biojs-vis-pdbviewer/external/jmol-14.2.4/jsmol/j2s/JS/PointGroup.js

A BioJS 2.0 component to view protein structures

Clazz.declarePackage ("JS");
Clazz.load (["JU.P3", "$.V3"], "JS.PointGroup", ["java.lang.Float", "java.util.Hashtable", "JU.Lst", "$.Quat", "$.SB", "JU.BSUtil", "$.Escape", "$.Logger", "$.Txt"], function () {
c$ = Clazz.decorateAsClass (function () {
this.drawInfo = null;
this.info = null;
this.textInfo = null;
this.drawType = "";
this.drawIndex = 0;
this.scale = NaN;
this.nAxes = null;
this.axes = null;
this.nAtoms = 0;
this.radius = 0;
this.distanceTolerance = 0.2;
this.linearTolerance = 8;
this.cosTolerance = 0.99;
this.name = "C_1?";
this.principalAxis = null;
this.principalPlane = null;
this.vTemp = null;
this.centerAtomIndex = -1;
this.haveInversionCenter = false;
this.center = null;
this.points = null;
this.atoms = null;
this.elements = null;
this.bsAtoms = null;
this.maxElement = 0;
this.eCounts = null;
this.nOps = 0;
if (!Clazz.isClassDefined ("JS.PointGroup.Operation")) {
JS.PointGroup.$PointGroup$Operation$ ();
}
Clazz.instantialize (this, arguments);
}, JS, "PointGroup");
Clazz.prepareFields (c$, function () {
this.nAxes =  Clazz.newIntArray (JS.PointGroup.maxAxis, 0);
this.axes =  new Array (JS.PointGroup.maxAxis);
this.vTemp =  new JU.V3 ();
this.center =  new JU.P3 ();
});
Clazz.defineMethod (c$, "getName", 
function () {
return this.name;
});
c$.getPointGroup = Clazz.defineMethod (c$, "getPointGroup", 
function (pgLast, atomset, bsAtoms, haveVibration, distanceTolerance, linearTolerance) {
var pg =  new JS.PointGroup ();
return (pg.set (pgLast, atomset, bsAtoms, haveVibration, distanceTolerance, linearTolerance) ? pg : pgLast);
}, "JS.PointGroup,~A,JU.BS,~B,~N,~N");
Clazz.makeConstructor (c$, 
 function () {
});
Clazz.defineMethod (c$, "isEqual", 
 function (pg) {
if (pg == null) return false;
if (this.linearTolerance != pg.linearTolerance || this.distanceTolerance != pg.distanceTolerance || this.nAtoms != pg.nAtoms || !this.bsAtoms.equals (pg.bsAtoms)) return false;
for (var i = 0; i < this.nAtoms; i++) {
if (this.elements[i] != pg.elements[i] || this.points[i].distance (pg.points[i]) != 0) return false;
}
return true;
}, "JS.PointGroup");
Clazz.defineMethod (c$, "set", 
 function (pgLast, atomset, bsAtoms, haveVibration, distanceTolerance, linearTolerance) {
this.distanceTolerance = distanceTolerance;
this.linearTolerance = linearTolerance;
this.bsAtoms = bsAtoms;
this.cosTolerance = (Math.cos (linearTolerance / 180 * 3.141592653589793));
if (!this.getAtomsAndElements (atomset, bsAtoms)) {
JU.Logger.error ("Too many atoms for point group calculation");
this.name = "point group not determined -- ac > 100 -- select fewer atoms and try again.";
return true;
}this.getElementCounts ();
if (haveVibration) {
var atomVibs =  new Array (this.points.length);
for (var i = this.points.length; --i >= 0; ) {
atomVibs[i] = JU.P3.newP (this.points[i]);
var v = this.atoms[i].getVibrationVector ();
if (v != null) atomVibs[i].add (v);
}
this.points = atomVibs;
}if (this.isEqual (pgLast)) return false;
this.findInversionCenter ();
if (this.isLinear (this.points)) {
if (this.haveInversionCenter) {
