diff --git a/modules/base/pymod/CMakeLists.txt b/modules/base/pymod/CMakeLists.txt
index 4eb36a9147d7d83b081d05f4abeb3ca0a2868467..22700288ae061f64b45fb741e13b5044b2bf8977 100644
--- a/modules/base/pymod/CMakeLists.txt
+++ b/modules/base/pymod/CMakeLists.txt
@@ -7,4 +7,4 @@ set(OST_BASE_PYMOD_SOURCES
pymod(NAME base OUTPUT_DIR ost
CPP ${OST_BASE_PYMOD_SOURCES}
- PY __init__.py settings.py)
+ PY __init__.py settings.py stutil.py)
diff --git a/modules/base/pymod/__init__.py b/modules/base/pymod/__init__.py
index 3d2137f7e76f6a66a8cf2041319d801742fafedf..aa723917bec0aed0d90e3c682ff200c39e90b72a 100644
--- a/modules/base/pymod/__init__.py
+++ b/modules/base/pymod/__init__.py
@@ -17,6 +17,7 @@
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
#------------------------------------------------------------------------------
from _base import *
+from stutil import *
from ost import geom
from ost import io
diff --git a/modules/base/pymod/stutil.py b/modules/base/pymod/stutil.py
new file mode 100644
index 0000000000000000000000000000000000000000..2f64beaefa3731c5689c73c585cbc3edb37d32f1
--- /dev/null
+++ b/modules/base/pymod/stutil.py
@@ -0,0 +1,95 @@
+import math
+from ost import mol
+
+def FloatValueExtract(func):
+ """
+ Decorator to wrap functions that take a list of float values. In addition to
+ passing in a list of float values directly, it is possible to extract the
+ values from attributes or generic properties.
+ """
+ def _dec(xs, prop=None, attr=None):
+ if prop!=None:
+ if len(xs)==0:
+ return func([])
+ assert attr==None
+ level=mol.Prop.Level.UNSPECIFIED
+ if isinstance(xs[0], mol.AtomBase):
+ level=mol.Prop.Level.ATOM
+ elif isinstance(xs[0], mol.ResidueBase):
+ level=mol.Prop.Level.RESIDUE
+ elif isinstance(xs[0], mol.ChainBase):
+ level=mol.Prop.Level.CHAIN
+ epm=mol.EntityPropertyMapper(prop, level)
+ vals=[]
+ for x in xs:
+ try:
+ vals.append(epm.Get(x))
+ except:
+ pass
+ return func(vals)
+ if attr!=None:
+ vals=[]
+ for x in xs:
+ try:
+ vals.append(getattr(x, attr))
+ except:
+ pass
+ return func(vals)
+ return func(xs)
+ return _dec
+
+@FloatValueExtract
+def Mean(xs):
+ """
+ Calculate mean of dataset
+ """
+ if len(xs)==0:
+ raise RuntimeError("Can't calculate mean of empty sequence")
+ return sum(xs)/len(xs)
+
+@FloatValueExtract
+def StdDev(xs):
+ """
+ Calculate standard-deviation of dataset
+
+ | sum[xi-<x>]^2 |
+ sigma=sqrt|---------------|
+ | n |
+ """
+ mean=Mean(xs)
+ return math.sqrt(sum([(x-mean)**2 for x in xs])/len(xs))
+
+@FloatValueExtract
+def Min(xs):
+ return min(xs)
+
+@FloatValueExtract
+def Max(xs):
+ return max(xs)
+
+def Correl(xs, ys):
+ """
+ Calculates the correlation coefficient between xs and ys as
+
+ sum[(xi-<x>)*(yi-<y>)]
+ r=----------------------
+ (n-1)*sx*sy
+
+ where <x>, <y> are the mean of dataset xs and ys, and, sx and sy are the
+ standard deviations.
+ """
+ if len(xs)!=len(ys):
+ raise RuntimeError("Can't calculate correl. Sequence lengths do not match.")
+ if len(xs)==1:
+ raise RuntimeError("Can't calculate correl of sequences with length 1.")
