diff --git a/examples/demos/the_hammer.py b/examples/demos/the_hammer.py
index 48970cefb16a8b9bee9a70395b2d5555f86e82cb..4f6266d287430788fa99d3b56647bba48c9d9588 100644
--- a/examples/demos/the_hammer.py
+++ b/examples/demos/the_hammer.py
@@ -1,7 +1,5 @@
from PyQt4 import QtCore
import math
-from ost import qa
-
# remove all objects from scene, just in case
scene.RemoveAll()
@@ -26,7 +24,7 @@ class Anim(QtCore.QTimer):
self.edi.SetTransform(geom.Mat4(rot))
self.edi.UpdateICS()
for a in self.b.view.atoms:
- score=qa.ClashScore(a.handle, self.a.view)
+ score=mol.alg.ClashScore(a.handle, self.a.view)
a.SetFloatProp('clash', score)
self.a.UpdatePositions()
self.b.ReapplyColorOps()
diff --git a/modules/conop/pymod/CMakeLists.txt b/modules/conop/pymod/CMakeLists.txt
index 57eeb82c986e9b2220fa1e1c188b65d07ca6886b..5affa4b457d780b7368b34a097bec832d2c3f36c 100644
--- a/modules/conop/pymod/CMakeLists.txt
+++ b/modules/conop/pymod/CMakeLists.txt
@@ -2,6 +2,7 @@ set(OST_CONOP_PYMOD_SOURCES
wrap_conop.cc
export_builder.cc
export_compound.cc
+ export_amino_acids.cc
export_conop.cc
export_ring_finder.cc
)
diff --git a/modules/conop/pymod/export_amino_acids.cc b/modules/conop/pymod/export_amino_acids.cc
new file mode 100644
index 0000000000000000000000000000000000000000..cf06f17324f53667243573edc8b26f6011f9b3c7
--- /dev/null
+++ b/modules/conop/pymod/export_amino_acids.cc
@@ -0,0 +1,84 @@
+//------------------------------------------------------------------------------
+// This file is part of the OpenStructure project <www.openstructure.org>
+//
+// Copyright (C) 2008-2011 by the OpenStructure authors
+//
+// This library is free software; you can redistribute it and/or modify it under
+// the terms of the GNU Lesser General Public License as published by the Free
+// Software Foundation; either version 3.0 of the License, or (at your option)
+// any later version.
+// This library is distributed in the hope that it will be useful, but WITHOUT
+// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+// details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with this library; if not, write to the Free Software Foundation, Inc.,
+// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+//------------------------------------------------------------------------------
+#include <boost/python.hpp>
+#include <boost/python/suite/indexing/vector_indexing_suite.hpp>
+#include <ost/conop/amino_acids.hh>
+
+using namespace boost::python;
+
+using namespace ost::conop;
+
+void export_AminoAcids()
+{
+ enum_<AminoAcid>("AminoAcid")
+ .value("ALA", ALA)
+ .value("ARG", ARG)
+ .value("ASN", ASN)
+ .value("ASP", ASP)
+ .value("GLN", GLN)
+ .value("GLU", GLU)
+ .value("LYS", LYS)
+ .value("SER", SER)
+ .value("CYS", CYS)
+ .value("TYR", TYR)
+ .value("THR", THR)
+ .value("VAL", VAL)
+ .value("ILE", ILE)
+ .value("LEU", LEU)
+ .value("GLY", GLY)
+ .value("PRO", PRO)
