My patches may2026

.gitignore

@@ -111,3 +111,6 @@ glucosepane/
 logs/
 homosapiens*
 homo_sapiens*/
+.DS_Store
+*.o
+contact_map

pyproject.toml

@@ -22,8 +22,8 @@ classifiers = [
     "Programming Language :: Python :: 3.11",
 ]
 dependencies = [
-    "numpy==1.25",
-    "vermouth==0.9.1", 
+    "numpy>=1.26",
+    "vermouth==0.9.6", 
     "pandas==2.2.2",
     "biopython==1.84",
     "scikit-learn",

src/colbuilder/colbuilder.py

@@ -89,11 +89,6 @@ def print_version(ctx: click.Context, param: click.Parameter, value: bool) -> No
     ctx.exit()
 
 
-from colbuilder.core.sequence.main_sequence import build_sequence
-from colbuilder.core.geometry.main_geometry import build_geometry_anywhere
-from colbuilder.core.topology.main_topology import build_topology
-
-
 def configure_loggers():
     """Configure external loggers to prevent duplicated output."""
     problematic_loggers = [
@@ -203,6 +198,7 @@ async def run_sequence_generation(config: ColbuilderConfig) -> Tuple[Optional[Pa
     """
     try:
         LOG.subsection("Generating Sequence")
+        from colbuilder.core.sequence.main_sequence import build_sequence
         return await build_sequence(config)
     except Exception as e:
         LOG.error(f"Sequence generation failed: {str(e)}")
@@ -234,6 +230,7 @@ async def run_geometry_generation(
     """
     try:
         LOG.subsection("Building Geometry or Mixing")
+        from colbuilder.core.geometry.main_geometry import build_geometry_anywhere
 
         current_file_manager = file_manager or FileManager(config)
 
@@ -324,6 +321,8 @@ async def run_topology_generation(
         TopologyGenerationError: If topology generation fails
     """
     try:
+        from colbuilder.core.topology.main_topology import build_topology
+
         if file_manager is None:
             file_manager = FileManager(config)
 
@@ -1157,4 +1156,4 @@ def main(**kwargs: Any) -> int:
 
 
 if __name__ == "__main__":
-    sys.exit(main())
+    sys.exit(main())

src/colbuilder/core/topology/amber.py

@@ -7,6 +7,7 @@
 """
 
 import os
+import re
 import shutil
 from pathlib import Path
 import asyncio
@@ -902,14 +903,20 @@ def write_itp(
 
         output_file = itp_file.parent / str(itp_file.name).replace("top", "itp")
 
+        # pdb2gmx -merge all writes a single moleculetype.  Older GROMACS
+        # versions name it "Protein_chain_A"; newer versions (>=2023) write
+        # just "Protein".  Match either so the topology body is copied
+        # regardless of GROMACS version.
+        molname_re = re.compile(r'^\s*Protein(?:_chain_\w+)?\s+\d+\s*$')
+
         with open(output_file, 'w') as f:
             write = False
             for line in itp_model:
                 if 'Include water topology' in line:
                     break
                 if write:
                     f.write(line)
-                elif 'Protein_chain_A' in line:
+                elif molname_re.match(line):
                     f.write('[ moleculetype ]\n')
                     f.write(f'{molecule_name}  3\n')
                     write = True