mirror of
https://github.com/molstar/molstar.git
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Initial pull-in of NGL Kinemage parser code. It is called by parser.ts and counts of objects are printed.
This commit is contained in:
Russ Taylor
800
src/mol-io/reader/kin/ngl-based-parser.ts
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800
src/mol-io/reader/kin/ngl-based-parser.ts
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@@ -0,0 +1,800 @@
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/**
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* Copyright (c) 2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
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* Based on earlier kin-parser.ts file from the NGL project (see second author notice below).
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* @file Ported NGL-based Kinemage file parser
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* @author ReliaSolve <russ@reliasolve.com>
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* @private
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*/
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/**
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* file Kin Parser
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* author Alexander Rose <alexander.rose@weirdbyte.de>
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*/
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// import { Debug, Log, ParserRegistry } from '../globals'
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// import { Vector3 } from 'three'
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// import Parser from './parser'
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function hsvToRgb (h: number, s: number, v: number) {
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h /= 360
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s /= 100
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v /= 100
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let r, g, b
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const i = Math.floor(h * 6)
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const f = h * 6 - i
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const p = v * (1 - s)
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const q = v * (1 - f * s)
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const t = v * (1 - (1 - f) * s)
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switch (i % 6) {
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case 0: r = v; g = t; b = p; break
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case 1: r = q; g = v; b = p; break
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case 2: r = p; g = v; b = t; break
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case 3: r = p; g = q; b = v; break
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case 4: r = t; g = p; b = v; break
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case 5: r = v; g = p; b = q; break
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}
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return [ r, g, b ] as number []
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}
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const ColorDict: {[k: string]: number[]} = {
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red: hsvToRgb(0, 100, 100),
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orange: hsvToRgb(20, 100, 100),
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gold: hsvToRgb(40, 100, 100),
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yellow: hsvToRgb(60, 100, 100),
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lime: hsvToRgb(80, 100, 100),
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green: hsvToRgb(120, 80, 100),
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sea: hsvToRgb(150, 100, 100),
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cyan: hsvToRgb(180, 100, 85),
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sky: hsvToRgb(210, 75, 95),
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blue: hsvToRgb(240, 70, 100),
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purple: hsvToRgb(275, 75, 100),
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magenta: hsvToRgb(300, 95, 100),
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hotpink: hsvToRgb(335, 100, 100),
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pink: hsvToRgb(350, 55, 100),
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peach: hsvToRgb(25, 75, 100),
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lilac: hsvToRgb(275, 55, 100),
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pinktint: hsvToRgb(340, 30, 100),
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peachtint: hsvToRgb(25, 50, 100),
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yellowtint: hsvToRgb(60, 50, 100),
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greentint: hsvToRgb(135, 40, 100),
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bluetint: hsvToRgb(220, 40, 100),
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lilactint: hsvToRgb(275, 35, 100),
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white: hsvToRgb(0, 0, 100),
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gray: hsvToRgb(0, 0, 50),
