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validation.ts
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validation.ts
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/**
* @file Validation
* @author Alexander Rose <alexander.rose@weirdbyte.de>
* @private
*/
import { Vector3, Color } from 'three'
import { Debug, Log } from '../globals'
import { defaults } from '../utils'
import { ClashPicker } from '../utils/picker'
import { uniformArray3 } from '../math/array-utils'
import { guessElement } from '../structure/structure-utils'
import AtomProxy from '../proxy/atom-proxy'
import Structure from '../structure/structure'
function getNamedItem(a: NamedNodeMap, name: string) {
const item = a.getNamedItem(name)
return item !== null ? item.value : ''
}
function getSele (a: NamedNodeMap, atomname?: string, useAltcode = false) {
const icode = getNamedItem(a, 'icode')
const chain = getNamedItem(a, 'chain')
const altcode = getNamedItem(a, 'altcode')
let sele = getNamedItem(a, 'resnum')
if (icode.trim()) sele += '^' + icode
if (chain.trim()) sele += ':' + chain
if (atomname) sele += '.' + atomname
if (useAltcode && altcode.trim()) sele += '%' + altcode
sele += '/' + (parseInt(getNamedItem(a, 'model')) - 1)
return sele
}
function setBitDict (dict: { [k: string]: number }, key: string, bit: number) {
if (dict[ key ] === undefined) {
dict[ key ] = bit
} else {
dict[ key ] |= bit
}
}
function hasAttrValue (attr: Attr|null, value: string) {
return attr !== null && attr.value === value
}
function getAtomSele (ap: AtomProxy) {
const icode = ap.inscode
const chain = ap.chainname
const atomname = ap.atomname
const altcode = ap.altloc
let sele = ap.resno + ''
if (icode) sele += '^' + icode
if (chain) sele += ':' + chain
if (atomname) sele += '.' + atomname
if (altcode) sele += '%' + altcode
sele += '/' + ap.modelIndex
return sele
}
function getProblemCount (clashDict: { [k: string]: { [k: string]: string } }, g: Element, ga: NamedNodeMap) {
let geoProblemCount = 0
const clashes = g.getElementsByTagName('clash')
for (let j = 0, jl = clashes.length; j < jl; ++j) {
if (clashDict[ getNamedItem(clashes[ j ].attributes, 'cid') ]) {
geoProblemCount += 1
break
}
}
const angleOutliers = g.getElementsByTagName('angle-outlier')
if (angleOutliers.length > 0) {
geoProblemCount += 1
}
const bondOutliers = g.getElementsByTagName('bond-outlier')
if (bondOutliers.length > 0) {
geoProblemCount += 1
}
const planeOutliers = g.getElementsByTagName('plane-outlier')
if (planeOutliers.length > 0) {
geoProblemCount += 1
}
if (hasAttrValue(ga.getNamedItem('rota'), 'OUTLIER')) {
geoProblemCount += 1
}
if (hasAttrValue(ga.getNamedItem('rama'), 'OUTLIER')) {
geoProblemCount += 1
}
if (hasAttrValue(ga.getNamedItem('RNApucker'), 'outlier')) {
geoProblemCount += 1
}
return geoProblemCount
}
class Validation {
rsrzDict: { [k: string]: number } = {}
rsccDict: { [k: string]: number } = {}
clashDict: { [k: string]: { [k: string]: string } } = {}
clashArray: { [k: string]: string }[] = []
geoDict: { [k: string]: number } = {}
geoAtomDict: { [k: string]: { [k: string]: number } } = {}
atomDict: { [k: string]: boolean|number } = {}
clashSele = 'NONE'
constructor (readonly name: string, readonlypath: string) {}
get type () { return 'validation' }
fromXml (xml: XMLDocument) {
if (Debug) Log.time('Validation.fromXml')
const rsrzDict = this.rsrzDict
const rsccDict = this.rsccDict
const clashDict = this.clashDict
const clashArray = this.clashArray
const geoDict = this.geoDict
const geoAtomDict = this.geoAtomDict
const atomDict = this.atomDict
const groups = xml.getElementsByTagName('ModelledSubgroup')
const _clashDict: { [k: string]: { [k: string]: string } } = {}
const clashList: string[] = []
if (Debug) Log.time('Validation.fromXml#clashDict')
for (let i = 0, il = groups.length; i < il; ++i) {
const g = groups[ i ]
const ga = g.attributes
const sele = getSele(ga)
if (ga.getNamedItem('rsrz') !== null) {
rsrzDict[ sele ] = parseFloat(getNamedItem(ga, 'rsrz'))
}
if (ga.getNamedItem('rscc') !== null) {
rsccDict[ sele ] = parseFloat(getNamedItem(ga, 'rscc'))
}
const seleAttr = xml.createAttribute('sele')
seleAttr.value = sele
ga.setNamedItem(seleAttr)
const clashes = g.getElementsByTagName('clash')
for (let j = 0, jl = clashes.length; j < jl; ++j) {
const ca = clashes[ j ].attributes
const atom = getNamedItem(ca, 'atom')
if (guessElement(atom) !== 'H') {
const cid = getNamedItem(ca, 'cid')
const atomSele = getSele(ga, atom, true)
atomDict[ atomSele ] = true
if (_clashDict[ cid ] === undefined) {
_clashDict[ cid ] = {
sele1: atomSele,
res1: sele
}
} else {
const c = _clashDict[ cid ]
if (c.res1 !== sele) {
c.sele2 = atomSele
c.res2 = sele
clashList.push(c.res1, sele)
clashDict[ cid ] = c
clashArray.push(c)
}
}
}
}
}
if (Debug) Log.timeEnd('Validation.fromXml#clashDict')
for (let i = 0, il = groups.length; i < il; ++i) {
const g = groups[ i ]
const ga = g.attributes
const sele = getNamedItem(ga, 'sele')
const isPolymer = getNamedItem(ga, 'seq') !== '.'