this.name = "D(infinity)h";
} else {
this.name = "C(infinity)v";
}this.vTemp.sub2 (this.points[1], this.points[0]);
this.addAxis (16, this.vTemp);
this.principalAxis = this.axes[16][0];
if (this.haveInversionCenter) {
this.axes[0] =  new Array (1);
this.principalPlane = this.axes[0][this.nAxes[0]++] = Clazz.innerTypeInstance (JS.PointGroup.Operation, this, null, this.vTemp);
}return true;
}this.axes[0] =  new Array (15);
var nPlanes = 0;
this.findCAxes ();
nPlanes = this.findPlanes ();
this.findAdditionalAxes (nPlanes);
var n = this.getHighestOrder ();
if (this.nAxes[17] > 1) {
if (this.nAxes[19] > 1) {
if (this.haveInversionCenter) {
this.name = "Ih";
} else {
this.name = "I";
}} else if (this.nAxes[18] > 1) {
if (this.haveInversionCenter) {
this.name = "Oh";
} else {
this.name = "O";
}} else {
if (nPlanes > 0) {
if (this.haveInversionCenter) {
this.name = "Th";
} else {
this.name = "Td";
}} else {
this.name = "T";
}}} else {
if (n < 2) {
if (nPlanes == 1) {
this.name = "Cs";
return true;
}if (this.haveInversionCenter) {
this.name = "Ci";
return true;
}this.name = "C1";
} else if ((n % 2) == 1 && this.nAxes[16] > 0 || (n % 2) == 0 && this.nAxes[16] > 1) {
this.principalAxis = this.setPrincipalAxis (n, nPlanes);
if (nPlanes == 0) {
if (n < 14) {
this.name = "S" + n;
} else {
this.name = "D" + (n - 14);
}} else {
if (n < 14) n = Clazz.doubleToInt (n / 2);
 else n -= 14;
if (nPlanes == n) {
this.name = "D" + n + "d";
} else {
this.name = "D" + n + "h";
}}} else if (nPlanes == 0) {
this.principalAxis = this.axes[n][0];
if (n < 14) {
this.name = "S" + n;
} else {
this.name = "C" + (n - 14);
}} else if (nPlanes == n - 14) {
this.principalAxis = this.axes[n][0];
this.name = "C" + nPlanes + "v";
} else {
this.principalAxis = this.axes[n < 14 ? n + 14 : n][0];
this.principalPlane = this.axes[0][0];
if (n < 14) n /= 2;
 else n -= 14;
this.name = "C" + n + "h";
}}return true;
}, "JS.PointGroup,~A,JU.BS,~B,~N,~N");
Clazz.defineMethod (c$, "setPrincipalAxis", 
 function (n, nPlanes) {
var principalPlane = this.setPrincipalPlane (n, nPlanes);
if (nPlanes == 0 && n < 14 || this.nAxes[n] == 1) {
if (nPlanes > 0 && n < 14) n = 14 + Clazz.doubleToInt (n / 2);
return this.axes[n][0];
}if (principalPlane == null) return null;
for (var i = 0; i < this.nAxes[16]; i++) if (this.isParallel (principalPlane.normalOrAxis, this.axes[16][i].normalOrAxis)) {
if (i != 0) {
var o = this.axes[16][0];
this.axes[16][0] = this.axes[16][i];
this.axes[16][i] = o;
}return this.axes[16][0];
}
return null;
}, "~N,~N");
Clazz.defineMethod (c$, "setPrincipalPlane", 
 function (n, nPlanes) {
if (nPlanes == 1) return this.principalPlane = this.axes[0][0];
if (nPlanes == 0 || nPlanes == n - 14) return null;
for (var i = 0; i < nPlanes; i++) for (var j = 0, nPerp = 0; j < nPlanes; j++) if (this.isPerpendicular (this.axes[0][i].normalOrAxis, this.axes[0][j].normalOrAxis) && ++nPerp > 2) {
if (i != 0) {
var o = this.axes[0][0];
this.axes[0][0] = this.axes[0][i];
this.axes[0][i] = o;
}return this.principalPlane = this.axes[0][0];
}

return null;
}, "~N,~N");
Clazz.defineMethod (c$, "getAtomsAndElements", 
 function (atomset, bsAtoms) {
var ac = JU.BSUtil.cardinalityOf (bsAtoms);