+ .value("MET", MET)
+ .value("HIS", HIS)
+ .value("PHE", PHE)
+ .value("TRP", TRP)
+ .export_values()
+ ;
+
+ class_<AminoAcidSet>("AminoAcidSet", init<>())
+ .def("Add", &AminoAcidSet::Add)
+ .def("Remove", &AminoAcidSet::Remove)
+ .def("Contains", &AminoAcidSet::Contains)
+ .def("Empty", &AminoAcidSet::Empty)
+ .def("CreatePolarSet",
+ &AminoAcidSet::CreatePolarSet).staticmethod("CreatePolarSet")
+ .def("CreateApolarSet",
+ &AminoAcidSet::CreateApolarSet).staticmethod("CreateApolarSet")
+ .def("CreateAromaticSet",
+ &AminoAcidSet::CreateAromaticSet).staticmethod("CreateAromaticSet")
+ .def("CreateThreeStateSet",
+ &AminoAcidSet::CreateThreeStateSet).staticmethod("CreateThreeStateSet")
+ .def("CreatePseudoSet",
+ &AminoAcidSet::CreatePseudoSet).staticmethod("CreatePseudoSet")
+ .def("CreateCompleteSet",
+ &AminoAcidSet::CreateCompleteSet).staticmethod("CreateCompleteSet")
+ .def("CreateSet", &AminoAcidSet::CreateSet).staticmethod("CreateSet")
+ .def(self_ns::str(self))
+ ;
+
+ class_<AminoAcidAlphabet>("AminoAcidAlphabet", init<>())
+ .def(vector_indexing_suite<AminoAcidAlphabet>())
+ ;
+
+ def("ResidueToAminoAcid",&ResidueToAminoAcid);
+ def("AminoAcidToResidueName",&AminoAcidToResidueName);
+ def("OneLetterCodeToResidueName",&OneLetterCodeToResidueName);
+ def("ResidueNameToOneLetterCode",&ResidueNameToOneLetterCode);
+ def("OneLetterCodeToAminoAcid",&OneLetterCodeToAminoAcid);
+}
+
diff --git a/modules/conop/src/CMakeLists.txt b/modules/conop/src/CMakeLists.txt
index e69c45689648a82ad4d086eb9e1657fa639d1131..65201bea130c811a12bd0a23b9c181e4d7fa795d 100644
--- a/modules/conop/src/CMakeLists.txt
+++ b/modules/conop/src/CMakeLists.txt
@@ -3,6 +3,7 @@ builder.hh
builder_fw.hh
conop.hh
heuristic_builder.hh
+amino_acids.hh
compound.hh
compound_lib.hh
module_config.hh
@@ -12,6 +13,7 @@ ring_finder.hh
set(OST_CONOP_SOURCES
builder.cc
+amino_acids.cc
conop.cc
heuristic_builder.cc
compound.cc
diff --git a/modules/qa/src/amino_acids.cc b/modules/conop/src/amino_acids.cc
similarity index 68%
rename from modules/qa/src/amino_acids.cc
rename to modules/conop/src/amino_acids.cc
index 7111844e3e4035c5fb3d255c23c0c4174c89cb76..7665e97b34240a78c886a06896fe48ef00026ed2 100644
--- a/modules/qa/src/amino_acids.cc
+++ b/modules/conop/src/amino_acids.cc
@@ -33,7 +33,7 @@
/*
Author: Marco Biasini
*/
-namespace ost { namespace qa {
+namespace ost { namespace conop {
using namespace boost::spirit;
@@ -41,26 +41,26 @@ namespace {
struct AminoAcidKeys : public symbols<AminoAcid> {
AminoAcidKeys() {
- add("ALA", Ala)
- ("ARG", Arg)
- ("ASN", Asn)
- ("ASP", Asp)
- ("GLN", Gln)
- ("GLU", Glu)
- ("LYS", Lys)
- ("SER", Ser)
- ("CYS", Cys)
- ("TYR", Tyr)
- ("THR", Thr)
- ("VAL", Val)
- ("ILE", Ile)
- ("LEU", Leu)
- ("PRO", Pro)
- ("GLY", Gly)
- ("MET", Met)
- ("HIS", His)
- ("TRP", Trp)
- ("PHE", Phe);
+ add("ALA", ALA)
+ ("ARG", ARG)
+ ("ASN", ASN)
+ ("ASP", ASP)
