mol-model: added sourceIndex to AtomicHierarchy

package-lock.json

@@ -458,7 +458,7 @@
     },
     "@types/valid-url": {
       "version": "1.0.2",
-      "resolved": "http://registry.npmjs.org/@types/valid-url/-/valid-url-1.0.2.tgz",
+      "resolved": "https://registry.npmjs.org/@types/valid-url/-/valid-url-1.0.2.tgz",
       "integrity": "sha1-YPpDXOJL/VuhB7jSqAeWrq86j0U=",
       "dev": true
     },
@@ -1693,7 +1693,7 @@
     },
     "camelcase-keys": {
       "version": "2.1.0",
-      "resolved": "http://registry.npmjs.org/camelcase-keys/-/camelcase-keys-2.1.0.tgz",
+      "resolved": "https://registry.npmjs.org/camelcase-keys/-/camelcase-keys-2.1.0.tgz",
       "integrity": "sha1-MIvur/3ygRkFHvodkyITyRuPkuc=",
       "dev": true,
       "requires": {
@@ -2574,7 +2574,7 @@
       "dependencies": {
         "node-fetch": {
           "version": "2.1.2",
-          "resolved": "https://registry.npmjs.org/node-fetch/-/node-fetch-2.1.2.tgz",
+          "resolved": "http://registry.npmjs.org/node-fetch/-/node-fetch-2.1.2.tgz",
           "integrity": "sha1-q4hOjn5X44qUR1POxwb3iNF2i7U=",
           "dev": true
         }
@@ -3069,7 +3069,7 @@
     },
     "duplexer": {
       "version": "0.1.1",
-      "resolved": "https://registry.npmjs.org/duplexer/-/duplexer-0.1.1.tgz",
+      "resolved": "http://registry.npmjs.org/duplexer/-/duplexer-0.1.1.tgz",
       "integrity": "sha1-rOb/gIwc5mtX0ev5eXessCM0z8E=",
       "dev": true
     },
@@ -3129,7 +3129,7 @@
     },
     "enabled": {
       "version": "1.0.2",
-      "resolved": "http://registry.npmjs.org/enabled/-/enabled-1.0.2.tgz",
+      "resolved": "https://registry.npmjs.org/enabled/-/enabled-1.0.2.tgz",
       "integrity": "sha1-ll9lE9LC0cX0ZStkouM5ZGf8L5M=",
       "dev": true,
       "requires": {
@@ -3611,7 +3611,7 @@
     },
     "fecha": {
       "version": "2.3.3",
-      "resolved": "http://registry.npmjs.org/fecha/-/fecha-2.3.3.tgz",
+      "resolved": "https://registry.npmjs.org/fecha/-/fecha-2.3.3.tgz",
       "integrity": "sha512-lUGBnIamTAwk4znq5BcqsDaxSmZ9nDVJaij6NvRt/Tg4R69gERA+otPKbS86ROw9nxVMw2/mp1fnaiWqbs6Sdg==",
       "dev": true
     },
@@ -4205,8 +4205,7 @@
         "ansi-regex": {
           "version": "2.1.1",
           "bundled": true,
-          "dev": true,
-          "optional": true
+          "dev": true
         },
         "aproba": {
           "version": "1.2.0",
@@ -4227,14 +4226,12 @@
         "balanced-match": {
           "version": "1.0.0",
           "bundled": true,
-          "dev": true,
-          "optional": true
+          "dev": true
         },
         "brace-expansion": {
           "version": "1.1.11",
           "bundled": true,
           "dev": true,
-          "optional": true,
           "requires": {
             "balanced-match": "^1.0.0",
             "concat-map": "0.0.1"
@@ -4249,20 +4246,17 @@
         "code-point-at": {
           "version": "1.1.0",
           "bundled": true,
-          "dev": true,
-          "optional": true
+          "dev": true
         },
         "concat-map": {
           "version": "0.0.1",
           "bundled": true,
-          "dev": true,
-          "optional": true
+          "dev": true
         },
         "console-control-strings": {
           "version": "1.1.0",
           "bundled": true,
-          "dev": true,
-          "optional": true
+          "dev": true
         },
         "core-util-is": {
           "version": "1.0.2",
@@ -4379,8 +4373,7 @@
         "inherits": {
           "version": "2.0.3",
           "bundled": true,
-          "dev": true,
-          "optional": true
+          "dev": true
         },
         "ini": {
           "version": "1.3.5",
@@ -4392,7 +4385,6 @@
           "version": "1.0.0",
           "bundled": true,
           "dev": true,
-          "optional": true,
           "requires": {
             "number-is-nan": "^1.0.0"
           }
@@ -4407,7 +4399,6 @@
           "version": "3.0.4",
           "bundled": true,
           "dev": true,
-          "optional": true,
           "requires": {
             "brace-expansion": "^1.1.7"
           }
@@ -4415,14 +4406,12 @@
         "minimist": {
           "version": "0.0.8",