+ mean_x=Mean(xs)
+ mean_y=Mean(ys)
+ sigma_x, sigma_y=(0.0, 0.0)
+ cross_term=0.0
+ for x, y in zip(xs, ys):
+ cross_term+=(x-mean_x)*(y-mean_y)
+ sigma_x+=(x-mean_x)**2
+ sigma_y+=(y-mean_y)**2
+ sigma_x=math.sqrt(sigma_x/len(xs))
+ sigma_y=math.sqrt(sigma_y/len(ys))
+ return cross_term/((len(xs)-1)*sigma_x*sigma_y)
diff --git a/modules/mol/base/pymod/CMakeLists.txt b/modules/mol/base/pymod/CMakeLists.txt
index 590af690986b9c300a28917bdbc0aea48f6f0cd9..29c336dca643d9bbafac80ad9fb5e3959e6ef48c 100644
--- a/modules/mol/base/pymod/CMakeLists.txt
+++ b/modules/mol/base/pymod/CMakeLists.txt
@@ -18,6 +18,7 @@ export_query_view_wrapper.cc
export_torsion.cc
export_visitor.cc
wrap_mol.cc
+export_entity_property_mapper.cc
)
pymod(NAME mol CPP ${OST_BASE_PYMOD_SOURCES} PY __init__.py)
diff --git a/modules/mol/base/pymod/export_entity_property_mapper.cc b/modules/mol/base/pymod/export_entity_property_mapper.cc
new file mode 100644
index 0000000000000000000000000000000000000000..fa271bed83a04df8773f8110e773b94e5a7676e1
--- /dev/null
+++ b/modules/mol/base/pymod/export_entity_property_mapper.cc
@@ -0,0 +1,68 @@
+#include <boost/python.hpp>
+
+#include <ost/mol/entity_property_mapper.hh>
+
+using namespace ost;
+using namespace ost::mol;
+using namespace boost::python;
+
+namespace {
+
+
+Real (EntityPropertyMapper::*get_ah_a)(const AtomHandle&) const=&EntityPropertyMapper::Get;
+Real (EntityPropertyMapper::*get_av_a)(const AtomView&) const=&EntityPropertyMapper::Get;
+Real (EntityPropertyMapper::*get_rh_a)(const ResidueHandle&) const=&EntityPropertyMapper::Get;
+Real (EntityPropertyMapper::*get_rv_a)(const ResidueView&) const=&EntityPropertyMapper::Get;
+Real (EntityPropertyMapper::*get_ch_a)(const ChainHandle&) const=&EntityPropertyMapper::Get;
+Real (EntityPropertyMapper::*get_cv_a)(const ChainView&) const=&EntityPropertyMapper::Get;
+
+
+Real (EntityPropertyMapper::*get_ah_b)(const AtomHandle&, Real) const=&EntityPropertyMapper::Get;
+Real (EntityPropertyMapper::*get_av_b)(const AtomView&, Real) const=&EntityPropertyMapper::Get;
+Real (EntityPropertyMapper::*get_rh_b)(const ResidueHandle&, Real) const=&EntityPropertyMapper::Get;
+Real (EntityPropertyMapper::*get_rv_b)(const ResidueView&, Real) const=&EntityPropertyMapper::Get;
+Real (EntityPropertyMapper::*get_ch_b)(const ChainHandle&, Real) const=&EntityPropertyMapper::Get;
+Real (EntityPropertyMapper::*get_cv_b)(const ChainView&, Real) const=&EntityPropertyMapper::Get;
+
+EntityPropertyMapper create_epm(const String& prop_name, char level)
+{
+ switch(level) {
+ case 'A':
+ case 'a':
+ return EntityPropertyMapper(prop_name, Prop::ATOM);
+ case 'R':
+ case 'r':
+ return EntityPropertyMapper(prop_name, Prop::RESIDUE);
+ case 'C':
+ case 'c':
+ return EntityPropertyMapper(prop_name, Prop::CHAIN);
+ case 'U':
+ case 'u':
+ return EntityPropertyMapper(prop_name, Prop::UNSPECIFIED);
+ default:
+ throw std::runtime_error(String("unknown property level '")+level+"'");
+ }
+}
+
+}
+
+void export_EntityPropertyMapper()
+{
+ class_<EntityPropertyMapper>("EntityPropertyMapper",
+ init<const String&,
+ Prop::Level>(arg("level")=Prop::UNSPECIFIED))
+ .def("__init__", &create_epm)
+ .def("Get", get_ah_a)
+ .def("Get", get_av_a)
+ .def("Get", get_rh_a)
+ .def("Get", get_rv_a)
+ .def("Get", get_ch_a)
+ .def("Get", get_cv_a)
+ .def("Get", get_ah_b)
+ .def("Get", get_av_b)
+ .def("Get", get_rh_b)
+ .def("Get", get_rv_b)
+ .def("Get", get_ch_b)
+ .def("Get", get_cv_b)
+ ;
+}
diff --git a/modules/mol/base/pymod/wrap_mol.cc b/modules/mol/base/pymod/wrap_mol.cc
index 82a449f681fbe98866c42acb0b8581fefd66d331..ce55b9942f8f5fd378ce11c78b924b6b5691a44d 100644
--- a/modules/mol/base/pymod/wrap_mol.cc
+++ b/modules/mol/base/pymod/wrap_mol.cc
@@ -41,6 +41,7 @@ void export_CoordGroup();
void export_PropertyID();
void export_BoundingBox();
void export_QueryViewWrapper();
+void export_EntityPropertyMapper();
BOOST_PYTHON_MODULE(_mol)
{
export_Entity();
@@ -61,7 +62,7 @@ BOOST_PYTHON_MODULE(_mol)
export_PropertyID();
export_BoundingBox();
export_QueryViewWrapper();
-
+ export_EntityPropertyMapper();
class_<Transform>("Transform", init<>())
.def("GetMatrix",&Transform::GetMatrix)
.def("GetTransposedMatrix",&Transform::GetTransposedMatrix)