openchemlib 9.0.1 → 9.1.0

package/dist/openchemlib.d.ts

@@ -2591,9 +2591,9 @@ export declare class Molecule {
    * stereo bond to indicate the proper configuration.
    * If the removal of a hydrogen atom would change an atom's implicit valence,
    * the atom's abnormal valence is set accordingly.
-   * @param is3D pass true, if atom coordinates are three dimensional
+   * @param is3D Deprecated: this parameter is unused and has no effect.
    */
-  removeExplicitHydrogens(is3D: boolean): void;
+  removeExplicitHydrogens(is3D?: boolean): void;
 
   /**
    * Separates all disconnected fragments of this Molecule into individual

package/dist/openchemlib.debug.js

@@ -62,6 +62,7 @@ var DrawContext = class {
     this.ctx.font = this.currentFont;
     this.currentColor = "#000000";
     this.currentLineWidth = 1;
+    this.canvasCache = /* @__PURE__ */ new Map();
   }
   clearRect(x, y, w, h) {
     this.ctx.clearRect(x, y, w, h);
@@ -157,13 +158,17 @@ var DrawContext = class {
         `drawImage call with ${arguments.length} arguments unimplemented`
       );
     }
-    const fullScaleCanvas = document.createElement("canvas");
-    const imageData = image.imageData;
-    fullScaleCanvas.width = imageData.width;
-    fullScaleCanvas.height = imageData.height;
-    const fullScaleContext = fullScaleCanvas.getContext("2d");
-    fullScaleContext.globalAlpha = 0;
-    fullScaleContext.putImageData(imageData, 0, 0);
+    let fullScaleCanvas = this.canvasCache.get(image);
+    if (!fullScaleCanvas) {
+      fullScaleCanvas = document.createElement("canvas");
+      const imageData = image.imageData;
+      fullScaleCanvas.width = imageData.width;
+      fullScaleCanvas.height = imageData.height;
+      const fullScaleContext = fullScaleCanvas.getContext("2d");
+      fullScaleContext.globalAlpha = 0;
+      fullScaleContext.putImageData(imageData, 0, 0);
+      this.canvasCache.set(image, fullScaleCanvas);
+    }
     this.ctx.drawImage(fullScaleCanvas, sx, sy, sw, sh, dx, dy, dw, dh);
   }
   isDarkBackground() {
@@ -176,6 +181,7 @@ var EditorArea = class {
   constructor(canvasElement, onChange) {
     this.canvasElement = canvasElement;
     this.changeListener = onChange;
+    this.drawContext = new DrawContext(this.canvasElement.getContext("2d"));
   }
   getBackgroundRGB() {
     return 16777215;
@@ -187,7 +193,7 @@ var EditorArea = class {
     return this.canvasElement.height;
   }
   getDrawContext() {
-    return new DrawContext(this.canvasElement.getContext("2d"));
+    return this.drawContext;
   }
   onChange(what, isUserEvent) {
     this.changeListener?.({ what, isUserEvent });
@@ -324,13 +330,14 @@ function getKeyFromEvent(ev, JavaEditorArea) {
 var Toolbar = class {
   constructor(canvasElement) {
     this.canvasElement = canvasElement;
+    this.drawContext = new DrawContext(this.canvasElement.getContext("2d"));
   }
   setDimensions(width, height) {
     this.canvasElement.width = width;
     this.canvasElement.height = height;
   }
   getDrawContext() {
-    return new DrawContext(this.canvasElement.getContext("2d"));
+    return this.drawContext;
   }
   getBackgroundRGB() {
     return 16777215;
@@ -714,7 +721,7 @@ function createEditor(parentElement, options, onChange, JavaEditorArea, JavaEdit
