remove blank divs in the report is the metrics aren't there

Author: keiran-rowell-unsw

assets/report_template.html

@@ -378,6 +378,7 @@
     <!-- Plots -->
     <div class="bg-gray-200 p-12 xl:p-16">
       <!-- Top row: Sequence Coverage (full width) -->
+      <!-- BEGIN_MSA_SECTION -->
       <div id="seq_coverage_container" class="flex justify-center mb-12 xl:mb-16">
         <div class="max-w-[720px] xl:max-w-[900px] 2xl:max-w-[1100px] w-full">
           <div class="text-3xl xl:text-4xl font-bold tracking-tight mb-4 xl:mb-6 text-center">
@@ -388,6 +389,7 @@
           </div>
         </div>
       </div>
+      <!-- END_MSA_SECTION -->
 
       <!-- Bottom row: pLDDT and PAE side by side -->
       <div class="flex flex-col xl:flex-row justify-center items-start gap-12 xl:gap-16 2xl:gap-20">
@@ -400,6 +402,7 @@
           </div>
         </div>
 
+        <!-- BEGIN_PAE_SECTION -->
         <div class="flex-1 max-w-[720px] xl:max-w-[850px] 2xl:max-w-[1000px]">
           <div class="text-3xl xl:text-4xl font-bold tracking-tight mb-4 xl:mb-6 text-center">
             Residue-pair alignment error - PAE
@@ -408,6 +411,7 @@
             <div id="pae_placeholder"></div>
           </div>
         </div>
+        <!-- END_PAE_SECTION -->
       </div>
     </div>
 

bin/generate_report.py

@@ -11,6 +11,7 @@
 import json
 import argparse
 import os
+import re
 from pathlib import Path
 
 prog_name_mapping = {
@@ -94,9 +95,11 @@ def generate_report(name, out_dir, structures, num_structs_limit=5, msa_files=No
             config=PLOTLY_CONFIG,
         )
 
-    # Replace placeholder divs with plot HTML
+    # Replace or remove optional sections
     if seq_cov_html:
         html = html.replace('<div id="seq_cov_placeholder"></div>', seq_cov_html, 1)
+    else:
+        html = re.sub(r'<!-- BEGIN_MSA_SECTION -->.*?<!-- END_MSA_SECTION -->', '', html, flags=re.DOTALL)
 
     # Generate the pLDDT plot and convert to HTML
     plddt_fig = generate_plddt_plot(parsed_structures)
@@ -116,6 +119,8 @@ def generate_report(name, out_dir, structures, num_structs_limit=5, msa_files=No
             config=PLOTLY_CONFIG,
         )
         html = html.replace('<div id="pae_placeholder"></div>', pae_html, 1)
+    else:
+        html = re.sub(r'<!-- BEGIN_PAE_SECTION -->.*?<!-- END_PAE_SECTION -->', '', html, flags=re.DOTALL)
 
     if write_htmls:
         with open(f"{out_dir}/{name}_coverage_pLDDT.html", "w") as out_file: