icn3d 3.54.0 → 3.54.1

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Files changed (4) hide show
  1. package/icn3d.js +132 -11
  2. package/icn3d.min.js +1 -1
  3. package/icn3d.module.js +132 -11
  4. package/package.json +1 -1
package/icn3d.js CHANGED
@@ -78278,6 +78278,8 @@ class CurveStripArrow {
78278
78278
  let scale = 1.8; // scale of the arrow width
78279
78279
  delta = delta * scale * (ic.axisDIV - cnt) / ic.axisDIV;
78280
78280
 
78281
+ if(!pntsCA[i] || !prevCOArray[i]) continue;
78282
+
78281
78283
  let v = new Vector3$1(pntsCA[i].x + prevCOArray[i].x * delta,
78282
78284
  pntsCA[i].y + prevCOArray[i].y * delta,
78283
78285
  pntsCA[i].z + prevCOArray[i].z * delta);
@@ -78299,7 +78301,7 @@ class CurveStripArrow {
78299
78301
  pntsCA[lastCAIndex].z + prevCOArray[lastCAIndex].z * delta);
78300
78302
 
78301
78303
  pnts[index].push(v);
78302
- colorsTmp.push(colors[i]);
78304
+ colorsTmp.push(colors[lastCAIndex]);
78303
78305
  if(index === 0) posIndex.push(positions[lastCAIndex]);
78304
78306
  }
78305
78307
 
@@ -79932,13 +79934,13 @@ class Tube {
79932
79934
  let maxDist2 = 3.0; // avoid tube between the residues in 3 residue helix
79933
79935
 
79934
79936
  let pnts_colors_radii = [];
79935
- let firstAtom, firstPos, prevAtom, prevPos;
79937
+ let firstAtom, firstPos, atom, prevAtom, prevPos;
79936
79938
  let half = Math.floor(ic.axisDIV / 2) - 1;
79937
79939
 
79938
79940
  for (let i = 0, il = atoms.length; i < il; ++i) {
79939
79941
  let pos = (tubePosArray) ? tubePosArray[i] : undefined;
79940
79942
 
79941
- let atom = atoms[i];
79943
+ atom = atoms[i];
79942
79944
  if ((atom.name === atomName) && !atom.het) {
79943
79945
  if(index == 0) {
79944
79946
  firstAtom = atom;
@@ -79965,7 +79967,61 @@ class Tube {
79965
79967
 
