- #1261 - initial implementation

Author: boriskovar-m2ms

docker-compose.dev.vector.yml

@@ -53,10 +53,10 @@ services:
       start_period: 10s
   web:
     container_name: web_dock
-    image: xchem/fragalysis-stack:latest
+    # image: xchem/fragalysis-stack:latest
     # image: alanbchristie/fragalysis-backend:1187.3
     # image: boriskovarm2ms/fragalysis-stack:experiment2
-    # image: kaliif/fragalysis-backend:latest
+    image: kaliif/fragalysis-backend:latest
     command: /bin/bash /code/launch-stack.sh
     volumes:
       - ../data/logs:/code/logs/

js/components/preview/molecule/observationCmpList.js

@@ -701,7 +701,7 @@ export const ObservationCmpList = memo(({ hideProjects }) => {
   let filteredLHSCompoundsList = useMemo(() => {
     const compounds = [];
     lhsCompoundsList.forEach(compound => {
-      const molsForCmp = joinedMoleculeLists.some(molecule => molecule.cmpd === compound.origId);
+      const molsForCmp = joinedMoleculeLists.some(molecule => molecule.cmpd === compound.compound);
       if (molsForCmp && compound.associatedObs.some(obs => joinedMoleculeLists.some(mol => mol.id === obs.id))) {
         compounds.push(compound);
       }
@@ -712,7 +712,7 @@ export const ObservationCmpList = memo(({ hideProjects }) => {
   useEffect(() => {
     if (isObservationDialogOpen && observationsForLHSCmp?.length > 0) {
       const cmpId = observationsForLHSCmp[0].cmpd;
-      const cmp = filteredLHSCompoundsList.find(c => c.origId === cmpId);
+      const cmp = filteredLHSCompoundsList.find(c => c.compound === cmpId);
       if (!cmp) {
         dispatch(setObservationsForLHSCmp([]));
         dispatch(setOpenObservationsDialog(false));
@@ -1214,9 +1214,6 @@ export const ObservationCmpList = memo(({ hideProjects }) => {
               >
                 {filteredLHSCompoundsList.map((data, index, array) => {
                   const molsForCmp = data.associatedObs;
-                  // const selected = allSelectedMolecules.some(
-                  //   molecule => molecule.cmpd === data.origId && molecule.canon_site_conf === data.canonSiteConf
-                  // );
                   const selected = allSelectedMolecules.some(molecule =>
                     data.associatedObs.some(obs => obs.id === molecule.id)
                   );

js/components/preview/tags/api/tagsApi.js

@@ -51,8 +51,8 @@ export const getCanonConformSites = async targetId => {
   });
 };
 
-export const getCompoundsLHS = async targetId => {
-  return api({ url: `${base_url}/api/cmpdimg/?target=${targetId}` }).then(response => {
+export const getPoses = async targetId => {
+  return api({ url: `${base_url}/api/poses/?target=${targetId}` }).then(response => {
     if (response?.data) {
       return response.data?.results;
     }

js/components/preview/tags/modal/tagEditor.js

@@ -144,12 +144,18 @@ export const TagEditor = memo(
     }
 
     const moleculesToEdit = moleculesToEditIds.map(id => dispatch(getMoleculeForId(id)));
-    let lhsCmp = null;
-    if (moleculesToEdit?.length > 0) {
-      const firstMolToEdit = moleculesToEdit[0];
-      const cmpId = firstMolToEdit.cmpd;
-      lhsCmp = lhsCompounds?.find(c => c.origId === cmpId && firstMolToEdit.canon_site_conf === c.canonSiteConf);
-    }
+    let poses = [];
+    moleculesToEdit?.forEach(m => {
+      const pose = lhsCompounds.find(p => p.site_observations.includes(m.id));
+      if (pose && !poses.find(p => p.id === pose.id)) {
+        poses.push(pose);
+      }
+    });
+    // if (moleculesToEdit?.length > 0) {
+    //   const firstMolToEdit = moleculesToEdit[0];
+    //   const cmpId = firstMolToEdit.cmpd;
+    //   lhsCmp = lhsCompounds?.find(c => c.compound === cmpId && firstMolToEdit.canon_site_conf === c.canonSiteConf);
+    // }
     moleculeTags = moleculeTags.sort(compareTagsAsc);
     const assignTagEditorOpen = useSelector(state => state.selectionReducers.tagEditorOpened);
 
@@ -206,7 +212,8 @@ export const TagEditor = memo(
           moleculesToEdit.forEach(m => {
             let newMol = { ...m };
             newMol.tags_set = newMol.tags_set.filter(id => id !== tag.id);
-            updateCmp(lhsCmp, newMol);
+            const pose = poses.find(p => p.site_observations.includes(m.id));
+            updateCmp(pose, newMol);
             dispatch(updateMoleculeInMolLists(newMol));
             const moleculeTag = getMoleculeTagForTag(moleculeTags, tag.id);
 
