Issue #833: transformations by assembly gen. and struct operators

public/3pcv.json

@@ -0,0 +1,4571 @@
+{
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+        },
+        "biomatrix": {
+            "matrix_list": [
+                {
+                    "matrix_id": "1",
+                    "apply_to_chain_list": [
+                        {
+                            "chain_id": "A",
+                            "new_chain_id": "A-2"
+                        }
+                    ],
+                    "transformation_matrix": {
+                        "rowx": {
+                            "x": 0,
+                            "y": 0,
+                            "z": 1,
+                            "t": 0
+                        },
+                        "rowy": {
+                            "x": -1,
+                            "y": 0,
+                            "z": 0,
+                            "t": 84.01474762
+                        },
+                        "rowz": {
+                            "x": 0,
+                            "y": -1,
+                            "z": 0,
+                            "t": 84.01474762
+                        }
+                    }
+                },
+                {
+                    "matrix_id": "2",
+                    "apply_to_chain_list": [
+                        {
+                            "chain_id": "A",
+                            "new_chain_id": "A-3"
+                        }
+                    ],
+                    "transformation_matrix": {
+                        "rowx": {
+                            "x": 0,
+                            "y": -1,
+                            "z": 0,
+                            "t": 84.01474762
+                        },
+                        "rowy": {
+                            "x": 0,
+                            "y": 0,
+                            "z": -1,
+                            "t": 84.01474762
+                        },
+                        "rowz": {
+                            "x": 1,
+                            "y": 0,
+                            "z": 0,
+                            "t": 0
+                        }
+                    }
+                }
+            ]
+        },
+        "ent_cif_mapping_results": {
+            "ent_cif_chain_map": {
+                "A": [
+                    "A"
+                ]
+            },
+            "cif_chain_derivatives": {
+                "A-2": "A",
+                "A-3": "A"
+            },
+            "pdbtm_derivatives_and_cif_chain_map": {
+                "B": [
+                    "A-2"
+                ],
+                "C": [
+                    "A-3"
+                ]
+            }
+        }
+    }
+}

src/TmFv3DApp/FeatureViewConfig.ts

@@ -26,6 +26,7 @@ import { TmRowTitleComponent } from "./tmdet-viewer/TmRowTitleComponent";
 
 export type TmFvConfigParams = {
     pdbEntry: string,
+    structureUrl?: string,
     pdbtmEntry: string,
     htpEntry: string,
     labelAsymId: string,
@@ -49,7 +50,8 @@ export async function createFeatureViewerConfing(params: TmFvConfigParams) {
         loadConfig: {
             loadMethod: LoadMethod.loadStructureFromUrl,
             loadParams: {
-                url: `https://www.ebi.ac.uk/pdbe/entry-files/download/${params.pdbEntry}_updated.cif`,
+                url: params.structureUrl
+                    ?? `https://www.ebi.ac.uk/pdbe/entry-files/download/${params.pdbEntry}_updated.cif`,
                 format: 'mmcif',
                 isBinary: false,
                 id: `${params.pdbEntry}_model`,

src/TmFv3DApp/TmTrajectoryHierarchyPreset.ts

@@ -56,7 +56,7 @@ export const TmDetRcsbPreset = TrajectoryHierarchyPresetProvider({
             .apply(StateTransforms.Model.StructureFromModel, props, { ref: 'assembly' })
             .commit();
 
-        applyTransformations(plugin, descriptor!);
+        //applyTransformations(plugin, descriptor!);
 
         const builder = plugin.builders.structure;
         const model = new StateObjectSelector(plugin.state.data.build().to('model').ref, plugin.state.data);

src/TmFv3DApp/index.html

@@ -40,11 +40,20 @@
           side1: "Outside",
           configData: "./zdh15_saguaro_7khm_B.json",
           annotationData: "./7khm.json"
+        },
+        "3pcv_A": {
+          title: 'TmSaguaro Example IV',
+          subtitle: '3pcv data',
+          elementId: "tmSaguaro",
+          pdbEntry: "3pcv",
+          labelAsymId: "A",
+          side1: "Outside",
+          configData: "./3pcv_saguaro_A.json",
+          annotationData: "./3pcv.json"
         }
       };
-      var item = getParam("entry", ".+_.+", "6bms_A");
-      console.log(configs);
-      console.log("itwem:", item);
+      var item = getParam("entry", ".+_.+", "3pcv_A");
+      console.log("Selected config item:", item);
       tmSaguaro.createRcsb3DViewer(configs[item]);
     </script>
 </head>

