diff --git a/modules/mol/mm/pymod/export_settings.cc b/modules/mol/mm/pymod/export_settings.cc index 42af757fcbf04c77909317881f22c9e99551d49c..3aba50adde1723a1387bc46cf25a87ef6afbbe8a 100644 --- a/modules/mol/mm/pymod/export_settings.cc +++ b/modules/mol/mm/pymod/export_settings.cc @@ -87,6 +87,7 @@ void export_MMSettings() .def_readwrite("solute_dielectric",&ost::mol::mm::MMSettings::solute_dielectric) .def_readwrite("reaction_field_dielectric",&ost::mol::mm::MMSettings::reaction_field_dielectric) .def_readwrite("use_dispersion_correction",&ost::mol::mm::MMSettings::use_dispersion_correction) + .def_readwrite("keep_ff_specific_naming",&ost::mol::mm::MMSettings::keep_ff_specific_naming) .def_readwrite("openmm_plugin_directory",&ost::mol::mm::MMSettings::openmm_plugin_directory) .def_readwrite("custom_plugin_directory",&ost::mol::mm::MMSettings::custom_plugin_directory) diff --git a/modules/mol/mm/src/mm_settings.hh b/modules/mol/mm/src/mm_settings.hh index a289d22fad3020f806fb327930f70199a0460ca1..c29ea463f0b3aa4d2e041a3b4afb888bbb489bcd 100644 --- a/modules/mol/mm/src/mm_settings.hh +++ b/modules/mol/mm/src/mm_settings.hh @@ -104,6 +104,7 @@ struct MMSettings{ solute_dielectric(1.0), //this is for GBSA reaction_field_dielectric(78.3), use_dispersion_correction(true), + keep_ff_specific_naming(true), openmm_plugin_directory("/usr/local/openmm/lib/plugins"), custom_plugin_directory("/usr/local/openmm/lib/plugins") @@ -153,6 +154,7 @@ struct MMSettings{ Real solute_dielectric; Real reaction_field_dielectric; bool use_dispersion_correction; + bool keep_ff_specific_naming; String openmm_plugin_directory; String custom_plugin_directory; }; diff --git a/modules/mol/mm/src/topology_creator.cc b/modules/mol/mm/src/topology_creator.cc index aa982f461f62fd0837f627b98bb4c8d5d5c5c15e..6cdf0e15d5f61a0efd244d5a17253ff56bd4472f 100644 --- a/modules/mol/mm/src/topology_creator.cc +++ b/modules/mol/mm/src/topology_creator.cc @@ -244,7 +244,6 @@ TopologyPtr TopologyCreator::Create(ost::mol::EntityHandle& ent, bound_to.push_back(temp); } - //let's set the proper masses top->SetMasses(atom_masses); @@ -944,6 +943,16 @@ TopologyPtr TopologyCreator::Create(ost::mol::EntityHandle& ent, top->SetFudgeQQ(ff->GetFudgeQQ()); top->SetFudgeLJ(ff->GetFudgeLJ()); + if(!settings->keep_ff_specific_naming){ + //let's rename to the pdb standard! + //first, we rename to the gromacs standars... + ff->AssignFFSpecificNames(ent,true); + //still call the assign gromacs names function... + MMModeller::AssignGromacsNaming(ent); + //let's finally do the renaming to PDB standard + MMModeller::AssignPDBNaming(ent); + } + return top;