molstar 4.2.0 → 4.4.0

package/lib/mol-gl/shader/direct-volume.frag.d.ts

@@ -4,4 +4,4 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author Michael Krone <michael.krone@uni-tuebingen.de>
  */
-export declare const directVolume_frag = "\nprecision highp float;\nprecision highp int;\n\n#include common\n#include light_frag_params\n\n#if dClipObjectCount != 0\n    uniform int uClipObjectType[dClipObjectCount];\n    uniform bool uClipObjectInvert[dClipObjectCount];\n    uniform vec3 uClipObjectPosition[dClipObjectCount];\n    uniform vec4 uClipObjectRotation[dClipObjectCount];\n    uniform vec3 uClipObjectScale[dClipObjectCount];\n#endif\n#include common_clip\n\n#include read_from_texture\n#include texture3d_from_1d_trilinear\n#include texture3d_from_2d_nearest\n#include texture3d_from_2d_linear\n\nuniform mat4 uProjection, uTransform, uModelView, uModel, uView;\nuniform vec3 uCameraDir;\n\nuniform sampler2D tDepth;\nuniform vec2 uDrawingBufferSize;\n\nvarying vec3 vOrigPos;\nvarying float vInstance;\nvarying vec4 vBoundingSphere;\nvarying mat4 vTransform;\n\nuniform mat4 uInvView;\nuniform vec3 uGridDim;\nuniform vec3 uBboxSize;\nuniform sampler2D tTransferTex;\nuniform float uTransferScale;\nuniform float uStepScale;\nuniform float uJumpLength;\n\nuniform int uObjectId;\nuniform int uVertexCount;\nuniform int uInstanceCount;\nuniform int uGroupCount;\n\n#if defined(dColorMarker)\n    uniform vec3 uHighlightColor;\n    uniform vec3 uSelectColor;\n    uniform vec3 uDimColor;\n    uniform float uHighlightStrength;\n    uniform float uSelectStrength;\n    uniform float uDimStrength;\n    uniform int uMarkerPriority;\n    uniform float uMarkerAverage;\n\n    uniform float uMarker;\n    uniform vec2 uMarkerTexDim;\n    uniform sampler2D tMarker;\n#endif\n\nuniform float uMetalness;\nuniform float uRoughness;\nuniform float uEmissive;\n\nuniform bool uFog;\nuniform float uFogNear;\nuniform float uFogFar;\nuniform vec3 uFogColor;\n\nuniform float uAlpha;\nuniform bool uTransparentBackground;\nuniform float uXrayEdgeFalloff;\nuniform float uExposure;\n\nuniform int uRenderMask;\n\nuniform float uNear;\nuniform float uFar;\nuniform float uIsOrtho;\n\nuniform vec3 uCellDim;\nuniform vec3 uCameraPosition;\nuniform mat4 uCartnToUnit;\n\n#if __VERSION__ != 100\n    // for webgl1 this is given as a 'define'\n    uniform int uMaxSteps;\n#endif\n\n#if defined(dGridTexType_2d)\n    precision highp sampler2D;\n    uniform sampler2D tGridTex;\n    uniform vec3 uGridTexDim;\n#elif defined(dGridTexType_3d)\n    precision highp sampler3D;\n    uniform sampler3D tGridTex;\n#endif\n\n#if defined(dColorType_uniform)\n    uniform vec3 uColor;\n#elif defined(dColorType_texture)\n    uniform vec2 uColorTexDim;\n    uniform sampler2D tColor;\n#endif\n\n#ifdef dOverpaint\n    #if defined(dOverpaintType_groupInstance) || defined(dOverpaintType_vertexInstance)\n        uniform vec2 uOverpaintTexDim;\n        uniform sampler2D tOverpaint;\n    #endif\n#endif\n\n#ifdef dUsePalette\n    uniform sampler2D tPalette;\n#endif\n\n#if defined(dGridTexType_2d)\n    vec4 textureVal(vec3 pos) {\n        return texture3dFrom2dLinear(tGridTex, pos + (vec3(0.5, 0.5, 0.0) / uGridDim), uGridDim, uGridTexDim.xy);\n    }\n    vec4 textureGroup(vec3 pos) {\n        return texture3dFrom2dNearest(tGridTex, pos + (vec3(0.5, 0.5, 0.0) / uGridDim), uGridDim, uGridTexDim.xy);\n    }\n#elif defined(dGridTexType_3d)\n    vec4 textureVal(vec3 pos) {\n        return texture(tGridTex, pos + (vec3(0.5) / uGridDim));\n    }\n    vec4 textureGroup(vec3 pos) {\n        return texelFetch(tGridTex, ivec3(pos * uGridDim), 0);\n    }\n#endif\n\nfloat calcDepth(const in vec3 pos) {\n    vec2 clipZW = pos.z * uProjection[2].zw + uProjection[3].zw;\n    return 0.5 + 0.5 * clipZW.x / clipZW.y;\n}\n\nfloat transferFunction(float value) {\n    return texture2D(tTransferTex, vec2(value, 0.0)).a;\n}\n\nfloat getDepth(const in vec2 coords) {\n    #ifdef depthTextureSupport\n        return texture2D(tDepth, coords).r;\n    #else\n        return unpackRGBAToDepth(texture2D(tDepth, coords));\n    #endif\n}\n\nconst float gradOffset = 0.5;\n\nvec3 v3m4(vec3 p, mat4 m) {\n    return (m * vec4(p, 1.0)).xyz;\n}\n\nfloat preFogAlphaBlended = 0.0;\n\nvec4 raymarch(vec3 startLoc, vec3 step, vec3 rayDir) {\n    mat3 normalMatrix = transpose3(inverse3(mat3(uModelView * vTransform)));\n    mat4 cartnToUnit = uCartnToUnit * inverse4(vTransform);\n    #if defined(dClipVariant_pixel) && dClipObjectCount != 0\n        mat4 modelTransform = uModel * vTransform * uTransform;\n    #endif\n    mat4 modelViewTransform = uModelView * vTransform * uTransform;\n\n    vec3 scaleVol = vec3(1.0) / uGridDim;\n    vec3 pos = startLoc;\n    vec4 cell;\n    float prevValue = -1.0;\n    float value = 0.0;\n    vec4 src = vec4(0.0);\n    vec4 dst = vec4(0.0);\n    float fragmentDepth;\n\n    vec3 posMin = vec3(0.0);\n    vec3 posMax = vec3(1.0) - vec3(1.0) / uGridDim;\n\n    vec3 unitPos;\n\n    vec3 nextPos;\n    float nextValue;\n\n    vec4 material;\n    vec4 overpaint;\n    float metalness = uMetalness;\n    float roughness = uRoughness;\n    float emissive = uEmissive;\n\n    vec3 gradient = vec3(1.0);\n    vec3 dx = vec3(gradOffset * scaleVol.x, 0.0, 0.0);\n    vec3 dy = vec3(0.0, gradOffset * scaleVol.y, 0.0);\n    vec3 dz = vec3(0.0, 0.0, gradOffset * scaleVol.z);\n\n    float maxDist = min(vBoundingSphere.w * 2.0, uFar - uNear);\n    float maxDistSq = maxDist * maxDist;\n\n    for (int i = 0; i < uMaxSteps; ++i) {\n        // break when beyond bounding-sphere or far-plane\n        vec3 distVec = startLoc - pos;\n        if (dot(distVec, distVec) > maxDistSq) break;\n\n        unitPos = v3m4(pos, cartnToUnit);\n\n        // continue when outside of grid\n        if (unitPos.x > posMax.x || unitPos.y > posMax.y || unitPos.z > posMax.z ||\n            unitPos.x < posMin.x || unitPos.y < posMin.y || unitPos.z < posMin.z\n        ) {\n            prevValue = value;\n            pos += step;\n            continue;\n        }\n\n        cell = textureVal(unitPos);\n        value = cell.a; // current voxel value\n\n        if (uJumpLength > 0.0 && value < 0.01) {\n            nextPos = pos + rayDir * uJumpLength;\n            nextValue = textureVal(v3m4(nextPos, cartnToUnit)).a;\n            if (nextValue < 0.01) {\n                prevValue = nextValue;\n                pos = nextPos;\n                continue;\n            }\n        }\n\n        vec4 mvPosition = modelViewTransform * vec4(unitPos * uGridDim, 1.0);\n        if (calcDepth(mvPosition.xyz) > getDepth(gl_FragCoord.xy / uDrawingBufferSize))\n            break;\n\n        #if defined(dClipVariant_pixel) && dClipObjectCount != 0\n            vec3 vModelPosition = v3m4(unitPos * uGridDim, modelTransform);\n            if (clipTest(vec4(vModelPosition, 0.0))) {\n                prevValue = value;\n                pos += step;\n                continue;\n            }\n        #endif\n\n        vec3 vViewPosition = mvPosition.xyz;\n        material.a = transferFunction(value);\n\n        #ifdef dPackedGroup\n            float group = unpackRGBToInt(textureGroup(floor(unitPos * uGridDim + 0.5) / uGridDim).rgb);\n        #else\n            vec3 g = floor(unitPos * uGridDim + 0.5);\n            // note that we swap x and z because the texture is flipped around y\n            #if defined(dAxisOrder_012)\n                float group = g.z + g.y * uGridDim.z + g.x * uGridDim.z * uGridDim.y; // 210\n            #elif defined(dAxisOrder_021)\n                float group = g.y + g.z * uGridDim.y + g.x * uGridDim.y * uGridDim.z; // 120\n            #elif defined(dAxisOrder_102)\n                float group = g.z + g.x * uGridDim.z + g.y * uGridDim.z * uGridDim.x; // 201\n            #elif defined(dAxisOrder_120)\n                float group = g.x + g.z * uGridDim.x + g.y * uGridDim.x * uGridDim.z; // 021\n            #elif defined(dAxisOrder_201)\n                float group = g.y + g.x * uGridDim.y + g.z * uGridDim.y * uGridDim.x; // 102\n            #elif defined(dAxisOrder_210)\n                float group = g.x + g.y * uGridDim.x + g.z * uGridDim.x * uGridDim.y; // 012\n            #endif\n        #endif\n\n        #if defined(dColorType_direct) && defined(dUsePalette)\n            material.rgb = texture2D(tPalette, vec2(value, 0.0)).rgb;\n        #elif defined(dColorType_uniform)\n            material.rgb = uColor;\n        #elif defined(dColorType_instance)\n            material.rgb = readFromTexture(tColor, vInstance, uColorTexDim).rgb;\n        #elif defined(dColorType_group)\n            material.rgb = readFromTexture(tColor, group, uColorTexDim).rgb;\n        #elif defined(dColorType_groupInstance)\n            material.rgb = readFromTexture(tColor, vInstance * float(uGroupCount) + group, uColorTexDim).rgb;\n        #elif defined(dColorType_vertex)\n            material.rgb = texture3dFrom1dTrilinear(tColor, unitPos, uGridDim, uColorTexDim, 0.0).rgb;\n        #elif defined(dColorType_vertexInstance)\n            material.rgb = texture3dFrom1dTrilinear(tColor, unitPos, uGridDim, uColorTexDim, vInstance * float(uVertexCount)).rgb;\n        #endif\n\n        #ifdef dOverpaint\n            #if defined(dOverpaintType_groupInstance)\n                overpaint = readFromTexture(tOverpaint, vInstance * float(uGroupCount) + group, uOverpaintTexDim);\n            #elif defined(dOverpaintType_vertexInstance)\n                overpaint = texture3dFrom1dTrilinear(tOverpaint, unitPos, uGridDim, uOverpaintTexDim, vInstance * float(uVertexCount));\n            #endif\n\n            material.rgb = mix(material.rgb, overpaint.rgb, overpaint.a);\n        #endif\n\n        #if defined(dIgnoreLight)\n            gl_FragColor.rgb = material.rgb;\n        #else\n            if (material.a >= 0.01) {\n                #ifdef dPackedGroup\n                    // compute gradient by central differences\n                    gradient.x = textureVal(unitPos - dx).a - textureVal(unitPos + dx).a;\n                    gradient.y = textureVal(unitPos - dy).a - textureVal(unitPos + dy).a;\n                    gradient.z = textureVal(unitPos - dz).a - textureVal(unitPos + dz).a;\n                #else\n                    gradient = cell.xyz * 2.0 - 1.0;\n                #endif\n                vec3 normal = -normalize(normalMatrix * normalize(gradient));\n                #include apply_light_color\n            } else {\n                gl_FragColor.rgb = material.rgb;\n            }\n        #endif\n\n        gl_FragColor.a = material.a * uAlpha * uTransferScale;\n\n        #if defined(dColorMarker)\n            float marker = uMarker;\n            if (uMarker == -1.0) {\n                marker = readFromTexture(tMarker, vInstance * float(uGroupCount) + group, uMarkerTexDim).a;\n                marker = floor(marker * 255.0 + 0.5); // rounding required to work on some cards on win\n            }\n        #endif\n        #include apply_marker_color\n\n        preFogAlphaBlended = (1.0 - preFogAlphaBlended) * gl_FragColor.a + preFogAlphaBlended;\n        fragmentDepth = calcDepth(mvPosition.xyz);\n        #include apply_fog\n\n        src = gl_FragColor;\n\n        if (!uTransparentBackground) {\n            // done in 'apply_fog' otherwise\n            src.rgb *= src.a;\n        }\n        dst = (1.0 - dst.a) * src + dst; // standard blending\n\n        // break if the color is opaque enough\n        if (dst.a > 0.95)\n            break;\n\n        pos += step;\n    }\n\n    return dst;\n}\n\n// TODO: support float texture for higher precision values???\n// TODO: support clipping exclusion texture support\n\nvoid main() {\n    #if defined(dRenderVariant_emissive)\n        discard;\n    #else\n        if (gl_FrontFacing)\n            discard;\n\n        vec3 rayDir = mix(normalize(vOrigPos - uCameraPosition), uCameraDir, uIsOrtho);\n        vec3 step = rayDir * uStepScale;\n\n        float boundingSphereNear = distance(vBoundingSphere.xyz, uCameraPosition) - vBoundingSphere.w;\n        float d = max(uNear, boundingSphereNear) - mix(0.0, distance(vOrigPos, uCameraPosition), uIsOrtho);\n        vec3 start = mix(uCameraPosition, vOrigPos, uIsOrtho) + (d * rayDir);\n        gl_FragColor = raymarch(start, step, rayDir);\n\n        float fragmentDepth = calcDepth((uModelView * vec4(start, 1.0)).xyz);\n        float preFogAlpha = clamp(preFogAlphaBlended, 0.0, 1.0);\n        #include wboit_write\n    #endif\n}\n";
