domain annotation server (prototype)

package-lock.json

@@ -1,5 +1,5 @@
 {
-  "name": "molio",
+  "name": "mol-star",
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@@ -182,6 +246,11 @@
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+      "integrity": "sha1-DPaLud318r55YcOoUXjLhdunjLQ="
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@@ -864,6 +966,16 @@
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@@ -1098,6 +1209,16 @@
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@@ -1158,6 +1279,24 @@
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@@ -1316,6 +1465,43 @@
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+      "resolved": "https://registry.npmjs.org/node-fetch/-/node-fetch-1.7.3.tgz",
+      "integrity": "sha512-NhZ4CsKx7cYm2vSrBAr2PvFOe6sWDf0UYLRqA6svUYg7+/TSfVAu49jYC4BvQ4Sms9SZgdqGBgroqfDhJdTyKQ==",
+      "requires": {
+        "encoding": "0.1.12",
+        "is-stream": "1.1.0"
+      }
+    },
     "node-int64": {
       "version": "0.4.0",
       "resolved": "https://registry.npmjs.org/node-int64/-/node-int64-0.4.0.tgz",
@@ -2991,6 +3252,14 @@
         "is-extendable": "0.1.1"
       }
     },
+    "on-finished": {
+      "version": "2.3.0",
+      "resolved": "https://registry.npmjs.org/on-finished/-/on-finished-2.3.0.tgz",
+      "integrity": "sha1-IPEzZIGwg811M3mSoWlxqi2QaUc=",
+      "requires": {
+        "ee-first": "1.1.1"
+      }
+    },
     "once": {
       "version": "1.4.0",
       "resolved": "https://registry.npmjs.org/once/-/once-1.4.0.tgz",
@@ -3127,6 +3396,11 @@
       "integrity": "sha1-m387DeMr543CQBsXVzzK8Pb1nZQ=",
       "dev": true
     },
+    "parseurl": {
+      "version": "1.3.2",
+      "resolved": "https://registry.npmjs.org/parseurl/-/parseurl-1.3.2.tgz",
+      "integrity": "sha1-/CidTtiZMRlGDBViUyYs3I3mW/M="
+    },
     "path-exists": {
       "version": "3.0.0",
       "resolved": "https://registry.npmjs.org/path-exists/-/path-exists-3.0.0.tgz",
@@ -3151,6 +3425,11 @@
       "integrity": "sha1-PBrfhx6pzWyUMbbqK9dKD/BVxME=",
       "dev": true
     },
+    "path-to-regexp": {
+      "version": "0.1.7",
+      "resolved": "https://registry.npmjs.org/path-to-regexp/-/path-to-regexp-0.1.7.tgz",
+      "integrity": "sha1-32BBeABfUi8V60SQ5yR6G/qmf4w="
+    },
     "path-type": {
       "version": "1.1.0",
       "resolved": "https://registry.npmjs.org/path-type/-/path-type-1.1.0.tgz",
@@ -3272,6 +3551,15 @@
       "integrity": "sha1-IS1b/hMYMGpCD2QCuOJv85ZHqEk=",
       "dev": true
     },
+    "proxy-addr": {
+      "version": "2.0.2",
+      "resolved": "https://registry.npmjs.org/proxy-addr/-/proxy-addr-2.0.2.tgz",
+      "integrity": "sha1-ZXFQT0e7mI7IGAJT+F3X4UlSvew=",
+      "requires": {
+        "forwarded": "0.1.2",
+        "ipaddr.js": "1.5.2"
+      }
+    },
     "prr": {
       "version": "0.0.0",
       "resolved": "https://registry.npmjs.org/prr/-/prr-0.0.0.tgz",
@@ -3293,8 +3581,7 @@
     "qs": {
       "version": "6.5.1",
       "resolved": "https://registry.npmjs.org/qs/-/qs-6.5.1.tgz",
-      "integrity": "sha512-eRzhrN1WSINYCDCbrz796z37LOe3m5tmW7RQf6oBntukAG1nmovJvhnwHHRMAfeoItc1m2Hk02WER2aQ/iqs+A==",
-      "dev": true
+      "integrity": "sha512-eRzhrN1WSINYCDCbrz796z37LOe3m5tmW7RQf6oBntukAG1nmovJvhnwHHRMAfeoItc1m2Hk02WER2aQ/iqs+A=="
     },
     "randomatic": {
       "version": "1.1.7",
@@ -3337,6 +3624,29 @@
         }
       }
     },
+    "range-parser": {
+      "version": "1.2.0",
+      "resolved": "https://registry.npmjs.org/range-parser/-/range-parser-1.2.0.tgz",
+      "integrity": "sha1-9JvmtIeJTdxA3MlKMi9hEJLgDV4="
+    },
+    "raw-body": {
+      "version": "2.3.2",
+      "resolved": "https://registry.npmjs.org/raw-body/-/raw-body-2.3.2.tgz",
