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some small fixes
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@thsa
thsa committed Aug 4, 2024
1 parent 2992022 commit 54ca309
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Showing 2 changed files with 49 additions and 28 deletions.
17 changes: 10 additions & 7 deletions src/main/java/org/openmolecules/fx/viewer3d/V3DMolecule.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -398,6 +398,9 @@ public BondRotationHelper getBondRotationHelper() {
return mBondRotationHelper;
}

private boolean isSurface(Node node) {
return node instanceof MeshView && !(node instanceof Cone);
}

/**
* @return center of gravity in local coordinate system
Expand Down Expand Up @@ -467,16 +470,16 @@ public void setHydrogenMode(MoleculeArchitect.HydrogenMode mode) {
* @param constructionMode one of the MoleculeArchitect.CONSTRUCTION_MODE... options
* @param hydrogenMode one of the MoleculeArchitect.HYDROGEN_MODE... options
*/
public void setMode(MoleculeArchitect.ConstructionMode constructionMode,
MoleculeArchitect.HydrogenMode hydrogenMode) {
public void setMode(MoleculeArchitect.ConstructionMode constructionMode, MoleculeArchitect.HydrogenMode hydrogenMode) {
if (constructionMode != mConstructionMode
|| hydrogenMode != mHydrogenMode) {
mConstructionMode = constructionMode;
mHydrogenMode = hydrogenMode;

for (int i=getChildren().size()-1; i>=0; i--)
if (!(getChildren().get(i) instanceof MeshView))
if (!isSurface(getChildren().get(i)))
getChildren().remove(i);

V3DMoleculeBuilder builder = new V3DMoleculeBuilder(this);
builder.setConstructionMode(constructionMode);
builder.setHydrogenMode(hydrogenMode);
Expand All @@ -492,7 +495,7 @@ public void setMode(MoleculeArchitect.ConstructionMode constructionMode,

public void reconstruct() {
for (int i=getChildren().size()-1; i>=0; i--)
if (!(getChildren().get(i) instanceof MeshView))
if (!isSurface(getChildren().get(i)))
getChildren().remove(i);
V3DMoleculeBuilder builder = new V3DMoleculeBuilder(this);
builder.setConstructionMode(mConstructionMode);
Expand Down Expand Up @@ -1107,7 +1110,7 @@ public void updateAppearance(Node node) {
if (!(node instanceof Shape3D))
return;

if (node instanceof MeshView && !(node instanceof Cone))
if (isSurface(node))
return;

Shape3D shape = (Shape3D)node;
Expand Down Expand Up @@ -1158,7 +1161,7 @@ public void updateAppearance(Node node) {
}

private Material getHiliteMaterial(Shape3D shape) {
if (shape instanceof MeshView) {
if (isSurface(shape)) {
NodeDetail detail = (NodeDetail)shape.getUserData();
if (detail.getMaterial().getDiffuseColor().getOpacity() == 1.0)
return sSolidHighlightedMaterial;
Expand All @@ -1171,7 +1174,7 @@ private Material getHiliteMaterial(Shape3D shape) {
}

private PhongMaterial getOverrideMaterial(Shape3D shape) {
if (!(shape instanceof MeshView)) {
if (!isSurface(shape)) {
NodeDetail detail = (NodeDetail)shape.getUserData();
if (detail != null
&& detail.getMaterial() == V3DMoleculeBuilder.getMaterial(MoleculeArchitect.getAtomARGB(1)))
Expand Down
60 changes: 39 additions & 21 deletions src/main/java/org/openmolecules/render/MoleculeArchitect.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -58,8 +58,8 @@ public enum ColorMode {ATOMIC_NO, WIRES;}
private static final int CONNECTION_POINT_COLOR = 0xFFCCCA90; // changed from 0xFFFF1493 to make it less look like oxygen