+ ("GLN", GLN)
+ ("GLU", GLU)
+ ("LYS", LYS)
+ ("SER", SER)
+ ("CYS", CYS)
+ ("TYR", TYR)
+ ("THR", THR)
+ ("VAL", VAL)
+ ("ILE", ILE)
+ ("LEU", LEU)
+ ("PRO", PRO)
+ ("GLY", GLY)
+ ("MET", MET)
+ ("HIS", HIS)
+ ("TRP", TRP)
+ ("PHE", PHE);
}
};
} // anon namespace
@@ -74,51 +74,51 @@ AminoAcid ResidueToAminoAcid(const mol::ResidueHandle& r) {
if (aa)
return *aa;
- return Xxx;
+ return XXX;
}
String AminoAcidToResidueName(AminoAcid aa)
{
switch(aa) {
- case Ala:
+ case ALA:
return "ALA";
- case Arg:
+ case ARG:
return "ARG";
- case Asn:
+ case ASN:
return "ASN";
- case Asp:
+ case ASP:
return "ASP";
- case Gln:
+ case GLN:
return "GLN";
- case Glu:
+ case GLU:
return "GLU";
- case Lys:
+ case LYS:
return "LYS";
- case Ser:
+ case SER:
return "SER";
- case Cys:
+ case CYS:
return "CYS";
- case Tyr:
+ case TYR:
return "TYR";
- case Trp:
+ case TRP:
return "TRP";
- case Thr:
+ case THR:
return "THR";
- case Val:
+ case VAL:
return "VAL";
- case Ile:
+ case ILE:
return "ILE";
- case Met:
+ case MET:
return "MET";
- case Leu:
+ case LEU:
return "LEU";
- case Gly:
+ case GLY:
return "GLY";
- case Pro:
+ case PRO:
return "PRO";
- case His:
+ case HIS:
return "HIS";
- case Phe:
+ case PHE:
return "PHE";
default:
return "UNK";
@@ -246,85 +246,85 @@ AminoAcid OneLetterCodeToAminoAcid(char olc)
char upper_olc=toupper(olc);
switch(upper_olc) {
case 'A':
- return Ala;
+ return ALA;
case 'R':
- return Arg;
+ return ARG;
case 'N':
- return Asn;
+ return ASN;
case 'D':
- return Asp;
+ return ASP;
case 'Q':
- return Gln;
+ return GLN;
case 'E':
- return Glu;
+ return GLU;
case 'K':
- return Lys;
+ return LYS;
case 'S':
- return Ser;
+ return SER;
case 'C':
- return Cys;
+ return CYS;
case 'Y':
- return Tyr;
+ return TYR;
case 'W':
- return Trp;
+ return TRP;
case 'T':
- return Thr;
+ return THR;
case 'V':
- return Val;
+ return VAL;
case 'I':
- return Ile;
+ return ILE;
case 'M':
- return Met;
+ return MET;
case 'L':
- return Leu;
+ return LEU;
case 'G':
- return Gly;
+ return GLY;
case 'P':
- return Pro;
+ return PRO;
case 'H':
- return His;
+ return HIS;
case 'F':
- return Phe;
+ return PHE;
default:
- return Xxx;
+ return XXX;
}
}
AminoAcidSet AminoAcidSet::CreatePolarSet()
{
AminoAcidSet polar;
- polar.Add(Arg);
- polar.Add(Asn);
- polar.Add(Asp);
- polar.Add(Gln);
- polar.Add(Glu);
- polar.Add(Ser);
- polar.Add(His);
- polar.Add(Lys);
- polar.Add(Thr);
+ polar.Add(ARG);
+ polar.Add(ASN);
+ polar.Add(ASP);
+ polar.Add(GLN);
+ polar.Add(GLU);
+ polar.Add(SER);
+ polar.Add(HIS);
+ polar.Add(LYS);
+ polar.Add(THR);
return polar;
}
AminoAcidSet AminoAcidSet::CreateAromaticSet()
{
AminoAcidSet aromatic;
- aromatic.Add(Trp);
- aromatic.Add(Tyr);
- aromatic.Add(Phe);
+ aromatic.Add(TRP);
+ aromatic.Add(TYR);
+ aromatic.Add(PHE);
return aromatic;
}
AminoAcidSet AminoAcidSet::CreateApolarSet()
{
AminoAcidSet apolar;
- apolar.Add(Ala);
- apolar.Add(Val);
