.gitlab-ci.yml

@@ -17,8 +17,8 @@ stages:
 .build:
   stage: build
   image: docker:24
-  needs: 
-    - format-pfam
+  # needs: 
+  #   - format-pfam
   variables:
     CONTEXT: "."
     DOCKERFILE: "Dockerfile"
@@ -56,6 +56,8 @@ get-pfam:
   artifacts:
     paths:
       - Pfam-A.hmm.dat
+  rules:
+    - if: $CI_COMMIT_BRANCH == "main"
 
 format-pfam:
   image: python:3.11
@@ -72,6 +74,8 @@ format-pfam:
   artifacts:
     paths:
       - content/_partials/_pfam-a-hmm.csv
+  rules:
+    - if: $CI_COMMIT_BRANCH == "main"    
 
 build:dev:
   extends: .build

components/Nav/PrevNext.vue

 <script setup lang="ts">
 const { surround } = useContent();
+const { mobile } = useDisplay();
 
 </script>
 <template>

components/PfamChips.vue

@@ -26,53 +26,42 @@ function constructPfamUrl(pfam: string) {
 }
 </script>
 <template>
-  <v-card flat class="d-flex justify-start align-center">
-    <template v-for="(pfam, index) in pfams" :key="pfam">
-      <v-chip
-        v-if="index < itemsToDisplay || itemsToDisplay < 0"
-        :href="constructPfamUrl(pfam)"
-        target="_blank"
-        color="info"
-        class="mr-1"
-      >
-        {{ pfam }}
-        <v-tooltip activator="parent" location="top">{{
-          pfamStore.get(pfam)?.DE ?? "none"
-        }}</v-tooltip></v-chip
-      >
+  <!-- class="d-inline-flex justify-start align-center" -->
+  <v-row>
+    <v-col>
+      <v-card flat color="transparent" density="compact" rounded="false">
+        <template v-for="(pfam, index) in pfams" :key="pfam">
+          <v-chip v-if="index < itemsToDisplay || itemsToDisplay < 0" :href="constructPfamUrl(pfam)" target="_blank"
+            color="info" class="mr-1 mb-1">
+            {{ pfam }}
+            <v-tooltip activator="parent" location="top">{{
+              pfamStore.get(pfam)?.DE ?? "none"
+            }}</v-tooltip></v-chip>
 
-      <template v-if="index === itemsToDisplay">
-        <v-chip
-          v-if="!show"
-          variant="text"
-          class="text-grey text-caption align-self-center px-1"
-          @click="show = !show"
-        >
-          (+{{ pfams.length - itemsToDisplay }} others)
-        </v-chip>
-      </template>
-    </template>
-    <template v-if="pfams.length > itemsToDisplay && show">
-      <template v-for="(pfam, index) in pfams" :key="pfam">
-        <v-chip
-          v-if="index >= itemsToDisplay"
-          :href="constructPfamUrl(pfam)"
-          target="_blank"
-          color="info"
-          class="mr-1"
-        >
-          {{ pfam }}
-          <v-tooltip activator="parent" location="top">{{
-            pfamStore.get(pfam)?.DE ?? "none"
-          }}</v-tooltip></v-chip
-        >
-      </template>
-    </template>
-    <v-btn
-      v-if="itemsToDisplay < pfams.length"
-      variant="text"
-      :icon="show ? 'mdi-chevron-up' : 'mdi-chevron-down'"
-      @click="show = !show"
-    ></v-btn>
-  </v-card>
+          <template v-if="index === itemsToDisplay">
+            <span>
+              <v-chip v-if="!show" variant="text" class="text-grey text-caption align-self-center px-1 "
+                @click="show = !show">
+                (+{{ pfams.length - itemsToDisplay }} others)
+              </v-chip>
+              <v-btn v-if="itemsToDisplay < pfams.length && !show" variant="text" :icon="'mdi-chevron-down'"
+                @click="show = !show"></v-btn>
+            </span>
+          </template>
+        </template>
+        <template v-if="pfams.length > itemsToDisplay && show">
+          <template v-for="(pfam, index) in pfams" :key="pfam">
+            <v-chip v-if="index >= itemsToDisplay" :href="constructPfamUrl(pfam)" target="_blank" color="info"
+              class="mr-1 mb-1">
+              {{ pfam }}
+              <v-tooltip activator="parent" location="top">{{
+                pfamStore.get(pfam)?.DE ?? "none"
+              }}</v-tooltip></v-chip>
+          </template>
+        </template>
+        <v-btn v-if="itemsToDisplay < pfams.length && show" variant="text" :icon="'mdi-chevron-up'"
+          @click="show = !show"></v-btn>
+      </v-card>
+    </v-col>
+  </v-row>
 </template>
\ No newline at end of file

