molstar 3.0.0-dev.9 → 3.1.0

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

@@ -1,11 +1,11 @@
 "use strict";
 /**
- * Copyright (c) 2017-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  * @author Michael Krone <michael.krone@uni-tuebingen.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.directVolume_frag = void 0;
-exports.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\nuniform vec3 uHighlightColor;\nuniform vec3 uSelectColor;\nuniform float uHighlightStrength;\nuniform float uSelectStrength;\nuniform int uMarkerPriority;\n\nuniform float uMarker;\nuniform vec2 uMarkerTexDim;\nuniform sampler2D tMarker;\n\nuniform float uMetalness;\nuniform float uRoughness;\n\nuniform float uFogNear;\nuniform float uFogFar;\nuniform vec3 uFogColor;\n\nuniform float uAlpha;\nuniform float uPickingAlphaThreshold;\nuniform bool uTransparentBackground;\nuniform float uXrayEdgeFalloff;\n\nuniform float uInteriorDarkening;\nuniform bool uInteriorColorFlag;\nuniform vec3 uInteriorColor;\n\nuniform bool uRenderWboit;\nuniform bool uDoubleSided;\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        if (!uRenderWboit) {\n            // in case of opaque volumes (and depth texture support)\n            return texture2D(tDepth, coords).r;\n        } else {\n            return unpackRGBAToDepth(texture2D(tDepth, coords));\n        }\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    #if !defined(dIgnoreLight)\n        mat3 normalMatrix = transpose3(inverse3(mat3(uModelView * vTransform)));\n    #endif\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\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), 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, isoPos, uGridDim, uColorTexDim, 0.0).rgb;\n        #elif defined(dColorType_vertexInstance)\n            material.rgb = texture3dFrom1dTrilinear(tColor, isoPos, 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, isoPos, uGridDim, uOverpaintTexDim, vInstance * float(uVertexCount));\n            #endif\n\n            material.rgb = mix(material.rgb, overpaint.rgb, overpaint.a);\n        #endif\n\n        #ifdef 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        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        #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 (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    bool interior = false;\n    #include wboit_write\n}\n";
+exports.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\nuniform vec3 uHighlightColor;\nuniform vec3 uSelectColor;\nuniform float uHighlightStrength;\nuniform float uSelectStrength;\nuniform int uMarkerPriority;\n\nuniform float uMarker;\nuniform vec2 uMarkerTexDim;\nuniform sampler2D tMarker;\n\nuniform float uMetalness;\nuniform float uRoughness;\n\nuniform float uFogNear;\nuniform float uFogFar;\nuniform vec3 uFogColor;\n\nuniform float uAlpha;\nuniform float uPickingAlphaThreshold;\nuniform bool uTransparentBackground;\nuniform float uXrayEdgeFalloff;\n\nuniform float uInteriorDarkening;\nuniform bool uInteriorColorFlag;\nuniform vec3 uInteriorColor;\n\nuniform bool uRenderWboit;\nuniform bool uDoubleSided;\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        if (!uRenderWboit) {\n            // in case of opaque volumes (and depth texture support)\n            return texture2D(tDepth, coords).r;\n        } else {\n            return unpackRGBAToDepth(texture2D(tDepth, coords));\n        }\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\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), 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, isoPos, uGridDim, uColorTexDim, 0.0).rgb;\n        #elif defined(dColorType_vertexInstance)\n            material.rgb = texture3dFrom1dTrilinear(tColor, isoPos, 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, isoPos, uGridDim, uOverpaintTexDim, vInstance * float(uVertexCount));\n            #endif\n\n            material.rgb = mix(material.rgb, overpaint.rgb, overpaint.a);\n        #endif\n\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\n        gl_FragColor.a = material.a * uAlpha * uTransferScale;\n\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        #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 (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    bool interior = false;\n    #include wboit_write\n}\n";
 //# sourceMappingURL=direct-volume.frag.js.map

package/lib/commonjs/mol-gl/shader/mesh.frag.d.ts

@@ -1,6 +1,6 @@
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
-export declare const mesh_frag = "\nprecision highp float;\nprecision highp int;\n\n#define bumpEnabled\n\n#include common\n#include common_frag_params\n#include color_frag_params\n#include light_frag_params\n#include normal_frag_params\n#include common_clip\n\nvoid main() {\n    #include clip_pixel\n\n    // Workaround for buggy gl_FrontFacing (e.g. on some integrated Intel GPUs)\n    vec3 fdx = dFdx(vViewPosition);\n    vec3 fdy = dFdy(vViewPosition);\n    vec3 faceNormal = normalize(cross(fdx,fdy));\n    bool frontFacing = dot(vNormal, faceNormal) > 0.0;\n\n    #if defined(dFlipSided)\n        interior = frontFacing;\n    #else\n        interior = !frontFacing;\n    #endif\n\n    float fragmentDepth = gl_FragCoord.z;\n    #include assign_material_color\n\n    #if defined(dRenderVariant_pick)\n        #include check_picking_alpha\n        gl_FragColor = material;\n    #elif defined(dRenderVariant_depth)\n        gl_FragColor = material;\n    #elif defined(dRenderVariant_marking)\n        gl_FragColor = material;\n    #elif defined(dRenderVariant_color)\n        #ifdef dIgnoreLight\n            gl_FragColor = material;\n        #else\n            #if defined(dFlatShaded)\n                vec3 normal = -faceNormal;\n            #else\n                vec3 normal = -normalize(vNormal);\n                if (uDoubleSided) normal *= float(frontFacing) * 2.0 - 1.0;\n            #endif\n            #include apply_light_color\n        #endif\n\n        #include apply_interior_color\n        #include apply_marker_color\n        #include apply_fog\n        #include wboit_write\n    #endif\n}\n";
+export declare const mesh_frag = "\nprecision highp float;\nprecision highp int;\n\n#define bumpEnabled\n\n#include common\n#include common_frag_params\n#include color_frag_params\n#include light_frag_params\n#include normal_frag_params\n#include common_clip\n\nvoid main() {\n    #include clip_pixel\n\n    // Workaround for buggy gl_FrontFacing (e.g. on some integrated Intel GPUs)\n    vec3 fdx = dFdx(vViewPosition);\n    vec3 fdy = dFdy(vViewPosition);\n    vec3 faceNormal = normalize(cross(fdx,fdy));\n    bool frontFacing = dot(vNormal, faceNormal) > 0.0;\n\n    #if defined(dFlipSided)\n        interior = frontFacing;\n    #else\n        interior = !frontFacing;\n    #endif\n\n    float fragmentDepth = gl_FragCoord.z;\n    #include assign_material_color\n\n    #if defined(dRenderVariant_pick)\n        #include check_picking_alpha\n        gl_FragColor = material;\n    #elif defined(dRenderVariant_depth)\n        gl_FragColor = material;\n    #elif defined(dRenderVariant_marking)\n        gl_FragColor = material;\n    #elif defined(dRenderVariant_color)\n        #if defined(dFlatShaded)\n            vec3 normal = -faceNormal;\n        #else\n            vec3 normal = -normalize(vNormal);\n            if (uDoubleSided) normal *= float(frontFacing) * 2.0 - 1.0;\n        #endif\n        #include apply_light_color\n\n        #include apply_interior_color\n        #include apply_marker_color\n        #include apply_fog\n        #include wboit_write\n    #endif\n}\n";

