caching

js/components/datasets/datasetMoleculeView.js

@@ -32,11 +32,12 @@ import {
   removeMoleculeFromCompoundsOfDatasetToBuy,
   setCrossReferenceCompoundName,
   setIsOpenCrossReferenceDialog,
-  setInspirationFragmentList
+  setInspirationFragmentList,
+  setInspirationMoleculeDataList
 } from './redux/actions';
 import { centerOnLigandByMoleculeID } from '../../reducers/ngl/dispatchActions';
 import { ArrowDownward, ArrowUpward, MyLocation } from '@material-ui/icons';
-import { isNumber, isString } from 'lodash';
+import { isString } from 'lodash';
 import { SvgTooltip } from '../common';
 import { OBJECT_TYPE } from '../nglView/constants';
 import { getRepresentationsByType } from '../nglView/generatingObjects';
@@ -265,6 +266,7 @@ export const DatasetMoleculeView = memo(
     const ref = useRef(null);
     const dispatch = useDispatch();
     const compoundsToBuyList = useSelector(state => state.datasetsReducers.compoundsToBuyDatasetMap[datasetID]);
+    const allInspirations = useSelector(state => state.datasetsReducers.allInspirations);
 
     const datasets = useSelector(state => state.datasetsReducers.datasets);
     const filteredScoreProperties = useSelector(state => state.datasetsReducers.filteredScoreProperties);
@@ -525,6 +527,16 @@ export const DatasetMoleculeView = memo(
       });
     };
 
+    const getInspirationsForMol = (datasetId, molId) => {
+      let inspirations = [];
+
+      if (allInspirations && allInspirations.hasOwnProperty(datasetId) && allInspirations[datasetId].hasOwnProperty(molId)) {
+        inspirations = allInspirations[datasetId][molId];
+      }
+
+      return inspirations;
+    };
+
     const handleClickOnDownArrow = () => {
       const refNext = ref.current.nextSibling;
       scrollToElement(refNext);
@@ -538,7 +550,9 @@ export const DatasetMoleculeView = memo(
 
       moveSelectedMoleculeSettings(nextItem, nextDatasetID);
       dispatch(moveSelectedMoleculeInspirationsSettings(data, nextItem));
-      dispatch(setInspirationFragmentList(nextItem.computed_inspirations));
+      const inspirations = getInspirationsForMol(datasetID, nextItem.id);
+      dispatch(setInspirationMoleculeDataList(inspirations));
+      // dispatch(setInspirationFragmentList(nextItem.computed_inspirations));
       dispatch(setCrossReferenceCompoundName(moleculeTitleNext));
       if (setRef && ref.current) {
         setRef(refNext);
@@ -560,7 +574,9 @@ export const DatasetMoleculeView = memo(
 
       moveSelectedMoleculeSettings(previousItem, previousDatasetID);
       dispatch(moveSelectedMoleculeInspirationsSettings(data, previousItem));
-      dispatch(setInspirationFragmentList(previousItem.computed_inspirations));
+      const inspirations = getInspirationsForMol(datasetID, previousItem.id);
+      dispatch(setInspirationMoleculeDataList(inspirations));
+      // dispatch(setInspirationFragmentList(previousItem.computed_inspirations));
       dispatch(setCrossReferenceCompoundName(moleculeTitlePrev));
       if (setRef && ref.current) {
         setRef(refPrevious);
@@ -752,7 +768,7 @@ export const DatasetMoleculeView = memo(
                             clickOnInspirations({
                               datasetID,
                               currentID,
-                              computed_inspirations: data && data.computed_inspirations
+                              computed_inspirations: getInspirationsForMol(datasetID, currentID)
                             })
                           );
                           if (setRef) {

js/components/datasets/inspirationDialog.js

@@ -24,11 +24,10 @@ import {
   removeDensity,
   removeVector
 } from '../preview/molecule/redux/dispatchActions';
-import { loadInspirationMoleculesDataList } from './redux/dispatchActions';
 import MoleculeView from '../preview/molecule/moleculeView';
 import { moleculeProperty } from '../preview/molecule/helperConstants';
 import { debounce } from 'lodash';
-import { setInspirationMoleculeDataList, setIsOpenInspirationDialog } from './redux/actions';
+import { setIsOpenInspirationDialog } from './redux/actions';
 import { Button } from '../common/Inputs/Button';
 import classNames from 'classnames';
 // import { useDisableUserInteraction } from '../helpers/useEnableUserInteracion';
@@ -37,7 +36,6 @@ import { NglContext } from '../nglView/nglProvider';
 import { VIEWS } from '../../constants/constants';
 import { Panel } from '../common/Surfaces/Panel';
 import { changeButtonClassname } from './helpers';
-import { getMoleculeList } from '../preview/molecule/redux/selectors';
 
 const useStyles = makeStyles(theme => ({
   paper: {
@@ -143,14 +141,10 @@ export const InspirationDialog = memo(
     const { getNglView } = useContext(NglContext);
     const stage = getNglView(VIEWS.MAJOR_VIEW) && getNglView(VIEWS.MAJOR_VIEW).stage;
 
