npm - molstar - Versions diffs - 2.3.7 → 2.4.1 - Mend

molstar 2.3.7 → 2.4.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (1699) hide show

package/lib/mol-model-formats/structure/pdb/assembly.js CHANGED Viewed

@@ -50,7 +50,7 @@ export function parseRemark350(lines, lineStart, lineEnd) {
         var line = getLine(i);
         if (line.substr(11, 12) === 'BIOMOLECULE:') {
             var id = line.substr(23).trim();
-            var details = "Biomolecule " + id;
+            var details = "Biomolecule ".concat(id);
             line = getLine(i + 1);
             if (line.substr(11, 30) !== 'APPLY THE FOLLOWING TO CHAINS:') {
                 i++;
@@ -86,7 +86,7 @@ export function parseRemark350(lines, lineStart, lineEnd) {
         }
         else if (line.substr(11, 33) === 'APPLYING THE FOLLOWING TO CHAINS:') {
             // variant in older PDB format version
-            current = PdbAssembly("" + asmId, "Biomolecule " + asmId);
+            current = PdbAssembly("".concat(asmId), "Biomolecule ".concat(asmId));
             assemblies.push(current);
             asmId += 1;
             group = { chains: [], operators: [] };
@@ -143,9 +143,9 @@ export function parseRemark350(lines, lineStart, lineEnd) {
                 };
                 for (var i = 0; i < 3; i++) {
                     for (var j = 0; j < 3; j++) {
-                        row["matrix[" + (i + 1) + "][" + (j + 1) + "]"] = '' + Mat4.getValue(oper.matrix, i, j);
+                        row["matrix[".concat(i + 1, "][").concat(j + 1, "]")] = '' + Mat4.getValue(oper.matrix, i, j);
                     }
-                    row["vector[" + (i + 1) + "]"] = '' + Mat4.getValue(oper.matrix, i, 3);
+                    row["vector[".concat(i + 1, "]")] = '' + Mat4.getValue(oper.matrix, i, 3);
                 }
                 pdbx_struct_oper_list_rows.push(row);
             }
@@ -159,13 +159,13 @@ export function parseRemark350(lines, lineStart, lineEnd) {
     };
     var _loop_1 = function (i) {
         var _loop_2 = function (j) {
-            var k_1 = "matrix[" + (i + 1) + "][" + (j + 1) + "]";
+            var k_1 = "matrix[".concat(i + 1, "][").concat(j + 1, "]");
             pdbx_struct_oper_list[k_1] = CifField.ofStrings(pdbx_struct_oper_list_rows.map(function (r) { return r[k_1]; }));
         };
         for (var j = 0; j < 3; j++) {
             _loop_2(j);
         }
-        var k = "vector[" + (i + 1) + "]";
+        var k = "vector[".concat(i + 1, "]");
         pdbx_struct_oper_list[k] = CifField.ofStrings(pdbx_struct_oper_list_rows.map(function (r) { return r[k]; }));
     };
     for (var i = 0; i < 3; i++) {
@@ -207,9 +207,9 @@ export function parseMtrix(lines, lineStart, lineEnd) {
         };
         for (var i = 0; i < 3; i++) {
             for (var j = 0; j < 3; j++) {
-                row["matrix[" + (i + 1) + "][" + (j + 1) + "]"] = '' + Mat4.getValue(oper, i, j);
+                row["matrix[".concat(i + 1, "][").concat(j + 1, "]")] = '' + Mat4.getValue(oper, i, j);
             }
-            row["vector[" + (i + 1) + "]"] = '' + Mat4.getValue(oper, i, 3);
+            row["vector[".concat(i + 1, "]")] = '' + Mat4.getValue(oper, i, 3);
         }
         struct_ncs_oper_rows.push(row);
     }
@@ -220,13 +220,13 @@ export function parseMtrix(lines, lineStart, lineEnd) {
     };
     var _loop_3 = function (i) {
         var _loop_4 = function (j) {
-            var k_2 = "matrix[" + (i + 1) + "][" + (j + 1) + "]";
+            var k_2 = "matrix[".concat(i + 1, "][").concat(j + 1, "]");
             struct_ncs_oper[k_2] = CifField.ofStrings(struct_ncs_oper_rows.map(function (r) { return r[k_2]; }));
         };
         for (var j = 0; j < 3; j++) {
             _loop_4(j);
         }
-        var k = "vector[" + (i + 1) + "]";
+        var k = "vector[".concat(i + 1, "]");
         struct_ncs_oper[k] = CifField.ofStrings(struct_ncs_oper_rows.map(function (r) { return r[k]; }));
     };
     for (var i = 0; i < 3; i++) {