package/lib/commonjs/mol-gl/shader/mesh.frag.js

@@ -1,10 +1,10 @@
 "use strict";
 /**
- * Copyright (c) 2018-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.mesh_frag = void 0;
-exports.mesh_frag = "\nprecision highp float;\nprecision highp int;\n\n#define bumpEnabled\n\n#include common\n#include common_frag_params\n#include color_frag_params\n#include light_frag_params\n#include normal_frag_params\n#include common_clip\n\nvoid main() {\n    #include clip_pixel\n\n    // Workaround for buggy gl_FrontFacing (e.g. on some integrated Intel GPUs)\n    vec3 fdx = dFdx(vViewPosition);\n    vec3 fdy = dFdy(vViewPosition);\n    vec3 faceNormal = normalize(cross(fdx,fdy));\n    bool frontFacing = dot(vNormal, faceNormal) > 0.0;\n\n    #if defined(dFlipSided)\n        interior = frontFacing;\n    #else\n        interior = !frontFacing;\n    #endif\n\n    float fragmentDepth = gl_FragCoord.z;\n    #include assign_material_color\n\n    #if defined(dRenderVariant_pick)\n        #include check_picking_alpha\n        gl_FragColor = material;\n    #elif defined(dRenderVariant_depth)\n        gl_FragColor = material;\n    #elif defined(dRenderVariant_marking)\n        gl_FragColor = material;\n    #elif defined(dRenderVariant_color)\n        #ifdef dIgnoreLight\n            gl_FragColor = material;\n        #else\n            #if defined(dFlatShaded)\n                vec3 normal = -faceNormal;\n            #else\n                vec3 normal = -normalize(vNormal);\n                if (uDoubleSided) normal *= float(frontFacing) * 2.0 - 1.0;\n            #endif\n            #include apply_light_color\n        #endif\n\n        #include apply_interior_color\n        #include apply_marker_color\n        #include apply_fog\n        #include wboit_write\n    #endif\n}\n";
+exports.mesh_frag = "\nprecision highp float;\nprecision highp int;\n\n#define bumpEnabled\n\n#include common\n#include common_frag_params\n#include color_frag_params\n#include light_frag_params\n#include normal_frag_params\n#include common_clip\n\nvoid main() {\n    #include clip_pixel\n\n    // Workaround for buggy gl_FrontFacing (e.g. on some integrated Intel GPUs)\n    vec3 fdx = dFdx(vViewPosition);\n    vec3 fdy = dFdy(vViewPosition);\n    vec3 faceNormal = normalize(cross(fdx,fdy));\n    bool frontFacing = dot(vNormal, faceNormal) > 0.0;\n\n    #if defined(dFlipSided)\n        interior = frontFacing;\n    #else\n        interior = !frontFacing;\n    #endif\n\n    float fragmentDepth = gl_FragCoord.z;\n    #include assign_material_color\n\n    #if defined(dRenderVariant_pick)\n        #include check_picking_alpha\n        gl_FragColor = material;\n    #elif defined(dRenderVariant_depth)\n        gl_FragColor = material;\n    #elif defined(dRenderVariant_marking)\n        gl_FragColor = material;\n    #elif defined(dRenderVariant_color)\n        #if defined(dFlatShaded)\n            vec3 normal = -faceNormal;\n        #else\n            vec3 normal = -normalize(vNormal);\n            if (uDoubleSided) normal *= float(frontFacing) * 2.0 - 1.0;\n        #endif\n        #include apply_light_color\n\n        #include apply_interior_color\n        #include apply_marker_color\n        #include apply_fog\n        #include wboit_write\n    #endif\n}\n";
 //# sourceMappingURL=mesh.frag.js.map