if (ac > 100) return false;
this.points =  new Array (ac);
this.atoms =  new Array (ac);
this.elements =  Clazz.newIntArray (ac, 0);
if (ac == 0) return true;
this.nAtoms = 0;
for (var i = bsAtoms.nextSetBit (0); i >= 0; i = bsAtoms.nextSetBit (i + 1)) {
this.points[this.nAtoms] = JU.P3.newP (atomset[i]);
this.atoms[this.nAtoms] = atomset[i];
var bondIndex = 1 + Math.max (3, atomset[i].getCovalentBondCount ());
this.elements[this.nAtoms] = atomset[i].getElementNumber () * bondIndex;
this.center.add (this.points[this.nAtoms++]);
}
this.center.scale (1 / this.nAtoms);
for (var i = this.nAtoms; --i >= 0; ) {
var r = this.center.distance (this.points[i]);
if (r < this.distanceTolerance) this.centerAtomIndex = i;
this.radius = Math.max (this.radius, r);
}
return true;
}, "~A,JU.BS");
Clazz.defineMethod (c$, "findInversionCenter", 
 function () {
this.haveInversionCenter = this.checkOperation (null, this.center, -1);
if (this.haveInversionCenter) {
this.axes[1] =  new Array (1);
this.axes[1][0] = Clazz.innerTypeInstance (JS.PointGroup.Operation, this, null);
}});
Clazz.defineMethod (c$, "checkOperation", 
 function (q, center, iOrder) {
var pt =  new JU.P3 ();
var nFound = 0;
var isInversion = (iOrder < 14);
out : for (var i = this.points.length; --i >= 0 && nFound < this.points.length; ) if (i == this.centerAtomIndex) {
nFound++;
} else {
var a1 = this.points[i];
var e1 = this.elements[i];
if (q != null) {
pt.sub2 (a1, center);
q.transformP2 (pt, pt).add (center);
} else {
pt.setT (a1);
}if (isInversion) {
this.vTemp.sub2 (center, pt);
pt.scaleAdd2 (2, this.vTemp, pt);
}if ((q != null || isInversion) && pt.distance (a1) < this.distanceTolerance) {
nFound++;
continue;
}for (var j = this.points.length; --j >= 0; ) {
if (j == i || this.elements[j] != e1) continue;
var a2 = this.points[j];
if (pt.distance (a2) < this.distanceTolerance) {
nFound++;
continue out;
}}
}
return nFound == this.points.length;
}, "JU.Quat,JU.P3,~N");
Clazz.defineMethod (c$, "isLinear", 
 function (atoms) {
var v1 = null;
if (atoms.length < 2) return false;
for (var i = atoms.length; --i >= 0; ) {
if (i == this.centerAtomIndex) continue;
if (v1 == null) {
v1 =  new JU.V3 ();
v1.sub2 (atoms[i], this.center);
v1.normalize ();
this.vTemp.setT (v1);
continue;
}this.vTemp.sub2 (atoms[i], this.center);
this.vTemp.normalize ();
if (!this.isParallel (v1, this.vTemp)) return false;
}
return true;
}, "~A");
Clazz.defineMethod (c$, "isParallel", 
 function (v1, v2) {
return (Math.abs (v1.dot (v2)) >= this.cosTolerance);
}, "JU.V3,JU.V3");
Clazz.defineMethod (c$, "isPerpendicular", 
 function (v1, v2) {
return (Math.abs (v1.dot (v2)) <= 1 - this.cosTolerance);
}, "JU.V3,JU.V3");
Clazz.defineMethod (c$, "getElementCounts", 
 function () {
for (var i = this.points.length; --i >= 0; ) {
var e1 = this.elements[i];
if (e1 > this.maxElement) this.maxElement = e1;
}
this.eCounts =  Clazz.newIntArray (++this.maxElement, 0);
for (var i = this.points.length; --i >= 0; ) this.eCounts[this.elements[i]]++;

});
Clazz.defineMethod (c$, "findCAxes", 
 function () {
var v1 =  new JU.V3 ();
var v2 =  new JU.V3 ();
var v3 =  new JU.V3 ();
for (var i = this.points.length; --i >= 0; ) {
