matterviz 0.3.5 → 0.3.6

package/dist/structure/export.js

@@ -1,727 +0,0 @@
-import { get_electro_neg_formula } from '../composition';
-import { download } from '../io/fetch';
-import * as math from '../math';
-import { Color, Group, Matrix4, Mesh, MeshStandardMaterial, ShaderMaterial } from 'three';
-import { GLTFExporter } from 'three/examples/jsm/exporters/GLTFExporter.js';
-import { OBJExporter } from 'three/examples/jsm/exporters/OBJExporter.js';
-// Type guard to check if a material has a color property (duck typing for bundler compatibility)
-// Uses duck typing to work across different Three.js instances (Threlte vs vanilla Three.js)
-export function has_color_property(mat) {
-    if (!(`color` in mat))
-        return false;
-    const color = mat.color;
-    if (!color || typeof color !== `object`)
-        return false;
-    // Check for Color-like object with numeric r/g/b channels (duck typing)
-    const color_obj = color;
-    const red_channel = color_obj.r;
-    const green_channel = color_obj.g;
-    const blue_channel = color_obj.b;
-    return (typeof red_channel === `number` &&
-        typeof green_channel === `number` &&
-        typeof blue_channel === `number`);
-}
-// Extract color from a ShaderMaterial by checking common color uniform patterns
-function extract_shader_color(shader_mat) {
-    const uniforms = shader_mat.uniforms;
-    if (!uniforms)
-        return null;
-    // Check for common color uniform names
-    for (const key of [`color`, `diffuse`, `baseColor`, `uColor`]) {
-        if (uniforms[key]?.value instanceof Color) {
-            return uniforms[key].value.clone();
-        }
-    }
-    // For gradient bonds, try to extract midpoint color from instanceColorStart/End attributes
-    // These are set as geometry attributes, not uniforms, so we return a default gray
-    return null;
-}
-// Convert ShaderMaterial to MeshStandardMaterial for export compatibility
-function convert_shader_to_standard(shader_mat) {
-    const extracted_color = extract_shader_color(shader_mat);
-    const standard_mat = new MeshStandardMaterial({
-        color: extracted_color ?? new Color(0.5, 0.5, 0.5),
-        metalness: 0.1,
-        roughness: 0.5,
-    });
-    standard_mat.name = shader_mat.name || `converted_shader_material`;
-    return standard_mat;
-}
-// Extract bond gradient colors from geometry attributes for a specific instance
-// Returns midpoint color between start and end colors for the bond
-export function extract_bond_color_for_instance(geometry, instance_idx) {
-    const color_start_attr = geometry.getAttribute(`instanceColorStart`);
-    const color_end_attr = geometry.getAttribute(`instanceColorEnd`);
-    if (!color_start_attr || !color_end_attr)
-        return null;
-    if (instance_idx < 0 || instance_idx >= color_start_attr.count)
-        return null;
-    // Get RGB values for this instance and compute midpoint color
-    const start_rgb = [
-        color_start_attr.getX(instance_idx),
-        color_start_attr.getY(instance_idx),
-        color_start_attr.getZ(instance_idx),
-    ];
-    const end_rgb = [
-        color_end_attr.getX(instance_idx),
-        color_end_attr.getY(instance_idx),
-        color_end_attr.getZ(instance_idx),
-    ];
-    const [mid_r, mid_g, mid_b] = math.scale(math.add(start_rgb, end_rgb), 0.5);
-    return new Color(mid_r, mid_g, mid_b);
-}
-// Remove custom/non-standard attributes from geometry that cause export issues
-// Standard GLTF attributes: position, normal, tangent, texcoord_N, color_N, joints_N, weights_N
-export function clean_geometry_for_export(geometry) {
-    const standard_attrs = new Set([
-        `position`,
-        `normal`,
-        `tangent`,
-        `uv`,
-        `uv1`,
-        `uv2`,
-        `uv3`,
-        `color`,
-        `skinIndex`,
-        `skinWeight`,
-    ]);
-    const attrs_to_remove = [];
-    for (const attr_name of Object.keys(geometry.attributes)) {
-        // Keep standard attributes and those starting with underscore (GLTF custom)
-        // But remove instance-specific attributes that cause accessor count mismatches
-        const lower_name = attr_name.toLowerCase();
-        if (lower_name.includes(`instance`) ||
-            (lower_name.includes(`color`) && !standard_attrs.has(lower_name)))
-            attrs_to_remove.push(attr_name);
-    }
-    for (const attr_name of attrs_to_remove) {
-        geometry.deleteAttribute(attr_name);
-    }
-}
-// Generate MTL (Wavefront Material) content from scene materials
-export function generate_mtl_content(scene) {
-    const lines = [`# MTL file generated by MatterViz`, ``];
-    const processed_materials = new Set();
-    scene.traverse((object) => {
-        if (!(object instanceof Mesh))
-            return;
-        const materials = Array.isArray(object.material) ? object.material : [object.material];
-        for (const mat of materials) {
-            // Skip if already processed or no name
-            const mat_name = mat.name || `default_material`;
-            if (processed_materials.has(mat_name))
-                continue;
-            processed_materials.add(mat_name);
-            lines.push(`newmtl ${mat_name}`);
-            // Get diffuse color (main color)
-            if (has_color_property(mat)) {
-                const color = mat.color;
-                lines.push(`Kd ${color.r.toFixed(6)} ${color.g.toFixed(6)} ${color.b.toFixed(6)}`);
-                // Ambient is typically a fraction of diffuse
-                lines.push(`Ka ${(color.r * 0.2).toFixed(6)} ${(color.g * 0.2).toFixed(6)} ${(color.b * 0.2).toFixed(6)}`);
-            }
-            else {
-                // Default white if no color
-                lines.push(`Kd 1.000000 1.000000 1.000000`);
-                lines.push(`Ka 0.200000 0.200000 0.200000`);
-            }
-            // Specular properties
-            lines.push(`Ks 0.500000 0.500000 0.500000`);
-            lines.push(`Ns 96.078431`); // Specular exponent
-            // Transparency (d = 1.0 is fully opaque)
-            const opacity = `opacity` in mat && typeof mat.opacity === `number` ? mat.opacity : 1.0;
-            lines.push(`d ${opacity.toFixed(6)}`);
-            // Illumination model (2 = highlight on)
-            lines.push(`illum 2`);
-            lines.push(``);
-        }
-    });
-    return lines.join(`\n`);
-}
-// Extract color from material, returning RGB values or null if not found
-function extract_material_color(mat) {
-    if (has_color_property(mat)) {
-        return { r: mat.color.r, g: mat.color.g, b: mat.color.b };
-    }
-    return null;
-}
-// Helper function to convert InstancedMesh to regular Mesh objects for export
-// This is necessary because GLB/OBJ exporters don't handle InstancedMesh properly
-// Note: Threlte's InstancedMesh sets isInstancedMesh=true but type remains "Mesh"
-// Type guard for InstancedMesh (Three.js uses isInstancedMesh property, not exposed in Object3D type)
-const is_instanced_mesh = (obj) => obj.isInstancedMesh || obj.type === `InstancedMesh`;
-function convert_instanced_meshes_to_regular(scene) {
-    // STEP 1: Collect material colors from ORIGINAL scene BEFORE cloning
-    // This is crucial because scene.clone() may not properly preserve Threlte's material colors
-    const material_colors = new Map();
-    const bond_colors_map = new Map();
-    scene.traverse((object) => {
-        const is_instanced = is_instanced_mesh(object);
-        if (!is_instanced)
-            return;
-        const instanced_mesh = object;
-        const mesh_id = instanced_mesh.uuid;
-        // Check if this is a shader material (bonds)
-        const mat = instanced_mesh.material;
-        const is_shader = Array.isArray(mat)
-            ? mat.some((m) => m instanceof ShaderMaterial)
-            : mat instanceof ShaderMaterial;
-        if (is_shader) {
-            // Extract bond colors for each instance from geometry attributes
-            const instance_colors = new Map();
-            for (let idx = 0; idx < instanced_mesh.count; idx++) {
-                const bond_color = extract_bond_color_for_instance(instanced_mesh.geometry, idx);
-                if (bond_color) {
-                    instance_colors.set(idx, bond_color);
-                }
-            }
-            bond_colors_map.set(mesh_id, instance_colors);
-        }
-        else {
-            // Extract shared material color for atoms
-            const single_mat = Array.isArray(mat) ? mat[0] : mat;
-            const color = extract_material_color(single_mat);