- apolar.Add(Leu);
- apolar.Add(Ile);
- apolar.Add(Gly);
- apolar.Add(Pro);
- apolar.Add(Cys);
- apolar.Add(Met);
+ apolar.Add(ALA);
+ apolar.Add(VAL);
+ apolar.Add(LEU);
+ apolar.Add(ILE);
+ apolar.Add(GLY);
+ apolar.Add(PRO);
+ apolar.Add(CYS);
+ apolar.Add(MET);
return apolar;
}
@@ -338,26 +338,26 @@ AminoAcidSet AminoAcidSet::CreateSet(AminoAcid aa)
std::vector<AminoAcidSet> AminoAcidSet::CreateCompleteSet() {
std::vector<AminoAcidSet> alphabet;
- alphabet.push_back(AminoAcidSet::CreateSet(Ala));
- alphabet.push_back(AminoAcidSet::CreateSet(Arg));
- alphabet.push_back(AminoAcidSet::CreateSet(Asn));
- alphabet.push_back(AminoAcidSet::CreateSet(Asp));
- alphabet.push_back(AminoAcidSet::CreateSet(Gln));
- alphabet.push_back(AminoAcidSet::CreateSet(Glu));
- alphabet.push_back(AminoAcidSet::CreateSet(Lys));
- alphabet.push_back(AminoAcidSet::CreateSet(Ser));
- alphabet.push_back(AminoAcidSet::CreateSet(Cys));
- alphabet.push_back(AminoAcidSet::CreateSet(Met));
- alphabet.push_back(AminoAcidSet::CreateSet(Trp));
- alphabet.push_back(AminoAcidSet::CreateSet(Tyr));
- alphabet.push_back(AminoAcidSet::CreateSet(Thr));
- alphabet.push_back(AminoAcidSet::CreateSet(Val));
- alphabet.push_back(AminoAcidSet::CreateSet(Ile));
- alphabet.push_back(AminoAcidSet::CreateSet(Leu));
- alphabet.push_back(AminoAcidSet::CreateSet(Gly));
- alphabet.push_back(AminoAcidSet::CreateSet(Pro));
- alphabet.push_back(AminoAcidSet::CreateSet(His));
- alphabet.push_back(AminoAcidSet::CreateSet(Phe));
+ alphabet.push_back(AminoAcidSet::CreateSet(ALA));
+ alphabet.push_back(AminoAcidSet::CreateSet(ARG));
+ alphabet.push_back(AminoAcidSet::CreateSet(ASN));
+ alphabet.push_back(AminoAcidSet::CreateSet(ASP));
+ alphabet.push_back(AminoAcidSet::CreateSet(GLN));
+ alphabet.push_back(AminoAcidSet::CreateSet(GLU));
+ alphabet.push_back(AminoAcidSet::CreateSet(LYS));
+ alphabet.push_back(AminoAcidSet::CreateSet(SER));
+ alphabet.push_back(AminoAcidSet::CreateSet(CYS));
+ alphabet.push_back(AminoAcidSet::CreateSet(MET));
+ alphabet.push_back(AminoAcidSet::CreateSet(TRP));
+ alphabet.push_back(AminoAcidSet::CreateSet(TYR));
+ alphabet.push_back(AminoAcidSet::CreateSet(THR));
+ alphabet.push_back(AminoAcidSet::CreateSet(VAL));
+ alphabet.push_back(AminoAcidSet::CreateSet(ILE));
+ alphabet.push_back(AminoAcidSet::CreateSet(LEU));
+ alphabet.push_back(AminoAcidSet::CreateSet(GLY));
+ alphabet.push_back(AminoAcidSet::CreateSet(PRO));
+ alphabet.push_back(AminoAcidSet::CreateSet(HIS));
+ alphabet.push_back(AminoAcidSet::CreateSet(PHE));
return alphabet;
}
@@ -375,26 +375,26 @@ std::vector<AminoAcidSet> AminoAcidSet::CreatePseudoSet() {
std::vector<AminoAcidSet> alphabet;
AminoAcidSet full_alphabet;
- full_alphabet.Add(Ala);
- full_alphabet.Add(Val);
- full_alphabet.Add(Leu);
- full_alphabet.Add(Ile);
- full_alphabet.Add(Gly);
- full_alphabet.Add(Pro);
- full_alphabet.Add(Cys);
- full_alphabet.Add(Met);