if (i == this.centerAtomIndex) continue;
var a1 = this.points[i];
var e1 = this.elements[i];
for (var j = this.points.length; --j > i; ) {
var a2 = this.points[j];
if (this.elements[j] != e1) continue;
v1.sub2 (a1, this.center);
v2.sub2 (a2, this.center);
v1.normalize ();
v2.normalize ();
if (this.isParallel (v1, v2)) {
this.getAllAxes (v1);
continue;
}if (this.nAxes[16] < JS.PointGroup.axesMaxN[16]) {
v3.ave (a1, a2);
v3.sub (this.center);
this.getAllAxes (v3);
}var order = (6.283185307179586 / v1.angle (v2));
var iOrder = Clazz.doubleToInt (Math.floor (order + 0.01));
var isIntegerOrder = (order - iOrder <= 0.02);
if (!isIntegerOrder || (iOrder = iOrder + 14) >= JS.PointGroup.maxAxis) continue;
if (this.nAxes[iOrder] < JS.PointGroup.axesMaxN[iOrder]) {
v3.cross (v1, v2);
this.checkAxisOrder (iOrder, v3, this.center);
}}
}
var vs =  new Array (this.nAxes[16] * 2);
for (var i = 0; i < vs.length; i++) vs[i] =  new JU.V3 ();

var n = 0;
for (var i = 0; i < this.nAxes[16]; i++) {
vs[n++].setT (this.axes[16][i].normalOrAxis);
vs[n].setT (this.axes[16][i].normalOrAxis);
vs[n++].scale (-1);
}
for (var i = vs.length; --i >= 2; ) for (var j = i; --j >= 1; ) for (var k = j; --k >= 0; ) {
v3.add2 (vs[i], vs[j]);
v3.add (vs[k]);
if (v3.length () < 1.0) continue;
this.checkAxisOrder (17, v3, this.center);
}


var nMin = 2147483647;
var iMin = -1;
for (var i = 0; i < this.maxElement; i++) {
if (this.eCounts[i] < nMin && this.eCounts[i] > 2) {
nMin = this.eCounts[i];
iMin = i;
}}
out : for (var i = 0; i < this.points.length - 2; i++) if (this.elements[i] == iMin) for (var j = i + 1; j < this.points.length - 1; j++) if (this.elements[j] == iMin) for (var k = j + 1; k < this.points.length; k++) if (this.elements[k] == iMin) {
v1.sub2 (this.points[i], this.points[j]);
v2.sub2 (this.points[i], this.points[k]);
v1.normalize ();
v2.normalize ();
v3.cross (v1, v2);
this.getAllAxes (v3);
v1.add2 (this.points[i], this.points[j]);
v1.add (this.points[k]);
v1.normalize ();
if (!this.isParallel (v1, v3)) this.getAllAxes (v1);
if (this.nAxes[19] == JS.PointGroup.axesMaxN[19]) break out;
}


vs =  new Array (this.maxElement);
for (var i = this.points.length; --i >= 0; ) {
var e1 = this.elements[i];
if (vs[e1] == null) vs[e1] =  new JU.V3 ();
 else if (this.haveInversionCenter) continue;
vs[e1].add (this.points[i]);
}
if (!this.haveInversionCenter) for (var i = 0; i < this.maxElement; i++) if (vs[i] != null) vs[i].scale (1 / this.eCounts[i]);

for (var i = 0; i < this.maxElement; i++) if (vs[i] != null) for (var j = 0; j < this.maxElement; j++) {
if (i == j || vs[j] == null) continue;
if (this.haveInversionCenter) v1.cross (vs[i], vs[j]);
 else v1.sub2 (vs[i], vs[j]);
this.checkAxisOrder (16, v1, this.center);
}

return this.getHighestOrder ();
});
Clazz.defineMethod (c$, "getAllAxes", 
 function (v3) {
for (var o = 16; o < JS.PointGroup.maxAxis; o++) if (this.nAxes[o] < JS.PointGroup.axesMaxN[o]) this.checkAxisOrder (o, v3, this.center);

}, "JU.V3");
Clazz.defineMethod (c$, "getHighestOrder", 
 function () {
var n = 0;
for (n = 14; --n > 1 && this.nAxes[n] == 0; ) {
}
if (n > 1) return (n + 14 < JS.PointGroup.maxAxis && this.nAxes[n + 14] > 0 ? n + 14 : n);
