new tentative

components/content/MolstarPdbePlugin.vue

@@ -159,8 +159,8 @@ const moleculeFormat: Ref<string> = ref("pdb")
 <template>
     <template v-if="uniq">
         <v-row>
-            <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"
+            <v-btn size="x-small" variant="text" icon="md:visibility" @click="setSelectedPdbToFirst()"></v-btn>
+            <v-btn :disabled="!structureToDownload" size="x-small" variant="text" icon="md:download" class="ml-1"
                 :href="structureToDownload"></v-btn>
         </v-row>
     </template>
@@ -191,8 +191,9 @@ const moleculeFormat: Ref<string> = ref("pdb")
                         <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" landscape :custom-data-url="selectedPdb"
-                                alphafold-view="true" :custom-data-format="moleculeFormat"></pdbe-molstar>
+                            <pdbe-molstar ref="pdbeMolstarComponent" landscape="true" hide-controls="true"
+                                :custom-data-url="selectedPdb" alphafold-view="true"
+                                :custom-data-format="moleculeFormat"></pdbe-molstar>
                         </v-sheet>
                     </v-col>
                     <v-col :cols="mobile ? 12 : undefined">
@@ -259,12 +260,12 @@ const moleculeFormat: Ref<string> = ref("pdb")
 
 
 <style>
-.msp-plugin .msp-plugin-content {
+/* .msp-plugin .msp-plugin-content {
     color: black !important;
-}
+} */
 
 div.msp-plugin-content.msp-layout-expanded {
-    z-index: 99 !important
+    z-index: 5 !important
 }
 
 .legendColor {

components/content/StructureDb.vue

@@ -6,12 +6,14 @@ import { useNumericalFilter } from "@/composables/useNumericalfilter"
 
 
 import { ServerDbTable } from "#components"
-const sortBy: Ref<SortItem[]> = ref([{ key: 'system', order: "asc" }])
+const sortBy: Ref<SortItem[]> = ref([{ key: 'System', order: "asc" }])
 const itemValue = ref("id");
-const facets: Ref<string[]> = ref(["system", "completed", "prediction_type",])
+const facets: Ref<string[]> = ref(["System", "subtype", "gene_name", "completed", "prediction_type",])
 const headers: Ref<Object[]> = ref([
     { title: 'Structure', key: 'structure', sortable: false, removable: false },
-    { title: "Type", key: "system", removable: false },
+    { title: "System", key: "System", removable: false },
+    { title: "Gene name", key: "gene_name", removable: false },
+    { title: "Subtype", key: "subtype", removable: false },
     // { title: "pdb file", key: "pdb" },
     // { title: "fasta", key: "fasta_file" },
     { title: "Proteins in structure", key: 'proteins_in_the_prediction', sortable: false, removable: true },
@@ -54,11 +56,11 @@ const dataTableServerProps = computed(() => {
 
 
 
-function namesToCollapsibleChips(names: string[], file: string | null = null) {
+function namesToCollapsibleChips(names: string[], systemDir: string, file: string | null = null) {
     if (file === null) {
-        return names.filter((it) => it !== "").map(it => ({ title: it.split("__").pop() }))
+        return names.filter((it) => it !== "").map(it => ({ title: it.split("__")[1] }))
     } else {
-        return names.filter((it) => it !== "").map(it => ({ title: it.split("__").pop(), href: `/wiki/${toSystemName(file)}/${file}` }))
+        return names.filter((it) => it !== "").map(it => ({ title: it.split("__")[1], href: `/wiki/${systemDir}/${file}` }))
     }
 }
 
@@ -68,14 +70,9 @@ function pdbNameToCif(pdbPath: string) {
 }
 
 function toSystemName(rawName: string) {
-    // split on -0 if exists else on _
-    if (rawName.includes("-0")) {
-
-        return rawName.split("-0")[0].toLocaleLowerCase()
-    } else {
-        return rawName.split("_")[0].toLocaleLowerCase()
-    }
-
+    // Does it work if it's a list of system genes ? 
+    // split on __ for systeme_vgenes
+    return rawName.split("__")[0].toLocaleLowerCase()
 