           "bundled": true,
-          "dev": true,
-          "optional": true
+          "dev": true
         },
         "minipass": {
           "version": "2.2.4",
           "bundled": true,
           "dev": true,
-          "optional": true,
           "requires": {
             "safe-buffer": "^5.1.1",
             "yallist": "^3.0.0"
@@ -4441,7 +4430,6 @@
           "version": "0.5.1",
           "bundled": true,
           "dev": true,
-          "optional": true,
           "requires": {
             "minimist": "0.0.8"
           }
@@ -4522,8 +4510,7 @@
         "number-is-nan": {
           "version": "1.0.1",
           "bundled": true,
-          "dev": true,
-          "optional": true
+          "dev": true
         },
         "object-assign": {
           "version": "4.1.1",
@@ -4535,7 +4522,6 @@
           "version": "1.4.0",
           "bundled": true,
           "dev": true,
-          "optional": true,
           "requires": {
             "wrappy": "1"
           }
@@ -4621,8 +4607,7 @@
         "safe-buffer": {
           "version": "5.1.1",
           "bundled": true,
-          "dev": true,
-          "optional": true
+          "dev": true
         },
         "safer-buffer": {
           "version": "2.1.2",
@@ -4658,7 +4643,6 @@
           "version": "1.0.2",
           "bundled": true,
           "dev": true,
-          "optional": true,
           "requires": {
             "code-point-at": "^1.0.0",
             "is-fullwidth-code-point": "^1.0.0",
@@ -4678,7 +4662,6 @@
           "version": "3.0.1",
           "bundled": true,
           "dev": true,
-          "optional": true,
           "requires": {
             "ansi-regex": "^2.0.0"
           }
@@ -4722,14 +4705,12 @@
         "wrappy": {
           "version": "1.0.2",
           "bundled": true,
-          "dev": true,
-          "optional": true
+          "dev": true
         },
         "yallist": {
           "version": "3.0.2",
           "bundled": true,
-          "dev": true,
-          "optional": true
+          "dev": true
         }
       }
     },
@@ -4789,7 +4770,7 @@
         },
         "strip-ansi": {
           "version": "3.0.1",
-          "resolved": "http://registry.npmjs.org/strip-ansi/-/strip-ansi-3.0.1.tgz",
+          "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-3.0.1.tgz",
           "integrity": "sha1-ajhfuIU9lS1f8F0Oiq+UJ43GPc8=",
           "dev": true,
           "requires": {
@@ -5088,7 +5069,7 @@
       "dependencies": {
         "minimist": {
           "version": "1.2.0",
-          "resolved": "https://registry.npmjs.org/minimist/-/minimist-1.2.0.tgz",
+          "resolved": "http://registry.npmjs.org/minimist/-/minimist-1.2.0.tgz",
           "integrity": "sha1-o1AIsg9BOD7sH7kU9M1d95omQoQ=",
           "dev": true
         },
@@ -5538,8 +5519,7 @@
             "ansi-regex": {
               "version": "2.1.1",
               "bundled": true,
-              "dev": true,
-              "optional": true
+              "dev": true
             },
             "aproba": {
               "version": "1.2.0",
@@ -5560,14 +5540,12 @@
             "balanced-match": {
               "version": "1.0.0",
               "bundled": true,
-              "dev": true,
-              "optional": true
+              "dev": true
             },
             "brace-expansion": {
               "version": "1.1.11",
               "bundled": true,
               "dev": true,
-              "optional": true,
               "requires": {
                 "balanced-match": "^1.0.0",
                 "concat-map": "0.0.1"
@@ -5582,20 +5560,17 @@
             "code-point-at": {
               "version": "1.1.0",
               "bundled": true,
-              "dev": true,
-              "optional": true
+              "dev": true
             },
             "concat-map": {
               "version": "0.0.1",
               "bundled": true,
-              "dev": true,
-              "optional": true
+              "dev": true
             },
             "console-control-strings": {
               "version": "1.1.0",
               "bundled": true,
-              "dev": true,
-              "optional": true
+              "dev": true
