From 34fb6a810445f8f94dbab7615e6ef57201b41f0d Mon Sep 17 00:00:00 2001
From: David Sehnal <david.sehnal@gmail.com>
Date: Wed, 13 Feb 2019 17:04:11 +0100
Subject: [PATCH] wip PDB parser
---
src/mol-io/reader/ccp4/parser.ts | 2 +-
src/mol-io/reader/cif/binary/parser.ts | 2 +-
src/mol-io/reader/cif/text/parser.ts | 2 +-
src/mol-io/reader/common/text/tokenizer.ts | 12 ++++----
src/mol-io/reader/csv/parser.ts | 2 +-
src/mol-io/reader/dsn6/parser.ts | 2 +-
src/mol-io/reader/gro/parser.ts | 4 +--
src/mol-io/reader/mol2/parser.ts | 2 +-
src/mol-io/reader/obj/parser.ts | 2 +-
src/mol-io/reader/pdb/parser.ts | 14 +++++++++
src/mol-io/reader/pdb/schema.ts | 11 +++++++
src/mol-io/reader/result.ts | 34 +++++++++++-----------
12 files changed, 57 insertions(+), 32 deletions(-)
create mode 100644 src/mol-io/reader/pdb/parser.ts
create mode 100644 src/mol-io/reader/pdb/schema.ts
diff --git a/src/mol-io/reader/ccp4/parser.ts b/src/mol-io/reader/ccp4/parser.ts
index 43cc24a83..d48c343e5 100644
--- a/src/mol-io/reader/ccp4/parser.ts
+++ b/src/mol-io/reader/ccp4/parser.ts
@@ -6,7 +6,7 @@
import { Task, RuntimeContext } from 'mol-task';
import { Ccp4File, Ccp4Header } from './schema'
-import Result from '../result'
+import { ReaderResult as Result } from '../result'
import { FileHandle } from '../../common/file-handle';
async function parseInternal(file: FileHandle, ctx: RuntimeContext): Promise<Result<Ccp4File>> {
diff --git a/src/mol-io/reader/cif/binary/parser.ts b/src/mol-io/reader/cif/binary/parser.ts
index 8a5f0ea1a..4cf3ae57f 100644
--- a/src/mol-io/reader/cif/binary/parser.ts
+++ b/src/mol-io/reader/cif/binary/parser.ts
@@ -7,7 +7,7 @@
import * as Data from '../data-model'
import { EncodedCategory, EncodedFile } from '../../../common/binary-cif'
import Field from './field'
-import Result from '../../result'
+import { ReaderResult as Result } from '../../result'
import decodeMsgPack from '../../../common/msgpack/decode'
import { Task } from 'mol-task'
diff --git a/src/mol-io/reader/cif/text/parser.ts b/src/mol-io/reader/cif/text/parser.ts
index 3ee75e270..96ce54472 100644
--- a/src/mol-io/reader/cif/text/parser.ts
+++ b/src/mol-io/reader/cif/text/parser.ts
@@ -25,7 +25,7 @@
import * as Data from '../data-model'
import Field from './field'
import { Tokens, TokenBuilder } from '../../common/text/tokenizer'
-import Result from '../../result'
+import { ReaderResult as Result } from '../../result'
import { Task, RuntimeContext, chunkedSubtask } from 'mol-task'
/**
diff --git a/src/mol-io/reader/common/text/tokenizer.ts b/src/mol-io/reader/common/text/tokenizer.ts
index 523bb9061..e88b68dd5 100644
--- a/src/mol-io/reader/common/text/tokenizer.ts
+++ b/src/mol-io/reader/common/text/tokenizer.ts
@@ -8,7 +8,9 @@
import { chunkedSubtask, RuntimeContext } from 'mol-task'
-export interface Tokenizer {
+export { Tokenizer }
+
+interface Tokenizer {
data: string,
position: number,
@@ -25,7 +27,7 @@ export interface Tokens {
indices: ArrayLike<number>
}
-export function Tokenizer(data: string): Tokenizer {
+function Tokenizer(data: string): Tokenizer {
return {
data,
position: 0,
@@ -36,7 +38,7 @@ export function Tokenizer(data: string): Tokenizer {
};
}
-export namespace Tokenizer {
+namespace Tokenizer {
export function getTokenString(state: Tokenizer) {
return state.data.substring(state.tokenStart, state.tokenEnd);
}
@@ -269,6 +271,4 @@ export namespace TokenBuilder {
indices: new Uint32Array(size)
}
}
-}
-
-export default Tokenizer
\ No newline at end of file
+}
\ No newline at end of file
diff --git a/src/mol-io/reader/csv/parser.ts b/src/mol-io/reader/csv/parser.ts
index d5bc68535..779aca07b 100644
--- a/src/mol-io/reader/csv/parser.ts
+++ b/src/mol-io/reader/csv/parser.ts
@@ -8,7 +8,7 @@
import { Tokens, TokenBuilder, Tokenizer } from '../common/text/tokenizer'
import * as Data from './data-model'
import Field from './field'
-import Result from '../result'
+import { ReaderResult as Result } from '../result'
import { Task, RuntimeContext, chunkedSubtask, } from 'mol-task'
const enum CsvTokenType {
diff --git a/src/mol-io/reader/dsn6/parser.ts b/src/mol-io/reader/dsn6/parser.ts
index a77c96866..35416d7a8 100644
--- a/src/mol-io/reader/dsn6/parser.ts
+++ b/src/mol-io/reader/dsn6/parser.ts
@@ -6,7 +6,7 @@
import { Task, RuntimeContext } from 'mol-task';
import { Dsn6File, Dsn6Header } from './schema'