for (n = JS.PointGroup.maxAxis; --n > 1 && this.nAxes[n] == 0; ) {
}
return n;
});
Clazz.defineMethod (c$, "checkAxisOrder", 
 function (iOrder, v, center) {
switch (iOrder) {
case 22:
if (this.nAxes[17] > 0) return false;
case 20:
case 18:
if (this.nAxes[19] > 0) return false;
break;
case 17:
if (this.nAxes[22] > 0) return false;
break;
case 19:
if (this.nAxes[18] > 0 || this.nAxes[20] > 0 || this.nAxes[22] > 0) return false;
break;
}
v.normalize ();
if (this.haveAxis (iOrder, v)) return false;
var q = JU.Quat.newVA (v, (iOrder < 14 ? 180 : 0) + Clazz.doubleToInt (360 / (iOrder % 14)));
if (!this.checkOperation (q, center, iOrder)) return false;
this.addAxis (iOrder, v);
switch (iOrder) {
case 16:
this.checkAxisOrder (4, v, center);
break;
case 17:
this.checkAxisOrder (3, v, center);
if (this.haveInversionCenter) this.addAxis (6, v);
break;
case 18:
this.addAxis (16, v);
this.checkAxisOrder (4, v, center);
this.checkAxisOrder (8, v, center);
break;
case 19:
this.checkAxisOrder (5, v, center);
if (this.haveInversionCenter) this.addAxis (10, v);
break;
case 20:
this.addAxis (16, v);
this.addAxis (17, v);
this.checkAxisOrder (3, v, center);
this.checkAxisOrder (6, v, center);
this.checkAxisOrder (12, v, center);
break;
case 22:
this.addAxis (16, v);
this.addAxis (18, v);
break;
}
return true;
}, "~N,JU.V3,JU.P3");
Clazz.defineMethod (c$, "addAxis", 
 function (iOrder, v) {
if (this.haveAxis (iOrder, v)) return;
if (this.axes[iOrder] == null) this.axes[iOrder] =  new Array (JS.PointGroup.axesMaxN[iOrder]);
this.axes[iOrder][this.nAxes[iOrder]++] = Clazz.innerTypeInstance (JS.PointGroup.Operation, this, null, v, iOrder);
}, "~N,JU.V3");
Clazz.defineMethod (c$, "haveAxis", 
 function (iOrder, v) {
if (this.nAxes[iOrder] == JS.PointGroup.axesMaxN[iOrder]) {
return true;
}if (this.nAxes[iOrder] > 0) for (var i = this.nAxes[iOrder]; --i >= 0; ) {
if (this.isParallel (v, this.axes[iOrder][i].normalOrAxis)) return true;
}
return false;
}, "~N,JU.V3");
Clazz.defineMethod (c$, "findPlanes", 
 function () {
var pt =  new JU.P3 ();
var v1 =  new JU.V3 ();
var v2 =  new JU.V3 ();
var v3 =  new JU.V3 ();
var nPlanes = 0;
var haveAxes = (this.getHighestOrder () > 1);
for (var i = this.points.length; --i >= 0; ) {
if (i == this.centerAtomIndex) continue;
var a1 = this.points[i];
var e1 = this.elements[i];
for (var j = this.points.length; --j > i; ) {
if (haveAxes && this.elements[j] != e1) continue;
var a2 = this.points[j];
pt.add2 (a1, a2);
pt.scale (0.5);
v1.sub2 (a1, this.center);
v2.sub2 (a2, this.center);
if (!this.isParallel (v1, v2)) {
v3.cross (v1, v2);
v3.normalize ();
nPlanes = this.getPlane (v3);
}v3.sub2 (a2, a1);
v3.normalize ();
nPlanes = this.getPlane (v3);
if (nPlanes == JS.PointGroup.axesMaxN[0]) return nPlanes;
}
}
if (haveAxes) for (var i = 16; i < JS.PointGroup.maxAxis; i++) for (var j = 0; j < this.nAxes[i]; j++) nPlanes = this.getPlane (this.axes[i][j].normalOrAxis);


return nPlanes;
});
Clazz.defineMethod (c$, "getPlane", 
 function (v3) {
if (!this.haveAxis (0, v3) && this.checkOperation (JU.Quat.newVA (v3, 180), this.center, -1)) this.axes[0][this.nAxes[0]++] = Clazz.innerTypeInstance (JS.PointGroup.Operation, this, null, v3);
