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41 results

sp-after.mol2

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  • 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
    }