 }
 
@@ -130,15 +127,16 @@ const plddtDistribution = computed(() => {
         </template>
 
         <template #[`item.proteins_in_the_prediction`]="{ item }">
-            <CollapsibleChips :items="namesToCollapsibleChips(item.proteins_in_the_prediction, item.fasta_file)">
+            <CollapsibleChips
+                :items="namesToCollapsibleChips(item.proteins_in_the_prediction, item.System_name_ok, item.fasta_file)">
             </CollapsibleChips>
         </template>
         <template #[`item.system_genes`]="{ item }">
-            <CollapsibleChips :items="namesToCollapsibleChips(item.system_genes)"></CollapsibleChips>
+            <CollapsibleChips :items="namesToCollapsibleChips(item.system_genes, item.System_name_ok)"></CollapsibleChips>
         </template>
         <template #[`item.structure`]="{ item }">
             <MolstarPdbePlugin v-if="item?.pdb && item.pdb !== 'na'"
-                :data-urls="[`/${toSystemName(item.system)}/${pdbNameToCif(item.pdb)}`]" uniq>
+                :data-urls="[`/${item.System_name_ok}/${pdbNameToCif(item.pdb)}`]" uniq>
             </MolstarPdbePlugin>
 
             <!-- <v-icon v-else color="warning" icon="md:dangerous"></v-icon> -->

data/system_case.yaml

+mmb_gp29_gp30: MMB_gp29_gp30
+pd-lambda-4: PD-Lambda-4
+zorya: Zorya
+radar: RADAR
+abie: AbiE
+pd-t4-3: PD-T4-3
+gaps6: GAPS6
+abia: AbiA
+pd-lambda-2: PD-Lambda-2
+pd-t4-5: PD-T4-5
+aditi: Aditi
+fs_hp_sdh_sah: FS_HP_SDH_sah
+gao_upx: Gao_Upx
+kiwa: Kiwa
+nhi: Nhi
+abiq: AbiQ
+pd-lambda-6: PD-Lambda-6
+isg15-like: ISG15-like
+pif: Pif
+gasdermin: GasderMIN
+mqsrac: MqsRAC
+pd-t4-8: PD-T4-8
+septu: Septu
+bunzi: Bunzi
+abir: AbiR
+fs_giy_yig: FS_GIY_YIG
+abij: AbiJ
+retron: Retron
+cas: CRISPR-Cas
+pd-t7-5: PD-T7-5
+fs_hp: FS_HP
+abiv: AbiV
+disarm: DISARM
+rst_2tm_1tm_tir: Rst_2TM_1TM_TIR
+pago: pAgo
+menshen: Menshen
+rst_3hp: Rst_3HP
+pd-t4-9: PD-T4-9
+viperin: Viperin
+gaps1: GAPS1
+fs_hsdr_like: FS_HsdR_like
+pd-t4-1: PD-T4-1
+pd-t4-10: PD-T4-10
+pd-t4-7: PD-T4-7
+rloc: RloC
+stk2: Stk2
+gao_qat: Gao_Qat
+pd-t7-1: PD-T7-1
+fs_sma: FS_Sma
+rst_tir-nlr: Rst_TIR-NLR
+gao_ppl: Gao_Ppl
+pd-t4-2: PD-T4-2
+sofic: SoFIC
+detocs: Detocs
+cbass: CBASS
+abig: AbiG
+gaps2: GAPS2
+abiu: AbiU
+abip2: AbiP2
+sefir: SEFIR
+borvo: Borvo
+old_exonuclease: Old_exonuclease
+rnlab: RnlAB
+abii: AbiI
+abid: AbiD
+prrc: PrrC
+rst_duf4238: Rst_DUF4238
+abi2: Abi2
+azaca: Azaca
+rst_hydrolase-3tm: Rst_Hydrolase-3Tm
+ddmde: DdmDE
+mads: MADS
+phrann_gp29_gp30: Phrann_gp29_gp30
+abil: AbiL
+olokun: Olokun
+pd-t7-3: PD-T7-3
+nixi: NixI
+pd-lambda-1: PD-Lambda-1
+dctpdeaminase: dCTPdeaminase
+eleos: Eleos
+drt: DRT
+pd-t4-6: PD-T4-6
+pd-t4-4: PD-T4-4
+0:title
+dartg: DarTG
+dpd: Dpd
+sanata: SanaTA
+mokosh: Mokosh
+paris: Paris
+dsr: Dsr
+abio: AbiO
+hna: Hna
+tiamat: Tiamat
+brex: BREX
+shango: Shango
+druantia: Druantia
+rosmerta: RosmerTA
+abit: AbiT
+psyrta: PsyrTA
+abik: AbiK
+thoeris: Thoeris
+pd-t7-2: PD-T7-2
+abib: AbiB
+lamassu-fam: Lamassu-Fam
+gao_iet: Gao_Iet
+avs: Avs
+spbk: SpbK
+pycsar: Pycsar
+wadjet: Wadjet
+rst_helicaseduf2290: Rst_HelicaseDUF2290
+gao_mza: Gao_Mza
+gao_ape: Gao_Ape
+mazef: MazEF
+pd-lambda-3: PD-Lambda-3
+abih: AbiH
+shedu: Shedu
+gao_her: Gao_Her
+shosta: ShosTA
+abic: AbiC
