molstar 3.0.0-dev.7 → 3.0.1

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

@@ -3,5 +3,5 @@
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
-export var image_frag = "\nprecision highp float;\nprecision highp int;\n\n#include common\n#include read_from_texture\n#include common_frag_params\n#include common_clip\n\nuniform vec2 uImageTexDim;\nuniform sampler2D tImageTex;\nuniform sampler2D tGroupTex;\n\nuniform vec2 uMarkerTexDim;\nuniform sampler2D tMarker;\n\nvarying vec2 vUv;\nvarying float vInstance;\n\n#if defined(dInterpolation_catmulrom) || defined(dInterpolation_mitchell) || defined(dInterpolation_bspline)\n    #define dInterpolation_cubic\n#endif\n\n#if defined(dInterpolation_cubic)\n    #if defined(dInterpolation_catmulrom) || defined(dInterpolation_mitchell)\n        #if defined(dInterpolation_catmulrom)\n            const float B = 0.0;\n            const float C = 0.5;\n        #elif defined(dInterpolation_mitchell)\n            const float B = 0.333;\n            const float C = 0.333;\n        #endif\n\n        float cubicFilter(float x){\n            float f = x;\n            if (f < 0.0) {\n                f = -f;\n            }\n            if (f < 1.0) {\n                return ((12.0 - 9.0 * B - 6.0 * C) * (f * f * f) +\n                    (-18.0 + 12.0 * B + 6.0 * C) * (f * f) +\n                    (6.0 - 2.0 * B)) / 6.0;\n            }else if (f >= 1.0 && f < 2.0){\n                return ((-B - 6.0 * C) * ( f * f * f)\n                    + (6.0 * B + 30.0 * C) * (f * f) +\n                    (-(12.0 * B) - 48.0 * C) * f +\n                    8.0 * B + 24.0 * C) / 6.0;\n            }else{\n                return 0.0;\n            }\n        }\n    #elif defined(dInterpolation_bspline)\n        float cubicFilter(float x) {\n            float f = x;\n            if (f < 0.0) {\n                f = -f;\n            }\n            if (f >= 0.0 && f <= 1.0){\n                return (2.0 / 3.0) + (0.5) * (f * f * f) - (f * f);\n            } else if (f > 1.0 && f <= 2.0) {\n                return 1.0 / 6.0 * pow((2.0 - f), 3.0);\n            }\n            return 1.0;\n        }\n    #endif\n\n    vec4 biCubic(sampler2D tex, vec2 texCoord) {\n        vec2 texelSize = 1.0 / uImageTexDim;\n        texCoord -= texelSize / 2.0;\n        vec4 nSum = vec4(0.0);\n        float nDenom = 0.0;\n        vec2 cell = fract(texCoord * uImageTexDim);\n        for (float m = -1.0; m <= 2.0; ++m) {\n            for (float n = -1.0; n <= 2.0; ++n) {\n                vec4 vecData = texture2D(tex, texCoord + texelSize * vec2(m, n));\n                float c = cubicFilter(m - cell.x) * cubicFilter(-n + cell.y);\n                nSum += vecData * c;\n                nDenom += c;\n            }\n        }\n        return nSum / nDenom;\n    }\n#endif\n\nvoid main() {\n    #include clip_pixel\n\n    #if defined(dInterpolation_cubic)\n        vec4 imageData = biCubic(tImageTex, vUv);\n    #else\n        vec4 imageData = texture2D(tImageTex, vUv);\n    #endif\n    imageData.a = clamp(imageData.a, 0.0, 1.0);\n    if (imageData.a > 0.9) imageData.a = 1.0;\n\n    float fragmentDepth = gl_FragCoord.z;\n    bool interior = false;\n\n    #if defined(dRenderVariant_pick)\n        if (imageData.a < 0.3)\n            discard;\n        if (uPickType == 1) {\n            gl_FragColor = vec4(encodeFloatRGB(float(uObjectId)), 1.0);\n        } else if (uPickType == 2) {\n            gl_FragColor = vec4(encodeFloatRGB(vInstance), 1.0);\n        } else {\n            gl_FragColor = vec4(texture2D(tGroupTex, vUv).rgb, 1.0);\n        }\n    #elif defined(dRenderVariant_depth)\n        if (imageData.a < 0.05)\n            discard;\n        gl_FragColor = packDepthToRGBA(gl_FragCoord.z);\n    #elif defined(dRenderVariant_marking)\n        float marker = uMarker;\n        if (uMarker == -1.0) {\n            float group = decodeFloatRGB(texture2D(tGroupTex, vUv).rgb);\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        if (uMarkingType == 1) {\n            if (marker > 0.0 || imageData.a < 0.05)\n                discard;\n            gl_FragColor = packDepthToRGBA(gl_FragCoord.z);\n        } else {\n            if (marker == 0.0 || imageData.a < 0.05)\n                discard;\n            float depthTest = 1.0;\n            if (uMarkingDepthTest) {\n                depthTest = (fragmentDepth >= getDepth(gl_FragCoord.xy / uDrawingBufferSize)) ? 1.0 : 0.0;\n            }\n            bool isHighlight = intMod(marker, 2.0) > 0.1;\n            gl_FragColor = vec4(0.0, depthTest, isHighlight ? 1.0 : 0.0, 1.0);\n        }\n    #elif defined(dRenderVariant_color)\n        if (imageData.a < 0.05)\n            discard;\n        gl_FragColor = imageData;\n        gl_FragColor.a *= uAlpha;\n\n        float marker = uMarker;\n        if (uMarker == -1.0) {\n            float group = decodeFloatRGB(texture2D(tGroupTex, vUv).rgb);\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\n        #include apply_marker_color\n        #include apply_fog\n        #include wboit_write\n    #endif\n}\n";
+export var image_frag = "\nprecision highp float;\nprecision highp int;\n\n#include common\n#include read_from_texture\n#include common_frag_params\n#include common_clip\n\nuniform vec2 uImageTexDim;\nuniform sampler2D tImageTex;\nuniform sampler2D tGroupTex;\n\nuniform vec2 uMarkerTexDim;\nuniform sampler2D tMarker;\n\nvarying vec2 vUv;\nvarying float vInstance;\n\n#if defined(dInterpolation_catmulrom) || defined(dInterpolation_mitchell) || defined(dInterpolation_bspline)\n    #define dInterpolation_cubic\n#endif\n\n#if defined(dInterpolation_cubic)\n    #if defined(dInterpolation_catmulrom) || defined(dInterpolation_mitchell)\n        #if defined(dInterpolation_catmulrom)\n            const float B = 0.0;\n            const float C = 0.5;\n        #elif defined(dInterpolation_mitchell)\n            const float B = 0.333;\n            const float C = 0.333;\n        #endif\n\n        float cubicFilter(float x){\n            float f = x;\n            if (f < 0.0) {\n                f = -f;\n            }\n            if (f < 1.0) {\n                return ((12.0 - 9.0 * B - 6.0 * C) * (f * f * f) +\n                    (-18.0 + 12.0 * B + 6.0 * C) * (f * f) +\n                    (6.0 - 2.0 * B)) / 6.0;\n            }else if (f >= 1.0 && f < 2.0){\n                return ((-B - 6.0 * C) * ( f * f * f)\n                    + (6.0 * B + 30.0 * C) * (f * f) +\n                    (-(12.0 * B) - 48.0 * C) * f +\n                    8.0 * B + 24.0 * C) / 6.0;\n            }else{\n                return 0.0;\n            }\n        }\n    #elif defined(dInterpolation_bspline)\n        float cubicFilter(float x) {\n            float f = x;\n            if (f < 0.0) {\n                f = -f;\n            }\n            if (f >= 0.0 && f <= 1.0){\n                return (2.0 / 3.0) + (0.5) * (f * f * f) - (f * f);\n            } else if (f > 1.0 && f <= 2.0) {\n                return 1.0 / 6.0 * pow((2.0 - f), 3.0);\n            }\n            return 1.0;\n        }\n    #endif\n\n    vec4 biCubic(sampler2D tex, vec2 texCoord) {\n        vec2 texelSize = 1.0 / uImageTexDim;\n        texCoord -= texelSize / 2.0;\n        vec4 nSum = vec4(0.0);\n        float nDenom = 0.0;\n        vec2 cell = fract(texCoord * uImageTexDim);\n        for (float m = -1.0; m <= 2.0; ++m) {\n            for (float n = -1.0; n <= 2.0; ++n) {\n                vec4 vecData = texture2D(tex, texCoord + texelSize * vec2(m, n));\n                float c = cubicFilter(m - cell.x) * cubicFilter(-n + cell.y);\n                nSum += vecData * c;\n                nDenom += c;\n            }\n        }\n        return nSum / nDenom;\n    }\n#endif\n\nvoid main() {\n    #include clip_pixel\n\n    #if defined(dInterpolation_cubic)\n        vec4 imageData = biCubic(tImageTex, vUv);\n    #else\n        vec4 imageData = texture2D(tImageTex, vUv);\n    #endif\n    imageData.a = clamp(imageData.a, 0.0, 1.0);\n    if (imageData.a > 0.9) imageData.a = 1.0;\n\n    float fragmentDepth = gl_FragCoord.z;\n    bool interior = false;\n\n    #if defined(dRenderVariant_pick)\n        if (imageData.a < 0.3)\n            discard;\n        if (uPickType == 1) {\n            gl_FragColor = vec4(packIntToRGB(float(uObjectId)), 1.0);\n        } else if (uPickType == 2) {\n            gl_FragColor = vec4(packIntToRGB(vInstance), 1.0);\n        } else {\n            gl_FragColor = vec4(texture2D(tGroupTex, vUv).rgb, 1.0);\n        }\n    #elif defined(dRenderVariant_depth)\n        if (imageData.a < 0.05)\n            discard;\n        gl_FragColor = packDepthToRGBA(gl_FragCoord.z);\n    #elif defined(dRenderVariant_marking)\n        float marker = uMarker;\n        if (uMarker == -1.0) {\n            float group = unpackRGBToInt(texture2D(tGroupTex, vUv).rgb);\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        if (uMarkingType == 1) {\n            if (marker > 0.0 || imageData.a < 0.05)\n                discard;\n            gl_FragColor = packDepthToRGBA(gl_FragCoord.z);\n        } else {\n            if (marker == 0.0 || imageData.a < 0.05)\n                discard;\n            float depthTest = 1.0;\n            if (uMarkingDepthTest) {\n                depthTest = (fragmentDepth >= getDepth(gl_FragCoord.xy / uDrawingBufferSize)) ? 1.0 : 0.0;\n            }\n            bool isHighlight = intMod(marker, 2.0) > 0.1;\n            gl_FragColor = vec4(0.0, depthTest, isHighlight ? 1.0 : 0.0, 1.0);\n        }\n    #elif defined(dRenderVariant_color)\n        if (imageData.a < 0.05)\n            discard;\n        gl_FragColor = imageData;\n        gl_FragColor.a *= uAlpha;\n\n        float marker = uMarker;\n        if (uMarker == -1.0) {\n            float group = unpackRGBToInt(texture2D(tGroupTex, vUv).rgb);\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\n        #include apply_marker_color\n        #include apply_fog\n        #include wboit_write\n    #endif\n}\n";
 //# sourceMappingURL=image.frag.js.map