79966
79968
  pnts_colors_radii.push(result);
79967
79969
  }
79968
- else {
79970
+ else {
79971
+ /*
79972
+ if(!isNaN(firstAtom.resi) && !isNaN(prevAtom.resi)) {
79973
+ let prevoneResid = firstAtom.structure + '_' + firstAtom.chain + '_' + (parseInt(firstAtom.resi) - 1).toString();
79974
+ let prevoneCoord = ic.firstAtomObjCls.getAtomCoordFromResi(prevoneResid, atomName);
79975
+ prevone = (prevoneCoord !== undefined) ? [prevoneCoord] : [];
79976
+
79977
+ let nextoneResid = prevAtom.structure + '_' + prevAtom.chain + '_' + (parseInt(prevAtom.resi) + 1).toString();
79978
+ let nexttwoResid = prevAtom.structure + '_' + prevAtom.chain + '_' + (parseInt(prevAtom.resi) + 2).toString();
79979
+ let nextthreeResid = prevAtom.structure + '_' + prevAtom.chain + '_' + (parseInt(prevAtom.resi) + 3).toString();
79980
+
79981
+ if(ic.residues.hasOwnProperty(nextoneResid)) {
79982
+ let nextAtom = ic.firstAtomObjCls.getAtomFromResi(nextoneResid, atomName);
79983
+ if(nextAtom !== undefined && nextAtom.ssbegin) { // include the residue
79984
+ nextoneResid = prevAtom.structure + '_' + prevAtom.chain + '_' + (parseInt(prevAtom.resi) + 2).toString();
79985
+ nexttwoResid = prevAtom.structure + '_' + prevAtom.chain + '_' + (parseInt(prevAtom.resi) + 3).toString();
79986
+
79987
+ pnts.push(nextAtom.coord);
79988
+ if(bCustom) {
79989
+ radii.push(this.getCustomtubesize(nextoneResid));
79990
+ }
79991
+ else {
79992
+ radii.push(this.getRadius(radius, nextAtom));
79993
+ }
79994
+ colors.push(nextAtom.color);
79995
+ }
79996
+ }
79997
+
79998
+ // add one more residue if only one residue is available and it's not part of helix/sheet
79999
+ if(pnts.length == 1 && ic.residues.hasOwnProperty(nextoneResid) && atom.ss == 'coil') {
80000
+ let nextAtom = ic.firstAtomObjCls.getAtomFromResi(nextoneResid, atomName);
80001
+
80002
+ if(nextAtom) {
80003
+ pnts.push(nextAtom.coord);
80004
+ colors.push(nextAtom.color);
80005
+
80006
+ let radiusFinal = this.getRadius(radius, atom);
80007
+ radii.push(radiusFinal);
80008
+
80009
+ nextoneResid = nexttwoResid;
80010
+ nexttwoResid = nextthreeResid;
80011
+ }
80012
+ }
80013
+
80014
+ let nextoneCoord = ic.firstAtomObjCls.getAtomCoordFromResi(nextoneResid, atomName);
80015
+ if(nextoneCoord !== undefined) {
80016
+ nexttwo.push(nextoneCoord);
80017
+ }
80018
+
80019
+ let nexttwoCoord = ic.firstAtomObjCls.getAtomCoordFromResi(nexttwoResid, atomName);
80020
+ if(nexttwoCoord !== undefined) {
80021
+ nexttwo.push(nexttwoCoord);
80022
+ }
80023
+ }
80024
+ */
79969
80025
  pnts_colors_radii.push({'pnts':pnts, 'colors':colors, 'radii':radii});
79970
80026
  }
79971
80027
  }
@@ -79989,6 +80045,24 @@ class Tube {
79989
80045
  }
79990
80046
  }
79991
80047
  else { // b factor, etc
80048
+ /*
80049
+ if(pnts.length == 0 && !isNaN(atom.resi)) {
80050
+ let prevoneResid = atom.structure + '_' + atom.chain + '_' + (parseInt(atom.resi) - 1).toString();
80051
+ if(ic.residues.hasOwnProperty(prevoneResid)) {
80052
+ prevAtom = ic.firstAtomObjCls.getAtomFromResi(prevoneResid, atomName);
80053
+ if(prevAtom !== undefined && prevAtom.ssend) { // include the residue
80054
+ pnts.push(prevAtom.coord);
80055
+ if(bCustom) {
80056
+ radii.push(this.getCustomtubesize(prevoneResid));
80057
+ }
80058
+ else {
80059
+ radii.push(this.getRadius(radius, prevAtom));
80060
+ }
80061
+ colors.push(prevAtom.color);
80062
+ }
80063
+ }
80064
+ }
80065
+ */
79992
80066
  pnts.push(atom.coord);
79993
80067
 
79994
80068
  let radiusFinal;
@@ -80037,6 +80111,47 @@ class Tube {
80037
80111
  }
80038
80112
  }
80039
80113
  else {
80114
+ /*
80115
+ prevone = [];
80116
+ if(firstAtom !== undefined && !isNaN(firstAtom.resi)) {
80117
+ let prevoneResid = firstAtom.structure + '_' + firstAtom.chain + '_' + (parseInt(firstAtom.resi) - 1).toString();
80118
+ let prevoneCoord = ic.firstAtomObjCls.getAtomCoordFromResi(prevoneResid, atomName);
80119
+ prevone = (prevoneCoord !== undefined) ? [prevoneCoord] : [];
80120
+ }
80121
+
80122
+ nexttwo = [];
80123
+ if(atom !== undefined && !isNaN(atom.resi)) {
80124
+ let nextoneResid = atom.structure + '_' + atom.chain + '_' + (parseInt(atom.resi) + 1).toString();
80125
+ let nexttwoResid = atom.structure + '_' + atom.chain + '_' + (parseInt(atom.resi) + 2).toString();
80126
+ let nextthreeResid = atom.structure + '_' + atom.chain + '_' + (parseInt(atom.resi) + 3).toString();
80127
+
80128
+ // add one more residue if only one residue is available
80129
+ if(pnts.length == 1 && ic.residues.hasOwnProperty(nextoneResid)) {
80130
+ let nextAtom = ic.firstAtomObjCls.getAtomFromResi(nextoneResid, atomName);
80131
+
80132
+ if(nextAtom) {
80133
+ pnts.push(nextAtom.coord);
80134
+ colors.push(nextAtom.color);
80135
+
80136
+ let radiusFinal = this.getRadius(radius, atom);
80137
+ radii.push(radiusFinal);
80138
+
80139
+ nextoneResid = nexttwoResid;
80140
+ nexttwoResid = nextthreeResid;
80141
+ }
80142
+ }
80143
+
80144
+ let nextoneCoord = ic.firstAtomObjCls.getAtomCoordFromResi(nextoneResid, atomName);
80145
+ if(nextoneCoord !== undefined) {
80146
+ nexttwo.push(nextoneCoord);
80147
+ }
80148
+
80149
+ let nexttwoCoord = ic.firstAtomObjCls.getAtomCoordFromResi(nexttwoResid, atomName);
80150
+ if(nexttwoCoord !== undefined) {
80151
+ nexttwo.push(nexttwoCoord);
80152
+ }
80153
+ }
80154
+ */
80040
80155
  pnts_colors_radii.push({'pnts':pnts, 'colors':colors, 'radii':radii});
80041
80156
  }
80042
80157
  }
@@ -80046,7 +80161,12 @@ class Tube {
80046
80161
  let colors = pnts_colors_radii[i].colors;
80047
80162
  let radii = pnts_colors_radii[i].radii;
80048
80163
 
