From 6d842b96a90df1326f5feae94c061f4f2da9de2a Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Wed, 4 Oct 2017 19:28:16 -0700
Subject: [PATCH] first attempt at cif dictionary parsing
---
src/reader/cif/data-model.ts | 16 ++++++++--
src/reader/cif/text/parser.ts | 60 +++++++++++++++++------------------
src/script.ts | 40 ++++++++++++++++++++---
3 files changed, 78 insertions(+), 38 deletions(-)
diff --git a/src/reader/cif/data-model.ts b/src/reader/cif/data-model.ts
index fdc54b5f6..666bdf88c 100644
--- a/src/reader/cif/data-model.ts
+++ b/src/reader/cif/data-model.ts
@@ -17,16 +17,28 @@ export function File(blocks: ArrayLike<Block>, name?: string): File {
export interface Block {
readonly header: string,
- readonly categories: { readonly [name: string]: Category }
+ readonly categories: Categories
+ readonly saveFrames: SafeFrame[]
}
-export function Block(categories: { readonly [name: string]: Category }, header: string): Block {
+export function Block(categories: Categories, header: string, saveFrames: SafeFrame[] = []): Block {
if (Object.keys(categories).some(k => k[0] !== '_')) {
throw new Error(`Category names must start with '_'.`);
}
+ return { header, categories, saveFrames };
+}
+
+export interface SafeFrame {
+ readonly header: string,
+ readonly categories: Categories
+}
+
+export function SafeFrame(categories: Categories, header: string): SafeFrame {
return { header, categories };
}
+export type Categories = { readonly [name: string]: Category }
+
export interface Category {
readonly rowCount: number,
getField(name: string): Field | undefined
diff --git a/src/reader/cif/text/parser.ts b/src/reader/cif/text/parser.ts
index d27dcd240..3b02bd78d 100644
--- a/src/reader/cif/text/parser.ts
+++ b/src/reader/cif/text/parser.ts
@@ -551,9 +551,12 @@ async function parseInternal(data: string, ctx: Computation.Context) {
let blockHeader: string = '';
let blockCategories = Object.create(null);
- //saveFrame = new DataBlock(data, "empty"),
- //inSaveFrame = false,
- //blockSaveFrames: any;
+ let inSaveFrame = false
+
+ // the next three initial values are never used in valid files
+ let saveFrames: Data.SafeFrame[] = [];
+ let saveCategories = Object.create(null);
+ let saveFrame: Data.SafeFrame = Data.SafeFrame(saveCategories, '');
ctx.update({ message: 'Parsing...', current: 0, max: data.length });
@@ -563,63 +566,58 @@ async function parseInternal(data: string, ctx: Computation.Context) {
// Data block
if (token === CifTokenType.Data) {
- // if (inSaveFrame) {
- // return error(tokenizer.currentLineNumber, "Unexpected data block inside a save frame.");
- // }
+ if (inSaveFrame) {
+ return error(tokenizer.lineNumber, "Unexpected data block inside a save frame.");
+ }
if (Object.keys(blockCategories).length > 0) {
- dataBlocks.push(Data.Block(blockCategories, blockHeader));
+ dataBlocks.push(Data.Block(blockCategories, blockHeader, saveFrames));
}
blockHeader = data.substring(tokenizer.tokenStart + 5, tokenizer.tokenEnd);
blockCategories = Object.create(null);
+ saveFrames = []
moveNext(tokenizer);
- }
- /* // Save frame
+ // Save frame
} else if (token === CifTokenType.Save) {
- id = data.substring(tokenizer.currentTokenStart + 5, tokenizer.currentTokenEnd);
-
- if (id.length === 0) {
- if (saveFrame.categories.length > 0) {
- blockSaveFrames = blockCategories.additionalData["saveFrames"];
- if (!blockSaveFrames) {
- blockSaveFrames = [];
- blockCategories.additionalData["saveFrames"] = blockSaveFrames;
- }
- blockSaveFrames[blockSaveFrames.length] = saveFrame;
+ const saveHeader = data.substring(tokenizer.tokenStart + 5, tokenizer.tokenEnd);
+ if (saveHeader.length === 0) {