+      "integrity": "sha1-vNYMd9Prk83gBQKVw/N5OJvIj4k=",
+      "requires": {
+        "bytes": "3.0.0",
+        "http-errors": "1.6.2",
+        "iconv-lite": "0.4.19",
+        "unpipe": "1.0.0"
+      },
+      "dependencies": {
+        "iconv-lite": {
+          "version": "0.4.19",
+          "resolved": "https://registry.npmjs.org/iconv-lite/-/iconv-lite-0.4.19.tgz",
+          "integrity": "sha512-oTZqweIP51xaGPI4uPa56/Pri/480R+mo7SeU+YETByQNhDG55ycFyNLIgta9vXhILrxXDmF7ZGhqZIcuN0gJQ=="
+        }
+      }
+    },
     "read-pkg": {
       "version": "1.1.0",
       "resolved": "https://registry.npmjs.org/read-pkg/-/read-pkg-1.1.0.tgz",
@@ -3637,8 +3947,7 @@
     "safe-buffer": {
       "version": "5.1.1",
       "resolved": "https://registry.npmjs.org/safe-buffer/-/safe-buffer-5.1.1.tgz",
-      "integrity": "sha512-kKvNJn6Mm93gAczWVJg7wH+wGYWNrDHdWvpUmHyEsgCtIwwo3bqPtV4tR5tuPaUhTOo/kvhVwd8XwwOllGYkbg==",
-      "dev": true
+      "integrity": "sha512-kKvNJn6Mm93gAczWVJg7wH+wGYWNrDHdWvpUmHyEsgCtIwwo3bqPtV4tR5tuPaUhTOo/kvhVwd8XwwOllGYkbg=="
     },
     "sane": {
       "version": "2.0.0",
@@ -3695,6 +4004,37 @@
       "integrity": "sha512-WfG/X9+oATh81XtllIo/I8gOiY9EXRdv1cQdyykeXK17YcUW3EXUAi2To4pcH6nZtJPr7ZOpM5OMyWJZm+8Rsg==",
       "dev": true
     },
+    "send": {
+      "version": "0.16.1",
+      "resolved": "https://registry.npmjs.org/send/-/send-0.16.1.tgz",
+      "integrity": "sha512-ElCLJdJIKPk6ux/Hocwhk7NFHpI3pVm/IZOYWqUmoxcgeyM+MpxHHKhb8QmlJDX1pU6WrgaHBkVNm73Sv7uc2A==",
+      "requires": {
+        "debug": "2.6.9",
+        "depd": "1.1.1",
+        "destroy": "1.0.4",
+        "encodeurl": "1.0.1",
+        "escape-html": "1.0.3",
+        "etag": "1.8.1",
+        "fresh": "0.5.2",
+        "http-errors": "1.6.2",
+        "mime": "1.4.1",
+        "ms": "2.0.0",
+        "on-finished": "2.3.0",
+        "range-parser": "1.2.0",
+        "statuses": "1.3.1"
+      }
+    },
+    "serve-static": {
+      "version": "1.13.1",
+      "resolved": "https://registry.npmjs.org/serve-static/-/serve-static-1.13.1.tgz",
+      "integrity": "sha512-hSMUZrsPa/I09VYFJwa627JJkNs0NrfL1Uzuup+GqHfToR2KcsXFymXSV90hoyw3M+msjFuQly+YzIH/q0MGlQ==",
+      "requires": {
+        "encodeurl": "1.0.1",
+        "escape-html": "1.0.3",
+        "parseurl": "1.3.2",
+        "send": "0.16.1"
+      }
+    },
     "set-blocking": {
       "version": "2.0.0",
       "resolved": "https://registry.npmjs.org/set-blocking/-/set-blocking-2.0.0.tgz",
@@ -3707,6 +4047,11 @@
       "integrity": "sha1-SysbJ+uAip+NzEgaWOXlb1mfP2E=",
       "dev": true
     },
+    "setprototypeof": {
+      "version": "1.1.0",
+      "resolved": "https://registry.npmjs.org/setprototypeof/-/setprototypeof-1.1.0.tgz",
+      "integrity": "sha512-BvE/TwpZX4FXExxOxZyRGQQv651MSwmWKZGqvmPcRIjDqWub67kTKuIMx43cZZrS/cBBzwBcNDWoFxt2XEFIpQ=="
+    },
     "shebang-command": {
       "version": "1.2.0",
       "resolved": "https://registry.npmjs.org/shebang-command/-/shebang-command-1.2.0.tgz",
@@ -3825,6 +4170,11 @@
         "tweetnacl": "0.14.5"
       }
     },
+    "statuses": {
+      "version": "1.3.1",
+      "resolved": "https://registry.npmjs.org/statuses/-/statuses-1.3.1.tgz",
+      "integrity": "sha1-+vUbnrdKrvOzrPStX2Gr8ky3uT4="
+    },
     "string_decoder": {
       "version": "1.0.3",
       "resolved": "https://registry.npmjs.org/string_decoder/-/string_decoder-1.0.3.tgz",
@@ -4155,32 +4505,32 @@
         "diff": "3.3.1",
         "glob": "7.1.2",
         "minimatch": "3.0.4",
-        "resolve": "1.4.0",
+        "resolve": "1.5.0",
         "semver": "5.4.1",
         "tslib": "1.7.1",
-        "tsutils": "2.12.1"