package/lib/commonjs/mol-gl/shader/spheres.frag.d.ts

@@ -1,6 +1,6 @@
 /**
- * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
-export declare const spheres_frag = "\nprecision highp float;\nprecision highp int;\n\n#define bumpEnabled\n\n#include common\n#include common_frag_params\n#include color_frag_params\n#include light_frag_params\n#include common_clip\n\nuniform mat4 uInvView;\n\nvarying float vRadius;\nvarying float vRadiusSq;\nvarying vec3 vPoint;\nvarying vec3 vPointViewPosition;\n\nvec3 cameraPos;\nvec3 cameraNormal;\n\nbool Impostor(out vec3 cameraPos, out vec3 cameraNormal){\n    vec3 cameraSpherePos = -vPointViewPosition;\n    cameraSpherePos.z += vRadius;\n\n    vec3 rayOrigin = mix(vec3(0.0, 0.0, 0.0), vPoint, uIsOrtho);\n    vec3 rayDirection = mix(normalize(vPoint), vec3(0.0, 0.0, 1.0), uIsOrtho);\n    vec3 cameraSphereDir = mix(cameraSpherePos, rayOrigin - cameraSpherePos, uIsOrtho);\n\n    float B = dot(rayDirection, cameraSphereDir);\n    float det = B * B + vRadiusSq - dot(cameraSphereDir, cameraSphereDir);\n\n    if (det < 0.0){\n        discard;\n        return false;\n    }\n\n    float sqrtDet = sqrt(det);\n    float posT = mix(B + sqrtDet, B + sqrtDet, uIsOrtho);\n    float negT = mix(B - sqrtDet, sqrtDet - B, uIsOrtho);\n\n    cameraPos = rayDirection * negT + rayOrigin;\n\n\n    if (calcDepth(cameraPos) <= 0.0) {\n        cameraPos = rayDirection * posT + rayOrigin;\n        interior = true;\n    } else {\n        interior = false;\n    }\n\n    cameraNormal = normalize(cameraPos - cameraSpherePos);\n    cameraNormal *= float(!interior) * 2.0 - 1.0;\n\n    return !interior;\n}\n\nvoid main(void){\n    #include clip_pixel\n\n    bool flag = Impostor(cameraPos, cameraNormal);\n    if (!uDoubleSided) {\n        if (interior) discard;\n    }\n\n    vec3 vViewPosition = cameraPos;\n    gl_FragDepthEXT = calcDepth(vViewPosition);\n    if (!flag && gl_FragDepthEXT >= 0.0) {\n        gl_FragDepthEXT = 0.0 + (0.0000001 / vRadius);\n    }\n\n    vec3 vModelPosition = (uInvView * vec4(vViewPosition, 1.0)).xyz;\n\n    if (gl_FragDepthEXT < 0.0) discard;\n    if (gl_FragDepthEXT > 1.0) discard;\n\n    float fragmentDepth = gl_FragDepthEXT;\n    #include assign_material_color\n\n    #if defined(dRenderVariant_pick)\n        #include check_picking_alpha\n        gl_FragColor = material;\n    #elif defined(dRenderVariant_depth)\n        gl_FragColor = material;\n    #elif defined(dRenderVariant_marking)\n        gl_FragColor = material;\n    #elif defined(dRenderVariant_color)\n        #ifdef dIgnoreLight\n            gl_FragColor = material;\n        #else\n            vec3 normal = -cameraNormal;\n            #include apply_light_color\n        #endif\n\n        #include apply_interior_color\n        #include apply_marker_color\n        #include apply_fog\n        #include wboit_write\n    #endif\n}\n";
+export declare const spheres_frag = "\nprecision highp float;\nprecision highp int;\n\n#define bumpEnabled\n\n#include common\n#include common_frag_params\n#include color_frag_params\n#include light_frag_params\n#include common_clip\n\nuniform mat4 uInvView;\n\nvarying float vRadius;\nvarying float vRadiusSq;\nvarying vec3 vPoint;\nvarying vec3 vPointViewPosition;\n\nvec3 cameraPos;\nvec3 cameraNormal;\n\nbool Impostor(out vec3 cameraPos, out vec3 cameraNormal){\n    vec3 cameraSpherePos = -vPointViewPosition;\n    cameraSpherePos.z += vRadius;\n\n    vec3 rayOrigin = mix(vec3(0.0, 0.0, 0.0), vPoint, uIsOrtho);\n    vec3 rayDirection = mix(normalize(vPoint), vec3(0.0, 0.0, 1.0), uIsOrtho);\n    vec3 cameraSphereDir = mix(cameraSpherePos, rayOrigin - cameraSpherePos, uIsOrtho);\n\n    float B = dot(rayDirection, cameraSphereDir);\n    float det = B * B + vRadiusSq - dot(cameraSphereDir, cameraSphereDir);\n\n    if (det < 0.0){\n        discard;\n        return false;\n    }\n\n    float sqrtDet = sqrt(det);\n    float posT = mix(B + sqrtDet, B + sqrtDet, uIsOrtho);\n    float negT = mix(B - sqrtDet, sqrtDet - B, uIsOrtho);\n\n    cameraPos = rayDirection * negT + rayOrigin;\n\n\n    if (calcDepth(cameraPos) <= 0.0) {\n        cameraPos = rayDirection * posT + rayOrigin;\n        interior = true;\n    } else {\n        interior = false;\n    }\n\n    cameraNormal = normalize(cameraPos - cameraSpherePos);\n    cameraNormal *= float(!interior) * 2.0 - 1.0;\n\n    return !interior;\n}\n\nvoid main(void){\n    #include clip_pixel\n\n    bool flag = Impostor(cameraPos, cameraNormal);\n    if (!uDoubleSided) {\n        if (interior) discard;\n    }\n\n    vec3 vViewPosition = cameraPos;\n    gl_FragDepthEXT = calcDepth(vViewPosition);\n    if (!flag && gl_FragDepthEXT >= 0.0) {\n        gl_FragDepthEXT = 0.0 + (0.0000001 / vRadius);\n    }\n\n    vec3 vModelPosition = (uInvView * vec4(vViewPosition, 1.0)).xyz;\n\n    if (gl_FragDepthEXT < 0.0) discard;\n    if (gl_FragDepthEXT > 1.0) discard;\n\n    float fragmentDepth = gl_FragDepthEXT;\n    #include assign_material_color\n\n    #if defined(dRenderVariant_pick)\n        #include check_picking_alpha\n        gl_FragColor = material;\n    #elif defined(dRenderVariant_depth)\n        gl_FragColor = material;\n    #elif defined(dRenderVariant_marking)\n        gl_FragColor = material;\n    #elif defined(dRenderVariant_color)\n        vec3 normal = -cameraNormal;\n        #include apply_light_color\n\n        #include apply_interior_color\n        #include apply_marker_color\n        #include apply_fog\n        #include wboit_write\n    #endif\n}\n";