-            if (color) {
-                material_colors.set(mesh_id, color);
-            }
-        }
-    });
-    // STEP 2: Clone the scene
-    const cloned_scene = scene.clone();
-    // STEP 3: Find all InstancedMesh objects in the cloned scene and build uuid mapping
-    const original_meshes = [];
-    const cloned_meshes = [];
-    scene.traverse((object) => {
-        if (is_instanced_mesh(object))
-            original_meshes.push(object);
-    });
-    cloned_scene.traverse((object) => {
-        if (is_instanced_mesh(object))
-            cloned_meshes.push(object);
-    });
-    // STEP 4: Convert each InstancedMesh to individual Mesh objects
-    for (let mesh_idx = 0; mesh_idx < cloned_meshes.length; mesh_idx++) {
-        const instanced_mesh = cloned_meshes[mesh_idx];
-        const original_mesh = original_meshes[mesh_idx];
-        const original_uuid = original_mesh?.uuid || instanced_mesh.uuid;
-        const parent = instanced_mesh.parent;
-        if (!parent || !instanced_mesh.instanceMatrix)
-            continue;
-        // Create a group to hold all the individual meshes
-        const group = new Group();
-        group.name = instanced_mesh.name;
-        // Get the base transform from the InstancedMesh
-        const base_matrix = new Matrix4();
-        base_matrix.copy(instanced_mesh.matrix);
-        // Get stored colors for this mesh
-        const stored_color = material_colors.get(original_uuid);
-        const stored_bond_colors = bond_colors_map.get(original_uuid);
-        // Check if material is a ShaderMaterial
-        const original_material = instanced_mesh.material;
-        const has_shader = Array.isArray(original_material)
-            ? original_material.some((mat) => mat instanceof ShaderMaterial)
-            : original_material instanceof ShaderMaterial;
-        // Create individual meshes for each instance
-        const instance_matrix = new Matrix4();
-        for (let idx = 0; idx < instanced_mesh.count; idx++) {
-            instanced_mesh.getMatrixAt(idx, instance_matrix);
-            // Clone geometry
-            const cloned_geometry = instanced_mesh.geometry.clone();
-            // Clean up custom attributes from shader-based geometries
-            if (has_shader) {
-                clean_geometry_for_export(cloned_geometry);
-            }
-            // Create material - always create fresh MeshStandardMaterial for reliability
-            const new_material = new MeshStandardMaterial({
-                metalness: 0.1,
-                roughness: 0.5,
-            });
-            new_material.name = `material_${mesh_idx}_${idx}`;
-            // Apply the correct color
-            const bond_color = stored_bond_colors?.get(idx);
-            if (bond_color) {
-                // Bond with gradient color - use stored midpoint color
-                new_material.color.copy(bond_color);
-            }
-            else if (stored_color) {
-                // Atom with shared material color
-                new_material.color.setRGB(stored_color.r, stored_color.g, stored_color.b);
-            }
-            else if (instanced_mesh.instanceColor) {
-                // Fallback: per-instance colors from instanceColor attribute
-                const color_r = instanced_mesh.instanceColor.getX(idx);
-                const color_g = instanced_mesh.instanceColor.getY(idx);
-                const color_b = instanced_mesh.instanceColor.getZ(idx);
-                new_material.color.setRGB(color_r, color_g, color_b);
-            }
-            // If no color found, material stays default white
-            const mesh = new Mesh(cloned_geometry, new_material);
-            // Combine base transform with instance transform
-            const combined_matrix = new Matrix4();
-            combined_matrix.multiplyMatrices(base_matrix, instance_matrix);
-            mesh.applyMatrix4(combined_matrix);
-            group.add(mesh);
-        }
-        // Replace the InstancedMesh with the Group in the parent
-        parent.remove(instanced_mesh);
-        parent.add(group);
-        // Update world matrices after scene graph modification
-        group.updateMatrixWorld(true);
-    }
-    // Update all world matrices in the modified scene
-    cloned_scene.updateMatrixWorld(true);
