Filters

The concept — six structure modifiers run in a fixed pipeline before display — is introduced in General → The structure model. This page covers driving them from code.

removeatoms → addhydrogen → missingbonds → disorder → symmetry → hydrogen

Key in viewer.modifiers	Class	Modes	Purpose
removeatoms	AtomLabelFilter	on, off	Strips explicitly excluded atoms (comma list, supports "A1>A10" ranges).
addhydrogen	IsolatedHydrogenFixer	on, off	Bonds orphan hydrogen atoms to a nearby heavy atom.
missingbonds	BondGenerator	keep, add, replace, create, ignore	Generates bonds from interatomic distances when the CIF doesn't list them.
disorder	DisorderFilter	all, group<rank>of<total>	Shows only one disorder group (plus non-disordered atoms) at a time.
symmetry	SymmetryGrower	none, hbonds, fragment, fragment-hbonds, cell, fragment-cell	Grows one additional symmetry sphere via bonds, H-bonds, or the whole unit cell.
hydrogen	HydrogenFilter	none, constant, anisotropic	Controls hydrogen atom display (hidden, constant-radius sphere, or real ADP).

Via a viewer

viewer.modifiers.hydrogen.mode = 'constant';
await viewer.updateStructure();

For filters whose mode change alters the structure's extent (symmetry, removeatoms), call viewer.loadStructure() instead so the camera resets — see CrystalViewer.

Standalone, without a viewer

HydrogenFilter, DisorderFilter, SymmetryGrower, AtomLabelFilter, and BondGenerator are all exported from the package root, so you can filter a CrystalStructure directly — useful for batch processing or non-visual tooling (they also work in Node via cifvis/nobrowser):

import { CIF, CrystalStructure, SymmetryGrower } from 'cifvis';

const cif = new CIF(cifText);
const structure = CrystalStructure.fromCIF(cif.getBlock(0));

const grower = new SymmetryGrower('fragment');
const grownStructure = grower.apply(structure);

Related utility exports

A few small helpers are exported alongside the filters:

Export	Purpose
formatValueEsd(value, su)	Formats a value and its standard uncertainty back into 1.234(5) notation.
tryToFixCifBlock(block)	Attempts common CIF repairs before CrystalStructure.fromCIF — see CIF files.
getDisorderIcon(mode)	Returns the built-in SVG icon for a disorder mode button.
generateDisorderGroupIcon(rank, total)	Generates an SVG icon for an arbitrary group<rank>of<total> disorder mode.