Merge pull request #151 from m2ms/#209

#209

js/components/nglView/redux/dispatchActions.js

@@ -60,6 +60,7 @@ export const toggleMoleculeGroup = (molGroupId, summaryViewStage, majorViewStage
     dispatch(
       clearAfterDeselectingMoleculeGroup({
         molGroupId,
+        currentMolGroup,
         majorViewStage
       })
     );

js/components/nglView/renderingObjects.js

@@ -35,7 +35,7 @@ const showMol = (stage, input_dict, object_name, representations, orientationMat
 
     if (orientationMatrix) {
       stage.viewerControls.orient(orientationMatrix);
-    } else {
+    } else if (orientationMatrix === undefined) {
       comp.autoView('ligand');
     }
     return assignRepresentationArrayToComp(reprArray, comp);
@@ -72,11 +72,11 @@ const renderComplex = (ol, representations, orientationMatrix) => {
   const reprArray = representations || createRepresentationsArray([repr2, repr3]);
   if (orientationMatrix) {
     stage.viewerControls.orient(orientationMatrix);
-  } else {
+  } else if (orientationMatrix === undefined) {
     comp.autoView('ligand');
+    //TODO setFocus should be in condition
+    comp.stage.setFocus(focus_let_temp);
   }
-  //TODO setFocus should be in condition
-  comp.stage.setFocus(focus_let_temp);
 
   return assignRepresentationArrayToComp(reprArray, comp);
 };
@@ -124,7 +124,7 @@ const showEvent = (stage, input_dict, object_name, representations, orientationM
 
         if (orientationMatrix) {
           stage.viewerControls.orient(orientationMatrix);
-        } else {
+        } else if (orientationMatrix === undefined) {
           comp.autoView('LIG');
         }
 
@@ -173,7 +173,7 @@ const showCylinder = (stage, input_dict, object_name, representations, orientati
   let comp = stage.addComponentFromObject(shape);
   if (orientationMatrix) {
     stage.viewerControls.orient(orientationMatrix);
-  } else {
+  } else if (orientationMatrix === undefined) {
     comp.autoView();
   }
   const reprArray =
@@ -196,7 +196,7 @@ const showArrow = (stage, input_dict, object_name, representations, orientationM
   let comp = stage.addComponentFromObject(shape);
   if (orientationMatrix) {
     stage.viewerControls.orient(orientationMatrix);
-  } else {
+  } else if (orientationMatrix === undefined) {
     comp.autoView();
   }
 
@@ -213,7 +213,7 @@ const showProtein = (stage, input_dict, object_name, representations, orientatio
 
     if (orientationMatrix) {
       stage.viewerControls.orient(orientationMatrix);
-    } else {
+    } else if (orientationMatrix === undefined) {
       comp.autoView();
     }
     return Promise.resolve(assignRepresentationArrayToComp(reprArray, comp));

js/components/preview/molecule/redux/dispatchActions.js

@@ -27,7 +27,7 @@ import { VIEWS } from '../../../../constants/constants';
 import { api } from '../../../../utils/api';
 import { selectVectorAndResetCompounds } from '../../../../reducers/selection/dispatchActions';
 import { colourList } from '../moleculeView';
-import { setMoleculeOrientation } from '../../../../reducers/ngl/actions';
+import { appendMoleculeOrientation } from '../../../../reducers/ngl/actions';
 import { setCompoundImage } from '../../summary/redux/actions';
 import { noCompoundImage } from '../../summary/redux/reducer';
 
@@ -79,7 +79,6 @@ const getViewUrl = (get_view, data) => {
 const handleVector = (json, stage, data) => (dispatch, getState) => {
   const state = getState();
   const to_select = state.selectionReducers.to_select;
-  const orientationMatrix = state.nglReducers.moleculeOrientations[data.site];
   var objList = generateObjectList(json['3d'], data);
   dispatch(setVectorList(objList));
   // loading vector objects
@@ -89,7 +88,7 @@ const handleVector = (json, stage, data) => (dispatch, getState) => {
         Object.assign({ display_div: VIEWS.MAJOR_VIEW }, getVectorWithColorByCountOfCompounds(item, to_select)),
         stage,
         undefined,
-        orientationMatrix
+        null
       )
     )
   );
@@ -129,15 +128,13 @@ export const removeVector = (stage, data) => (dispatch, getState) => {
   dispatch(removeFromVectorOnList(generateMoleculeId(data)));
 };
 