-    // Convert any remaining ShaderMaterials to standard materials (e.g. non-instanced bonds)
-    // Also clean up custom geometry attributes that cause export validation errors
-    cloned_scene.traverse((object) => {
-        if (object instanceof Mesh) {
-            let has_shader_material = false;
-            if (object.material instanceof ShaderMaterial) {
-                object.material = convert_shader_to_standard(object.material);
-                has_shader_material = true;
-            }
-            else if (Array.isArray(object.material)) {
-                has_shader_material = object.material.some((mat) => mat instanceof ShaderMaterial);
-                object.material = object.material.map((mat) => mat instanceof ShaderMaterial ? convert_shader_to_standard(mat) : mat);
-            }
-            // Clean up custom attributes from geometries that had shader materials
-            if (has_shader_material && object.geometry) {
-                clean_geometry_for_export(object.geometry);
-            }
-        }
-    });
-    return cloned_scene;
-}
-// Generate a filename for structure exports based on structure metadata
-// Sanitize string for use in filenames by removing problematic characters.
-const sanitize_filename_part = (text) => text
-    .replace(/<\/?[^>]+>/g, ``) // strip HTML tags
-    .replace(/[/\\:*?"<>|]/g, `_`) // replace filesystem-invalid chars
-    .replace(/_+/g, `_`) // condense consecutive underscores
-    .replace(/^_|_$/g, ``); // remove leading/trailing underscores
-export function create_structure_filename(structure, extension) {
-    if (!structure)
-        return `structure.${extension}`;
-    const parts = [];
-    // Helper to sanitize and push non-empty parts
-    const safe_push = (value) => {
-        const sanitized = value ? sanitize_filename_part(value) : ``;
-        if (sanitized)
-            parts.push(sanitized);
-    };
-    safe_push(structure.id);
-    // Add formula (plain text to avoid HTML in filenames)
-    const formula = get_electro_neg_formula(structure, true);
-    if (formula && formula !== `Unknown`) {
-        safe_push(formula.replaceAll(` `, ``));
-    }
-    // Add space group if available
-    if (`symmetry` in structure &&
-        structure.symmetry &&
-        typeof structure.symmetry === `object` &&
-        `space_group_symbol` in structure.symmetry) {
-        const space_group = structure.symmetry.space_group_symbol;
-        if (space_group && typeof space_group === `string`) {
-            safe_push(space_group.replaceAll(` `, ``));
-        }
-    }
-    // Add lattice system if available
-    if (`lattice` in structure &&
-        structure.lattice &&
-        typeof structure.lattice === `object` &&
-        `lattice_system` in structure.lattice) {
-        const lattice_system = structure.lattice.lattice_system;
-        if (lattice_system && typeof lattice_system === `string`) {
-            safe_push(lattice_system);
-        }
-    }
-    // Add number of sites
-    if (structure.sites?.length)
-        parts.push(`${structure.sites.length}sites`);
-    const base_name = parts.length > 0 ? parts.join(`-`) : `structure`;
-    return `${base_name}.${extension}`;
-}
-// Generate XYZ content string without saving
-export function structure_to_xyz_str(structure) {
-    if (!structure?.sites)
-        throw new Error(`No structure or sites to export`);
-    const lines = [];
-    // First line: number of atoms
-    lines.push(String(structure.sites.length));
-    // Second line: comment (structure ID, formula, or default)
-    const comment_parts = [];
-    if (structure.id)
-        comment_parts.push(structure.id);
-    const formula = get_electro_neg_formula(structure, true);
-    if (formula && formula !== `Unknown`)
-        comment_parts.push(formula);
-    // Include extended XYZ lattice information when available so round-trips preserve lattice
-    if (`lattice` in structure && structure.lattice?.matrix?.length === 3) {
-        const lattice_values = structure.lattice.matrix
-            .flat()
-            .map((value) => (Number.isFinite(value) ? value : 0).toFixed(8))
-            .join(` `);
-        comment_parts.push(`Lattice="${lattice_values}"`);
-    }