package/lib/mol-model-formats/structure/pdb/assembly.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/lib/mol-model-formats/structure/pdb/conect.js CHANGED Viewed

@@ -41,7 +41,7 @@ export function parseConect(lines, lineStart, lineEnd, sites) {
             // as double/triple bonds, e.g. CONECT 1529 1528 1528 is a double bond
             if (bondIndex[idxB] !== undefined)
                 continue;
-            id.push("covale" + k);
+            id.push("covale".concat(k));
             conn_type_id.push('covale');
             ptnr1_label_asym_id.push(sites.label_asym_id.str(idxA));
             ptnr1_auth_seq_id.push(sites.auth_seq_id.int(idxA));

package/lib/mol-model-formats/structure/pdb/conect.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"conect.js","sourceRoot":"","sources":["../../../../src/mol-model-formats/structure/pdb/conect.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,WAAW,EAAE,QAAQ,EAAE,MAAM,4BAA4B,CAAC;AAInE,MAAM,UAAU,WAAW,CAAC,KAAa,EAAE,SAAiB,EAAE,OAAe,EAAE,KAA4D;IACvI,IAAM,KAAK,GAA4B,EAAE,CAAC;IAC1C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,GAAG,KAAK,CAAC,EAAG,CAAC,QAAQ,EAAE,CAAC,GAAG,EAAE,EAAE,EAAE,CAAC,EAAE;QAClD,KAAK,CAAC,KAAK,CAAC,EAAG,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC;KAC/B;IAED,IAAM,OAAO,GAAG,UAAC,CAAS,IAAK,OAAA,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,GAAG,CAAC,CAAC,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,EAApE,CAAoE,CAAC;IAEpG,IAAM,EAAE,GAAa,EAAE,CAAC;IACxB,IAAM,YAAY,GAAa,EAAE,CAAC;IAElC,IAAM,mBAAmB,GAAa,EAAE,CAAC;IACzC,IAAM,kBAAkB,GAAa,EAAE,CAAC;IACxC,IAAM,iBAAiB,GAAa,EAAE,CAAC;IACvC,IAAM,mBAAmB,GAAa,EAAE,CAAC;IAEzC,IAAM,mBAAmB,GAAa,EAAE,CAAC;IACzC,IAAM,kBAAkB,GAAa,EAAE,CAAC;IACxC,IAAM,iBAAiB,GAAa,EAAE,CAAC;IACvC,IAAM,mBAAmB,GAAa,EAAE,CAAC;IAEzC,IAAM,GAAG,GAAG,CAAC,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,EAAE,CAAC,CAAC;IAE7B,IAAI,CAAC,GAAG,CAAC,CAAC;IAEV,KAAK,IAAI,CAAC,GAAG,SAAS,EAAE,CAAC,GAAG,OAAO,EAAE,CAAC,EAAE,EAAE;QACtC,IAAM,IAAI,GAAG,OAAO,CAAC,CAAC,CAAC,CAAC;QACxB,IAAM,IAAI,GAAG,KAAK,CAAC,QAAQ,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;QAEhD,IAAM,SAAS,GAA0B,EAAE,CAAC;QAE5C,IAAI,IAAI,KAAK,SAAS;YAAE,SAAS;QAEjC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,EAAE;YACxB,IAAM,GAAG,GAAG,QAAQ,CAAC,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC;YAC7C,IAAI,MAAM,CAAC,KAAK,CAAC,GAAG,CAAC;gBAAE,SAAS;YAEhC,IAAM,IAAI,GAAG,KAAK,CAAC,GAAG,CAAC,CAAC;YACxB,IAAI,IAAI,KAAK,SAAS;gBAAE,SAAS;YACjC,IAAI,IAAI,GAAG,IAAI;gBAAE,SAAS;YAE1B,sEAAsE;YACtE,sEAAsE;YACtE,IAAI,SAAS,CAAC,IAAI,CAAC,KAAK,SAAS;gBAAE,SAAS;YAE5C,EAAE,CAAC,IAAI,CAAC,~~WAAS~~,~~CAAG~~,CAAC,CAAC;YACtB,YAAY,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC;YAE5B,mBAAmB,CAAC,IAAI,CAAC,KAAK,CAAC,aAAc,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC;YACzD,iBAAiB,CAAC,IAAI,CAAC,KAAK,CAAC,WAAY,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC;YACrD,kBAAkB,CAAC,IAAI,CAAC,KAAK,CAAC,YAAa,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC;YACvD,mBAAmB,CAAC,IAAI,CAAC,KAAK,CAAC,aAAc,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC;YAEzD,mBAAmB,CAAC,IAAI,CAAC,KAAK,CAAC,aAAc,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC;YACzD,iBAAiB,CAAC,IAAI,CAAC,KAAK,CAAC,WAAY,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC;YACrD,kBAAkB,CAAC,IAAI,CAAC,KAAK,CAAC,YAAa,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC;YACvD,mBAAmB,CAAC,IAAI,CAAC,KAAK,CAAC,aAAc,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC;YAEzD,CAAC,IAAI,CAAC,CAAC;SACV;KACJ;IAED,IAAM,WAAW,GAA6D;QAC1E,EAAE,EAAE,QAAQ,CAAC,SAAS,CAAC,EAAE,CAAC;QAC1B,YAAY,EAAE,QAAQ,CAAC,SAAS,CAAC,YAAY,CAAC;QAE9C,mBAAmB,EAAE,QAAQ,CAAC,SAAS,CAAC,mBAAmB,CAAC;QAC5D,iBAAiB,EAAE,QAAQ,CAAC,SAAS,CAAC,iBAAiB,CAAC;QACxD,kBAAkB,EAAE,QAAQ,CAAC,SAAS,CAAC,kBAAkB,CAAC;QAC1D,mBAAmB,EAAE,QAAQ,CAAC,SAAS,CAAC,mBAAmB,CAAC;QAE5D,mBAAmB,EAAE,QAAQ,CAAC,SAAS,CAAC,mBAAmB,CAAC;QAC5D,kBAAkB,EAAE,QAAQ,CAAC,SAAS,CAAC,kBAAkB,CAAC;QAC1D,iBAAiB,EAAE,QAAQ,CAAC,SAAS,CAAC,iBAAiB,CAAC;QACxD,mBAAmB,EAAE,QAAQ,CAAC,SAAS,CAAC,mBAAmB,CAAC;KAC/D,CAAC;IAEF,OAAO,WAAW,CAAC,QAAQ,CAAC,aAAa,EAAE,WAAW,CAAC,CAAC;AAC5D,CAAC"}
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package/lib/mol-model-formats/structure/pdb/entity.js CHANGED Viewed

@@ -97,7 +97,7 @@ export function parseHetnam(lines, lineStart, lineEnd) {
         var het = line.substr(11, 3).trim();
         var name_1 = line.substr(15).trim();
         if (hetnams.has(het)) {
-            hetnams.set(het, hetnams.get(het) + " " + name_1);
+            hetnams.set(het, "".concat(hetnams.get(het), " ").concat(name_1));
         }
         else {
             hetnams.set(het, name_1);

package/lib/mol-model-formats/structure/pdb/entity.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/lib/mol-model-formats/structure/property/assembly.js CHANGED Viewed