package/lib/mol-gl/shader/marching-cubes/isosurface.frag.d.ts

@@ -1 +1 @@
-export declare const isosurface_frag = "\nprecision highp float;\nprecision highp int;\nprecision highp sampler2D;\n\n#if __VERSION__ == 100\n    uniform sampler2D tActiveVoxelsPyramid;\n#else\n    precision highp isampler2D;\n    uniform isampler2D tActiveVoxelsPyramid;\n#endif\n\nuniform sampler2D tActiveVoxelsBase;\nuniform sampler2D tVolumeData;\nuniform sampler2D tTriIndices;\n\nuniform float uIsoValue;\nuniform float uLevels;\nuniform float uSize;\nuniform float uCount;\nuniform bool uInvert;\n\nuniform vec3 uGridDim;\nuniform vec3 uGridTexDim;\nuniform mat4 uGridTransform;\n\n// scale to volume data coord\nuniform vec2 uScale;\n\n#include common\n\n// cube corners (excluding origin)\nconst vec3 c1 = vec3(1., 0., 0.);\nconst vec3 c2 = vec3(1., 1., 0.);\nconst vec3 c3 = vec3(0., 1., 0.);\nconst vec3 c4 = vec3(0., 0., 1.);\nconst vec3 c5 = vec3(1., 0., 1.);\nconst vec3 c6 = vec3(1., 1., 1.);\nconst vec3 c7 = vec3(0., 1., 1.);\n\nvec3 index3dFrom2d(vec2 coord) {\n    vec2 gridTexPos = coord * uGridTexDim.xy;\n    vec2 columnRow = ivec2Div(gridTexPos, uGridDim.xy);\n    vec2 posXY = gridTexPos - columnRow * uGridDim.xy;\n    float posZ = columnRow.y * intDiv(uGridTexDim.x, uGridDim.x) + columnRow.x;\n    return vec3(posXY, posZ);\n}\n\nvec4 texture3dFrom2dNearest(sampler2D tex, vec3 pos, vec3 gridDim, vec2 texDim) {\n    float zSlice = floor(pos.z * gridDim.z + 0.5); // round to nearest z-slice\n    float column = intDiv(intMod(zSlice * gridDim.x, texDim.x), gridDim.x);\n    float row = intDiv(zSlice * gridDim.x, texDim.x);\n    vec2 coord = (vec2(column * gridDim.x, row * gridDim.y) + (pos.xy * gridDim.xy)) / (texDim / uScale);\n    return texture2D(tex, coord + 0.5 / (texDim / uScale));\n}\n\nvec4 voxel(vec3 pos) {\n    pos = min(max(vec3(0.0), pos), uGridDim - vec3(1.0));\n    return texture3dFrom2dNearest(tVolumeData, pos / uGridDim, uGridDim, uGridTexDim.xy);\n}\n\nvec4 voxelPadded(vec3 pos) {\n    pos = min(max(vec3(0.0), pos), uGridDim - vec3(vec2(2.0), 1.0)); // remove xy padding\n    return texture3dFrom2dNearest(tVolumeData, pos / uGridDim, uGridDim, uGridTexDim.xy);\n}\n\nint idot2(const in ivec2 a, const in ivec2 b) {\n    return a.x * b.x + a.y * b.y;\n}\n\nint idot4(const in ivec4 a, const in ivec4 b) {\n    return a.x * b.x + a.y * b.y + a.z * b.z + a.w * b.w;\n}\n\n#if __VERSION__ == 100\n    int pyramidVoxel(vec2 pos) {\n        return int(decodeFloatRGB(texture2D(tActiveVoxelsPyramid, pos / (vec2(1.0, 0.5) * uSize)).rgb));\n    }\n#else\n    int pyramidVoxel(vec2 pos) {\n        return texture2D(tActiveVoxelsPyramid, pos / (vec2(1.0, 0.5) * uSize)).r;\n    }\n#endif\n\nvec4 baseVoxel(vec2 pos) {\n    return texture2D(tActiveVoxelsBase, pos / uSize);\n}\n\nvoid main(void) {\n    // get 1D index\n    int vI = int(gl_FragCoord.x) + int(gl_FragCoord.y) * int(uSize);\n\n    // ignore 1D indices outside of the grid\n    if(vI >= int(uCount)) discard;\n\n    ivec2 offset = ivec2(int(uSize) - 2, 0);\n\n    int start = 0;\n    ivec4 starts = ivec4(0);\n    ivec4 ends = ivec4(0);\n    int diff = 2;\n    ivec4 m = ivec4(0);\n    ivec2 position = ivec2(0);\n    ivec4 vI4 = ivec4(vI);\n\n    ivec2 relativePosition = ivec2(0);\n    int end = 0;\n    ivec2 pos1 = ivec2(0);\n    ivec2 pos2 = ivec2(0);\n    ivec2 pos3 = ivec2(0);\n    ivec2 pos4 = ivec2(0);\n    ivec3 vI3 = ivec3(vI);\n    ivec3 mask = ivec3(0);\n\n    // traverse the different levels of the pyramid\n    for(int i = 1; i < 14; i++) {\n        if(float(i) >= uLevels) break;\n\n        offset.x -= diff;\n        diff *= 2;\n        relativePosition = position + offset;\n\n        end = start + pyramidVoxel(vec2(relativePosition));\n        pos1 = ivec2(relativePosition);\n        starts.x = start;\n        ends.x = end;\n        pos2 = ivec2(relativePosition + ivec2(1, 0));\n        starts.y = ends.x;\n        ends.y = ends.x + pyramidVoxel(vec2(pos2));\n        pos3 = relativePosition + ivec2(0, 1);\n        starts.z = ends.y;\n        ends.z = ends.y + pyramidVoxel(vec2(pos3));\n        pos4 = relativePosition + ivec2(1, 1);\n        starts.w = ends.z;\n        mask = ivec3(greaterThanEqual(vI3, starts.rgb)) * ivec3(lessThan(vI3, ends.rgb));\n        m = ivec4(mask, 1 - int(any(bvec3(mask))));\n\n        relativePosition = m.x * pos1 + m.y * pos2 + m.z * pos3 + m.w * pos4;\n        start = idot4(m, starts);\n        position = 2 * (relativePosition - offset);\n    }\n\n    end = start + int(baseVoxel(vec2(position)).r * 255.0);\n    pos1 = position;\n    starts.x = start;\n    ends.x = end;\n    pos2 = position + ivec2(1, 0);\n    starts.y = ends.x;\n    ends.y = ends.x + int(baseVoxel(vec2(pos2)).r * 255.0);\n    pos3 = position + ivec2(0, 1);\n    starts.z = ends.y;\n    ends.z = ends.y + int(baseVoxel(vec2(pos3)).r * 255.0);\n    pos4 = position + ivec2(1, 1);\n    starts.w = ends.z;\n    mask = ivec3(greaterThanEqual(vI3, starts.rgb)) * ivec3(lessThan(vI3, ends.rgb));\n    m = ivec4(mask, 1 - int(any(bvec3(mask))));\n    position = m.x * pos1 + m.y * pos2 + m.z * pos3 + m.w * pos4;\n\n    vec2 coord2d = (vec2(position) / uSize) / uScale;\n    vec3 coord3d = floor(index3dFrom2d(coord2d) + 0.5);\n\n    float edgeIndex = floor(baseVoxel(vec2(position)).a * 255.0 + 0.5);\n\n    // current vertex for the up to 15 MC cases\n    int currentVertex = vI - idot4(m, starts);\n\n    // ensure winding-order is the same for negative and positive iso-levels\n    if (uInvert) {\n        int v = imod(currentVertex + 1, 3);\n        if (v == 1) currentVertex += 2;\n        else if (v == 0) currentVertex -= 2;\n    }\n\n    // get index into triIndices table\n    int mcIndex = 16 * int(edgeIndex) + currentVertex;\n    vec4 mcData = texture2D(tTriIndices, vec2(imod(mcIndex, 64), mcIndex / 64) / 64.);\n\n    // bit mask to avoid conditionals (see comment below) for getting MC case corner\n    vec4 m0 = vec4(floor(mcData.a * 255.0 + 0.5));\n\n    // get edge value masks\n    vec4 m1 = vec4(equal(m0, vec4(0., 1., 2., 3.)));\n    vec4 m2 = vec4(equal(m0, vec4(4., 5., 6., 7.)));\n    vec4 m3 = vec4(equal(m0, vec4(8., 9., 10., 11.)));\n\n    // apply bit masks\n    vec3 b0 = coord3d +\n                m1.y * c1 +\n                m1.z * c2 +\n                m1.w * c3 +\n                m2.x * c4 +\n                m2.y * c5 +\n                m2.z * c6 +\n                m2.w * c7 +\n                m3.y * c1 +\n                m3.z * c2 +\n                m3.w * c3;\n    vec3 b1 = coord3d +\n                m1.x * c1 +\n                m1.y * c2 +\n                m1.z * c3 +\n                m2.x * c5 +\n                m2.y * c6 +\n                m2.z * c7 +\n                m2.w * c4 +\n                m3.x * c4 +\n                m3.y * c5 +\n                m3.z * c6 +\n                m3.w * c7;\n\n    // the conditionals that are avoided by above bitmasks\n    // vec3 b0 = coord3d;\n    // vec3 b1 = coord3d;\n    // if (mcIndex == 0.0) {\n    //     b1 += c1;\n    // } else if (mcIndex == 1.0) {\n    //     b0 += c1; b1 += c2;\n    // } else if (mcIndex == 2.0) {\n    //     b0 += c2; b1 += c3;\n    // } else if (mcIndex == 3.0) {\n    //     b0 += c3;\n    // } else if (mcIndex == 4.0) {\n    //     b0 += c4; b1 += c5;\n    // } else if (mcIndex == 5.0) {\n    //     b0 += c5; b1 += c6;\n    // } else if (mcIndex == 6.0) {\n    //     b0 += c6; b1 += c7;\n    // } else if (mcIndex == 7.0) {\n    //     b0 += c7; b1 += c4;\n    // } else if (mcIndex == 8.0) {\n    //     b1 += c4;\n    // } else if (mcIndex == 9.0) {\n    //     b0 += c1; b1 += c5;\n    // } else if (mcIndex == 10.0) {\n    //     b0 += c2; b1 += c6;\n    // } else if (mcIndex == 11.0) {\n    //     b0 += c3; b1 += c7;\n    // }\n    // b0 = floor(b0 + 0.5);\n    // b1 = floor(b1 + 0.5);\n\n    vec4 d0 = voxel(b0);\n    vec4 d1 = voxel(b1);\n\n    float v0 = d0.a;\n    float v1 = d1.a;\n\n    float t = (uIsoValue - v0) / (v0 - v1);\n    gl_FragData[0].xyz = (uGridTransform * vec4(b0 + t * (b0 - b1), 1.0)).xyz;\n\n    // group id\n    #if __VERSION__ == 100\n        // webgl1 does not support 'flat' interpolation (i.e. no interpolation)\n        // so we ensure a constant group id per triangle here\n        #ifdef dPackedGroup\n            gl_FragData[1] = vec4(voxel(coord3d).rgb, 1.0);\n        #else\n            vec3 gridDim = uGridDim - vec3(1.0, 1.0, 0.0); // remove xy padding\n            float group = coord3d.z + coord3d.y * gridDim.z + coord3d.x * gridDim.z * gridDim.y;\n            gl_FragData[1] = vec4(group > 16777215.5 ? vec3(1.0) : encodeFloatRGB(group), 1.0);\n        #endif\n    #else\n        #ifdef dPackedGroup\n            gl_FragData[1] = vec4(t < 0.5 ? d0.rgb : d1.rgb, 1.0);\n        #else\n            vec3 b = t < 0.5 ? b0 : b1;\n            vec3 gridDim = uGridDim - vec3(1.0, 1.0, 0.0); // remove xy padding\n            float group = b.z + b.y * gridDim.z + b.x * gridDim.z * gridDim.y;\n            gl_FragData[1] = vec4(group > 16777215.5 ? vec3(1.0) : encodeFloatRGB(group), 1.0);\n        #endif\n    #endif\n\n    // normals from gradients\n    vec3 n0 = -normalize(vec3(\n        voxelPadded(b0 - c1).a - voxelPadded(b0 + c1).a,\n        voxelPadded(b0 - c3).a - voxelPadded(b0 + c3).a,\n        voxelPadded(b0 - c4).a - voxelPadded(b0 + c4).a\n    ));\n    vec3 n1 = -normalize(vec3(\n        voxelPadded(b1 - c1).a - voxelPadded(b1 + c1).a,\n        voxelPadded(b1 - c3).a - voxelPadded(b1 + c3).a,\n        voxelPadded(b1 - c4).a - voxelPadded(b1 + c4).a\n    ));\n    gl_FragData[2].xyz = -vec3(\n        n0.x + t * (n0.x - n1.x),\n        n0.y + t * (n0.y - n1.y),\n        n0.z + t * (n0.z - n1.z)\n    );\n\n    // ensure normal-direction is the same for negative and positive iso-levels\n    if (uInvert) {\n        gl_FragData[2].xyz *= -1.0;\n    }\n\n    // apply normal matrix\n    gl_FragData[2].xyz *= transpose3(inverse3(mat3(uGridTransform)));\n}\n";