-    const comment = comment_parts.length > 0 ? comment_parts.join(` `) : `Generated from structure`;
-    lines.push(comment);
-    // Cache converter for fractional→Cartesian (if lattice available)
-    const frac_to_cart = `lattice` in structure && structure.lattice?.matrix?.length === 3
-        ? math.create_frac_to_cart(structure.lattice.matrix)
-        : null;
-    // Atom lines: element symbol followed by x, y, z coordinates
-    for (const site of structure.sites) {
-        // Extract element symbol from species
-        let element_symbol = `X`; // default fallback
-        if (site.species && Array.isArray(site.species) && site.species.length > 0) {
-            // species is an array of Species objects with element property
-            const first_species = site.species[0];
-            if (first_species && `element` in first_species && first_species.element)
-                element_symbol = first_species.element;
-        }
-        // Get coordinates - prefer xyz; fallback to abc (converted to cartesian if lattice available)
-        let coords;
-        if (site.xyz && Array.isArray(site.xyz) && site.xyz.length >= 3) {
-            coords = site.xyz.slice(0, 3);
-        }
-        else if (site.abc?.length >= 3 && frac_to_cart) {
-            coords = frac_to_cart(site.abc);
-        }
-        else
-            coords = [0, 0, 0]; // fallback
-        // Format coordinates to reasonable precision
-        const [x, y, z] = coords.map((coord) => coord.toFixed(6));
-        lines.push(`${element_symbol} ${x} ${y} ${z}`);
-    }
-    return lines.join(`\n`);
-}
-// Generate a valid CIF data block name from structure formula
-// CIF block names can contain alphanumerics, underscores, but no spaces or special chars
-function get_cif_block_name(structure) {
-    try {
-        // Count atoms per element (rounded to nearest integer for occupancy)
-        const element_counts = {};
-        for (const site of structure.sites) {
-            if (!site.species || !Array.isArray(site.species))
-                continue;
-            for (const species of site.species) {
-                if (!species.element)
-                    continue;
-                const count = species.occu ?? 1;
-                element_counts[species.element] = (element_counts[species.element] ?? 0) + count;
-            }
-        }
-        // Sort elements alphabetically and build formula string
-        const elements = Object.keys(element_counts).sort();
-        if (elements.length === 0)
-            throw new Error(`No elements found`);
-        const formula = elements
-            .map((el) => {
-            const count = Math.round(element_counts[el]);
-            if (count === 0)
-                return null; // filter out near-zero occupancies
-            return count === 1 ? el : `${el}${count}`;
-        })
-            .filter((part) => part !== null)
-            .join(``);
-        if (!formula)
-            throw new Error(`All occupancies round to zero`);
-        return formula;
-    }
-    catch {
-        // Fall back to structure.id (sanitized) or generic name
-        if (structure.id) {
-            // Remove invalid CIF characters (keep alphanumerics and underscores)
-            // and condense consecutive underscores for cleaner block names
-            return structure.id.replace(/[^a-zA-Z0-9_]/g, `_`).replace(/_+/g, `_`);
-        }
-        return `structure`;
-    }
-}
-// Generate CIF content string without saving
-export function structure_to_cif_str(structure) {
-    if (!structure?.sites)
-        throw new Error(`No structure or sites to export`);
-    if (!(`lattice` in structure) || !structure.lattice) {
-        throw new Error(`No lattice information for CIF export`);
-    }
-    const lines = [];
-    // CIF header with data block (required by pymatgen and CIF spec)
-    lines.push(`# CIF file generated by MatterViz`);
-    const block_name = get_cif_block_name(structure);
-    lines.push(`data_${block_name}`);
-    lines.push(``);
-    // Cell parameters
-    const lattice = structure.lattice;
-    if (lattice.a && lattice.b && lattice.c) {
-        lines.push(`_cell_length_a ${lattice.a.toFixed(6)}`);
-        lines.push(`_cell_length_b ${lattice.b.toFixed(6)}`);
-        lines.push(`_cell_length_c ${lattice.c.toFixed(6)}`);