@@ -235,7 +242,8 @@ export const TagEditor = memo(
             if (!m.tags_set.some(id => id === tag.id)) {
               let newMol = { ...m };
               newMol.tags_set.push(tag.id);
-              updateCmp(lhsCmp, newMol);
+              const pose = poses.find(p => p.site_observations.includes(m.id));
+              updateCmp(pose, newMol);
               dispatch(updateMoleculeInMolLists(newMol));
               const moleculeTag = getMoleculeTagForTag(moleculeTags, tag.id);
               let mtObject = molTagObjects.find(mto => mto.tag === tag.tag);

js/components/preview/tags/redux/dispatchActions.js

@@ -39,7 +39,8 @@ import {
   getTagCategories,
   getCompoundsLHS,
   getCanonSites,
-  getCanonConformSites
+  getCanonConformSites,
+  getPoses
 } from '../api/tagsApi';
 import {
   getMoleculeTagForTag,
@@ -126,7 +127,7 @@ export const storeData = data => (dispatch, getState) => {
   dispatch(setTagSelectorData(categories, tags));
 
   let allMolecules = [];
-  data.molecules.forEach(mol => { });
+  data.molecules.forEach(mol => {});
 };
 
 export const updateTagProp = (tag, value, prop) => (dispatch, getState) => {
@@ -192,7 +193,7 @@ export const loadMoleculesAndTagsNew = targetId => async (dispatch, getState) =>
   }
   const tagCategories = await getTagCategories();
   // const canonSitesList = await getCanonSites(targetId);
-  const canonConformSitest = await getCanonConformSites(targetId);
+  // const canonConformSitest = await getCanonConformSites(targetId);
 
   const data = await getAllDataNew(targetId);
   let allMolecules = [];
@@ -231,59 +232,42 @@ export const loadMoleculesAndTagsNew = targetId => async (dispatch, getState) =>
   dispatch(setTagSelectorData(tagCategories, tags));
   dispatch(setAllDataLoaded(true));
 
-  return getCompoundsLHS(targetId).then(compounds => {
-    const expandedCompounds = [];
-    let newIdStart = Math.max(...compounds?.map(c => c.id)) + 1;
-    compounds?.forEach(c => {
-      const siteObs = allMolecules.filter(m => m.cmpd === c.id);
-      const canonConformSites = siteObs?.map(so => {
-        return {
-          smiles: so.smiles,
-          code: so.code,
-          canon_site_conf: so.canon_site_conf,
-          canon_site: canonConformSitest.find(ccf => ccf.id === so.canon_site_conf)?.canon_site
-        };
-      });
-      canonConformSites?.forEach(cs => {
-        let newObject = { ...c };
-
-        newObject['smiles'] = cs.smiles;
-        // newObject['code'] = `${cs.code}/${cs.canon_site}`;
-        newObject['code'] = `${cs.code}`;
-        newObject['origId'] = c.id;
-        newObject['id'] = newIdStart++;
-        newObject['canonSiteConf'] = cs.canon_site_conf;
-        newObject['canonSite'] = cs.canon_site;
-
-        const associatedObs = siteObs
-          .filter(
-            so =>
-              canonConformSitest.find(ccf => ccf.id === so.canon_site_conf)?.canon_site === newObject.canonSite &&
-              so.cmpd === c.id
-          )
-          .map(so => {
-            return {
-              ...so,
-              canon_site: canonConformSitest.find(ccf => ccf.id === so.canon_site_conf)?.canon_site
-            };
-          })
-          .sort((a, b) => {
-            if (a.code < b.code) {
-              return -1;
-            }
-            if (a.code > b.code) {
-              return 1;
-            }
-            return 0;
-          });
-        newObject['associatedObs'] = associatedObs;
+  return getPoses(targetId).then(poses => {
+    const modifiedPoses = [];
+    // let newIdStart = Math.max(...poses?.map(c => c.id)) + 1;
+    poses?.forEach(pose => {
+      const siteObs = allMolecules.filter(m => pose.site_observations.includes(m.id));
+      const firstObs = siteObs[0];
+      // const canonConformSites = siteObs?.map(so => {
+      //   return {
+      //     smiles: so.smiles,
+      //     code: so.code,
+      //     canon_site_conf: so.canon_site_conf,
+      //     canon_site: canonConformSitest.find(ccf => ccf.id === so.canon_site_conf)?.canon_site
+      //   };
+      // });
+      let newObject = { ...pose };
+      newObject['smiles'] = firstObs?.smiles;
+      newObject['code'] = `${pose.display_name}`;
+      // newObject['id'] = newIdStart++;
+      // newObject['origId'] = pose.id;
+      newObject['canonSiteConf'] = firstObs?.canon_site_conf;
+      newObject['canonSite'] = pose.canon_site;
 
-        if (!expandedCompounds.find(ec => ec.origId === newObject.origId && ec.canonSite === newObject.canonSite)) {
-          expandedCompounds.push(newObject);
+      const associatedObs = siteObs.sort((a, b) => {
+        if (a.code < b.code) {
+          return -1;
         }
+        if (a.code > b.code) {
+          return 1;
+        }
+        return 0;
       });
+      newObject['associatedObs'] = associatedObs;
+
+      modifiedPoses.push(newObject);
     });
-    expandedCompounds.sort((a, b) => {
+    modifiedPoses.sort((a, b) => {
       if (a.code < b.code) {
         return -1;
       }
@@ -292,6 +276,6 @@ export const loadMoleculesAndTagsNew = targetId => async (dispatch, getState) =>
       }
       return 0;
     });
-    dispatch(setLHSCompoundsLIst(expandedCompounds));
+    dispatch(setLHSCompoundsLIst(modifiedPoses));
   });
 };