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Fix extended stereo #20

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b7d87f9
updated how stereo works
tylerperyea Dec 8, 2023
aaa9b51
merged
tylerperyea Dec 8, 2023
20e7936
updated version
tylerperyea Dec 8, 2023
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6 changes: 3 additions & 3 deletions pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,7 @@

<groupId>gov.nih.ncats</groupId>
<artifactId>molwitch-renderer</artifactId>
<version>1.0.15</version>
<version>1.0.16-SNAPSHOT</version>

<name>Molwitch Renderer</name>

Expand Down Expand Up @@ -93,7 +93,7 @@
<dependency>
<groupId>gov.nih.ncats</groupId>
<artifactId>molwitch</artifactId>
<version>0.6.5</version>
<version>0.6.6-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
Expand All @@ -116,7 +116,7 @@
<dependency>
<groupId>gov.nih.ncats</groupId>
<artifactId>molwitch-cdk</artifactId>
<version>1.0.14</version>
<version>1.0.15-SNAPSHOT</version>
<scope>test</scope>
</dependency>
<dependency>
Expand Down
185 changes: 129 additions & 56 deletions src/main/java/gov/nih/ncats/molwitch/renderer/NchemicalRenderer.java
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Original file line number Diff line number Diff line change
Expand Up @@ -18,15 +18,6 @@

package gov.nih.ncats.molwitch.renderer;

import gov.nih.ncats.molwitch.*;
import gov.nih.ncats.molwitch.SGroup.SGroupBracket;
import gov.nih.ncats.molwitch.SGroup.SGroupType;
import gov.nih.ncats.molwitch.Bond.BondType;
import gov.nih.ncats.molwitch.isotopes.NISTIsotopeFactory;
import gov.nih.ncats.molwitch.renderer.Graphics2DParent.*;
import gov.nih.ncats.molwitch.renderer.RendererOptions.DrawOptions;
import gov.nih.ncats.molwitch.renderer.RendererOptions.DrawProperties;

import java.awt.BasicStroke;
import java.awt.Color;
import java.awt.Font;
Expand All @@ -46,17 +37,38 @@
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Objects;
import java.util.Optional;
import java.util.OptionalInt;
import java.util.Map.Entry;
import java.util.Set;
import java.util.function.Function;
import java.util.function.Predicate;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import java.util.stream.Collectors;

import gov.nih.ncats.molwitch.Atom;
import gov.nih.ncats.molwitch.AtomCoordinates;
import gov.nih.ncats.molwitch.Bond;
import gov.nih.ncats.molwitch.Bond.BondType;
import gov.nih.ncats.molwitch.Bond.DoubleBondStereo;
import gov.nih.ncats.molwitch.Chemical;
import gov.nih.ncats.molwitch.Chirality;
import gov.nih.ncats.molwitch.MolwitchException;
import gov.nih.ncats.molwitch.SGroup;
import gov.nih.ncats.molwitch.SGroup.SGroupBracket;
import gov.nih.ncats.molwitch.SGroup.SGroupType;
import gov.nih.ncats.molwitch.Stereocenter;
import gov.nih.ncats.molwitch.isotopes.NISTIsotopeFactory;
import gov.nih.ncats.molwitch.renderer.Graphics2DParent.AffineTransformParent;
import gov.nih.ncats.molwitch.renderer.Graphics2DParent.GeneralPathParent;
import gov.nih.ncats.molwitch.renderer.Graphics2DParent.GeomGenerator;
import gov.nih.ncats.molwitch.renderer.Graphics2DParent.LineParent;
import gov.nih.ncats.molwitch.renderer.Graphics2DParent.Point2DParent;
import gov.nih.ncats.molwitch.renderer.Graphics2DParent.Rectangle2DParent;
import gov.nih.ncats.molwitch.renderer.RendererOptions.DrawOptions;
import gov.nih.ncats.molwitch.renderer.RendererOptions.DrawProperties;