+export declare const directVolume_frag = "\nprecision highp float;\nprecision highp int;\n\n#include common\n#include light_frag_params\n\n#if dClipObjectCount != 0\n    uniform int uClipObjectType[dClipObjectCount];\n    uniform bool uClipObjectInvert[dClipObjectCount];\n    uniform vec3 uClipObjectPosition[dClipObjectCount];\n    uniform vec4 uClipObjectRotation[dClipObjectCount];\n    uniform vec3 uClipObjectScale[dClipObjectCount];\n#endif\n#include common_clip\n\n#include read_from_texture\n#include texture3d_from_1d_trilinear\n#include texture3d_from_2d_nearest\n#include texture3d_from_2d_linear\n\nuniform mat4 uProjection, uTransform, uModelView, uModel, uView;\nuniform vec3 uCameraDir;\n\nuniform sampler2D tDepth;\nuniform vec2 uDrawingBufferSize;\n\nvarying vec3 vOrigPos;\nvarying float vInstance;\nvarying vec4 vBoundingSphere;\nvarying mat4 vTransform;\n\nuniform mat4 uInvView;\nuniform vec3 uGridDim;\nuniform vec3 uBboxSize;\nuniform sampler2D tTransferTex;\nuniform float uTransferScale;\nuniform float uStepScale;\nuniform float uJumpLength;\n\nuniform int uObjectId;\nuniform int uVertexCount;\nuniform int uInstanceCount;\nuniform int uGroupCount;\n\n#if defined(dColorMarker)\n    uniform vec3 uHighlightColor;\n    uniform vec3 uSelectColor;\n    uniform vec3 uDimColor;\n    uniform float uHighlightStrength;\n    uniform float uSelectStrength;\n    uniform float uDimStrength;\n    uniform int uMarkerPriority;\n    uniform float uMarkerAverage;\n\n    uniform float uMarker;\n    uniform vec2 uMarkerTexDim;\n    uniform sampler2D tMarker;\n#endif\n\nuniform float uMetalness;\nuniform float uRoughness;\nuniform float uEmissive;\n\nuniform bool uFog;\nuniform float uFogNear;\nuniform float uFogFar;\nuniform vec3 uFogColor;\n\nuniform float uAlpha;\nuniform bool uTransparentBackground;\nuniform float uXrayEdgeFalloff;\nuniform float uCelSteps;\nuniform float uExposure;\n\nuniform int uRenderMask;\n\nuniform float uNear;\nuniform float uFar;\nuniform float uIsOrtho;\n\nuniform vec3 uCellDim;\nuniform vec3 uCameraPosition;\nuniform mat4 uCartnToUnit;\n\n#if __VERSION__ != 100\n    // for webgl1 this is given as a 'define'\n    uniform int uMaxSteps;\n#endif\n\n#if defined(dGridTexType_2d)\n    precision highp sampler2D;\n    uniform sampler2D tGridTex;\n    uniform vec3 uGridTexDim;\n#elif defined(dGridTexType_3d)\n    precision highp sampler3D;\n    uniform sampler3D tGridTex;\n#endif\n\n#if defined(dColorType_uniform)\n    uniform vec3 uColor;\n#elif defined(dColorType_texture)\n    uniform vec2 uColorTexDim;\n    uniform sampler2D tColor;\n#endif\n\n#ifdef dOverpaint\n    #if defined(dOverpaintType_groupInstance) || defined(dOverpaintType_vertexInstance)\n        uniform vec2 uOverpaintTexDim;\n        uniform sampler2D tOverpaint;\n    #endif\n#endif\n\n#ifdef dUsePalette\n    uniform sampler2D tPalette;\n#endif\n\n#if defined(dGridTexType_2d)\n    vec4 textureVal(vec3 pos) {\n        return texture3dFrom2dLinear(tGridTex, pos + (vec3(0.5, 0.5, 0.0) / uGridDim), uGridDim, uGridTexDim.xy);\n    }\n    vec4 textureGroup(vec3 pos) {\n        return texture3dFrom2dNearest(tGridTex, pos + (vec3(0.5, 0.5, 0.0) / uGridDim), uGridDim, uGridTexDim.xy);\n    }\n#elif defined(dGridTexType_3d)\n    vec4 textureVal(vec3 pos) {\n        return texture(tGridTex, pos + (vec3(0.5) / uGridDim));\n    }\n    vec4 textureGroup(vec3 pos) {\n        return texelFetch(tGridTex, ivec3(pos * uGridDim), 0);\n    }\n#endif\n\nfloat calcDepth(const in vec3 pos) {\n    vec2 clipZW = pos.z * uProjection[2].zw + uProjection[3].zw;\n    return 0.5 + 0.5 * clipZW.x / clipZW.y;\n}\n\nfloat transferFunction(float value) {\n    return texture2D(tTransferTex, vec2(value, 0.0)).a;\n}\n\nfloat getDepth(const in vec2 coords) {\n    #ifdef depthTextureSupport\n        return texture2D(tDepth, coords).r;\n    #else\n        return unpackRGBAToDepth(texture2D(tDepth, coords));\n    #endif\n}\n\nconst float gradOffset = 0.5;\n\nvec3 v3m4(vec3 p, mat4 m) {\n    return (m * vec4(p, 1.0)).xyz;\n}\n\nfloat preFogAlphaBlended = 0.0;\n\nvec4 raymarch(vec3 startLoc, vec3 step, vec3 rayDir) {\n    mat3 normalMatrix = transpose3(inverse3(mat3(uModelView * vTransform)));\n    mat4 cartnToUnit = uCartnToUnit * inverse4(vTransform);\n    #if defined(dClipVariant_pixel) && dClipObjectCount != 0\n        mat4 modelTransform = uModel * vTransform * uTransform;\n    #endif\n    mat4 modelViewTransform = uModelView * vTransform * uTransform;\n\n    vec3 scaleVol = vec3(1.0) / uGridDim;\n    vec3 pos = startLoc;\n    vec4 cell;\n    float prevValue = -1.0;\n    float value = 0.0;\n    vec4 src = vec4(0.0);\n    vec4 dst = vec4(0.0);\n    float fragmentDepth;\n\n    vec3 posMin = vec3(0.0);\n    vec3 posMax = vec3(1.0) - vec3(1.0) / uGridDim;\n\n    vec3 unitPos;\n\n    vec3 nextPos;\n    float nextValue;\n\n    vec4 material;\n    vec4 overpaint;\n    float metalness = uMetalness;\n    float roughness = uRoughness;\n    float emissive = uEmissive;\n\n    vec3 gradient = vec3(1.0);\n    vec3 dx = vec3(gradOffset * scaleVol.x, 0.0, 0.0);\n    vec3 dy = vec3(0.0, gradOffset * scaleVol.y, 0.0);\n    vec3 dz = vec3(0.0, 0.0, gradOffset * scaleVol.z);\n\n    float maxDist = min(vBoundingSphere.w * 2.0, uFar - uNear);\n    float maxDistSq = maxDist * maxDist;\n\n    for (int i = 0; i < uMaxSteps; ++i) {\n        // break when beyond bounding-sphere or far-plane\n        vec3 distVec = startLoc - pos;\n        if (dot(distVec, distVec) > maxDistSq) break;\n\n        unitPos = v3m4(pos, cartnToUnit);\n\n        // continue when outside of grid\n        if (unitPos.x > posMax.x || unitPos.y > posMax.y || unitPos.z > posMax.z ||\n            unitPos.x < posMin.x || unitPos.y < posMin.y || unitPos.z < posMin.z\n        ) {\n            prevValue = value;\n            pos += step;\n            continue;\n        }\n\n        cell = textureVal(unitPos);\n        value = cell.a; // current voxel value\n\n        if (uJumpLength > 0.0 && value < 0.01) {\n            nextPos = pos + rayDir * uJumpLength;\n            nextValue = textureVal(v3m4(nextPos, cartnToUnit)).a;\n            if (nextValue < 0.01) {\n                prevValue = nextValue;\n                pos = nextPos;\n                continue;\n            }\n        }\n\n        vec4 mvPosition = modelViewTransform * vec4(unitPos * uGridDim, 1.0);\n        if (calcDepth(mvPosition.xyz) > getDepth(gl_FragCoord.xy / uDrawingBufferSize))\n            break;\n\n        #if defined(dClipVariant_pixel) && dClipObjectCount != 0\n            vec3 vModelPosition = v3m4(unitPos * uGridDim, modelTransform);\n            if (clipTest(vec4(vModelPosition, 0.0))) {\n                prevValue = value;\n                pos += step;\n                continue;\n            }\n        #endif\n\n        vec3 vViewPosition = mvPosition.xyz;\n        material.a = transferFunction(value);\n\n        #ifdef dPackedGroup\n            float group = unpackRGBToInt(textureGroup(floor(unitPos * uGridDim + 0.5) / uGridDim).rgb);\n        #else\n            vec3 g = floor(unitPos * uGridDim + 0.5);\n            // note that we swap x and z because the texture is flipped around y\n            #if defined(dAxisOrder_012)\n                float group = g.z + g.y * uGridDim.z + g.x * uGridDim.z * uGridDim.y; // 210\n            #elif defined(dAxisOrder_021)\n                float group = g.y + g.z * uGridDim.y + g.x * uGridDim.y * uGridDim.z; // 120\n            #elif defined(dAxisOrder_102)\n                float group = g.z + g.x * uGridDim.z + g.y * uGridDim.z * uGridDim.x; // 201\n            #elif defined(dAxisOrder_120)\n                float group = g.x + g.z * uGridDim.x + g.y * uGridDim.x * uGridDim.z; // 021\n            #elif defined(dAxisOrder_201)\n                float group = g.y + g.x * uGridDim.y + g.z * uGridDim.y * uGridDim.x; // 102\n            #elif defined(dAxisOrder_210)\n                float group = g.x + g.y * uGridDim.x + g.z * uGridDim.x * uGridDim.y; // 012\n            #endif\n        #endif\n\n        #if defined(dColorType_direct) && defined(dUsePalette)\n            material.rgb = texture2D(tPalette, vec2(value, 0.0)).rgb;\n        #elif defined(dColorType_uniform)\n            material.rgb = uColor;\n        #elif defined(dColorType_instance)\n            material.rgb = readFromTexture(tColor, vInstance, uColorTexDim).rgb;\n        #elif defined(dColorType_group)\n            material.rgb = readFromTexture(tColor, group, uColorTexDim).rgb;\n        #elif defined(dColorType_groupInstance)\n            material.rgb = readFromTexture(tColor, vInstance * float(uGroupCount) + group, uColorTexDim).rgb;\n        #elif defined(dColorType_vertex)\n            material.rgb = texture3dFrom1dTrilinear(tColor, unitPos, uGridDim, uColorTexDim, 0.0).rgb;\n        #elif defined(dColorType_vertexInstance)\n            material.rgb = texture3dFrom1dTrilinear(tColor, unitPos, uGridDim, uColorTexDim, vInstance * float(uVertexCount)).rgb;\n        #endif\n\n        #ifdef dOverpaint\n            #if defined(dOverpaintType_groupInstance)\n                overpaint = readFromTexture(tOverpaint, vInstance * float(uGroupCount) + group, uOverpaintTexDim);\n            #elif defined(dOverpaintType_vertexInstance)\n                overpaint = texture3dFrom1dTrilinear(tOverpaint, unitPos, uGridDim, uOverpaintTexDim, vInstance * float(uVertexCount));\n            #endif\n\n            material.rgb = mix(material.rgb, overpaint.rgb, overpaint.a);\n        #endif\n\n        #if defined(dIgnoreLight)\n            gl_FragColor.rgb = material.rgb;\n        #else\n            if (material.a >= 0.01) {\n                #ifdef dPackedGroup\n                    // compute gradient by central differences\n                    gradient.x = textureVal(unitPos - dx).a - textureVal(unitPos + dx).a;\n                    gradient.y = textureVal(unitPos - dy).a - textureVal(unitPos + dy).a;\n                    gradient.z = textureVal(unitPos - dz).a - textureVal(unitPos + dz).a;\n                #else\n                    gradient = cell.xyz * 2.0 - 1.0;\n                #endif\n                vec3 normal = -normalize(normalMatrix * normalize(gradient));\n                #include apply_light_color\n            } else {\n                gl_FragColor.rgb = material.rgb;\n            }\n        #endif\n\n        gl_FragColor.a = material.a * uAlpha * uTransferScale;\n\n        #if defined(dColorMarker)\n            float marker = uMarker;\n            if (uMarker == -1.0) {\n                marker = readFromTexture(tMarker, vInstance * float(uGroupCount) + group, uMarkerTexDim).a;\n                marker = floor(marker * 255.0 + 0.5); // rounding required to work on some cards on win\n            }\n        #endif\n        #include apply_marker_color\n\n        preFogAlphaBlended = (1.0 - preFogAlphaBlended) * gl_FragColor.a + preFogAlphaBlended;\n        fragmentDepth = calcDepth(mvPosition.xyz);\n        #include apply_fog\n\n        src = gl_FragColor;\n\n        if (!uTransparentBackground) {\n            // done in 'apply_fog' otherwise\n            src.rgb *= src.a;\n        }\n        dst = (1.0 - dst.a) * src + dst; // standard blending\n\n        // break if the color is opaque enough\n        if (dst.a > 0.95)\n            break;\n\n        pos += step;\n    }\n\n    return dst;\n}\n\n// TODO: support float texture for higher precision values???\n// TODO: support clipping exclusion texture support\n\nvoid main() {\n    #if defined(dRenderVariant_emissive)\n        discard;\n    #else\n        if (gl_FrontFacing)\n            discard;\n\n        vec3 rayDir = mix(normalize(vOrigPos - uCameraPosition), uCameraDir, uIsOrtho);\n        vec3 step = rayDir * uStepScale;\n\n        float boundingSphereNear = distance(vBoundingSphere.xyz, uCameraPosition) - vBoundingSphere.w;\n        float d = max(uNear, boundingSphereNear) - mix(0.0, distance(vOrigPos, uCameraPosition), uIsOrtho);\n        vec3 start = mix(uCameraPosition, vOrigPos, uIsOrtho) + (d * rayDir);\n        gl_FragColor = raymarch(start, step, rayDir);\n\n        float fragmentDepth = calcDepth((uModelView * vec4(start, 1.0)).xyz);\n        float preFogAlpha = clamp(preFogAlphaBlended, 0.0, 1.0);\n        #include wboit_write\n    #endif\n}\n";