-export const addComplex = (stage, data, colourToggle) => (dispatch, getState) => {
-  const state = getState();
-  const orientationMatrix = state.nglReducers.moleculeOrientations[data.site];
+export const addComplex = (stage, data, colourToggle) => dispatch => {
   dispatch(
     loadObject(
       Object.assign({ display_div: VIEWS.MAJOR_VIEW }, generateComplexObject(data, colourToggle, base_url)),
       stage,
       undefined,
-      orientationMatrix
+      null
     )
   ).finally(() => {
     const currentOrientation = stage.viewerControls.getOrientation();
@@ -164,13 +161,13 @@ export const addLigand = (stage, data, colourToggle) => (dispatch, getState) =>
       Object.assign({ display_div: VIEWS.MAJOR_VIEW }, generateMoleculeObject(data, colourToggle)),
       stage,
       undefined,
-      orientationMatrix
+      orientationMatrix !== undefined ? null : undefined
     )
   ).finally(() => {
     const currentOrientation = stage.viewerControls.getOrientation();
     dispatch(setOrientation(VIEWS.MAJOR_VIEW, currentOrientation));
 
-    dispatch(setMoleculeOrientation(data.site, currentOrientation));
+    dispatch(appendMoleculeOrientation(data.site, currentOrientation));
   });
   dispatch(appendFragmentDisplayList(generateMoleculeId(data)));
 };
@@ -180,7 +177,7 @@ export const removeLigand = (stage, data) => dispatch => {
   dispatch(removeFromFragmentDisplayList(generateMoleculeId(data)));
 };
 
-export const selectFirstMolecule = (majorView, moleculeList) => (dispatch, getState) => {
+export const selectFirstMolecule = (majorView, moleculeList) => dispatch => {
   if (moleculeList) {
     const firstMolecule = moleculeList[0];
     dispatch(addLigand(majorView, firstMolecule, colourList[0]));

js/components/preview/moleculeGroups/redux/dispatchActions.js

@@ -8,6 +8,9 @@ import {
 } from '../../../../reducers/ngl/dispatchActions';
 import { getJoinedMoleculeList } from '../../molecule/redux/selectors';
 import {
+  removeFromComplexList,
+  removeFromFragmentDisplayList,
+  removeFromVectorOnList,
   resetSelectionState,
   setComplexList,
   setFilterSettings,
@@ -17,15 +20,18 @@ import {
   setVectorList,
   setVectorOnList
 } from '../../../../reducers/selection/actions';
-import { setCountOfRemainingMoleculeGroups } from '../../../../reducers/ngl/actions';
+import { removeMoleculeOrientation, setCountOfRemainingMoleculeGroups } from '../../../../reducers/ngl/actions';
 import { setMolGroupList, setMolGroupOn } from '../../../../reducers/api/actions';
 import { getUrl, loadFromServer } from '../../../../utils/genericList';
 import { OBJECT_TYPE } from '../../../nglView/constants';
 import { SCENES } from '../../../../reducers/ngl/constants';
 import { setSortDialogOpen } from '../../molecule/redux/actions';
 import { resetCurrentCompoundsSettings } from '../../compounds/redux/actions';
 
-export const clearAfterDeselectingMoleculeGroup = ({ molGroupId, majorViewStage }) => (dispatch, getState) => {
+export const clearAfterDeselectingMoleculeGroup = ({ molGroupId, currentMolGroup, majorViewStage }) => (
+  dispatch,
+  getState
+) => {
   dispatch(setObjectSelection([molGroupId]));
 
   let site;
@@ -63,6 +69,20 @@ export const clearAfterDeselectingMoleculeGroup = ({ molGroupId, majorViewStage
     });
 
   dispatch(setObjectSelection(undefined));
+
+  // remove molecule orientation for given site
+  dispatch(removeMoleculeOrientation(site));
+
+  // remove all selected ALCV of given site
+  currentMolGroup.mol_id.forEach(moleculeID => {
+    // remove Ligand, Complex, Vectors from selection
+    //Ligand
+    dispatch(removeFromFragmentDisplayList({ id: moleculeID }));
+    // Complex
+    dispatch(removeFromComplexList({ id: moleculeID }));
+    // Vectors
+    dispatch(removeFromVectorOnList({ id: moleculeID }));
+  });
 };
 
 export const saveMoleculeGroupsToNglView = (molGroupList, stage) => dispatch => {
@@ -200,6 +220,7 @@ export const onSelectMoleculeGroup = ({ moleculeGroup, stageSummaryView, majorVi
     dispatch(
       clearAfterDeselectingMoleculeGroup({
         molGroupId: moleculeGroup.id,
+        currentMolGroup,
         majorViewStage
       })
     );

js/reducers/ngl/actions.js

@@ -75,7 +75,17 @@ export const decrementCountOfPendingNglObjects = () => ({
   type: CONSTANTS.DECREMENT_COUNT_OF_PENDING_NGL_OBJECTS
 });
 