src/TmFv3DApp/index.ts

@@ -35,6 +35,7 @@ async function createConfig(configParams: any): Promise<RcsbFv3DCustomInterface>
         side1: configParams.side1,
         htpEntry: configParams.htpEntry,
         pdbEntry: configParams.pdbEntry,
+        structureUrl: configParams.structureUrl!,
         labelAsymId: labelAsymId,
         pdbtmEntry: `${pdbEntry}_${labelAsymId}`
     };

src/TmFv3DApp/tmdet-extension/symmetry.ts

@@ -13,14 +13,13 @@ import { mmCIF_Schema } from 'molstar/lib/mol-io/reader/cif/schema/mmcif';
 import { Model } from 'molstar/lib/mol-model/structure';
 import { ModelSymmetry } from 'molstar/lib/mol-model-formats/structure/property/symmetry';
 import { PDBTMDescriptor } from './types';
-import { DebugUtil } from './debug-utils';
-
+import { Mat3, Mat4, Vec3 } from 'molstar/lib/mol-math/linear-algebra';
+import { transformationForStateTransform } from './transformation';
 
 export function registerTmDetSymmetry(pdbtmDescriptor: PDBTMDescriptor) {
     ModelSymmetry.Provider.formatRegistry.remove('mmCIF');
-    const excludedChains = constructChainListFromOperations(pdbtmDescriptor);
     ModelSymmetry.Provider.formatRegistry.add('mmCIF',  function(model: Model) {
-        return tmDetSymmetryFromMmCif(model, excludedChains);
+        return tmDetSymmetryFromMmCif(model, pdbtmDescriptor);
     });
 }
 
@@ -45,23 +44,28 @@ function constructChainListFromOperations(pdbtmDescriptor: PDBTMDescriptor): str
     return excludedChains;
 }
 
-function tmDetSymmetryFromMmCif(model: Model, excludedChains: string[]) {
+function tmDetSymmetryFromMmCif(model: Model, pdbtmDescriptor: PDBTMDescriptor) {
     if (!MmcifFormat.is(model.sourceData)) return;
 
     let data = model.sourceData.data.db;
+    let excludedChains: string[] = constructChainListFromOperations(pdbtmDescriptor);
     excludedChains = union(
         excludedChains,
         Array.from(data.pdbx_nonpoly_scheme.asym_id.toArray())
     );
+    const structureOperations: StructureOperation[] = collectOperations(pdbtmDescriptor);
+    console.log("Structure Operators:", structureOperations);
 
     const updated_pdbx_struct_assembly_gen = createPdbxStructAssemblyGen(
+        structureOperations,
         data.pdbx_struct_assembly_gen,
         excludedChains
     );
-    DebugUtil.log('Non-poly entities:', Table.formatToString(data.pdbx_entity_nonpoly));
-    DebugUtil.log('Non-poly chains:', data.pdbx_nonpoly_scheme.asym_id.toArray());
+    console.log('Non-poly entities:', Table.formatToString(data.pdbx_entity_nonpoly));
+    console.log('Non-poly chains:', data.pdbx_nonpoly_scheme.asym_id.toArray());
 
-    const only_identity_operation = createPdbxStructOperList(data.pdbx_struct_oper_list);
+    const updated_struct_oper_list = createPdbxStructOperList(structureOperations, data.pdbx_struct_oper_list);
+    console.log('Orig. struct oper list:', data.pdbx_struct_oper_list);
 
     return ModelSymmetry.fromData({
         symmetry: data.symmetry,
@@ -70,60 +74,110 @@ function tmDetSymmetryFromMmCif(model: Model, excludedChains: string[]) {
         atom_sites: data.atom_sites,
         pdbx_struct_assembly: data.pdbx_struct_assembly,
         pdbx_struct_assembly_gen: updated_pdbx_struct_assembly_gen,
-        pdbx_struct_oper_list: only_identity_operation
+        pdbx_struct_oper_list: updated_struct_oper_list
     });
 }
 
