Merge remote-tracking branch 'remotes/origin/allfunctionality' into #486

js/components/preview/compounds/redux/dispatchActions.js

@@ -44,17 +44,17 @@ export const selectAllCompounds = () => (dispatch, getState) => {
     for (let index in currentVectorCompoundsFiltered[key]) {
       if (index !== 'vector') {
         for (let indexOfCompound in currentVectorCompoundsFiltered[key][index]) {
+          let compoundId = parseInt(indexOfCompound);
           var thisObj = {
             smiles: currentVectorCompoundsFiltered[key][index][indexOfCompound].end,
             vector: currentVectorCompoundsFiltered[key].vector.split('_')[0],
             mol: smiles,
             class: parseInt(currentCompoundClass),
-            indexOfCompound: indexOfCompound,
-            index: index
+            compoundId: compoundId
           };
           items.push(thisObj);
-          dispatch(appendToBuyList(thisObj, index, true));
-          dispatch(addSelectedCompoundClass(currentCompoundClass, parseInt(indexOfCompound)));
+          dispatch(appendToBuyList(thisObj, compoundId, true));
+          dispatch(addSelectedCompoundClass(currentCompoundClass, compoundId));
         }
       }
     }
@@ -215,28 +215,29 @@ export const handleClickOnCompound = ({ event, data, majorViewStage, index }) =>
   }
 };
 
-export const handleBuyList = ({ isSelected, data, index }) => async (dispatch, getState) => {
+export const handleBuyList = ({ isSelected, data, compoundId }) => (dispatch, getState) => {
   const state = getState();
   const currentCompoundClass = state.previewReducers.compounds.currentCompoundClass;
 
-  dispatch(setHighlightedCompoundId(index));
+  dispatch(setHighlightedCompoundId(compoundId));
 
   if (isSelected === false) {
-    await dispatch(removeSelectedCompoundClass(index));
-    dispatch(removeFromToBuyList(data, index, true));
+    dispatch(removeSelectedCompoundClass(compoundId));
+    dispatch(removeFromToBuyList(data, compoundId, true));
   } else {
-    await dispatch(addSelectedCompoundClass(currentCompoundClass, index));
-    dispatch(appendToBuyList(Object.assign({}, data, { class: currentCompoundClass }), index, true));
+    dispatch(addSelectedCompoundClass(currentCompoundClass, compoundId));
+    dispatch(appendToBuyList(Object.assign({}, data, { class: currentCompoundClass }), compoundId, true));
   }
 };
 
-export const handleBuyListAll = ({ isSelected, items, majorViewStage }) => async (dispatch, getState) => {
+export const handleBuyListAll = ({ isSelected, items, majorViewStage }) => (dispatch, getState) => {
   if (isSelected === false) {
     dispatch(clearCompounds(items, majorViewStage));
   } else {
     for (var item in items) {
-      dispatch(appendToBuyList(item, item.index, true));
-      dispatch(addSelectedCompoundClass(item.class, item.indexOfCompound));
+      let index = item.compoundId;
+      dispatch(appendToBuyList(item, index, true));
+      dispatch(addSelectedCompoundClass(item.class, index));
     }
     dispatch(appendToBuyListAll(items));
   }

js/components/preview/molecule/moleculeList.js

@@ -292,9 +292,6 @@ export const MoleculeList = memo(({ height, setFilterItemsHeight, filterItemsHei
     }
   }, [getJoinedMoleculeList, getAllMoleculeList, searchString]);
 
-  // Used for MoleculeListSortFilterDialog when using textSearch
-  const joinedMoleculeListsCopy = useMemo(() => [...joinedMoleculeLists], [joinedMoleculeLists]);
-
   const addSelectedMoleculesFromUnselectedSites = useCallback((joinedMoleculeLists, list) => {
     const result = [...joinedMoleculeLists];
     list?.forEach(moleculeID => {
@@ -451,6 +448,8 @@ export const MoleculeList = memo(({ height, setFilterItemsHeight, filterItemsHei
       setFilterItemsHeight(0);
     }
   }, [isActiveFilter, setFilterItemsHeight]);
+
+  const joinedMoleculeListsCopy = useMemo(() => [...joinedMoleculeLists], [joinedMoleculeLists]);
 
   useEffect(() => {
     if (!joinedMoleculeListsCopy.length) {

js/components/preview/viewerControls/displayControls/index.js

@@ -10,6 +10,8 @@ import {
   addComponentRepresentation,
   removeComponentRepresentation,
   updateComponentRepresentation,
+  updateComponentRepresentationVisibility,
+  updateComponentRepresentationVisibilityAll,
   changeComponentRepresentation
 } from '../../../../reducers/ngl/actions';
 import { deleteObject } from '../../../../reducers/ngl/dispatchActions';
@@ -52,7 +54,10 @@ export default memo(({ open, onClose }) => {
         const newVisibility = !r.getVisibility();
         // update in redux
         representation.params.visible = newVisibility;
-        dispatch(updateComponentRepresentation(parentKey, representation.uuid, representation));
+        dispatch(updateComponentRepresentation(parentKey, representation.uuid, representation, '', true));
+        dispatch(
+          updateComponentRepresentationVisibility(parentKey, representation.uuid, representation, newVisibility)
+        );
         // update in nglView
         r.setVisibility(newVisibility);
       }
@@ -121,7 +126,7 @@ export default memo(({ open, onClose }) => {
     const targetObject = objectsInView[parentKey];
     const nglView = getNglView(objectsInView[parentKey].display_div);
     const comp = nglView.stage.getComponentsByName(parentKey).first;
-    comp.eachRepresentation(representation => dispatch(removeComponentRepresentation(parentKey, representation)));
+    comp.eachRepresentation(representation => dispatch(removeComponentRepresentation(parentKey, representation, true)));
 