//import java.awt.image.BufferedImage;
/**
Expand All @@ -68,6 +80,9 @@ class NchemicalRenderer extends AbstractChemicalRenderer {
public static final ARGBColor transparent = new ARGBColor(0, 0, 0, 0);
private String protProperty = "AMINO_ACID_SEQUENCE";
private static Font defaultFont;

private static float FONT_SIZE_LABEL_FUDGE = 0.7f;


static {
try {
Expand Down Expand Up @@ -262,6 +277,8 @@ public void renderChem(Graphics2D g9, Chemical c, int x, int y, int width, int h

boolean wedgeJoin = displayParams.getDrawOption(DrawOptions.DRAW_STEREO_WEDGE_JOIN);

boolean drawStereoBondLabels = displayParams.getDrawOption(DrawOptions.DRAW_STEREO_WEDGE_JOIN);



boolean PROP_DASH_SPACING = displayParams.getDrawOption(DrawOptions.DRAW_CONSTANT_DASH_WIDTH);
Expand All @@ -273,6 +290,7 @@ public void renderChem(Graphics2D g9, Chemical c, int x, int y, int width, int h
boolean drawTerminalCarbons = displayParams.getDrawOption(DrawOptions.DRAW_TERMINAL_CARBON);
boolean drawColorScheme = !displayParams.getDrawOption(DrawOptions.DRAW_GREYSCALE);
boolean drawStereoLabels = displayParams.getDrawOption(DrawOptions.DRAW_STEREO_LABELS);
boolean drawStereoLabelsEZ = displayParams.getDrawOption(DrawOptions.DRAW_STEREO_LABELS_EZ) && drawStereoLabels;
boolean stereoFromMap = displayParams.getDrawOption(DrawOptions.DRAW_STEREO_GIVEN_BY_MAP);
boolean highlightMapAtoms = displayParams.getDrawOption(DrawOptions.DRAW_HIGHLIGHT_MAPPED);
boolean highlightHalo = displayParams.getDrawOption(DrawOptions.DRAW_HIGHLIGHT_WITH_HALO);
Expand Down Expand Up @@ -557,7 +575,7 @@ public void renderChem(Graphics2D g9, Chemical c, int x, int y, int width, int h


float bondWidth = (float) (DEF_STROKE_PERCENT * resize * BONDAVG);
float braketFrac = 0.7f;
float braketFrac = FONT_SIZE_LABEL_FUDGE;
float braketWidth = (float) (DEF_STROKE_PERCENT * resize * BONDAVG * braketFrac);
BasicStroke solid = new BasicStroke(bondWidth, BasicStroke.CAP_ROUND, BasicStroke.JOIN_ROUND);
BasicStroke solidHalo = new BasicStroke((float) (bondWidth + HALO_RADIUS_MULTIPLY * resize * BONDAVG),
Expand Down Expand Up @@ -599,7 +617,10 @@ public void renderChem(Graphics2D g9, Chemical c, int x, int y, int width, int h
}
}else {
final List<Stereocenter> allStereocenters = c.getAllStereocenters();
stereoMap = allStereocenters.stream().filter(Stereocenter::isDefined).map(Stereocenter::getCenterAtom).filter(a -> a.getChirality() != null)
stereoMap = allStereocenters.stream()
// .filter(Stereocenter::isDefined)
.map(Stereocenter::getCenterAtom)
.filter(a -> a.getChirality() != null)
.collect(Collectors.toMap(Atom::getAtomIndexInParent, a -> a.getChirality()));
}

