Minor fixes in doc and unusable default parameter in svd_superpose

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();
 

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