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brown: hsvToRgb(20, 45, 75),
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deadwhite: [ 1, 1, 1 ],
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deadblack: [ 0, 0, 0 ],
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invisible: [ 0, 0, 0 ]
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}
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const reWhitespaceComma = /[\s,]+/
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const reCurlyWhitespace = /[^{}\s]*{[^{}]+}|[^{}\s]+/g
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const reTrimCurly = /^{+|}+$/g
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const reTrimQuotes = /^['"]+|['"]+$/g
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const reCollapseEqual = /\s*=\s*/g
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function parseListDef (line: string) {
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let name
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let defaultColor
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let master = []
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let width
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line = line.replace(reCollapseEqual, '=')
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const lm = line.match(reCurlyWhitespace) as RegExpMatchArray
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for (let j = 1; j < lm.length; ++j) {
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const e = lm[ j ]
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if (e[ 0 ] === '{') {
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name = e.substring(1, e.length - 1)
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} else {
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const es = e.split('=')
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if (es.length === 2) {
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if (es[ 0 ] === 'color') {
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defaultColor = ColorDict[ es[ 1 ] ]
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} else if (es[ 0 ] === 'width') {
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width = parseInt(es[ 1 ])
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} else if (es[ 0 ] === 'master') {
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master.push(es[ 1 ].replace(reTrimCurly, ''))
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}
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}
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}
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}
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return {
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listName: name,
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listColor: defaultColor,
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listMasters: master,
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listWidth: width
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}
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}
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function parseListElm (line: string) {
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line = line.trim()
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const idx1 = line.indexOf('{')
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const idx2 = line.indexOf('}')
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const ls = line.substr(idx2 + 1).split(reWhitespaceComma)
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const label = line.substr(idx1 + 1, idx2 - 1)
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const position = [
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parseFloat(ls[ ls.length - 3 ]),
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parseFloat(ls[ ls.length - 2 ]),
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parseFloat(ls[ ls.length - 1 ])
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]
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let color, width, radius
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let lineBreak = false
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let triangleBreak = false
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for (let lsindex = 4; lsindex <= ls.length; lsindex++) {
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const literal = ls[ ls.length - lsindex ]
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if (literal in ColorDict) {
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color = ColorDict[ ls[ ls.length - lsindex ] ]
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}
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if (literal.startsWith('width')) {
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width = parseInt(literal.substring(5))
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}
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if (literal.startsWith('r=')) {
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radius = parseFloat(literal.split('=')[1])
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}
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if (literal.startsWith('P')) {