             },
             "core-util-is": {
               "version": "1.0.2",
@@ -5712,8 +5687,7 @@
             "inherits": {
               "version": "2.0.3",
               "bundled": true,
-              "dev": true,
-              "optional": true
+              "dev": true
             },
             "ini": {
               "version": "1.3.5",
@@ -5725,7 +5699,6 @@
               "version": "1.0.0",
               "bundled": true,
               "dev": true,
-              "optional": true,
               "requires": {
                 "number-is-nan": "^1.0.0"
               }
@@ -5740,7 +5713,6 @@
               "version": "3.0.4",
               "bundled": true,
               "dev": true,
-              "optional": true,
               "requires": {
                 "brace-expansion": "^1.1.7"
               }
@@ -5748,14 +5720,12 @@
             "minimist": {
               "version": "0.0.8",
               "bundled": true,
-              "dev": true,
-              "optional": true
+              "dev": true
             },
             "minipass": {
               "version": "2.3.5",
               "bundled": true,
               "dev": true,
-              "optional": true,
               "requires": {
                 "safe-buffer": "^5.1.2",
                 "yallist": "^3.0.0"
@@ -5774,7 +5744,6 @@
               "version": "0.5.1",
               "bundled": true,
               "dev": true,
-              "optional": true,
               "requires": {
                 "minimist": "0.0.8"
               }
@@ -5855,8 +5824,7 @@
             "number-is-nan": {
               "version": "1.0.1",
               "bundled": true,
-              "dev": true,
-              "optional": true
+              "dev": true
             },
             "object-assign": {
               "version": "4.1.1",
@@ -5868,7 +5836,6 @@
               "version": "1.4.0",
               "bundled": true,
               "dev": true,
-              "optional": true,
               "requires": {
                 "wrappy": "1"
               }
@@ -5954,8 +5921,7 @@
             "safe-buffer": {
               "version": "5.1.2",
               "bundled": true,
-              "dev": true,
-              "optional": true
+              "dev": true
             },
             "safer-buffer": {
               "version": "2.1.2",
@@ -5991,7 +5957,6 @@
               "version": "1.0.2",
               "bundled": true,
               "dev": true,
-              "optional": true,
               "requires": {
                 "code-point-at": "^1.0.0",
                 "is-fullwidth-code-point": "^1.0.0",
@@ -6011,7 +5976,6 @@
               "version": "3.0.1",
               "bundled": true,
               "dev": true,
-              "optional": true,
               "requires": {
                 "ansi-regex": "^2.0.0"
               }
@@ -6055,14 +6019,12 @@
             "wrappy": {
               "version": "1.0.2",
               "bundled": true,
-              "dev": true,
-              "optional": true
+              "dev": true
             },
             "yallist": {
               "version": "3.0.3",
               "bundled": true,
-              "dev": true,
-              "optional": true
+              "dev": true
             }
           }
         },
@@ -10083,7 +10045,7 @@
     },
     "meow": {
       "version": "3.7.0",
-      "resolved": "http://registry.npmjs.org/meow/-/meow-3.7.0.tgz",
+      "resolved": "https://registry.npmjs.org/meow/-/meow-3.7.0.tgz",
       "integrity": "sha1-cstmi0JSKCkKu/qFaJJYcwioAfs=",
       "dev": true,
       "requires": {
@@ -10267,7 +10229,7 @@
     },
     "minimist": {
       "version": "0.0.8",
-      "resolved": "https://registry.npmjs.org/minimist/-/minimist-0.0.8.tgz",
+      "resolved": "http://registry.npmjs.org/minimist/-/minimist-0.0.8.tgz",
       "integrity": "sha1-hX/Kv8M5fSYluCKCYuhqp6ARsF0=",
       "dev": true
     },
@@ -10330,7 +10292,7 @@
     },
     "mkdirp": {
       "version": "0.5.1",
-      "resolved": "https://registry.npmjs.org/mkdirp/-/mkdirp-0.5.1.tgz",
+      "resolved": "http://registry.npmjs.org/mkdirp/-/mkdirp-0.5.1.tgz",