package/lib/mol-gl/shader/direct-volume.frag.js

@@ -76,6 +76,7 @@ uniform vec3 uFogColor;
 uniform float uAlpha;
 uniform bool uTransparentBackground;
 uniform float uXrayEdgeFalloff;
+uniform float uCelSteps;
 uniform float uExposure;
 
 uniform int uRenderMask;

package/lib/mol-gl/shader/dof.frag.d.ts

@@ -0,0 +1,7 @@
+/**
+ * Copyright (c) 2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Ludovic Autin <autin@scripps.edu>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+export declare const dof_frag = "\nprecision highp float;\nprecision highp int;\nprecision highp sampler2D;\n\n#include common\n\nuniform sampler2D tColor;\nuniform sampler2D tDepthOpaque;\nuniform sampler2D tDepthTransparent;\n\nuniform vec2 uTexSize;\nuniform vec4 uBounds;\n\nuniform float uBlurSpread;\nuniform float uInFocus;\nuniform float uPPM;\n\nuniform float uNear; // Near plane\nuniform float uFar;  // Far plane\n\nuniform mat4 uInvProjection; // Inverse projection\nuniform mat4 uProjection; // projection\n\nuniform int uMode; // 0-planar, 1-spherical\nuniform vec3 uCenter; // Center of focus sphere in view space\n\n// Function to convert depth value from depth buffer to view space Z\nfloat getViewZ(const in float depth) {\n    #if dOrthographic == 1\n        return orthographicDepthToViewZ(depth, uNear, uFar);\n    #else\n        return perspectiveDepthToViewZ(depth, uNear, uFar);\n    #endif\n}\n\n// Retrieve depth from opaque depth texture\nfloat getDepthOpaque(const in vec2 coords) {\n    #ifdef depthTextureSupport\n        return texture2D(tDepthOpaque, coords).r;\n    #else\n        return unpackRGBAToDepth(texture2D(tDepthOpaque, coords));\n    #endif\n}\n\n// Retrieve depth from transparent depth texture\nfloat getDepthTransparent(const in vec2 coords) {\n    return unpackRGBAToDepth(texture2D(tDepthTransparent, coords));\n}\n\nbool isBackground(const in float depth) {\n    return depth == 1.0;\n}\n\nfloat getDepth(const in vec2 coords) {\n    return min(getDepthOpaque(coords), getDepthTransparent(coords));\n}\n\nfloat getCOC(vec2 uv) {\n    float depth = getDepth(uv);\n    float viewDist = getViewZ(depth);\n    vec3 aposition = screenSpaceToViewSpace(vec3(uv.xy, depth), uInvProjection);\n    float focusDist = length(aposition - uCenter);\n    float coc = 0.0;  // Circle of Confusion\n    if (uMode == 0) { // planar Depth of field\n        coc = (abs(viewDist) - uInFocus) / uPPM;  //focus distance, focus range\n    } else if(uMode == 1) { // spherical Depth of field\n        coc = focusDist / uPPM ;\n    }\n    coc = clamp(coc, -1.0, 1.0);\n    return coc;\n}\n\n// Simple box blur for blurring the image\nvec3 getBlurredImage(vec2 coords) {\n    vec4 blurColor = vec4(0);\n    vec2 texelSize = vec2(1.0 / uTexSize.x, 1.0 / uTexSize.y);\n    float count = 0.0;\n    for (int x = 0; x < int(dBlurSize); x++) {\n        for (int y = 0; y < int(dBlurSize); y++) {\n            vec2 offset = vec2(float(x) - float(dBlurSize) / 2.0, float(y) - float(dBlurSize) / 2.0);\n            vec2 uvPixel = coords.xy + offset * texelSize * uBlurSpread;\n            float coc = getCOC(uvPixel);\n            coc = smoothstep(0.0, 1.0, abs(coc));\n            // mix blurColor with new color with weight coc\n            blurColor.rgb = blurColor.rgb + texture2D(tColor, uvPixel).xyz * coc;\n            count+=coc;\n        }\n    }\n    blurColor = blurColor / count;\n    return blurColor.rgb;\n}\n\n// simplification from https://catlikecoding.com/unity/tutorials/advanced-rendering/depth-of-field/\nvoid main() {\n    vec2 uv = gl_FragCoord.xy / uTexSize;\n    vec4 color = texture2D(tColor, uv);\n    float depth = getDepth(uv);\n\n    float viewDist = getViewZ(depth);\n\n    vec3 aposition = screenSpaceToViewSpace(vec3(uv.xy, depth), uInvProjection);\n    float focusDist = length(aposition - uCenter);\n    vec3 blurColor = getBlurredImage(uv);\n\n    float coc = getCOC(uv); // Circle of Confusion\n\n    // for debugging the coc\n    // color.rgb = (coc < 0.0) ? (1.0 - abs(coc)) * vec3(1.0,0.0,0.0) : vec3(0.0, 1.0 - coc, 0.0) ;//mix(color.rgb, blurColor.rgb, abs(coc));\n    color.rgb = mix(color.rgb, blurColor, smoothstep(0.0, 1.0, abs(coc))); // Smooth blending based on CoC\n    gl_FragColor = color;\n}\n";