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lineBreak = true
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}
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if (literal.startsWith('X')) {
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triangleBreak = true
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}
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}
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// const color = line[ idx2 + 1 ] === ' ' ? undefined : ColorDict[ ls[ 0 ] ]
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return {
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label: label,
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position: position,
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color: color,
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radius: radius,
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width: width,
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isLineBreak: lineBreak,
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isTriangleBreak: triangleBreak
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}
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}
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function parseStr (line: string) {
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const start = line.indexOf('{')
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const end = line.indexOf('}')
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return line.substring(
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start !== -1 ? start + 1 : 0,
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end !== -1 ? end : undefined
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).trim()
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}
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function parseFlag (line: string) {
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const end = line.indexOf('}')
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return end === -1 ? undefined : line.substr(end + 1).trim()
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}
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function parseGroup (line: string) {
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let name:string = ''
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let master:string[] = []
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let flags: {[k: string]: string|boolean} = {}
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line = line.replace(reCollapseEqual, '=')
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const lm = line.match(reCurlyWhitespace) as RegExpMatchArray
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for (let j = 1; j < lm.length; ++j) {
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const e = lm[ j ]
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if (e[ 0 ] === '{') {
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name = e.substring(1, e.length - 1)
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} else {
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const es = e.split('=')
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if (es.length === 2) {
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if (es[ 0 ] === 'master') {
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master.push(es[ 1 ].replace(reTrimCurly, ''))
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} else {
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flags[ es[ 0 ] ] = es[ 1 ].replace(reTrimCurly, '')
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}
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} else {
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flags[ es[ 0 ] ] = true
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}
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}
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}
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return { groupName: name,
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groupFlags: flags,
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groupMasters: master
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}
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}
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interface RibbonObject {
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labelArray: string[],
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positionArray: number[],
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breakArray: boolean[],
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colorArray: number[],
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name?: string,
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masterArray: any[]
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}
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function convertKinTriangleArrays (ribbonObject: RibbonObject) {
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// have to convert ribbons/triangle lists from stripdrawmode to normal drawmode
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// index [ 0 1 2 3 4 5 6 7 8 91011 ]
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// label [ 0 1 2 3 4 5 ] to [ 0 1 2 1 2 3 2 3 4 3 4 5 ]