-    }
-    if (lattice.alpha && lattice.beta && lattice.gamma) {
-        lines.push(`_cell_angle_alpha ${lattice.alpha.toFixed(6)}`);
-        lines.push(`_cell_angle_beta ${lattice.beta.toFixed(6)}`);
-        lines.push(`_cell_angle_gamma ${lattice.gamma.toFixed(6)}`);
-    }
-    // Space group information
-    if (`symmetry` in structure &&
-        structure.symmetry &&
-        typeof structure.symmetry === `object`) {
-        const symmetry = structure.symmetry;
-        const { space_group_number, space_group_symbol } = symmetry;
-        if (typeof space_group_symbol === `string` && space_group_symbol) {
-            lines.push(`_space_group_name_H-M_alt ${space_group_symbol}`);
-        }
-        if ((typeof space_group_number === `number` || typeof space_group_number === `string`) &&
-            space_group_number) {
-            lines.push(`_space_group_IT_number ${space_group_number}`);
-        }
-    }
-    lines.push(``);
-    // Atom site loop header
-    lines.push(`loop_`);
-    lines.push(`_atom_site_label`);
-    lines.push(`_atom_site_type_symbol`);
-    lines.push(`_atom_site_fract_x`);
-    lines.push(`_atom_site_fract_y`);
-    lines.push(`_atom_site_fract_z`);
-    lines.push(`_atom_site_occupancy`);
-    // Cache inverse transpose for Cartesian→fractional conversion (avoids recomputing per site)
-    const cart_to_frac = lattice.matrix?.length === 3 ? math.create_cart_to_frac(lattice.matrix) : null;
-    // Atom sites
-    for (let idx = 0; idx < structure.sites.length; idx++) {
-        const site = structure.sites[idx];
-        if (!site)
-            continue; // Skip if site is undefined
-        // Extract element symbol from species
-        let element_symbol = `X`; // default fallback
-        let occupancy = 1;
-        if (site.species && Array.isArray(site.species) && site.species.length > 0) {
-            const first_species = site.species[0];
-            if (first_species && `element` in first_species && first_species.element) {
-                element_symbol = first_species.element;
-                occupancy = first_species?.occu ?? 1;
-            }
-        }
-        // Get fractional coordinates
-        let frac_coords;
-        if (site.abc && Array.isArray(site.abc) && site.abc.length >= 3) {
-            frac_coords = site.abc.slice(0, 3);
-        }
-        else if (site.xyz?.length >= 3 && cart_to_frac) {
-            frac_coords = cart_to_frac(site.xyz);
-        }
-        else
-            throw new Error(`No valid coordinates found for site ${idx}`);
-        // Format: label element_symbol x y z
-        const label = site.label || `${element_symbol}${idx + 1}`;
-        lines.push(`${label} ${element_symbol} ${frac_coords[0].toFixed(8)} ${frac_coords[1].toFixed(8)} ${frac_coords[2].toFixed(8)} ${occupancy.toFixed(8)}`);
-    }
-    return lines.join(`\n`);
-}
-// Generate VASP POSCAR content string without saving
-export function structure_to_poscar_str(structure) {
-    if (!structure?.sites)
-        throw new Error(`No structure or sites to export`);
-    if (!(`lattice` in structure) || !structure.lattice) {
-        throw new Error(`No lattice information for POSCAR export`);
-    }
-    const lines = [];
-    // Use plain text formula for POSCAR title to avoid HTML tags
-    const formula = get_electro_neg_formula(structure, true);
-    const title = structure.id ||
-        (formula && formula !== `Unknown` ? formula : null) ||
-        `Generated from structure`;
-    lines.push(title);
-    lines.push(`1.0`); // Scale factor (1.0 for direct coordinates)
-    const lattice = structure.lattice;
-    if (lattice.matrix && Array.isArray(lattice.matrix) && lattice.matrix.length >= 3) {
-        // Convert 3x3 matrix to 3 vectors
-        const matrix = lattice.matrix;
-        lines.push(`${matrix[0][0].toFixed(8)} ${matrix[0][1].toFixed(8)} ${matrix[0][2].toFixed(8)}`);
-        lines.push(`${matrix[1][0].toFixed(8)} ${matrix[1][1].toFixed(8)} ${matrix[1][2].toFixed(8)}`);
-        lines.push(`${matrix[2][0].toFixed(8)} ${matrix[2][1].toFixed(8)} ${matrix[2][2].toFixed(8)}`);
-    }
-    else {
-        throw new Error(`No valid lattice matrix for POSCAR export`);
-    }
-    // Count atoms by element
-    const element_counts = new Map();