- full_alphabet.Add(Trp);
- full_alphabet.Add(Tyr);
- full_alphabet.Add(Phe);
- full_alphabet.Add(Arg);
- full_alphabet.Add(Asn);
- full_alphabet.Add(Asp);
- full_alphabet.Add(Gln);
- full_alphabet.Add(Glu);
- full_alphabet.Add(Ser);
- full_alphabet.Add(His);
- full_alphabet.Add(Lys);
- full_alphabet.Add(Thr);
+ full_alphabet.Add(ALA);
+ full_alphabet.Add(VAL);
+ full_alphabet.Add(LEU);
+ full_alphabet.Add(ILE);
+ full_alphabet.Add(GLY);
+ full_alphabet.Add(PRO);
+ full_alphabet.Add(CYS);
+ full_alphabet.Add(MET);
+ full_alphabet.Add(TRP);
+ full_alphabet.Add(TYR);
+ full_alphabet.Add(PHE);
+ full_alphabet.Add(ARG);
+ full_alphabet.Add(ASN);
+ full_alphabet.Add(ASP);
+ full_alphabet.Add(GLN);
+ full_alphabet.Add(GLU);
+ full_alphabet.Add(SER);
+ full_alphabet.Add(HIS);
+ full_alphabet.Add(LYS);
+ full_alphabet.Add(THR);
alphabet.push_back(full_alphabet);
return alphabet;
@@ -431,7 +431,7 @@ AminoAcidSet::Iterator AminoAcidSet::Begin() const
{
// find first bit that is set
int start=0;
- while (start<=Xxx+1 && !(bits_ & (1 << start))) {
+ while (start<=XXX+1 && !(bits_ & (1 << start))) {
++start;
}
return AminoAcidSetIterator(bits_, start);
@@ -439,7 +439,7 @@ AminoAcidSet::Iterator AminoAcidSet::Begin() const
AminoAcidSet::Iterator AminoAcidSet::End() const
{
- return AminoAcidSetIterator(bits_, Xxx+1);
+ return AminoAcidSetIterator(bits_, XXX+1);
}
bool AminoAcidSet::operator==(const AminoAcidSet& rhs) const
diff --git a/modules/qa/src/amino_acids.hh b/modules/conop/src/amino_acids.hh
similarity index 81%
rename from modules/qa/src/amino_acids.hh
rename to modules/conop/src/amino_acids.hh
index 03521fa40eb3fcd3c9fa3770d0b73693f39cc2ba..aa778e3c0090f20a56752e9dbf87b2f210e8dc53 100644
--- a/modules/qa/src/amino_acids.hh
+++ b/modules/conop/src/amino_acids.hh
@@ -16,8 +16,8 @@
// along with this library; if not, write to the Free Software Foundation, Inc.,
// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
//------------------------------------------------------------------------------
-#ifndef OST_QA_AMINO_ACIDS_HH
-#define OST_QA_AMINO_ACIDS_HH
+#ifndef OST_CONOP_AMINO_ACIDS_HH
+#define OST_CONOP_AMINO_ACIDS_HH
/*
Author: Marco Biasini
*/
@@ -26,35 +26,35 @@
#include <ost/mol/residue_handle.hh>
#include <ost/mol/torsion_handle.hh>
-#include <ost/qa/module_config.hh>
-namespace ost { namespace qa {
+#include <ost/conop/module_config.hh>
+
+namespace ost { namespace conop {
// convenience enum for standard set of 20 amino acids
// Xxx signifies an unknown amino acid.
typedef enum {
- Ala, Arg, Asn,
- Asp, Gln, Glu,
- Lys, Ser, Cys,
- Met, Trp, Tyr,
- Thr, Val, Ile,
- Leu, Gly, Pro,
- His, Phe, Xxx
-
+ ALA, ARG, ASN,
+ ASP, GLN, GLU,
+ LYS, SER, CYS,
+ MET, TRP, TYR,
+ THR, VAL, ILE,
+ LEU, GLY, PRO,
+ HIS, PHE, XXX
} AminoAcid;
/// \brief from residue name to amino acid.
///
/// for non standard amino acids Xxx is returned.
