molstar 3.0.0-dev.6 → 3.0.0

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

@@ -3,4 +3,4 @@
  *
  * @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                #ifdef dDoubleSided\n                    normal = normal * (float(frontFacing) * 2.0 - 1.0);\n                #endif\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        #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";

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

@@ -3,5 +3,5 @@
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
-export var 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                #ifdef dDoubleSided\n                    normal = normal * (float(frontFacing) * 2.0 - 1.0);\n                #endif\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 var 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";
 //# sourceMappingURL=mesh.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) && !defined(dDoubleSided) // TODO checking dDoubleSided should not be required, ASR\n        transformedNormal = -transformedNormal;\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) && !defined(dDoubleSided) // TODO checking dDoubleSided should not be required, ASR\n        transformedNormal = -transformedNormal;\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/spheres.frag.d.ts

@@ -3,4 +3,4 @@
  *
  * @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    #ifndef dDoubleSided\n        if (interior)\n            discard;\n    #endif\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        #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";

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

@@ -3,5 +3,5 @@
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
-export var 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    #ifndef dDoubleSided\n        if (interior)\n            discard;\n    #endif\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 var 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";
 //# sourceMappingURL=spheres.frag.js.map

package/lib/mol-gl/shader-code.d.ts

@@ -20,6 +20,7 @@ export interface ShaderExtensions {
 declare type FragOutTypes = {
     [k in number]: 'vec4' | 'ivec4';
 };
+declare type IgnoreDefine = (name: string, variant: string, defines: ShaderDefines) => boolean;
 export interface ShaderCode {
     readonly id: number;
     readonly name: string;
@@ -28,8 +29,9 @@ export interface ShaderCode {
     readonly extensions: ShaderExtensions;
     /** Fragment shader output type only applicable for webgl2 */
     readonly outTypes: FragOutTypes;
+    readonly ignoreDefine?: IgnoreDefine;
 }
-export declare function ShaderCode(name: string, vert: string, frag: string, extensions?: ShaderExtensions, outTypes?: FragOutTypes): ShaderCode;
+export declare function ShaderCode(name: string, vert: string, frag: string, extensions?: ShaderExtensions, outTypes?: FragOutTypes, ignoreDefine?: IgnoreDefine): ShaderCode;
 export declare const PointsShaderCode: ShaderCode;
 export declare const SpheresShaderCode: ShaderCode;
 export declare const CylindersShaderCode: ShaderCode;