       "integrity": "sha1-MAV0OOrGz3+MR2fzhkjWaX11yQM=",
       "dev": true,
       "requires": {
@@ -10484,7 +10446,7 @@
       "dependencies": {
         "semver": {
           "version": "5.3.0",
-          "resolved": "http://registry.npmjs.org/semver/-/semver-5.3.0.tgz",
+          "resolved": "https://registry.npmjs.org/semver/-/semver-5.3.0.tgz",
           "integrity": "sha1-myzl094C0XxgEq0yaqa00M9U+U8=",
           "dev": true
         }
@@ -10630,7 +10592,7 @@
         },
         "chalk": {
           "version": "1.1.3",
-          "resolved": "http://registry.npmjs.org/chalk/-/chalk-1.1.3.tgz",
+          "resolved": "https://registry.npmjs.org/chalk/-/chalk-1.1.3.tgz",
           "integrity": "sha1-qBFcVeSnAv5NFQq9OHKCKn4J/Jg=",
           "dev": true,
           "requires": {
@@ -10742,7 +10704,7 @@
         },
         "strip-ansi": {
           "version": "3.0.1",
-          "resolved": "http://registry.npmjs.org/strip-ansi/-/strip-ansi-3.0.1.tgz",
+          "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-3.0.1.tgz",
           "integrity": "sha1-ajhfuIU9lS1f8F0Oiq+UJ43GPc8=",
           "dev": true,
           "requires": {
@@ -11100,7 +11062,7 @@
     },
     "p-is-promise": {
       "version": "1.1.0",
-      "resolved": "http://registry.npmjs.org/p-is-promise/-/p-is-promise-1.1.0.tgz",
+      "resolved": "https://registry.npmjs.org/p-is-promise/-/p-is-promise-1.1.0.tgz",
       "integrity": "sha1-nJRWmJ6fZYgBewQ01WCXZ1w9oF4=",
       "dev": true
     },
@@ -12695,7 +12657,7 @@
         },
         "strip-ansi": {
           "version": "3.0.1",
-          "resolved": "http://registry.npmjs.org/strip-ansi/-/strip-ansi-3.0.1.tgz",
+          "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-3.0.1.tgz",
           "integrity": "sha1-ajhfuIU9lS1f8F0Oiq+UJ43GPc8=",
           "dev": true,
           "requires": {
@@ -12819,7 +12781,7 @@
       "dependencies": {
         "source-map": {
           "version": "0.4.4",
-          "resolved": "http://registry.npmjs.org/source-map/-/source-map-0.4.4.tgz",
+          "resolved": "https://registry.npmjs.org/source-map/-/source-map-0.4.4.tgz",
           "integrity": "sha1-66T12pwNyZneaAMti092FzZSA2s=",
           "dev": true,
           "requires": {
@@ -13546,7 +13508,7 @@
       "dependencies": {
         "minimist": {
           "version": "1.2.0",
-          "resolved": "https://registry.npmjs.org/minimist/-/minimist-1.2.0.tgz",
+          "resolved": "http://registry.npmjs.org/minimist/-/minimist-1.2.0.tgz",
           "integrity": "sha1-o1AIsg9BOD7sH7kU9M1d95omQoQ=",
           "dev": true
         }
@@ -13596,7 +13558,7 @@
     },
     "tar": {
       "version": "2.2.1",
-      "resolved": "http://registry.npmjs.org/tar/-/tar-2.2.1.tgz",
+      "resolved": "https://registry.npmjs.org/tar/-/tar-2.2.1.tgz",
       "integrity": "sha1-jk0qJWwOIYXGsYrWlK7JaLg8sdE=",
       "dev": true,
       "requires": {
@@ -14708,8 +14670,7 @@
             "ansi-regex": {
               "version": "2.1.1",
               "bundled": true,
-              "dev": true,
-              "optional": true
+              "dev": true
             },
             "aproba": {
               "version": "1.2.0",
@@ -14730,14 +14691,12 @@
             "balanced-match": {
               "version": "1.0.0",
               "bundled": true,
-              "dev": true,
-              "optional": true
+              "dev": true
             },
             "brace-expansion": {
               "version": "1.1.11",
               "bundled": true,
               "dev": true,
-              "optional": true,
               "requires": {
                 "balanced-match": "^1.0.0",
                 "concat-map": "0.0.1"
@@ -14752,20 +14711,17 @@
             "code-point-at": {
               "version": "1.1.0",
               "bundled": true,
-              "dev": true,
-              "optional": true
+              "dev": true
             },
             "concat-map": {
               "version": "0.0.1",
               "bundled": true,
-              "dev": true,
-              "optional": true
+              "dev": true
             },
             "console-control-strings": {
               "version": "1.1.0",