     userSelect: "none",
     webkitUserSelect: "none"
   });
-  const shadowRoot = rootElement.attachShadow({ mode: "closed" });
+  const shadowRoot = rootElement.attachShadow({ mode: "open" });
   shadowRoot.adoptedStyleSheets = [getEditorStylesheet()];
   let toolbarCanvas = null;
   if (!readOnly) {
@@ -11418,7 +11425,7 @@ function getExports($wnd) {
     return aromaticPi > 1;
   };
   _.idCodeCreate = function idCodeCreate() {
-    var EZCount, THCount, a, a$array, a$index, a$max, atom, atom0, atom1, atom10, atom11, atom2, atom3, atom4, atom5, atom6, atom7, atom8, atom9, atomList, base, bond, bond0, bond1, bond2, bond3, bond4, bondOrder, chargedAtoms, connBits, conns, count, customLabel, dbits, dif, hIndex, i, i0, i1, isAromaticSPBond, j, label_0, lbits, maxLength, maxdif, nbits, nitrogens, otherAtoms, oxygens, parity;
+    var EZCount, THCount, a, a$array, a$index, a$max, atom, atom0, atom1, atom10, atom11, atom2, atom3, atom4, atom5, atom6, atom7, atom8, atom9, atomList, base, bond, bond0, bond1, bond2, bond3, bond4, bondOrder, chargedAtoms, connBits, conns, count, customLabel, dbits, dif, hIndex, i, i0, isAromaticSPBond, j, label_0, lbits, maxLength, maxdif, nbits, nitrogens, otherAtoms, oxygens, parity;
     this.encodeBitsStart(false);
     this.encodeBits(9, 4);
     nbits = $wnd.Math.max(carc2.getNeededBits(this.mMol.getAtoms_0()), carc2.getNeededBits(this.mMol.getBonds_0()));
@@ -11721,12 +11728,11 @@ function getExports($wnd) {
     if (this.mAllHydrogensAreExplicit && (this.mMode & 16) != 0) {
       count = 0;
       connBits = 0;
-      for (i1 = 0; i1 < this.mMol.getAtoms_0(); i1++) {
-        atom = this.mGraphAtom[i1];
+      for (atom7 = 0; atom7 < this.mMol.getAtoms_0(); atom7++) {
         conns = 0;
-        for (j = this.mMol.getConnAtoms_0(atom); j < this.mMol.getAllConnAtoms_0(atom); j++) {
-          if (this.mMol.isSelectedAtom_0(this.mMol.getConnAtom_0(atom, j))) {
-            hIndex = j - this.mMol.getConnAtoms_0(atom);
+        for (j = this.mMol.getConnAtoms_0(this.mGraphAtom[atom7]); j < this.mMol.getAllConnAtoms_0(this.mGraphAtom[atom7]); j++) {
+          if (this.mMol.isSelectedAtom_0(this.mMol.getConnAtom_0(this.mGraphAtom[atom7], j))) {
+            hIndex = j - this.mMol.getConnAtoms_0(this.mGraphAtom[atom7]);
             conns |= 1 << hIndex;
             connBits = $wnd.Math.max(connBits, hIndex + 1);
           }
@@ -11738,12 +11744,11 @@ function getExports($wnd) {
         this.encodeFeatureNo(38);
         this.encodeBits(fromInt_0(count), nbits);
         this.encodeBits(fromInt_0(connBits), 3);
-        for (i = 0; i < this.mMol.getAtoms_0(); i++) {
-          atom = this.mGraphAtom[i];
+        for (atom = 0; atom < this.mMol.getAtoms_0(); atom++) {
           conns = 0;
-          for (j = this.mMol.getConnAtoms_0(atom); j < this.mMol.getAllConnAtoms_0(atom); j++) {
-            if (this.mMol.isSelectedAtom_0(this.mMol.getConnAtom_0(atom, j))) {
-              hIndex = j - this.mMol.getConnAtoms_0(atom);
+          for (j = this.mMol.getConnAtoms_0(this.mGraphAtom[atom]); j < this.mMol.getAllConnAtoms_0(this.mGraphAtom[atom]); j++) {
+            if (this.mMol.isSelectedAtom_0(this.mMol.getConnAtom_0(this.mGraphAtom[atom], j))) {