Expand Down Expand Up @@ -711,18 +732,18 @@ public void renderChem(Graphics2D g9, Chemical c, int x, int y, int width, int h
if (assumeStarRelative) {
attach2 = "(R*)";
}
if (!assumeRelative)
break;
case Unknown:
case Parity_Either:
//from TP: The big thing is that if the molecule is marked as racemic or (+/-) stereochemistry,
// //then it's definitely either R or S
if (Chemical.StereochemistryType.RACEMIC.equals(stereochemistryType) || Chemical.OpticalActivity.PLUS_MINUS.equals(opticalActivity)) {
if (assumeRelative) {
attach2 = "(RS)";
ncol = colorPalette.getStereoColorKnown();
} else {
attach2 = "(*)";
ncol = colorPalette.getStereoColorUnknown();
}
break;
case r:
attach2 = "(r)";
ncol = colorPalette.getStereoColorKnown();
if (assumeStarRelative) {
attach2 = "(r*)";
}
if (assumeRelative) {
attach2 = "(rs)";
}
break;
case S:
Expand All @@ -731,15 +752,25 @@ public void renderChem(Graphics2D g9, Chemical c, int x, int y, int width, int h
if (assumeStarRelative) {
attach2 = "(S*)";
}
if (!assumeRelative) {
break;
if (assumeRelative) {
attach2 = "(SR)";
}
break;
case s:
attach2 = "(s)";
ncol = colorPalette.getStereoColorKnown();
if (assumeStarRelative) {
attach2 = "(s*)";
}
if (assumeRelative) {
attach2 = "(sr)";
}
attach2 = "(*)";
ncol = colorPalette.getStereoColorUnknown();
// case ChemicalAtom.STEREO_SR:
// attach2 = "(SR)";
// ncol = STEREO_COLOR_KNOWN;
// break;
break;
case Unknown:
case Parity_Either:
attach2 = "(*)";
ncol = colorPalette.getStereoColorUnknown();
break;

default:
}
Expand All @@ -760,7 +791,7 @@ public void renderChem(Graphics2D g9, Chemical c, int x, int y, int width, int h
}
forceDraw = true;
//System.out.printf("setting font to %.4f\n", (fsize * 0.7f));
g2.setFont(defaultFont.deriveFont(fsize * 0.7f));
g2.setFont(defaultFont.deriveFont(fsize * FONT_SIZE_LABEL_FUDGE));
fm = g2.getFontMetrics();
} else {
// should restrict full atom highlight for
Expand All @@ -777,7 +808,7 @@ public void renderChem(Graphics2D g9, Chemical c, int x, int y, int width, int h
attachments.add(attach2);
// attachmentLOC.add(1|2|4|8);
attachmentLOC.add(-1);
attachmentSIZE.add(.7f);
attachmentSIZE.add(FONT_SIZE_LABEL_FUDGE);
if (stereoColoring) {
attachmentCOL.add(ncol);
} else {
Expand Down Expand Up @@ -1087,6 +1118,7 @@ public void renderChem(Graphics2D g9, Chemical c, int x, int y, int width, int h
bp.DEF_NUM_DASH = DEF_NUM_DASH;
bp.bondWidth = bondWidth;
bp.DEF_SPLIT_RATIO = DEF_SPLIT_RATIO;
bp.fsize=fsize;
bp.DrawDashWedge = DrawDashWedge;
bp.drawLastDashLineOnNonSymbols = drawLastDashLineOnNonSymbols;

Expand All @@ -1097,6 +1129,8 @@ public void renderChem(Graphics2D g9, Chemical c, int x, int y, int width, int h
bp.wedgeJoin = wedgeJoin;
bp.solidREC = solidREC;
bp.maxWedgeWidth = maxW;
bp.drawStereoBondLabels=drawStereoLabelsEZ;
bp.colorPalette=colorPalette;

if (highlightHalo) {
bp.highlightHalo = true;
Expand Down Expand Up @@ -1317,7 +1351,7 @@ private void drawBracketedSgroup(Graphics2DTemp g2, float maxX, float maxY, floa

if(supsOpt.isPresent() || subs.isPresent()){
//System.out.printf("g2.setFont(defaultFont.deriveFont(fsize * 0.7f)); %.5f", (fsize * 0.7f));
g2.setFont(defaultFont.deriveFont(fsize * 0.7f));
g2.setFont(defaultFont.deriveFont(fsize * FONT_SIZE_LABEL_FUDGE));
fm = g2.getFontMetrics();