+export declare const isosurface_frag = "\nprecision highp float;\nprecision highp int;\nprecision highp sampler2D;\n\n#if __VERSION__ == 100\n    uniform sampler2D tActiveVoxelsPyramid;\n#else\n    precision highp isampler2D;\n    uniform isampler2D tActiveVoxelsPyramid;\n#endif\n\nuniform sampler2D tActiveVoxelsBase;\nuniform sampler2D tVolumeData;\nuniform sampler2D tTriIndices;\n\nuniform float uIsoValue;\nuniform float uLevels;\nuniform float uSize;\nuniform float uCount;\nuniform bool uInvert;\n\nuniform vec3 uGridDim;\nuniform vec3 uGridTexDim;\nuniform mat4 uGridTransform;\n\n// scale to volume data coord\nuniform vec2 uScale;\n\n#include common\n\n// cube corners (excluding origin)\nconst vec3 c1 = vec3(1., 0., 0.);\nconst vec3 c2 = vec3(1., 1., 0.);\nconst vec3 c3 = vec3(0., 1., 0.);\nconst vec3 c4 = vec3(0., 0., 1.);\nconst vec3 c5 = vec3(1., 0., 1.);\nconst vec3 c6 = vec3(1., 1., 1.);\nconst vec3 c7 = vec3(0., 1., 1.);\n\nvec3 index3dFrom2d(vec2 coord) {\n    vec2 gridTexPos = coord * uGridTexDim.xy;\n    vec2 columnRow = ivec2Div(gridTexPos, uGridDim.xy);\n    vec2 posXY = gridTexPos - columnRow * uGridDim.xy;\n    float posZ = columnRow.y * intDiv(uGridTexDim.x, uGridDim.x) + columnRow.x;\n    return vec3(posXY, posZ);\n}\n\nvec4 texture3dFrom2dNearest(sampler2D tex, vec3 pos, vec3 gridDim, vec2 texDim) {\n    float zSlice = floor(pos.z * gridDim.z + 0.5); // round to nearest z-slice\n    float column = intDiv(intMod(zSlice * gridDim.x, texDim.x), gridDim.x);\n    float row = intDiv(zSlice * gridDim.x, texDim.x);\n    vec2 coord = (vec2(column * gridDim.x, row * gridDim.y) + (pos.xy * gridDim.xy)) / (texDim / uScale);\n    return texture2D(tex, coord + 0.5 / (texDim / uScale));\n}\n\nvec4 voxel(vec3 pos) {\n    pos = min(max(vec3(0.0), pos), uGridDim - vec3(1.0));\n    return texture3dFrom2dNearest(tVolumeData, pos / uGridDim, uGridDim, uGridTexDim.xy);\n}\n\nvec4 voxelPadded(vec3 pos) {\n    pos = min(max(vec3(0.0), pos), uGridDim - vec3(vec2(2.0), 1.0)); // remove xy padding\n    return texture3dFrom2dNearest(tVolumeData, pos / uGridDim, uGridDim, uGridTexDim.xy);\n}\n\nint idot2(const in ivec2 a, const in ivec2 b) {\n    return a.x * b.x + a.y * b.y;\n}\n\nint idot4(const in ivec4 a, const in ivec4 b) {\n    return a.x * b.x + a.y * b.y + a.z * b.z + a.w * b.w;\n}\n\n#if __VERSION__ == 100\n    int pyramidVoxel(vec2 pos) {\n        return int(unpackRGBToInt(texture2D(tActiveVoxelsPyramid, pos / (vec2(1.0, 0.5) * uSize)).rgb));\n    }\n#else\n    int pyramidVoxel(vec2 pos) {\n        return texture2D(tActiveVoxelsPyramid, pos / (vec2(1.0, 0.5) * uSize)).r;\n    }\n#endif\n\nvec4 baseVoxel(vec2 pos) {\n    return texture2D(tActiveVoxelsBase, pos / uSize);\n}\n\nvec4 getGroup(const in vec3 p) {\n    vec3 gridDim = uGridDim - vec3(1.0, 1.0, 0.0); // remove xy padding\n    // note that we swap x and z because the texture is flipped around y\n    #if defined(dAxisOrder_012)\n        float group = p.z + p.y * gridDim.z + p.x * gridDim.z * gridDim.y; // 210\n    #elif defined(dAxisOrder_021)\n        float group = p.y + p.z * gridDim.y + p.x * gridDim.y * gridDim.z; // 120\n    #elif defined(dAxisOrder_102)\n        float group = p.z + p.x * gridDim.z + p.y * gridDim.z * gridDim.x; // 201\n    #elif defined(dAxisOrder_120)\n        float group = p.x + p.z * gridDim.x + p.y * gridDim.x * gridDim.z; // 021\n    #elif defined(dAxisOrder_201)\n        float group = p.y + p.x * gridDim.y + p.z * gridDim.y * gridDim.x; // 102\n    #elif defined(dAxisOrder_210)\n        float group = p.x + p.y * gridDim.x + p.z * gridDim.x * gridDim.y; // 012\n    #endif\n    return vec4(group > 16777215.5 ? vec3(1.0) : packIntToRGB(group), 1.0);\n}\n\nvoid main(void) {\n    // get 1D index\n    int vI = int(gl_FragCoord.x) + int(gl_FragCoord.y) * int(uSize);\n\n    // ignore 1D indices outside of the grid\n    if(vI >= int(uCount)) discard;\n\n    ivec2 offset = ivec2(int(uSize) - 2, 0);\n\n    int start = 0;\n    ivec4 starts = ivec4(0);\n    ivec4 ends = ivec4(0);\n    int diff = 2;\n    ivec4 m = ivec4(0);\n    ivec2 position = ivec2(0);\n    ivec4 vI4 = ivec4(vI);\n\n    ivec2 relativePosition = ivec2(0);\n    int end = 0;\n    ivec2 pos1 = ivec2(0);\n    ivec2 pos2 = ivec2(0);\n    ivec2 pos3 = ivec2(0);\n    ivec2 pos4 = ivec2(0);\n    ivec3 vI3 = ivec3(vI);\n    ivec3 mask = ivec3(0);\n\n    // traverse the different levels of the pyramid\n    for(int i = 1; i < 14; i++) {\n        if(float(i) >= uLevels) break;\n\n        offset.x -= diff;\n        diff *= 2;\n        relativePosition = position + offset;\n\n        end = start + pyramidVoxel(vec2(relativePosition));\n        pos1 = ivec2(relativePosition);\n        starts.x = start;\n        ends.x = end;\n        pos2 = ivec2(relativePosition + ivec2(1, 0));\n        starts.y = ends.x;\n        ends.y = ends.x + pyramidVoxel(vec2(pos2));\n        pos3 = relativePosition + ivec2(0, 1);\n        starts.z = ends.y;\n        ends.z = ends.y + pyramidVoxel(vec2(pos3));\n        pos4 = relativePosition + ivec2(1, 1);\n        starts.w = ends.z;\n        mask = ivec3(greaterThanEqual(vI3, starts.rgb)) * ivec3(lessThan(vI3, ends.rgb));\n        m = ivec4(mask, 1 - int(any(bvec3(mask))));\n\n        relativePosition = m.x * pos1 + m.y * pos2 + m.z * pos3 + m.w * pos4;\n        start = idot4(m, starts);\n        position = 2 * (relativePosition - offset);\n    }\n\n    end = start + int(baseVoxel(vec2(position)).r * 255.0);\n    pos1 = position;\n    starts.x = start;\n    ends.x = end;\n    pos2 = position + ivec2(1, 0);\n    starts.y = ends.x;\n    ends.y = ends.x + int(baseVoxel(vec2(pos2)).r * 255.0);\n    pos3 = position + ivec2(0, 1);\n    starts.z = ends.y;\n    ends.z = ends.y + int(baseVoxel(vec2(pos3)).r * 255.0);\n    pos4 = position + ivec2(1, 1);\n    starts.w = ends.z;\n    mask = ivec3(greaterThanEqual(vI3, starts.rgb)) * ivec3(lessThan(vI3, ends.rgb));\n    m = ivec4(mask, 1 - int(any(bvec3(mask))));\n    position = m.x * pos1 + m.y * pos2 + m.z * pos3 + m.w * pos4;\n\n    vec2 coord2d = (vec2(position) / uSize) / uScale;\n    vec3 coord3d = floor(index3dFrom2d(coord2d) + 0.5);\n\n    float edgeIndex = floor(baseVoxel(vec2(position)).a * 255.0 + 0.5);\n\n    // current vertex for the up to 15 MC cases\n    int currentVertex = vI - idot4(m, starts);\n\n    // ensure winding-order is the same for negative and positive iso-levels\n    if (uInvert) {\n        int v = imod(currentVertex + 1, 3);\n        if (v == 1) currentVertex += 2;\n        else if (v == 0) currentVertex -= 2;\n    }\n\n    // get index into triIndices table\n    int mcIndex = 16 * int(edgeIndex) + currentVertex;\n    vec4 mcData = texture2D(tTriIndices, vec2(imod(mcIndex, 64), mcIndex / 64) / 64.);\n\n    // bit mask to avoid conditionals (see comment below) for getting MC case corner\n    vec4 m0 = vec4(floor(mcData.a * 255.0 + 0.5));\n\n    // get edge value masks\n    vec4 m1 = vec4(equal(m0, vec4(0., 1., 2., 3.)));\n    vec4 m2 = vec4(equal(m0, vec4(4., 5., 6., 7.)));\n    vec4 m3 = vec4(equal(m0, vec4(8., 9., 10., 11.)));\n\n    // apply bit masks\n    vec3 b0 = coord3d +\n                m1.y * c1 +\n                m1.z * c2 +\n                m1.w * c3 +\n                m2.x * c4 +\n                m2.y * c5 +\n                m2.z * c6 +\n                m2.w * c7 +\n                m3.y * c1 +\n                m3.z * c2 +\n                m3.w * c3;\n    vec3 b1 = coord3d +\n                m1.x * c1 +\n                m1.y * c2 +\n                m1.z * c3 +\n                m2.x * c5 +\n                m2.y * c6 +\n                m2.z * c7 +\n                m2.w * c4 +\n                m3.x * c4 +\n                m3.y * c5 +\n                m3.z * c6 +\n                m3.w * c7;\n\n    // the conditionals that are avoided by above bitmasks\n    // vec3 b0 = coord3d;\n    // vec3 b1 = coord3d;\n    // if (mcIndex == 0.0) {\n    //     b1 += c1;\n    // } else if (mcIndex == 1.0) {\n    //     b0 += c1; b1 += c2;\n    // } else if (mcIndex == 2.0) {\n    //     b0 += c2; b1 += c3;\n    // } else if (mcIndex == 3.0) {\n    //     b0 += c3;\n    // } else if (mcIndex == 4.0) {\n    //     b0 += c4; b1 += c5;\n    // } else if (mcIndex == 5.0) {\n    //     b0 += c5; b1 += c6;\n    // } else if (mcIndex == 6.0) {\n    //     b0 += c6; b1 += c7;\n    // } else if (mcIndex == 7.0) {\n    //     b0 += c7; b1 += c4;\n    // } else if (mcIndex == 8.0) {\n    //     b1 += c4;\n    // } else if (mcIndex == 9.0) {\n    //     b0 += c1; b1 += c5;\n    // } else if (mcIndex == 10.0) {\n    //     b0 += c2; b1 += c6;\n    // } else if (mcIndex == 11.0) {\n    //     b0 += c3; b1 += c7;\n    // }\n    // b0 = floor(b0 + 0.5);\n    // b1 = floor(b1 + 0.5);\n\n    vec4 d0 = voxel(b0);\n    vec4 d1 = voxel(b1);\n\n    float v0 = d0.a;\n    float v1 = d1.a;\n\n    float t = (uIsoValue - v0) / (v0 - v1);\n    gl_FragData[0].xyz = (uGridTransform * vec4(b0 + t * (b0 - b1), 1.0)).xyz;\n\n    // group id\n    #if __VERSION__ == 100\n        // webgl1 does not support 'flat' interpolation (i.e. no interpolation)\n        // so we ensure a constant group id per triangle here\n        #ifdef dPackedGroup\n            gl_FragData[1] = vec4(voxel(coord3d).rgb, 1.0);\n        #else\n            gl_FragData[1] = getGroup(coord3d);\n        #endif\n    #else\n        #ifdef dPackedGroup\n            gl_FragData[1] = vec4(t < 0.5 ? d0.rgb : d1.rgb, 1.0);\n        #else\n            gl_FragData[1] = getGroup(t < 0.5 ? b0 : b1);\n        #endif\n    #endif\n\n    // normals from gradients\n    vec3 n0 = -normalize(vec3(\n        voxelPadded(b0 - c1).a - voxelPadded(b0 + c1).a,\n        voxelPadded(b0 - c3).a - voxelPadded(b0 + c3).a,\n        voxelPadded(b0 - c4).a - voxelPadded(b0 + c4).a\n    ));\n    vec3 n1 = -normalize(vec3(\n        voxelPadded(b1 - c1).a - voxelPadded(b1 + c1).a,\n        voxelPadded(b1 - c3).a - voxelPadded(b1 + c3).a,\n        voxelPadded(b1 - c4).a - voxelPadded(b1 + c4).a\n    ));\n    gl_FragData[2].xyz = -vec3(\n        n0.x + t * (n0.x - n1.x),\n        n0.y + t * (n0.y - n1.y),\n        n0.z + t * (n0.z - n1.z)\n    );\n\n    // ensure normal-direction is the same for negative and positive iso-levels\n    if (uInvert) {\n        gl_FragData[2].xyz *= -1.0;\n    }\n\n    // apply normal matrix\n    gl_FragData[2].xyz *= transpose3(inverse3(mat3(uGridTransform)));\n}\n";