@@ -91,7 +91,7 @@ function getAssemblyOperators(matrices, operatorNames, startIndex, assemblyId) {
             Mat4.mul(m, m, matrices.get(op[i]));
         }
         index++;
-        operators[operators.length] = SymmetryOperator.create("ASM_" + index, m, { assembly: { id: assemblyId, operId: index, operList: op } });
+        operators[operators.length] = SymmetryOperator.create("ASM_".concat(index), m, { assembly: { id: assemblyId, operId: index, operList: op } });
     }
     return operators;
 }

package/lib/mol-model-formats/structure/property/assembly.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ 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package/lib/mol-model-formats/structure/property/symmetry.js CHANGED Viewed

@@ -67,7 +67,7 @@ function getNcsOperators(struct_ncs_oper) {
         if (struct_ncs_oper.code.value(i) === 'given' && !Mat3.isIdentity(m) && !Vec3.isZero(v))
             continue;
         var ncsId = id.value(i);
-        opers[opers.length] = SymmetryOperator.ofRotationAndOffset("ncs_" + ncsId, m, v, ncsId);
+        opers[opers.length] = SymmetryOperator.ofRotationAndOffset("ncs_".concat(ncsId), m, v, ncsId);
     }
     return opers;
 }

package/lib/mol-model-formats/structure/property/symmetry.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/lib/mol-model-formats/volume/ccp4.js CHANGED Viewed

@@ -29,7 +29,7 @@ function getTypedArrayCtor(header) {
         case TypedArrayValueType.Int16: return Int16Array;
         case TypedArrayValueType.Uint16: return Uint16Array;
     }
-    throw Error(valueType + " is not a supported value format.");
+    throw Error("".concat(valueType, " is not a supported value format."));
 }
 export function volumeFromCcp4(source, params) {
     var _this = this;

package/lib/mol-model-formats/volume/ccp4.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/lib/mol-model-props/common/custom-element-property.js CHANGED Viewed

@@ -68,7 +68,7 @@ var CustomElementProperty;
                 color: color,
                 props: props,
                 contextHash: contextHash,
-                description: "Assign element colors based on '" + modelProperty.label + "' data."
+                description: "Assign element colors based on '".concat(modelProperty.label, "' data.")
             };
         }
         return {

package/lib/mol-model-props/common/custom-element-property.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/lib/mol-model-props/common/custom-property.js CHANGED Viewed

@@ -48,7 +48,7 @@ var CustomProperty;
         Registry.prototype.get = function (name) {
             var prop = this.providers.get(name);
             if (!prop) {
-                throw new Error("Custom property '" + name + "' is not registered.");
+                throw new Error("Custom property '".concat(name, "' is not registered."));
             }
             return this.providers.get(name);
         };

package/lib/mol-model-props/common/custom-property.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/lib/mol-model-props/computed/interactions/common.js CHANGED Viewed

@@ -91,7 +91,7 @@ var InteractionsInterContacts = /** @class */ (function (_super) {
         return this.elementKeyIndex.get(this.getElementKey(index, unit.id)) || [];
     };
     InteractionsInterContacts.prototype.getElementKey = function (index, unitId) {
-        return index + "|" + unitId;
+        return "".concat(index, "|").concat(unitId);
     };
     return InteractionsInterContacts;
 }(InterUnitGraph));

package/lib/mol-model-props/computed/interactions/common.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ 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package/lib/mol-model-props/computed/interactions/hydrogen-bonds.d.ts CHANGED Viewed

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author Fred Ludlow <Fred.Ludlow@astx.com>

package/lib/mol-model-props/computed/interactions/hydrogen-bonds.js CHANGED Viewed