if(subs.isPresent()){
Expand Down Expand Up @@ -1420,6 +1454,23 @@ private static Rectangle2D drawString(Graphics2DTemp g2, String s, float x, floa
return null;
}
}

private static Rectangle2D getStringBounds(Graphics2DTemp g2, String s, float x, float y) {
boolean glyph = true;
if (glyph) {
GlyphVector gv = g2.getFont().createGlyphVector(g2.getFontRenderContext(), s.toCharArray());
Rectangle2D r2 = gv.getLogicalBounds();
// g2.drawGlyphVector(gv, x, y);
return new Rectangle2D.Double(r2.getMinX() + x, r2.getMinY() + y, r2.getWidth(), r2.getHeight());
// r2=g2.getTransform().createTransformedShape(r2).getBounds2D();
// r2
// return r2;

} else {
g2.drawString(s, x, y);
return null;
}
}

private static String formatSuperAtomLabel(String label){
StringBuilder builder = new StringBuilder(label);
Expand Down Expand Up @@ -1539,13 +1590,18 @@ private static class AtomDrawProps {
}

private static class BondProps {
public ColorPalette colorPalette;


public double maxWedgeWidth;
float DEF_DBL_BOND_GAP;
float DEF_DBL_BOND_DISTANCE;
float BONDAVG;
float DEF_NUM_DASH;
float bondWidth;
float DEF_SPLIT_RATIO;
float fsize;


boolean DrawDashWedge;
boolean PROP_DASH_SPACING;
Expand Down Expand Up @@ -1609,6 +1665,7 @@ private void drawBonds(Graphics2DTemp g2, Chemical c, List<double[]> toAdd, Stro

float dxdbl = dx / 4.f;
float dydbl = dy / 4.f;
double inv1=1;

float[] doubleBPos = new float[2];
centerTransform.transform(xy, 5, doubleBPos, 0, 1);
Expand Down Expand Up @@ -1640,6 +1697,7 @@ private void drawBonds(Graphics2DTemp g2, Chemical c, List<double[]> toAdd, Stro
tx = dbcy[0];
dbcy[0] = dbcy[1];
dbcy[1] = tx;
inv1=-1;
}
float rat = DEF_DBL_BOND_DISTANCE * 2;
/*
Expand Down Expand Up @@ -1804,27 +1862,42 @@ private void drawBonds(Graphics2DTemp g2, Chemical c, List<double[]> toAdd, Stro
}
//TEMP testing ability to draw text
if(drawStereoBondLabels && cb.getBondType()== BondType.DOUBLE) {

String bondStereo =cb.getDoubleBondStereo().name();
String bsPieces[] = bondStereo.split("\\_");
FontMetrics metrics = g2.getFontMetrics();
int labelWidth = metrics.stringWidth(bsPieces[0]);
double x = Math.min(cb.getAtom1().getAtomCoordinates().getX(), cb.getAtom2().getAtomCoordinates().getX()) +
Math.abs( cb.getAtom1().getAtomCoordinates().getX()-cb.getAtom2().getAtomCoordinates().getX())/2;
System.out.printf("atom1 x %.2f atom2 x %.2f middle %.2f\n", cb.getAtom1().getAtomCoordinates().getX(),
cb.getAtom2().getAtomCoordinates().getX(), x);
double y = Math.min(cb.getAtom1().getAtomCoordinates().getY(), cb.getAtom2().getAtomCoordinates().getY()) + Math.abs( cb.getAtom1().getAtomCoordinates().getY()-cb.getAtom2().getAtomCoordinates().getY())/2;
System.out.printf("atom1 y %.2f atom2 y %.2f middle %.2f\n", cb.getAtom1().getAtomCoordinates().getY(),
cb.getAtom2().getAtomCoordinates().getY(), y);
float fudgeFactor=240;
float xPos= (float) (x- labelWidth +1.5* fudgeFactor);
float yPos = (float) (y + metrics.getHeight()/2 )+fudgeFactor;
System.out.printf("Going to draw string '%s' at %.2f, %.2f\n", bsPieces[0],
xPos, yPos);
ARGBColor colorBefore= g2.getARGBColor();
g2.setColor(new ARGBColor(0, 255, 0, 250));
drawString(g2, bsPieces[0], xPos, yPos);
g2.setColor(colorBefore);
DoubleBondStereo dbs=cb.getDoubleBondStereo();
if(dbs!=DoubleBondStereo.NONE) {