+              hIndex = j - this.mMol.getConnAtoms_0(this.mGraphAtom[atom]);
               conns |= 1 << hIndex;
             }
           }
@@ -16028,7 +16033,7 @@ function getExports($wnd) {
   _.invalidateHelperArrays_0 = function invalidateHelperArrays(helperBits) {
     this.mValidHelperArrays &= ~helperBits;
   };
-  _.is3D_0 = function is3D_0() {
+  _.is3D_0 = function is3D() {
     var atom;
     for (atom = 0; atom < this.mAllAtoms; atom++)
       if (this.mCoordinates[atom].z_0 != 0)
@@ -19067,10 +19072,7 @@ function getExports($wnd) {
     }
     return preferredBond;
   };
-  _.removeExplicitHydrogens_0 = function removeExplicitHydrogens() {
-    this.removeExplicitHydrogens_1(true, false);
-  };
-  _.removeExplicitHydrogens_1 = function removeExplicitHydrogens_0(hasValid2DCoords, hasValid3DCoords) {
+  _.removeExplicitHydrogens_0 = function removeExplicitHydrogens(hasValid2DCoords) {
     var abnormalValence, atom, explicitAbnormalValence, newAbnormalValence;
     this.ensureHelperArrays_0(hasValid2DCoords ? 15 : 1);
     this.mAllAtoms = this.mAtoms;
@@ -19711,7 +19713,7 @@ function getExports($wnd) {
     this.parse_2(mol, idcode, coordinates, 0, 0);
   };
   _.parse_2 = function parse_2(mol, idcode, coordinates, idcodeStart, coordsStart) {
-    var EZCount, THCount, abits, allAtoms, allBonds, aromState, aromaticSPBond, atom, atom0, atom1, atom2, atomList, atomicNo, atoms, avbl, avblDefault, avblInt, base, bbits, binCount, bond, bond$array, bond$index, bond$max, bond0, bondOrder, bondType, bondTypes, bridgeData, charge, chargedAtoms, closureBonds, connBits, coords2DAvailable, coordsAre3D, coordsAreAbsolute, count, dataType, dbits, decodeOldCoordinates, decodedDX, decodedDY, dif, dx, dy, dz, e, eNeighbours, f, factor, from, hCount, hint, hydrogen, hydrogenCount, i, i0, i1, i10, i11, i12, i13, i14, i15, i16, i17, i18, i19, i2, i20, i21, i22, i23, i24, i25, i26, i27, i28, i29, i3, i30, i31, i32, i33, i34, i35, i36, i37, i38, i39, i4, i40, i41, i42, i43, i5, i6, i7, i8, i9, index_0, isDelocalizedBond, j, label_0, lbits, mass, neighbours, nitrogens, no, offset, otherAtoms, oxygens, parity, piElectrons, resolutionBits, ringSize, ringState, selectedHydrogenBits, stereoState, targetAVBL, version2, xInt, xOffset, yInt, yOffset, zInt, zOffset;
+    var EZCount, THCount, abits, allAtoms, allBonds, aromState, aromaticSPBond, atom, atom0, atom1, atom2, atomList, atomicNo, atoms, avbl, avblDefault, avblInt, base, bbits, binCount, bond, bond$array, bond$index, bond$max, bond0, bondOrder, bondType, bondTypes, bridgeData, charge, chargedAtoms, closureBonds, connBits, conns, coords2DAvailable, coordsAre3D, coordsAreAbsolute, count, dataType, dbits, decodeOldCoordinates, decodedDX, decodedDY, dif, dx, dy, dz, e, eNeighbours, f, factor, from, hCount, hint, hydrogen, hydrogenCount, i, i0, i1, i10, i11, i12, i13, i14, i15, i16, i17, i18, i19, i2, i20, i21, i22, i23, i24, i25, i26, i27, i28, i29, i3, i30, i31, i32, i33, i34, i35, i36, i37, i38, i39, i4, i40, i41, i42, i43, i5, i6, i7, i8, i9, index_0, isDelocalizedBond, j, label_0, lbits, mass, neighbours, nitrogens, no, offset, otherAtoms, oxygens, parity, piElectrons, resolutionBits, ringSize, ringState, selectedHydrogenBits, stereoState, targetAVBL, version2, xInt, xOffset, yInt, yOffset, zInt, zOffset;