package/lib/mol-gl/shader/marching-cubes/isosurface.frag.js

@@ -1,2 +1,2 @@
-export var isosurface_frag = "\nprecision highp float;\nprecision highp int;\nprecision highp sampler2D;\n\n#if __VERSION__ == 100\n    uniform sampler2D tActiveVoxelsPyramid;\n#else\n    precision highp isampler2D;\n    uniform isampler2D tActiveVoxelsPyramid;\n#endif\n\nuniform sampler2D tActiveVoxelsBase;\nuniform sampler2D tVolumeData;\nuniform sampler2D tTriIndices;\n\nuniform float uIsoValue;\nuniform float uLevels;\nuniform float uSize;\nuniform float uCount;\nuniform bool uInvert;\n\nuniform vec3 uGridDim;\nuniform vec3 uGridTexDim;\nuniform mat4 uGridTransform;\n\n// scale to volume data coord\nuniform vec2 uScale;\n\n#include common\n\n// cube corners (excluding origin)\nconst vec3 c1 = vec3(1., 0., 0.);\nconst vec3 c2 = vec3(1., 1., 0.);\nconst vec3 c3 = vec3(0., 1., 0.);\nconst vec3 c4 = vec3(0., 0., 1.);\nconst vec3 c5 = vec3(1., 0., 1.);\nconst vec3 c6 = vec3(1., 1., 1.);\nconst vec3 c7 = vec3(0., 1., 1.);\n\nvec3 index3dFrom2d(vec2 coord) {\n    vec2 gridTexPos = coord * uGridTexDim.xy;\n    vec2 columnRow = ivec2Div(gridTexPos, uGridDim.xy);\n    vec2 posXY = gridTexPos - columnRow * uGridDim.xy;\n    float posZ = columnRow.y * intDiv(uGridTexDim.x, uGridDim.x) + columnRow.x;\n    return vec3(posXY, posZ);\n}\n\nvec4 texture3dFrom2dNearest(sampler2D tex, vec3 pos, vec3 gridDim, vec2 texDim) {\n    float zSlice = floor(pos.z * gridDim.z + 0.5); // round to nearest z-slice\n    float column = intDiv(intMod(zSlice * gridDim.x, texDim.x), gridDim.x);\n    float row = intDiv(zSlice * gridDim.x, texDim.x);\n    vec2 coord = (vec2(column * gridDim.x, row * gridDim.y) + (pos.xy * gridDim.xy)) / (texDim / uScale);\n    return texture2D(tex, coord + 0.5 / (texDim / uScale));\n}\n\nvec4 voxel(vec3 pos) {\n    pos = min(max(vec3(0.0), pos), uGridDim - vec3(1.0));\n    return texture3dFrom2dNearest(tVolumeData, pos / uGridDim, uGridDim, uGridTexDim.xy);\n}\n\nvec4 voxelPadded(vec3 pos) {\n    pos = min(max(vec3(0.0), pos), uGridDim - vec3(vec2(2.0), 1.0)); // remove xy padding\n    return texture3dFrom2dNearest(tVolumeData, pos / uGridDim, uGridDim, uGridTexDim.xy);\n}\n\nint idot2(const in ivec2 a, const in ivec2 b) {\n    return a.x * b.x + a.y * b.y;\n}\n\nint idot4(const in ivec4 a, const in ivec4 b) {\n    return a.x * b.x + a.y * b.y + a.z * b.z + a.w * b.w;\n}\n\n#if __VERSION__ == 100\n    int pyramidVoxel(vec2 pos) {\n        return int(decodeFloatRGB(texture2D(tActiveVoxelsPyramid, pos / (vec2(1.0, 0.5) * uSize)).rgb));\n    }\n#else\n    int pyramidVoxel(vec2 pos) {\n        return texture2D(tActiveVoxelsPyramid, pos / (vec2(1.0, 0.5) * uSize)).r;\n    }\n#endif\n\nvec4 baseVoxel(vec2 pos) {\n    return texture2D(tActiveVoxelsBase, pos / uSize);\n}\n\nvoid main(void) {\n    // get 1D index\n    int vI = int(gl_FragCoord.x) + int(gl_FragCoord.y) * int(uSize);\n\n    // ignore 1D indices outside of the grid\n    if(vI >= int(uCount)) discard;\n\n    ivec2 offset = ivec2(int(uSize) - 2, 0);\n\n    int start = 0;\n    ivec4 starts = ivec4(0);\n    ivec4 ends = ivec4(0);\n    int diff = 2;\n    ivec4 m = ivec4(0);\n    ivec2 position = ivec2(0);\n    ivec4 vI4 = ivec4(vI);\n\n    ivec2 relativePosition = ivec2(0);\n    int end = 0;\n    ivec2 pos1 = ivec2(0);\n    ivec2 pos2 = ivec2(0);\n    ivec2 pos3 = ivec2(0);\n    ivec2 pos4 = ivec2(0);\n    ivec3 vI3 = ivec3(vI);\n    ivec3 mask = ivec3(0);\n\n    // traverse the different levels of the pyramid\n    for(int i = 1; i < 14; i++) {\n        if(float(i) >= uLevels) break;\n\n        offset.x -= diff;\n        diff *= 2;\n        relativePosition = position + offset;\n\n        end = start + pyramidVoxel(vec2(relativePosition));\n        pos1 = ivec2(relativePosition);\n        starts.x = start;\n        ends.x = end;\n        pos2 = ivec2(relativePosition + ivec2(1, 0));\n        starts.y = ends.x;\n        ends.y = ends.x + pyramidVoxel(vec2(pos2));\n        pos3 = relativePosition + ivec2(0, 1);\n        starts.z = ends.y;\n        ends.z = ends.y + pyramidVoxel(vec2(pos3));\n        pos4 = relativePosition + ivec2(1, 1);\n        starts.w = ends.z;\n        mask = ivec3(greaterThanEqual(vI3, starts.rgb)) * ivec3(lessThan(vI3, ends.rgb));\n        m = ivec4(mask, 1 - int(any(bvec3(mask))));\n\n        relativePosition = m.x * pos1 + m.y * pos2 + m.z * pos3 + m.w * pos4;\n        start = idot4(m, starts);\n        position = 2 * (relativePosition - offset);\n    }\n\n    end = start + int(baseVoxel(vec2(position)).r * 255.0);\n    pos1 = position;\n    starts.x = start;\n    ends.x = end;\n    pos2 = position + ivec2(1, 0);\n    starts.y = ends.x;\n    ends.y = ends.x + int(baseVoxel(vec2(pos2)).r * 255.0);\n    pos3 = position + ivec2(0, 1);\n    starts.z = ends.y;\n    ends.z = ends.y + int(baseVoxel(vec2(pos3)).r * 255.0);\n    pos4 = position + ivec2(1, 1);\n    starts.w = ends.z;\n    mask = ivec3(greaterThanEqual(vI3, starts.rgb)) * ivec3(lessThan(vI3, ends.rgb));\n    m = ivec4(mask, 1 - int(any(bvec3(mask))));\n    position = m.x * pos1 + m.y * pos2 + m.z * pos3 + m.w * pos4;\n\n    vec2 coord2d = (vec2(position) / uSize) / uScale;\n    vec3 coord3d = floor(index3dFrom2d(coord2d) + 0.5);\n\n    float edgeIndex = floor(baseVoxel(vec2(position)).a * 255.0 + 0.5);\n\n    // current vertex for the up to 15 MC cases\n    int currentVertex = vI - idot4(m, starts);\n\n    // ensure winding-order is the same for negative and positive iso-levels\n    if (uInvert) {\n        int v = imod(currentVertex + 1, 3);\n        if (v == 1) currentVertex += 2;\n        else if (v == 0) currentVertex -= 2;\n    }\n\n    // get index into triIndices table\n    int mcIndex = 16 * int(edgeIndex) + currentVertex;\n    vec4 mcData = texture2D(tTriIndices, vec2(imod(mcIndex, 64), mcIndex / 64) / 64.);\n\n    // bit mask to avoid conditionals (see comment below) for getting MC case corner\n    vec4 m0 = vec4(floor(mcData.a * 255.0 + 0.5));\n\n    // get edge value masks\n    vec4 m1 = vec4(equal(m0, vec4(0., 1., 2., 3.)));\n    vec4 m2 = vec4(equal(m0, vec4(4., 5., 6., 7.)));\n    vec4 m3 = vec4(equal(m0, vec4(8., 9., 10., 11.)));\n\n    // apply bit masks\n    vec3 b0 = coord3d +\n                m1.y * c1 +\n                m1.z * c2 +\n                m1.w * c3 +\n                m2.x * c4 +\n                m2.y * c5 +\n                m2.z * c6 +\n                m2.w * c7 +\n                m3.y * c1 +\n                m3.z * c2 +\n                m3.w * c3;\n    vec3 b1 = coord3d +\n                m1.x * c1 +\n                m1.y * c2 +\n                m1.z * c3 +\n                m2.x * c5 +\n                m2.y * c6 +\n                m2.z * c7 +\n                m2.w * c4 +\n                m3.x * c4 +\n                m3.y * c5 +\n                m3.z * c6 +\n                m3.w * c7;\n\n    // the conditionals that are avoided by above bitmasks\n    // vec3 b0 = coord3d;\n    // vec3 b1 = coord3d;\n    // if (mcIndex == 0.0) {\n    //     b1 += c1;\n    // } else if (mcIndex == 1.0) {\n    //     b0 += c1; b1 += c2;\n    // } else if (mcIndex == 2.0) {\n    //     b0 += c2; b1 += c3;\n    // } else if (mcIndex == 3.0) {\n    //     b0 += c3;\n    // } else if (mcIndex == 4.0) {\n    //     b0 += c4; b1 += c5;\n    // } else if (mcIndex == 5.0) {\n    //     b0 += c5; b1 += c6;\n    // } else if (mcIndex == 6.0) {\n    //     b0 += c6; b1 += c7;\n    // } else if (mcIndex == 7.0) {\n    //     b0 += c7; b1 += c4;\n    // } else if (mcIndex == 8.0) {\n    //     b1 += c4;\n    // } else if (mcIndex == 9.0) {\n    //     b0 += c1; b1 += c5;\n    // } else if (mcIndex == 10.0) {\n    //     b0 += c2; b1 += c6;\n    // } else if (mcIndex == 11.0) {\n    //     b0 += c3; b1 += c7;\n    // }\n    // b0 = floor(b0 + 0.5);\n    // b1 = floor(b1 + 0.5);\n\n    vec4 d0 = voxel(b0);\n    vec4 d1 = voxel(b1);\n\n    float v0 = d0.a;\n    float v1 = d1.a;\n\n    float t = (uIsoValue - v0) / (v0 - v1);\n    gl_FragData[0].xyz = (uGridTransform * vec4(b0 + t * (b0 - b1), 1.0)).xyz;\n\n    // group id\n    #if __VERSION__ == 100\n        // webgl1 does not support 'flat' interpolation (i.e. no interpolation)\n        // so we ensure a constant group id per triangle here\n        #ifdef dPackedGroup\n            gl_FragData[1] = vec4(voxel(coord3d).rgb, 1.0);\n        #else\n            vec3 gridDim = uGridDim - vec3(1.0, 1.0, 0.0); // remove xy padding\n            float group = coord3d.z + coord3d.y * gridDim.z + coord3d.x * gridDim.z * gridDim.y;\n            gl_FragData[1] = vec4(group > 16777215.5 ? vec3(1.0) : encodeFloatRGB(group), 1.0);\n        #endif\n    #else\n        #ifdef dPackedGroup\n            gl_FragData[1] = vec4(t < 0.5 ? d0.rgb : d1.rgb, 1.0);\n        #else\n            vec3 b = t < 0.5 ? b0 : b1;\n            vec3 gridDim = uGridDim - vec3(1.0, 1.0, 0.0); // remove xy padding\n            float group = b.z + b.y * gridDim.z + b.x * gridDim.z * gridDim.y;\n            gl_FragData[1] = vec4(group > 16777215.5 ? vec3(1.0) : encodeFloatRGB(group), 1.0);\n        #endif\n    #endif\n\n    // normals from gradients\n    vec3 n0 = -normalize(vec3(\n        voxelPadded(b0 - c1).a - voxelPadded(b0 + c1).a,\n        voxelPadded(b0 - c3).a - voxelPadded(b0 + c3).a,\n        voxelPadded(b0 - c4).a - voxelPadded(b0 + c4).a\n    ));\n    vec3 n1 = -normalize(vec3(\n        voxelPadded(b1 - c1).a - voxelPadded(b1 + c1).a,\n        voxelPadded(b1 - c3).a - voxelPadded(b1 + c3).a,\n        voxelPadded(b1 - c4).a - voxelPadded(b1 + c4).a\n    ));\n    gl_FragData[2].xyz = -vec3(\n        n0.x + t * (n0.x - n1.x),\n        n0.y + t * (n0.y - n1.y),\n        n0.z + t * (n0.z - n1.z)\n    );\n\n    // ensure normal-direction is the same for negative and positive iso-levels\n    if (uInvert) {\n        gl_FragData[2].xyz *= -1.0;\n    }\n\n    // apply normal matrix\n    gl_FragData[2].xyz *= transpose3(inverse3(mat3(uGridTransform)));\n}\n";
+export var isosurface_frag = "\nprecision highp float;\nprecision highp int;\nprecision highp sampler2D;\n\n#if __VERSION__ == 100\n    uniform sampler2D tActiveVoxelsPyramid;\n#else\n    precision highp isampler2D;\n    uniform isampler2D tActiveVoxelsPyramid;\n#endif\n\nuniform sampler2D tActiveVoxelsBase;\nuniform sampler2D tVolumeData;\nuniform sampler2D tTriIndices;\n\nuniform float uIsoValue;\nuniform float uLevels;\nuniform float uSize;\nuniform float uCount;\nuniform bool uInvert;\n\nuniform vec3 uGridDim;\nuniform vec3 uGridTexDim;\nuniform mat4 uGridTransform;\n\n// scale to volume data coord\nuniform vec2 uScale;\n\n#include common\n\n// cube corners (excluding origin)\nconst vec3 c1 = vec3(1., 0., 0.);\nconst vec3 c2 = vec3(1., 1., 0.);\nconst vec3 c3 = vec3(0., 1., 0.);\nconst vec3 c4 = vec3(0., 0., 1.);\nconst vec3 c5 = vec3(1., 0., 1.);\nconst vec3 c6 = vec3(1., 1., 1.);\nconst vec3 c7 = vec3(0., 1., 1.);\n\nvec3 index3dFrom2d(vec2 coord) {\n    vec2 gridTexPos = coord * uGridTexDim.xy;\n    vec2 columnRow = ivec2Div(gridTexPos, uGridDim.xy);\n    vec2 posXY = gridTexPos - columnRow * uGridDim.xy;\n    float posZ = columnRow.y * intDiv(uGridTexDim.x, uGridDim.x) + columnRow.x;\n    return vec3(posXY, posZ);\n}\n\nvec4 texture3dFrom2dNearest(sampler2D tex, vec3 pos, vec3 gridDim, vec2 texDim) {\n    float zSlice = floor(pos.z * gridDim.z + 0.5); // round to nearest z-slice\n    float column = intDiv(intMod(zSlice * gridDim.x, texDim.x), gridDim.x);\n    float row = intDiv(zSlice * gridDim.x, texDim.x);\n    vec2 coord = (vec2(column * gridDim.x, row * gridDim.y) + (pos.xy * gridDim.xy)) / (texDim / uScale);\n    return texture2D(tex, coord + 0.5 / (texDim / uScale));\n}\n\nvec4 voxel(vec3 pos) {\n    pos = min(max(vec3(0.0), pos), uGridDim - vec3(1.0));\n    return texture3dFrom2dNearest(tVolumeData, pos / uGridDim, uGridDim, uGridTexDim.xy);\n}\n\nvec4 voxelPadded(vec3 pos) {\n    pos = min(max(vec3(0.0), pos), uGridDim - vec3(vec2(2.0), 1.0)); // remove xy padding\n    return texture3dFrom2dNearest(tVolumeData, pos / uGridDim, uGridDim, uGridTexDim.xy);\n}\n\nint idot2(const in ivec2 a, const in ivec2 b) {\n    return a.x * b.x + a.y * b.y;\n}\n\nint idot4(const in ivec4 a, const in ivec4 b) {\n    return a.x * b.x + a.y * b.y + a.z * b.z + a.w * b.w;\n}\n\n#if __VERSION__ == 100\n    int pyramidVoxel(vec2 pos) {\n        return int(unpackRGBToInt(texture2D(tActiveVoxelsPyramid, pos / (vec2(1.0, 0.5) * uSize)).rgb));\n    }\n#else\n    int pyramidVoxel(vec2 pos) {\n        return texture2D(tActiveVoxelsPyramid, pos / (vec2(1.0, 0.5) * uSize)).r;\n    }\n#endif\n\nvec4 baseVoxel(vec2 pos) {\n    return texture2D(tActiveVoxelsBase, pos / uSize);\n}\n\nvec4 getGroup(const in vec3 p) {\n    vec3 gridDim = uGridDim - vec3(1.0, 1.0, 0.0); // remove xy padding\n    // note that we swap x and z because the texture is flipped around y\n    #if defined(dAxisOrder_012)\n        float group = p.z + p.y * gridDim.z + p.x * gridDim.z * gridDim.y; // 210\n    #elif defined(dAxisOrder_021)\n        float group = p.y + p.z * gridDim.y + p.x * gridDim.y * gridDim.z; // 120\n    #elif defined(dAxisOrder_102)\n        float group = p.z + p.x * gridDim.z + p.y * gridDim.z * gridDim.x; // 201\n    #elif defined(dAxisOrder_120)\n        float group = p.x + p.z * gridDim.x + p.y * gridDim.x * gridDim.z; // 021\n    #elif defined(dAxisOrder_201)\n        float group = p.y + p.x * gridDim.y + p.z * gridDim.y * gridDim.x; // 102\n    #elif defined(dAxisOrder_210)\n        float group = p.x + p.y * gridDim.x + p.z * gridDim.x * gridDim.y; // 012\n    #endif\n    return vec4(group > 