components/content/ListSystems.vue

@@ -37,7 +37,7 @@ const { initPfam } = usePfamStore();
 initPfam();
 </script>
 <template>
-  <v-card>
+  <v-card >
     <v-toolbar density="compact">
       <v-toolbar-title>Defense Systems</v-toolbar-title>
 
@@ -58,14 +58,7 @@ initPfam();
       </template>
       <template #[`item.PFAM`]="{ item }">
 
-        <pfam-chips v-if="item.columns?.PFAM" :pfam-string="item.columns.PFAM"></pfam-chips>
-      </template>
-      <template #expanded-row="{ columns, item }">
-        <tr>
-          <td :colspan="columns.length" class="v-data-table__td v-data-table-column--align-start">
-            <pfam-chips :pfam-string="item.columns.PFAM" :items-to-display="-1"></pfam-chips>
-          </td>
-        </tr>
+        <pfam-chips v-if="item?.PFAM" :pfam-string="item.PFAM"></pfam-chips>
       </template>
     </v-data-table-virtual>
   </v-card>

components/content/MolstarPdbePlugin.vue

@@ -3,34 +3,66 @@ import { withTrailingSlash, withLeadingSlash, joinURL } from 'ufo'
 import { useRuntimeConfig, computed } from '#imports'
 export interface Props {
     height?: number
-    dataUrl: string
+    dataUrls?: string[]
+    dataUrl?: string
 }
+// const selectedPdb = ref('')
+const refinedDataUrls = computed(() => {
 
-const refinedDataUrl = computed(() => {
-    if (props.dataUrl?.startsWith('/') && !props.dataUrl.startsWith('//')) {
-        const _base = withLeadingSlash(withTrailingSlash(useRuntimeConfig().app.baseURL))
-        if (_base !== '/' && !props.dataUrl.startsWith(_base)) {
-            return joinURL(_base, props.dataUrl)
+    function refinedUrl(url: string) {
+        if (url?.startsWith('/') && !url.startsWith('//')) {
+            const _base = withLeadingSlash(withTrailingSlash(useRuntimeConfig().app.baseURL))
+            if (_base !== '/' && !url.startsWith(_base)) {
+                return joinURL(_base, url)
+            }
         }
+        return url
     }
-    return props.dataUrl
+
+    let urls: string[] = []
+
+    if (props?.dataUrls && props?.dataUrls?.length > 0) {
+        urls = [...props.dataUrls.map((dataUrl) => {
+            return refinedUrl(dataUrl)
+        })]
+    }
+    if (props?.dataUrl) {
+        urls = [...urls, refinedUrl(props.dataUrl)]
+    }
+    return urls
+
+
 })
 
+// const selectedPdb = ref(refinedDataUrls.value?.length > 0 ? refinedDataUrls.value[0] : null)
 const props = withDefaults(defineProps<Props>(), {
     height: 600,
 })
 
-const { width } = useDisplay()
+const { width, height } = useDisplay()
 
 const maxWidth = ref(1300)
 
-
+const dialog = ref(false)
+// const show = ref(false)
 
 const computedWidth = computed(() => {
     if (width > maxWidth) return maxWidth
     return width
 })
 
+const computedHeight = computed(() => {
+    return height.value - 250
+})
+
+function closeStructure() {
+    selectedPdb.value = null
+    dialog.value = false
+
+
+}
+
+
 useHead({
     link: [
         {
@@ -54,15 +86,62 @@ useHead({
     ]
 })
 