     mol.clear_0();
     if (jsEquals(idcode, null) || idcodeStart < 0 || idcodeStart >= idcode.length)
       return;
@@ -20182,8 +20184,11 @@ function getExports($wnd) {
           no = this.decodeBits(abits);
           connBits = this.decodeBits(3);
           selectedHydrogenBits = initUnidimensionalArray(cggl.I_classLit, { 6: 1, 4: 1, 1: 1 }, 5, allAtoms, 15, 1);
-          for (i = 0; i < no; i++)
-            selectedHydrogenBits[this.decodeBits(abits)] = this.decodeBits(connBits);
+          for (i = 0; i < no; i++) {
+            atom = this.decodeBits(abits);
+            conns = this.decodeBits(connBits);
+            selectedHydrogenBits[atom] = conns;
+          }
           break;
       }
     }
@@ -27342,7 +27347,7 @@ function getExports($wnd) {
       }
     }
     if (!this.mMakeHydrogenExplicit && (this.mSmartsFeatureFound || this.mSmartsMode == 2))
-      this.mMol.removeExplicitHydrogens_0();
+      this.mMol.removeExplicitHydrogens_0(false);
     this.mMol.ensureHelperArrays_0(1);
     this.correctValenceExceededNitrogen();
     this.locateAromaticDoubleBonds(allowSmarts, this.mSmartsFeatureFound);
@@ -32202,7 +32207,7 @@ function getExports($wnd) {
     if (isNull(this.mRandom))
       this.mRandom = new ju.Random();
     if ((this.mMode & 2) != 0)
-      mol.removeExplicitHydrogens_1(false, false);
+      mol.removeExplicitHydrogens_0(false);
     this.mMol = mol;
     this.mMol.ensureHelperArrays_0(7);
     this.mFFP = ffp;
@@ -33990,15 +33995,16 @@ function getExports($wnd) {
   defineClass(430, 1, { 117: 1, 1: 1 }, carcfm.AngleBend);
   _.$init_80 = function $init_80() {
   };
-  _.getEnergy_0 = function getEnergy_0(pos) {
-    var angle, c2, cb, theta;
+  _.getEnergy_0 = function getEnergy_0(pos, detail) {
+    var angle, c2, cb, e, theta;
     theta = new carcfm.Vector3_4(pos, this.a2, this.a1).angle_0(new carcfm.Vector3_4(pos, this.a2, this.a3));
     angle = jl.toDegrees(theta) - this.theta0;
     cb = -6981317e-9;
     c2 = 143.9325 * 0.017453292519943295 * 0.017453292519943295;
-    if (this.isLinear)
-      return 143.9325 * this.ka * (1 + $wnd.Math.cos(theta));
-    return 0.5 * 0.043844346773450435 * this.ka * angle * angle * (1 + -6981317e-9 * angle);
+    e = this.isLinear ? 143.9325 * this.ka * (1 + $wnd.Math.cos(theta)) : 0.5 * 0.043844346773450435 * this.ka * angle * angle * (1 + -6981317e-9 * angle);
+    if (isNotNull(detail))
+      detail.append_9("angleBend	" + caru.toString_20(jl.toDegrees(theta)) + "	" + caru.toString_20(this.theta0) + "	" + this.a1 + "," + this.a2 + "," + this.a3 + "	" + caru.toString_20(e) + "\n");
+    return e;
   };
   _.getGradient = function getGradient(pos, grad) {
     var angleTerm, c2, cb, cosTheta, dCos_dS, dE_dTheta, dist0, dist1, r0, r1, sinTheta, sinThetaSq;
@@ -34087,14 +34093,17 @@ function getExports($wnd) {
   defineClass(256, 1, { 117: 1, 1: 1 }, carcfm.BondStretch);
   _.$init_86 = function $init_86() {
   };
-  _.getEnergy_0 = function getEnergy_1(pos) {
-    var c1, c3, cs, diff, dist;
+  _.getEnergy_0 = function getEnergy_1(pos, detail) {
+    var c1, c3, cs, diff, dist, e;
     c1 = 143.9325;
     cs = -2;
     c3 = 7 / 12;