16777215.5 ? vec3(1.0) : packIntToRGB(group), 1.0);\n}\n\nvoid main(void) {\n    // get 1D index\n    int vI = int(gl_FragCoord.x) + int(gl_FragCoord.y) * int(uSize);\n\n    // ignore 1D indices outside of the grid\n    if(vI >= int(uCount)) discard;\n\n    ivec2 offset = ivec2(int(uSize) - 2, 0);\n\n    int start = 0;\n    ivec4 starts = ivec4(0);\n    ivec4 ends = ivec4(0);\n    int diff = 2;\n    ivec4 m = ivec4(0);\n    ivec2 position = ivec2(0);\n    ivec4 vI4 = ivec4(vI);\n\n    ivec2 relativePosition = ivec2(0);\n    int end = 0;\n    ivec2 pos1 = ivec2(0);\n    ivec2 pos2 = ivec2(0);\n    ivec2 pos3 = ivec2(0);\n    ivec2 pos4 = ivec2(0);\n    ivec3 vI3 = ivec3(vI);\n    ivec3 mask = ivec3(0);\n\n    // traverse the different levels of the pyramid\n    for(int i = 1; i < 14; i++) {\n        if(float(i) >= uLevels) break;\n\n        offset.x -= diff;\n        diff *= 2;\n        relativePosition = position + offset;\n\n        end = start + pyramidVoxel(vec2(relativePosition));\n        pos1 = ivec2(relativePosition);\n        starts.x = start;\n        ends.x = end;\n        pos2 = ivec2(relativePosition + ivec2(1, 0));\n        starts.y = ends.x;\n        ends.y = ends.x + pyramidVoxel(vec2(pos2));\n        pos3 = relativePosition + ivec2(0, 1);\n        starts.z = ends.y;\n        ends.z = ends.y + pyramidVoxel(vec2(pos3));\n        pos4 = relativePosition + ivec2(1, 1);\n        starts.w = ends.z;\n        mask = ivec3(greaterThanEqual(vI3, starts.rgb)) * ivec3(lessThan(vI3, ends.rgb));\n        m = ivec4(mask, 1 - int(any(bvec3(mask))));\n\n        relativePosition = m.x * pos1 + m.y * pos2 + m.z * pos3 + m.w * pos4;\n        start = idot4(m, starts);\n        position = 2 * (relativePosition - offset);\n    }\n\n    end = start + int(baseVoxel(vec2(position)).r * 255.0);\n    pos1 = position;\n    starts.x = start;\n    ends.x = end;\n    pos2 = position + ivec2(1, 0);\n    starts.y = ends.x;\n    ends.y = ends.x + int(baseVoxel(vec2(pos2)).r * 255.0);\n    pos3 = position + ivec2(0, 1);\n    starts.z = ends.y;\n    ends.z = ends.y + int(baseVoxel(vec2(pos3)).r * 255.0);\n    pos4 = position + ivec2(1, 1);\n    starts.w = ends.z;\n    mask = ivec3(greaterThanEqual(vI3, starts.rgb)) * ivec3(lessThan(vI3, ends.rgb));\n    m = ivec4(mask, 1 - int(any(bvec3(mask))));\n    position = m.x * pos1 + m.y * pos2 + m.z * pos3 + m.w * pos4;\n\n    vec2 coord2d = (vec2(position) / uSize) / uScale;\n    vec3 coord3d = floor(index3dFrom2d(coord2d) + 0.5);\n\n    float edgeIndex = floor(baseVoxel(vec2(position)).a * 255.0 + 0.5);\n\n    // current vertex for the up to 15 MC cases\n    int currentVertex = vI - idot4(m, starts);\n\n    // ensure winding-order is the same for negative and positive iso-levels\n    if (uInvert) {\n        int v = imod(currentVertex + 1, 3);\n        if (v == 1) currentVertex += 2;\n        else if (v == 0) currentVertex -= 2;\n    }\n\n    // get index into triIndices table\n    int mcIndex = 16 * int(edgeIndex) + currentVertex;\n    vec4 mcData = texture2D(tTriIndices, vec2(imod(mcIndex, 64), mcIndex / 64) / 64.);\n\n    // bit mask to avoid conditionals (see comment below) for getting MC case corner\n    vec4 m0 = vec4(floor(mcData.a * 255.0 + 0.5));\n\n    // get edge value masks\n    vec4 m1 = vec4(equal(m0, vec4(0., 1., 2., 3.)));\n    vec4 m2 = vec4(equal(m0, vec4(4., 5., 6., 7.)));\n    vec4 m3 = vec4(equal(m0, vec4(8., 9., 10., 11.)));\n\n    // apply bit masks\n    vec3 b0 = coord3d +\n                m1.y * c1 +\n                m1.z * c2 +\n                m1.w * c3 +\n                m2.x * c4 +\n                m2.y * c5 +\n                m2.z * c6 +\n                m2.w * c7 +\n                m3.y * c1 +\n                m3.z * c2 +\n                m3.w * c3;\n    vec3 b1 = coord3d +\n                m1.x * c1 +\n                m1.y * c2 +\n                m1.z * c3 +\n                m2.x * c5 +\n                m2.y * c6 +\n                m2.z * c7 +\n                m2.w * c4 +\n                m3.x * c4 +\n                m3.y * c5 +\n                m3.z * c6 +\n                m3.w * c7;\n\n    // the conditionals that are avoided by above bitmasks\n    // vec3 b0 = coord3d;\n    // vec3 b1 = coord3d;\n    // if (mcIndex == 0.0) {\n    //     b1 += c1;\n    // } else if (mcIndex == 1.0) {\n    //     b0 += c1; b1 += c2;\n    // } else if (mcIndex == 2.0) {\n    //     b0 += c2; b1 += c3;\n    // } else if (mcIndex == 3.0) {\n    //     b0 += c3;\n    // } else if (mcIndex == 4.0) {\n    //     b0 += c4; b1 += c5;\n    // } else if (mcIndex == 5.0) {\n    //     b0 += c5; b1 += c6;\n    // } else if (mcIndex == 6.0) {\n    //     b0 += c6; b1 += c7;\n    // } else if (mcIndex == 7.0) {\n    //     b0 += c7; b1 += c4;\n    // } else if (mcIndex == 8.0) {\n    //     b1 += c4;\n    // } else if (mcIndex == 9.0) {\n    //     b0 += c1; b1 += c5;\n    // } else if (mcIndex == 10.0) {\n    //     b0 += c2; b1 += c6;\n    // } else if (mcIndex == 11.0) {\n    //     b0 += c3; b1 += c7;\n    // }\n    // b0 = floor(b0 + 0.5);\n    // b1 = floor(b1 + 0.5);\n\n    vec4 d0 = voxel(b0);\n    vec4 d1 = voxel(b1);\n\n    float v0 = d0.a;\n    float v1 = d1.a;\n\n    float t = (uIsoValue - v0) / (v0 - v1);\n    gl_FragData[0].xyz = (uGridTransform * vec4(b0 + t * (b0 - b1), 1.0)).xyz;\n\n    // group id\n    #if __VERSION__ == 100\n        // webgl1 does not support 'flat' interpolation (i.e. no interpolation)\n        // so we ensure a constant group id per triangle here\n        #ifdef dPackedGroup\n            gl_FragData[1] = vec4(voxel(coord3d).rgb, 1.0);\n        #else\n            gl_FragData[1] = getGroup(coord3d);\n        #endif\n    #else\n        #ifdef dPackedGroup\n            gl_FragData[1] = vec4(t < 0.5 ? d0.rgb : d1.rgb, 1.0);\n        #else\n            gl_FragData[1] = getGroup(t < 0.5 ? b0 : b1);\n        #endif\n    #endif\n\n    // normals from gradients\n    vec3 n0 = -normalize(vec3(\n        voxelPadded(b0 - c1).a - voxelPadded(b0 + c1).a,\n        voxelPadded(b0 - c3).a - voxelPadded(b0 + c3).a,\n        voxelPadded(b0 - c4).a - voxelPadded(b0 + c4).a\n    ));\n    vec3 n1 = -normalize(vec3(\n        voxelPadded(b1 - c1).a - voxelPadded(b1 + c1).a,\n        voxelPadded(b1 - c3).a - voxelPadded(b1 + c3).a,\n        voxelPadded(b1 - c4).a - voxelPadded(b1 + c4).a\n    ));\n    gl_FragData[2].xyz = -vec3(\n        n0.x + t * (n0.x - n1.x),\n        n0.y + t * (n0.y - n1.y),\n        n0.z + t * (n0.z - n1.z)\n    );\n\n    // ensure normal-direction is the same for negative and positive iso-levels\n    if (uInvert) {\n        gl_FragData[2].xyz *= -1.0;\n    }\n\n    // apply normal matrix\n    gl_FragData[2].xyz *= transpose3(inverse3(mat3(uGridTransform)));\n}\n";
 //# sourceMappingURL=isosurface.frag.js.map