               "bundled": true,
-              "dev": true,
-              "optional": true
+              "dev": true
             },
             "core-util-is": {
               "version": "1.0.2",
@@ -14882,8 +14838,7 @@
             "inherits": {
               "version": "2.0.3",
               "bundled": true,
-              "dev": true,
-              "optional": true
+              "dev": true
             },
             "ini": {
               "version": "1.3.5",
@@ -14895,7 +14850,6 @@
               "version": "1.0.0",
               "bundled": true,
               "dev": true,
-              "optional": true,
               "requires": {
                 "number-is-nan": "^1.0.0"
               }
@@ -14910,7 +14864,6 @@
               "version": "3.0.4",
               "bundled": true,
               "dev": true,
-              "optional": true,
               "requires": {
                 "brace-expansion": "^1.1.7"
               }
@@ -14918,14 +14871,12 @@
             "minimist": {
               "version": "0.0.8",
               "bundled": true,
-              "dev": true,
-              "optional": true
+              "dev": true
             },
             "minipass": {
               "version": "2.3.5",
               "bundled": true,
               "dev": true,
-              "optional": true,
               "requires": {
                 "safe-buffer": "^5.1.2",
                 "yallist": "^3.0.0"
@@ -14944,7 +14895,6 @@
               "version": "0.5.1",
               "bundled": true,
               "dev": true,
-              "optional": true,
               "requires": {
                 "minimist": "0.0.8"
               }
@@ -15025,8 +14975,7 @@
             "number-is-nan": {
               "version": "1.0.1",
               "bundled": true,
-              "dev": true,
-              "optional": true
+              "dev": true
             },
             "object-assign": {
               "version": "4.1.1",
@@ -15038,7 +14987,6 @@
               "version": "1.4.0",
               "bundled": true,
               "dev": true,
-              "optional": true,
               "requires": {
                 "wrappy": "1"
               }
@@ -15124,8 +15072,7 @@
             "safe-buffer": {
               "version": "5.1.2",
               "bundled": true,
-              "dev": true,
-              "optional": true
+              "dev": true
             },
             "safer-buffer": {
               "version": "2.1.2",
@@ -15161,7 +15108,6 @@
               "version": "1.0.2",
               "bundled": true,
               "dev": true,
-              "optional": true,
               "requires": {
                 "code-point-at": "^1.0.0",
                 "is-fullwidth-code-point": "^1.0.0",
@@ -15181,7 +15127,6 @@
               "version": "3.0.1",
               "bundled": true,
               "dev": true,
-              "optional": true,
               "requires": {
                 "ansi-regex": "^2.0.0"
               }
@@ -15225,14 +15170,12 @@
             "wrappy": {
               "version": "1.0.2",
               "bundled": true,
-              "dev": true,
-              "optional": true
+              "dev": true
             },
             "yallist": {
               "version": "3.0.3",
               "bundled": true,
-              "dev": true,
-              "optional": true
+              "dev": true
             }
           }
         },
@@ -16011,7 +15954,7 @@
     },
     "whatwg-fetch": {
       "version": "2.0.4",
-      "resolved": "https://registry.npmjs.org/whatwg-fetch/-/whatwg-fetch-2.0.4.tgz",
+      "resolved": "http://registry.npmjs.org/whatwg-fetch/-/whatwg-fetch-2.0.4.tgz",
       "integrity": "sha512-dcQ1GWpOD/eEQ97k66aiEVpNnapVj90/+R+SXTPYGHpYBBypfKJEQjLrvMZ7YXbKm21gXd4NcuxUTjiv1YtLng==",
       "dev": true
     },
@@ -16154,7 +16097,7 @@
     },
     "wrap-ansi": {
       "version": "2.1.0",
-      "resolved": "https://registry.npmjs.org/wrap-ansi/-/wrap-ansi-2.1.0.tgz",
+      "resolved": "http://registry.npmjs.org/wrap-ansi/-/wrap-ansi-2.1.0.tgz",
       "integrity": "sha1-2Pw9KE3QV5T+hJc8rs3Rz4JP3YU=",
       "dev": true,
       "requires": {

