From 9430784bfa2aac5cb5305b9a972913634306e09f Mon Sep 17 00:00:00 2001
From: Gerardo Tauriello <gerardo.tauriello@unibas.ch>
Date: Mon, 30 May 2016 13:10:40 +0200
Subject: [PATCH] Minor fixes in doc and unusable default parameter in
svd_superpose
---
modules/mol/alg/src/svd_superpose.cc | 4 ++--
modules/mol/mm/doc/forcefield.rst | 4 +++-
2 files changed, 5 insertions(+), 3 deletions(-)
diff --git a/modules/mol/alg/src/svd_superpose.cc b/modules/mol/alg/src/svd_superpose.cc
index 89d6fcfdb..59adf6141 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 9ddbe77ff..444ff0243 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
--
GitLab