return this.nAxes[0];
}, "JU.V3");
Clazz.defineMethod (c$, "findAdditionalAxes", 
 function (nPlanes) {
var planes = this.axes[0];
var Cn = 0;
if (nPlanes > 1 && ((Cn = nPlanes + 14) < JS.PointGroup.maxAxis) && this.nAxes[Cn] == 0) {
this.vTemp.cross (planes[0].normalOrAxis, planes[1].normalOrAxis);
if (!this.checkAxisOrder (Cn, this.vTemp, this.center) && nPlanes > 2) {
this.vTemp.cross (planes[1].normalOrAxis, planes[2].normalOrAxis);
this.checkAxisOrder (Cn - 1, this.vTemp, this.center);
}}if (this.nAxes[16] == 0 && nPlanes > 2) {
for (var i = 0; i < nPlanes - 1; i++) {
for (var j = i + 1; j < nPlanes; j++) {
this.vTemp.add2 (planes[1].normalOrAxis, planes[2].normalOrAxis);
this.checkAxisOrder (16, this.vTemp, this.center);
}
}
}}, "~N");
Clazz.defineMethod (c$, "getInfo", 
function (modelIndex, asDraw, asInfo, type, index, scaleFactor) {
this.info = (asInfo ?  new java.util.Hashtable () : null);
var v =  new JU.V3 ();
var op;
if (scaleFactor == 0) scaleFactor = 1;
this.scale = scaleFactor;
var nType =  Clazz.newIntArray (4, 2, 0);
for (var i = 1; i < JS.PointGroup.maxAxis; i++) for (var j = this.nAxes[i]; --j >= 0; ) nType[this.axes[i][j].type][0]++;


var sb =  new JU.SB ().append ("# ").appendI (this.nAtoms).append (" atoms\n");
if (asDraw) {
var haveType = (type != null && type.length > 0);
this.drawType = type = (haveType ? type : "");
this.drawIndex = index;
var anyProperAxis = (type.equalsIgnoreCase ("Cn"));
var anyImproperAxis = (type.equalsIgnoreCase ("Sn"));
sb.append ("set perspectivedepth off;\n");
var m = "_" + modelIndex + "_";
if (!haveType) sb.append ("draw pg0").append (m).append ("* delete;draw pgva").append (m).append ("* delete;draw pgvp").append (m).append ("* delete;");
if (!haveType || type.equalsIgnoreCase ("Ci")) sb.append ("draw pg0").append (m).append (this.haveInversionCenter ? "inv " : " ").append (JU.Escape.eP (this.center)).append (this.haveInversionCenter ? "\"i\";\n" : ";\n");
var offset = 0.1;
for (var i = 2; i < JS.PointGroup.maxAxis; i++) {
if (i == 14) offset = 0.1;
if (this.nAxes[i] == 0) continue;
var label = this.axes[i][0].getLabel ();
offset += 0.25;
var scale = scaleFactor * this.radius + offset;
if (!haveType || type.equalsIgnoreCase (label) || anyProperAxis && i >= 14 || anyImproperAxis && i < 14) for (var j = 0; j < this.nAxes[i]; j++) {
if (index > 0 && j + 1 != index) continue;
op = this.axes[i][j];
v.add2 (op.normalOrAxis, this.center);
if (op.type == 2) scale = -scale;
sb.append ("draw pgva").append (m).append (label).append ("_").appendI (j + 1).append (" width 0.05 scale ").appendF (scale).append (" ").append (JU.Escape.eP (v));
v.scaleAdd2 (-2, op.normalOrAxis, v);
var isPA = (this.principalAxis != null && op.index == this.principalAxis.index);
sb.append (JU.Escape.eP (v)).append ("\"").append (label).append (isPA ? "*" : "").append ("\" color ").append (isPA ? "red" : op.type == 2 ? "blue" : "yellow").append (";\n");
}
}
if (!haveType || type.equalsIgnoreCase ("Cs")) for (var j = 0; j < this.nAxes[0]; j++) {
if (index > 0 && j + 1 != index) continue;
op = this.axes[0][j];
sb.append ("draw pgvp").append (m).appendI (j + 1).append ("disk scale ").appendF (scaleFactor * this.radius * 2).append (" CIRCLE PLANE ").append (JU.Escape.eP (this.center));
