Add parsing of PDB and PDBDEV ids from the database2 table

salilab · May 10, 2024 · 0e176aa · 0e176aa
1 parent 71ceb76
commit 0e176aa
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Showing 5 changed files with 61 additions and 10 deletions.
diff --git a/ihm_validation/mmcif_io.py b/ihm_validation/mmcif_io.py
@@ -112,6 +112,26 @@ def get_id_from_entry(self) -> str:
                     entry = entry_init.strip()
         return entry
 
+    def get_pdb_id(self) -> str:
+        """Check database2 table for PDB ID"""
+        entry_id = None
+        if len(self.system.databases) > 0:
+            for db in self.system.databases:
+                if db.id == 'PDB':
+                    entry_id =  db.code
+
+        return entry_id
+
+    def get_pdb_dev_id(self) -> str:
+        """Check database2 table for PDB ID"""
+        entry_id = None
+        if len(self.system.databases) > 0:
+            for db in self.system.databases:
+                if db.id == 'PDB-Dev':
+                    entry_id =  db.code
+
+        return entry_id
+
     def get_primary_citation_info(self) -> tuple:
         '''get title and authors for the primary citation'''
         title, authors = None, None

diff --git a/ihm_validation/report.py b/ihm_validation/report.py
@@ -24,7 +24,7 @@
 import numpy as np
 from selenium import webdriver
 
-REPORT_VERSION = '1.1'
+REPORT_VERSION = '1.2-dev'
 
 class WriteReport(object):
     def __init__(self, mmcif_file, db, cache, nocache=False):
@@ -87,6 +87,8 @@ def run_entry_composition(self, Template_Dict: dict) -> dict:
                                       entry_id[6:])]
         Template_Dict['ID_R'] = (
             entry_id[0:6]+'_'+entry_id[6:]).split()
+        Template_Dict['PDB_ID'] = self.input.get_pdb_id()
+        Template_Dict['PDBDEV_ID'] = self.input.get_pdb_dev_id()
         Template_Dict['Molecule'] = self.input.get_struc_title()
         Template_Dict['Authors'] = self.input.get_authors()
         title, authors = self.input.get_primary_citation_info()
@@ -493,7 +495,6 @@ def run_supplementary_table(self,
             Template_Dict['clustering'] = None
         Template_Dict['location'] = location
         Template_Dict['complex_name'] = self.input.get_struc_title()
-        Template_Dict['PDB_ID'] = self.input.get_id()
         Template_Dict['Subunits'] = utility.get_subunits(
             self.input.get_composition())
         Template_Dict['datasets'] = utility.get_datasets(self.input.get_dataset_details(

diff --git a/templates/full_validation_pdf.html b/templates/full_validation_pdf.html
@@ -167,12 +167,24 @@ <h2 align="center">{{ date }}</h2>
           <div class="card-header" style="background-color: #FFFFFF;">
             <div class="bs-example" class="text-center">
               <table class="table table-bordered" style="height: 16rem;">
-                <thead>
+                {% if PDB_ID is not none %} 
                   <tr>
-                    <th align="center" class="text-center" style="text-align:center; vertical-align: middle;">PDB ID</th>
-                    <th align="center" class="text-center" style="text-align:center; vertical-align: middle;">{{ ID_T }}</th>
+                    <td align="center" class="text-center" style="text-align:center; vertical-align: middle;">PDB ID</td>
+                    <td align="center" class="text-center" style="text-align:center; vertical-align: middle;">{{ PDB_ID }}</td>
                   </tr>
-                </thead>
+                {% endif %}
+                {% if PDBDEV_ID is not none %} 
+                  <tr>
+                    <td align="center" class="text-center" style="text-align:center; vertical-align: middle;">PDBDEV ID</td>
+                    <td align="center" class="text-center" style="text-align:center; vertical-align: middle;">{{ PDBDEV_ID }}</td>
+                  </tr>
+                {% endif %}
+                {% if ((PDB_ID is none) and (PDBDEV_ID is none))  %} 
+                  <tr>
+                    <td align="center" class="text-center" style="text-align:center; vertical-align: middle;">Entry ID</td>
+                    <td align="center" class="text-center" style="text-align:center; vertical-align: middle;">{{ ID_T }}</td>
+                  </tr>
+                {% endif %}
                 <tr>
                   <td class="align-middle" class="text-center" style="text-align:center; vertical-align: middle;">Structure Name</td>
                   <td class="align-middle" class="text-center" style="text-align:center; vertical-align: middle;">{{ Molecule }}</td>

diff --git a/templates/main.html b/templates/main.html
@@ -36,12 +36,24 @@ <h5 align="center" style="text-align: center";>Download Summary Table</h5>
       <div class="card-header" style="background-color:#FFFFFF; border-color:#003366;">
         <div class="bs-example" class="text-center">
           <table class="table table-bordered" style="border-color:#003366; height: 25rem;">
-            <thead>
+            {% if PDB_ID is not none %} 
               <tr>
-                <th align="center" class="text-center">PDB ID</th>
-                <th align="center" class="text-center">{{ID_T}}</th>
+                <td align="center" class="text-center">PDB ID</td>
+                <td align="center" class="text-center">{{PDB_ID}}</td>
               </tr>
-            </thead>
+            {% endif %}
+            {% if PDBDEV_ID is not none %} 
+              <tr>
+                <td align="center" class="text-center">PDBDEV ID</td>
+                <td align="center" class="text-center">{{PDBDEV_ID}}</td>
+              </tr>
+            {% endif %}
+            {% if ((PDB_ID is none) and (PDBDEV_ID is none))  %} 
+              <tr>
+                <td align="center" class="text-center">Entry ID</td>
+                <td align="center" class="text-center">{{ID_T}}</td>
+              </tr>
+            {% endif %}
             <tr>
               <td class="align-middle" class="text-center">Structure title</td>
               <td class="align-middle" class="text-center">{{Molecule}} </td>

diff --git a/templates/summary_validation_pdf.html b/templates/summary_validation_pdf.html
@@ -65,7 +65,13 @@
       </style>
    </head>
    <body>
+    {% if PDB_ID is not none %}
+      <h3 class="center">Summary of integrative structure determination of {{complex_name}} ({{PDB_ID}}) </h3>
+    {% elif PDBDEV_ID is not none %}
+      <h3 class="center">Summary of integrative structure determination of {{complex_name}} ({{PDBDEV_ID}}) </h3>
+    {% else %}
       <h3 class="center">Summary of integrative structure determination of {{complex_name}} ({{ID_T}}) </h3>
+    {% endif %}
       <div class="ex1">
          <table ID=t01>
          <tr bgcolor ='silver'>