+dazbog: Dazbog
+gao_tery: Gao_TerY
+hachiman: Hachiman
+sspbcde: SspBCDE
+lit: Lit
+rm: RM
+card_nlr: CARD_NLR
+gaps4: GAPS4
+abin: AbiN
+pd-t7-4: PD-T7-4
+charlie_gp32: Charlie_gp32
+fs_hepn_tm: FS_HEPN_TM
+rst_rt-nitrilase-tm: Rst_RT-nitrilase-Tm
+uzume: Uzume
+mok_hok_sok: Mok_Hok_Sok
+dodola: Dodola
+dgtpase: dGTPase
+butters_gp57r: Butters_gp57r
+bsta: BstA
+gao_tmn: Gao_Tmn
+panchino_gp28: Panchino_gp28
+caprel: CapRel
+nlr: NLR
+pd-lambda-5: PD-Lambda-5
+dnd: Dnd
+abiz: AbiZ
+gabija: Gabija
+jukab: JukAB
+gao_hhe: Gao_Hhe
+rst_gop_beta_cll: Rst_gop_beta_cll
+pfiat: PfiAT
+gao_rl: Gao_RL
+rexab: RexAB
+butters_gp30_gp31: Butters_gp30_gp31

packages/df-wiki-cli/df_wiki_cli/content/main.py

@@ -4,7 +4,8 @@ import json
 import pandas as pd
 import shutil
 import csv
-import yaml
+import matplotlib.pyplot as plt
+from pandas.errors import ParserError
 from typing_extensions import Annotated
 from typing import Optional, List
 from pathlib import Path
@@ -88,17 +89,6 @@ def structure(
             resolve_path=True,
         ),
     ],
-    map: Annotated[
-        Path,
-        typer.Option(
-            exists=True,
-            file_okay=True,
-            dir_okay=True,
-            writable=False,
-            readable=True,
-            resolve_path=True,
-        ),
-    ],
     dir: Annotated[
         Path,
         typer.Option(
@@ -122,13 +112,10 @@ def structure(
         ),
     ],
 ):
-    with open(map, "r") as map_f:
-        system_to_dir = yaml.safe_load(map_f)
-
     with open(stat, "r") as stat_f:
         reader = csv.DictReader(stat_f)
         for row in reader:
-            dir_name = system_to_dir[row["system"]]
+            dir_name = row["System_name_ok"]
             pdb_path_file = Path(row["pdb"])
             cif_file_name = Path(str(pdb_path_file).split(".pdb")[0] + ".cif")
             files = [
@@ -143,11 +130,21 @@ def structure(
             for f in files:
                 str_f = str(f["f"])
                 if str_f and str_f != "." and str_f != "" and str_f != "na":
-                    # console.print("--" + str(f["f"]) + "--")
-                    # console.print(f"[green] copy {f['f'].name} to {target_dir}")
                     file_to_copy = dir / f["d"] / f["f"]
                     if file_to_copy.exists():
-                        shutil.copy2(file_to_copy, target_dir)
+                        if f["d"] == "PAE":
+                            png_file = str(file_to_copy).split(".tsv")[0] + ".png"
+                            try:
+                                pae2png(file_to_copy, png_file)
+                            except ParserError as err:
+                                console.print(
+                                    f"[red] file {str(file_to_copy.name)} cannot be parsed"
+                                )
+                                print(err)
+                            else:
+                                shutil.copy2(png_file, target_dir)
+                        else:
+                            shutil.copy2(file_to_copy, target_dir)
                     else:
                         console.print(
                             f"[red] file {str(file_to_copy.name)} does not exist"
@@ -229,3 +226,16 @@ def systems(
 
