add(new Bounds(logicalBounds.getMinX(), logicalBounds.getMinY(),
logicalBounds.getMaxX(), logicalBounds.getMaxY()));
}

return group;
}

Expand Down Expand Up @@ -539,7 +553,7 @@ private static IRenderingElement recolor(IRenderingElement element, Color color)
* @param stroke the stroke width
* @return generated outer glow
*/
private static IRenderingElement outerGlow(IRenderingElement element, Color color, double glowWidth, double stroke) {
static IRenderingElement outerGlow(IRenderingElement element, Color color, double glowWidth, double stroke) {
if (element instanceof ElementGroup) {
ElementGroup orgGroup = (ElementGroup) element;
ElementGroup newGroup = new ElementGroup();
Expand Down

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