     dist = new carcfm.Vector3_3(pos, this.a1).distance_0(new carcfm.Vector3_3(pos, this.a2));
     diff = (dist - this.r0) * (dist - this.r0);
-    return 0.5 * 143.9325 * this.kb * diff * (1 + -2 * (dist - this.r0) + 0.5833333333333334 * -2 * -2 * diff);
+    e = 0.5 * 143.9325 * this.kb * diff * (1 + -2 * (dist - this.r0) + 0.5833333333333334 * -2 * -2 * diff);
+    if (isNotNull(detail))
+      detail.append_9("bondStretch	" + caru.toString_20(dist) + "	" + caru.toString_20(this.r0) + "	" + this.a1 + "," + this.a2 + "	" + caru.toString_20(e) + "\n");
+    return e;
   };
   _.getGradient = function getGradient_0(pos, grad) {
     var c1, c3, cs, dE_dr, dist, distTerm, i;
@@ -34219,14 +34228,17 @@ function getExports($wnd) {
   defineClass(431, 1, { 117: 1, 1: 1 }, carcfm.Electrostatic);
   _.$init_87 = function $init_87() {
   };
-  _.getEnergy_0 = function getEnergy_2(pos) {
-    var corr_dist, diel, dist;
+  _.getEnergy_0 = function getEnergy_2(pos, detail) {
+    var corr_dist, diel, dist, e;
     dist = new carcfm.Vector3_4(pos, this.a1, this.a2).length_2();
     corr_dist = dist + 0.05;
     diel = 332.0716;
     if (this.distModel)
       corr_dist *= corr_dist;
-    return diel * this.charge_term / corr_dist * (jsEquals(this.rel_0, (carcfm.$clinit_Separation$Relation(), carcfm.ONE_FOUR)) ? 0.75 : 1);
+    e = diel * this.charge_term / corr_dist * (jsEquals(this.rel_0, (carcfm.$clinit_Separation$Relation(), carcfm.ONE_FOUR)) ? 0.75 : 1);
+    if (isNotNull(detail))
+      detail.append_9("electrostatic	" + caru.toString_20(dist) + "		" + this.a1 + "," + this.a2 + "	" + caru.toString_20(e) + "\n");
+    return e;
   };
   _.getGradient = function getGradient_1(pos, grad) {
     var corr_dist, dE_dr, dGrad, dist, i;
@@ -34296,14 +34308,22 @@ function getExports($wnd) {
     this.mEnergies = new ju.ArrayList();
   };
   _.getTotalEnergy_0 = function getTotalEnergy() {
-    return this.getTotalEnergy_1(this.mPos);
+    return this.getTotalEnergy_2(this.mPos, null);
   };
   _.getTotalEnergy_1 = function getTotalEnergy_0(pos) {
-    var term, term$iterator, total;
+    return this.getTotalEnergy_2(pos, null);
+  };
+  _.getTotalEnergy_2 = function getTotalEnergy_1(pos, detail) {
+    var no, term, term$iterator, total;
+    if (isNotNull(detail))
+      detail.append_9("no	type	is_property	opt_property	atoms	energy\n");
     total = 0;
+    no = 0;
     for (term$iterator = this.mEnergies.iterator(); term$iterator.hasNext_0(); ) {
       term = castTo(term$iterator.next_3(), 117);
-      total += term.getEnergy_0(pos);
+      if (isNotNull(detail))
+        detail.append_5(++no).append_9("	");
+      total += term.getEnergy_0(pos, detail);
     }
     return total;
   };
@@ -34435,15 +34455,18 @@ function getExports($wnd) {
   defineClass(212, 1, { 117: 1, 1: 1 }, carcfm.OutOfPlane);
   _.$init_90 = function $init_90() {
   };
-  _.getEnergy_0 = function getEnergy_3(pos) {
-    var c2, chi, n, rji, rjk, rjl;
+  _.getEnergy_0 = function getEnergy_3(pos, detail) {
+    var c2, chi, e, n, rji, rjk, rjl;
     rji = new carcfm.Vector3_4(pos, this.ac, this.a1).normalise();
     rjk = new carcfm.Vector3_4(pos, this.ac, this.a2).normalise();
     rjl = new carcfm.Vector3_4(pos, this.ac, this.a3).normalise();