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2019-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author Fred Ludlow <Fred.Ludlow@astx.com>
@@ -46,10 +46,7 @@ function addUnitHydrogenDonors(structure, unit, builder) {
     var totalH = getUnitValenceModel(structure, unit).totalH;
     var elements = unit.elements;
     var _a = unit.model.atomicConformation, x = _a.x, y = _a.y, z = _a.z;
-    var elementAromaticRingIndices = unit.rings.elementAromaticRingIndices;
     for (var i = 0, il = elements.length; i < il; ++i) {
-        if (elementAromaticRingIndices.has(i))
-            continue;
         var element = typeSymbol(unit, i);
         if ((
         // include both nitrogen atoms in histidine due to
@@ -100,13 +97,10 @@ function addUnitHydrogenAcceptors(structure, unit, builder) {
     var _a = getUnitValenceModel(structure, unit), charge = _a.charge, implicitH = _a.implicitH, idealGeometry = _a.idealGeometry;
     var elements = unit.elements;
     var _b = unit.model.atomicConformation, x = _b.x, y = _b.y, z = _b.z;
-    var elementAromaticRingIndices = unit.rings.elementAromaticRingIndices;
     var add = function (i) {
         builder.add(5 /* HydrogenAcceptor */, 0 /* None */, x[elements[i]], y[elements[i]], z[elements[i]], i);
     };
     for (var i = 0, il = elements.length; i < il; ++i) {
-        if (elementAromaticRingIndices.has(i))
-            continue;
         var element = typeSymbol(unit, i);
         if (element === "O" /* O */) {
             // Basically assume all oxygen atoms are acceptors!

package/lib/mol-model-props/computed/interactions/hydrogen-bonds.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/lib/mol-model-props/computed/interactions/refine.js CHANGED Viewed

@@ -82,8 +82,8 @@ function hydrophobicRefiner(structure, interactions) {
         var elementB = infoB.members[infoB.offsets[infoB.feature]];
         var residueA = infoA.unit.getResidueIndex(elementA);
         var residueB = infoB.unit.getResidueIndex(elementB);
-        var keyA = elementA + "|" + infoA.unit.id + "|" + residueB + "|" + infoB.unit.id + "|A";
-        var keyB = elementB + "|" + infoB.unit.id + "|" + residueA + "|" + infoA.unit.id + "|B";
+        var keyA = "".concat(elementA, "|").concat(infoA.unit.id, "|").concat(residueB, "|").concat(infoB.unit.id, "|A");
+        var keyB = "".concat(elementB, "|").concat(infoB.unit.id, "|").concat(residueA, "|").concat(infoA.unit.id, "|B");
         var dist = Features.distance(infoA, infoB);
         handleResidueContact(dist, edge, keyA, map, set);
         handleResidueContact(dist, edge, keyB, map, set);

package/lib/mol-model-props/computed/interactions/refine.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/lib/mol-model-props/computed/representations/interactions-inter-unit-cylinder.d.ts CHANGED Viewed

@@ -19,14 +19,14 @@ export declare const InteractionsInterUnitParams: {
     dashCap: PD.BooleanParam;
     stubCap: PD.BooleanParam;
     radialSegments: PD.Numeric;
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     doubleSided: PD.BooleanParam;
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
 };
 export declare type InteractionsInterUnitParams = typeof InteractionsInterUnitParams;
 export declare function InteractionsInterUnitVisual(materialId: number): ComplexVisual<InteractionsInterUnitParams>;

package/lib/mol-model-props/computed/representations/interactions-intra-unit-cylinder.d.ts CHANGED Viewed

@@ -19,14 +19,14 @@ export declare const InteractionsIntraUnitParams: {
     dashCap: PD.BooleanParam;
     stubCap: PD.BooleanParam;
     radialSegments: PD.Numeric;
-    unitKinds: PD.MultiSelect<"spheres" | "atomic" | "gaussians">;
+    unitKinds: PD.MultiSelect<"spheres" | "gaussians" | "atomic">;
     doubleSided: PD.BooleanParam;
     flipSided: PD.BooleanParam;
     flatShaded: PD.BooleanParam;
     ignoreLight: PD.BooleanParam;
     xrayShaded: PD.BooleanParam;
     alpha: PD.Numeric;
-    quality: PD.Select<"custom" | "auto" | "highest" | "higher" | "high" | "medium" | "low" | "lower" | "lowest">;
+    quality: PD.Select<"auto" | "medium" | "high" | "low" | "custom" | "highest" | "higher" | "lower" | "lowest">;
 };
 export declare type InteractionsIntraUnitParams = typeof InteractionsIntraUnitParams;
 export declare function InteractionsIntraUnitVisual(materialId: number): UnitsVisual<InteractionsIntraUnitParams>;