-export const setMoleculeOrientation = (moleculeGroupID, orientation) => ({
-  type: CONSTANTS.SET_MOLECULE_ORIENTATION,
+export const appendMoleculeOrientation = (moleculeGroupID, orientation) => ({
+  type: CONSTANTS.APPEND_MOLECULE_ORIENTATION,
   payload: { moleculeGroupID, orientation }
 });
+
+export const setMoleculeOrientations = moleculeOrientations => ({
+  type: CONSTANTS.SET_MOLECULE_ORIENTATIONS,
+  payload: moleculeOrientations
+});
+
+export const removeMoleculeOrientation = moleculeGroupID => ({
+  type: CONSTANTS.REMOVE_MOLECULE_ORIENTATION,
+  payload: moleculeGroupID
+});

js/reducers/ngl/constants.js

@@ -23,7 +23,9 @@ export const CONSTANTS = {
   INCREMENT_COUNT_OF_PENDING_NGL_OBJECTS: prefix + 'INCREMENT_COUNT_OF_PENDING_NGL_OBJECTS',
   DECREMENT_COUNT_OF_PENDING_NGL_OBJECTS: prefix + 'DECREMENT_COUNT_OF_PENDING_NGL_OBJECTS',
 
-  SET_MOLECULE_ORIENTATION: prefix + 'SET_MOLECULE_ORIENTATION'
+  SET_MOLECULE_ORIENTATIONS: prefix + 'SET_MOLECULE_ORIENTATIONS',
+  APPEND_MOLECULE_ORIENTATION: prefix + 'SET_MOLECULE_ORIENTATION',
+  REMOVE_MOLECULE_ORIENTATION: prefix + 'REMOVE_MOLECULE_ORIENTATION'
 };
 
 export const SCENES = {

js/reducers/ngl/dispatchActions.js

@@ -7,6 +7,7 @@ import {
   resetStateToDefaultScene,
   resetStateToSessionScene,
   saveCurrentStateAsDefaultScene,
+  setMoleculeOrientations,
   setNglOrientation,
   setNglViewParams,
   setProteinLoadingState
@@ -141,5 +142,10 @@ export const reloadNglViewFromScene = (stage, display_div, scene, sessionData) =
     if (newOrientation) {
       stage.viewerControls.orient(newOrientation.elements);
     }
+
+    // set molecule orientations
+    if (currentScene.moleculeOrientations) {
+      dispatch(setMoleculeOrientations(currentScene.moleculeOrientations));
+    }
   });
 };

js/reducers/ngl/nglReducers.js

@@ -196,14 +196,24 @@ export default function nglReducers(state = INITIAL_STATE, action = {}) {
     case CONSTANTS.INCREMENT_COUNT_OF_PENDING_NGL_OBJECTS:
       return Object.assign({}, state, { countOfPendingNglObjects: state.countOfPendingNglObjects + 1 });
 
-    case CONSTANTS.SET_MOLECULE_ORIENTATION:
+    case CONSTANTS.SET_MOLECULE_ORIENTATIONS:
+      return Object.assign({}, state, { moleculeOrientations: action.payload });
+
+    case CONSTANTS.APPEND_MOLECULE_ORIENTATION:
       const newMoleculeOrientations = state.moleculeOrientations;
 
       if (newMoleculeOrientations[action.payload.moleculeGroupID] === undefined) {
         newMoleculeOrientations[action.payload.moleculeGroupID] = action.payload.orientation;
       }
       return Object.assign({}, state, { moleculeOrientations: newMoleculeOrientations });
 
+    case CONSTANTS.REMOVE_MOLECULE_ORIENTATION:
+      const diminishedMoleculeOrientations = state.moleculeOrientations;
+      if (diminishedMoleculeOrientations[action.payload] !== undefined) {
+        delete diminishedMoleculeOrientations[action.payload];
+      }
+      return Object.assign({}, state, { moleculeOrientations: diminishedMoleculeOrientations });
+
     default:
       return state;
   }

package.json

@@ -1,6 +1,6 @@
 {
   "name": "fragalysis-frontend",
-  "version": "0.4.0",
+  "version": "0.4.2",
   "description": "Frontend for fragalysis",
   "main": "webpack.config.js",
   "scripts": {