-DLLEXPORT_OST_QA AminoAcid ResidueToAminoAcid(const mol::ResidueHandle& r);
+DLLEXPORT_OST_CONOP AminoAcid ResidueToAminoAcid(const mol::ResidueHandle& r);
// \brief from amino acid to residue name
-DLLEXPORT_OST_QA String AminoAcidToResidueName(AminoAcid aa);
+DLLEXPORT_OST_CONOP String AminoAcidToResidueName(AminoAcid aa);
-DLLEXPORT_OST_QA String OneLetterCodeToResidueName(char olc);
+DLLEXPORT_OST_CONOP String OneLetterCodeToResidueName(char olc);
-DLLEXPORT_OST_QA AminoAcid OneLetterCodeToAminoAcid(char olc);
+DLLEXPORT_OST_CONOP AminoAcid OneLetterCodeToAminoAcid(char olc);
-char DLLEXPORT_OST_QA ResidueNameToOneLetterCode(String rn);
+char DLLEXPORT_OST_CONOP ResidueNameToOneLetterCode(String rn);
class AminoAcidSetIterator : public std::iterator<std::forward_iterator_tag,
AminoAcid> {
@@ -86,16 +86,14 @@ private:
void Advance()
{
++curr_;
- while (curr_<=Xxx && !(bits_ & (1 << curr_))) { ++curr_; }
+ while (curr_<=XXX && !(bits_ & (1 << curr_))) { ++curr_; }
}
unsigned int bits_;
int curr_;
};
-
-
/// \brief Amino acid bit set
-class DLLEXPORT_OST_QA AminoAcidSet {
+class DLLEXPORT_OST_CONOP AminoAcidSet {
public:
typedef AminoAcidSetIterator Iterator;
@@ -152,9 +150,11 @@ private:
unsigned int bits_;
};
-DLLEXPORT_OST_QA std::ostream& operator<<(std::ostream& os,
+DLLEXPORT_OST_CONOP std::ostream& operator<<(std::ostream& os,
const AminoAcidSet& aa_set);
+typedef std::vector<AminoAcidSet> AminoAcidAlphabet;
+
}}
#endif
diff --git a/modules/mol/alg/pymod/CMakeLists.txt b/modules/mol/alg/pymod/CMakeLists.txt
index 30fae2eb199a4ff4f4c461eefcd5bfc4f00d12c8..a1880895f2096619147137d66cfa94c0480ce7f2 100644
--- a/modules/mol/alg/pymod/CMakeLists.txt
+++ b/modules/mol/alg/pymod/CMakeLists.txt
@@ -1,6 +1,7 @@
set(OST_MOL_ALG_PYMOD_SOURCES
wrap_mol_alg.cc
export_svd_superpose.cc
+ export_clash.cc
)
set(OST_MOL_ALG_PYMOD_MODULES
diff --git a/modules/qa/pymod/export_clash.cc b/modules/mol/alg/pymod/export_clash.cc
similarity index 95%
rename from modules/qa/pymod/export_clash.cc
rename to modules/mol/alg/pymod/export_clash.cc
index 82be0e395f0954cdbdbc227fb6e727ab68de2dcb..0720999be1cf7e65eb42ddb256768f3072f9f2f1 100644
--- a/modules/qa/pymod/export_clash.cc
+++ b/modules/mol/alg/pymod/export_clash.cc
@@ -17,11 +17,12 @@
// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
//------------------------------------------------------------------------------
#include <boost/python.hpp>
+
using namespace boost::python;
-#include <ost/qa/clash_score.hh>
+#include <ost/mol/alg/clash_score.hh>
-using namespace ost::qa;
+using namespace ost::mol::alg;
using namespace ost;
namespace {
diff --git a/modules/mol/alg/pymod/wrap_mol_alg.cc b/modules/mol/alg/pymod/wrap_mol_alg.cc
index c41707f1aea60ab41c726a473ee1840835244506..2d409899673e6feeb6d46caf76d6a1d6b2bbc35b 100644
--- a/modules/mol/alg/pymod/wrap_mol_alg.cc
+++ b/modules/mol/alg/pymod/wrap_mol_alg.cc
@@ -27,7 +27,7 @@ using namespace boost::python;
using namespace ost;
void export_svdSuperPose();
-
+void export_Clash();
#if OST_IMG_ENABLED
void export_entity_to_density();
#endif
@@ -56,4 +56,6 @@ BOOST_PYTHON_MODULE(_mol_alg)
arg("end")=-1, arg("ref")=-1));
// def("ConstructCBetas", one_arg, args("entity_handle"));
def("ConstructCBetas", &ost::mol::alg::ConstructCBetas, (arg("entity_handle"), arg("include_gly")=false));
+
+ export_Clash();
}
diff --git a/modules/mol/alg/src/CMakeLists.txt b/modules/mol/alg/src/CMakeLists.txt
index 9ba04a5ee60442edc6ab9522b23222b46a8331f0..f2a23bdd6fbde06023483b25fe210329336a52ee 100644
--- a/modules/mol/alg/src/CMakeLists.txt
+++ b/modules/mol/alg/src/CMakeLists.txt
@@ -6,10 +6,12 @@ set(OST_MOL_ALG_HEADERS
superpose_frames.hh
filter_clashes.hh
construct_cbeta.hh
+ clash_score.hh
)
set(OST_MOL_ALG_SOURCES
svd_superpose.cc
+ clash_score.cc
sec_structure_segments.cc
local_dist_test.cc
superpose_frames.cc
diff --git a/modules/qa/src/clash_score.cc b/modules/mol/alg/src/clash_score.cc
similarity index 76%
rename from modules/qa/src/clash_score.cc
rename to modules/mol/alg/src/clash_score.cc
index e942da7e0fd636f219c4e2a43d3fa9787e4c7360..81e97c6322b9bade135b26cd7e33a74a79240eaa 100644
--- a/modules/qa/src/clash_score.cc
+++ b/modules/mol/alg/src/clash_score.cc
@@ -21,20 +21,20 @@
#include <ost/mol/iterator.hh>
#include "clash_score.hh"
-namespace ost { namespace qa {
+namespace ost { namespace mol { namespace alg {
namespace {
template <typename T, typename I>
-Real do_clash_score(const T& ent_a, const mol::EntityView& ent_b)
+Real do_clash_score(const T& ent_a, const EntityView& ent_b)
{
Real energy=0.0;
for (I i=ent_a.AtomsBegin(), e=ent_a.AtomsEnd(); i!=e; ++i) {
- mol::AtomViewList clashees=ent_b.FindWithin((*i).GetPos(),
+ AtomViewList clashees=ent_b.FindWithin((*i).GetPos(),
(*i).GetRadius()+1.7);
- for (mol::AtomViewList::iterator j=clashees.begin(),
+ for (AtomViewList::iterator j=clashees.begin(),
e2=clashees.end(); j!=e2; ++j) {
energy+=StericEnergy((*j).GetPos(), (*j).GetRadius()-0.25,
(*i).GetPos(), (*i).GetRadius()-0.25);
@@ -62,22 +62,22 @@ Real StericEnergy(const geom::Vec3& pos1, Real r1,
return 57.273*(1.0-sqrt(distance_sqr)/rr);
}
-Real ClashScore(const mol::EntityView& ent_a, const mol::EntityView& ent_b)
+Real ClashScore(const EntityView& ent_a, const EntityView& ent_b)
{
- return do_clash_score<mol::EntityView, mol::AtomViewIter>(ent_a, ent_b);
+ return do_clash_score<EntityView, AtomViewIter>(ent_a, ent_b);
}
-Real ClashScore(const mol::EntityHandle& ent_a, const mol::EntityView& ent_b)
+Real ClashScore(const EntityHandle& ent_a, const EntityView& ent_b)
{
- return do_clash_score<mol::EntityHandle, mol::AtomHandleIter>(ent_a, ent_b);
+ return do_clash_score<EntityHandle, AtomHandleIter>(ent_a, ent_b);
}
-Real ClashScore(const mol::AtomHandle& atom, const mol::EntityView& ent_b)
+Real ClashScore(const AtomHandle& atom, const EntityView& ent_b)
{
Real energy=0.0;
- mol::AtomViewList clashees=ent_b.FindWithin(atom.GetPos(),
+ AtomViewList clashees=ent_b.FindWithin(atom.GetPos(),
atom.GetRadius()+2.0);
- for (mol::AtomViewList::iterator j=clashees.begin(),
+ for (AtomViewList::iterator j=clashees.begin(),
e2=clashees.end(); j!=e2; ++j) {
energy+=StericEnergy((*j).GetPos(), (*j).GetRadius(),
atom.GetPos(), atom.GetRadius());
@@ -85,4 +85,4 @@ Real ClashScore(const mol::AtomHandle& atom, const mol::EntityView& ent_b)
return energy;
}
-}}
+}}}
diff --git a/modules/qa/src/clash_score.hh b/modules/mol/alg/src/clash_score.hh
similarity index 83%
rename from modules/qa/src/clash_score.hh
rename to modules/mol/alg/src/clash_score.hh
index fea13bbeaab037354a044a3ba537b29f95e4d581..ba1700295b341ded0caa6ae727f1ff2c86c5c5e6 100644
--- a/modules/qa/src/clash_score.hh
+++ b/modules/mol/alg/src/clash_score.hh
@@ -16,8 +16,8 @@
// along with this library; if not, write to the Free Software Foundation, Inc.,
// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
//------------------------------------------------------------------------------
-#ifndef OST_QA_CLASH_SCORE_HH
-#define OST_QA_CLASH_SCORE_HH
+#ifndef OST_MOL_ALG_CLASH_SCORE_HH
+#define OST_MOL_ALG_CLASH_SCORE_HH
/*
Author: Marco Biasini
@@ -25,9 +25,9 @@
#include <ost/mol/entity_view.hh>
#include <ost/mol/entity_handle.hh>
-#include <ost/qa/module_config.hh>
+#include <ost/mol/alg/module_config.hh>
-namespace ost { namespace qa {
+namespace ost { namespace mol { namespace alg {
/// \defgroup Clash Steric Clash Score Calculation
///
@@ -41,20 +41,20 @@ namespace ost { namespace qa {
/// For each atom of ent_a the interaction with atoms of ent_b calculated.