private static final int COLOR_NONE = 0x00000000; // don't draw objects with this color
private final static int[] ATOM_ARGB = { CONNECTION_POINT_COLOR,
COLOR_NONE, 0xFFD9FFFF, 0xFFCC80FF, 0xFFC2FF00, 0xFFFFB5B5, // ?, H,He,Li, Be,B
private final static int[] ATOM_ARGB = { COLOR_NONE,
0xFFFFFFFF, 0xFFD9FFFF, 0xFFCC80FF, 0xFFC2FF00, 0xFFFFB5B5, // ?, H,He,Li, Be,B
0xFF909090, 0xFF3050F8, 0xFFFF0D0D, 0xFF90E050, 0xFFB3E3F5, 0xFFAB5CF2, // C, N, O, F,Ne,Na
0xFF8AFF00, 0xFFBFA6A6, 0xFFF0C8A0, 0xFFFF8000, 0xFFFFFF30, 0xFF1FF01F, // Mg,Al,Si, P, S,Cl
0xFF80D1E3, 0xFF8F40D4, 0xFF3DFF00, 0xFFE6E6E6, 0xFFBFC2C7, 0xFFA6A6AB, // Ar, K,Ca,Sc,Ti, V
Expand Down Expand Up @@ -186,16 +186,17 @@ && includeAtom(mMol.getBondAtom(1, bond)))
buildBond(bond);

for (int atom=fromAtom; atom<toAtom; atom++) {
if (includeAtom(atom)
&& (mConstructionMode != ConstructionMode.WIRES || mMol.getConnAtoms(atom) == 0)) {
if (includeAtom(atom)) {
int atomicNo = mMol.getAtomicNo(atom);
if (atomicNo == 0 || "*".equals(mMol.getAtomCustomLabel(atom))) {
boolean isAttachmentPoint = (atomicNo == 0 || "*".equals(mMol.getAtomCustomLabel(atom)));
if (isAttachmentPoint) {
double radius = mMol.isMarkedAtom(atom) ? VDWRadii.getVDWRadius(atomicNo)/4
: (mConstructionMode == ConstructionMode.WIRES) ? VDWRadii.getVDWRadius(atomicNo)/6
: (mConstructionMode == ConstructionMode.BALLS) ? VDWRadii.getVDWRadius(atomicNo)*0.95 // to avoid collision with vdw-radii based surface
: VDWRadii.getVDWRadius(atomicNo)/4;
buildConnection(atom, radius);
buildAttachmentPoint(atom, radius);
}
else {
else if (mConstructionMode != ConstructionMode.WIRES || mMol.getConnAtoms(atom) == 0) {
double radius = mMol.isMarkedAtom(atom) ? VDWRadii.getVDWRadius(atomicNo)/4
: (mConstructionMode == ConstructionMode.BALL_AND_STICKS) ? VDWRadii.getVDWRadius(atomicNo)/4
: (mConstructionMode == ConstructionMode.STICKS) ?
Expand All @@ -222,16 +223,17 @@ && includeAtom(mol.getBondAtom(1, bond)))
}

for (Integer atom:atoms) {
if (includeAtom(atom)
&& (mConstructionMode != ConstructionMode.WIRES || mMol.getConnAtoms(atom) == 0)) {
if (includeAtom(atom)) {
int atomicNo = mol.getAtomicNo(atom);
if (atomicNo == 0 || "*".equals(mMol.getAtomCustomLabel(atom))) {
boolean isAttachmentPoint = (atomicNo == 0 || "*".equals(mMol.getAtomCustomLabel(atom)));
if (isAttachmentPoint) {
double radius = mMol.isMarkedAtom(atom) ? VDWRadii.getVDWRadius(atomicNo)/4
: (mConstructionMode == ConstructionMode.WIRES) ? VDWRadii.getVDWRadius(atomicNo)/6
: (mConstructionMode == ConstructionMode.BALLS) ? VDWRadii.getVDWRadius(atomicNo)*0.95 // to avoid collision with vdw-radii based surface
: VDWRadii.getVDWRadius(atomicNo)/4;
buildConnection(atom, radius);
buildAttachmentPoint(atom, radius);
}
else {
else if (mConstructionMode != ConstructionMode.WIRES || mMol.getConnAtoms(atom) == 0) {
double radius = mol.isMarkedAtom(atom) ? VDWRadii.getVDWRadius(atomicNo)/4
: (mConstructionMode == ConstructionMode.BALL_AND_STICKS) ? VDWRadii.getVDWRadius(atomicNo)/4
: (mConstructionMode == ConstructionMode.STICKS) ?
Expand Down Expand Up @@ -259,7 +261,7 @@ private boolean includeAtom(int atom) {
/**
* @param atom wild card atom drawn as cone, which defines a connection to some other not included part of the molecule
*/
private void buildConnection(int atom, double radius) {
private void buildAttachmentPoint(int atom, double radius) {
Coordinates c1 = getCoordinates(atom);

if (mMol.getConnAtoms(atom) == 0) {
Expand Down Expand Up @@ -320,21 +322,37 @@ private void buildBond(int bond) {
}