+const pdbeMolstarComponent = ref(null)
+// const selectedPdb = ref("/wiki/avs/AVAST_I,AVAST_I__Avs1A,0,V-plddts_85.07081.pdb")
+const selectedPdb = ref(null)
+
+watch(selectedPdb, (selectedPdb, prevSelectPdb) => {
+    if (selectedPdb !== null) {
+        dialog.value = true
+        if (pdbeMolstarComponent.value?.viewerInstance) {
+            const viewerInstance = pdbeMolstarComponent.value.viewerInstance
+
+            // show.value = true
+
+            const customData = { url: selectedPdb, format: "pdb", binary: false }
+
+            viewerInstance.visual.update({ customData })
+
+        }
+
+    }
+})
+
 </script>
 
 
 <template>
-    <v-sheet class="d-flex align-center justify-center flex-wrap text-center mx-auto px-4 my-3" height="500"
-        :max-width="1300" :width="computedWidth - 950" position="relative">
-        <pdbe-molstar :custom-data-url="refinedDataUrl" custom-data-format="pdb" hide-expand-icon="true"
-            hide-controls="true" landscape="true" sequence-panel></pdbe-molstar>
-    </v-sheet>
+    <v-row><v-col><v-select v-model="selectedPdb" label="Select PDB" :items="refinedDataUrls"
+                hide-details="auto"></v-select></v-col></v-row>
+
+    <v-row justify="center">
+        <v-dialog v-model="dialog" transition="dialog-bottom-transition" fullscreen :scrim="false">
+            <v-card flat :rounded="false">
+                <v-toolbar>
+                    <v-toolbar-title>Strucutures</v-toolbar-title>
+                    <v-select v-model="selectedPdb" label="Select PDB" :items="refinedDataUrls"
+                        hide-details="auto"></v-select>
+                    <v-spacer></v-spacer>
+
+                    <v-btn :disabled="!selectedPdb" icon="md:download" :href="selectedPdb"></v-btn>
+                    <v-btn icon @click="closeStructure">
+                        <v-icon>mdi-close</v-icon>
+                    </v-btn>
+
+                </v-toolbar>
+                <v-card-text>
+
+                    <v-sheet v-if="selectedPdb"
+                        class="d-flex align-center justify-center flex-wrap text-center mx-auto px-4 my-3"
+                        :height="computedHeight" :max-width="1300" :width="computedWidth" position="relative">
+                        <pdbe-molstar ref="pdbeMolstarComponent" hide-controls :custom-data-url="selectedPdb"
+                            custom-data-format="pdb"></pdbe-molstar>
+                    </v-sheet>
+                </v-card-text>
+
+            </v-card>
+        </v-dialog>
+    </v-row>
 </template>
 
 

composables/useFetchArticle.ts

@@ -89,14 +89,14 @@ export function useFetchArticle(doi: string) {
 
         if (store.articles.size === 0) {
             const localArticles = await queryContent('/_partials/_articles').where({ _partial: true }).findOne()
-            if (localArticles.body && store.articles.size <= 0) {
-                for (const article of localArticles.body) {
+            console.log(localArticles)
+            if (localArticles?.articles && store.articles.size <= 0) {
+                for (const article of localArticles.articles) {
                     store.add(article)
                 }
             }
         }
 
-
         if (store.articles.has(doi)) {
             srcArticle.value = store.articles.get(doi)
             return

content/3.defense-systems/abia.md

@@ -34,6 +34,33 @@ Among the 22k complete genomes of RefSeq, this system is present in 50 genomes (
 
 *Proportion of genome encoding the AbiA system for the 14 phyla with more than 50 genomes in the RefSeq database.* *Pie chart of the repartition of all the subsystems found in the RefSeq database.*
 
+## Structure
+
+### AbiA_large
+
+::molstar-pdbe-plugin
+---
+height: 700
+dataUrl: /abia/AbiA_large__AbiA_large-plddts_90.82916.pdb
+---
+::
+
+### AbiA_small
+
+::molstar-pdbe-plugin
+---
+height: 700
+dataUrl: /abia/AbiA_small,AbiA_small__AbiA_SLATT,0,DF-plddts_94.13374.pdb
+---
+::
+
+::molstar-pdbe-plugin
+---
+height: 700
+dataUrl: /abia/AbiA_small,AbiA_small__AbiA_small,0,DF-plddts_89.82347.pdb
+---
+::
+
 ## Experimental validation
 