package/lib/commonjs/mol-gl/shader/spheres.frag.js

@@ -1,10 +1,10 @@
 "use strict";
 /**
- * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2019-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.spheres_frag = void 0;
-exports.spheres_frag = "\nprecision highp float;\nprecision highp int;\n\n#define bumpEnabled\n\n#include common\n#include common_frag_params\n#include color_frag_params\n#include light_frag_params\n#include common_clip\n\nuniform mat4 uInvView;\n\nvarying float vRadius;\nvarying float vRadiusSq;\nvarying vec3 vPoint;\nvarying vec3 vPointViewPosition;\n\nvec3 cameraPos;\nvec3 cameraNormal;\n\nbool Impostor(out vec3 cameraPos, out vec3 cameraNormal){\n    vec3 cameraSpherePos = -vPointViewPosition;\n    cameraSpherePos.z += vRadius;\n\n    vec3 rayOrigin = mix(vec3(0.0, 0.0, 0.0), vPoint, uIsOrtho);\n    vec3 rayDirection = mix(normalize(vPoint), vec3(0.0, 0.0, 1.0), uIsOrtho);\n    vec3 cameraSphereDir = mix(cameraSpherePos, rayOrigin - cameraSpherePos, uIsOrtho);\n\n    float B = dot(rayDirection, cameraSphereDir);\n    float det = B * B + vRadiusSq - dot(cameraSphereDir, cameraSphereDir);\n\n    if (det < 0.0){\n        discard;\n        return false;\n    }\n\n    float sqrtDet = sqrt(det);\n    float posT = mix(B + sqrtDet, B + sqrtDet, uIsOrtho);\n    float negT = mix(B - sqrtDet, sqrtDet - B, uIsOrtho);\n\n    cameraPos = rayDirection * negT + rayOrigin;\n\n\n    if (calcDepth(cameraPos) <= 0.0) {\n        cameraPos = rayDirection * posT + rayOrigin;\n        interior = true;\n    } else {\n        interior = false;\n    }\n\n    cameraNormal = normalize(cameraPos - cameraSpherePos);\n    cameraNormal *= float(!interior) * 2.0 - 1.0;\n\n    return !interior;\n}\n\nvoid main(void){\n    #include clip_pixel\n\n    bool flag = Impostor(cameraPos, cameraNormal);\n    if (!uDoubleSided) {\n        if (interior) discard;\n    }\n\n    vec3 vViewPosition = cameraPos;\n    gl_FragDepthEXT = calcDepth(vViewPosition);\n    if (!flag && gl_FragDepthEXT >= 0.0) {\n        gl_FragDepthEXT = 0.0 + (0.0000001 / vRadius);\n    }\n\n    vec3 vModelPosition = (uInvView * vec4(vViewPosition, 1.0)).xyz;\n\n    if (gl_FragDepthEXT < 0.0) discard;\n    if (gl_FragDepthEXT > 1.0) discard;\n\n    float fragmentDepth = gl_FragDepthEXT;\n    #include assign_material_color\n\n    #if defined(dRenderVariant_pick)\n        #include check_picking_alpha\n        gl_FragColor = material;\n    #elif defined(dRenderVariant_depth)\n        gl_FragColor = material;\n    #elif defined(dRenderVariant_marking)\n        gl_FragColor = material;\n    #elif defined(dRenderVariant_color)\n        #ifdef dIgnoreLight\n            gl_FragColor = material;\n        #else\n            vec3 normal = -cameraNormal;\n            #include apply_light_color\n        #endif\n\n        #include apply_interior_color\n        #include apply_marker_color\n        #include apply_fog\n        #include wboit_write\n    #endif\n}\n";
+exports.spheres_frag = "\nprecision highp float;\nprecision highp int;\n\n#define bumpEnabled\n\n#include common\n#include common_frag_params\n#include color_frag_params\n#include light_frag_params\n#include common_clip\n\nuniform mat4 uInvView;\n\nvarying float vRadius;\nvarying float vRadiusSq;\nvarying vec3 vPoint;\nvarying vec3 vPointViewPosition;\n\nvec3 cameraPos;\nvec3 cameraNormal;\n\nbool Impostor(out vec3 cameraPos, out vec3 cameraNormal){\n    vec3 cameraSpherePos = -vPointViewPosition;\n    cameraSpherePos.z += vRadius;\n\n    vec3 rayOrigin = mix(vec3(0.0, 0.0, 0.0), vPoint, uIsOrtho);\n    vec3 rayDirection = mix(normalize(vPoint), vec3(0.0, 0.0, 1.0), uIsOrtho);\n    vec3 cameraSphereDir = mix(cameraSpherePos, rayOrigin - cameraSpherePos, uIsOrtho);\n\n    float B = dot(rayDirection, cameraSphereDir);\n    float det = B * B + vRadiusSq - dot(cameraSphereDir, cameraSphereDir);\n\n    if (det < 0.0){\n        discard;\n        return false;\n    }\n\n    float sqrtDet = sqrt(det);\n    float posT = mix(B + sqrtDet, B + sqrtDet, uIsOrtho);\n    float negT = mix(B - sqrtDet, sqrtDet - B, uIsOrtho);\n\n    cameraPos = rayDirection * negT + rayOrigin;\n\n\n    if (calcDepth(cameraPos) <= 0.0) {\n        cameraPos = rayDirection * posT + rayOrigin;\n        interior = true;\n    } else {\n        interior = false;\n    }\n\n    cameraNormal = normalize(cameraPos - cameraSpherePos);\n    cameraNormal *= float(!interior) * 2.0 - 1.0;\n\n    return !interior;\n}\n\nvoid main(void){\n    #include clip_pixel\n\n    bool flag = Impostor(cameraPos, cameraNormal);\n    if (!uDoubleSided) {\n        if (interior) discard;\n    }\n\n    vec3 vViewPosition = cameraPos;\n    gl_FragDepthEXT = calcDepth(vViewPosition);\n    if (!flag && gl_FragDepthEXT >= 0.0) {\n        gl_FragDepthEXT = 0.0 + (0.0000001 / vRadius);\n    }\n\n    vec3 vModelPosition = (uInvView * vec4(vViewPosition, 1.0)).xyz;\n\n    if (gl_FragDepthEXT < 0.0) discard;\n    if (gl_FragDepthEXT > 1.0) discard;\n\n    float fragmentDepth = gl_FragDepthEXT;\n    #include assign_material_color\n\n    #if defined(dRenderVariant_pick)\n        #include check_picking_alpha\n        gl_FragColor = material;\n    #elif defined(dRenderVariant_depth)\n        gl_FragColor = material;\n    #elif defined(dRenderVariant_marking)\n        gl_FragColor = material;\n    #elif defined(dRenderVariant_color)\n        vec3 normal = -cameraNormal;\n        #include apply_light_color\n\n        #include apply_interior_color\n        #include apply_marker_color\n        #include apply_fog\n        #include wboit_write\n    #endif\n}\n";
 //# sourceMappingURL=spheres.frag.js.map

