diff --git a/package.json b/package.json
index 31ad572ad994ae22ff0b852798a91c6d15b35d76..ae74e31e7843cfcee96df6862a932c6d13e567e9 100644
--- a/package.json
+++ b/package.json
@@ -13,7 +13,8 @@
"test": "./node_modules/.bin/jest",
"dist": "./node_modules/.bin/uglifyjs build/js/molio.dev.js -cm > dist/molio.js && cp build/js/molio.esm.js dist/molio.esm.js",
"script": "./node_modules/.bin/rollup build/js/src/script.js -e fs -f cjs -o build/js/script.js",
- "runscript": "npm run script && node build/js/script.js"
+ "runscript": "npm run script && node build/js/script.js",
+ "download-dics": "./node_modules/.bin/download -o build/dics http://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic && ./node_modules/.bin/download -o build/dics http://mmcif.wwpdb.org/dictionaries/ascii/mmcif_ddl.dic"
},
"jest": {
"moduleFileExtensions": [
@@ -29,7 +30,8 @@
"license": "MIT",
"devDependencies": {
"@types/jest": "^21.1.2",
- "@types/node": "^8.0.32",
+ "@types/node": "^8.0.34",
+ "download-cli": "^1.0.5",
"jest": "^21.2.1",
"rollup": "^0.50.0",
"rollup-plugin-buble": "^0.16.0",
@@ -37,10 +39,11 @@
"rollup-plugin-json": "^2.3.0",
"rollup-plugin-node-resolve": "^3.0.0",
"rollup-watch": "^4.3.1",
- "ts-jest": "^21.0.1",
+ "ts-jest": "^21.1.2",
"tslint": "^5.7.0",
"typescript": "^2.5.3",
- "uglify-js": "^3.1.3"
+ "uglify-js": "^3.1.3",
+ "util.promisify": "^1.0.0"
},
"dependencies": {}
}
diff --git a/src/reader/cif/schema/utils.ts b/src/reader/cif/schema/utils.ts
index 42093d8391390b99cc3a7f6e5efb2161dd362af1..94d68bb2c7b464432cca2c374f2655f2e8fe2df7 100644
--- a/src/reader/cif/schema/utils.ts
+++ b/src/reader/cif/schema/utils.ts
@@ -1,6 +1,6 @@
// import dic from './dic'
-import { Field, Category } from '../schema'
+import { Field, Block, Category } from '../schema'
import * as Data from '../data-model'
const pooledStr = Field.pooledStr()
@@ -8,7 +8,7 @@ const str = Field.str()
const int = Field.int()
const float = Field.float()
-function getFieldType (type: string) {
+export function getFieldType (type: string) {
switch (type) {
case 'code':
case 'ucode':
@@ -63,38 +63,102 @@ function getFieldType (type: string) {
return str
}
+type SafeFrameCategories = { [category: string]: Data.SafeFrame }
+type SafeFrameLinks = { [k: string]: string }
+
+interface SafeFrameData {
+ categories: SafeFrameCategories
+ links: SafeFrameLinks
+}
+
+// get field from given or linked category
+function getField ( category: string, field: string, d: Data.SafeFrame, ctx: SafeFrameData): Data.Field|undefined {
+ const { categories, links } = ctx
+
+ const cat = d.categories[category]
+ if (cat) {
+ return cat.getField(field)
+ } else {
+ if (d.header in links) {
+ return getField(category, field, categories[links[d.header]], ctx)
+ } else {
+ // console.log(`no links found for '${d.header}'`)
+ }
+ }
+}
+
+// function getEnums (d: Data.SafeFrame, ctx: SafeFrameData): string[]|undefined {
+// const value = getField('_item_enumeration', 'value', d, ctx)
+// if (value) {
+// const enums: string[] = []
+// for (let i = 0; i < value.rowCount; ++i) {
+// enums.push(value.str(i))
+// // console.log(value.str(i))
+// }
+// return enums
+// } else {
+// // console.log(`item_enumeration.value not found for '${d.header}'`)
+// }
+// }
+
+function getCode (d: Data.SafeFrame, ctx: SafeFrameData): string|undefined {
+ const code = getField('_item_type', 'code', d, ctx)
+ if (code) {
+ let c = code.str(0)
+ // if (c === 'ucode') {
+ // const enums = getEnums(d, ctx)
+ // if (enums) c += `: ${enums.join('|')}`
+ // }
+ return c
+ } else {
+ console.log(`item_type.code not found for '${d.header}'`)
+ }
+}
+
export function getSchema (dic: Data.Block) { // todo Block needs to be specialized with safe frames as well
- const schema: { [category: string]: Category.Schema } = {}
+ const schema: Block.Schema = {} // { [category: string]: Category.Schema } = {}
+ const categories: SafeFrameCategories = {}
+ const links: SafeFrameLinks = {}
dic.saveFrames.forEach(d => {
- if (d.header[0] !== '_') {
- schema[d.header] = {}
- } else {
- const categoryName = d.header.substring(1, d.header.indexOf('.'))