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// convertedindex [ 0 1 2 3 4 5 6 7 8 91011121314151617181920212223242526 ]
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// index [ 0 1 2 3 4 5 6 7 8 91011121314 ] [ 0 1 2 3 4 5 6 7 8 3 4 5 6 7 8 91011 6 7 8 91011121314 ]
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// position/color [ 0 0 0 1 1 1 2 2 2 3 3 3 4 4 4 ] to [ 0 0 0 1 1 1 2 2 2 1 1 1 2 2 2 3 3 3 2 2 2 3 3 3 4 4 4 ]
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let { labelArray, positionArray, colorArray, breakArray } = ribbonObject
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let convertedLabels = []
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for (let i = 0; i < (labelArray.length - 2) * 3; ++i) {
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convertedLabels[i] = labelArray[i - Math.floor(i / 3) * 2]
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}
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let convertedBreaks = []
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for (let i = 0; i < (breakArray.length - 2) * 3; ++i) {
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convertedBreaks[i] = breakArray[i - Math.floor(i / 3) * 2]
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}
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let convertedPositions = []
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for (let i = 0; i < (positionArray.length / 3 - 2) * 9; ++i) {
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convertedPositions[i] = positionArray[i - Math.floor(i / 9) * 6]
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}
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let convertedColors = []
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for (let i = 0; i < (colorArray.length / 3 - 2) * 9; ++i) {
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convertedColors[i] = colorArray[i - Math.floor(i / 9) * 6]
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}
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let vector3Positions = []
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for (let i = 0; i < (convertedPositions.length) / 3; ++i) {
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vector3Positions.push([convertedPositions[i * 3], convertedPositions[i * 3] + 1, convertedPositions[i * 3] + 2])
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}
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//let normals = []
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//for (let i = 0; i < vector3Positions.length - 1; ++i) {
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// let normalVec3 = vector3Positions[i].cross(vector3Positions[i + 1])
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// normals.push(normalVec3.x)
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// normals.push(normalVec3.y)
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// normals.push(normalVec3.z)
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//}
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return {
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name: ribbonObject.name,
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masterArray: ribbonObject.masterArray,
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labelArray: convertedLabels,
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positionArray: convertedPositions,
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breakArray: convertedBreaks,
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colorArray: convertedColors
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}
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}
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function removePointBreaksTriangleArrays (convertedRibbonObject: RibbonObject) {
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// after converting ribbon/triangle arrys to drawmode, removed point break triangles
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// label [ 0 1 2 3 4 5 ] to [ 0 1 2 1 2 3 2 3 4 3 4 5 ]
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// position/color [ 0 0 0 1 1 1 2 2 2 3 3 3 4 4 4 ] to [ 0 0 0 1 1 1 2 2 2 1 1 1 2 2 2 3 3 3 2 2 2 3 3 3 4 4 4 ]
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let { labelArray, positionArray, colorArray, breakArray } = convertedRibbonObject
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let editedLabels = []
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let editedPositions = []
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let editedColors = []
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let editedBreaks = []
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for (let i = 0; i < breakArray.length / 3; i++) {
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let breakPointer = i * 3
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let positionPointer = i * 9
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if (!breakArray[breakPointer+1]&&!breakArray[breakPointer+2]) {
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editedLabels.push(labelArray[breakPointer])
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editedLabels.push(labelArray[breakPointer+1])
