From 7030b108e78e1c986937a8cc03dc812a861a7ed8 Mon Sep 17 00:00:00 2001
From: Valerio Mariani <valerio.mariani@unibas.ch>
Date: Wed, 28 Nov 2012 15:25:10 +0100
Subject: [PATCH] Refactored iinterface and export of ClashingDistance class
---
modules/mol/alg/doc/molalg.rst | 11 ++++++++++-
modules/mol/alg/pymod/__init__.py | 4 ++--
modules/mol/alg/pymod/wrap_mol_alg.cc | 7 ++++++-
modules/mol/alg/src/filter_clashes.cc | 6 ++++++
modules/mol/alg/src/filter_clashes.hh | 3 +++
5 files changed, 27 insertions(+), 4 deletions(-)
diff --git a/modules/mol/alg/doc/molalg.rst b/modules/mol/alg/doc/molalg.rst
index 66b142940..5a3e5e7c9 100644
--- a/modules/mol/alg/doc/molalg.rst
+++ b/modules/mol/alg/doc/molalg.rst
@@ -276,7 +276,7 @@ The following function detects steric clashes in atomic structures. Two atoms ar
:param clash_distance: minimum clashing distance (in Angstroms)
:param tolerance: tolerance threshold (in Angstroms)
- .. method GetClashingDistance()
+ .. method:: GetClashingDistance()
Recovers a reference distance and a tolerance threshold from the list
@@ -285,6 +285,15 @@ The following function detects steric clashes in atomic structures. Two atoms ar
:returns: a tuple containing the minimum clashing distance and the tolerance threshold
+ .. method:: GetAdjustedClashingDistance()
+
+ Recovers a reference distance from the list, already adjusted by the tolerance threshold
+
+ :param ele1: string containing the first element's name
+ :param ele2: string containing the second element's name
+
+ :returns: the adjusted minimum clashing distance
+
.. method:: GetMaxAdjustedDistance()
Returns the longest clashing distance in the list, after adjustment with tolerance threshold
diff --git a/modules/mol/alg/pymod/__init__.py b/modules/mol/alg/pymod/__init__.py
index 126d0196f..36d93a720 100644
--- a/modules/mol/alg/pymod/__init__.py
+++ b/modules/mol/alg/pymod/__init__.py
@@ -6,11 +6,11 @@ import ost.mol.alg.structure_analysis
import ost.mol.alg.helix_kinks
# Fills a list of reference clashing distances from a file (requires a path to the file)
-def FillClashingDistancesFromFile(filename,default_clashing_distance,default_tolerance):
+def FillClashingDistancesFromFile(filename):
fh=open(filename,'r')
lines=fh.readlines()
fh.close()
- return FillClashingDistances(lines,default_clashing_distance,default_tolerance)
+ return FillClashingDistances(lines)
# Fills a list of bond stereo-chemical statistics from a file (requires a path to the file)
def FillBondStereoChemicalParamsFromFile(filename):
diff --git a/modules/mol/alg/pymod/wrap_mol_alg.cc b/modules/mol/alg/pymod/wrap_mol_alg.cc
index 08ad6631e..bdf141aa5 100644
--- a/modules/mol/alg/pymod/wrap_mol_alg.cc
+++ b/modules/mol/alg/pymod/wrap_mol_alg.cc
@@ -24,6 +24,7 @@
#include <ost/mol/alg/superpose_frames.hh>
#include <ost/mol/alg/filter_clashes.hh>
#include <ost/mol/alg/consistency_checks.hh>
+#include <ost/export_helper/pair_to_tuple_conv.hh>
using namespace boost::python;
using namespace ost;
@@ -60,7 +61,7 @@ ost::mol::alg::StereoChemicalParams fill_stereochemical_params_wrapper (const St
return ost::mol::alg::FillStereoChemicalParams(header,stereo_chemical_props_file_vector);
}
-ost::mol::alg::ClashingDistances fill_clashing_distances_wrapper (const list& stereo_chemical_props_file, Real min_default_distance, Real min_distance_tolerance)
+ost::mol::alg::ClashingDistances fill_clashing_distances_wrapper (const list& stereo_chemical_props_file)
{
int stereo_chemical_props_file_length = boost::python::extract<int>(stereo_chemical_props_file.attr("__len__")());
std::vector<String> stereo_chemical_props_file_vector(stereo_chemical_props_file_length);
@@ -103,6 +104,9 @@ BOOST_PYTHON_MODULE(_ost_mol_alg)
export_entity_to_density();
#endif
+ to_python_converter<std::pair<Real,Real>,
+ PairToTupleConverter<Real, Real> >();
+
def("LocalDistDiffTest", lddt_a, (arg("sequence_separation")=0,arg("local_lddt_property_string")=""));
def("LocalDistDiffTest", lddt_c, (arg("local_lddt_property_string")=""));
def("LocalDistDiffTest", lddt_b, (arg("ref_index")=0, arg("mdl_index")=1));
@@ -124,6 +128,7 @@ BOOST_PYTHON_MODULE(_ost_mol_alg)
class_<mol::alg::ClashingDistances> ("ClashingDistances",init<>())
.def("SetClashingDistance",&mol::alg::ClashingDistances::SetClashingDistance)
.def("GetClashingDistance",&mol::alg::ClashingDistances::GetClashingDistance)
+ .def("GetAdjustedClashingDistance",&mol::alg::ClashingDistances::GetAdjustedClashingDistance)
.def("GetMaxAdjustedDistance",&mol::alg::ClashingDistances::GetMaxAdjustedDistance)
.def("IsEmpty",&mol::alg::ClashingDistances::IsEmpty)
diff --git a/modules/mol/alg/src/filter_clashes.cc b/modules/mol/alg/src/filter_clashes.cc
index 235464544..dc450498e 100644
--- a/modules/mol/alg/src/filter_clashes.cc
+++ b/modules/mol/alg/src/filter_clashes.cc
@@ -108,6 +108,12 @@ std::pair<Real,Real> ClashingDistances::GetClashingDistance(const String& ele1,c
return find_ci->second;
}
+Real ClashingDistances::GetAdjustedClashingDistance(const String& ele1,const String& ele2) const
+{
+ std::pair <Real,Real> clash_dist = GetClashingDistance(ele1,ele2);
+ return clash_dist.first-clash_dist.second;
+}
+
void ClashingDistances::PrintAllDistances() const
{
for (std::map <String,std::pair<float,float> >::const_iterator index = min_distance_.begin();index != min_distance_.end();++index) {
diff --git a/modules/mol/alg/src/filter_clashes.hh b/modules/mol/alg/src/filter_clashes.hh
index f9d7473b6..e294cd489 100644
--- a/modules/mol/alg/src/filter_clashes.hh
+++ b/modules/mol/alg/src/filter_clashes.hh
@@ -40,6 +40,9 @@ public:
/// \brief Recovers a reference distance and a tolerance threshold (respectively) from the list
std::pair<Real,Real> GetClashingDistance(const String& ele1,const String& ele2) const;
+ /// \brief Recovers a reference distance already adjusted by the tolerance threshold from the list
+ Real GetAdjustedClashingDistance(const String& ele1,const String& ele2) const;
+
/// \brief Recovers the longest distance in the list, corrected by tolerance
Real GetMaxAdjustedDistance() const;
--
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