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Commit 0f2f8286 authored by Remi PLANEL's avatar Remi PLANEL
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remove icon warning when no struct

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Pipeline #119173 passed
Stage: delete-release
Stage: build-df-cli
Stage: lint
Stage: get-data
Stage: deploy-meilisearch
Stage: update-meilisearch-indexes
Stage: get-meili-key
Stage: build
Stage: build-wiki
Stage: deploy
Stage: load-website
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.gitlab-ci.yml
+ 2
− 2
View file @ 0f2f8286
......@@ -441,8 +441,8 @@ load-website:prod:
- kubectl --namespace ${NAMESPACE} cp .output/public/ ${WIKI_POD}:/website
- kubectl --namespace ${NAMESPACE} cp scripts/copy-structure-data.sh ${WIKI_POD}:/structure-data/sanitized-dump
- kubectl --namespace ${NAMESPACE} exec ${WIKI_POD} -- bash /structure-data/sanitized-dump/copy-structure-data.sh
- kubectl --namespace ${NAMESPACE} exec ${WIKI_POD} -- bash -c 'cd /structure-data/sanitized-dump && find * -type d -exec sh -c "for d in $@; do (cd /usr/share/nginx/html/$d; cp --archive --recursive --symbolic-link /structure-data/sanitized-dump/$d/* .) done" argv0 {} +'
- kubectl --namespace ${NAMESPACE} exec ${WIKI_POD} -- bash -c 'cd /structure-data/sanitized-dump && bash copy-structure-data.sh'
# - kubectl --namespace ${NAMESPACE} exec ${WIKI_POD} -- bash -c 'cd /structure-data/sanitized-dump && find * -type d -exec sh -c "for d in $@; do (cd /usr/share/nginx/html/$d; cp --archive --recursive --symbolic-link /structure-data/sanitized-dump/$d/* .) done" argv0 {} +'
......
components/content/MolstarPdbePlugin.vue
+ 93
− 92
View file @ 0f2f8286
......@@ -157,102 +157,103 @@ const moleculeFormat: Ref<string> = ref("pdb")
<template>
<span class="d-flex flex-wrap align-center justify-center">
<template v-if="uniq">
<v-row>
<template v-if="uniq">
<v-btn size="x-small" variant="tonal" icon="md:visibility" @click="setSelectedPdbToFirst()"></v-btn>
<v-btn :disabled="!structureToDownload" size="x-small" variant="tonal" icon="md:download" class="ml-1"
:href="structureToDownload"></v-btn>
</template>
<v-select v-else v-model="selectedPdb" label="Select PDB" :items="refinedDataUrls" hide-details="auto">
</v-select>
<v-btn size="x-small" variant="tonal" icon="md:visibility" @click="setSelectedPdbToFirst()"></v-btn>
<v-btn :disabled="!structureToDownload" size="x-small" variant="tonal" icon="md:download" class="ml-1"
:href="structureToDownload"></v-btn>
</v-row>
<v-dialog v-model="dialog" transition="dialog-bottom-transition" fullscreen :scrim="false">
<v-card flat :rounded="false">
<v-toolbar>
<v-toolbar-title>Structures</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="structureToDownload"></v-btn>
<v-btn icon @click="closeStructure">
<v-icon>mdi-close</v-icon>
</v-btn>
</v-toolbar>
<v-card-text>
<v-row>
<v-col :cols="mobile ? 12 : 'auto'">
<v-sheet v-if="selectedPdb"
class="d-flex align-center justify-center flex-wrap text-center mx-auto px-4 my-3"
:height="computedHeight" :width="computedWidth" position="relative">
<pdbe-molstar ref="pdbeMolstarComponent" hide-controls="true" landscape="true"
:custom-data-url="selectedPdb" alphafold-view="true"
:custom-data-format="moleculeFormat"></pdbe-molstar>
</v-sheet>
</v-col>
<v-col :cols="mobile ? 12 : undefined">
<v-img :src="selectedPaePath"></v-img>
<!-- <PlotFigure v-if="sanitizedPaeData?.length > 0 && paeError === null" defer
</template>
<v-row v-else>
<span class="d-flex flex-wrap align-center justify-center">
<v-select v-model="selectedPdb" label="Select PDB" :items="refinedDataUrls" hide-details="auto">
</v-select>
</span>
</v-row>
<v-dialog v-model="dialog" transition="dialog-bottom-transition" fullscreen :scrim="false">
<v-card flat :rounded="false">
<v-toolbar>
<v-toolbar-title>Structures</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="structureToDownload"></v-btn>
<v-btn icon @click="closeStructure">
<v-icon>mdi-close</v-icon>
</v-btn>
</v-toolbar>
<v-card-text>
<v-row>
<v-col :cols="mobile ? 12 : 'auto'">
<v-sheet v-if="selectedPdb"
class="d-flex align-center justify-center flex-wrap text-center mx-auto px-4 my-3"
:height="computedHeight" :width="computedWidth" position="relative">
<pdbe-molstar ref="pdbeMolstarComponent" hide-controls="true" landscape="true"
:custom-data-url="selectedPdb" alphafold-view="true"
:custom-data-format="moleculeFormat"></pdbe-molstar>
</v-sheet>
</v-col>
<v-col :cols="mobile ? 12 : undefined">
<v-img :src="selectedPaePath"></v-img>
<!-- <PlotFigure v-if="sanitizedPaeData?.length > 0 && paeError === null" defer
:options="plotPaeOptions"></PlotFigure>
<v-alert v-else type="warning" variant="tonal">{{ paeError }}</v-alert> -->
<v-card flat color="transparent">
<v-card-title>Model Confidence</v-card-title>
<v-card-text>
AlphaFold produces a per-residue model
confidence score (pLDDT) between 0 and 100. Some regions below 50 pLDDT may be
unstructured
in isolation.