package/lib/mol-gl/shader/mesh.vert.d.ts

@@ -3,4 +3,4 @@
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
-export declare const mesh_vert = "\nprecision highp float;\nprecision highp int;\nprecision highp sampler2D;\n\n#include common\n#include read_from_texture\n#include common_vert_params\n#include color_vert_params\n#include common_clip\n#include texture3d_from_2d_linear\n\n#ifdef dGeoTexture\n    uniform vec2 uGeoTexDim;\n    uniform sampler2D tPosition;\n    uniform sampler2D tGroup;\n    uniform sampler2D tNormal;\n#else\n    attribute vec3 aPosition;\n    attribute float aGroup;\n    attribute vec3 aNormal;\n#endif\nattribute mat4 aTransform;\nattribute float aInstance;\n\nvarying vec3 vNormal;\n\nvoid main(){\n    #include assign_group\n    #include assign_marker_varying\n    #include assign_clipping_varying\n    #include assign_position\n    #include assign_color_varying\n    #include clip_instance\n\n    #ifdef dGeoTexture\n        vec3 normal = readFromTexture(tNormal, VertexID, uGeoTexDim).xyz;\n    #else\n        vec3 normal = aNormal;\n    #endif\n    mat3 normalMatrix = transpose3(inverse3(mat3(modelView)));\n    vec3 transformedNormal = normalize(normalMatrix * normalize(normal));\n    #if defined(dFlipSided)\n        if (!uDoubleSided) { // TODO checking uDoubleSided should not be required, ASR\n            transformedNormal = -transformedNormal;\n        }\n    #endif\n    vNormal = transformedNormal;\n}\n";
+export declare const mesh_vert = "\nprecision highp float;\nprecision highp int;\nprecision highp sampler2D;\n\n#include common\n#include read_from_texture\n#include common_vert_params\n#include color_vert_params\n#include common_clip\n#include texture3d_from_2d_linear\n\n#ifdef dGeometryType_textureMesh\n    uniform vec2 uGeoTexDim;\n    uniform sampler2D tPosition;\n    uniform sampler2D tGroup;\n    uniform sampler2D tNormal;\n#else\n    attribute vec3 aPosition;\n    attribute float aGroup;\n    attribute vec3 aNormal;\n#endif\nattribute mat4 aTransform;\nattribute float aInstance;\n\nvarying vec3 vNormal;\n\nvoid main(){\n    #include assign_group\n    #include assign_marker_varying\n    #include assign_clipping_varying\n    #include assign_position\n    #include assign_color_varying\n    #include clip_instance\n\n    #ifdef dGeometryType_textureMesh\n        vec3 normal = readFromTexture(tNormal, VertexID, uGeoTexDim).xyz;\n    #else\n        vec3 normal = aNormal;\n    #endif\n    mat3 normalMatrix = transpose3(inverse3(mat3(modelView)));\n    vec3 transformedNormal = normalize(normalMatrix * normalize(normal));\n    #if defined(dFlipSided)\n        if (!uDoubleSided) { // TODO checking uDoubleSided should not be required, ASR\n            transformedNormal = -transformedNormal;\n        }\n    #endif\n    vNormal = transformedNormal;\n}\n";

package/lib/mol-gl/shader/mesh.vert.js

@@ -3,5 +3,5 @@
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
-export var mesh_vert = "\nprecision highp float;\nprecision highp int;\nprecision highp sampler2D;\n\n#include common\n#include read_from_texture\n#include common_vert_params\n#include color_vert_params\n#include common_clip\n#include texture3d_from_2d_linear\n\n#ifdef dGeoTexture\n    uniform vec2 uGeoTexDim;\n    uniform sampler2D tPosition;\n    uniform sampler2D tGroup;\n    uniform sampler2D tNormal;\n#else\n    attribute vec3 aPosition;\n    attribute float aGroup;\n    attribute vec3 aNormal;\n#endif\nattribute mat4 aTransform;\nattribute float aInstance;\n\nvarying vec3 vNormal;\n\nvoid main(){\n    #include assign_group\n    #include assign_marker_varying\n    #include assign_clipping_varying\n    #include assign_position\n    #include assign_color_varying\n    #include clip_instance\n\n    #ifdef dGeoTexture\n        vec3 normal = readFromTexture(tNormal, VertexID, uGeoTexDim).xyz;\n    #else\n        vec3 normal = aNormal;\n    #endif\n    mat3 normalMatrix = transpose3(inverse3(mat3(modelView)));\n    vec3 transformedNormal = normalize(normalMatrix * normalize(normal));\n    #if defined(dFlipSided)\n        if (!uDoubleSided) { // TODO checking uDoubleSided should not be required, ASR\n            transformedNormal = -transformedNormal;\n        }\n    #endif\n    vNormal = transformedNormal;\n}\n";
+export var mesh_vert = "\nprecision highp float;\nprecision highp int;\nprecision highp sampler2D;\n\n#include common\n#include read_from_texture\n#include common_vert_params\n#include color_vert_params\n#include common_clip\n#include texture3d_from_2d_linear\n\n#ifdef dGeometryType_textureMesh\n    uniform vec2 uGeoTexDim;\n    uniform sampler2D tPosition;\n    uniform sampler2D tGroup;\n    uniform sampler2D tNormal;\n#else\n    attribute vec3 aPosition;\n    attribute float aGroup;\n    attribute vec3 aNormal;\n#endif\nattribute mat4 aTransform;\nattribute float aInstance;\n\nvarying vec3 vNormal;\n\nvoid main(){\n    #include assign_group\n    #include assign_marker_varying\n    #include assign_clipping_varying\n    #include assign_position\n    #include assign_color_varying\n    #include clip_instance\n\n    #ifdef dGeometryType_textureMesh\n        vec3 normal = readFromTexture(tNormal, VertexID, uGeoTexDim).xyz;\n    #else\n        vec3 normal = aNormal;\n    #endif\n    mat3 normalMatrix = transpose3(inverse3(mat3(modelView)));\n    vec3 transformedNormal = normalize(normalMatrix * normalize(normal));\n    #if defined(dFlipSided)\n        if (!uDoubleSided) { // TODO checking uDoubleSided should not be required, ASR\n            transformedNormal = -transformedNormal;\n        }\n    #endif\n    vNormal = transformedNormal;\n}\n";
 //# sourceMappingURL=mesh.vert.js.map

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

@@ -160,7 +160,7 @@ import { mesh_frag } from './shader/mesh.frag';
 export var MeshShaderCode = ShaderCode('mesh', mesh_vert, mesh_frag, { drawBuffers: 'optional' }, {}, ignoreDefine);
 import { directVolume_vert } from './shader/direct-volume.vert';
 import { directVolume_frag } from './shader/direct-volume.frag';
-export var DirectVolumeShaderCode = ShaderCode('direct-volume', directVolume_vert, directVolume_frag, { fragDepth: 'optional', drawBuffers: 'optional' });
+export var DirectVolumeShaderCode = ShaderCode('direct-volume', directVolume_vert, directVolume_frag, { fragDepth: 'optional', drawBuffers: 'optional' }, {}, ignoreDefine);
 import { image_vert } from './shader/image.vert';
 import { image_frag } from './shader/image.frag';
 export var ImageShaderCode = ShaderCode('image', image_vert, image_frag, { drawBuffers: 'optional' }, {}, ignoreDefineUnlit);

package/lib/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 5.354, IHM 1.17, MA 1.3.3.
  *
  * @author molstar/ciftools package
  */

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

@@ -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 5.354, IHM 1.17, MA 1.3.3.
  *
  * @author molstar/ciftools package
  */

package/lib/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 5.354, IHM 1.17, MA 1.3.3.
  *
  * @author molstar/ciftools package
  */

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

@@ -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 5.354, IHM 1.17, MA 1.3.3.
  *
  * @author molstar/ciftools package
  */

package/lib/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 5.354, IHM 1.17, MA 1.3.3.
  *
  * @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<"AFDB" | "CAS" | "CSD" | "EMDB" | "ICSD" | "MA" | "MDF" | "MODBASE" | "NDB" | "NBS" | "PDB" | "PDF" | "RCSB" | "SMR" | "EBI" | "PDBE" | "BMRB" | "WWPDB" | "PDB_ACC">;
         /**
          * The code assigned by the database identified in
          * _database_2.database_id.