-    const element_symbols = [];
-    for (const site of structure.sites) {
-        let element_symbol = `X`; // default fallback
-        if (site.species && Array.isArray(site.species) && site.species.length > 0) {
-            const first_species = site.species[0];
-            if (first_species && `element` in first_species && first_species.element) {
-                element_symbol = first_species.element;
-            }
-        }
-        if (!element_counts.has(element_symbol)) {
-            element_counts.set(element_symbol, 0);
-            element_symbols.push(element_symbol);
-        }
-        element_counts.set(element_symbol, Number(element_counts.get(element_symbol)) + 1);
-    }
-    // Element symbols line
-    lines.push(element_symbols.join(` `));
-    // Atom counts line
-    lines.push(element_symbols.map((el) => element_counts.get(el)).join(` `));
-    // Check if any site has selective dynamics
-    const has_selective_dynamics = structure.sites.some((site) => site.properties?.selective_dynamics);
-    if (has_selective_dynamics) {
-        lines.push(`Selective dynamics`);
-    }
-    // Coordinate mode (Direct = fractional coordinates)
-    lines.push(`Direct`);
-    // Cache inverse transpose for Cartesian→fractional conversion (avoids recomputing per site)
-    const cart_to_frac = lattice.matrix?.length === 3 ? math.create_cart_to_frac(lattice.matrix) : null;
-    // Atom coordinates grouped by element
-    for (const element_symbol of element_symbols) {
-        for (const site of structure.sites) {
-            let site_element = `X`;
-            if (site.species && Array.isArray(site.species) && site.species.length > 0) {
-                const first_species = site.species[0];
-                if (first_species && `element` in first_species && first_species.element) {
-                    site_element = first_species.element;
-                }
-            }
-            if (site_element === element_symbol) {
-                // Get fractional coordinates
-                let frac_coords;
-                if (site.abc && Array.isArray(site.abc) && site.abc.length >= 3) {
-                    frac_coords = site.abc.slice(0, 3);
-                }
-                else if (site.xyz?.length >= 3 && cart_to_frac) {
-                    frac_coords = cart_to_frac(site.xyz.slice(0, 3));
-                }
-                else {
-                    throw new Error(`No valid coordinates found for site`);
-                }
-                let selective_dynamics_str = ``;
-                if (has_selective_dynamics) {
-                    const sel_dyn = (site.properties?.selective_dynamics ?? [
-                        true,
-                        true,
-                        true,
-                    ]);
-                    selective_dynamics_str = ` ${sel_dyn[0] ? `T` : `F`} ${sel_dyn[1] ? `T` : `F`} ${sel_dyn[2] ? `T` : `F`}`;
-                }
-                lines.push(`${frac_coords[0].toFixed(8)} ${frac_coords[1].toFixed(8)} ${frac_coords[2].toFixed(8)}${selective_dynamics_str}`);
-            }
-        }
-    }
-    return lines.join(`\n`);
-}
-// Generate JSON content string without saving
-export function structure_to_json_str(structure) {
-    if (!structure)
-        throw new Error(`No structure to export`);
-    return JSON.stringify(structure, null, 2);
-}
-// Export structure as CIF format
-export function export_structure_as_cif(structure) {
-    try {
-        const content = structure_to_cif_str(structure);
-        const filename = create_structure_filename(structure, `cif`);
-        download(content, filename, `chemical/x-cif`);
-    }
-    catch (error) {
-        console.error(`Failed to export CIF:`, error);
-    }
-}
-// Export structure as VASP POSCAR format
-export function export_structure_as_poscar(structure) {
-    try {
-        const content = structure_to_poscar_str(structure);
-        const filename = create_structure_filename(structure, `poscar`);
-        download(content, filename, `text/plain`);
-    }
-    catch (error) {
-        console.error(`Failed to export POSCAR:`, error);
-    }
-}
-// Export structure as XYZ format. Format specification:
-// - Line 1: Number of atoms
-// - Line 2: Comment line (structure ID, formula, etc.)