src/mol-model-formats/structure/mmcif/atomic.ts

@@ -16,11 +16,8 @@ import { ElementSymbol } from 'mol-model/structure/model/types';
 import { Entities } from 'mol-model/structure/model/properties/common';
 import { getAtomicRanges } from 'mol-model/structure/model/properties/utils/atomic-ranges';
 import { getAtomicDerivedData } from 'mol-model/structure/model/properties/utils/atomic-derived';
-import { ModelFormat } from '../format';
-import mmCIF_Format = ModelFormat.mmCIF
 import { FormatData } from './parser';
 
-
 type AtomSite = mmCIF_Database['atom_site']
 
 function findHierarchyOffsets(atom_site: AtomSite) {
@@ -45,13 +42,14 @@ function findHierarchyOffsets(atom_site: AtomSite) {
     return { residues, chains };
 }
 
-function createHierarchyData(atom_site: AtomSite, offsets: { residues: ArrayLike<number>, chains: ArrayLike<number> }): AtomicData {
+function createHierarchyData(atom_site: AtomSite, sourceIndex: Column<number>, offsets: { residues: ArrayLike<number>, chains: ArrayLike<number> }): AtomicData {
     const atoms = Table.ofColumns(AtomsSchema, {
         type_symbol: Column.ofArray({ array: Column.mapToArray(atom_site.type_symbol, ElementSymbol), schema: Column.Schema.Aliased<ElementSymbol>(Column.Schema.str) }),
         label_atom_id: atom_site.label_atom_id,
         auth_atom_id: atom_site.auth_atom_id,
         label_alt_id: atom_site.label_alt_id,
-        pdbx_formal_charge: atom_site.pdbx_formal_charge
+        pdbx_formal_charge: atom_site.pdbx_formal_charge,
+        sourceIndex
     });
     const residues = Table.view(atom_site, ResiduesSchema, offsets.residues);
     // Optimize the numeric columns
@@ -80,9 +78,9 @@ function isHierarchyDataEqual(a: AtomicData, b: AtomicData) {
         && Table.areEqual(a.atoms as Table<AtomsSchema>, b.atoms as Table<AtomsSchema>)
 }
 
-export function getAtomicHierarchyAndConformation(format: mmCIF_Format, atom_site: AtomSite, entities: Entities, formatData: FormatData, previous?: Model) {
+export function getAtomicHierarchyAndConformation(atom_site: AtomSite, sourceIndex: Column<number>, entities: Entities, formatData: FormatData, previous?: Model) {
     const hierarchyOffsets = findHierarchyOffsets(atom_site);
-    const hierarchyData = createHierarchyData(atom_site, hierarchyOffsets);
+    const hierarchyData = createHierarchyData(atom_site, sourceIndex, hierarchyOffsets);
 
     if (previous && isHierarchyDataEqual(previous.atomicHierarchy, hierarchyData)) {
         return {

src/mol-model-formats/structure/mmcif/ihm.ts

@@ -21,6 +21,7 @@ export interface IHMData {
     model_name: string,
     entities: Entities,
     atom_site: mmCIF['atom_site'],
+    atom_site_sourceIndex: Column<number>,
     ihm_sphere_obj_site: mmCIF['ihm_sphere_obj_site'],
     ihm_gaussian_obj_site: mmCIF['ihm_gaussian_obj_site']
 }

src/mol-model-formats/structure/mmcif/parser.ts

@@ -169,8 +169,8 @@ function getFormatData(format: mmCIF_Format): FormatData {
     }
 }
 