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

@@ -110,41 +110,69 @@ function replaceCounts(str, defines) {
 function preprocess(str, defines) {
     return unrollLoops(replaceCounts(str, defines));
 }
-export function ShaderCode(name, vert, frag, extensions, outTypes) {
+export function ShaderCode(name, vert, frag, extensions, outTypes, ignoreDefine) {
     if (extensions === void 0) { extensions = {}; }
     if (outTypes === void 0) { outTypes = {}; }
-    return { id: shaderCodeId(), name: name, vert: addIncludes(vert), frag: addIncludes(frag), extensions: extensions, outTypes: outTypes };
+    return { id: shaderCodeId(), name: name, vert: addIncludes(vert), frag: addIncludes(frag), extensions: extensions, outTypes: outTypes, ignoreDefine: ignoreDefine };
 }
 // Note: `drawBuffers` need to be 'optional' for wboit
+function ignoreDefine(name, variant, defines) {
+    var _a;
+    if (variant.startsWith('color')) {
+        if (name === 'dLightCount') {
+            return !!((_a = defines.dIgnoreLight) === null || _a === void 0 ? void 0 : _a.ref.value);
+        }
+    }
+    else {
+        return [
+            'dColorType', 'dUsePalette',
+            'dLightCount',
+            'dOverpaintType', 'dOverpaint',
+            'dSubstanceType', 'dSubstance',
+        ].includes(name);
+    }
+    return false;
+}
+;
+function ignoreDefineUnlit(name, variant, defines) {
+    if (name === 'dLightCount')
+        return true;
+    return ignoreDefine(name, variant, defines);
+}
+;
 import { points_vert } from './shader/points.vert';
 import { points_frag } from './shader/points.frag';
-export var PointsShaderCode = ShaderCode('points', points_vert, points_frag, { drawBuffers: 'optional' });
+export var PointsShaderCode = ShaderCode('points', points_vert, points_frag, { drawBuffers: 'optional' }, {}, ignoreDefineUnlit);
 import { spheres_vert } from './shader/spheres.vert';
 import { spheres_frag } from './shader/spheres.frag';
-export var SpheresShaderCode = ShaderCode('spheres', spheres_vert, spheres_frag, { fragDepth: 'required', drawBuffers: 'optional' });
+export var SpheresShaderCode = ShaderCode('spheres', spheres_vert, spheres_frag, { fragDepth: 'required', drawBuffers: 'optional' }, {}, ignoreDefine);
 import { cylinders_vert } from './shader/cylinders.vert';
 import { cylinders_frag } from './shader/cylinders.frag';
-export var CylindersShaderCode = ShaderCode('cylinders', cylinders_vert, cylinders_frag, { fragDepth: 'required', drawBuffers: 'optional' });
+export var CylindersShaderCode = ShaderCode('cylinders', cylinders_vert, cylinders_frag, { fragDepth: 'required', drawBuffers: 'optional' }, {}, ignoreDefine);
 import { text_vert } from './shader/text.vert';
 import { text_frag } from './shader/text.frag';
-export var TextShaderCode = ShaderCode('text', text_vert, text_frag, { drawBuffers: 'optional' });
+export var TextShaderCode = ShaderCode('text', text_vert, text_frag, { drawBuffers: 'optional' }, {}, ignoreDefineUnlit);
 import { lines_vert } from './shader/lines.vert';
 import { lines_frag } from './shader/lines.frag';
-export var LinesShaderCode = ShaderCode('lines', lines_vert, lines_frag, { drawBuffers: 'optional' });
+export var LinesShaderCode = ShaderCode('lines', lines_vert, lines_frag, { drawBuffers: 'optional' }, {}, ignoreDefineUnlit);
 import { mesh_vert } from './shader/mesh.vert';
 import { mesh_frag } from './shader/mesh.frag';
-export var MeshShaderCode = ShaderCode('mesh', mesh_vert, mesh_frag, { drawBuffers: 'optional' });
+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' });
-function getDefinesCode(defines) {
+export var ImageShaderCode = ShaderCode('image', image_vert, image_frag, { drawBuffers: 'optional' }, {}, ignoreDefineUnlit);
+function getDefinesCode(defines, ignore) {
+    var _a;
     if (defines === undefined)
         return '';
+    var variant = (((_a = defines.dRenderVariant) === null || _a === void 0 ? void 0 : _a.ref.value) || '');
     var lines = [];
     for (var name_1 in defines) {
+        if (ignore === null || ignore === void 0 ? void 0 : ignore(name_1, variant, defines))
+            continue;
         var define = defines[name_1];
         var v = define.ref.value;
         if (v !== undefined) {
@@ -229,7 +257,8 @@ function transformGlsl300Frag(frag) {
     return frag.replace(/gl_FragData\[([0-9]+)\]/g, 'out_FragData$1');
 }
 export function addShaderDefines(gl, extensions, defines, shaders) {
-    var header = getDefinesCode(defines);
+    var vertHeader = getDefinesCode(defines, shaders.ignoreDefine);
+    var fragHeader = getDefinesCode(defines, shaders.ignoreDefine);
     var vertPrefix = isWebGL2(gl) ? glsl300VertPrefix : '';
     var fragPrefix = isWebGL2(gl)
         ? getGlsl300FragPrefix(gl, extensions, shaders.extensions, shaders.outTypes)
@@ -238,8 +267,8 @@ export function addShaderDefines(gl, extensions, defines, shaders) {
     return {
         id: shaderCodeId(),
         name: shaders.name,
-        vert: "".concat(vertPrefix).concat(header).concat(preprocess(shaders.vert, defines)),
-        frag: "".concat(fragPrefix).concat(header).concat(preprocess(frag, defines)),
+        vert: "".concat(vertPrefix).concat(vertHeader).concat(preprocess(shaders.vert, defines)),
+        frag: "".concat(fragPrefix).concat(fragHeader).concat(preprocess(frag, defines)),
         extensions: shaders.extensions,
         outTypes: shaders.outTypes
     };