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

@@ -1,7 +1,7 @@
 /**
  * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.352, IHM 1.17, CARB draft.
+ * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.355, IHM 1.17, MA 1.3.4.
  *
  * @author molstar/ciftools package
  */

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

@@ -2,7 +2,7 @@
 /**
  * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.352, IHM 1.17, CARB draft.
+ * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.355, IHM 1.17, MA 1.3.4.
  *
  * @author molstar/ciftools package
  */

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

@@ -1,7 +1,7 @@
 /**
  * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.352, IHM 1.17, CARB draft.
+ * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.355, IHM 1.17, MA 1.3.4.
  *
  * @author molstar/ciftools package
  */

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

@@ -2,7 +2,7 @@
 /**
  * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.352, IHM 1.17, CARB draft.
+ * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.355, IHM 1.17, MA 1.3.4.
  *
  * @author molstar/ciftools package
  */

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

@@ -1,7 +1,7 @@
 /**
  * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.353, IHM 1.17, MA 1.3.3.
+ * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.355, IHM 1.17, MA 1.3.4.
  *
  * @author molstar/ciftools package
  */
@@ -670,7 +670,7 @@ export declare const mmCIF_Schema: {
         /**
          * An abbreviation that identifies the database.
          */
-        database_id: Schema.Aliased<"CAS" | "CSD" | "EMDB" | "ICSD" | "MDF" | "NDB" | "NBS" | "PDB" | "PDF" | "RCSB" | "EBI" | "PDBE" | "BMRB" | "WWPDB" | "PDB_ACC">;
+        database_id: Schema.Aliased<"AlphaFoldDB" | "CAS" | "CSD" | "EMDB" | "ICSD" | "ModelArchive" | "MDF" | "MODBASE" | "NDB" | "NBS" | "PDB" | "PDF" | "RCSB" | "SWISS-MODEL_REPOSITORY" | "EBI" | "PDBE" | "BMRB" | "WWPDB" | "PDB_ACC">;
         /**
          * The code assigned by the database identified in
          * _database_2.database_id.

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

@@ -2,7 +2,7 @@
 /**
  * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.353, IHM 1.17, MA 1.3.3.
+ * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.355, IHM 1.17, MA 1.3.4.
  *
  * @author molstar/ciftools package
  */

package/lib/commonjs/mol-io/reader/mol/parser.d.ts

@@ -1,7 +1,8 @@
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Panagiotis Tourlas <panagiot_tourlov@hotmail.com>
  */
 import { Column } from '../../../mol-data/db';
 import { Task } from '../../../mol-task';
@@ -18,6 +19,7 @@ export interface MolFile {
         readonly y: Column<number>;
         readonly z: Column<number>;
         readonly type_symbol: Column<string>;
+        readonly formal_charge: Column<number>;
     };
     readonly bonds: {
         readonly count: number;
@@ -25,7 +27,27 @@ export interface MolFile {
         readonly atomIdxB: Column<number>;
         readonly order: Column<number>;
     };
+    readonly formalCharges: {
+        readonly atomIdx: Column<number>;
+        readonly charge: Column<number>;
+    };
 }
+/**
+ * @param key - The value found at the atom block.
+ * @returns The actual formal charge based on the mapping.
+ */
+export declare function formalChargeMapper(key: number): 0 | 1 | 3 | 2 | -3 | -1 | -2;
 export declare function handleAtoms(tokenizer: Tokenizer, count: number): MolFile['atoms'];
 export declare function handleBonds(tokenizer: Tokenizer, count: number): MolFile['bonds'];
+interface FormalChargesRawData {
+    atomIdx: Array<number>;
+    charge: Array<number>;
+}
+export declare function handleFormalCharges(tokenizer: Tokenizer, lineStart: number, formalCharges: FormalChargesRawData): void;
+/** Call an appropriate handler based on the property type.
+ * (For now it only calls the formal charge handler, additional handlers can
+ * be added for other properties.)
+ */
+export declare function handlePropertiesBlock(tokenizer: Tokenizer): MolFile['formalCharges'];
 export declare function parseMol(data: string): Task<Result<MolFile>>;
+export {};