-function createStandardModel(format: mmCIF_Format, atom_site: AtomSite, entities: Entities, formatData: FormatData, previous?: Model): Model {
-    const atomic = getAtomicHierarchyAndConformation(format, atom_site, entities, formatData, previous);
+function createStandardModel(format: mmCIF_Format, atom_site: AtomSite, sourceIndex: Column<number>, entities: Entities, formatData: FormatData, previous?: Model): Model {
+    const atomic = getAtomicHierarchyAndConformation(atom_site, sourceIndex, entities, formatData, previous);
     if (previous && atomic.sameAsPrevious) {
         return {
             ...previous,
@@ -209,7 +209,7 @@ function createStandardModel(format: mmCIF_Format, atom_site: AtomSite, entities
 }
 
 function createModelIHM(format: mmCIF_Format, data: IHMData, formatData: FormatData): Model {
-    const atomic = getAtomicHierarchyAndConformation(format, data.atom_site, data.entities, formatData);
+    const atomic = getAtomicHierarchyAndConformation(data.atom_site, data.atom_site_sourceIndex, data.entities, formatData);
     const coarse = getIHMCoarse(data, formatData);
 
     return {
@@ -255,8 +255,8 @@ async function readStandard(ctx: RuntimeContext, format: mmCIF_Format, formatDat
     let modelStart = 0;
     while (modelStart < atomCount) {
         const modelEnd = findModelEnd(format.data.atom_site.pdbx_PDB_model_num, modelStart);
-        const atom_site = await sortAtomSite(ctx, format.data.atom_site, modelStart, modelEnd);
-        const model = createStandardModel(format, atom_site, entities, formatData, models.length > 0 ? models[models.length - 1] : void 0);
+        const { atom_site, sourceIndex } = await sortAtomSite(ctx, format.data.atom_site, modelStart, modelEnd);
+        const model = createStandardModel(format, atom_site, sourceIndex, entities, formatData, models.length > 0 ? models[models.length - 1] : void 0);
         attachProps(model);
         models.push(model);
         modelStart = modelEnd;
@@ -265,14 +265,17 @@ async function readStandard(ctx: RuntimeContext, format: mmCIF_Format, formatDat
 }
 
 function splitTable<T extends Table<any>>(table: T, col: Column<number>) {
-    const ret = new Map<number, T>()
+    const ret = new Map<number, { table: T, start: number, end: number }>()
     const rowCount = table._rowCount;
     let modelStart = 0;
     while (modelStart < rowCount) {
         const modelEnd = findModelEnd(col, modelStart);
         const id = col.value(modelStart);
-        const window = Table.window(table, table._schema, modelStart, modelEnd) as T;
-        ret.set(id, window);
+        ret.set(id, {
+            table: Table.window(table, table._schema, modelStart, modelEnd) as T,
+            start: modelStart,
+            end: modelEnd
+        });
         modelStart = modelEnd;
     }
     return ret;
@@ -286,8 +289,9 @@ async function readIHM(ctx: RuntimeContext, format: mmCIF_Format, formatData: Fo
         throw new Error('expected _atom_site.ihm_model_id to be defined')
     }
 
-    // TODO: will IHM require sorting or will we trust it?
     const atom_sites = splitTable(format.data.atom_site, format.data.atom_site.ihm_model_id);
+    // TODO: will coarse IHM records require sorting or will we trust it?
+    // ==> Probably implement a sort as as well and store the sourceIndex same as with atomSite
     const sphere_sites = splitTable(format.data.ihm_sphere_obj_site, format.data.ihm_sphere_obj_site.model_id);
     const gauss_sites = splitTable(format.data.ihm_gaussian_obj_site, format.data.ihm_gaussian_obj_site.model_id);
 