-// - Remaining lines: Element symbol followed by x, y, z coordinates (in Angstrom)
-export function export_structure_as_xyz(structure) {
-    try {
-        const xyz_content = structure_to_xyz_str(structure);
-        const filename = create_structure_filename(structure, `xyz`);
-        download(xyz_content, filename, `text/plain`);
-    }
-    catch (error) {
-        console.error(`Error exporting XYZ:`, error);
-    }
-}
-// Export structure in pymatgen JSON format
-export function export_structure_as_json(structure) {
-    try {
-        const data = structure_to_json_str(structure);
-        const filename = create_structure_filename(structure, `json`);
-        download(data, filename, `application/json`);
-    }
-    catch (error) {
-        console.error(`Error exporting JSON:`, error);
-    }
-}
-// Export Three.js scene as GLB (binary GLTF) file
-// GLB preserves materials and colors, making it ideal for element visualization
-export function export_structure_as_glb(scene, structure) {
-    try {
-        if (!scene) {
-            console.warn(`No scene available for GLB export`);
-            return;
-        }
-        // Convert instanced meshes to regular meshes for export
-        const export_scene = convert_instanced_meshes_to_regular(scene);
-        const exporter = new GLTFExporter();
-        const filename = create_structure_filename(structure, `glb`);
-        // Export as binary GLB format
-        exporter.parse(export_scene, (result) => {
-            if (result instanceof ArrayBuffer) {
-                const blob = new Blob([result], { type: `model/gltf-binary` });
-                download(blob, filename, `model/gltf-binary`);
-            }
-            else {
-                console.error(`GLB export returned unexpected format`);
-            }
-        }, (error) => {
-            console.error(`GLB export failed:`, error);
-        }, { binary: true });
-    }
-    catch (error) {
-        console.error(`Error exporting GLB:`, error);
-    }
-}
-// Export Three.js scene as OBJ (Wavefront Object) file with accompanying MTL file for materials
-// OBJ exports geometry with material references, MTL contains color definitions
-export function export_structure_as_obj(scene, structure) {
-    try {
-        if (!scene) {
-            console.warn(`No scene available for OBJ export`);
-            return;
-        }
-        // Convert instanced meshes to regular meshes for export
-        const export_scene = convert_instanced_meshes_to_regular(scene);
-        const obj_exporter = new OBJExporter();
-        const base_filename = create_structure_filename(structure, ``).replace(/\.$/, ``);
-        const obj_filename = `${base_filename}.obj`;
-        const mtl_filename = `${base_filename}.mtl`;
-        // Generate OBJ content with material library reference
-        let obj_content = obj_exporter.parse(export_scene);
-        // Add material library reference at the beginning of the OBJ file
-        obj_content = `mtllib ${mtl_filename}\n${obj_content}`;
-        // Generate MTL content with material color definitions
-        const mtl_content = generate_mtl_content(export_scene);
-        // Download both files
-        const obj_blob = new Blob([obj_content], { type: `text/plain` });
-        const mtl_blob = new Blob([mtl_content], { type: `text/plain` });
-        download(obj_blob, obj_filename, `text/plain`);
-        // Small delay to prevent some browsers from blocking rapid successive downloads as potential abuse.
-        // A more robust solution might be to zip both files together.
-        setTimeout(() => download(mtl_blob, mtl_filename, `text/plain`), 100);
-    }
-    catch (error) {
-        console.error(`Error exporting OBJ:`, error);
-    }
-}