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editedLabels.push(labelArray[breakPointer+2])
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editedBreaks.push(breakArray[breakPointer])
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editedBreaks.push(breakArray[breakPointer+1])
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editedBreaks.push(breakArray[breakPointer+2])
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editedPositions.push(positionArray[positionPointer])
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editedPositions.push(positionArray[positionPointer+1])
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editedPositions.push(positionArray[positionPointer+2])
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editedPositions.push(positionArray[positionPointer+3])
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editedPositions.push(positionArray[positionPointer+4])
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editedPositions.push(positionArray[positionPointer+5])
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editedPositions.push(positionArray[positionPointer+6])
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editedPositions.push(positionArray[positionPointer+7])
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editedPositions.push(positionArray[positionPointer+8])
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editedColors.push(colorArray[positionPointer])
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editedColors.push(colorArray[positionPointer+1])
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editedColors.push(colorArray[positionPointer+2])
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editedColors.push(colorArray[positionPointer+3])
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editedColors.push(colorArray[positionPointer+4])
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editedColors.push(colorArray[positionPointer+5])
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editedColors.push(colorArray[positionPointer+6])
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editedColors.push(colorArray[positionPointer+7])
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editedColors.push(colorArray[positionPointer+8])
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} else {
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//console.log('X triangle break found')
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//console.log('skipping: '+positionArray[positionPointer]+','+positionArray[positionPointer+1]+','+positionArray[positionPointer+2]+','
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// +positionArray[positionPointer+3]+','+positionArray[positionPointer+4]+','+positionArray[positionPointer+5]+','
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// +positionArray[positionPointer+6]+','+positionArray[positionPointer+7]+','+positionArray[positionPointer+8])
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}
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}
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return {
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name: convertedRibbonObject.name,
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masterArray: convertedRibbonObject.masterArray,
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labelArray: editedLabels,
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positionArray: editedPositions,
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breakArray: editedBreaks,
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colorArray: editedColors
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}
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}
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interface Kinemage {
|
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kinemage?: number,
|
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onewidth?: any,
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'1viewid'?: string,
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pdbfile?: string,
|
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text: string,
|
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texts: string[],
|
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captions: string[],
|
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caption: string,
|
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groupDict: {[k:string]: {[k:string]: boolean}},
|
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subgroupDict: {[k: string]: any},
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masterDict: {[k:string]: {indent: boolean, visible: boolean}},
|
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pointmasterDict: {[k: string]: any},
|
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dotLists: DotList[],
|
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vectorLists: VectorList[],
|
||||
ballLists: any[],
|
||||
ribbonLists: RibbonObject[]
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}
|
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|
||||
interface DotList {
|
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name?: string,
|
||||
masterArray: any[],
|
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labelArray: any[],
|
||||