private void buildBallAndStickBond(int bond, double d, double b, double c) {
int color = BALL_AND_STICK_STICK_COLOR;
int atom1 = mMol.getBondAtom(0, bond);
int atom2 = mMol.getBondAtom(1, bond);
int color1 = (getAtomColor(atom1) == COLOR_NONE) ? COLOR_NONE : BALL_AND_STICK_STICK_COLOR;
int color2 = (getAtomColor(atom2) == COLOR_NONE) ? COLOR_NONE : BALL_AND_STICK_STICK_COLOR;

if (color1 == COLOR_NONE && color2 == COLOR_NONE)
return;

if (color1 != COLOR_NONE) {
center.between(mMol.getCoordinates(atom1), mMol.getCoordinates(atom2), 0.25);
d /= 2.0;
}
if (color2 != COLOR_NONE) {
center.between(mMol.getCoordinates(atom1), mMol.getCoordinates(atom2), 0.75);
d /= 2.0;
}

int order = mMol.getBondOrder(bond);
if (order == 1) {
double dd = 2*calculateBondReduction(bond, 0.2);
if (dd < d)
mBuilder.addCylinder(bondRole(bond), BALL_AND_STICK_SBOND_RADIUS, d-dd, center, b, c, color);
mBuilder.addCylinder(bondRole(bond), BALL_AND_STICK_SBOND_RADIUS, d-dd, center, b, c, BALL_AND_STICK_STICK_COLOR);
return;
}

if (order == 2) {
Coordinates ds = calculateDoubleBondShift(bond).scale(BALL_AND_STICK_DBOND_SHIFT);
double dd = calculateBondReduction(bond, 0.20+0.10);
if (dd != 0f) {
mBuilder.addCylinder(bondRole(bond), BALL_AND_STICK_DBOND_RADIUS, d-dd, point1.set(center).add(ds), b, c, color);
mBuilder.addCylinder(bondRole(bond), BALL_AND_STICK_DBOND_RADIUS, d-dd, point1.set(center).sub(ds), b, c, color);
mBuilder.addCylinder(bondRole(bond), BALL_AND_STICK_DBOND_RADIUS, d-dd, point1.set(center).add(ds), b, c, BALL_AND_STICK_STICK_COLOR);
mBuilder.addCylinder(bondRole(bond), BALL_AND_STICK_DBOND_RADIUS, d-dd, point1.set(center).sub(ds), b, c, BALL_AND_STICK_STICK_COLOR);
}
return;
}
Expand All @@ -344,11 +362,11 @@ private void buildBallAndStickBond(int bond, double d, double b, double c) {
double dd1 = 2*calculateBondReduction(bond, 0.11);
double dd2 = 2*calculateBondReduction(bond, 0.22+0.07);
if (dd2 < d)
mBuilder.addCylinder(bondRole(bond), BALL_AND_STICK_TBOND_RADIUS, d-dd2, point1.set(center).add(ds), b, c, color);
mBuilder.addCylinder(bondRole(bond), BALL_AND_STICK_TBOND_RADIUS, d-dd2, point1.set(center).add(ds), b, c, BALL_AND_STICK_STICK_COLOR);
if (dd1 < d)
mBuilder.addCylinder(bondRole(bond), BALL_AND_STICK_TBOND_RADIUS, d-dd1, center, b, c, color);
mBuilder.addCylinder(bondRole(bond), BALL_AND_STICK_TBOND_RADIUS, d-dd1, center, b, c, BALL_AND_STICK_STICK_COLOR);
if (dd2 < d)
mBuilder.addCylinder(bondRole(bond), BALL_AND_STICK_TBOND_RADIUS, d-dd2, point1.set(center).sub(ds), b, c, color);
mBuilder.addCylinder(bondRole(bond), BALL_AND_STICK_TBOND_RADIUS, d-dd2, point1.set(center).sub(ds), b, c, BALL_AND_STICK_STICK_COLOR);
return;
}

Expand All @@ -359,7 +377,7 @@ private void buildBallAndStickBond(int bond, double d, double b, double c) {
Coordinates p2 = getCoordinates(mMol.getBondAtom(1, bond));
point1.between(p1, p2, dd/d);
point2.between(p2, p1, dd/d);
buildDottedBond(bond, color, color, point1, point2, BALL_AND_STICK_DOT_RADIUS, d-2*dd);
buildDottedBond(bond, color1, color2, point1, point2, BALL_AND_STICK_DOT_RADIUS, d-2*dd);
}
return;
}
Expand Down

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