+        "tsutils": "2.12.2"
       },
       "dependencies": {
         "resolve": {
-          "version": "1.4.0",
-          "resolved": "https://registry.npmjs.org/resolve/-/resolve-1.4.0.tgz",
-          "integrity": "sha512-aW7sVKPufyHqOmyyLzg/J+8606v5nevBgaliIlV7nUpVMsDnoBGV/cbSLNjZAg9q0Cfd/+easKVKQ8vOu8fn1Q==",
+          "version": "1.5.0",
+          "resolved": "https://registry.npmjs.org/resolve/-/resolve-1.5.0.tgz",
+          "integrity": "sha512-hgoSGrc3pjzAPHNBg+KnFcK2HwlHTs/YrAGUr6qgTVUZmXv1UEXXl0bZNBKMA9fud6lRYFdPGz0xXxycPzmmiw==",
           "dev": true,
           "requires": {
             "path-parse": "1.0.5"
           }
-        },
-        "tsutils": {
-          "version": "2.12.1",
-          "resolved": "https://registry.npmjs.org/tsutils/-/tsutils-2.12.1.tgz",
-          "integrity": "sha1-9Nlc4zkciXHkblTEzw7bCiHdWyQ=",
-          "dev": true,
-          "requires": {
-            "tslib": "1.7.1"
-          }
         }
       }
     },
+    "tsutils": {
+      "version": "2.12.2",
+      "resolved": "https://registry.npmjs.org/tsutils/-/tsutils-2.12.2.tgz",
+      "integrity": "sha1-rVikhl0X7D3bZjG2ylO+FKVlb/M=",
+      "dev": true,
+      "requires": {
+        "tslib": "1.7.1"
+      }
+    },
     "tunnel-agent": {
       "version": "0.6.0",
       "resolved": "https://registry.npmjs.org/tunnel-agent/-/tunnel-agent-0.6.0.tgz",
@@ -4206,6 +4556,15 @@
         "prelude-ls": "1.1.2"
       }
     },
+    "type-is": {
+      "version": "1.6.15",
+      "resolved": "https://registry.npmjs.org/type-is/-/type-is-1.6.15.tgz",
+      "integrity": "sha1-yrEPtJCeRByChC6v4a1kbIGARBA=",
+      "requires": {
+        "media-typer": "0.3.0",
+        "mime-types": "2.1.17"
+      }
+    },
     "typescript": {
       "version": "2.6.1",
       "resolved": "https://registry.npmjs.org/typescript/-/typescript-2.6.1.tgz",
@@ -4213,9 +4572,9 @@
       "dev": true
     },
     "uglify-js": {
-      "version": "3.1.6",
-      "resolved": "https://registry.npmjs.org/uglify-js/-/uglify-js-3.1.6.tgz",
-      "integrity": "sha512-/rseyxEKEVMBo8279lqpoJgD6C/i/CIi+9TJDvWmb+Xo6mqMKwjA8Io3IMHlcXQzj99feR6zrN8m3wqqvm/nYA==",
+      "version": "3.1.7",
+      "resolved": "https://registry.npmjs.org/uglify-js/-/uglify-js-3.1.7.tgz",
+      "integrity": "sha512-ZRs/A6LJhLac7SN3Hv22LXEtndFliqTkfTilYSx84cxHXoC2bbhdSOsUZqRvfwEAjlIE4AK8pLd47+RxINCTjg==",
       "dev": true,
       "requires": {
         "commander": "2.11.0",
@@ -4253,6 +4612,11 @@
       "integrity": "sha1-+nG63UQ3r0wUiEHjs7Fl+enlkLc=",
       "dev": true
     },
+    "unpipe": {
+      "version": "1.0.0",
+      "resolved": "https://registry.npmjs.org/unpipe/-/unpipe-1.0.0.tgz",
+      "integrity": "sha1-sr9O6FFKrmFltIF4KdIbLvSZBOw="
+    },
     "url-parse-lax": {
       "version": "1.0.0",
       "resolved": "https://registry.npmjs.org/url-parse-lax/-/url-parse-lax-1.0.0.tgz",
@@ -4284,6 +4648,11 @@
         "object.getownpropertydescriptors": "2.0.3"
       }
     },
+    "utils-merge": {
+      "version": "1.0.1",
+      "resolved": "https://registry.npmjs.org/utils-merge/-/utils-merge-1.0.1.tgz",
+      "integrity": "sha1-n5VxD1CiZ5R7LMwSR0HBAoQn5xM="
+    },
     "uuid": {
       "version": "3.1.0",
       "resolved": "https://registry.npmjs.org/uuid/-/uuid-3.1.0.tgz",
@@ -4300,6 +4669,11 @@
         "spdx-expression-parse": "1.0.4"
       }
     },
+    "vary": {
+      "version": "1.1.2",
+      "resolved": "https://registry.npmjs.org/vary/-/vary-1.1.2.tgz",
+      "integrity": "sha1-IpnwLG3tMNSllhsLn3RSShj2NPw="
+    },
     "verror": {
       "version": "1.10.0",
       "resolved": "https://registry.npmjs.org/verror/-/verror-1.10.0.tgz",