- const itemName = d.header.substring(d.header.indexOf('.') + 1)
- let fields
- if (categoryName in schema) {
- fields = schema[categoryName]
- } else {
- fields = {}
- schema[categoryName] = fields
- }
- // console.log(util.inspect(d.categories, {showHidden: false, depth: 1}))
- const item_type = d.categories['_item_type']
- if (item_type) {
- const code = item_type.getField('code')
- if (code) {
- fields[itemName] = getFieldType(code.str(0))
- } else {
- console.log(`item_type.code not found for '${d.header}'`)
+ if (d.header[0] !== '_') return
+ categories[d.header] = d
+ const item_linked = d.categories['_item_linked']
+ if (item_linked) {
+ const child_name = item_linked.getField('child_name')
+ const parent_name = item_linked.getField('parent_name')
+ if (child_name && parent_name) {
+ for (let i = 0; i < item_linked.rowCount; ++i) {
+ const childName = child_name.str(i)
+ const parentName = parent_name.str(i)
+ if (childName in links && links[childName] !== parentName) {
+ console.log(`${childName} linked to ${links[childName]}, ignoring link to ${parentName}`)
+ }
+ links[childName] = parentName
}
- } else {
- // TODO check for _item_linked.parent_name and use its type
- console.log(`item_type not found for '${d.header}'`)
}
+ }
+ })
+ Object.keys(categories).forEach(fullName => {
+ const d = categories[fullName]
+ const categoryName = d.header.substring(1, d.header.indexOf('.'))
+ const itemName = d.header.substring(d.header.indexOf('.') + 1)
+ let fields
+ if (categoryName in schema) {
+ fields = schema[categoryName]
+ } else {
+ fields = {}
+ schema[categoryName] = fields
+ }
+
+ const code = getCode(d, { categories, links })
+ if (code) {
+ fields[itemName] = getFieldType(code)
+ } else {
+ console.log(`could not determine code for '${d.header}'`)
}
})
- return schema
+ return schema as Block.Instance<any>
}
diff --git a/src/script.ts b/src/script.ts
index 06868a492c54fa9971cfd113a919448c5a9051f8..4f5615a1225f9a77ac08b37cb9e05e8c35f85840 100644
--- a/src/script.ts
+++ b/src/script.ts
@@ -8,9 +8,13 @@
import * as util from 'util'
import * as fs from 'fs'
+require('util.promisify').shim();
+const readFileAsync = util.promisify(fs.readFile);
+
import Gro from './reader/gro/parser'
import CIF from './reader/cif/index'
+import { apply as applySchema } from './reader/cif/schema'
import { getSchema } from './reader/cif/schema/utils'
const file = '1crn.gro'
@@ -76,13 +80,9 @@ async function runGro(input: string) {
console.log(residueNumber.length, residueNumber[0], residueNumber[residueNumber.length - 1])
}
-export function _gro() {
- fs.readFile(`./examples/${file}`, 'utf8', function (err, input) {
- if (err) {
- return console.log(err);
- }
- runGro(input)
- });
+export async function _gro() {
+ const input = await readFileAsync(`./examples/${file}`, 'utf8')
+ runGro(input)
}
// _gro()
@@ -108,35 +108,38 @@ async function runCIF(input: string | Uint8Array) {
console.log(mmcif.atom_site.Cartn_x.value(0));
console.log(mmcif.entity.type.toArray());
console.log(mmcif.pdbx_struct_oper_list.matrix.value(0));
+
+ const schema = await _dic()
+ if (schema) {
+ const mmcif2 = applySchema(schema, data)
+ // console.log(util.inspect(mmcif2.atom_site, {showHidden: false, depth: 3}))
+ console.log(mmcif2.atom_site.Cartn_x.value(0));
+ console.log(mmcif2.entity.type.toArray());
+ // console.log(mmcif2.pdbx_struct_oper_list.matrix.value(0)); // TODO
+ } else {
+ console.log('error getting mmcif schema from dic')
+ }
}
-export function _cif() {
+export async function _cif() {
let path = `./examples/1cbs_updated.cif`;
- path = '../test/3j3q.cif' // lets have a relative path for big test files
- fs.readFile(path, 'utf8', function (err, input) {
- if (err) {
- return console.log(err);
- }
- console.log('------------------');
- console.log('Text CIF:');
- runCIF(input);
- });
+ // path = '../test/3j3q.cif' // lets have a relative path for big test files
+ const input = await readFileAsync(path, 'utf8')
+ console.log('------------------');
+ console.log('Text CIF:');
+ runCIF(input);
path = `./examples/1cbs_full.bcif`;
// const path = 'c:/test/quick/3j3q.cif';
- fs.readFile(path, function (err, input) {
- if (err) {
- return console.log(err);
- }
- console.log('------------------');
- console.log('BinaryCIF:');
- const data = new Uint8Array(input.byteLength);
- for (let i = 0; i < input.byteLength; i++) data[i] = input[i];
- runCIF(input);
- });
+ const input2 = await readFileAsync(path)
+ console.log('------------------');
+ console.log('BinaryCIF:');
+ const data = new Uint8Array(input2.byteLength);
+ for (let i = 0; i < input2.byteLength; i++) data[i] = input2[i];
+ runCIF(input2);
}
-// _cif();
+_cif();
async function runDic(input: string | Uint8Array) {
console.time('parseDic');
@@ -151,23 +154,21 @@ async function runDic(input: string | Uint8Array) {
}
const schema = getSchema(parsed.result.blocks[0])
- // console.log(util.inspect(schema, {showHidden: false, depth: 1}))
- console.log(util.inspect(Object.keys(schema).length, {showHidden: false, depth: 1}))
+ console.log(util.inspect(schema, {showHidden: false, depth: 3}))
+ // console.log(util.inspect(Object.keys(schema).length, {showHidden: false, depth: 1}))
+
+ return schema
}
-export function _dic() {
- let path = '../test/mmcif_pdbx_v50.dic'
- fs.readFile(path, 'utf8', function (err, input) {
- if (err) {
- return console.log(err);
- }
- console.log('------------------');
- console.log('Text DIC:');
- runDic(input);
- });
+export async function _dic() {
+ let path = './build/dics/mmcif_pdbx_v50.dic'
+ const input = await readFileAsync(path, 'utf8')
+ console.log('------------------');
+ console.log('Text DIC:');
+ return runDic(input);
}
-_dic();
+// _dic();
import Computation from './utils/computation'
const comp = Computation.create(async ctx => {