package/lib/commonjs/mol-io/reader/mol/parser.js

@@ -1,22 +1,70 @@
 "use strict";
 /**
- * Copyright (c) 2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
+ * @author Panagiotis Tourlas <panagiot_tourlov@hotmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.parseMol = exports.handleBonds = exports.handleAtoms = void 0;
+exports.parseMol = exports.handlePropertiesBlock = exports.handleFormalCharges = exports.handleBonds = exports.handleAtoms = exports.formalChargeMapper = void 0;
 var tslib_1 = require("tslib");
 var db_1 = require("../../../mol-data/db");
 var mol_task_1 = require("../../../mol-task");
 var token_1 = require("../common/text/column/token");
 var tokenizer_1 = require("../common/text/tokenizer");
 var result_1 = require("../result");
+/*
+    The atom lines in a .mol file have the following structure:
+
+    xxxxx.xxxxyyyyy.yyyyzzzzz.zzzz aaaddcccssshhhbbbvvvHHHrrriiimmmnnneee
+    ---------------------------------------------------------------------
+
+    Below is a breakdown of each component and its start/end indices:
+
+    xxxxx.xxxx  (X COORDINATE, 1-10)
+    yyyyy.yyyy  (Y COORDINATE, 10-20)
+    zzzzz.zzzz  (Z COORDINATE, 20-30)
+    _           (30 IS EMPTY)
+    aaa         (ATOM SYMBOL, 31-34)
+    dd          (MASS DIFF, 34-36)
+    ccc         (FORMAL CHARGE, 36-39)
+    sss         (ATOM STEREO PARITY, 39-42)
+    hhh         (HYDROGEN COUNT+1, 42-45)
+    bbb         (STEREO CARE BOX, 45-48)
+    vvv         (VALENCE, 48-51)
+    HHH         (H0 DESIGNATOR, 51-54)
+    rrr         (UNUSED, 54-57)
+    iii         (UNUSED, 57-60)
+    mmm         (ATOM-ATOM MAPPING NUMBER, 60-63)
+    nnn         (INVERSION/RETENTION FLAG, 63-66)
+    eee         (EXACT CHANGE FLAG, 66-69)
+*/
+/**
+ * @param key - The value found at the atom block.
+ * @returns The actual formal charge based on the mapping.
+ */
+function formalChargeMapper(key) {
+    switch (key) {
+        case 7: return -3;
+        case 6: return -2;
+        case 5: return -1;
+        case 0: return 0;
+        case 3: return 1;
+        case 2: return 2;
+        case 1: return 3;
+        case 4: return 0;
+        default:
+            console.error("Value ".concat(key, " is outside the 0-7 range, defaulting to 0."));
+            return 0;
+    }
+}
+exports.formalChargeMapper = formalChargeMapper;
 function handleAtoms(tokenizer, count) {
     var x = tokenizer_1.TokenBuilder.create(tokenizer.data, count * 2);
     var y = tokenizer_1.TokenBuilder.create(tokenizer.data, count * 2);
     var z = tokenizer_1.TokenBuilder.create(tokenizer.data, count * 2);
     var type_symbol = tokenizer_1.TokenBuilder.create(tokenizer.data, count * 2);
+    var formal_charge = tokenizer_1.TokenBuilder.create(tokenizer.data, count * 2);
     for (var i = 0; i < count; ++i) {
         tokenizer_1.Tokenizer.markLine(tokenizer);
         var s = tokenizer.tokenStart, position = tokenizer.position;
@@ -28,6 +76,8 @@ function handleAtoms(tokenizer, count) {
         tokenizer_1.TokenBuilder.addUnchecked(z, tokenizer.tokenStart, tokenizer.tokenEnd);
         tokenizer_1.Tokenizer.trim(tokenizer, s + 31, s + 34);
         tokenizer_1.TokenBuilder.addUnchecked(type_symbol, tokenizer.tokenStart, tokenizer.tokenEnd);
+        tokenizer_1.Tokenizer.trim(tokenizer, s + 36, s + 39);
+        tokenizer_1.TokenBuilder.addUnchecked(formal_charge, tokenizer.tokenStart, tokenizer.tokenEnd);
         tokenizer.position = position;
     }
     return {
@@ -35,7 +85,8 @@ function handleAtoms(tokenizer, count) {
         x: (0, token_1.TokenColumnProvider)(x)(db_1.Column.Schema.float),
         y: (0, token_1.TokenColumnProvider)(y)(db_1.Column.Schema.float),
         z: (0, token_1.TokenColumnProvider)(z)(db_1.Column.Schema.float),
-        type_symbol: (0, token_1.TokenColumnProvider)(type_symbol)(db_1.Column.Schema.str)
+        type_symbol: (0, token_1.TokenColumnProvider)(type_symbol)(db_1.Column.Schema.str),
+        formal_charge: (0, token_1.TokenColumnProvider)(formal_charge)(db_1.Column.Schema.int)
     };
 }
 exports.handleAtoms = handleAtoms;
@@ -62,6 +113,65 @@ function handleBonds(tokenizer, count) {
     };
 }
 exports.handleBonds = handleBonds;
+function handleFormalCharges(tokenizer, lineStart, formalCharges) {
+    tokenizer_1.Tokenizer.trim(tokenizer, lineStart + 6, lineStart + 9);
+    var numOfCharges = parseInt(tokenizer_1.Tokenizer.getTokenString(tokenizer));
+    for (var i = 0; i < numOfCharges; ++i) {
+        /*
+        M  CHG  3   1  -1   2   0   2  -1
+                |   |   |   |   |
+                |   |   |   |   |__charge2 (etc.)
+                |   |   |   |
+                |   |   |   |__atomIdx2
+                |   |   |
+                |   |   |__charge1
+                |   |
+                |   |__atomIdx1 (cursor at position 12)
+                |
+                |___numOfCharges
+        */
+        var offset = 9 + (i * 8);
+        tokenizer_1.Tokenizer.trim(tokenizer, lineStart + offset, lineStart + offset + 4);
+        var _atomIdx = tokenizer_1.Tokenizer.getTokenString(tokenizer);
+        formalCharges.atomIdx.push(+_atomIdx);
+        tokenizer_1.Tokenizer.trim(tokenizer, lineStart + offset + 4, lineStart + offset + 8);
+        var _charge = tokenizer_1.Tokenizer.getTokenString(tokenizer);
+        formalCharges.charge.push(+_charge);
+    }
+    /* Once the line is read, move to the next one. */
+    tokenizer_1.Tokenizer.eatLine(tokenizer);
+}
+exports.handleFormalCharges = handleFormalCharges;
+/** Call an appropriate handler based on the property type.
+ * (For now it only calls the formal charge handler, additional handlers can
+ * be added for other properties.)
+ */
+function handlePropertiesBlock(tokenizer) {
+    var _atomIdx = [];
+    var _charge = [];
+    var _formalCharges = { atomIdx: _atomIdx, charge: _charge };
+    while (tokenizer.position < tokenizer.length) {
+        var s = tokenizer.position;
+        tokenizer_1.Tokenizer.trim(tokenizer, s + 3, s + 6);
+        var propertyType = tokenizer_1.Tokenizer.getTokenString(tokenizer);
+        if (propertyType === 'END')
+            break;
+        tokenizer_1.Tokenizer.eatLine(tokenizer);
+        switch (propertyType) {
+            case 'CHG':
+                handleFormalCharges(tokenizer, s, _formalCharges);
+                break;
+            default:
+                break;
+        }
+    }
+    var formalCharges = {
+        atomIdx: db_1.Column.ofIntArray(_formalCharges.atomIdx),
+        charge: db_1.Column.ofIntArray(_formalCharges.charge)
+    };
+    return formalCharges;
+}
+exports.handlePropertiesBlock = handlePropertiesBlock;
 function parseInternal(data) {
     var tokenizer = (0, tokenizer_1.Tokenizer)(data);
     var title = tokenizer_1.Tokenizer.readLine(tokenizer).trim();
@@ -71,12 +181,14 @@ function parseInternal(data) {
     var atomCount = +counts.substr(0, 3), bondCount = +counts.substr(3, 3);
     var atoms = handleAtoms(tokenizer, atomCount);
     var bonds = handleBonds(tokenizer, bondCount);
+    var formalCharges = handlePropertiesBlock(tokenizer);
     var result = {
         title: title,
         program: program,
         comment: comment,
         atoms: atoms,
-        bonds: bonds
+        bonds: bonds,
+        formalCharges: formalCharges,
     };
     return result_1.ReaderResult.success(result);
 }