package/lib/mol-gl/shader/dof.frag.js

@@ -0,0 +1,119 @@
+/**
+ * Copyright (c) 2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Ludovic Autin <autin@scripps.edu>
+ * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ */
+export const dof_frag = `
+precision highp float;
+precision highp int;
+precision highp sampler2D;
+
+#include common
+
+uniform sampler2D tColor;
+uniform sampler2D tDepthOpaque;
+uniform sampler2D tDepthTransparent;
+
+uniform vec2 uTexSize;
+uniform vec4 uBounds;
+
+uniform float uBlurSpread;
+uniform float uInFocus;
+uniform float uPPM;
+
+uniform float uNear; // Near plane
+uniform float uFar;  // Far plane
+
+uniform mat4 uInvProjection; // Inverse projection
+uniform mat4 uProjection; // projection
+
+uniform int uMode; // 0-planar, 1-spherical
+uniform vec3 uCenter; // Center of focus sphere in view space
+
+// Function to convert depth value from depth buffer to view space Z
+float getViewZ(const in float depth) {
+    #if dOrthographic == 1
+        return orthographicDepthToViewZ(depth, uNear, uFar);
+    #else
+        return perspectiveDepthToViewZ(depth, uNear, uFar);
+    #endif
+}
+
+// Retrieve depth from opaque depth texture
+float getDepthOpaque(const in vec2 coords) {
+    #ifdef depthTextureSupport
+        return texture2D(tDepthOpaque, coords).r;
+    #else
+        return unpackRGBAToDepth(texture2D(tDepthOpaque, coords));
+    #endif
+}
+
+// Retrieve depth from transparent depth texture
+float getDepthTransparent(const in vec2 coords) {
+    return unpackRGBAToDepth(texture2D(tDepthTransparent, coords));
+}
+
+bool isBackground(const in float depth) {
+    return depth == 1.0;
+}
+
+float getDepth(const in vec2 coords) {
+    return min(getDepthOpaque(coords), getDepthTransparent(coords));
+}
+
+float getCOC(vec2 uv) {
+    float depth = getDepth(uv);
+    float viewDist = getViewZ(depth);
+    vec3 aposition = screenSpaceToViewSpace(vec3(uv.xy, depth), uInvProjection);
+    float focusDist = length(aposition - uCenter);
+    float coc = 0.0;  // Circle of Confusion
+    if (uMode == 0) { // planar Depth of field
+        coc = (abs(viewDist) - uInFocus) / uPPM;  //focus distance, focus range
+    } else if(uMode == 1) { // spherical Depth of field
+        coc = focusDist / uPPM ;
+    }
+    coc = clamp(coc, -1.0, 1.0);
+    return coc;
+}
+
+// Simple box blur for blurring the image
+vec3 getBlurredImage(vec2 coords) {
+    vec4 blurColor = vec4(0);
+    vec2 texelSize = vec2(1.0 / uTexSize.x, 1.0 / uTexSize.y);
+    float count = 0.0;
+    for (int x = 0; x < int(dBlurSize); x++) {
+        for (int y = 0; y < int(dBlurSize); y++) {
+            vec2 offset = vec2(float(x) - float(dBlurSize) / 2.0, float(y) - float(dBlurSize) / 2.0);
+            vec2 uvPixel = coords.xy + offset * texelSize * uBlurSpread;
+            float coc = getCOC(uvPixel);
+            coc = smoothstep(0.0, 1.0, abs(coc));
+            // mix blurColor with new color with weight coc
+            blurColor.rgb = blurColor.rgb + texture2D(tColor, uvPixel).xyz * coc;
+            count+=coc;
+        }
+    }
+    blurColor = blurColor / count;
+    return blurColor.rgb;
+}
+
+// simplification from https://catlikecoding.com/unity/tutorials/advanced-rendering/depth-of-field/
+void main() {
+    vec2 uv = gl_FragCoord.xy / uTexSize;
+    vec4 color = texture2D(tColor, uv);
+    float depth = getDepth(uv);
+
+    float viewDist = getViewZ(depth);
+
+    vec3 aposition = screenSpaceToViewSpace(vec3(uv.xy, depth), uInvProjection);
+    float focusDist = length(aposition - uCenter);
+    vec3 blurColor = getBlurredImage(uv);
+
+    float coc = getCOC(uv); // Circle of Confusion
+
+    // for debugging the coc
+    // color.rgb = (coc < 0.0) ? (1.0 - abs(coc)) * vec3(1.0,0.0,0.0) : vec3(0.0, 1.0 - coc, 0.0) ;//mix(color.rgb, blurColor.rgb, abs(coc));
+    color.rgb = mix(color.rgb, blurColor, smoothstep(0.0, 1.0, abs(coc))); // Smooth blending based on CoC
+    gl_FragColor = color;
+}
+`;

package/lib/mol-gl/shader/ssao-blur.frag.d.ts

@@ -5,4 +5,4 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author Ludovic Autin <ludovic.autin@gmail.com>
  */
-export declare const ssaoBlur_frag = "\nprecision highp float;\nprecision highp int;\nprecision highp sampler2D;\n\nuniform sampler2D tSsaoDepth;\nuniform vec2 uTexSize;\nuniform vec4 uBounds;\n\nuniform float uKernel[dOcclusionKernelSize];\n\nuniform float uBlurDirectionX;\nuniform float uBlurDirectionY;\n\nuniform mat4 uInvProjection;\nuniform float uNear;\nuniform float uFar;\n\n#include common\n\nfloat getViewZ(const in float depth) {\n    #if dOrthographic == 1\n        return orthographicDepthToViewZ(depth, uNear, uFar);\n    #else\n        return perspectiveDepthToViewZ(depth, uNear, uFar);\n    #endif\n}\n\nbool isBackground(const in float depth) {\n    return depth == 1.0;\n}\n\nbool outsideBounds(const in vec2 p) {\n    return p.x < uBounds.x || p.y < uBounds.y || p.x > uBounds.z || p.y > uBounds.w;\n}\n\nfloat getPixelSize(const in vec2 coords, const in float depth) {\n    vec3 viewPos0 = screenSpaceToViewSpace(vec3(coords, depth), uInvProjection);\n    vec3 viewPos1 = screenSpaceToViewSpace(vec3(coords + vec2(1.0, 0.0) / uTexSize, depth), uInvProjection);\n    return distance(viewPos0, viewPos1);\n}\n\nvoid main(void) {\n    vec2 coords = gl_FragCoord.xy / uTexSize;\n\n    vec2 packedDepth = texture2D(tSsaoDepth, coords).zw;\n\n    if (outsideBounds(coords)) {\n        gl_FragColor = vec4(packUnitIntervalToRG(1.0), packedDepth);\n        return;\n    }\n\n    float selfDepth = unpackRGToUnitInterval(packedDepth);\n    // if background and if second pass\n    if (isBackground(selfDepth) && uBlurDirectionY != 0.0) {\n        gl_FragColor = vec4(packUnitIntervalToRG(1.0), packedDepth);\n        return;\n    }\n\n    float selfViewZ = getViewZ(selfDepth);\n    float pixelSize = getPixelSize(coords, selfDepth);\n    // max diff depth between two pixels\n    float maxDiffViewZ = 1.0;\n\n    vec2 offset = vec2(uBlurDirectionX, uBlurDirectionY) / uTexSize;\n\n    float sum = 0.0;\n    float kernelSum = 0.0;\n    // only if kernelSize is odd\n    for (int i = -dOcclusionKernelSize / 2; i <= dOcclusionKernelSize / 2; i++) {\n        if (abs(float(i)) > 1.0 && abs(float(i)) * pixelSize > 0.8) continue;\n\n        vec2 sampleCoords = coords + float(i) * offset;\n        if (outsideBounds(sampleCoords)) {\n            continue;\n        }\n\n        vec4 sampleSsaoDepth = texture2D(tSsaoDepth, sampleCoords);\n\n        float sampleDepth = unpackRGToUnitInterval(sampleSsaoDepth.zw);\n        if (isBackground(sampleDepth)) {\n            continue;\n        }\n\n        float sampleViewZ = getViewZ(sampleDepth);\n        if (abs(selfViewZ - sampleViewZ) > maxDiffViewZ) {\n            continue;\n        }\n\n        float kernel = uKernel[int(abs(float(i)))]; // abs is not defined for int in webgl1\n        float sampleValue = unpackRGToUnitInterval(sampleSsaoDepth.xy);\n\n        sum += kernel * sampleValue;\n        kernelSum += kernel;\n    }\n    gl_FragColor = vec4(packUnitIntervalToRG(sum / kernelSum), packedDepth);\n}\n";
+export declare const ssaoBlur_frag = "\nprecision highp float;\nprecision highp int;\nprecision highp sampler2D;\n\nuniform sampler2D tSsaoDepth;\nuniform vec2 uTexSize;\nuniform vec4 uBounds;\n\nuniform float uKernel[dOcclusionKernelSize];\nuniform float uBlurDepthBias;\n\nuniform float uBlurDirectionX;\nuniform float uBlurDirectionY;\n\nuniform mat4 uInvProjection;\nuniform float uNear;\nuniform float uFar;\n\n#include common\n\nfloat getViewZ(const in float depth) {\n    #if dOrthographic == 1\n        return orthographicDepthToViewZ(depth, uNear, uFar);\n    #else\n        return perspectiveDepthToViewZ(depth, uNear, uFar);\n    #endif\n}\n\nbool isBackground(const in float depth) {\n    return depth == 1.0;\n}\n\nbool isNearClip(const in float depth) {\n    return depth == 0.0;\n}\n\nbool outsideBounds(const in vec2 p) {\n    return p.x < uBounds.x || p.y < uBounds.y || p.x > uBounds.z || p.y > uBounds.w;\n}\n\nfloat getPixelSize(const in vec2 coords, const in float depth) {\n    vec3 viewPos0 = screenSpaceToViewSpace(vec3(coords, depth), uInvProjection);\n    vec3 viewPos1 = screenSpaceToViewSpace(vec3(coords + vec2(1.0, 0.0) / uTexSize, depth), uInvProjection);\n    return distance(viewPos0, viewPos1);\n}\n\nvoid main(void) {\n    vec2 coords = gl_FragCoord.xy / uTexSize;\n\n    vec2 packedDepth = texture2D(tSsaoDepth, coords).zw;\n\n    if (outsideBounds(coords)) {\n        gl_FragColor = vec4(packUnitIntervalToRG(1.0), packedDepth);\n        return;\n    }\n\n    float selfDepth = unpackRGToUnitInterval(packedDepth);\n    // (if background and if second pass) or if near clip\n    if ((isBackground(selfDepth) && uBlurDirectionY != 0.0) || isNearClip(selfDepth)) {\n        gl_FragColor = vec4(packUnitIntervalToRG(1.0), packedDepth);\n        return;\n    }\n\n    float selfViewZ = getViewZ(selfDepth);\n    float pixelSize = getPixelSize(coords, selfDepth);\n\n    vec2 offset = vec2(uBlurDirectionX, uBlurDirectionY) / uTexSize;\n\n    float sum = 0.0;\n    float kernelSum = 0.0;\n    // only if kernelSize is odd\n    for (int i = -dOcclusionKernelSize / 2; i <= dOcclusionKernelSize / 2; i++) {\n        if (abs(float(i)) > 1.0 && abs(float(i)) * pixelSize > 0.8) continue;\n\n        vec2 sampleCoords = coords + float(i) * offset;\n        if (outsideBounds(sampleCoords)) {\n            continue;\n        }\n\n        vec4 sampleSsaoDepth = texture2D(tSsaoDepth, sampleCoords);\n\n        float sampleDepth = unpackRGToUnitInterval(sampleSsaoDepth.zw);\n        if (isBackground(sampleDepth) || isNearClip(sampleDepth)) {\n            continue;\n        }\n\n        float sampleViewZ = getViewZ(sampleDepth);\n        if (abs(selfViewZ - sampleViewZ) >= uBlurDepthBias) {\n            continue;\n        }\n\n        float kernel = uKernel[int(abs(float(i)))]; // abs is not defined for int in webgl1\n        float sampleValue = unpackRGToUnitInterval(sampleSsaoDepth.xy);\n\n        sum += kernel * sampleValue;\n        kernelSum += kernel;\n    }\n    gl_FragColor = vec4(packUnitIntervalToRG(sum / kernelSum), packedDepth);\n}\n";

package/lib/mol-gl/shader/ssao-blur.frag.js

@@ -15,6 +15,7 @@ uniform vec2 uTexSize;
 uniform vec4 uBounds;
 
 uniform float uKernel[dOcclusionKernelSize];
+uniform float uBlurDepthBias;
 
 uniform float uBlurDirectionX;
 uniform float uBlurDirectionY;
@@ -37,6 +38,10 @@ bool isBackground(const in float depth) {
     return depth == 1.0;
 }
 