80049
- this.createTubeSub(pnts, colors, radii, bHighlight, bNonCoil);
80164
+ if(tubePosArray) {
80165
+ this.createTubeSub(pnts, colors, radii, bHighlight, bNonCoil);
80166
+ }
80167
+ else {
80168
+ this.createTubeSub(pnts, colors, radii, bHighlight, bNonCoil, true);
80169
+ }
80050
80170
  }
80051
80171
 
80052
80172
  pnts_colors_radii = [];
@@ -80105,7 +80225,7 @@ class Tube {
80105
80225
  };
80106
80226
 
80107
80227
  // modified from iview (http://istar.cse.cuhk.edu.hk/iview/)
80108
- createTubeSub(_pnts, colors, radii, bHighlight, bNonCoil) { let ic = this.icn3d, me = ic.icn3dui;
80228
+ createTubeSub(_pnts, colors, radii, bHighlight, bNonCoil, bSubdivide) { let ic = this.icn3d, me = ic.icn3dui;
80109
80229
  if(me.bNode) return;
80110
80230
 
80111
80231
  if (_pnts.length < 2) return;
@@ -80118,8 +80238,8 @@ class Tube {
80118
80238
  let offset = 0, offset2 = 0, offset3 = 0;
80119
80239
 
80120
80240
  let pnts;
80121
- /*
80122
- if(!bSubdivided) {
80241
+
80242
+ if(bSubdivide) {
80123
80243
  let pnts_clrs = me.subdivideCls.subdivide(_pnts, colors, axisDiv);
80124
80244
 
80125
80245
  pnts = pnts_clrs[0];
@@ -80128,8 +80248,6 @@ class Tube {
80128
80248
  else {
80129
80249
  pnts = _pnts;
80130
80250
  }
80131
- */
80132
- pnts = _pnts;
80133
80251
 
80134
80252
  let constRadiius;
80135
80253
  // a threshold to stop drawing the tube if it's less than this ratio of radius
@@ -80612,7 +80730,10 @@ class Strand {
80612
80730
 
80613
80731
  bSheetSegment = prevCoorO ? (ss === 'sheet') : (atom.ss === 'sheet');
80614
80732
  bHelixSegment = prevCoorO ? (ss === 'helix') : (atom.ss === 'helix');
80615
- this.createStrand_base(posArray, pntsAllSub, pntsCAAllSub, prevCOArrayAllSub, colorsAllSub, positionsSub, missingResArray, fill, bHighlight, bRibbon, num, bSheetSegment, bHelixSegment, bFullAtom, thickness);
80733
+ // skip the 2-residue joint between two adjacent SS (sheet end -> helix begin)
80734
+ if(!(ssend && atom.ssbegin)) {
80735
+ this.createStrand_base(posArray, pntsAllSub, pntsCAAllSub, prevCOArrayAllSub, colorsAllSub, positionsSub, missingResArray, fill, bHighlight, bRibbon, num, bSheetSegment, bHelixSegment, bFullAtom, thickness);
80736
+ }
80616
80737
  posArray = [];
80617
80738
  missingResArray = [];
80618
80739
  } // end if (atom.ssbegin || atom.ssend)