Examples with StereoMolecule com.actelion.research.chem.StereoMolecule used on opensource projects

Example 16 with StereoMolecule

use of com.actelion.research.chem.StereoMolecule in project openchemlib by Actelion.

the class SelectionAction method moveAtomsAndBonds.

private boolean moveAtomsAndBonds(double dx, double dy, boolean force) {
    boolean ok = false;
    StereoMolecule mol = model.getMolecule();
    if (mol != null) {
        if (mol != null && atom != -1 || force) {
            translateAtoms(mol, dx, dy, true);
            ok = true;
        } else if (mol != null && bond != -1 || force) {
            translateBonds(mol, dx, dy, true);
            ok = true;
        }
    }
    return ok;
}

Example 17 with StereoMolecule

use of com.actelion.research.chem.StereoMolecule in project openchemlib by Actelion.

the class SelectionAction method deselectAllAtoms.

private void deselectAllAtoms() {
    StereoMolecule mol = model.getMolecule();
    deselectAtoms(mol);
}

Example 18 with StereoMolecule

use of com.actelion.research.chem.StereoMolecule in project openchemlib by Actelion.

the class SelectionAction method onDoubleClick.

@Override
public boolean onDoubleClick(IMouseEvent evt) {
    // StereoMolecule mol = model.getSelectedMolecule();
    java.awt.geom.Point2D pt = new Point2D.Double(evt.getX(), evt.getY());
    StereoMolecule mol = model.getMoleculeAt(pt, true);
    if (mol != null) {
        int atom = mol.findAtom((float) pt.getX(), (float) pt.getY());
        int bond = mol.findBond((float) pt.getX(), (float) pt.getY());
        boolean mShiftIsDown = evt.isShiftDown();
        int mMode = model.getMode();
        if (mol.isFragment()) {
            if (atom != -1) {
                return showAtomQFDialog(atom);
            } else if (bond != -1) {
                return showBondQFDialog(bond);
            }
        // else if (mCurrentHiliteObject != null) {
        // if (!mShiftIsDown) {
        // for (int i = 0; i < mol.getAllAtoms(); i++)
        // mol.setAtomSelection(i, false);
        // for (int i = 0; i < mDrawingObjectList.size(); i++)
        // ((AbstractDrawingObject) mDrawingObjectList.get(i)).setSelected(false);
        // }
        // 
        // mCurrentHiliteObject.setSelected(true);
        // update(UPDATE_REDRAW);
        // }
        } else {
            int rootAtom = -1;
            if (atom != -1) {
                rootAtom = atom;
            } else if (bond != -1) {
                rootAtom = mol.getBondAtom(0, bond);
            }
            if (rootAtom != -1) /*|| mCurrentHiliteObject != null*/
            {
                if (!mShiftIsDown) {
                    deselectAllAtoms();
                    if (model.isReaction()) {
                        model.selectFragmentByAtom(rootAtom);
                    } else {
                        for (int i = 0; i < mol.getAllAtoms(); i++) {
                            mol.setAtomSelection(i, true);
                        }
                    }
                // if (mDrawingObjectList != null)
                // for (AbstractDrawingObject drawingObject : mDrawingObjectList)
                // drawingObject.setSelected(false);
                }
                // }
                return true;
            }
        }
    } else {
        IDrawingObject drawingObject = model.getSelectedDrawingObject();
        if (drawingObject != null) {
            // System.out.printf("Doubleclick on seleted object\n");
            if (evt.isShiftDown()) {
                deselectAllAtoms();
                deselectAllDrawingObjects();
            // model.setSelectedDrawingObject(null);
            }
            drawingObject.setSelected(true);
            model.setSelectedDrawingObject(drawingObject);
        }
    }
    return false;
}

Example 19 with StereoMolecule

use of com.actelion.research.chem.StereoMolecule in project openchemlib by Actelion.

the class SelectionAction method selectFromPolygonRegion.

private void selectFromPolygonRegion() {
    StereoMolecule mol = model.getMolecule();
    for (int i = 0; i < mol.getAllAtoms(); i++) {
        boolean isSelected = polygon.contains(mol.getAtomX(i), mol.getAtomY(i));
        mol.setAtomSelection(i, isSelected);
    // model.setSelectedMolecule(mol);
    }
    List<IDrawingObject> drawables = model.getDrawingObjects();
    for (IDrawingObject d : drawables) {
        Rectangle2D r = d.getBoundingRect();
        if (polygon.contains(r.getCenterX(), r.getCenterY()))
            d.setSelected(true);
    }
}

Example 20 with StereoMolecule

use of com.actelion.research.chem.StereoMolecule in project openchemlib by Actelion.

the class UpBondAction method onChangeBond.

public void onChangeBond(int bond) {
    StereoMolecule mol = model.getMolecule();
    if (mol != null) {
        mol.changeBond(bond, Molecule.cBondTypeUp);
        mol.ensureHelperArrays(Molecule.cHelperNeighbours);
    }
}