positionArray: any[],
|
||||
colorArray: any[]
|
||||
}
|
||||
|
||||
interface VectorList {
|
||||
name?: string,
|
||||
masterArray: any[],
|
||||
label1Array: string[],
|
||||
label2Array: string[],
|
||||
position1Array: number[],
|
||||
position2Array: number[],
|
||||
color1Array: number[],
|
||||
color2Array: number[],
|
||||
width: number[]
|
||||
}
|
||||
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class KinParser {
|
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/// @brief Property that is filled in by the constructor as it parses the file. Read by the caller.
|
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kinemage: Kinemage
|
||||
|
||||
/// @brief Constructor for the KinParser class.
|
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/// @param data The string data to be parsed, including all lines in the file.
|
||||
constructor(data: string) {
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||||
this._parse(data);
|
||||
}
|
||||
|
||||
private _parse (data: string) {
|
||||
// http://kinemage.biochem.duke.edu/software/king.php
|
||||
|
||||
const kinemage: Kinemage = {
|
||||
kinemage: undefined,
|
||||
onewidth: undefined,
|
||||
'1viewid': undefined,
|
||||
pdbfile: undefined,
|
||||
texts: [],
|
||||
text: '',
|
||||
captions: [],
|
||||
caption: '',
|
||||
groupDict: {},
|
||||
subgroupDict: {},
|
||||
masterDict: {},
|
||||
pointmasterDict: {},
|
||||
dotLists: [],
|
||||
vectorLists: [],
|
||||
ballLists: [],
|
||||
ribbonLists: []
|
||||
}
|
||||
this.kinemage = kinemage
|
||||
|
||||
let currentGroupMasters: string[]
|
||||
let currentSubgroupMasters: string[]
|
||||
|
||||
let isDotList = false
|
||||
let prevDotLabel = ''
|
||||
let dotDefaultColor: number[]
|
||||
let dotLabel: string[], dotPosition: number[], dotColor: number[]
|
||||
|
||||
let isVectorList = false
|
||||
let prevVecLabel = ''
|
||||
let prevVecPosition: number[]|null = null
|
||||
let prevVecColor: number[]|null = null
|
||||
let vecDefaultColor: number[], vecDefaultWidth: number[]
|
||||
let vecLabel1: string[], vecLabel2: string[], vecPosition1: number[], vecPosition2: number[], vecColor1: number[], vecColor2: number[]
|
||||
|
||||
let isBallList = false
|
||||
let prevBallLabel = ''
|
||||
let ballRadius: number[], ballDefaultColor: number[]
|
||||
let ballLabel: string[], ballPosition: number[], ballColor: number[]
|
||||
|
||||
let isRibbonList = false
|
||||
let prevRibbonPointLabel = ''
|
||||
|
||||
let ribbonListDefaultColor: number[]
|
||||
let ribbonPointLabelArray: string[], ribbonPointPositionArray: number[], ribbonPointBreakArray: boolean[], ribbonPointColorArray: number[]
|
||||
|
||||
let isText = false
|
||||
let isCaption = false
|
||||
|
||||
// @vectorlist {mc} color= white master= {mainchain}
|
||||
// { n thr A 1 B13.79 1crnFH} P 17.047, 14.099, 3.625 { n thr A 1 B13.79 1crnFH} L 17.047, 14.099, 3.625
|
||||
|
||||
// @dotlist {x} color=white master={vdw contact} master={dots}
|
||||
// { CB THR 1 A}sky 'P' 18.915,14.199,5.024
|
||||
|
||||
function _parseChunkOfLines (_i: number, _n: number, lines: string[]) {
|
||||
for (let i = _i; i < _n; ++i) {
|
||||
const line = lines[ i ]
|
||||
|
||||
if (line[ 0 ] === '@') {
|
||||
isDotList = false
|
||||
isVectorList = false
|
||||
isBallList = false
|
||||
isRibbonList = false
|
||||
isText = false
|
||||
isCaption = false
|
||||
}
|
||||
|
||||
if (!line) {
|
||||
isDotList = false
|
||||
isVectorList = false
|
||||
isBallList = false
|
||||
isRibbonList = false
|
||||
} else if (line.startsWith('@dotlist')) {
|
||||
// @dotlist {x} color=white master={vdw contact} master={dots}
|
||||
|
||||
let { listColor, listName, listMasters } = parseListDef(line)
|
||||
|
||||
isDotList = true
|
||||
prevDotLabel = ''
|
||||
dotLabel = []
|
||||
dotPosition = []
|
||||
dotColor = []
|
||||
dotDefaultColor = listColor as number[]
|
||||
|
||||
if (currentGroupMasters) {
|
||||
listMasters = listMasters.concat(currentGroupMasters)
|
||||
}
|
||||
if (currentSubgroupMasters) {
|
||||
listMasters = listMasters.concat(currentSubgroupMasters)
|
||||
}
|
||||
|
||||
kinemage.dotLists.push({
|
||||
name: listName,
|
||||
masterArray: listMasters,
|
||||
labelArray: dotLabel,
|
||||
positionArray: dotPosition,
|
||||
colorArray: dotColor
|
||||
})
|
||||
} else if (line.startsWith('@vectorlist')) {
|
||||
// @vectorlist {x} color=white master={small overlap} master={dots}
|
||||
|
||||
let { listMasters, listName, listWidth, listColor } = parseListDef(line)
|
||||
|
||||
if (listMasters) {
|
||||
listMasters.forEach(function (name: string) {
|
||||
if (!kinemage.masterDict[ name ]) {
|
||||
kinemage.masterDict[ name ] = {
|
||||
indent: false,
|
||||
visible: false
|
||||
}
|
||||
}
|
||||
})
|
||||
}
|
||||
|
||||
isVectorList = true
|
||||
prevVecLabel = ''
|
||||
prevVecPosition = null
|
||||
prevVecColor = null
|
||||
vecLabel1 = []
|
||||
vecLabel2 = []
|
||||
vecPosition1 = []
|
||||
vecPosition2 = []
|
||||
vecColor1 = []
|
||||
vecColor2 = []
|
||||
vecDefaultColor = listColor as number[]
|
||||
vecDefaultWidth = []
|
||||
if (listWidth) {
|
||||
vecDefaultWidth.push(listWidth)
|
||||
}
|
||||
|
||||
if (currentGroupMasters) {
|
||||
listMasters = listMasters.concat(currentGroupMasters)
|
||||
}
|
||||
if (currentSubgroupMasters) {
|