+bool isNearClip(const in float depth) {
+    return depth == 0.0;
+}
+
 bool outsideBounds(const in vec2 p) {
     return p.x < uBounds.x || p.y < uBounds.y || p.x > uBounds.z || p.y > uBounds.w;
 }
@@ -58,16 +63,14 @@ void main(void) {
     }
 
     float selfDepth = unpackRGToUnitInterval(packedDepth);
-    // if background and if second pass
-    if (isBackground(selfDepth) && uBlurDirectionY != 0.0) {
+    // (if background and if second pass) or if near clip
+    if ((isBackground(selfDepth) && uBlurDirectionY != 0.0) || isNearClip(selfDepth)) {
         gl_FragColor = vec4(packUnitIntervalToRG(1.0), packedDepth);
         return;
     }
 
     float selfViewZ = getViewZ(selfDepth);
     float pixelSize = getPixelSize(coords, selfDepth);
-    // max diff depth between two pixels
-    float maxDiffViewZ = 1.0;
 
     vec2 offset = vec2(uBlurDirectionX, uBlurDirectionY) / uTexSize;
 
@@ -85,12 +88,12 @@ void main(void) {
         vec4 sampleSsaoDepth = texture2D(tSsaoDepth, sampleCoords);
 
         float sampleDepth = unpackRGToUnitInterval(sampleSsaoDepth.zw);
-        if (isBackground(sampleDepth)) {
+        if (isBackground(sampleDepth) || isNearClip(sampleDepth)) {
             continue;
         }
 
         float sampleViewZ = getViewZ(sampleDepth);
-        if (abs(selfViewZ - sampleViewZ) > maxDiffViewZ) {
+        if (abs(selfViewZ - sampleViewZ) >= uBlurDepthBias) {
             continue;
         }
 

package/lib/mol-gl/shader-code.js

@@ -134,7 +134,7 @@ function ignoreDefine(name, variant, defines) {
             'dLightCount', 'dXrayShaded',
             'dOverpaintType', 'dOverpaint',
             'dSubstanceType', 'dSubstance',
-            'dColorMarker',
+            'dColorMarker', 'dCelShaded'
         ];
         if (variant !== 'emissive') {
             ignore.push('dEmissiveType', 'dEmissive');

package/lib/mol-gl/webgl/context.js

@@ -271,6 +271,7 @@ export function createContext(gl, props = {}) {
         contextRestored,
         setContextLost: () => {
             isContextLost = true;
+            timer.clear();
         },
         handleContextRestored: (extraResets) => {
             Object.assign(extensions, createExtensions(gl));

package/lib/mol-gl/webgl/render-item.d.ts

@@ -41,12 +41,12 @@ declare const GraphicsRenderVariant: {
     emissive: string;
 };
 export type GraphicsRenderVariant = keyof typeof GraphicsRenderVariant;
-export declare const GraphicsRenderVariants: ("color" | "emissive" | "depth" | "pick" | "marking")[];
+export declare const GraphicsRenderVariants: GraphicsRenderVariant[];
 declare const ComputeRenderVariant: {
     compute: string;
 };
 export type ComputeRenderVariant = keyof typeof ComputeRenderVariant;
-export declare const ComputeRenderVariants: "compute"[];
+export declare const ComputeRenderVariants: ComputeRenderVariant[];
 export type Transparency = 'blended' | 'wboit' | 'dpoit' | undefined;
 export type GraphicsRenderItem = RenderItem<GraphicsRenderVariant>;
 export declare function createGraphicsRenderItem(ctx: WebGLContext, drawMode: DrawMode, shaderCode: ShaderCode, schema: RenderableSchema, values: RenderableValues, materialId: number, transparency: Transparency): RenderItem<"color" | "emissive" | "depth" | "pick" | "marking">;

package/lib/mol-gl/webgl/timer.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2022-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2022-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */

package/lib/mol-gl/webgl/timer.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2022-2023 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2022-2024 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -22,6 +22,9 @@ class MovingAverage {
     stats() {
         return Object.fromEntries(this.avgs.entries());
     }
+    clear() {
+        this.avgs.clear();
+    }
     constructor(count) {
         this.count = count;
         this.avgs = new Map();
@@ -58,8 +61,12 @@ export function createTimer(gl, extensions, stats, options) {
             dtq.deleteQuery(query);
         });
         pending.clear();
+        stack.length = 0;
+        gpuAvgs.clear();
+        cpuAvgs.clear();
         measures = [];
         current = null;
+        capturingStats = false;
     };
     const add = () => {
         if (!dtq)

package/lib/mol-io/common/simple-buffer.d.ts

@@ -4,7 +4,6 @@
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author David Sehnal <david.sehnal@gmail.com>
  */
-/// <reference types="node" />
 export interface SimpleBuffer extends Uint8Array {
     readInt8: (offset: number) => number;
     readUInt8: (offset: number) => number;

package/lib/mol-io/reader/cif/schema/bird.d.ts

@@ -1,7 +1,7 @@
 /**
  * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.391, IHM 1.25, MA 1.4.6.
+ * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.395, IHM 1.25, MA 1.4.6.
  *
  * @author molstar/ciftools package
  */

package/lib/mol-io/reader/cif/schema/bird.js

@@ -1,7 +1,7 @@
 /**
  * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.391, IHM 1.25, MA 1.4.6.
+ * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.395, IHM 1.25, MA 1.4.6.
  *
  * @author molstar/ciftools package
  */

package/lib/mol-io/reader/cif/schema/ccd.d.ts

@@ -1,7 +1,7 @@
 /**
  * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.391, IHM 1.25, MA 1.4.6.
+ * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.395, IHM 1.25, MA 1.4.6.
  *
  * @author molstar/ciftools package
  */

package/lib/mol-io/reader/cif/schema/ccd.js

@@ -1,7 +1,7 @@
 /**
  * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.391, IHM 1.25, MA 1.4.6.
+ * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.395, IHM 1.25, MA 1.4.6.
  *
  * @author molstar/ciftools package
  */

package/lib/mol-io/reader/cif/schema/mmcif.d.ts

@@ -1,7 +1,7 @@
 /**
  * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.391, IHM 1.25, MA 1.4.6.
+ * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.395, IHM 1.25, MA 1.4.6.
  *
  * @author molstar/ciftools package
  */
@@ -780,6 +780,14 @@ export declare const mmCIF_Schema: {
          * the entry.
          */
         pdbx_number_of_molecules: Schema.Int;
+        /**
+         * An identifier for the parent entity if this entity
+         * is part of a complex entity.  For instance a chimeric
+         * entity may be decomposed into several independent
+         * chemical entities where each component entity was
+         * obtained from a different source.
+         */
+        pdbx_parent_entity_id: Schema.Str;
         /**
          * Details about any entity mutation(s).
          */

package/lib/mol-io/reader/cif/schema/mmcif.js

@@ -1,7 +1,7 @@
 /**
  * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.391, IHM 1.25, MA 1.4.6.
+ * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.395, IHM 1.25, MA 1.4.6.
  *
  * @author molstar/ciftools package
  */
@@ -789,6 +789,14 @@ export const mmCIF_Schema = {
          * the entry.
          */
         pdbx_number_of_molecules: int,
+        /**
+         * An identifier for the parent entity if this entity
+         * is part of a complex entity.  For instance a chimeric
+         * entity may be decomposed into several independent
+         * chemical entities where each component entity was
+         * obtained from a different source.
+         */
+        pdbx_parent_entity_id: str,
         /**
          * Details about any entity mutation(s).
          */

package/lib/mol-io/reader/common/text/column/fixed.d.ts

@@ -5,5 +5,5 @@
  */
 import { Column } from '../../../../../mol-data/db';
 import { Tokens } from '../tokenizer';
-export declare function FixedColumnProvider(lines: Tokens): <T extends Column.Schema<any>>(offset: number, width: number, type: T) => Column<T["T"]>;
+export declare function FixedColumnProvider(lines: Tokens): <T extends Column.Schema>(offset: number, width: number, type: T) => Column<T["T"]>;
 export declare function FixedColumn<T extends Column.Schema>(lines: Tokens, offset: number, width: number, schema: T): Column<T['T']>;

package/lib/mol-io/reader/common/text/column/token.d.ts

@@ -6,7 +6,7 @@
  */
 import { Column } from '../../../../../mol-data/db';
 import { Tokens } from '../tokenizer';
-export declare function TokenColumnProvider(tokens: Tokens): <T extends Column.Schema<any>>(type: T) => Column<T["T"]>;
+export declare function TokenColumnProvider(tokens: Tokens): <T extends Column.Schema>(type: T) => Column<T["T"]>;
 export declare function TokenColumn<T extends Column.Schema>(tokens: Tokens, schema: T): Column<T['T']>;
 export declare function areValuesEqualProvider(tokens: Tokens): (rowA: number, rowB: number) => boolean;
 export declare function areTokensEmpty(tokens: Tokens): boolean;

package/lib/mol-io/reader/ply/schema.d.ts

@@ -24,7 +24,7 @@ export declare const PlyTypeByteLength: {
 };
 export type PlyType = keyof typeof PlyTypeByteLength;
 export declare const PlyTypes: Set<string>;
-export declare function PlyType(str: string): "double" | "float" | "char" | "int" | "uint8" | "int8" | "uint16" | "int16" | "uint32" | "int32" | "float32" | "ushort" | "uchar" | "short" | "uint" | "float64";
+export declare function PlyType(str: string): PlyType;
 export interface PlyFile {
     readonly comments: ReadonlyArray<string>;
     readonly elementNames: ReadonlyArray<string>;

package/lib/mol-math/linear-algebra/3d/minimize-rmsd.js

@@ -53,7 +53,8 @@ function computeN(state) {
     const cA = state.centerA;
     const cB = state.centerB;
     let sizeSq = 0.0;
-    for (let i = 0, _l = state.a.x.length; i < _l; i++) {
+    const L = Math.min(state.a.x.length, state.b.x.length);
+    for (let i = 0; i < L; i++) {
         const aX = xsA[i] - cA[0], aY = ysA[i] - cA[1], aZ = zsA[i] - cA[2];
         const bX = xsB[i] - cB[0], bY = ysB[i] - cB[1], bZ = zsB[i] - cB[2];
         sizeSq += aX * aX + aY * aY + aZ * aZ + bX * bX + bY * bY + bZ * bZ;

package/lib/mol-model/loci.d.ts

@@ -103,7 +103,7 @@ declare namespace Loci {
     export type Granularity = keyof typeof Granularity;
     export const GranularityOptions: ["element" | "operator" | "residue" | "entity" | "chain" | "model" | "structure" | "elementInstances" | "residueInstances" | "chainInstances", string][];
     /** Exclude `Instances` granularity kinds */
-    export function simpleGranularity(granularity: Granularity): "element" | "operator" | "residue" | "entity" | "chain" | "model" | "structure" | "elementInstances" | "residueInstances" | "chainInstances";
+    export function simpleGranularity(granularity: Granularity): Granularity;
     export function applyGranularity(loci: Loci, granularity: Granularity): Loci;
     /**
      * Converts structure related loci to StructureElement.Loci and applies