-function createPdbxStructAssemblyGen(pdbx_struct_assembly_gen: Table<mmCIF_Schema['pdbx_struct_assembly_gen']>,
+function createPdbxStructAssemblyGen(
+    structureOperations: StructureOperation[],
+    pdbx_struct_assembly_gen: Table<mmCIF_Schema['pdbx_struct_assembly_gen']>,
     excludedChains: string[]): Table<mmCIF_Schema['pdbx_struct_assembly_gen']> {
 
     const asym_id_list_column = createAsymIdColumn(
         pdbx_struct_assembly_gen, excludedChains
     );
+    const assembly_id: string[] = [];
+    const asym_id_list: string[][] = [];
+    const oper_expression: string[] = [];
+
+    // we create only one assembly - maybe in multiple rows
+    assembly_id.push("1");
+    asym_id_list.push(asym_id_list_column);
+    oper_expression.push("0"); // this is the basic membrane plane transformation
+
+    const chainMap = new Map<string, string[]>();
+    // collect each operator for each chain
+    structureOperations.slice(1).forEach(function (operation: StructureOperation) {
+        if (!chainMap.has(operation.chainId)) {
+            chainMap.set(operation.chainId, [ operation.id.toString() ]);
+        } else {
+            chainMap.get(operation.chainId)?.push(operation.id.toString());
+        }
+    });
+    // fill columns of table
+    chainMap.forEach(function(operators, chain) {
+        assembly_id.push("1");
+        asym_id_list.push([ chain ]);
+        oper_expression.push(operators.join(","));
+    });
+
 
     // create table with new column
     let updated_pdbx_struct_assembly_gen = Table.ofColumns(
         pdbx_struct_assembly_gen._schema,
         {
-            assembly_id: Column.ofStringArray([ '1' ]),
-            asym_id_list: asym_id_list_column,
-            //oper_expression: data.pdbx_struct_assembly_gen.oper_expression
-            // NOTE: we expect here pdbx_struct_assembly_gen has only one row
-            oper_expression: Column.ofStringArray([ '1' ])
+            assembly_id: Column.ofStringArray(assembly_id),
+            asym_id_list: Column.ofStringListArray(asym_id_list),
+            oper_expression: Column.ofStringArray(oper_expression)
         }
     );
-    DebugUtil.log('Orig. assembly_gen', Table.formatToString(pdbx_struct_assembly_gen));
-    DebugUtil.log('Updated assembly_gen', Table.formatToString(updated_pdbx_struct_assembly_gen));
+    console.log('Orig. assembly_gen', Table.formatToString(pdbx_struct_assembly_gen));
+    console.log('Updated assembly_gen', Table.formatToString(updated_pdbx_struct_assembly_gen));
 
     return updated_pdbx_struct_assembly_gen;
 }
 
-function createPdbxStructOperList(pdbx_struct_oper_list: Table<mmCIF_Schema['pdbx_struct_oper_list']>):
+function createPdbxStructOperList(
+    structureOperations: StructureOperation[],
+    pdbx_struct_oper_list: Table<mmCIF_Schema['pdbx_struct_oper_list']>):
     Table<mmCIF_Schema['pdbx_struct_oper_list']> {
 
+    const id: string[] = [];
+    const type: string[] = [];
+    const name: string[] = [];
+    const symmetry_operation: string[] = [];
+    const matrix: number[][] = [];
+    const vector: number[][] = [];
+
+    structureOperations.forEach(function (operation: StructureOperation) {
+        id.push(operation.id.toString());
+        type.push(".");
+        const operationName = (operation.id == 0)
+            ? "Membrane transformation as identity operation"
+            : `${operation.chainId} -> ${operation.newChainId}`;
+        name.push(operationName);
+        symmetry_operation.push(".");
+
+        const rotation: number[] = Mat3.toArray(operation.operator.rotation, [], 0);
+        const translation: number[] = Vec3.toArray(operation.operator.translation, [], 0);;
+        matrix.push(rotation);
+        vector.push(translation);
+    });
+
+
     let updated_pdbx_struct_oper_list = Table.ofColumns(
         pdbx_struct_oper_list._schema,
         {
-            id: Column.ofStringArray([ '1' ]),
+            id: Column.ofStringArray(id),
             type: Column.ofArray({
-                array: [ 'identity operation' ],
+                array: type,
                 schema: pdbx_struct_oper_list.type.schema
             }),
-            name: Column.ofStringArray([ '1_555' ]),
-            symmetry_operation: Column.ofStringArray([ 'x,y,z' ]),
+            name: Column.ofStringArray(name),
+            symmetry_operation: Column.ofStringArray(symmetry_operation),
             matrix:  Column.ofArray({
-                array: [[ 1, 0, 0, 0, 1, 0, 0, 0, 1 ]],
+                array: matrix,
                 schema: pdbx_struct_oper_list.matrix.schema
             }),
             vector: Column.ofArray({
-                array: [ [ 0, 0, 0 ] ],
+                array: vector,
                 schema: pdbx_struct_oper_list.vector.schema
             })
         }
     );
 