-    const inspirationFragmentList = useSelector(state => state.datasetsReducers.inspirationFragmentList);
-
     const isLoadingInspirationListOfMolecules = useSelector(
       state => state.datasetsReducers.isLoadingInspirationListOfMolecules
     );
     const inspirationMoleculeDataList = useSelector(state => state.datasetsReducers.inspirationMoleculeDataList);
-    const allInspirationMoleculeDataList = useSelector(state => state.datasetsReducers.allInspirationMoleculeDataList);
-    const getJoinedMoleculeList = useSelector(state => getMoleculeList(state));
 
     const ligandList = useSelector(state => state.selectionReducers.fragmentDisplayList);
     const proteinList = useSelector(state => state.selectionReducers.proteinList);
@@ -162,16 +156,6 @@ export const InspirationDialog = memo(
     const dispatch = useDispatch();
     // const disableUserInteraction = useDisableUserInteraction();
 
-    useEffect(() => {
-      if (inspirationFragmentList && inspirationFragmentList.length > 0) {
-        dispatch(loadInspirationMoleculesDataList(inspirationFragmentList)).catch(error => {
-          throw new Error(error);
-        });
-      } else {
-        dispatch(setInspirationMoleculeDataList([]));
-      }
-    }, [dispatch, inspirationFragmentList]);
-
     let debouncedFn;
 
     const handleSearch = event => {
@@ -224,8 +208,6 @@ export const InspirationDialog = memo(
     const selectMoleculeSite = moleculeGroupSite => {};
 
     const removeOfAllSelectedTypes = () => {
-      let molecules = [...getJoinedMoleculeList, ...allInspirationMoleculeDataList];
-
       proteinList?.forEach(moleculeID => {
         let foundedMolecule = moleculeList?.find(mol => mol.id === moleculeID);
         foundedMolecule = foundedMolecule && Object.assign({ isInspiration: true }, foundedMolecule);

js/components/datasets/redux/actions.js

@@ -248,6 +248,11 @@ export const setInspirationMoleculeDataList = (moleculeList = []) => ({
   payload: moleculeList
 });
 
+export const setAllInspirations = (allInspirationsMap) => ({
+  type: constants.SET_ALL_INSPIRATIONS,
+  payload: allInspirationsMap
+});
+
 export const setAllInspirationMoleculeDataList = (moleculeList = []) => ({
   type: constants.SET_ALL_INSPIRATION_MOLECULE_DATA_LIST,
   payload: moleculeList

js/components/datasets/redux/constants.js

@@ -29,6 +29,7 @@ export const constants = {
   SET_INSPIRATION_LIST: prefix + 'SET_INSPIRATION_LIST',
   APPEND_INSPIRATION_LIST: prefix + 'APPEND_INSPIRATION_LIST',
   REMOVE_FROM_INSPIRATION_LIST: prefix + 'REMOVE_FROM_INSPIRATION_LIST',
+  SET_ALL_INSPIRATIONS: prefix + 'SET_ALL_INSPIRATIONS',
 
   APPEND_TO_SCORE_DATASET_MAP: prefix + 'APPEND_TO_SCORE_DATASET_MAP',
   REMOVE_FROM_SCORE_DATASET_MAP: prefix + 'REMOVE_FROM_SCORE_DATASET_MAP',

js/components/datasets/redux/dispatchActions.js

@@ -386,7 +386,7 @@ export const clearDatasetSettings = datasetID => dispatch => {
 
 export const clickOnInspirations = ({ datasetID, currentID, computed_inspirations = [] }) => dispatch => {
   dispatch(setInspirationList(datasetID, [currentID]));
-  dispatch(setInspirationFragmentList(computed_inspirations));
+  dispatch(setInspirationMoleculeDataList(computed_inspirations));
   dispatch(setIsOpenInspirationDialog(true));
 };
 

js/components/datasets/redux/reducer.js

@@ -30,6 +30,7 @@ export const INITIAL_STATE = {
   isLoadingInspirationListOfMolecules: false,
   inspirationMoleculeDataList: [],
   allInspirationMoleculeDataList: [],
+  allInspirations: {},
 