package/lib/mol-model/sequence/alignment/alignment.d.ts

@@ -3,10 +3,11 @@
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
+import { SubstitutionMatrix } from './substitution-matrix';
 declare const DefaultAlignmentOptions: {
     gapPenalty: number;
     gapExtensionPenalty: number;
-    substMatrix: "default" | "blosum62" | "blosum62x";
+    substMatrix: SubstitutionMatrix | "default";
 };
 export type AlignmentOptions = typeof DefaultAlignmentOptions;
 export declare function align(seqA: ArrayLike<string>, seqB: ArrayLike<string>, options?: Partial<AlignmentOptions>): {

package/lib/mol-model/structure/model/types/saccharides.js

@@ -5,4 +5,4 @@
  *
  * @author molstar/cli/chem-comp-dict/create-saccharides
  */
-export const SaccharideNames = new Set(['145', '147', '149', '289', '291', '293', '445', '475', '491', '510', '604', '045', '05L', '07E', '07Y', '08U', '09X', '0AT', '0BD', '0H0', '0HX', '0LP', '0MK', '0NZ', '0TS', '0UB', '0V4', '0WK', '0XY', '0YT', '10M', '12E', '14T', '15L', '16F', '16G', '16O', '17T', '18D', '18O', '18T', '1AR', '1BW', '1CF', '1FT', '1GL', '1GN', '1JB', '1LL', '1NA', '1S3', '1S4', '1SD', '1X4', '20S', '20X', '22O', '22S', '23V', '24S', '25E', '26M', '26O', '26Q', '26R', '26V', '26W', '26Y', '27C', '2DG', '2DR', '2F8', '2FG', '2FL', '2FP', '2GL', '2GS', '2H5', '2HA', '2M4', '2M5', '2M8', '2OS', '2SI', '2WP', '2WS', '32O', '34V', '38J', '3BU', '3CM', '3DO', '3DY', '3FM', '3GR', '3HD', '3J3', '3J4', '3LJ', '3LR', '3MF', '3MG', '3MK', '3R3', '3S6', '3SA', '3YW', '40J', '42D', '44S', '46D', '46M', '46Z', '48Z', '49A', '49S', '49T', '49V', '4AM', '4CQ', '4GC', '4GL', '4GP', '4JA', '4N2', '4NN', '4QY', '4R1', '4RS', '4SG', '4U0', '4U1', '4U2', '4UZ', '4V5', '50A', '51N', '56N', '57S', '5DI', '5GF', '5GO', '5II', '5KQ', '5KS', '5KT', '5KV', '5L2', '5L3', '5LS', '5LT', '5MM', '5N6', '5QP', '5RP', '5SA', '5SP', '5TH', '5TJ', '5TK', '5TM', '61J', '62I', '64K', '66O', '6BG', '6C2', '6DM', '6GB', '6GP', '6GR', '6K3', '6KH', '6KL', '6KS', '6KU', '6KW', '6LA', '6LS', '6LW', '6MJ', '6MN', '6PG', '6PY', '6PZ', '6S2', '6SA', '6UD', '6Y6', '6YR', '6ZC', '73E', '79J', '7CV', '7D1', '7GP', '7JZ', '7K2', '7K3', '7NU', '7SA', '83Y', '89Y', '8B7', '8B9', '8EX', '8GA', '8GG', '8GP', '8I4', '8LM', '8LR', '8OQ', '8PK', '8S0', '8YV', '95Z', '96O', '98U', '9AM', '9C1', '9CD', '9GP', '9KJ', '9MR', '9OK', '9PG', '9QG', '9QZ', '9RN', '9S7', '9SG', '9SJ', '9SM', '9SP', '9T1', '9T7', '9VP', '9WJ', '9WN', '9WZ', '9YW', 'A0K', 'A1AIO', 'A1Q', 'A2G', 'A5C', 'A6P', 'AAL', 'AAO', 'ABC', 'ABD', 'ABE', 'ABF', 'ABL', 'AC1', 'ACG', 'ACR', 'ACX', 'ADA', 'ADG', 'ADR', 'AF1', 'AFD', 'AFL', 'AFO', 'AFP', 'AFR', 'AGC', 'AGH', 'AGL', 'AGR', 'AH2', 'AH8', 'AHG', 'AHM', 'AHR', 'AIG', 'ALL', 'ALX', 'AMG', 'AMN', 'AMU', 'AMV', 'ANA', 'AOG', 'AOS', 'AQA', 'ARA', 'ARB', 'ARE', 'ARI', 'ARW', 'ASC', 'ASG', 'ASO', 'AXP', 'AXR', 'AY9', 'AZC', 'B0D', 'B16', 'B1H', 'B1N', 'B2G', 'B4G', 'B6D', 'B7G', 'B8D', 'B9D', 'BBK', 'BBV', 'BCD', 'BCW', 'BDF', 'BDG', 'BDP', 'BDR', 'BDZ', 'BEM', 'BFN', 'BFP', 'BG6', 'BG8', 'BGC', 'BGL', 'BGN', 'BGP', 'BGS', 'BHG', 'BM3', 'BM7', 'BMA', 'BMX', 'BND', 'BNG', 'BNX', 'BO1', 'BOG', 'BQY', 'BRI', 'BS7', 'BTG', 'BTU', 'BW3', 'BWG', 'BXF', 'BXP', 'BXX', 'BXY', 'BZD', 'C3B', 'C3G', 'C3X', 'C4B', 'C4W', 'C4X', 'C5X', 'CAP', 'CBF', 'CBI', 'CBK', 'CDR', 'CE5', 'CE6', 'CE8', 'CEG', 'CEX', 'CEY', 'CEZ', 'CGF', 'CJB', 'CKB', 'CKP', 'CNP', 'CR1', 'CR6', 'CRA', 'CT3', 'CTO', 'CTR', 'CTT', 'D0N', 'D1M', 'D5E', 'D6G', 'DAF', 'DAG', 'DAN', 'DDA', 'DDB', 'DDL', 'DEG', 'DEL', 'DFR', 'DFX', 'DG0', 'DGC', 'DGD', 'DGM', 'DGO', 'DGS', 'DGU', 'DIG', 'DJB', 'DJE', 'DK4', 'DKX', 'DKZ', 'DL6', 'DLD', 'DLF', 'DLG', 'DMU', 'DNO', 'DO8', 'DOM', 'DP5', 'DPC', 'DQQ', 'DQR', 'DR2', 'DR3', 'DR4', 'DR5', 'DRI', 'DSR', 'DT6', 'DVC', 'DYM', 'E3M', 'E4P', 'E5G', 'EAG', 'EBG', 'EBQ', 'EEN', 'EEQ', 'EGA', 'EJT', 'EMP', 'EMZ', 'EPG', 'EQP', 'EQV', 'ERE', 'ERI', 'ETT', 'EUS', 'F1P', 'F1X', 'F55', 'F58', 'F6P', 'F8X', 'FBP', 'FCA', 'FCB', 'FCT', 'FDP', 'FDQ', 'FFC', 'FFX', 'FIF', 'FIX', 'FK9', 'FKD', 'FMF', 'FMO', 'FNG', 'FNY', 'FRU', 'FSA', 'FSI', 'FSM', 'FSR', 'FSW', 'FU4', 'FUB', 'FUC', 'FUD', 'FUF', 'FUL', 'FUY', 'FVQ', 'FX1', 'FYJ', 'G0S', 'G16', 'G1P', 'G20', 'G28', 'G2F', 'G3F', 'G3I', 'G4D', 'G4S', 'G6D', 'G6P', 'G6S', 'G7P', 'G8Z', 'GAA', 'GAC', 'GAD', 'GAF', 'GAL', 'GAT', 'GBH', 'GC1', 'GC4', 'GC9', 'GCB', 'GCD', 'GCN', 'GCO', 'GCS', 'GCT', 'GCU', 'GCV', 'GCW', 'GDA', 'GDL', 'GE1', 'GE3', 'GFP', 'GIV', 'GL0', 'GL1', 'GL2', 'GL4', 'GL5', 'GL6', 'GL7', 'GL9', 'GLA', 'GLB', 'GLC', 'GLD', 'GLF', 'GLG', 'GLO', 'GLP', 'GLS', 'GLT', 'GLW', 'GM0', 'GMB', 'GMH', 'GMT', 'GMZ', 'GN1', 'GN4', 'GNS', 'GNX', 'GP0', 'GP1', 'GP4', 'GPH', 'GPK', 'GPM', 'GPO', 'GPQ', 'GPU', 'GPV', 'GPW', 'GQ1', 'GRF', 'GRX', 'GS1', 'GS4', 'GS9', 'GSA', 'GSD', 'GTE', 'GTH', 'GTK', 'GTM', 'GTR', 'GU0', 'GU1', 'GU2', 'GU3', 'GU4', 'GU5', 'GU6', 'GU8', 'GU9', 'GUF', 'GUL', 'GUP', 'GUZ', 'GXL', 'GXV', 'GYE', 'GYG', 'GYP', 'GYU', 'GYV', 'GZL', 'H1M', 'H1S', 'H2P', 'H3S', 'H53', 'H6Q', 'H6Z', 'HBZ', 'HD4', 'HDL', 'HMS', 'HNV', 'HNW', 'HSG', 'HSH', 'HSJ', 'HSQ', 'HSR', 'HSU', 'HSX', 'HSY', 'HSZ', 'HTG', 'HTM', 'HVC', 'I57', 'IAB', 'IDC', 'IDF', 'IDG', 'IDR', 'IDS', 'IDT', 'IDU', 'IDX', 'IDY', 'IEM', 'IN1', 'IPT', 'ISD', 'ISL', 'ISX', 'IVG', 'IXD', 'J5B', 'JFZ', 'JHM', 'JLT', 'JRV', 'JS2', 'JSV', 'JV4', 'JVA', 'JVS', 'JZR', 'K5B', 'K99', 'KBA', 'KBG', 'KD5', 'KDA', 'KDB', 'KDD', 'KDE', 'KDF', 'KDM', 'KDN', 'KDO', 'KDR', 'KFN', 'KG1', 'KGM', 'KHP', 'KME', 'KO1', 'KO2', 'KOT', 'KQC', 'KTU', 'L1L', 'L6N', 'L6S', 'L6T', 'LAG', 'LAH', 'LAI', 'LAK', 'LAO', 'LAT', 'LB2', 'LBS', 'LBT', 'LCN', 'LDY', 'LEC', 'LER', 'LFC', 'LFR', 'LGC', 'LGU', 'LKA', 'LKS', 'LM2', 'LMO', 'LMT', 'LMU', 'LNV', 'LOG', 'LOX', 'LPK', 'LRH', 'LSM', 'LTG', 'LTM', 'LVO', 'LVZ', 'LXB', 'LXC', 'LXZ', 'LZ0', 'M1F', 'M1P', 'M2F', 'M3M', 'M3N', 'M55', 'M6D', 'M6P', 'M7B', 'M7P', 'M8C', 'MA1', 'MA2', 'MA3', 'MA8', 'MAB', 'MAF', 'MAG', 'MAL', 'MAN', 'MAT', 'MAV', 'MAW', 'MBE', 'MBF', 'MBG', 'MCU', 'MDA', 'MDP', 'MFA', 'MFB', 'MFU', 'MG5', 'MGA', 'MGC', 'MGL', 'MGS', 'MJJ', 'MLB', 'MLR', 'MMA', 'MMN', 'MN0', 'MNA', 'MQG', 'MQT', 'MRH', 'MRP', 'MSX', 'MTT', 'MUB', 'MUG', 'MUR', 'MVP', 'MXY', 'MXZ', 'MYG', 'N1L', 'N3U', 'N9S', 'NA1', 'NAA', 'NAG', 'NBG', 'NBX', 'NBY', 'NDG', 'NED', 'NFG', 'NG1', 'NG6', 'NGA', 'NGB', 'NGC', 'NGE', 'NGF', 'NGK', 'NGL', 'NGR', 'NGS', 'NGY', 'NGZ', 'NHF', 'NLC', 'NM6', 'NM9', 'NNG', 'NPF', 'NSQ', 'NT1', 'NTF', 'NTO', 'NTP', 'NXD', 'NYT', 'O1G', 'OAK', 'OEL', 'OI7', 'OPM', 'ORP', 'OSU', 'OTG', 'OTN', 'OTU', 'OX2', 'P53', 'P6P', 'P8E', 'PA1', 'PA5', 'PAV', 'PDX', 'PH5', 'PKM', 'PNA', 'PNG', 'PNJ', 'PNW', 'PPC', 'PRP', 'PSG', 'PSJ', 'PSV', 'PTQ', 'PUF', 'PZU', 'QDK', 'QIF', 'QKH', 'QPS', 'QV4', 'R1P', 'R1X', 'R2B', 'R2G', 'R5P', 'RAA', 'RAE', 'RAF', 'RAM', 'RAO', 'RAT', 'RB5', 'RBL', 'RCD', 'RDP', 'REL', 'RER', 'RF5', 'RG1', 'RGG', 'RHA', 'RHC', 'RI2', 'RIB', 'RIP', 'RM4', 'RNS', 'RNT', 'ROB', 'ROR', 'RP3', 'RP5', 'RP6', 'RPA', 'RR7', 'RRJ', 'RRY', 'RST', 'RTG', 'RTV', 'RUB', 'RUG', 'RUU', 'RV7', 'RVG', 'RVM', 'RWI', 'RY7', 'RZM', 'S6P', 'S7P', 'S81', 'SA0', 'SCG', 'SCR', 'SDD', 'SDY', 'SEJ', 'SF6', 'SF9', 'SFJ', 'SFU', 'SG4', 'SG5', 'SG6', 'SG7', 'SGA', 'SGC', 'SGD', 'SGN', 'SGS', 'SHB', 'SHD', 'SHG', 'SI3', 'SIA', 'SID', 'SIO', 'SIZ', 'SLB', 'SLM', 'SLT', 'SMD', 'SN5', 'SNG', 'SOE', 'SOG', 'SOL', 'SOR', 'SR1', 'SSG', 'SSH', 'STW', 'STZ', 'SUC', 'SUP', 'SUS', 'SWE', 'SZZ', 'T68', 'T6D', 'T6P', 'T6T', 'TA6', 'TAG', 'TCB', 'TCG', 'TDG', 'TEU', 'TF0', 'TFU', 'TGA', 'TGK', 'TGR', 'TGY', 'TH1', 'TM5', 'TM6', 'TM9', 'TMR', 'TMX', 'TNX', 'TOA', 'TOC', 'TQY', 'TRE', 'TRV', 'TS8', 'TT7', 'TTV', 'TTZ', 'TU4', 'TUG', 'TUJ', 'TUP', 'TUR', 'TVD', 'TVG', 'TVM', 'TVS', 'TVV', 'TVY', 'TW7', 'TWA', 'TWD', 'TWG', 'TWJ', 'TWY', 'TXB', 'TY6', 'TYV', 'U1Y', 'U2A', 'U2D', 'U63', 'U8V', 'U97', 'U9A', 'U9D', 'U9G', 'U9J', 'U9M', 'UAP', 'UBH', 'UBO', 'UCD', 'UDC', 'UEA', 'V3M', 'V3P', 'V71', 'VDF', 'VG1', 'VJ1', 'VJ4', 'VKN', 'VTB', 'W9T', 'WIA', 'WOO', 'WUN', 'WZ1', 'WZ2', 'WZ4', 'X0X', 'X1P', 'X1X', 'X2F', 'X2Y', 'X34', 'X4S', 'X5S', 'X6X', 'X6Y', 'XBP', 'XDP', 'XDX', 'XGP', 'XIL', 'XKJ', 'XLF', 'XLS', 'XMM', 'XS2', 'XUL', 'XXM', 'XXR', 'XXX', 'XY6', 'XY9', 'XYB', 'XYF', 'XYL', 'XYP', 'XYS', 'XYT', 'XYZ', 'YDR', 'YIO', 'YJM', 'YKR', 'YO5', 'YX0', 'YX1', 'YYB', 'YYD', 'YYH', 'YYJ', 'YYK', 'YYM', 'YYQ', 'YYR', 'YZ0', 'YZT', 'Z0F', 'Z15', 'Z16', 'Z2D', 'Z2T', 'Z3K', 'Z3L', 'Z3Q', 'Z3U', 'Z4K', 'Z4R', 'Z4S', 'Z4U', 'Z4V', 'Z4W', 'Z4Y', 'Z57', 'Z5J', 'Z5L', 'Z61', 'Z6G', 'Z6H', 'Z6J', 'Z6W', 'Z8H', 'Z8T', 'Z9D', 'Z9E', 'Z9H', 'Z9K', 'Z9L', 'Z9M', 'Z9N', 'Z9W', 'ZB0', 'ZB1', 'ZB2', 'ZB3', 'ZCD', 'ZCZ', 'ZD0', 'ZDC', 'ZDM', 'ZDO', 'ZEE', 'ZEL', 'ZGE', 'ZMR', 'UMQ', 'SQD']);