v.add2 (op.normalOrAxis, this.center);
sb.append (JU.Escape.eP (v)).append (" color translucent yellow;\n");
v.add2 (op.normalOrAxis, this.center);
sb.append ("draw pgvp").append (m).appendI (j + 1).append ("ring width 0.05 scale ").appendF (scaleFactor * this.radius * 2).append (" arc ").append (JU.Escape.eP (v));
v.scaleAdd2 (-2, op.normalOrAxis, v);
sb.append (JU.Escape.eP (v));
v.add3 (0.011, 0.012, 0.013);
sb.append (JU.Escape.eP (v)).append ("{0 360 0.5} color ").append (this.principalPlane != null && op.index == this.principalPlane.index ? "red" : "blue").append (";\n");
}
sb.append ("# name=").append (this.name);
sb.append (", nCi=").appendI (this.haveInversionCenter ? 1 : 0);
sb.append (", nCs=").appendI (this.nAxes[0]);
sb.append (", nCn=").appendI (nType[1][0]);
sb.append (", nSn=").appendI (nType[2][0]);
sb.append (": ");
for (var i = JS.PointGroup.maxAxis; --i >= 2; ) if (this.nAxes[i] > 0) {
sb.append (" n").append (i < 14 ? "S" : "C").appendI (i % 14);
sb.append ("=").appendI (this.nAxes[i]);
}
sb.append (";\n");
this.drawInfo = sb.toString ();
return this.drawInfo;
}var n = 0;
var nTotal = 1;
var ctype = (this.haveInversionCenter ? "Ci" : "center");
if (this.haveInversionCenter) nTotal++;
if (this.info == null) sb.append ("\n\n").append (this.name).append ("\t").append (ctype).append ("\t").append (JU.Escape.eP (this.center));
 else this.info.put (ctype, this.center);
for (var i = JS.PointGroup.maxAxis; --i >= 0; ) {
if (this.nAxes[i] > 0) {
n = JS.PointGroup.nUnique[i];
var label = this.axes[i][0].getLabel ();
if (this.info == null) sb.append ("\n\n").append (this.name).append ("\tn").append (label).append ("\t").appendI (this.nAxes[i]).append ("\t").appendI (n);
 else this.info.put ("n" + label, Integer.$valueOf (this.nAxes[i]));
n *= this.nAxes[i];
nTotal += n;
nType[this.axes[i][0].type][1] += n;
var vinfo = (this.info == null ? null :  new JU.Lst ());
for (var j = 0; j < this.nAxes[i]; j++) {
if (vinfo == null) sb.append ("\n").append (this.name).append ("\t").append (label).append ("_").appendI (j + 1).append ("\t").appendO (this.axes[i][j].normalOrAxis);
 else vinfo.addLast (this.axes[i][j].normalOrAxis);
}
if (this.info != null) this.info.put (label, vinfo);
}}
if (this.info == null) {
sb.append ("\n");
sb.append ("\n").append (this.name).append ("\ttype\tnType\tnUnique");
sb.append ("\n").append (this.name).append ("\tE\t  1\t  1");
n = (this.haveInversionCenter ? 1 : 0);
sb.append ("\n").append (this.name).append ("\tCi\t  ").appendI (n).append ("\t  ").appendI (n);
sb.append ("\n").append (this.name).append ("\tCs\t");
JU.Txt.rightJustify (sb, "    ", this.nAxes[0] + "\t");
JU.Txt.rightJustify (sb, "    ", this.nAxes[0] + "\n");
sb.append (this.name).append ("\tCn\t");
JU.Txt.rightJustify (sb, "    ", nType[1][0] + "\t");
JU.Txt.rightJustify (sb, "    ", nType[1][1] + "\n");
sb.append (this.name).append ("\tSn\t");
JU.Txt.rightJustify (sb, "    ", nType[2][0] + "\t");
JU.Txt.rightJustify (sb, "    ", nType[2][1] + "\n");
sb.append (this.name).append ("\t\tTOTAL\t");
JU.Txt.rightJustify (sb, "    ", nTotal + "\n");