package.json

@@ -24,15 +24,20 @@
     "transform": {
       "\\.ts$": "<rootDir>/node_modules/ts-jest/preprocessor.js"
     },
-    "moduleDirectories": ["node_modules", "build/node_modules"], 
+    "moduleDirectories": [
+      "node_modules",
+      "build/node_modules"
+    ],
     "testRegex": "\\.spec\\.ts$"
   },
   "author": "",
   "license": "MIT",
   "devDependencies": {
     "@types/benchmark": "^1.0.30",
+    "@types/express": "^4.0.39",
     "@types/jest": "^21.1.5",
     "@types/node": "^8.0.47",
+    "@types/node-fetch": "^1.6.7",
     "benchmark": "^2.1.4",
     "download-cli": "^1.0.5",
     "jest": "^21.2.1",
@@ -45,8 +50,11 @@
     "ts-jest": "^21.1.4",
     "tslint": "^5.8.0",
     "typescript": "^2.6.1",
-    "uglify-js": "^3.1.6",
+    "uglify-js": "^3.1.7",
     "util.promisify": "^1.0.0"
   },
-  "dependencies": {}
+  "dependencies": {
+    "express": "^4.16.2",
+    "node-fetch": "^1.7.3"
+  }
 }

src/apps/domain-annotation-server/mapping.ts

@@ -0,0 +1,102 @@
+/**
+ * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { Table } from 'mol-base/collections/database'
+import { CIFEncoder, create as createEncoder } from 'mol-io/writer/cif'
+import * as S from './schemas'
+import { getCategoryInstanceProvider } from './utils'
+
+export default function create(allData: any) {
+    const mols = Object.keys(allData);
+    if (!mols.length) return '#';
+
+    const data = allData[mols[0]];
+
+    const enc = createEncoder();
+    enc.startDataBlock(mols[0]);
+
+    for (const cat of Object.keys(S.categories)) {
+        writeDomain(enc, getDomain(cat, (S.categories as any)[cat], data));
+    }
+    return enc.getData();
+}
+
+interface DomainAnnotation {
+    name: string,
+    domains: Table<any>,
+    mappings: Table<S.mapping>
+}
+type MappingRow = Table.Row<S.mapping>;
+
+function writeDomain(enc: CIFEncoder<any>, domain: DomainAnnotation | undefined) {
+    if (!domain) return;
+    enc.writeCategory(getCategoryInstanceProvider(`pdbx_${domain.name}_domain_annotation`, domain.domains));
+    enc.writeCategory(getCategoryInstanceProvider(`pdbx_${domain.name}_domain_mapping`, domain.mappings));
+}
+
+function getMappings(startId: number, group_id: number, mappings: any): MappingRow[] {
+    const rows: MappingRow[] = [];
+
+    const n = (v: any) => v === null ? void 0 : v;
+
+    for (const entry of mappings) {
+        if (entry.start && entry.end) {
+            rows.push({
+                id: startId++,
+                group_id,
+                label_entity_id: '' + entry.entity_id,
+                label_asym_id: entry.struct_asym_id,
+                auth_asym_id: entry.chain_id,
+                beg_label_seq_id: n(entry.start.residue_number),
+                beg_auth_seq_id: n(entry.start.author_residue_number),
+                pdbx_beg_PDB_ins_code: entry.start.author_insertion_code,
+                end_label_seq_id: n(entry.end.residue_number),
+                end_auth_seq_id: n(entry.end.author_residue_number),
+                pdbx_end_PDB_ins_code: entry.end.author_insertion_code
+            });