   // cross reference
   isOpenCrossReferenceDialog: false,
@@ -341,6 +342,9 @@ export const datasetsReducers = (state = INITIAL_STATE, action = {}) => {
       }
       return Object.assign({}, state, { inspirationFragmentList: [...diminishedInspirationFragmentList] });
 
+    case constants.SET_ALL_INSPIRATIONS:
+      return {...state, allInspirations: action.payload};
+
     case constants.APPEND_MOLECULE_TO_COMPOUNDS_TO_BUY_OF_DATASET:
       const setOfMolecules = new Set(state.compoundsToBuyDatasetMap[action.payload.datasetID]);
       setOfMolecules.add(action.payload.moleculeID);

js/components/nglView/renderingObjects.js

@@ -6,6 +6,7 @@ import {
   defaultFocus
 } from './generatingObjects';
 import { concatStructures, Selection, Shape, Matrix4 } from 'ngl';
+import {addToPdbCache} from '../../reducers/ngl/actions';
 
 const showSphere = ({ stage, input_dict, object_name, representations }) => {
   let colour = input_dict.colour;
@@ -80,18 +81,53 @@ const renderHitProtein = (ol, representations, orientationMatrix) => {
   return assignRepresentationArrayToComp(reprArray, comp);
 };
 
-const showHitProtein = ({ stage, input_dict, object_name, representations, orientationMatrix }) => {
+const loadPdbFile = (url) => {
+  return fetch(url).then(response => response.text()).then(str => {
+    return new Blob([str], { type: 'text/plain' })
+  });
+};
+
+const getNameOfPdb = (url) => {
+  const parts = url.split('/');
+  const last = parts[parts.length - 1];
+  return last;
+};
+
+const getPdb = (url) => (dispatch, getState) => {
+  const state = getState();
+
+  const pdbCache = state.nglReducers.pdbCache;
+  const pdbName = getNameOfPdb(url);
+  if (pdbCache.hasOwnProperty(pdbName)) {
+    return new Promise((resolve, reject) => {
+      resolve(pdbCache[pdbName])
+    });
+  } else {
+    return loadPdbFile(url).then(b => {
+      dispatch(addToPdbCache(pdbName, b));
+      return b;
+    });
+  };
+};
+
+const showHitProtein = ({ stage, input_dict, object_name, representations, orientationMatrix, dispatch }) => {
   let stringBlob = new Blob([input_dict.sdf_info], { type: 'text/plain' });
-  return Promise.all([
-    stage.loadFile(input_dict.prot_url, { ext: 'pdb', defaultAssembly: 'BU1' }),
-    stage.loadFile(stringBlob, { ext: 'sdf' }),
-    stage,
-    defaultFocus,
-    object_name,
-    input_dict.colour
-  ]).then(ol => renderHitProtein(ol, representations, orientationMatrix));
+
+  return dispatch(getPdb(input_dict.prot_url)).then(pdbBlob => {
+    return Promise.all([
+      stage.loadFile(pdbBlob, { ext: 'pdb', defaultAssembly: 'BU1' }),
+      stage.loadFile(stringBlob, { ext: 'sdf' }),
+      stage,
+      defaultFocus,
+      object_name,
+      input_dict.colour
+    ]);
+  }).then(ol => {
+    renderHitProtein(ol, representations, orientationMatrix)
+  });
 };
 
+
 const renderComplex = (ol, representations, orientationMatrix) => {
   let cs = concatStructures(
     ol[4],

js/components/preview/Preview.js

@@ -31,7 +31,7 @@ import { loadDatasetCompoundsWithScores, loadDataSets } from '../datasets/redux/
 import { SelectedCompoundList } from '../datasets/selectedCompoundsList';
 import { DatasetSelectorMenuButton } from '../datasets/datasetSelectorMenuButton';
 import ArrowDropDownIcon from '@material-ui/icons/ArrowDropDown';
-import { setMoleculeListIsLoading, replaceAllMoleculeLists } from '../datasets/redux/actions';
+import { setMoleculeListIsLoading, setAllInspirations } from '../datasets/redux/actions';
 
 const hitNavigatorWidth = 504;
 