     n = rji.cross_0(rjk).normalise();
     chi = 57.29577951308232 * $wnd.Math.asin(n.dot_0(rjl));
     c2 = 143.9325 * 0.017453292519943295 * 0.017453292519943295;
-    return 0.5 * c2 * this.koop * chi * chi;
+    e = 0.5 * c2 * this.koop * chi * chi;
+    if (isNotNull(detail))
+      detail.append_9("outOfPlane	" + caru.toString_20(chi) + "		" + this.a1 + "," + this.a2 + "," + this.a3 + "	" + caru.toString_20(e) + "\n");
+    return e;
   };
   _.getGradient = function getGradient_2(pos, grad) {
     var c2, chi, cosChi, cosChiSq, cosTheta, dE_dChi, dji, djk, djl, i, n, rji, rjk, rjl, sinChi, sinTheta, sinThetaSq, t1, t2, t3, term1, term2, tg1, tg3, tg4;
@@ -34785,13 +34808,16 @@ function getExports($wnd) {
   defineClass(432, 1, { 117: 1, 1: 1 }, carcfm.StretchBend);
   _.$init_95 = function $init_95() {
   };
-  _.getEnergy_0 = function getEnergy_4(pos) {
-    var dist1, dist2, factor, theta;
+  _.getEnergy_0 = function getEnergy_4(pos, detail) {
+    var dist1, dist2, e, factor, theta;
     dist1 = new carcfm.Vector3_4(pos, this.a2, this.a1).length_2();
     dist2 = new carcfm.Vector3_4(pos, this.a2, this.a3).length_2();
     theta = new carcfm.Vector3_4(pos, this.a2, this.a1).angle_0(new carcfm.Vector3_4(pos, this.a2, this.a3));
     factor = 143.9325 * 0.017453292519943295 * (jl.toDegrees(theta) - this.theta0);
-    return factor * (dist1 - this.r0i) * this.kba_ijk + factor * (dist2 - this.r0k) * this.kba_kji;
+    e = factor * (dist1 - this.r0i) * this.kba_ijk + factor * (dist2 - this.r0k) * this.kba_kji;
+    if (isNotNull(detail))
+      detail.append_9("stretchBend	" + caru.toString_20(dist1) + "," + caru.toString_20(dist2) + "," + caru.toString_20(jl.toDegrees(theta)) + "	" + caru.toString_20(this.r0i) + "," + caru.toString_20(this.r0k) + "," + caru.toString_20(this.theta0) + "	" + this.a1 + "," + this.a2 + "," + this.a3 + "	" + caru.toString_20(e) + "\n");
+    return e;
   };
   _.getGradient = function getGradient_3(pos, grad) {
     var angleTerm, c5, cosTheta, dCos_dS1, dCos_dS2, dCos_dS3, dCos_dS4, dCos_dS5, dCos_dS6, dist1, dist2, distTerm, p12, p32, sinTheta, sinThetaSq;
@@ -34910,8 +34936,8 @@ function getExports($wnd) {
   defineClass(433, 1, { 117: 1, 1: 1 }, carcfm.TorsionAngle);
   _.$init_97 = function $init_97() {
   };
-  _.getEnergy_0 = function getEnergy_5(pos) {
-    var cos2Phi, cos3Phi, cosPhi, r1, r2, r3, r4, t1, t2;
+  _.getEnergy_0 = function getEnergy_5(pos, detail) {
+    var cos2Phi, cos3Phi, cosPhi, e, r1, r2, r3, r4, t1, t2;
     r1 = new carcfm.Vector3_4(pos, this.a1, this.a2);
     r2 = new carcfm.Vector3_4(pos, this.a3, this.a2);
     r3 = new carcfm.Vector3_4(pos, this.a2, this.a3);
@@ -34921,7 +34947,10 @@ function getExports($wnd) {
     cosPhi = t1.cosAngle(t2);
     cos2Phi = 2 * cosPhi * cosPhi - 1;
     cos3Phi = cosPhi * (2 * cos2Phi - 1);
-    return 0.5 * (this.v1 * (1 + cosPhi) + this.v2 * (1 - cos2Phi) + this.v3 * (1 + cos3Phi));
+    e = 0.5 * (this.v1 * (1 + cosPhi) + this.v2 * (1 - cos2Phi) + this.v3 * (1 + cos3Phi));
+    if (isNotNull(detail))
+      detail.append_9("torsion	" + caru.toString_20(jl.toDegrees(t1.angle_0(t2))) + "		" + this.a1 + "," + this.a2 + "," + this.a3 + "," + this.a4 + "	" + caru.toString_20(e) + "\n");
+    return e;