||||
listMasters = listMasters.concat(currentSubgroupMasters)
|
||||
}
|
||||
|
||||
kinemage.vectorLists.push({
|
||||
name: listName,
|
||||
masterArray: listMasters,
|
||||
label1Array: vecLabel1,
|
||||
label2Array: vecLabel2,
|
||||
position1Array: vecPosition1,
|
||||
position2Array: vecPosition2,
|
||||
color1Array: vecColor1,
|
||||
color2Array: vecColor2,
|
||||
width: vecDefaultWidth
|
||||
})
|
||||
} else if (line.startsWith('@balllist')) {
|
||||
let { listName, listColor, listMasters } = parseListDef(line)
|
||||
|
||||
if (listMasters) {
|
||||
listMasters.forEach(function (name: string) {
|
||||
if (!kinemage.masterDict[ name ]) {
|
||||
kinemage.masterDict[ name ] = {
|
||||
indent: false,
|
||||
visible: false
|
||||
}
|
||||
}
|
||||
})
|
||||
}
|
||||
|
||||
isBallList = true
|
||||
|
||||
prevBallLabel = ''
|
||||
ballLabel = []
|
||||
ballRadius = []
|
||||
ballPosition = []
|
||||
ballColor = []
|
||||
ballDefaultColor = listColor as number[]
|
||||
|
||||
if (currentGroupMasters) {
|
||||
listMasters = listMasters.concat(currentGroupMasters)
|
||||
}
|
||||
if (currentSubgroupMasters) {
|
||||
listMasters = listMasters.concat(currentSubgroupMasters)
|
||||
}
|
||||
|
||||
kinemage.ballLists.push({
|
||||
name: listName,
|
||||
masterArray: listMasters,
|
||||
labelArray: ballLabel,
|
||||
radiusArray: ballRadius,
|
||||
positionArray: ballPosition,
|
||||
colorArray: ballColor
|
||||
})
|
||||
} else if (line.startsWith('@ribbonlist')||line.startsWith('@trianglelist')) {
|
||||
let { listMasters, listName, listColor } = parseListDef(line)
|
||||
|
||||
if (listMasters) {
|
||||
listMasters.forEach(function (name: string) {
|
||||
if (!kinemage.masterDict[ name ]) {
|
||||
kinemage.masterDict[ name ] = {
|
||||
indent: false,
|
||||
visible: false
|
||||
}
|
||||
}
|
||||
})
|
||||
}
|
||||
isRibbonList = true
|
||||
prevRibbonPointLabel = ''
|
||||
ribbonPointLabelArray = []
|
||||
ribbonPointPositionArray = []
|
||||
ribbonPointBreakArray = []
|
||||
ribbonPointColorArray = []
|
||||
ribbonListDefaultColor = listColor as number[]
|
||||
|
||||
if (currentGroupMasters) {
|
||||
listMasters = listMasters.concat(currentGroupMasters)
|
||||
}
|
||||
if (currentSubgroupMasters) {
|
||||
listMasters = listMasters.concat(currentSubgroupMasters)
|
||||
}
|
||||
|
||||
kinemage.ribbonLists.push({
|
||||
name: listName,
|
||||
masterArray: listMasters,
|
||||
labelArray: ribbonPointLabelArray,
|
||||
positionArray: ribbonPointPositionArray,
|
||||
breakArray: ribbonPointBreakArray,
|
||||
colorArray: ribbonPointColorArray
|
||||
})
|
||||
} else if (line.startsWith('@text')) {
|
||||
isText = true
|
||||
kinemage.texts.push(line.substr(5))
|
||||
} else if (line.startsWith('@caption')) {
|
||||
isCaption = true
|
||||
kinemage.captions.push(line.substr(8))
|
||||
} else if (isDotList) {
|
||||
// { CB THR 1 A}sky 'P' 18.915,14.199,5.024
|
||||
|
||||
let { label, color, position } = parseListElm(line)
|
||||
|
||||
if (label === '"') {
|
||||
label = prevDotLabel
|
||||
} else {
|
||||
prevDotLabel = label
|
||||
}
|
||||
|
||||
if (color === undefined) {
|
||||
color = dotDefaultColor
|
||||
}
|
||||
|
||||
dotLabel.push(label)
|
||||
dotPosition.push(...position)
|
||||
dotColor.push(...color)
|
||||
} else if (isVectorList) {
|
||||
// { n thr A 1 B13.79 1crnFH} P 17.047, 14.099, 3.625 { n thr A 1 B13.79 1crnFH} L 17.047, 14.099, 3.625
|
||||
|
||||
let doubleLine = line.replace(/(?!^){/g, '\n{')
|
||||
let splitLine = doubleLine.split(/\n/)
|
||||
|
||||
for (var i2 = 0; i2 < splitLine.length; i2++) {
|
||||
let singlePointLine = splitLine[i2]
|
||||
let { label, color, width, position, isLineBreak } = parseListElm(singlePointLine)
|
||||
|
||||
if (label === '"') {
|
||||
label = prevVecLabel
|
||||
} else {
|
||||
prevVecLabel = label
|
||||
}
|
||||
|
||||
if (color === undefined) {
|
||||
color = vecDefaultColor
|
||||
}
|
||||
|
||||
if (!isLineBreak) {
|
||||
if (prevVecPosition !== null) {
|
||||
if (width) {
|
||||
vecDefaultWidth.push(width)
|
||||
}
|
||||
|
||||
vecLabel1.push(prevVecLabel)
|
||||
vecPosition1.push(...prevVecPosition)
|
||||
vecColor1.push(...prevVecColor as number[])
|
||||
|
||||
vecLabel2.push(label)
|
||||
vecPosition2.push(...position)
|
||||
vecColor2.push(...color)
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
prevVecLabel = label
|
||||
prevVecPosition = position
|
||||
prevVecColor = color
|
||||
}
|
||||
} else if (isBallList) {
|
||||
// {cb arg A 1 1.431 -106.80} r=1.431 39.085, 8.083, 22.182
|
||||
|
||||
let { label, radius, color, position } = parseListElm(line)
|
||||
|
||||
if (label === '"') {
|
||||
label = prevBallLabel
|
||||
} else {
|
||||
prevBallLabel = label
|
||||
}
|
||||
|
||||
if (radius === undefined) {
|
||||
radius = 1 // temporary default radius
|
||||
}
|
||||
|
||||
if (color === undefined) {
|
||||
color = ballDefaultColor
|
||||
}
|
||||
|
||||
ballLabel.push(label)
|
||||
ballRadius.push(radius)
|
||||
ballPosition.push(...position)
|
||||
ballColor.push(...color)
|
||||
} else if (isRibbonList) {
|
||||
let { label, color, position, isTriangleBreak } = parseListElm(line)
|
||||
|
||||
if (label === '"') {
|
||||
label = prevRibbonPointLabel
|
||||
} else {
|
||||
prevRibbonPointLabel = label
|
||||
}
|
||||
|
||||