     // remove from nglReducer and selectionReducer
     dispatch(deleteObject(targetObject, nglView.stage, true));
@@ -144,10 +149,12 @@ export default memo(({ open, onClose }) => {
           // update in nglView
           r.setVisibility(newVisibility);
           // update in redux
-          dispatch(updateComponentRepresentation(parentKey, representation.uuid, representation));
+          dispatch(updateComponentRepresentation(parentKey, representation.uuid, representation, '', true));
         }
       });
     });
+
+    dispatch(updateComponentRepresentationVisibilityAll(parentKey, newVisibility));
   };
 
   const hasAllRepresentationVisibled = parentKey => {

js/components/preview/viewerControls/settingsControls.js

@@ -86,7 +86,7 @@ export const SettingControls = memo(({ open, onClose }) => {
               step={1}
               min={0}
               max={100}
-              onChange={(e, value) => dispatch(setNglClipFar(value, viewParams[NGL_PARAMS.cli], majorView))}
+              onChange={(e, value) => dispatch(setNglClipFar(value, viewParams[NGL_PARAMS.clipFar], majorView))}
             />
           </Grid>
         </Grid>

js/reducers/ngl/actions.js

@@ -10,12 +10,41 @@ export const deleteNglObject = target => ({
   target
 });
 
-export const updateComponentRepresentation = (objectInViewID, representationID, newRepresentation, change) => ({
+export const updateComponentRepresentationVisibility = (
+  objectInViewID,
+  representationID,
+  representation,
+  newVisibility,
+  skipTracking = false
+) => ({
+  type: CONSTANTS.UPDATE_COMPONENT_REPRESENTATION_VISIBILITY,
+  representationID,
+  representation,
+  newVisibility,
+  objectInViewID,
+  skipTracking
+});
+
+export const updateComponentRepresentationVisibilityAll = (objectInViewID, newVisibility, skipTracking = false) => ({
+  type: CONSTANTS.UPDATE_COMPONENT_REPRESENTATION_VISIBILITY_ALL,
+  newVisibility,
+  objectInViewID,
+  skipTracking
+});
+
+export const updateComponentRepresentation = (
+  objectInViewID,
+  representationID,
+  newRepresentation,
+  change,
+  skipTracking = false
+) => ({
   type: CONSTANTS.UPDATE_COMPONENT_REPRESENTATION,
   representationID,
   newRepresentation,
   objectInViewID,
-  change
+  change,
+  skipTracking
 });
 
 export const addComponentRepresentation = (objectInViewID, newRepresentation, skipTracking = false) => ({
@@ -51,7 +80,7 @@ export const setNglViewParams = (key, value, stage = undefined, objectId = undef
   };
 };
 
-export const setBackgroundColor = (color) => {
+export const setBackgroundColor = color => {
   return {
     type: CONSTANTS.SET_BACKGROUND_COLOR,
     payload: color

js/reducers/ngl/constants.js

@@ -4,6 +4,8 @@ export const CONSTANTS = {
   LOAD_OBJECT: prefix + 'LOAD_OBJECT',
   DELETE_OBJECT: prefix + 'DELETE_OBJECT',
   // NGL Component Representation
+  UPDATE_COMPONENT_REPRESENTATION_VISIBILITY: prefix + 'UPDATE_COMPONENT_REPRESENTATION_VISIBILITY',
+  UPDATE_COMPONENT_REPRESENTATION_VISIBILITY_ALL: prefix + 'UPDATE_COMPONENT_REPRESENTATION_VISIBILITY_ALL',
   UPDATE_COMPONENT_REPRESENTATION: prefix + 'UPDATE_COMPONENT_REPRESENTATION',
   REMOVE_COMPONENT_REPRESENTATION: prefix + 'REMOVE_COMPONENT_REPRESENTATION',
   ADD_COMPONENT_REPRESENTATION: prefix + 'ADD_COMPONENT_REPRESENTATION',

js/reducers/tracking/constants.js

@@ -49,6 +49,8 @@ export const actionType = {
   COMPOUND_SELECTED: 'COMPOUND_SELECTED',
   COMPOUND_DESELECTED: 'COMPOUND_DESELECTED',
   REPRESENTATION_UPDATED: 'REPRESENTATION_UPDATED',
+  REPRESENTATION_VISIBILITY_UPDATED: 'REPRESENTATION_VISIBILITY_UPDATED',
+  REPRESENTATION_VISIBILITY_ALL_UPDATED: 'REPRESENTATION_VISIBILITY_ALL_UPDATED',
   REPRESENTATION_ADDED: 'REPRESENTATION_ADDED',
   REPRESENTATION_REMOVED: 'REPRESENTATION_REMOVED',
   REPRESENTATION_CHANGED: 'REPRESENTATION_CHANGED',
@@ -76,11 +78,13 @@ export const actionDescription = {
   SELECTED: 'was selected',
   DESELECTED: 'was deselected',
   HIDDEN: 'hidden',
+  VISIBLE: 'visible',
   CANCELED: 'canceled',
   ADDED: 'was added',
   REMOVED: 'was removed',
   CHANGED: 'was changed',
   UPDATED: 'was updated',
+  VISIBILITY: 'visiblity',
   TO_SHOPPING_CART: 'to shopping cart',
   FROM_SHOPPING_CART: 'from shopping cart',
   LIGAND: 'Ligand',
@@ -94,8 +98,7 @@ export const actionDescription = {
   TARGET: 'Target',
   ALL: 'All',
   LIGANDS: 'Ligands',
-  SIDECHAINS: 'Sidechains',
-  INTERACTIONS: 'Interactions'
+  SIDECHAINS: 'Sidechains'
 };
 
 export const actionObjectType = {