</v-card-text>
<v-list>
<v-list-item>
<template #prepend>
<div class="legendColor mr-2" style="background-color: rgb(0, 83, 214);">
&nbsp;</div>
</template>
<v-list-item-title>
Very high (pLDDT > 90)
</v-list-item-title>
</v-list-item>
<v-list-item>
<template #prepend>
<div class="legendColor mr-2" style="background-color: rgb(101, 203, 243);">
&nbsp;</div>
</template>
<v-list-item-title>
High (90 > pLDDT > 70)
</v-list-item-title>
</v-list-item>
<v-list-item>
<template #prepend>
<div class="legendColor mr-2" style="background-color: rgb(255, 219, 19);">
&nbsp;</div>
</template>
<v-list-item-title>
Low (70 > pLDDT > 50) </v-list-item-title>
</v-list-item>
<v-list-item>
<template #prepend>
<div class="legendColor mr-2" style="background-color: rgb(255, 125, 69);">
&nbsp;</div>
</template>
<v-list-item-title>
Very low (pLDDT &lt; 50) </v-list-item-title>
</v-list-item>
</v-list>
</v-card>
</v-col>
</v-row>
</v-card-text>
</v-card>
</v-dialog>
</span>
<v-card flat color="transparent">
<v-card-title>Model Confidence</v-card-title>
<v-card-text>
AlphaFold produces a per-residue model
confidence score (pLDDT) between 0 and 100. Some regions below 50 pLDDT may be
unstructured
in isolation.
</v-card-text>
<v-list>
<v-list-item>
<template #prepend>
<div class="legendColor mr-2" style="background-color: rgb(0, 83, 214);">
&nbsp;</div>
</template>
<v-list-item-title>
Very high (pLDDT > 90)
</v-list-item-title>
</v-list-item>
<v-list-item>
<template #prepend>
<div class="legendColor mr-2" style="background-color: rgb(101, 203, 243);">
&nbsp;</div>
</template>
<v-list-item-title>
High (90 > pLDDT > 70)
</v-list-item-title>
</v-list-item>
<v-list-item>
<template #prepend>
<div class="legendColor mr-2" style="background-color: rgb(255, 219, 19);">
&nbsp;</div>
</template>
<v-list-item-title>
Low (70 > pLDDT > 50) </v-list-item-title>
</v-list-item>
<v-list-item>
<template #prepend>
<div class="legendColor mr-2" style="background-color: rgb(255, 125, 69);">
&nbsp;</div>
</template>
<v-list-item-title>
Very low (pLDDT &lt; 50) </v-list-item-title>
</v-list-item>
</v-list>
</v-card>
</v-col>
</v-row>
</v-card-text>
</v-card>
</v-dialog>
</template>
......
components/content/StructureDb.vue
+ 3
− 3
View file @ 0f2f8286
......@@ -140,9 +140,9 @@ const plddtDistribution = computed(() => {
<MolstarPdbePlugin v-if="item?.pdb && item.pdb !== 'na'"
:data-urls="[`/${toSystemName(item.system)}/${pdbNameToCif(item.pdb)}`]" uniq>
</MolstarPdbePlugin>
<span v-else class="d-flex flex-wrap align-center justify-center">
<v-icon color="warning" icon="md:dangerous"></v-icon>
</span>
<!-- <v-icon v-else color="warning" icon="md:dangerous"></v-icon> -->
</template>
<template #[`item.completed`]="{ item }">
<v-icon v-if="item.completed" color="success" icon="md:check"></v-icon>
......
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