@@ -296,13 +300,26 @@ async function readIHM(ctx: RuntimeContext, format: mmCIF_Format, formatData: Fo
     const { model_id, model_name } = ihm_model_list;
     for (let i = 0; i < ihm_model_list._rowCount; i++) {
         const id = model_id.value(i);
+
+        let atom_site, atom_site_sourceIndex;
+        if (atom_sites.has(id)) {
+            const e = atom_sites.get(id)!;
+            const { atom_site: sorted, sourceIndex } = await sortAtomSite(ctx, e.table, e.start, e.end);
+            atom_site = sorted;
+            atom_site_sourceIndex = sourceIndex;
+        } else {
+            atom_site = Table.window(format.data.atom_site, format.data.atom_site._schema, 0, 0);
+            atom_site_sourceIndex = Column.ofIntArray([]);
+        }
+
         const data: IHMData = {
             model_id: id,
             model_name: model_name.value(i),
             entities: entities,
-            atom_site: atom_sites.has(id) ? atom_sites.get(id)! : Table.window(format.data.atom_site, format.data.atom_site._schema, 0, 0),
-            ihm_sphere_obj_site: sphere_sites.has(id) ? sphere_sites.get(id)! : Table.window(format.data.ihm_sphere_obj_site, format.data.ihm_sphere_obj_site._schema, 0, 0),
-            ihm_gaussian_obj_site: gauss_sites.has(id) ? gauss_sites.get(id)! : Table.window(format.data.ihm_gaussian_obj_site, format.data.ihm_gaussian_obj_site._schema, 0, 0)
+            atom_site,
+            atom_site_sourceIndex,
+            ihm_sphere_obj_site: sphere_sites.has(id) ? sphere_sites.get(id)!.table : Table.window(format.data.ihm_sphere_obj_site, format.data.ihm_sphere_obj_site._schema, 0, 0),
+            ihm_gaussian_obj_site: gauss_sites.has(id) ? gauss_sites.get(id)!.table : Table.window(format.data.ihm_gaussian_obj_site, format.data.ihm_gaussian_obj_site._schema, 0, 0)
         };
         const model = createModelIHM(format, data, formatData);
         attachProps(model);

src/mol-model-formats/structure/mmcif/sort.ts

@@ -9,6 +9,8 @@ import { createRangeArray, makeBuckets } from 'mol-data/util';
 import { Column, Table } from 'mol-data/db';
 import { RuntimeContext } from 'mol-task';
 
+export type SortedAtomSite = mmCIF_Database['atom_site'] & { sourceIndex: Column<number> }
+
 function isIdentity(xs: ArrayLike<number>) {
     for (let i = 0, _i = xs.length; i < _i; i++) {
         if (xs[i] !== i) return false;
@@ -36,8 +38,11 @@ export async function sortAtomSite(ctx: RuntimeContext, atom_site: mmCIF_Databas
     }
 
     if (isIdentity(indices) && indices.length === atom_site._rowCount) {
-        return atom_site;
+        return { atom_site, sourceIndex: Column.ofIntArray(indices) };
     }
 
-    return Table.view(atom_site, atom_site._schema, indices) as mmCIF_Database['atom_site'];
+    return {
+        atom_site: Table.view(atom_site, atom_site._schema, indices) as mmCIF_Database['atom_site'],
+        sourceIndex: Column.ofIntArray(indices)
+    };
 }

src/mol-model/structure/model/properties/atomic/hierarchy.ts

@@ -38,7 +38,14 @@ export const AtomsSchema = {
      * The net integer charge assigned to this atom.
      * This is the formal charge assignment normally found in chemical diagrams.
      */
-    pdbx_formal_charge: mmCIF.atom_site.pdbx_formal_charge
+    pdbx_formal_charge: mmCIF.atom_site.pdbx_formal_charge,
+
+    /**
+     * The index of this atom in the input data.
+     * Required because of sorting of atoms.
+     */
+    sourceIndex: Column.Schema.int
+
     // id, occupancy and B_iso_or_equiv are part of conformation
 };