   };
   _.getGradient = function getGradient_4(pos, grad) {
     var cosPhi, d, dCos_dT, dE_dPhi, r, sin2Phi, sin3Phi, sinPhi, sinPhiSq, sinTerm, t;
@@ -35009,8 +35038,8 @@ function getExports($wnd) {
   defineClass(434, 1, { 117: 1, 1: 1 }, carcfm.VanDerWaals);
   _.$init_98 = function $init_98() {
   };
-  _.getEnergy_0 = function getEnergy_6(pos) {
-    var aTerm, aTerm2, aTerm7, bTerm, dist, dist2, dist7, rstar_ij2, rstar_ij7, vdw1, vdw1m1, vdw2, vdw2m1;
+  _.getEnergy_0 = function getEnergy_6(pos, detail) {
+    var aTerm, aTerm2, aTerm7, bTerm, dist, dist2, dist7, e, rstar_ij2, rstar_ij7, vdw1, vdw1m1, vdw2, vdw2m1;
     dist = new carcfm.Vector3_4(pos, this.a1, this.a2).length_2();
     vdw1 = 1.07;
     vdw1m1 = 1.07 - 1;
@@ -35024,7 +35053,10 @@ function getExports($wnd) {
     rstar_ij2 = this.rstar_ij * this.rstar_ij;
     rstar_ij7 = rstar_ij2 * rstar_ij2 * rstar_ij2 * this.rstar_ij;
     bTerm = 1.12 * rstar_ij7 / (dist7 + 0.1200000000000001 * rstar_ij7) - 2;
-    return aTerm7 * bTerm * this.well_depth;
+    e = aTerm7 * bTerm * this.well_depth;
+    if (isNotNull(detail))
+      detail.append_9("vanDerWaals	" + caru.toString_20(dist) + "		" + this.a1 + "," + this.a2 + "	" + caru.toString_20(e) + "\n");
+    return e;
   };
   _.getGradient = function getGradient_5(pos, grad) {
     var dE_dr, dGrad, dist, i, q, q2, q6, q7, q7pvdw2m1, t, t2, t7, vdw1, vdw1m1, vdw2, vdw2m1, vdw2t7;
@@ -46835,7 +46867,7 @@ function getExports($wnd) {
   _._minimise = function _minimise(maxIts, gradTol, funcTol) {
     return this.oclMmff.minimise_0(maxIts, gradTol, funcTol);
   };
-  _.getTotalEnergy = function getTotalEnergy_1() {
+  _.getTotalEnergy = function getTotalEnergy_2() {
     return this.oclMmff.getTotalEnergy_0();
   };
   _.size = function size_4() {
@@ -47499,7 +47531,7 @@ function getExports($wnd) {
     inventor.invent(this.oclMolecule);
     this.oclMolecule.setStereoBondsFromParity_0();
   };
-  _.is3D = function is3D_1() {
+  _.is3D = function is3D_0() {
     return this.oclMolecule.is3D_0();
   };
   _.isAlkaliMetal = function isAlkaliMetal_0(atom) {
@@ -47649,8 +47681,8 @@ function getExports($wnd) {
   _.removeBondHiliting = function removeBondHiliting_0() {
     this.oclMolecule.removeBondHiliting_0();
   };
-  _.removeExplicitHydrogens = function removeExplicitHydrogens_1(is3D) {
-    this.oclMolecule.removeExplicitHydrogens_1(true, is3D);
+  _.removeExplicitHydrogens = function removeExplicitHydrogens_0() {
+    this.oclMolecule.removeExplicitHydrogens_0(true);
   };
   _.removeQueryFeatures = function removeQueryFeatures_0() {
     return this.oclMolecule.removeQueryFeatures_0();
@@ -64774,21 +64806,21 @@ function getExports($wnd) {
   };
   ooccg.addHydrogenAtoms = function addHydrogenAtoms(mol) {
     ooccg.$clinit_ConformerGenerator();
-    var atom, atom0, atom1, hydrogenBondLength, i, implicitHydrogen, oldStereoHelperBits;
+    var atom, atom0, atom1, bondLength, i, implicitHydrogen, oldStereoHelperBits;
     oldStereoHelperBits = mol.getHelperArrayStatus_0() & 248;
     mol.ensureHelperArrays_0(1);
     implicitHydrogen = initUnidimensionalArray(cggl.I_classLit, { 6: 1, 4: 1, 1: 1 }, 5, mol.getAtoms_0(), 15, 1);
     for (atom0 = 0; atom0 < mol.getAtoms_0(); atom0++)
