propagate the skip flag

bin/polyply

@@ -138,6 +138,9 @@ def main(): # pylint: disable=too-many-locals,too-many-statements
                               help='file with grid-points', default=None)
     system_group.add_argument('-mi', dest='maxiter', type=int,
                               help='max number of trys to grow a molecule', default=800)
+    system_group.add_argument('-skip_filter', action='store_true', dest='skip_filter',
+                              help='do not group residues by isomophism when making '
+                                   'templates but just resname')
     system_group.add_argument('-start', dest='start', nargs='+', type=str,
                               default=[],
                               help=('Specify which residue to build first. The syntax is '

polyply/tests/test_generate_templates.py

@@ -155,7 +155,7 @@ def test_run_molecule():
           top = polyply.src.topology.Topology.from_gmx_topfile(TEST_DATA / "topology_test" / "system.top", "test")
           top.gen_pairs()
           top.convert_nonbond_to_sig_eps()
-          GenerateTemplates(topology=top, max_opt=10).run_molecule(top.molecules[0])
+          GenerateTemplates(topology=top, skip_filter=False, max_opt=10).run_molecule(top.molecules[0])
           assert "PMMA" in top.volumes
           assert "PMMA" in top.molecules[0].templates