+ if (Object.keys(saveCategories).length > 0) {
+ saveFrames[saveFrames.length] = saveFrame
}
inSaveFrame = false;
} else {
if (inSaveFrame) {
- return error(tokenizer.currentLineNumber, "Save frames cannot be nested.");
+ return error(tokenizer.lineNumber, "Save frames cannot be nested.");
}
inSaveFrame = true;
- saveFrame = new DataBlock(data, id);
+ saveCategories = Object.create(null);
+ saveFrame = Data.SafeFrame(saveCategories, saveHeader);
}
moveNext(tokenizer);
- // Loop
- } */ else if (token === CifTokenType.Loop) {
- const cat = await handleLoop(tokenizer, /*inSaveFrame ? saveFrame : */ blockCategories);
+ // Loop
+ } else if (token === CifTokenType.Loop) {
+ const cat = await handleLoop(tokenizer, inSaveFrame ? saveCategories : blockCategories);
if (cat.hasError) {
return error(cat.errorLine, cat.errorMessage);
}
- // Single row
+ // Single row
} else if (token === CifTokenType.ColumnName) {
- const cat = handleSingle(tokenizer, /*inSaveFrame ? saveFrame :*/ blockCategories);
+ const cat = handleSingle(tokenizer, inSaveFrame ? saveCategories : blockCategories);
if (cat.hasError) {
return error(cat.errorLine, cat.errorMessage);
}
- // Out of options
+ // Out of options
} else {
return error(tokenizer.lineNumber, 'Unexpected token. Expected data_, loop_, or data name.');
}
}
// Check if the latest save frame was closed.
- // if (inSaveFrame) {
- // return error(tokenizer.currentLineNumber, "Unfinished save frame (`" + saveFrame.header + "`).");
- // }
+ if (inSaveFrame) {
+ return error(tokenizer.lineNumber, "Unfinished save frame (`" + saveFrame.header + "`).");
+ }
if (Object.keys(blockCategories).length > 0) {
- dataBlocks.push(Data.Block(blockCategories, blockHeader));
+ dataBlocks.push(Data.Block(blockCategories, blockHeader, saveFrames));
}
return result(Data.File(dataBlocks));
diff --git a/src/script.ts b/src/script.ts
index f4cf5a07a..724767d15 100644
--- a/src/script.ts
+++ b/src/script.ts
@@ -5,7 +5,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-// import * as util from 'util'
+import * as util from 'util'
import * as fs from 'fs'
import Gro from './reader/gro/parser'
@@ -74,7 +74,7 @@ async function runGro(input: string) {
console.log(residueNumber.length, residueNumber[0], residueNumber[residueNumber.length - 1])
}
-function _gro() {
+export function _gro() {
fs.readFile(`./examples/${file}`, 'utf8', function (err, input) {
if (err) {
return console.log(err);
@@ -83,7 +83,7 @@ function _gro() {
});
}
-_gro()
+// _gro()
async function runCIF(input: string | Uint8Array) {
console.time('parseCIF');
@@ -110,7 +110,7 @@ async function runCIF(input: string | Uint8Array) {
export function _cif() {
let path = `./examples/1cbs_updated.cif`;
- path = 'c:/test/quick/3j3q.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);
@@ -134,7 +134,37 @@ export function _cif() {
});
}
-_cif();
+// _cif();
+
+async function runDic(input: string | Uint8Array) {
+ console.time('parseDic');
+ const comp = typeof input === 'string' ? CIF.parseText(input) : CIF.parseBinary(input);
+
+ const ctx = Computation.observable({ updateRateMs: 250, observer: p => showProgress('DIC', p) });
+ const parsed = await comp(ctx);
+ console.timeEnd('parseDic');
+ if (parsed.isError) {
+ console.log(parsed);
+ return;
+ }
+
+ const data = parsed.result.blocks[0];
+ console.log(util.inspect(data.saveFrames, {showHidden: false, depth: 3}))
+}
+
+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);
+ });
+}
+
+_dic();
import Computation from './utils/computation'
const comp = Computation.create(async ctx => {
--
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