@@ -130,19 +130,18 @@ const Preview = memo(({ isStateLoaded, hideProjects }) => {
       const keys = Object.keys(moleculeLists);
       keys.forEach(key => {
         let dataset = moleculeLists[key];
-        let mols = [];
+        let mols = {};
         dataset.forEach(dsMol => {
           let inspirations = [];
           dsMol.computed_inspirations.forEach(id => {
             let lhsMol = allMolsMap[id];
             inspirations.push(lhsMol);
           });
-          dsMol.inspirations = inspirations;
-          mols.push(dsMol);
+          mols[dsMol.id] = inspirations;
         });
         allDatasets[key] = mols;
       });
-      dispatch(replaceAllMoleculeLists(allDatasets));
+      dispatch(setAllInspirations(allDatasets));
     }
   }, [all_mol_lists, moleculeLists, isLoadingMoleculeList, linearizeMoleculesLists, dispatch]);
 

js/reducers/ngl/actions.js

@@ -1,6 +1,8 @@
 /**
  * Created by abradley on 03/03/2018.
  */
+import { constant } from 'lodash';
+import { constants } from '../selection/constants';
 import { CONSTANTS } from './constants';
 
 export const loadNglObject = (target, representations) => ({ type: CONSTANTS.LOAD_OBJECT, target, representations });
@@ -85,3 +87,8 @@ export const removeMoleculeOrientation = moleculeGroupID => ({
   type: CONSTANTS.REMOVE_MOLECULE_ORIENTATION,
   payload: moleculeGroupID
 });
+
+export const addToPdbCache = (name, cacheItem) => ({
+  type: CONSTANTS.ADD_TO_PDB_CACHE,
+  payload: {name: name, cacheItem: cacheItem}
+});

js/reducers/ngl/actions.test.js

@@ -297,35 +297,6 @@ describe("testing ngl reducer's actions", () => {
     expect(result.nglOrientations).toStrictEqual(defaultScene[SCENES.defaultScene].nglOrientations);
   });
 
-  /*
-  it('should reset current state to session scene', () => {
-    expect.hasAssertions();
-    const sessionScene = {
-      objectsInView: {
-        molecule_1: {
-          properties: [{ a: 'dfg' }],
-          representations: [
-            {
-              lastKnownID: 78904,
-              uuid: 9903,
-              other: 'fdjsdj'
-            },
-            {
-              lastKnownID: 178904,
-              uuid: 19903,
-              other: '1fdjsdj'
-            }
-          ]
-        }
-      },
-      nglOrientations: { a: [24, 566] }
-    };
-
-    let result = nglReducers(initialState, actions.setNglStateFromCurrentSnapshot(sessionScene));
-    expect(result.objectsInView).toStrictEqual(sessionScene.objectsInView);
-    expect(result.nglOrientations).toStrictEqual(sessionScene.nglOrientations);
-  });
-*/
   it('should remove all ngl view components', () => {
     expect.hasAssertions();
     let result = nglReducers(initialState, actions.removeAllNglComponents());

js/reducers/ngl/constants.js

@@ -22,7 +22,9 @@ export const CONSTANTS = {
 
   SET_MOLECULE_ORIENTATIONS: prefix + 'SET_MOLECULE_ORIENTATIONS',
   APPEND_MOLECULE_ORIENTATION: prefix + 'SET_MOLECULE_ORIENTATION',
-  REMOVE_MOLECULE_ORIENTATION: prefix + 'REMOVE_MOLECULE_ORIENTATION'
+  REMOVE_MOLECULE_ORIENTATION: prefix + 'REMOVE_MOLECULE_ORIENTATION',
+
+  ADD_TO_PDB_CACHE: prefix + 'ADD_TO_PDB_CACHE'
 };
 
 export const SCENES = {

js/reducers/ngl/dispatchActions.js

@@ -45,7 +45,8 @@ export const loadObject = ({
       object_name: versionFixedTarget.name,
       representations: previousRepresentations,
       orientationMatrix,
-      markAsRightSideLigand
+      markAsRightSideLigand,
+      dispatch
     })
       .then(representations => {
          dispatch(loadNglObject(versionFixedTarget, representations))

js/reducers/ngl/nglReducers.js

@@ -1,6 +1,5 @@
 import { BACKGROUND_COLOR, NGL_PARAMS } from '../../components/nglView/constants';
 import { CONSTANTS } from './constants';
-import NglView from '../../components/nglView/nglView';
 import { VIEWS } from '../../constants/constants';
 
 export const INITIAL_STATE = {
@@ -39,7 +38,8 @@ export const INITIAL_STATE = {
     [VIEWS.MAJOR_VIEW]: 0,
     [VIEWS.SUMMARY_VIEW]: 0
   },
-  moleculeOrientations: {}
+  moleculeOrientations: {},
+  pdbCache: {}
 };
 
 export default function nglReducers(state = INITIAL_STATE, action = {}) {
@@ -174,6 +174,11 @@ export default function nglReducers(state = INITIAL_STATE, action = {}) {
       }
       return Object.assign({}, state, { moleculeOrientations: diminishedMoleculeOrientations });
 
+    case CONSTANTS.ADD_TO_PDB_CACHE:
+      return {...state, pdbCache: {
+        ...state.pdbCache, [action.payload.name]: action.payload.cacheItem
+      }};
+
     default:
       return state;
   }