+export const SaccharideNames = new Set(['145', '147', '149', '289', '291', '293', '445', '475', '491', '510', '604', '045', '05L', '07E', '07Y', '08U', '09X', '0AT', '0BD', '0H0', '0HX', '0LP', '0MK', '0NZ', '0TS', '0UB', '0V4', '0WK', '0XY', '0YT', '10M', '12E', '14T', '15L', '16F', '16G', '16O', '17T', '18D', '18O', '18T', '1AR', '1BW', '1CF', '1FT', '1GL', '1GN', '1JB', '1LL', '1NA', '1S3', '1S4', '1SD', '1X4', '20S', '20X', '22O', '22S', '23V', '24S', '25E', '26M', '26O', '26Q', '26R', '26V', '26W', '26Y', '27C', '2DG', '2DR', '2F8', '2FG', '2FL', '2FP', '2GL', '2GS', '2H5', '2HA', '2M4', '2M5', '2M8', '2OS', '2SI', '2WP', '2WS', '32O', '34V', '38J', '3BU', '3CM', '3DO', '3DY', '3FM', '3GR', '3HD', '3J3', '3J4', '3LJ', '3LR', '3MF', '3MG', '3MK', '3R3', '3S6', '3SA', '3YW', '40J', '42D', '44S', '46D', '46M', '46Z', '48Z', '49A', '49S', '49T', '49V', '4AM', '4CQ', '4GC', '4GL', '4GP', '4JA', '4N2', '4NN', '4QY', '4R1', '4RS', '4SG', '4U0', '4U1', '4U2', '4UZ', '4V5', '50A', '51N', '56N', '57S', '5DI', '5GF', '5GO', '5II', '5KQ', '5KS', '5KT', '5KV', '5L2', '5L3', '5LS', '5LT', '5MM', '5N6', '5QP', '5RP', '5SA', '5SP', '5TH', '5TJ', '5TK', '5TM', '61J', '62I', '64K', '66O', '6BG', '6C2', '6DM', '6GB', '6GP', '6GR', '6K3', '6KH', '6KL', '6KS', '6KU', '6KW', '6LA', '6LS', '6LW', '6MJ', '6MN', '6PG', '6PY', '6PZ', '6S2', '6SA', '6UD', '6Y6', '6YR', '6ZC', '73E', '79J', '7CV', '7D1', '7GP', '7JZ', '7K2', '7K3', '7NU', '7SA', '83Y', '89Y', '8B7', '8B9', '8EX', '8GA', '8GG', '8GP', '8I4', '8LM', '8LR', '8OQ', '8PK', '8S0', '8YV', '95Z', '96O', '98U', '9AM', '9C1', '9CD', '9GP', '9KJ', '9MR', '9OK', '9PG', '9QG', '9QZ', '9RN', '9S7', '9SG', '9SJ', '9SM', '9SP', '9T1', '9T7', '9VP', '9WJ', '9WN', '9WZ', '9YW', 'A0K', 'A1AIO', 'A1H0Z', 'A1Q', 'A2G', 'A5C', 'A6P', 'AAL', 'AAO', 'ABC', 'ABD', 'ABE', 'ABF', 'ABL', 'AC1', 'ACG', 'ACR', 'ACX', 'ADA', 'ADG', 'ADR', 'AF1', 'AFD', 'AFL', 'AFO', 'AFP', 'AFR', 'AGC', 'AGH', 'AGL', 'AGR', 'AH2', 'AH8', 'AHG', 'AHM', 'AHR', 'AIG', 'ALL', 'ALX', 'AMG', 'AMN', 'AMU', 'AMV', 'ANA', 'AOG', 'AOS', 'AQA', 'ARA', 'ARB', 'ARE', 'ARI', 'ARW', 'ASC', 'ASG', 'ASO', 'AXP', 'AXR', 'AY9', 'AZC', 'B0D', 'B16', 'B1H', 'B1N', 'B2G', 'B4G', 'B6D', 'B7G', 'B8D', 'B9D', 'BBK', 'BBV', 'BCD', 'BCW', 'BDF', 'BDG', 'BDP', 'BDR', 'BDZ', 'BEM', 'BFN', 'BFP', 'BG6', 'BG8', 'BGC', 'BGL', 'BGN', 'BGP', 'BGS', 'BHG', 'BM3', 'BM7', 'BMA', 'BMX', 'BND', 'BNG', 'BNX', 'BO1', 'BOG', 'BQY', 'BRI', 'BS7', 'BTG', 'BTU', 'BW3', 'BWG', 'BXF', 'BXP', 'BXX', 'BXY', 'BZD', 'C3B', 'C3G', 'C3X', 'C4B', 'C4W', 'C4X', 'C5X', 'CAP', 'CBF', 'CBI', 'CBK', 'CDR', 'CE5', 'CE6', 'CE8', 'CEG', 'CEX', 'CEY', 'CEZ', 'CGF', 'CJB', 'CKB', 'CKP', 'CNP', 'CR1', 'CR6', 'CRA', 'CT3', 'CTO', 'CTR', 'CTT', 'D0N', 'D1M', 'D5E', 'D6G', 'DAF', 'DAG', 'DAN', 'DDA', 'DDB', 'DDL', 'DEG', 'DEL', 'DFR', 'DFX', 'DG0', 'DGC', 'DGD', 'DGM', 'DGO', 'DGS', 'DGU', 'DIG', 'DJB', 'DJE', 'DK4', 'DKX', 'DKZ', 'DL6', 'DLD', 'DLF', 'DLG', 'DMU', 'DNO', 'DO8', 'DOM', 'DP5', 'DPC', 'DQQ', 'DQR', 'DR2', 'DR3', 'DR4', 'DR5', 'DRI', 'DSR', 'DT6', 'DVC', 'DYM', 'E3M', 'E4P', 'E5G', 'EAG', 'EBG', 'EBQ', 'EEN', 'EEQ', 'EGA', 'EJT', 'EMP', 'EMZ', 'EPG', 'EQP', 'EQV', 'ERE', 'ERI', 'ETT', 'EUS', 'F1P', 'F1X', 'F55', 'F58', 'F6P', 'F8X', 'FBP', 'FCA', 'FCB', 'FCT', 'FDP', 'FDQ', 'FFC', 'FFX', 'FIF', 'FIX', 'FK9', 'FKD', 'FMF', 'FMO', 'FNG', 'FNY', 'FRU', 'FSA', 'FSI', 'FSM', 'FSR', 'FSW', 'FU4', 'FUB', 'FUC', 'FUD', 'FUF', 'FUL', 'FUY', 'FVQ', 'FX1', 'FYJ', 'G0S', 'G16', 'G1P', 'G20', 'G28', 'G2F', 'G3F', 'G3I', 'G4D', 'G4S', 'G6D', 'G6P', 'G6S', 'G7P', 'G8Z', 'GAA', 'GAC', 'GAD', 'GAF', 'GAL', 'GAT', 'GBH', 'GC1', 'GC4', 'GC9', 'GCB', 'GCD', 'GCN', 'GCO', 'GCS', 'GCT', 'GCU', 'GCV', 'GCW', 'GDA', 'GDL', 'GE1', 'GE3', 'GFP', 'GIV', 'GL0', 'GL1', 'GL2', 'GL4', 'GL5', 'GL6', 'GL7', 'GL9', 'GLA', 'GLB', 'GLC', 'GLD', 'GLF', 'GLG', 'GLO', 'GLP', 'GLS', 'GLT', 'GLW', 'GM0', 'GMB', 'GMH', 'GMT', 'GMZ', 'GN1', 'GN4', 'GNS', 'GNX', 'GP0', 'GP1', 'GP4', 'GPH', 'GPK', 'GPM', 'GPO', 'GPQ', 'GPU', 'GPV', 'GPW', 'GQ1', 'GRF', 'GRX', 'GS1', 'GS4', 'GS9', 'GSA', 'GSD', 'GTE', 'GTH', 'GTK', 'GTM', 'GTR', 'GU0', 'GU1', 'GU2', 'GU3', 'GU4', 'GU5', 'GU6', 'GU8', 'GU9', 'GUF', 'GUL', 'GUP', 'GUZ', 'GXL', 'GXV', 'GYE', 'GYG', 'GYP', 'GYU', 'GYV', 'GZL', 'H1M', 'H1S', 'H2P', 'H3S', 'H53', 'H6Q', 'H6Z', 'HBZ', 'HD4', 'HDL', 'HMS', 'HNV', 'HNW', 'HSG', 'HSH', 'HSJ', 'HSQ', 'HSR', 'HSU', 'HSX', 'HSY', 'HSZ', 'HTG', 'HTM', 'HVC', 'I57', 'IAB', 'IDC', 'IDF', 'IDG', 'IDR', 'IDS', 'IDT', 'IDU', 'IDX', 'IDY', 'IEM', 'IN1', 'IPT', 'ISD', 'ISL', 'ISX', 'IVG', 'IXD', 'J5B', 'JFZ', 'JHM', 'JLT', 'JRV', 'JS2', 'JSV', 'JV4', 'JVA', 'JVS', 'JZR', 'K5B', 'K99', 'KBA', 'KBG', 'KD5', 'KDA', 'KDB', 'KDD', 'KDE', 'KDF', 'KDM', 'KDN', 'KDO', 'KDR', 'KFN', 'KG1', 'KGM', 'KHP', 'KME', 'KO1', 'KO2', 'KOT', 'KQC', 'KTU', 'L1L', 'L6N', 'L6S', 'L6T', 'LAG', 'LAH', 'LAI', 'LAK', 'LAO', 'LAT', 'LB2', 'LBS', 'LBT', 'LCN', 'LDY', 'LEC', 'LER', 'LFC', 'LFR', 'LGC', 'LGU', 'LKA', 'LKS', 'LM2', 'LMO', 'LMT', 'LMU', 'LNV', 'LOG', 'LOX', 'LPK', 'LRH', 'LSM', 'LTG', 'LTM', 'LVO', 'LVZ', 'LXB', 'LXC', 'LXZ', 'LZ0', 'M1F', 'M1P', 'M2F', 'M3M', 'M3N', 'M55', 'M6D', 'M6P', 'M7B', 'M7P', 'M8C', 'MA1', 'MA2', 'MA3', 'MA8', 'MAB', 'MAF', 'MAG', 'MAL', 'MAN', 'MAT', 'MAV', 'MAW', 'MBE', 'MBF', 'MBG', 'MCU', 'MDA', 'MDP', 'MFA', 'MFB', 'MFU', 'MG5', 'MGA', 'MGC', 'MGL', 'MGS', 'MJJ', 'MLB', 'MLR', 'MMA', 'MMN', 'MN0', 'MNA', 'MQG', 'MQT', 'MRH', 'MRP', 'MSX', 'MTT', 'MUB', 'MUG', 'MUR', 'MVP', 'MXY', 'MXZ', 'MYG', 'N1L', 'N3U', 'N9S', 'NA1', 'NAA', 'NAG', 'NBG', 'NBX', 'NBY', 'NDG', 'NED', 'NFG', 'NG1', 'NG6', 'NGA', 'NGB', 'NGC', 'NGE', 'NGF', 'NGK', 'NGL', 'NGR', 'NGS', 'NGY', 'NGZ', 'NHF', 'NLC', 'NM6', 'NM9', 'NNG', 'NPF', 'NSQ', 'NT1', 'NTF', 'NTO', 'NTP', 'NXD', 'NYT', 'O1G', 'OAK', 'OEL', 'OI7', 'OPM', 'ORP', 'OSU', 'OTG', 'OTN', 'OTU', 'OX2', 'P53', 'P6P', 'P8E', 'PA1', 'PA5', 'PAV', 'PDX', 'PH5', 'PKM', 'PNA', 'PNG', 'PNJ', 'PNW', 'PPC', 'PRP', 'PSG', 'PSJ', 'PSV', 'PTQ', 'PUF', 'PZU', 'QDK', 'QIF', 'QKH', 'QPS', 'QV4', 'R1P', 'R1X', 'R2B', 'R2G', 'R5P', 'RAA', 'RAE', 'RAF', 'RAM', 'RAO', 'RAT', 'RB5', 'RBL', 'RCD', 'RDP', 'REL', 'RER', 'RF5', 'RG1', 'RGG', 'RHA', 'RHC', 'RI2', 'RIB', 'RIP', 'RM4', 'RNS', 'RNT', 'ROB', 'ROR', 'RP3', 'RP5', 'RP6', 'RPA', 'RR7', 'RRJ', 'RRY', 'RST', 'RTG', 'RTV', 'RUB', 'RUG', 'RUU', 'RV7', 'RVG', 'RVM', 'RWI', 'RY7', 'RZM', 'S6P', 'S7P', 'S81', 'SA0', 'SCG', 'SCR', 'SDD', 'SDY', 'SEJ', 'SF6', 'SF9', 'SFJ', 'SFU', 'SG4', 'SG5', 'SG6', 'SG7', 'SGA', 'SGC', 'SGD', 'SGN', 'SGS', 'SHB', 'SHD', 'SHG', 'SI3', 'SIA', 'SID', 'SIO', 'SIZ', 'SLB', 'SLM', 'SLT', 'SMD', 'SN5', 'SNG', 'SOE', 'SOG', 'SOL', 'SOR', 'SR1', 'SSG', 'SSH', 'STW', 'STZ', 'SUC', 'SUP', 'SUS', 'SWE', 'SZZ', 'T68', 'T6D', 'T6P', 'T6T', 'TA6', 'TAG', 'TCB', 'TCG', 'TDG', 'TEU', 'TF0', 'TFU', 'TGA', 'TGK', 'TGR', 'TGY', 'TH1', 'TM5', 'TM6', 'TM9', 'TMR', 'TMX', 'TNX', 'TOA', 'TOC', 'TQY', 'TRE', 'TRV', 'TS8', 'TT7', 'TTV', 'TTZ', 'TU4', 'TUG', 'TUJ', 'TUP', 'TUR', 'TVD', 'TVG', 'TVM', 'TVS', 'TVV', 'TVY', 'TW7', 'TWA', 'TWD', 'TWG', 'TWJ', 'TWY', 'TXB', 'TY6', 'TYV', 'U1Y', 'U2A', 'U2D', 'U63', 'U8V', 'U97', 'U9A', 'U9D', 'U9G', 'U9J', 'U9M', 'UAP', 'UBH', 'UBO', 'UCD', 'UDC', 'UEA', 'V3M', 'V3P', 'V71', 'VDF', 'VG1', 'VJ1', 'VJ4', 'VKN', 'VTB', 'W9T', 'WIA', 'WOO', 'WUN', 'WZ1', 'WZ2', 'WZ4', 'X0X', 'X1P', 'X1X', 'X2F', 'X2Y', 'X34', 'X4S', 'X5S', 'X6X', 'X6Y', 'XBP', 'XDP', 'XDX', 'XGP', 'XIL', 'XKJ', 'XLF', 'XLS', 'XMM', 'XS2', 'XUL', 'XXM', 'XXR', 'XXX', 'XY6', 'XY9', 'XYB', 'XYF', 'XYL', 'XYP', 'XYS', 'XYT', 'XYZ', 'YDR', 'YIO', 'YJM', 'YKR', 'YO5', 'YX0', 'YX1', 'YYB', 'YYD', 'YYH', 'YYJ', 'YYK', 'YYM', 'YYQ', 'YYR', 'YZ0', 'YZT', 'Z0F', 'Z15', 'Z16', 'Z2D', 'Z2T', 'Z3K', 'Z3L', 'Z3Q', 'Z3U', 'Z4K', 'Z4R', 'Z4S', 'Z4U', 'Z4V', 'Z4W', 'Z4Y', 'Z57', 'Z5J', 'Z5L', 'Z61', 'Z6G', 'Z6H', 'Z6J', 'Z6W', 'Z8H', 'Z8T', 'Z9D', 'Z9E', 'Z9H', 'Z9K', 'Z9L', 'Z9M', 'Z9N', 'Z9W', 'ZB0', 'ZB1', 'ZB2', 'ZB3', 'ZCD', 'ZCZ', 'ZD0', 'ZDC', 'ZDM', 'ZDO', 'ZEE', 'ZEL', 'ZGE', 'ZMR', 'UMQ', 'SQD']);