 AbiA systems were experimentally validated using:

content/3.defense-systems/abib.md

@@ -29,6 +29,17 @@ Among the 22k complete genomes of RefSeq, this system is present in 13 genomes (
 
 *Proportion of genome encoding the AbiB system for the 14 phyla with more than 50 genomes in the RefSeq database.* 
 
+## Structure
+
+### AbiB
+
+::molstar-pdbe-plugin
+---
+height: 700
+dataUrl: /abib/AbiB__AbiB-plddts_74.5545.pdb
+---
+::
+
 ## Experimental validation
 
 AbiB systems were experimentally validated using:

content/3.defense-systems/abic.md

@@ -30,6 +30,17 @@ Among the 22k complete genomes of RefSeq, this system is present in 196 genomes
 
 *Proportion of genome encoding the AbiC system for the 14 phyla with more than 50 genomes in the RefSeq database.* 
 
+## Structure
+
+### AbiC
+
+::molstar-pdbe-plugin
+---
+height: 700
+dataUrl: /abic/AbiC__AbiC-plddts_83.80335.pdb
+---
+::
+
 ## Experimental validation
 
 AbiC systems were experimentally validated using:

content/3.defense-systems/abid.md

@@ -30,6 +30,17 @@ Among the 22k complete genomes of RefSeq, this system is present in 2748 genomes
 
 *Proportion of genome encoding the AbiD system for the 14 phyla with more than 50 genomes in the RefSeq database.* 
 
+## Structure
+
+### AbiD
+
+::molstar-pdbe-plugin
+---
+height: 700
+dataUrl: /abid/AbiD__AbiD-plddts_91.87407.pdb
+---
+::
+
 ## Experimental validation
 
 AbiD systems were experimentally validated using:

content/3.defense-systems/abie.md

@@ -42,6 +42,24 @@ Among the 22k complete genomes of RefSeq, this system is present in 3742 genomes
 
 *Proportion of genome encoding the AbiE system for the 14 phyla with more than 50 genomes in the RefSeq database.* 
 
+## Structure
+
+### AbiE
+
+::molstar-pdbe-plugin
+---
+height: 700
+dataUrl: /abie/AbiE,AbiE__AbiEi,0,V-plddts_85.81224.pdb
+---
+::
+
+::molstar-pdbe-plugin
+---
+height: 700
+dataUrl: /abie/AbiE,AbiE__AbiEii,0,V-plddts_90.73768.pdb
+---
+::
+
 ## Experimental validation
 
 AbiE systems were experimentally validated using:

content/3.defense-systems/abig.md

@@ -30,6 +30,24 @@ Among the 22k complete genomes of RefSeq, this system is present in 33 genomes (
 
 *Proportion of genome encoding the AbiG system for the 14 phyla with more than 50 genomes in the RefSeq database.* 
 
+## Structure
+
+### AbiG
+
+::molstar-pdbe-plugin
+---
+height: 700
+dataUrl: /abig/AbiG,AbiG__AbiGi,0,V-plddts_92.08021.pdb
+---
+::
+
+::molstar-pdbe-plugin
+---
+height: 700
+dataUrl: /abig/AbiG,AbiG__AbiGii,0,V-plddts_88.01846.pdb
+---
+::
+
 ## Experimental validation
 
 AbiG systems were experimentally validated using:

content/3.defense-systems/abih.md

@@ -32,6 +32,17 @@ Among the 22k complete genomes of RefSeq, this system is present in 1277 genomes
 
 *Proportion of genome encoding the AbiH system for the 14 phyla with more than 50 genomes in the RefSeq database.* 
 
+## Structure
+
+### AbiH
+
+::molstar-pdbe-plugin
+---
+height: 700
+dataUrl: /abih/AbiH__AbiH-plddts_91.3485.pdb
+---
+::
+
 ## Experimental validation
 
