diff --git a/modules/mol/alg/src/svd_superpose.cc b/modules/mol/alg/src/svd_superpose.cc index 89d6fcfdb50ef748af8c97c5a7a5041359efc8f7..59adf6141d3fcab79dd11753127ea49833c101e7 100644 --- a/modules/mol/alg/src/svd_superpose.cc +++ b/modules/mol/alg/src/svd_superpose.cc @@ -434,7 +434,7 @@ SuperpositionResult MeanSquareMinimizer::IterativeMinimize(int ncycles, Real dis SuperpositionResult SuperposeAtoms(const mol::AtomViewList& atoms1, const mol::AtomViewList& atoms2, - bool apply_transform=true) + bool apply_transform) { MeanSquareMinimizer msm = MeanSquareMinimizer::FromAtomLists(atoms1, atoms2); SuperpositionResult result = msm.MinimizeOnce(); @@ -454,7 +454,7 @@ SuperpositionResult SuperposeAtoms(const mol::AtomViewList& atoms1, SuperpositionResult SuperposeSVD(const mol::EntityView& ev1, const mol::EntityView& ev2, - bool apply_transform=true) { + bool apply_transform) { AtomViewList atoms1 = ev1.GetAtomList(); AtomViewList atoms2 = ev2.GetAtomList(); diff --git a/modules/mol/mm/doc/forcefield.rst b/modules/mol/mm/doc/forcefield.rst index 9ddbe77ff15a7543604a5993c0232df551ca3d22..444ff0243e473a3c2d6ab82cd2ec7b4eed37aecf 100644 --- a/modules/mol/mm/doc/forcefield.rst +++ b/modules/mol/mm/doc/forcefield.rst @@ -149,12 +149,14 @@ results into :class:`~ost.mol.mm.Forcefield` objects. from ost.mol import mm - # create parameters for TYR using PDB's component dictionary + # create parameters for RVP using PDB's component dictionary mm.antechamber.RunAntechamber('RVP', 'components.cif', base_out_dir='ligands') # create force field ff = mm.Forcefield() ff = mm.antechamber.AddFromPath(ff, 'ligands/RVP') + # equivalent: ff = mm.antechamber.AddFromFiles(ff, 'ligands/RVP/frcmod', + # 'ligands/RVP/out.mpdb') # since Antechamber cannot deal with ions, you can do it manually ff = mm.antechamber.AddIon(ff, 'CL', 'CL', 35.45, -1.0, 0.4401, 0.4184) # save it