package/lib/commonjs/mol-io/reader/sdf/parser-v3-util.d.ts

@@ -1,3 +1,9 @@
+/**
+ * Copyright (c) 2021-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Jason Pattle <jpattle@exscientia.co.uk>
+ * @author Panagiotis Tourlas <panagiot_tourlov@hotmail.com>
+ */
 import { MolFile } from '../mol/parser';
 import { Tokenizer } from '../common/text/tokenizer';
 export declare function isV3(versionLine: string): boolean;

package/lib/commonjs/mol-io/reader/sdf/parser-v3-util.js

@@ -1,4 +1,10 @@
 "use strict";
+/**
+ * Copyright (c) 2021-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author Jason Pattle <jpattle@exscientia.co.uk>
+ * @author Panagiotis Tourlas <panagiot_tourlov@hotmail.com>
+ */
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.handleBondsV3 = exports.handleAtomsV3 = exports.handleCountsV3 = exports.isV3 = void 0;
 var db_1 = require("../../../mol-data/db");
@@ -49,6 +55,9 @@ function handleAtomsV3(tokenizer, atomCount) {
         y: (0, token_1.TokenColumnProvider)(y)(db_1.Column.Schema.float),
         z: (0, token_1.TokenColumnProvider)(z)(db_1.Column.Schema.float),
         type_symbol: (0, token_1.TokenColumnProvider)(type_symbol)(db_1.Column.Schema.str),
+        /* No support for formal charge parsing in V3000 molfiles at the moment,
+        so all charges default to 0.*/
+        formal_charge: db_1.Column.ofConst(0, atomCount, db_1.Column.Schema.int)
     };
 }
 exports.handleAtomsV3 = handleAtomsV3;

package/lib/commonjs/mol-io/reader/sdf/parser.d.ts

@@ -1,8 +1,10 @@
 /**
- * Copyright (c) 2020-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Jason Pattle <jpattle@exscientia.co.uk>
+ * @author Panagiotis Tourlas <panagiot_tourlov@hotmail.com>
  */
 import { Column } from '../../../mol-data/db';
 import { MolFile } from '../mol/parser';

package/lib/commonjs/mol-io/reader/sdf/parser.js

@@ -1,9 +1,11 @@
 "use strict";
 /**
- * Copyright (c) 2020-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2020-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Sebastian Bittrich <sebastian.bittrich@rcsb.org>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author Jason Pattle <jpattle@exscientia.co.uk>
+ * @author Panagiotis Tourlas <panagiot_tourlov@hotmail.com>
  */
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.parseSdf = void 0;
@@ -72,11 +74,18 @@ function handleMolFile(tokenizer) {
         }
         return;
     }
+    /* No support for formal charge parsing in V3000 molfiles at the moment,
+    so all charges default to 0.*/
+    var nullFormalCharges = {
+        atomIdx: db_1.Column.ofConst(0, atomCount, db_1.Column.Schema.int),
+        charge: db_1.Column.ofConst(0, atomCount, db_1.Column.Schema.int)
+    };
     var atoms = molIsV3 ? (0, parser_v3_util_1.handleAtomsV3)(tokenizer, atomCount) : (0, parser_1.handleAtoms)(tokenizer, atomCount);
     var bonds = molIsV3 ? (0, parser_v3_util_1.handleBondsV3)(tokenizer, bondCount) : (0, parser_1.handleBonds)(tokenizer, bondCount);
+    var formalCharges = molIsV3 ? nullFormalCharges : (0, parser_1.handlePropertiesBlock)(tokenizer);
     var dataItems = handleDataItems(tokenizer);
     return {
-        molFile: { title: title, program: program, comment: comment, atoms: atoms, bonds: bonds },
+        molFile: { title: title, program: program, comment: comment, atoms: atoms, bonds: bonds, formalCharges: formalCharges },
         dataItems: dataItems
     };
 }