       implicitHydrogen[atom0] = mol.getImplicitHydrogens_1(atom0);
-    hydrogenBondLength = 0.8 * mol.getAverageBondLength_0();
     for (atom1 = 0; atom1 < implicitHydrogen.length; atom1++)
       if (implicitHydrogen[atom1] != 0)
         for (i = 0; i < implicitHydrogen[atom1]; i++)
           mol.addBond_1(atom1, mol.addAtom_2(1), 1);
     mol.ensureHelperArrays_0(1);
+    bondLength = 0.8 * mol.getAverageBondLength_0();
     for (atom = 0; atom < implicitHydrogen.length; atom++)
       if (implicitHydrogen[atom] != 0)
-        ooccg.setHydrogenLocations(mol, atom, implicitHydrogen[atom], hydrogenBondLength);
+        ooccg.setHydrogenLocations(mol, atom, implicitHydrogen[atom], bondLength);
     if ((oldStereoHelperBits & 8) != 0)
       mol.setParitiesValid_0(oldStereoHelperBits);
   };
@@ -64802,7 +64834,7 @@ function getExports($wnd) {
     ooccg.$clinit_ConformerGenerator();
     return compare_25(b2_1.getSmallerSideAtoms().length, b1_0.getSmallerSideAtoms().length);
   };
-  ooccg.setHydrogenLocations = function setHydrogenLocations(mol, atom, newHydrogenCount, avbl) {
+  ooccg.setHydrogenLocations = function setHydrogenLocations(mol, atom, newHydrogenCount, bondLength) {
     var a1, a2, angle, angleIncrement, biggestAngleDif, bond, dif, firstNewHydrogenConnIndex, hydrogenAngle, i, i0, i1, newHydrogen, startAngle, stereoBondAngle, stereoBondCount, stereoBondIndex;
     firstNewHydrogenConnIndex = mol.getAllConnAtoms_0(atom) - newHydrogenCount;
     stereoBondIndex = -1;
@@ -64855,8 +64887,8 @@ function getExports($wnd) {
         }
       }
       newHydrogen = mol.getConnAtom_0(atom, firstNewHydrogenConnIndex + i);
-      mol.setAtomX_0(newHydrogen, mol.getAtomX_0(atom) + avbl * $wnd.Math.sin(hydrogenAngle));
-      mol.setAtomY_0(newHydrogen, mol.getAtomY_0(atom) + avbl * $wnd.Math.cos(hydrogenAngle));
+      mol.setAtomX_0(newHydrogen, mol.getAtomX_0(atom) + bondLength * $wnd.Math.sin(hydrogenAngle));
+      mol.setAtomY_0(newHydrogen, mol.getAtomY_0(atom) + bondLength * $wnd.Math.cos(hydrogenAngle));
     }
   };
   defineClass(230, 1, { 1: 1 }, ooccg.ConformerGenerator_0);
@@ -67287,7 +67319,7 @@ function getExports($wnd) {
     this.$init_419();
     this.mMol = mol;
     if (!keepHydrogen)
-      this.mMol.removeExplicitHydrogens_0();
+      this.mMol.removeExplicitHydrogens_0(true);
     this.mMol.ensureHelperArrays_0(15);
     this.mRuleList = new ju.ArrayList();
     this.mSkipRule = initUnidimensionalArray(cggl.Z_classLit, { 9: 1, 4: 1, 1: 1 }, 5, (ooccs.$clinit_ConformationRule(), ooccs.RULE_NAME).length, 16, 1);
@@ -69752,7 +69784,7 @@ function getExports($wnd) {
   $sendStats("moduleStartup", "end");
   $gwt && $gwt.permProps && __gwtModuleFunction.__moduleStartupDone($gwt.permProps);
   const toReturn = $wnd["OCL"];
-  toReturn.version = "9.0.1";
+  toReturn.version = "9.1.0";
   return toReturn;
 }
 var isBrowserWindow = typeof window !== "undefined" && typeof window.document !== "undefined";
@@ -69894,8 +69926,8 @@ export {
 };
 /**
  * openchemlib - Manipulate molecules
- * @version v9.0.1
- * @date 2025-04-28T14:22:13.313Z
+ * @version v9.1.0
+ * @date 2025-04-30T14:40:58.380Z
  * @link https://github.com/cheminfo/openchemlib-js
  * @license BSD-3-Clause
 */