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

@@ -21,18 +21,19 @@ export interface RenderItem<T extends string> {
 declare const GraphicsRenderVariant: {
     colorBlended: string;
     colorWboit: string;
-    pickObject: string;
-    pickInstance: string;
-    pickGroup: string;
+    pick: string;
     depth: string;
-    markingDepth: string;
-    markingMask: string;
+    marking: string;
 };
 export declare type GraphicsRenderVariant = keyof typeof GraphicsRenderVariant;
+export declare const GraphicsRenderVariants: ("depth" | "colorBlended" | "colorWboit" | "pick" | "marking")[];
+export declare const GraphicsRenderVariantsBlended: ("depth" | "colorBlended" | "colorWboit" | "pick" | "marking")[];
+export declare const GraphicsRenderVariantsWboit: ("depth" | "colorBlended" | "colorWboit" | "pick" | "marking")[];
 declare const ComputeRenderVariant: {
     compute: string;
 };
 export declare type ComputeRenderVariant = keyof typeof ComputeRenderVariant;
+export declare const ComputeRenderVariants: "compute"[];
 declare function createValueChanges(): {
     attributes: boolean;
     defines: boolean;
@@ -41,7 +42,7 @@ declare function createValueChanges(): {
 };
 declare type ValueChanges = ReturnType<typeof createValueChanges>;
 export declare type GraphicsRenderItem = RenderItem<GraphicsRenderVariant>;
-export declare function createGraphicsRenderItem(ctx: WebGLContext, drawMode: DrawMode, shaderCode: ShaderCode, schema: RenderableSchema, values: RenderableValues, materialId: number): RenderItem<"depth" | "colorBlended" | "colorWboit" | "pickObject" | "pickInstance" | "pickGroup" | "markingDepth" | "markingMask">;
+export declare function createGraphicsRenderItem(ctx: WebGLContext, drawMode: DrawMode, shaderCode: ShaderCode, schema: RenderableSchema, values: RenderableValues, materialId: number, variants: GraphicsRenderVariant[]): RenderItem<"depth" | "colorBlended" | "colorWboit" | "pick" | "marking">;
 export declare type ComputeRenderItem = RenderItem<ComputeRenderVariant>;
 export declare function createComputeRenderItem(ctx: WebGLContext, drawMode: DrawMode, shaderCode: ShaderCode, schema: RenderableSchema, values: RenderableValues, materialId?: number): RenderItem<"compute">;
 /**

package/lib/mol-gl/webgl/render-item.js

@@ -29,10 +29,12 @@ export function getDrawMode(ctx, drawMode) {
     }
 }
 //
-var GraphicsRenderVariant = { 'colorBlended': '', 'colorWboit': '', 'pickObject': '', 'pickInstance': '', 'pickGroup': '', 'depth': '', 'markingDepth': '', 'markingMask': '' };
-var GraphicsRenderVariants = Object.keys(GraphicsRenderVariant);
-var ComputeRenderVariant = { 'compute': '' };
-var ComputeRenderVariants = Object.keys(ComputeRenderVariant);
+var GraphicsRenderVariant = { colorBlended: '', colorWboit: '', pick: '', depth: '', marking: '' };
+export var GraphicsRenderVariants = Object.keys(GraphicsRenderVariant);
+export var GraphicsRenderVariantsBlended = GraphicsRenderVariants.filter(function (v) { return v !== 'colorWboit'; });
+export var GraphicsRenderVariantsWboit = GraphicsRenderVariants.filter(function (v) { return v !== 'colorBlended'; });
+var ComputeRenderVariant = { compute: '' };
+export var ComputeRenderVariants = Object.keys(ComputeRenderVariant);
 function createProgramVariant(ctx, variant, defineValues, shaderCode, schema) {
     defineValues = __assign(__assign({}, defineValues), { dRenderVariant: ValueCell.create(variant) });
     if (schema.dRenderVariant === undefined) {
@@ -54,8 +56,8 @@ function resetValueChanges(valueChanges) {
     valueChanges.elements = false;
     valueChanges.textures = false;
 }
-export function createGraphicsRenderItem(ctx, drawMode, shaderCode, schema, values, materialId) {
-    return createRenderItem(ctx, drawMode, shaderCode, schema, values, materialId, GraphicsRenderVariants);
+export function createGraphicsRenderItem(ctx, drawMode, shaderCode, schema, values, materialId, variants) {
+    return createRenderItem(ctx, drawMode, shaderCode, schema, values, materialId, variants);
 }
 export function createComputeRenderItem(ctx, drawMode, shaderCode, schema, values, materialId) {
     if (materialId === void 0) { materialId = -1; }

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

@@ -48,8 +48,15 @@ export function createResources(gl, state, stats, extensions) {
         return wrapCached(shaderCache.get({ type: type, source: source }));
     }
     var programCache = createReferenceCache(function (props) {
+        var _a;
         var array = [props.shaderCode.id];
-        Object.keys(props.defineValues).forEach(function (k) { return array.push(hashString(k), defineValueHash(props.defineValues[k].ref.value)); });
+        var variant = (((_a = props.defineValues.dRenderVariant) === null || _a === void 0 ? void 0 : _a.ref.value) || '');
+        Object.keys(props.defineValues).forEach(function (k) {
+            var _a, _b;
+            if (!((_b = (_a = props.shaderCode).ignoreDefine) === null || _b === void 0 ? void 0 : _b.call(_a, k, variant, props.defineValues))) {
+                array.push(hashString(k), defineValueHash(props.defineValues[k].ref.value));
+            }
+        });
         return hashFnv32a(array).toString();
     }, function (props) { return wrap('program', createProgram(gl, state, extensions, getShader, props)); }, function (program) { program.destroy(); });
     return {

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>