-    DebugUtil.log('Orig. pdbx_struct_oper_list', Table.formatToString(pdbx_struct_oper_list));
-    DebugUtil.log('Updated pdbx_struct_oper_list', Table.formatToString(updated_pdbx_struct_oper_list));
+    console.log('Orig. pdbx_struct_oper_list', Table.formatToString(pdbx_struct_oper_list));
+    console.log('Updated pdbx_struct_oper_list', Table.formatToString(updated_pdbx_struct_oper_list));
 
     return updated_pdbx_struct_oper_list;
 }
@@ -137,10 +191,10 @@ function createAsymIdColumn(pdbx_struct_assembly_gen: Table<mmCIF_Schema['pdbx_s
         asym_id_list = asym_id_list.concat(currentAsymIdList);
     }
     asym_id_list = minus(asym_id_list, excludedChains);
-    DebugUtil.log('Excluded chains:', excludedChains);
-    DebugUtil.log('Included chains:', asym_id_list);
+    console.log('Excluded chains:', excludedChains);
+    console.log('Included chains:', asym_id_list);
 
-    return Column.ofStringListArray([ asym_id_list ]);
+    return asym_id_list;
 }
 
 // difference of two string arrays (interpreted as sets)
@@ -156,3 +210,82 @@ function union(a: string[], b: string[]): string[] {
     b.forEach(item => a_set.add(item));
     return Array.from(a_set.values());
 }
+
+
+//////////////////////////////////////////////////////////////////////
+
+
+/*
+ * Construction of struct operators
+ */
+
+/**
+ * Type to contain operation properties.
+ */
+type StructureOperation = {
+    id: number,
+    chainId: string,
+    newChainId: string,
+    operator: {
+        rotation: Mat3,
+        translation: Vec3
+    }
+}
+
+function collectOperations(descriptor: PDBTMDescriptor): StructureOperation[] {
+
+    const operations: StructureOperation[] = [];
+    const annotations = descriptor.additional_entry_annotations;
+
+    const membraneTransformation = transformationForStateTransform(descriptor.additional_entry_annotations.membrane.transformation_matrix);
+    operations.push({
+        id: 0,
+        chainId: "Any chain with identity operation",
+        newChainId: ".",
+        operator: mat4ToRotationAndTranslation(membraneTransformation)
+    });
+
+    let operationId: number = 1;
+
+    if (annotations?.biomatrix?.matrix_list) {
+        annotations.biomatrix.matrix_list.forEach(function(mx) {
+            mx.apply_to_chain_list.forEach(function(chainPair) {
+                let id  = chainPair.chain_id;
+                let newId = chainPair.new_chain_id;
+                if (annotations.biomatrix.chain_deletes?.includes(newId)) {
+                    console.log(`${id} -> ${newId} transformation skipped due to delete rule`);
+                    return;
+                }
+                const mtx = transformationForStateTransform(mx.transformation_matrix);
+                const composedTransformation = Mat4.mul(Mat4(), membraneTransformation, mtx);
+
+                const operator: StructureOperation = {
+                    id: operationId,
+                    chainId: id,
+                    newChainId: newId,
+                    operator: mat4ToRotationAndTranslation(composedTransformation)
+                };
+                operations.push(operator);
+                operationId++;
+            });
+        });
+    }
+
+    return operations;
+}
+
+/**
+ * Convert Mat4 object to array representation of its 3x4 part.
+ * Rotation matrix 3x3 and translation vector 3x1.
+ *
+ * @param mat4 Mat4 object
+ * @returns Object with rotation matrix and translation vector
+ */
+function mat4ToRotationAndTranslation(mat4: Mat4) {
+    return {
+        rotation: Mat3.fromMat4(
+            Mat3.zero(), Mat4.extractRotation(Mat4.zero(), mat4)
+        ),
+        translation: Mat4.getTranslation(Vec3.zero(), mat4)
+    };
+}

src/TmFv3DApp/tmdet-extension/tmdet-color-theme.ts

@@ -212,6 +212,9 @@ function loadRegionColorsFromStyleSheets(prefix: string = 'ult_'): void {
 }
 
 export function updateSiteColors(side1: "Inside"|"Outside"|null): void {
+
+    console.log(`updateSiteColors: side1: ${side1}`);
+
     if (!side1) {
         console.error('updateSiteColors: side1 is undefined or null');
         return;