Implementation of the Martini3 Go-model

bin/martinize2

@@ -191,6 +191,7 @@ def martinize(system, mappings, to_ff, delete_unknown=False):
     vermouth.LocateChargeDummies().run_system(system)
     return system
 
+
 def _cys_argument(value):
     """
     Convert and validate the value of the cys option for argparse.
@@ -960,7 +961,8 @@ def entry():
                               res_dist=args.go_res_dist,)
 
         defines = ("GO_VIRT",)
-        itp_paths = ["go_atomtypes.itp", "go_nbparams.itp"]
+        itp_paths = {"atomtypes": "go_atomtypes.itp",
+                     "nonbond_params": "go_nbparams.itp"}
     else:
         # don't write non-bonded interactions
         itp_paths = []
@@ -1028,7 +1030,8 @@ def entry():
         # sites for the biasing
         if not args.go:
             vermouth.rcsu.go_vs_includes.VirtualSiteCreator().run_system(system)
-            itp_paths = ["virtual_sites_atomtypes.itp", "virtual_sites_nonbond_params.itp"]
+            itp_paths = {"atomtypes": "virtual_sites_atomtypes.itp",
+                         "nonbond_params": "virtual_sites_nonbond_params.itp"}
         # now we add a bias by defining specific virtual-site water interactions
         vermouth.processors.ComputeWaterBias(args.water_bias,
                                              { s:float(eps) for s, eps in args.water_bias_eps},

vermouth/gmx/topology.py

@@ -110,7 +110,13 @@
                     comments = ""
                 itp_file.write(f"{a1} {a2} 1 {nb1:3.8F} {nb2:3.8F} {comments}\n")
 
-def write_gmx_topology(system, top_path, itp_paths=[], C6C12=False, defines=(), header=()):
+def write_gmx_topology(system,
+                       top_path,
+                       itp_paths={"nonbond_params": "extra_nbparams.itp",
+                                  "atomtypes": "extra_atomtypes.itp"},
+                       C6C12=False,
+                       defines=(),
+                       header=()):
     """
     Writes a Gromacs .top file for the specified system. Gromacs topology
     files are defined by directives for example `[ atomtypes ]`. However,
@@ -126,9 +132,10 @@
     system: vermouth.system.System
     top_path: pathlib.Path
         path for topology file
-    itp_paths: list[pathlib.Path]
+    itp_paths: dict[str, pathlib.Path]
         list of paths for writing the topology parameters
-        like atomtypes.
+        like atomtypes with the key being the name of the
+        directive.
     C6C12: bool
         write non-bonded interaction parameters using LJ
         C6C12 form
@@ -138,18 +145,17 @@
         any comment lines to include at the beginning
     """
     if not system.molecules:
         raise ValueError("No molecule in the system. Nothing to write.")
 
-    itp_paths = itp_paths[::-1]
     include_string = ""
     # First we write the atomtypes directive
     if "atomtypes" in system.gmx_topology_params:
-        _path = itp_paths.pop()
+        _path = itp_paths['atomtypes']
         write_atomtypes(system, _path, C6C12)
         include_string += f'\n #include "{_path}"'
     # Next we write the nonbond_params directive
     if "nonbond_params" in system.gmx_topology_params:
-        _path = itp_paths.pop()
+        _path = itp_paths['nonbond_params']
         write_nonbond_params(system, _path, C6C12)
         include_string += f'\n #include "{_path}"\n'
     # Write the ITP files for the molecule types, and prepare writing the
@@ -184,11 +190,11 @@
                 header[-1] = header[-1] + "\n"
                 header.append("Please cite the following papers:")
                 for citation in molecule.citations:
                     cite_string = citation_formatter(
                         molecule.force_field.citations[citation]
                     )
                     LOGGER.info("Please cite: " + cite_string)
                     header.append(cite_string)
                 vermouth.gmx.itp.write_molecule_itp(molecule, outfile, header=header)
             this_moltype_len = len(molecule.meta["moltype"])
             if this_moltype_len > max_name_length:

vermouth/tests/gmx/test_topology.py

@@ -185,7 +185,7 @@ def test_toplevel_topology(tmp_path, dummy_molecule):
                        outpath,
                        header=['first header comment', 'second header comment'],
                        defines=('random', ),
-                       itp_paths=[atompath, nbpath],
+                       itp_paths={"atomtypes": atompath, "nonbond_params": nbpath},
                        # at this level C6C12 doesn't matter; it gets
                        # checked in previous texts
                        C6C12=False)

vermouth/tests/test_vs_generation.py

@@ -41,7 +41,7 @@ def test_no_system_error(test_molecule):
     processor = VirtualSiteCreator()
     test_molecule.meta['moltype'] = "random"
     # no system
-    with pytest.raises(IOError):
+    with pytest.raises(ValueError):
         processor.run_molecule(test_molecule)
 
 def test_return_no_nodes():