if (isPolymer) {
const geoProblemCount = getProblemCount(clashDict, g, ga)
if (geoProblemCount > 0) {
geoDict[ sele ] = geoProblemCount
}
} else {
const clashes = g.getElementsByTagName('clash')
const mogBondOutliers = g.getElementsByTagName('mog-bond-outlier')
const mogAngleOutliers = g.getElementsByTagName('mog-angle-outlier')
if (mogBondOutliers.length > 0 || mogAngleOutliers.length > 0 || clashes.length > 0) {
const atomDict = {}
geoAtomDict[ sele ] = atomDict
for (let j = 0, jl = clashes.length; j < jl; ++j) {
const ca = clashes[ j ].attributes
if (clashDict[ getNamedItem(ca, 'cid') ]) {
setBitDict(atomDict, getNamedItem(ca, 'atom'), 1)
}
}
for (let j = 0, jl = mogBondOutliers.length; j < jl; ++j) {
const mbo = mogBondOutliers[ j ].attributes
getNamedItem(mbo, 'atoms').split(',').forEach(function (atomname) {
setBitDict(atomDict, atomname, 2)
})
}
for (let j = 0, jl = mogAngleOutliers.length; j < jl; ++j) {
const mao = mogAngleOutliers[ j ].attributes
getNamedItem(mao, 'atoms').split(',').forEach(function (atomname) {
setBitDict(atomDict, atomname, 4)
})
}
}
}
}
this.clashSele = clashList.length ? clashList.join(' OR ') : 'NONE'
if (Debug) Log.timeEnd('Validation.fromXml')
}
getClashData (params: { color: number|string|Color, structure: Structure }) {
if (Debug) Log.time('Validation.getClashData')
const p = params || {}
const s = p.structure
const atomSet = s.atomSet! // TODO
const c = new Color(defaults(p.color, '#f0027f'))
const ap1 = s.getAtomProxy()
const ap2 = s.getAtomProxy()
const vDir = new Vector3()
const vPos1 = new Vector3()
const vPos2 = new Vector3()
const clashArray = this.clashArray
const n = clashArray.length
const position1 = new Float32Array(n * 3)
const position2 = new Float32Array(n * 3)
const color = uniformArray3(n, c.r, c.g, c.b) as Float32Array
const radius = new Float32Array(n)
const picking = new Float32Array(n)
if (Debug) Log.time('Validation.getClashData#atomDict')
const atomDict = this.atomDict
s.eachAtom(function (ap) {
const sele = getAtomSele(ap)
if (atomDict[ sele ] === true) {
atomDict[ sele ] = ap.index
}
})
if (Debug) Log.timeEnd('Validation.getClashData#atomDict')
let i = 0
clashArray.forEach(function (c, idx) {
ap1.index = atomDict[ c.sele1 ] as number // TODO
ap2.index = atomDict[ c.sele2 ] as number // TODO
if (ap1.index === undefined || ap2.index === undefined ||
!atomSet.isSet(ap1.index, ap2.index)) return
vDir.subVectors(ap2 as any, ap1 as any).setLength(ap1.vdw) // TODO
vPos1.copy(ap1 as any).add(vDir) // TODO
vDir.subVectors(ap1 as any, ap2 as any).setLength(ap2.vdw) // TODO
vPos2.copy(ap2 as any).add(vDir) // TODO
const dHalf = ap1.distanceTo(ap2) / 2
const r1 = Math.sqrt(ap1.vdw * ap1.vdw - dHalf * dHalf)
const r2 = Math.sqrt(ap2.vdw * ap2.vdw - dHalf * dHalf)
vPos1.toArray(position1 as any, i * 3) // TODO
vPos2.toArray(position2 as any, i * 3)
radius[ i ] = (r1 + r2) / 2
picking[ i ] = idx
++i
})
if (Debug) Log.timeEnd('Validation.getClashData')
return {
position1: position1.subarray(0, i * 3),
position2: position2.subarray(0, i * 3),
color: color.subarray(0, i * 3),
color2: color.subarray(0, i * 3),
radius: radius.subarray(0, i),
picking: new ClashPicker(picking.subarray(0, i), this, s)
}
}
}
export default Validation