 AbiH systems were experimentally validated using:

content/3.defense-systems/abii.md

@@ -31,6 +31,17 @@ Among the 22k complete genomes of RefSeq, this system is present in 8 genomes (0
 
 *Proportion of genome encoding the AbiI system for the 14 phyla with more than 50 genomes in the RefSeq database.* 
 
+## Structure
+
+### AbiI
+
+::molstar-pdbe-plugin
+---
+height: 700
+dataUrl: /abii/AbiI__AbiI-plddts_90.31131.pdb
+---
+::
+
 ## Experimental validation
 
 AbiI systems were experimentally validated using:

content/3.defense-systems/abij.md

@@ -32,6 +32,17 @@ Among the 22k complete genomes of RefSeq, this system is present in 807 genomes
 
 *Proportion of genome encoding the AbiJ system for the 14 phyla with more than 50 genomes in the RefSeq database.* 
 
+## Structure
+
+### AbiJ
+
+::molstar-pdbe-plugin
+---
+height: 700
+dataUrl: /abij/AbiJ__AbiJ-plddts_85.12535.pdb
+---
+::
+
 ## Experimental validation
 
 AbiJ systems were experimentally validated using:

content/3.defense-systems/abik.md

@@ -32,6 +32,17 @@ Among the 22k complete genomes of RefSeq, this system is present in 107 genomes
 
 *Proportion of genome encoding the AbiK system for the 14 phyla with more than 50 genomes in the RefSeq database.* 
 
+## Structure
+
+### AbiK
+
+::molstar-pdbe-plugin
+---
+height: 700
+dataUrl: /abik/AbiK__AbiK-plddts_91.42521.pdb
+---
+::
+
 ## Experimental validation
 
 AbiK systems were experimentally validated using:

content/3.defense-systems/abil.md

@@ -32,6 +32,24 @@ Among the 22k complete genomes of RefSeq, this system is present in 783 genomes
 
 *Proportion of genome encoding the AbiL system for the 14 phyla with more than 50 genomes in the RefSeq database.* 
 
+## Structure
+
+### AbiL
+
+::molstar-pdbe-plugin
+---
+height: 700
+dataUrl: /abil/AbiL,AbiL__AbiLi,0,V-plddts_89.17612.pdb
+---
+::
+
+::molstar-pdbe-plugin
+---
+height: 700
+dataUrl: /abil/AbiL,AbiL__AbiLii,0,V-plddts_86.69766.pdb
+---
+::
+
 ## Experimental validation
 
 AbiL systems were experimentally validated using:

content/3.defense-systems/abin.md

@@ -31,6 +31,17 @@ Among the 22k complete genomes of RefSeq, this system is present in 167 genomes
 
 *Proportion of genome encoding the AbiN system for the 14 phyla with more than 50 genomes in the RefSeq database.* 
 
+## Structure
+
+### AbiN
+
+::molstar-pdbe-plugin
+---
+height: 700
+dataUrl: /abin/AbiN__AbiN-plddts_84.27216.pdb
+---
+::
+
 ## Experimental validation
 
 AbiN systems were experimentally validated using:

content/3.defense-systems/abio.md

@@ -32,6 +32,17 @@ Among the 22k complete genomes of RefSeq, this system is present in 109 genomes
 
 *Proportion of genome encoding the AbiO system for the 14 phyla with more than 50 genomes in the RefSeq database.* 
 
+## Structure
+
+### AbiO
+
+::molstar-pdbe-plugin
+---
+height: 700
+dataUrl: /abio/AbiO__AbiO-plddts_87.43501.pdb
+---
+::
+
 ## Experimental validation
 
 AbiO systems were experimentally validated using:

content/3.defense-systems/abip2.md

@@ -32,6 +32,17 @@ Among the 22k complete genomes of RefSeq, this system is present in 299 genomes
 
 *Proportion of genome encoding the AbiP2 system for the 14 phyla with more than 50 genomes in the RefSeq database.* 
 
+## Structure
+
+### AbiP2
+
+::molstar-pdbe-plugin
+---
+height: 700
+dataUrl: /abip2/AbiP2__AbiP2-plddts_93.08218.pdb
+---
+::
+
 ## Experimental validation
 
 AbiP2 systems were experimentally validated using: