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Commit 01071bcf authored by David Sehnal's avatar David Sehnal
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Merge branch 'master' into structure-data-model

parents 1575e514 df27c595
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package.json
+ 7
− 4
View file @ 01071bcf
...@@ -13,7 +13,8 @@ ...@@ -13,7 +13,8 @@
"test": "./node_modules/.bin/jest", "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", "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", "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": { "jest": {
"moduleFileExtensions": [ "moduleFileExtensions": [
...@@ -29,7 +30,8 @@ ...@@ -29,7 +30,8 @@
"license": "MIT", "license": "MIT",
"devDependencies": { "devDependencies": {
"@types/jest": "^21.1.2", "@types/jest": "^21.1.2",
"@types/node": "^8.0.32", "@types/node": "^8.0.34",
"download-cli": "^1.0.5",
"jest": "^21.2.1", "jest": "^21.2.1",
"rollup": "^0.50.0", "rollup": "^0.50.0",
"rollup-plugin-buble": "^0.16.0", "rollup-plugin-buble": "^0.16.0",
...@@ -37,10 +39,11 @@ ...@@ -37,10 +39,11 @@
"rollup-plugin-json": "^2.3.0", "rollup-plugin-json": "^2.3.0",
"rollup-plugin-node-resolve": "^3.0.0", "rollup-plugin-node-resolve": "^3.0.0",
"rollup-watch": "^4.3.1", "rollup-watch": "^4.3.1",
"ts-jest": "^21.0.1", "ts-jest": "^21.1.2",
"tslint": "^5.7.0", "tslint": "^5.7.0",
"typescript": "^2.5.3", "typescript": "^2.5.3",
"uglify-js": "^3.1.3" "uglify-js": "^3.1.3",
"util.promisify": "^1.0.0"
}, },
"dependencies": {} "dependencies": {}
} }
src/reader/cif/schema/utils.ts
+ 91
− 27
View file @ 01071bcf
// import dic from './dic' // import dic from './dic'
import { Field, Category } from '../schema' import { Field, Block, Category } from '../schema'
import * as Data from '../data-model' import * as Data from '../data-model'
const pooledStr = Field.pooledStr() const pooledStr = Field.pooledStr()
...@@ -8,7 +8,7 @@ const str = Field.str() ...@@ -8,7 +8,7 @@ const str = Field.str()
const int = Field.int() const int = Field.int()
const float = Field.float() const float = Field.float()
function getFieldType (type: string) { export function getFieldType (type: string) {
switch (type) { switch (type) {
case 'code': case 'code':
case 'ucode': case 'ucode':
...@@ -63,38 +63,102 @@ function getFieldType (type: string) { ...@@ -63,38 +63,102 @@ function getFieldType (type: string) {
return str 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 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 => { dic.saveFrames.forEach(d => {
if (d.header[0] !== '_') { if (d.header[0] !== '_') return
schema[d.header] = {} categories[d.header] = d
} else { const item_linked = d.categories['_item_linked']
const categoryName = d.header.substring(1, d.header.indexOf('.')) if (item_linked) {
const itemName = d.header.substring(d.header.indexOf('.') + 1) const child_name = item_linked.getField('child_name')
let fields const parent_name = item_linked.getField('parent_name')
if (categoryName in schema) { if (child_name && parent_name) {
fields = schema[categoryName] for (let i = 0; i < item_linked.rowCount; ++i) {
} else { const childName = child_name.str(i)
fields = {} const parentName = parent_name.str(i)
schema[categoryName] = fields if (childName in links && links[childName] !== parentName) {
} console.log(`${childName} linked to ${links[childName]}, ignoring link to ${parentName}`)
// console.log(util.inspect(d.categories, {showHidden: false, depth: 1})) }
const item_type = d.categories['_item_type'] links[childName] = parentName
if (item_type) {
const code = item_type.getField('code')
if (code) {
fields[itemName] = getFieldType(code.str(0))
} else {
console.log(`item_type.code not found for '${d.header}'`)
} }
} 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>
} }
src/script.ts
+ 42
− 41
View file @ 01071bcf
...@@ -8,9 +8,13 @@ ...@@ -8,9 +8,13 @@
import * as util from 'util' import * as util from 'util'
import * as fs from 'fs' import * as fs from 'fs'