this.textInfo = sb.toString ();
return this.textInfo;
}this.info.put ("name", this.name);
this.info.put ("nAtoms", Integer.$valueOf (this.nAtoms));
this.info.put ("nTotal", Integer.$valueOf (nTotal));
this.info.put ("nCi", Integer.$valueOf (this.haveInversionCenter ? 1 : 0));
this.info.put ("nCs", Integer.$valueOf (this.nAxes[0]));
this.info.put ("nCn", Integer.$valueOf (nType[1][0]));
this.info.put ("nSn", Integer.$valueOf (nType[2][0]));
this.info.put ("distanceTolerance", Float.$valueOf (this.distanceTolerance));
this.info.put ("linearTolerance", Float.$valueOf (this.linearTolerance));
this.info.put ("detail", sb.toString ().$replace ('\n', ';'));
if (this.principalAxis != null && this.principalAxis.index > 0) this.info.put ("principalAxis", this.principalAxis.normalOrAxis);
if (this.principalPlane != null && this.principalPlane.index > 0) this.info.put ("principalPlane", this.principalPlane.normalOrAxis);
return this.info;
}, "~N,~B,~B,~S,~N,~N");
Clazz.defineMethod (c$, "isDrawType", 
function (type, index, scale) {
return (this.drawInfo != null && this.drawType.equals (type == null ? "" : type) && this.drawIndex == index && this.scale == scale);
}, "~S,~N,~N");
c$.$PointGroup$Operation$ = function () {
Clazz.pu$h(self.c$);
c$ = Clazz.decorateAsClass (function () {
Clazz.prepareCallback (this, arguments);
this.type = 0;
this.order = 0;
this.index = 0;
this.normalOrAxis = null;
Clazz.instantialize (this, arguments);
}, JS.PointGroup, "Operation");
Clazz.makeConstructor (c$, 
function () {
this.index = ++this.b$["JS.PointGroup"].nOps;
this.type = 3;
this.order = 1;
if (JU.Logger.debugging) JU.Logger.debug ("new operation -- " + JS.PointGroup.typeNames[this.type]);
});
Clazz.makeConstructor (c$, 
function (a, b) {
this.index = ++this.b$["JS.PointGroup"].nOps;
this.type = (b < 14 ? 2 : 1);
this.order = b % 14;
this.normalOrAxis = JU.Quat.newVA (a, 180).getNormal ();
if (JU.Logger.debugging) JU.Logger.debug ("new operation -- " + (this.order == b ? "S" : "C") + this.order + " " + this.normalOrAxis);
}, "JU.V3,~N");
Clazz.makeConstructor (c$, 
function (a) {
if (a == null) return;
this.index = ++this.b$["JS.PointGroup"].nOps;
this.type = 0;
this.normalOrAxis = JU.Quat.newVA (a, 180).getNormal ();
if (JU.Logger.debugging) JU.Logger.debug ("new operation -- plane " + this.normalOrAxis);
}, "JU.V3");
Clazz.defineMethod (c$, "getLabel", 
function () {
switch (this.type) {
case 0:
return "Cs";
case 2:
return "S" + this.order;
default:
return "C" + this.order;
}
});
c$ = Clazz.p0p ();
};
Clazz.defineStatics (c$,
"axesMaxN", [15, 0, 0, 1, 3, 1, 10, 0, 1, 0, 6, 0, 1, 0, 0, 0, 15, 10, 6, 6, 10, 0, 1],
"nUnique", [1, 0, 0, 2, 2, 4, 2, 0, 4, 0, 4, 0, 4, 0, 0, 0, 1, 2, 2, 4, 2, 0, 4],
"s3", 3,
"s4", 4,
"s5", 5,
"s6", 6,
"s8", 8,
"s10", 10,
"s12", 12,
"firstProper", 14,
"c2", 16,
"c3", 17,
"c4", 18,
"c5", 19,
"c6", 20,
"c8", 22);
c$.maxAxis = c$.prototype.maxAxis = JS.PointGroup.axesMaxN.length;
Clazz.defineStatics (c$,
"ATOM_COUNT_MAX", 100,
"OPERATION_PLANE", 0,
"OPERATION_PROPER_AXIS", 1,
"OPERATION_IMPROPER_AXIS", 2,
"OPERATION_INVERSION_CENTER", 3,
"typeNames", ["plane", "proper axis", "improper axis", "center of inversion"]);
});