package/lib/commonjs/mol-io/writer/cif/encoder/binary.js

@@ -173,8 +173,15 @@ function getFieldData(field, arrayCtor, totalCount, data) {
                 allPresent = false;
             }
             else {
-                mask[offset] = 0 /* Present */;
-                array[offset] = getter(key, d, offset);
+                var value = getter(key, d, offset);
+                if (typeof value === 'string' && !value) {
+                    mask[offset] = 1 /* NotPresent */;
+                    allPresent = false;
+                }
+                else {
+                    mask[offset] = 0 /* Present */;
+                }
+                array[offset] = value;
             }
             offset++;
         }

package/lib/commonjs/mol-math/geometry/primitives/sphere3d.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>

package/lib/commonjs/mol-math/geometry/primitives/sphere3d.js

@@ -1,6 +1,6 @@
 "use strict";
 /**
- * Copyright (c) 2018-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2018-2022 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author David Sehnal <david.sehnal@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -10,6 +10,8 @@ exports.Sphere3D = void 0;
 var tslib_1 = require("tslib");
 var linear_algebra_1 = require("../../linear-algebra");
 var int_1 = require("../../../mol-data/int");
+var axes3d_1 = require("./axes3d");
+var principal_axes_1 = require("../../linear-algebra/matrix/principal-axes");
 function Sphere3D() {
     return Sphere3D.zero();
 }
@@ -197,11 +199,22 @@ exports.Sphere3D = Sphere3D;
             return out;
         }
         if (hasExtrema(sphere)) {
+            var positions = new Float32Array(sphere.extrema.length * 3);
+            for (var i = 0; i < sphere.extrema.length; i++) {
+                linear_algebra_1.Vec3.toArray(sphere.extrema[i], positions, i * 3);
+            }
+            var axes_1 = principal_axes_1.PrincipalAxes.calculateMomentsAxes(positions);
+            axes3d_1.Axes3D.scale(axes_1, axes3d_1.Axes3D.normalize(axes_1, axes_1), delta);
             setExtrema(out, sphere.extrema.map(function (e) {
                 linear_algebra_1.Vec3.sub(tmpDir, e, sphere.center);
-                var dist = linear_algebra_1.Vec3.distance(sphere.center, e);
-                linear_algebra_1.Vec3.normalize(tmpDir, tmpDir);
-                return linear_algebra_1.Vec3.scaleAndAdd((0, linear_algebra_1.Vec3)(), sphere.center, tmpDir, dist + delta);
+                var out = linear_algebra_1.Vec3.clone(e);
+                var sA = linear_algebra_1.Vec3.dot(tmpDir, axes_1.dirA) < 0 ? -1 : 1;
+                linear_algebra_1.Vec3.scaleAndAdd(out, out, axes_1.dirA, sA);
+                var sB = linear_algebra_1.Vec3.dot(tmpDir, axes_1.dirB) < 0 ? -1 : 1;
+                linear_algebra_1.Vec3.scaleAndAdd(out, out, axes_1.dirB, sB);
+                var sC = linear_algebra_1.Vec3.dot(tmpDir, axes_1.dirC) < 0 ? -1 : 1;
+                linear_algebra_1.Vec3.scaleAndAdd(out, out, axes_1.dirC, sC);
+                return out;
             }));
         }
         return out;

package/lib/commonjs/mol-math/geometry/symmetry-operator.d.ts

@@ -42,7 +42,7 @@ declare namespace SymmetryOperator {
         hkl?: Vec3;
         spgrOp?: number;
     };
-    function create(name: string, matrix: Mat4, info?: CreateInfo): SymmetryOperator;
+    function create(name: string, matrix: Mat4, info?: CreateInfo | SymmetryOperator): SymmetryOperator;
     function checkIfRotationAndTranslation(rot: Mat3, offset: Vec3): boolean;
     function ofRotationAndOffset(name: string, rot: Mat3, offset: Vec3, ncsId?: number): SymmetryOperator;
     function lerpFromIdentity(out: Mat4, op: SymmetryOperator, t: number): Mat4;

package/lib/commonjs/mol-math/geometry/symmetry-operator.js

@@ -22,8 +22,9 @@ var SymmetryOperator;
         var _hkl = hkl ? vec3_1.Vec3.clone(hkl) : (0, vec3_1.Vec3)();
         spgrOp = (0, mol_util_1.defaults)(spgrOp, -1);
         ncsId = ncsId || -1;
-        var suffix = getSuffix(info);
-        if (mat4_1.Mat4.isIdentity(matrix))
+        var isIdentity = mat4_1.Mat4.isIdentity(matrix);
+        var suffix = getSuffix(info, isIdentity);
+        if (isIdentity)
             return { name: name, assembly: assembly, matrix: matrix, inverse: mat4_1.Mat4.identity(), isIdentity: true, hkl: _hkl, spgrOp: spgrOp, ncsId: ncsId, suffix: suffix };
         if (!mat4_1.Mat4.isRotationAndTranslation(matrix, SymmetryOperator.RotationTranslationEpsilon)) {
             console.warn("Symmetry operator (".concat(name, ") should be a composition of rotation and translation."));
@@ -31,11 +32,16 @@ var SymmetryOperator;
         return { name: name, assembly: assembly, matrix: matrix, inverse: mat4_1.Mat4.invert((0, mat4_1.Mat4)(), matrix), isIdentity: false, hkl: _hkl, spgrOp: spgrOp, ncsId: ncsId, suffix: suffix };
     }
     SymmetryOperator.create = create;
-    function getSuffix(info) {
+    function isSymmetryOperator(x) {
+        return !!x && !!x.matrix && !!x.inverse && typeof x.name === 'string';
+    }
+    function getSuffix(info, isIdentity) {
         if (!info)
             return '';
         if (info.assembly) {
-            return "_".concat(info.assembly.operId);
+            if (isSymmetryOperator(info))
+                return info.suffix;
+            return isIdentity ? '' : "_".concat(info.assembly.operId);
         }
         if (typeof info.spgrOp !== 'undefined' && typeof info.hkl !== 'undefined' && info.spgrOp !== -1) {
             var _a = info.hkl, i = _a[0], j = _a[1], k = _a[2];