String bondStereo =cb.getDoubleBondStereo().name();

float xPos = .5f*(p1[0]+p2[0]);
float yPos = .5f*(p1[1]+p2[1]);


ARGBColor colorBefore= g2.getARGBColor();
if(dbs.isDefined()) {
g2.setColor(colorPalette.getStereoColorKnown());
bondStereo=bondStereo.split("\\_")[0];
}else {
g2.setColor(colorPalette.getStereoColorUnknown());
bondStereo="E/Z";
}
float invD=(float)inv1;
g2.setFont(defaultFont.deriveFont(Font.BOLD,fsize * FONT_SIZE_LABEL_FUDGE));
//get the rectangle that it would be drawn on
Rectangle2D bounds = getStringBounds(g2, bondStereo,
xPos
+ rat * invD* dydbl
, yPos
- invD* rat * dxdbl
);
float centerSubtractX= (float) (bounds.getWidth())/2;
float centerSubtractY= -(float) (bounds.getHeight())/2;
drawString(g2, bondStereo,
xPos-centerSubtractX
+ rat * invD* dydbl
, yPos-centerSubtractY
- invD* rat * dxdbl
);
g2.setColor(colorBefore);
}
}
}

Expand Down
8 changes: 8 additions & 0 deletions src/main/java/gov/nih/ncats/molwitch/renderer/RendererOptions.java
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Original file line number Diff line number Diff line change
Expand Up @@ -43,6 +43,9 @@ public enum DrawOptions{
DRAW_IMPLICIT_HYDROGEN(true, "PROP_KEY_DRAW_IMPLICIT_HYDROGEN"),
DRAW_TERMINAL_CARBON(true, "PROP_KEY_DRAW_TERMINAL_CARBON"),
DRAW_STEREO_BONDS(true, "PROP_KEY_DRAW_STEREO_BONDS"),



DRAW_PROPORTIONAL_ATOM_RADIUS(false, "PROP_KEY_DRAW_PROPORTIONAL_ATOM_RADIUS"),
DRAW_PROPORTION_AVERAGE_BOND_LENGTH(true, "PROP_KEY_DRAW_PROPORTION_AVERAGE_BOND_LENGTH"),
DRAW_CENTER_ALL_DOUBLE_BONDS(false, "PROP_KEY_DRAW_CENTER_ALL_DOUBLE_BONDS"),
Expand Down Expand Up @@ -77,7 +80,11 @@ public enum DrawOptions{


DRAW_GREYSCALE(false, "PROP_KEY_DRAW_GREYSCALE"),

DRAW_STEREO_LABELS(false, "PROP_KEY_DRAW_STEREO_LABELS"),
DRAW_STEREO_LABELS_EZ(true, "PROP_KEY_STEREO_LABELS_EZ"),


DRAW_STEREO_GIVEN_BY_MAP(false, "PROP_KEY_DRAW_STEREO_GIVEN_BY_MAP"),
DRAW_HIGHLIGHT_MAPPED(false, "PROP_KEY_DRAW_HIGHLIGHT_MAPPED"),
DRAW_HIGHLIGHT_WITH_HALO(false, "PROP_KEY_DRAW_HIGHLIGHT_WITH_HALO"),
Expand Down Expand Up @@ -427,6 +434,7 @@ public RendererOptions resetToDefaults() {
public RendererOptions turnOffStereo() {
setDrawOption(DrawOptions.DRAW_STEREO_LABELS, false);
setDrawOption(DrawOptions.DRAW_STEREO_LABELS_PARENTHESES, false);

fireChangeListeners();
return this;
}
Expand Down