             json_object = json.dumps(systems, indent=2)
             ty.write(json_object)
+
+
+def pae2png(tsv_file, png_file):
+    v = pd.read_table(tsv_file, index_col=0, low_memory=False)
+    fig, ax = plt.subplots(1, 1, figsize=(4, 3), facecolor=None)
+    m = ax.matshow(v, cmap="Greens_r", vmin=0, vmax=35, aspect="auto", origin="lower")
+    cbar = plt.colorbar(m, ax=ax, fraction=0.046, pad=0.04)
+    ax.set_xlabel("Scored Residues")
+    ax.set_ylabel("Aligned Residues")
+    cbar.set_label("Expected Position Error (Å)")
+    plt.tight_layout()
+    plt.savefig(png_file, dpi=150, facecolor=None, transparent=True)
+    plt.close()

packages/df-wiki-cli/df_wiki_cli/meilisearch/__init__.py

@@ -45,7 +45,10 @@ NaFloat = Annotated[Optional[float], BeforeValidator(na_to_none)]
 
 class StrucutreStatistics(BaseModel):
     id: int
-    system: str
+    System_name_ok: str
+    System: str
+    gene_name: str
+    subtype: str
     proteins_in_the_prediction: List[str]
     prediction_type: str
     batch: int
@@ -150,7 +153,16 @@ def update_structure(
     )
     print(pagination_settings_task)
     attr_task = index.update_filterable_attributes(
-        body=["system", "completed", "prediction_type", "plddts", "iptm+ptm", "pDockQ"]
+        body=[
+            "System",
+            "gene_name",
+            "subtype",
+            "completed",
+            "prediction_type",
+            "plddts",
+            "iptm+ptm",
+            "pDockQ",
+        ]
     )
     params = {
         "maxValuesPerFacet": 1000000,
@@ -161,7 +173,10 @@ def update_structure(
     print(attr_task)
     index.update_sortable_attributes(
         [
-            "system",
+            "System_name_ok",
+            "System",
+            "gene_name",
+            "subtype",
             "completed",
             "plddts",
             "nb_sys",
@@ -170,7 +185,6 @@ def update_structure(
             "system_number_of_genes",
             "iptm+ptm",
             "pDockQ",
-            "type",
         ]
     )
     index.update_typo_tolerance({"enabled": False})

packages/df-wiki-cli/pyproject.toml

 [tool.poetry]
 name = "df-wiki-cli"
-version = "0.1.3"
+version = "0.1.4"
 description = ""
 authors = ["Remi  PLANEL <rplanel@pasteur.fr>"]
 readme = "README.md"
@@ -17,6 +17,7 @@ meilisearch = "^0.28.4"
 pydantic = "^2.4.2"
 pydantic-yaml = "^1.2.0"
 python-frontmatter = "^1.0.1"
+matplotlib = "^3.8.2"
 
 
 [tool.poetry.group.dev.dependencies]