require('util.promisify').shim();
const readFileAsync = util.promisify(fs.readFile);
import Gro from './reader/gro/parser' import Gro from './reader/gro/parser'
import CIF from './reader/cif/index' import CIF from './reader/cif/index'
import { apply as applySchema } from './reader/cif/schema'
import { getSchema } from './reader/cif/schema/utils' import { getSchema } from './reader/cif/schema/utils'
const file = '1crn.gro' const file = '1crn.gro'
...@@ -76,13 +80,9 @@ async function runGro(input: string) { ...@@ -76,13 +80,9 @@ async function runGro(input: string) {
console.log(residueNumber.length, residueNumber[0], residueNumber[residueNumber.length - 1]) console.log(residueNumber.length, residueNumber[0], residueNumber[residueNumber.length - 1])
} }
export function _gro() { export async function _gro() {
fs.readFile(`./examples/${file}`, 'utf8', function (err, input) { const input = await readFileAsync(`./examples/${file}`, 'utf8')
if (err) { runGro(input)
return console.log(err);
}
runGro(input)
});
} }
// _gro() // _gro()
...@@ -108,35 +108,38 @@ async function runCIF(input: string | Uint8Array) { ...@@ -108,35 +108,38 @@ async function runCIF(input: string | Uint8Array) {
console.log(mmcif.atom_site.Cartn_x.value(0)); console.log(mmcif.atom_site.Cartn_x.value(0));
console.log(mmcif.entity.type.toArray()); console.log(mmcif.entity.type.toArray());
console.log(mmcif.pdbx_struct_oper_list.matrix.value(0)); 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`; let path = `./examples/1cbs_updated.cif`;
path = '../test/3j3q.cif' // lets have a relative path for big test files // path = '../test/3j3q.cif' // lets have a relative path for big test files
fs.readFile(path, 'utf8', function (err, input) { const input = await readFileAsync(path, 'utf8')
if (err) { console.log('------------------');
return console.log(err); console.log('Text CIF:');
} runCIF(input);
console.log('------------------');
console.log('Text CIF:');
runCIF(input);
});
path = `./examples/1cbs_full.bcif`; path = `./examples/1cbs_full.bcif`;
// const path = 'c:/test/quick/3j3q.cif'; // const path = 'c:/test/quick/3j3q.cif';
fs.readFile(path, function (err, input) { const input2 = await readFileAsync(path)
if (err) { console.log('------------------');
return console.log(err); console.log('BinaryCIF:');
} const data = new Uint8Array(input2.byteLength);
console.log('------------------'); for (let i = 0; i < input2.byteLength; i++) data[i] = input2[i];
console.log('BinaryCIF:'); runCIF(input2);
const data = new Uint8Array(input.byteLength);
for (let i = 0; i < input.byteLength; i++) data[i] = input[i];
runCIF(input);
});
} }
// _cif(); _cif();
async function runDic(input: string | Uint8Array) { async function runDic(input: string | Uint8Array) {
console.time('parseDic'); console.time('parseDic');
...@@ -151,23 +154,21 @@ async function runDic(input: string | Uint8Array) { ...@@ -151,23 +154,21 @@ async function runDic(input: string | Uint8Array) {
} }
const schema = getSchema(parsed.result.blocks[0]) const schema = getSchema(parsed.result.blocks[0])
// console.log(util.inspect(schema, {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})) // console.log(util.inspect(Object.keys(schema).length, {showHidden: false, depth: 1}))
return schema
} }
export function _dic() { export async function _dic() {
let path = '../test/mmcif_pdbx_v50.dic' let path = './build/dics/mmcif_pdbx_v50.dic'
fs.readFile(path, 'utf8', function (err, input) { const input = await readFileAsync(path, 'utf8')
if (err) { console.log('------------------');
return console.log(err); console.log('Text DIC:');
} return runDic(input);
console.log('------------------');
console.log('Text DIC:');
runDic(input);
});
} }
_dic(); // _dic();
import Computation from './utils/computation' import Computation from './utils/computation'
const comp = Computation.create(async ctx => { const comp = Computation.create(async ctx => {
......
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