+        } else {
+            rows.push({
+                id: startId++,
+                group_id,
+                label_entity_id: '' + entry.entity_id,
+                label_asym_id: entry.struct_asym_id,
+                auth_asym_id: entry.chain_id
+            } as any);
+        }
+    }
+    return rows;
+}
+
+function getDomainInfo(id: string, mapping_group_id: number, data: any, schema: any) {
+    const props = Object.create(null);
+    for (const k of Object.keys(schema)) props[k] = data[k];
+    return { id, mapping_group_id, identifier: data.identifier, ...props };
+}
+
+function getDomain(name: string, schema: any, allData: any) {
+    if (!allData[name]) return void 0;
+
+    const data = allData[name];
+
+    const domains: any[] = [];
+    const mappings: MappingRow[] = [];
+
+    let mappingSerialId = 1, mapping_group_id = 1;
+
+    for (const id of Object.keys(data)) {
+        const domain = data[id];
+        domains.push(getDomainInfo(id, mapping_group_id, domain, schema));
+        mappings.push(...getMappings(mappingSerialId, mapping_group_id, domain.mappings));
+        mappingSerialId = mappings.length + 1;
+        mapping_group_id++;
+    }
+
+    return domains.length > 0 ? {
+        name,
+        domains: Table.ofRows({ ...S.Base, ...schema }, domains),
+        mappings: Table.ofRows(S.mapping, mappings)
+    } : void 0;
+}

src/apps/domain-annotation-server/schemas.ts

@@ -0,0 +1,89 @@
+/**
+ * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { Column } from 'mol-base/collections/database'
+
+import Type = Column.Type
+
+export const Base = {
+    id: Type.str,
+    identifier: Type.str,
+    mapping_group_id: Type.int
+}
+export type Base = typeof Base
+
+export const mapping = {
+    id: Type.int,
+    group_id: Type.int,
+
+    label_entity_id: Type.str,
+    label_asym_id: Type.str,
+    auth_asym_id: Type.str,
+
+    beg_label_seq_id: Type.int,
+    beg_auth_seq_id: Type.int,
+    pdbx_beg_PDB_ins_code: Type.str,
+
+    end_label_seq_id: Type.int,
+    end_auth_seq_id: Type.int,
+    pdbx_end_PDB_ins_code: Type.str
+}
+export type mapping = typeof mapping
+
+export const Pfam = {
+    description: Type.str
+}
+export type Pfam = typeof Pfam
+
+export const InterPro = {
+    name: Type.str
+}
+export type InterPro = typeof InterPro
+
+export const CATH = {
+    name: Type.str,
+    homology: Type.str,
+    architecture: Type.str,
+    identifier: Type.str,
+    class: Type.str,
+    topology: Type.str,
+}
+export type CATH = typeof CATH
+
+export const EC = {
+    accepted_name: Type.str,
+    reaction: Type.str,
+    systematic_name: Type.str
+}
+export type EC = typeof EC
+
+export const UniProt = {
+    name: Type.str
+}
+export type UniProt = typeof UniProt
+
+export const SCOP = {
+    sccs: Type.str,
+    description: Type.str
+}
+export type SCOP = typeof SCOP
+
+export const GO = {
+    category: Type.str,
+    definition: Type.str,
+    name: Type.str
+}
+export type GO = typeof GO
+
+export const categories = {
+    Pfam,
+    InterPro,
+    CATH,
+    EC,
+    UniProt,
+    SCOP,
+    GO
+}