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

@@ -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 5.354, IHM 1.17, MA 1.3.3.
  *
  * @author molstar/ciftools package
  */

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

@@ -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 { __awaiter, __generator } from "tslib";
 import { Column } from '../../../mol-data/db';
@@ -9,11 +10,57 @@ import { Task } from '../../../mol-task';
 import { TokenColumnProvider as TokenColumn } from '../common/text/column/token';
 import { TokenBuilder, Tokenizer } from '../common/text/tokenizer';
 import { ReaderResult as Result } from '../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.
+ */
+export 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;
+    }
+}
 export function handleAtoms(tokenizer, count) {
     var x = TokenBuilder.create(tokenizer.data, count * 2);
     var y = TokenBuilder.create(tokenizer.data, count * 2);
     var z = TokenBuilder.create(tokenizer.data, count * 2);
     var type_symbol = TokenBuilder.create(tokenizer.data, count * 2);
+    var formal_charge = TokenBuilder.create(tokenizer.data, count * 2);
     for (var i = 0; i < count; ++i) {
         Tokenizer.markLine(tokenizer);
         var s = tokenizer.tokenStart, position = tokenizer.position;
@@ -25,6 +72,8 @@ export function handleAtoms(tokenizer, count) {
         TokenBuilder.addUnchecked(z, tokenizer.tokenStart, tokenizer.tokenEnd);
         Tokenizer.trim(tokenizer, s + 31, s + 34);
         TokenBuilder.addUnchecked(type_symbol, tokenizer.tokenStart, tokenizer.tokenEnd);
+        Tokenizer.trim(tokenizer, s + 36, s + 39);
+        TokenBuilder.addUnchecked(formal_charge, tokenizer.tokenStart, tokenizer.tokenEnd);
         tokenizer.position = position;
     }
     return {
@@ -32,7 +81,8 @@ export function handleAtoms(tokenizer, count) {
         x: TokenColumn(x)(Column.Schema.float),
         y: TokenColumn(y)(Column.Schema.float),
         z: TokenColumn(z)(Column.Schema.float),
-        type_symbol: TokenColumn(type_symbol)(Column.Schema.str)
+        type_symbol: TokenColumn(type_symbol)(Column.Schema.str),
+        formal_charge: TokenColumn(formal_charge)(Column.Schema.int)
     };
 }
 export function handleBonds(tokenizer, count) {
@@ -57,6 +107,63 @@ export function handleBonds(tokenizer, count) {
         order: TokenColumn(order)(Column.Schema.int)
     };
 }
+export function handleFormalCharges(tokenizer, lineStart, formalCharges) {
+    Tokenizer.trim(tokenizer, lineStart + 6, lineStart + 9);
+    var numOfCharges = parseInt(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.trim(tokenizer, lineStart + offset, lineStart + offset + 4);
+        var _atomIdx = Tokenizer.getTokenString(tokenizer);
+        formalCharges.atomIdx.push(+_atomIdx);
+        Tokenizer.trim(tokenizer, lineStart + offset + 4, lineStart + offset + 8);
+        var _charge = Tokenizer.getTokenString(tokenizer);
+        formalCharges.charge.push(+_charge);
+    }
+    /* Once the line is read, move to the next one. */
+    Tokenizer.eatLine(tokenizer);
+}
+/** 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 function handlePropertiesBlock(tokenizer) {
+    var _atomIdx = [];
+    var _charge = [];
+    var _formalCharges = { atomIdx: _atomIdx, charge: _charge };
+    while (tokenizer.position < tokenizer.length) {
+        var s = tokenizer.position;
+        Tokenizer.trim(tokenizer, s + 3, s + 6);
+        var propertyType = Tokenizer.getTokenString(tokenizer);
+        if (propertyType === 'END')
+            break;
+        Tokenizer.eatLine(tokenizer);
+        switch (propertyType) {
+            case 'CHG':
+                handleFormalCharges(tokenizer, s, _formalCharges);
+                break;
+            default:
+                break;
+        }
+    }
+    var formalCharges = {
+        atomIdx: Column.ofIntArray(_formalCharges.atomIdx),
+        charge: Column.ofIntArray(_formalCharges.charge)
+    };
+    return formalCharges;
+}
 function parseInternal(data) {
     var tokenizer = Tokenizer(data);
     var title = Tokenizer.readLine(tokenizer).trim();
@@ -66,12 +173,14 @@ 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.success(result);
 }

package/lib/mol-io/reader/mol2/parser.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2020 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 Zepei Xu <xuzepei19950617@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>

package/lib/mol-io/reader/mol2/parser.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017-2020 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 Zepei Xu <xuzepei19950617@gmail.com>
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
@@ -241,9 +241,38 @@ function handleBonds(state) {
         });
     });
 }
+function handleCrysin(state) {
+    var tokenizer = state.tokenizer;
+    while (tokenizer.position < tokenizer.data.length) {
+        var l = getTokenString(tokenizer);
+        if (l === '@<TRIPOS>MOLECULE') {
+            return;
+        }
+        else if (l === '@<TRIPOS>CRYSIN') {
+            break;
+        }
+        else {
+            markLine(tokenizer);
+        }
+    }
+    if (tokenizer.position >= tokenizer.data.length)
+        return;
+    markLine(tokenizer);
+    var values = getTokenString(tokenizer).trim().split(reWhitespace);
+    return {
+        a: parseFloat(values[0]),
+        b: parseFloat(values[1]),
+        c: parseFloat(values[2]),
+        alpha: parseFloat(values[3]),
+        beta: parseFloat(values[4]),
+        gamma: parseFloat(values[5]),
+        spaceGroup: parseInt(values[6], 10),
+        setting: parseInt(values[7], 10),
+    };
+}
 function parseInternal(ctx, data, name) {
     return __awaiter(this, void 0, void 0, function () {
-        var tokenizer, structures, state, atoms, bonds, result;
+        var tokenizer, structures, state, atoms, bonds, crysin, result;
         return __generator(this, function (_a) {
             switch (_a.label) {
                 case 0:
@@ -261,7 +290,8 @@ function parseInternal(ctx, data, name) {
                     return [4 /*yield*/, handleBonds(state)];
                 case 3:
                     bonds = _a.sent();
-                    structures.push({ molecule: state.molecule, atoms: atoms, bonds: bonds });
+                    crysin = handleCrysin(state);
+                    structures.push({ molecule: state.molecule, atoms: atoms, bonds: bonds, crysin: crysin });
                     skipWhitespace(tokenizer);
                     while (getTokenString(tokenizer) !== '@<TRIPOS>MOLECULE' && tokenizer.position < tokenizer.data.length) {
                         markLine(tokenizer);

package/lib/mol-io/reader/mol2/schema.d.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017 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>
  */
@@ -37,10 +37,21 @@ export interface Mol2Bonds {
     bond_type: Column<string>;
     status_bits: Column<string>;
 }
+export interface Mol2Crysin {
+    a: number;
+    b: number;
+    c: number;
+    alpha: number;
+    beta: number;
+    gamma: number;
+    spaceGroup: number;
+    setting: number;
+}
 export interface Mol2Structure {
     molecule: Readonly<Mol2Molecule>;
     atoms: Readonly<Mol2Atoms>;
     bonds: Readonly<Mol2Bonds>;
+    crysin?: Readonly<Mol2Crysin>;
 }
 export interface Mol2File {
     name: string;

package/lib/mol-io/reader/mol2/schema.js

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017 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>
  */

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

@@ -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 { Column } from '../../../mol-data/db';
 import { Tokenizer, TokenBuilder } from '../common/text/tokenizer';
 import { TokenColumnProvider as TokenColumn } from '../common/text/column/token';
@@ -44,6 +50,9 @@ export function handleAtomsV3(tokenizer, atomCount) {
         y: TokenColumn(y)(Column.Schema.float),
         z: TokenColumn(z)(Column.Schema.float),
         type_symbol: TokenColumn(type_symbol)(Column.Schema.str),
+        /* No support for formal charge parsing in V3000 molfiles at the moment,
+        so all charges default to 0.*/
+        formal_charge: Column.ofConst(0, atomCount, Column.Schema.int)
     };
 }
 export function handleBondsV3(tokenizer, bondCount) {

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

@@ -1,12 +1,14 @@
 /**
- * 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 { __awaiter, __generator } from "tslib";
 import { Column } from '../../../mol-data/db';
-import { handleAtoms, handleBonds } from '../mol/parser';
+import { handleAtoms, handleBonds, handlePropertiesBlock } from '../mol/parser';
 import { Task } from '../../../mol-task';
 import { ReaderResult as Result } from '../result';
 import { Tokenizer, TokenBuilder } from '../common/text/tokenizer';
@@ -69,11 +71,18 @@ 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: Column.ofConst(0, atomCount, Column.Schema.int),
+        charge: Column.ofConst(0, atomCount, Column.Schema.int)
+    };
     var atoms = molIsV3 ? handleAtomsV3(tokenizer, atomCount) : handleAtoms(tokenizer, atomCount);
     var bonds = molIsV3 ? handleBondsV3(tokenizer, bondCount) : handleBonds(tokenizer, bondCount);
+    var formalCharges = molIsV3 ? nullFormalCharges : 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
     };
 }