-import Result from '../result'
+import { ReaderResult as Result } from '../result'
import { FileHandle } from '../../common/file-handle';
function parseBrixHeader(str: string): Dsn6Header {
diff --git a/src/mol-io/reader/gro/parser.ts b/src/mol-io/reader/gro/parser.ts
index 6183a9a5f..0367a3ee8 100644
--- a/src/mol-io/reader/gro/parser.ts
+++ b/src/mol-io/reader/gro/parser.ts
@@ -6,10 +6,10 @@
*/
import { Column } from 'mol-data/db'
-import Tokenizer from '../common/text/tokenizer'
+import { Tokenizer } from '../common/text/tokenizer'
import FixedColumn from '../common/text/column/fixed'
import * as Schema from './schema'
-import Result from '../result'
+import { ReaderResult as Result } from '../result'
import { Task, RuntimeContext } from 'mol-task'
interface State {
diff --git a/src/mol-io/reader/mol2/parser.ts b/src/mol-io/reader/mol2/parser.ts
index 297e15026..45e0b6cca 100644
--- a/src/mol-io/reader/mol2/parser.ts
+++ b/src/mol-io/reader/mol2/parser.ts
@@ -15,7 +15,7 @@ import { Column } from 'mol-data/db'
import { TokenBuilder, Tokenizer } from '../common/text/tokenizer'
import TokenColumn from '../common/text/column/token'
import * as Schema from './schema'
-import Result from '../result'
+import { ReaderResult as Result } from '../result'
import { Task, RuntimeContext, chunkedSubtask } from 'mol-task'
const { skipWhitespace, eatValue, markLine, getTokenString, readLine } = Tokenizer;
diff --git a/src/mol-io/reader/obj/parser.ts b/src/mol-io/reader/obj/parser.ts
index 046143b30..a8b113a33 100644
--- a/src/mol-io/reader/obj/parser.ts
+++ b/src/mol-io/reader/obj/parser.ts
@@ -4,7 +4,7 @@
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
-import Result from '../result'
+import { ReaderResult as Result } from '../result'
import { Task, RuntimeContext } from 'mol-task'
import { Mesh } from 'mol-geo/geometry/mesh/mesh';
diff --git a/src/mol-io/reader/pdb/parser.ts b/src/mol-io/reader/pdb/parser.ts
new file mode 100644
index 000000000..4936fe9c9
--- /dev/null
+++ b/src/mol-io/reader/pdb/parser.ts
@@ -0,0 +1,14 @@
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { PdbFile } from './schema';
+import { Task } from 'mol-task';
+import { ReaderResult } from '../result';
+import { Tokenizer } from '../common/text/tokenizer';
+
+export function parse(data: string): Task<ReaderResult<PdbFile>> {
+ return Task.create('Parse PDB', async ctx => ReaderResult.success({ lines: await Tokenizer.readAllLinesAsync(data, ctx) }));
+}
\ No newline at end of file
diff --git a/src/mol-io/reader/pdb/schema.ts b/src/mol-io/reader/pdb/schema.ts
new file mode 100644
index 000000000..d5ab67905
--- /dev/null
+++ b/src/mol-io/reader/pdb/schema.ts
@@ -0,0 +1,11 @@
+/**
+ * Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+import { Tokens } from '../common/text/tokenizer';
+
+export interface PdbFile {
+ lines: Tokens
+}
\ No newline at end of file
diff --git a/src/mol-io/reader/result.ts b/src/mol-io/reader/result.ts
index 4eb76dd37..255ae0c9e 100644
--- a/src/mol-io/reader/result.ts
+++ b/src/mol-io/reader/result.ts
@@ -5,7 +5,7 @@
* @author David Sehnal <david.sehnal@gmail.com>
*/
-type ReaderResult<T> = Success<T> | Error
+type ReaderResult<T> = ReaderResult.Success<T> | ReaderResult.Error
namespace ReaderResult {
export function error<T>(message: string, line = -1): ReaderResult<T> {
@@ -15,28 +15,28 @@ namespace ReaderResult {
export function success<T>(result: T, warnings: string[] = []): ReaderResult<T> {
return new Success<T>(result, warnings);
}
-}
-export class Error {
- isError: true = true;
+ export class Error {
+ isError: true = true;
- toString() {
- if (this.line >= 0) {
- return `[Line ${this.line}] ${this.message}`;
+ toString() {
+ if (this.line >= 0) {
+ return `[Line ${this.line}] ${this.message}`;
+ }
+ return this.message;
}
- return this.message;
- }
- constructor(
- public message: string,
- public line: number) {
+ constructor(
+ public message: string,
+ public line: number) {
+ }
}
-}
-export class Success<T> {
- isError: false = false;
+ export class Success<T> {
+ isError: false = false;
- constructor(public result: T, public warnings: string[]) { }
+ constructor(public result: T, public warnings: string[]) { }
+ }
}
-export default ReaderResult
\ No newline at end of file
+export { ReaderResult }
\ No newline at end of file
--
GitLab