Select Git revision
util.ts 2.94 KiB
/**
* Copyright (c) 2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* @author Alexander Rose <alexander.rose@weirdbyte.de>
*/
import { Model, ResidueIndex, ElementIndex } from './model';
import { MoleculeType, AtomRole, MoleculeTypeAtomRoleId } from './model/types';
import { Vec3 } from 'mol-math/linear-algebra';
import { Unit } from './structure';
import Matrix from 'mol-math/linear-algebra/matrix/matrix';
export function getMoleculeType(model: Model, rI: ResidueIndex) {
const compId = model.atomicHierarchy.residues.label_comp_id.value(rI)
const chemCompMap = model.properties.chemicalComponentMap
const cc = chemCompMap.get(compId)
return cc ? cc.moleculeType : MoleculeType.unknown
}
export function getAtomIdForAtomRole(moleculeType: MoleculeType, atomRole: AtomRole) {
const m = MoleculeTypeAtomRoleId[moleculeType]
if (m !== undefined) {
const a = m[atomRole]
if (a !== undefined) return a
}
return ''
}
export function getElementIndexForAtomId(model: Model, rI: ResidueIndex, atomId: string): ElementIndex | -1 {
const { offsets } = model.atomicHierarchy.residueAtomSegments
const { label_atom_id } = model.atomicHierarchy.atoms
for (let j = offsets[rI], _j = offsets[rI + 1]; j < _j; j++) {
if (label_atom_id.value(j) === atomId) return j as ElementIndex
}
return -1
}
export function getElementIndexForAtomRole(model: Model, rI: ResidueIndex, atomRole: AtomRole) {
const atomId = getAtomIdForAtomRole(getMoleculeType(model, rI), atomRole)
return getElementIndexForAtomId(model, rI, atomId)
}
export function residueLabel(model: Model, rI: number) {
const { residues, chains, residueAtomSegments, chainAtomSegments } = model.atomicHierarchy
const { label_comp_id, label_seq_id } = residues
const { label_asym_id } = chains
const cI = chainAtomSegments.index[residueAtomSegments.offsets[rI]]
return `${label_asym_id.value(cI)} ${label_comp_id.value(rI)} ${label_seq_id.value(rI)}`
}
const centerPos = Vec3.zero()
const centerMin = Vec3.zero()
export function getCenterAndRadius(centroid: Vec3, unit: Unit, indices: ArrayLike<number>) {
const pos = unit.conformation.position
const { elements } = unit
Vec3.set(centroid, 0, 0, 0)
for (let i = 0, il = indices.length; i < il; ++i) {
pos(elements[indices[i]], centerPos)
Vec3.add(centroid, centroid, centerPos)
Vec3.min(centerMin, centerMin, centerPos)
}
Vec3.scale(centroid, centroid, 1/indices.length)
return Vec3.distance(centerMin, centroid)
}
const matrixPos = Vec3.zero()
export function getPositionMatrix(unit: Unit, indices: ArrayLike<number>) {
const pos = unit.conformation.position
const mat = Matrix.create(3, indices.length)
const { elements } = unit
for (let i = 0, il = indices.length; i < il; ++i) {
pos(elements[indices[i]], matrixPos)
Vec3.toArray(matrixPos, mat.data, i * 3)
}
return mat
}