package/lib/mol-model/structure/model/types.d.ts

@@ -111,9 +111,9 @@ export declare function getComponentType(compId: string): ChemCompType;
 export declare function getDefaultChemicalComponent(compId: string): ChemicalComponent;
 export declare function getEntityType(compId: string): mmCIF_Schema['entity']['type']['T'];
 export declare function getEntitySubtype(compId: string, compType: ChemCompType): EntitySubtype;
-export declare function isPolymer(moleculeType: MoleculeType): boolean;
-export declare function isNucleic(moleculeType: MoleculeType): boolean;
-export declare function isProtein(moleculeType: MoleculeType): boolean;
+export declare function isPolymer(moleculeType: MoleculeType): moleculeType is MoleculeType.Protein | MoleculeType.RNA | MoleculeType.DNA | MoleculeType.PNA;
+export declare function isNucleic(moleculeType: MoleculeType): moleculeType is MoleculeType.RNA | MoleculeType.DNA | MoleculeType.PNA;
+export declare function isProtein(moleculeType: MoleculeType): moleculeType is MoleculeType.Protein;
 export type SecondaryStructureType = BitFlags<SecondaryStructureType.Flag>;
 export declare namespace SecondaryStructureType {
     const is: (ss: SecondaryStructureType, f: Flag) => boolean;