Added support for custom atomic labels, radii and colors in the NGL-based structure viewer.

Changelog: Added

gui/src/components/visualization/StructureBuilder.js

+/*
+ * Copyright The NOMAD Authors.
+ *
+ * This file is part of NOMAD. See https://nomad-lab.eu for further info.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+/**
+ * This class is used for building the required NGL stores (atomStore,
+ * residueStore, chainStore, modelStore) for a Structure. The blueprint for this
+ * class comes from the NGL package (ngl/src/structure/structure-builder.ts)
+ * which is not not exported from the minified package.
+ */
+class StructureBuilder {
+  constructor(structure) {
+    this.currentModelindex = null
+    this.currentChainid = null
+    this.currentResname = null
+    this.currentResno = null
+    this.currentInscode = undefined
+    this.currentHetero = null
+
+    this.previousResname = ''
+    this.previousHetero = null
+
+    this.ai = -1
+    this.ri = -1
+    this.ci = -1
+    this.mi = -1
+    this.structure = structure
+  }
+
+  addResidueType(ri) {
+    const atomStore = this.structure.atomStore
+    const residueStore = this.structure.residueStore
+    const residueMap = this.structure.residueMap
+    const cc = this.structure.chemCompMap?.dict[this.previousResname]
+
+    const count = residueStore.atomCount[ri]
+    const offset = residueStore.atomOffset[ri]
+    const atomTypeIdList = new Array(count)
+    for (let i = 0; i < count; ++i) {
+      atomTypeIdList[i] = atomStore.atomTypeId[offset + i]
+    }
+    const chemCompType = cc?.chemCompType
+    const bonds = cc ? this.structure.chemCompMap?.getBonds(this.previousResname, atomTypeIdList) : undefined
+    residueStore.residueTypeId[ri] = residueMap.add(
+      this.previousResname, atomTypeIdList, this.previousHetero, chemCompType, bonds
+    )
+  }
+
+  addAtom(modelindex, chainname, chainid, resname, resno, hetero, sstruc, inscode) {
+    const atomStore = this.structure.atomStore
+    const residueStore = this.structure.residueStore
+    const chainStore = this.structure.chainStore
+    const modelStore = this.structure.modelStore
+
+    let addModel = false
+    let addChain = false
+    let addResidue = false
+
+    if (this.currentModelindex !== modelindex) {
+      addModel = true
+      addChain = true
+      addResidue = true
+      this.mi += 1
+      this.ci += 1
+      this.ri += 1
+    } else if (this.currentChainid !== chainid) {
+      addChain = true
+      addResidue = true
+      this.ci += 1
+      this.ri += 1
+    } else if (this.currentResno !== resno || this.currentResname !== resname || this.currentInscode !== inscode) {
+      addResidue = true
+      this.ri += 1
+    }
+    this.ai += 1
+
+    if (addModel) {
+      modelStore.growIfFull()
+      modelStore.chainOffset[this.mi] = this.ci
+      modelStore.chainCount[this.mi] = 0
+      modelStore.count += 1
+      chainStore.modelIndex[this.ci] = this.mi
+    }
+
+    if (addChain) {
+      chainStore.growIfFull()
+      chainStore.setChainname(this.ci, chainname)
+      chainStore.setChainid(this.ci, chainid)
+      chainStore.residueOffset[this.ci] = this.ri
+      chainStore.residueCount[this.ci] = 0
+      chainStore.count += 1
+      chainStore.modelIndex[this.ci] = this.mi
+      modelStore.chainCount[this.mi] += 1
+      residueStore.chainIndex[this.ri] = this.ci
+    }
+
+    if (addResidue) {
+      this.previousResname = this.currentResname
+      this.previousHetero = this.currentHetero
+      if (this.ri > 0) this.addResidueType(this.ri - 1)
+      residueStore.growIfFull()
+      residueStore.resno[this.ri] = resno
+      if (sstruc !== undefined) {
+        residueStore.sstruc[this.ri] = sstruc.charCodeAt(0)
+      }
+      if (inscode !== undefined) {
+        residueStore.inscode[this.ri] = inscode.charCodeAt(0)
+      }
+      residueStore.atomOffset[this.ri] = this.ai
+      residueStore.atomCount[this.ri] = 0
+      residueStore.count += 1
+      residueStore.chainIndex[this.ri] = this.ci
+      chainStore.residueCount[this.ci] += 1
+    }
+
+    atomStore.count += 1
+    atomStore.residueIndex[this.ai] = this.ri
+    residueStore.atomCount[this.ri] += 1
+
+    this.currentModelindex = modelindex
+    this.currentChainid = chainid
+    this.currentResname = resname
+    this.currentResno = resno
+    this.currentInscode = inscode
+    this.currentHetero = hetero
+  }
+
+  finalize() {
+    this.previousResname = this.currentResname
+    this.previousHetero = this.currentHetero
+    if (this.ri > -1) this.addResidueType(this.ri)
+  }
+}
+
+export default StructureBuilder