if (color === undefined) {
|
||||
color = ribbonListDefaultColor
|
||||
}
|
||||
|
||||
ribbonPointLabelArray.push(label)
|
||||
ribbonPointPositionArray.push(...position)
|
||||
ribbonPointBreakArray.push(isTriangleBreak)
|
||||
ribbonPointColorArray.push(...color)
|
||||
} else if (isText) {
|
||||
kinemage.texts.push(line)
|
||||
} else if (isCaption) {
|
||||
kinemage.captions.push(line)
|
||||
} else if (line.startsWith('@kinemage')) {
|
||||
kinemage.kinemage = parseInt(line.substr(9).trim())
|
||||
} else if (line.startsWith('@onewidth')) {
|
||||
kinemage.onewidth = true
|
||||
} else if (line.startsWith('@1viewid')) {
|
||||
kinemage[ '1viewid' ] = parseStr(line)
|
||||
} else if (line.startsWith('@pdbfile')) {
|
||||
kinemage.pdbfile = parseStr(line)
|
||||
} else if (line.startsWith('@group')) {
|
||||
let { groupName, groupFlags, groupMasters } = parseGroup(line)
|
||||
if (!kinemage.groupDict[ groupName as string ]) {
|
||||
kinemage.groupDict[ groupName as string ] = {
|
||||
dominant: false,
|
||||
animate: false
|
||||
}
|
||||
currentGroupMasters = groupMasters
|
||||
}
|
||||
|
||||
if (currentGroupMasters) {
|
||||
currentGroupMasters.forEach(function (master) {
|
||||
if (!kinemage.masterDict[ master ]) {
|
||||
kinemage.masterDict[ master ] = {
|
||||
indent: false,
|
||||
visible: false
|
||||
}
|
||||
}
|
||||
})
|
||||
}
|
||||
|
||||
for (let key in groupFlags as {[k: string]: boolean}) {
|
||||
kinemage.groupDict[ groupName as string ][ key ] = (groupFlags as {[k: string]: boolean})[ key ]
|
||||
}
|
||||
} else if (line.startsWith('@subgroup')) {
|
||||
const { groupName, groupFlags, groupMasters } = parseGroup(line)
|
||||
|
||||
if (!kinemage.subgroupDict[ groupName as string ]) {
|
||||
kinemage.subgroupDict[ groupName as string ] = {
|
||||
dominant: false,
|
||||
animate: false
|
||||
}
|
||||
currentSubgroupMasters = groupMasters
|
||||
}
|
||||
|
||||
if (currentSubgroupMasters) {
|
||||
currentSubgroupMasters.forEach(function (master) {
|
||||
if (!kinemage.masterDict[ master ]) {
|
||||
kinemage.masterDict[ master ] = {
|
||||
indent: false,
|
||||
visible: false
|
||||
}
|
||||
}
|
||||
})
|
||||
}
|
||||
|
||||
for (let key in groupFlags as {[k: string]: boolean}) {
|
||||
kinemage.subgroupDict[ groupName as string ][ key ] = (groupFlags as {[k: string]: boolean})[ key ]
|
||||
}
|
||||
} else if (line.startsWith('@master')) {
|
||||
const name = parseStr(line)
|
||||
const flag = parseFlag(line)
|
||||
|
||||
if (!kinemage.masterDict[ name ]) {
|
||||
kinemage.masterDict[ name ] = {
|
||||
indent: false,
|
||||
visible: false
|
||||
}
|
||||
}
|
||||
|
||||
if (flag === 'on') {
|
||||
kinemage.masterDict[ name ].visible = true
|
||||
} else if (flag === 'off') {
|
||||
kinemage.masterDict[ name ].visible = false
|
||||
} else if (flag === 'indent') {
|
||||
kinemage.masterDict[ name ].indent = true
|
||||
} else if (!flag) {
|
||||
// nothing to do
|
||||
}
|
||||
} else if (line.startsWith('@pointmaster')) {
|
||||
const { groupName, groupFlags } = parseGroup(line)
|
||||
|
||||
kinemage.pointmasterDict[ groupName as string] = {
|
||||
id: Object.keys(groupFlags as {[k: string]: boolean})[ 0 ].replace(reTrimQuotes, '')
|
||||
}
|
||||
} else {
|
||||
console.log(line)
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
// Break the file into a list of lines and then parse them all.
|
||||
const lines = data.split(/\r?\n/)
|
||||
_parseChunkOfLines(0, lines.length, lines);
|
||||
|
||||
kinemage.text = kinemage.texts.join('\n').trim()
|
||||
kinemage.caption = kinemage.captions.join('\n').trim()
|
||||
if (kinemage.ribbonLists) {
|
||||
let convertedLists: RibbonObject[] = []
|
||||
kinemage.ribbonLists.forEach(function (listObject) {
|
||||
convertedLists.push(removePointBreaksTriangleArrays(convertKinTriangleArrays(listObject)))
|
||||
})
|
||||
kinemage.ribbonLists = convertedLists
|
||||
}
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
export default KinParser
|
||||
@@ -7,6 +7,7 @@
|
||||
import { ReaderResult as Result } from '../result';
|
||||
import { Task, RuntimeContext } from '../../../mol-task';
|
||||
import { KinFile, KinType, KinElement } from './schema';
|
||||
import KinParser from './ngl-based-parser';
|
||||
import { Tokenizer, TokenBuilder, Tokens } from '../common/text/tokenizer';
|
||||
import { Column } from '../../../mol-data/db';
|
||||
import { TokenColumn } from '../common/text/column/token';
|
||||
@@ -239,6 +240,14 @@ function parseListElement(state: State, spec: ListElementSpec) {
|
||||
}
|
||||
|
||||
async function parseInternal(data: string, ctx: RuntimeContext): Promise<Result<KinFile>> {
|
||||
|
||||
console.log('XXX Constructing KinParser');
|
||||
const NGLParser = new KinParser(data);
|
||||
console.log('XXX Getting data from KinParser');
|
||||
const kinData = NGLParser.kinemage;
|
||||
console.log(`XXX Number of vector lists: ${kinData.vectorLists.length}, ballLists: ${kinData.ballLists.length}, ribbonLists: ${kinData.ribbonLists.length}`);
|
||||
|
||||
/// @todo Replace this with code that pulls from the NGL-based data and constructs a KinFile
|
||||
const state = State(data, ctx);
|
||||
ctx.update({ message: 'Parsing...', current: 0, max: data.length });
|
||||
parseHeader(state);
|
||||
|
||||
Reference in New Issue
Block a user