src/apps/domain-annotation-server/server.ts

@@ -0,0 +1,48 @@
+/**
+ * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import * as express from 'express'
+import fetch from 'node-fetch'
+import createMapping from './mapping'
+
+async function getMappings(id: string) {
+    const data = await fetch(`https://www.ebi.ac.uk/pdbe/api/mappings/${id}`);
+    const json = await data.json();
+    return createMapping(json);
+};
+
+
+let PORT = process.env.port || 1338;
+
+const app = express();
+
+const PREFIX = '/'
+
+app.get(`${PREFIX}/:id`, async (req, res) => {
+    try {
+        console.log('Requesting ' + req.params.id);
+        const mapping = await getMappings(req.params.id);
+        res.writeHead(200, {
+            'Content-Type': 'text/plain; charset=utf-8',
+            'Access-Control-Allow-Origin': '*',
+            'Access-Control-Allow-Headers': 'X-Requested-With'
+        });
+        res.end(mapping);
+    } catch {
+        console.log('Failed ' + req.params.id);
+        res.writeHead(404, { 'Access-Control-Allow-Origin': '*', 'Access-Control-Allow-Headers': 'X-Requested-With' });
+        res.end();
+    }
+});
+
+app.get(`${PREFIX}`, (req, res) => {
+    res.writeHead(200, { 'Content-Type': 'text/plain; charset=utf-8' });
+    res.end('Usage: /pdb_id, e.g. /1tqn');
+})
+
+app.listen(PORT);
+
+console.log('Running on port ' + PORT);

src/apps/domain-annotation-server/test.ts

@@ -0,0 +1,14 @@
+/**
+ * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import fetch from 'node-fetch'
+import createMapping from './mapping'
+
+(async function () {
+    const data = await fetch('https://www.ebi.ac.uk/pdbe/api/mappings/1tqn?pretty=true');
+    const json = await data.json();
+    console.log(createMapping(json));
+}());

src/apps/domain-annotation-server/utils.ts

@@ -0,0 +1,43 @@
+/**
+ * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { Table } from 'mol-base/collections/database'
+import Iterator from 'mol-base/collections/iterator'
+import * as Encoder from 'mol-io/writer/cif'
+
+function columnValue(k: string) {
+    return (i: number, d: any) => d[k].value(i);
+}
+
+function columnValueKind(k: string) {
+    return (i: number, d: any) => d[k].valueKind(i);
+}
+
+function ofSchema(schema: Table.Schema) {
+    const fields: Encoder.FieldDefinition[] = [];
+    for (const k of Object.keys(schema)) {
+        const t = schema[k];
+        // TODO: matrix/vector/support
+        const type = t.kind === 'str' ? Encoder.FieldType.Str : t.kind === 'int' ? Encoder.FieldType.Int : Encoder.FieldType.Float;
+        fields.push({ name: k, type, value: columnValue(k), valueKind: columnValueKind(k) })
+    }
+    return fields;
+}
+
+function ofTable<S extends Table.Schema>(name: string, table: Table<S>): Encoder.CategoryDefinition<number> {
+    return { name, fields: ofSchema(table._schema) }
+}
+
+export function getCategoryInstanceProvider(name: string, table: Table<any>): Encoder.CategoryProvider {
+    return () => {
+        return {
+            data: table,
+            definition: ofTable(name, table),
+            keys: () => Iterator.Range(0, table._rowCount - 1),
+            rowCount: table._rowCount
+        };
+    }
+}

src/mol-io/writer/cif/encoder.ts

@@ -57,7 +57,7 @@ export interface CategoryProvider {
     (ctx: any): CategoryInstance
 }
 
-export interface CIFEncoder<T, Context> extends Encoder<T> {
+export interface CIFEncoder<T = string | Uint8Array, Context = any> extends Encoder<T> {
     startDataBlock(header: string): void,
     writeCategory(category: CategoryProvider, contexts?: Context[]): void,
     getData(): T