/// \return 0.0 if there are no clashes and a positive clash score otherwise.
/// \sa \ref the_hammer.py "The Hammer Example"
-Real DLLEXPORT_OST_QA ClashScore(const mol::EntityView& ent_a, const mol::EntityView& ent_b);
+Real DLLEXPORT_OST_MOL_ALG ClashScore(const mol::EntityView& ent_a, const mol::EntityView& ent_b);
/// \brief calculate clash score between full entity and view
-Real DLLEXPORT_OST_QA ClashScore(const mol::EntityHandle& ent_a,
+Real DLLEXPORT_OST_MOL_ALG ClashScore(const mol::EntityHandle& ent_a,
const mol::EntityView& ent_b);
//// \brief calculate clash score of one single atom
///
/// \return floating point between 0 and 10
/// \sa \ref the_hammer.py "The Hammer Example"
-Real DLLEXPORT_OST_QA ClashScore(const mol::AtomHandle& atom,
+Real DLLEXPORT_OST_MOL_ALG ClashScore(const mol::AtomHandle& atom,
const mol::EntityView& ent_b);
/// \brief calculate steric energy of two atoms
-Real DLLEXPORT_OST_QA StericEnergy(const geom::Vec3& pos1, Real r1,
+Real DLLEXPORT_OST_MOL_ALG StericEnergy(const geom::Vec3& pos1, Real r1,
const geom::Vec3& pos2, Real r2);
//@}
@@ -62,6 +62,6 @@ Real DLLEXPORT_OST_QA StericEnergy(const geom::Vec3& pos1, Real r1,
///
/// Dynamic recalculation of clash score for a moving object. The real-valued
/// clash score is then color-mapped onto the objects.
-}}
+}}}
#endif
diff --git a/modules/qa/CMakeLists.txt b/modules/qa/CMakeLists.txt
deleted file mode 100644
index 6955f55f9b8d0237224a2d4aab25aa3b5310003d..0000000000000000000000000000000000000000
--- a/modules/qa/CMakeLists.txt
+++ /dev/null
@@ -1,2 +0,0 @@
-add_subdirectory(src)
-add_subdirectory(pymod)
\ No newline at end of file
diff --git a/modules/qa/pymod/CMakeLists.txt b/modules/qa/pymod/CMakeLists.txt
deleted file mode 100644
index c9681924294521ffbe8119f585f24bb9e7a3f120..0000000000000000000000000000000000000000
--- a/modules/qa/pymod/CMakeLists.txt
+++ /dev/null
@@ -1,13 +0,0 @@
-set(OST_QA_PYMOD_SOURCES
- export_interaction.cc
- export_torsion.cc
- export_packing.cc
- export_reduced.cc
- export_utilities.cc
- wrap_qa.cc
- export_clash.cc
-)
-set(OST_QA_PYMOD_MODULES
-__init__.py
-)
-pymod(NAME qa CPP ${OST_QA_PYMOD_SOURCES} PY ${OST_QA_PYMOD_MODULES})
diff --git a/modules/qa/pymod/__init__.py b/modules/qa/pymod/__init__.py
deleted file mode 100644
index 6e144e870165d695cb921ac8493706179b9bbb25..0000000000000000000000000000000000000000
--- a/modules/qa/pymod/__init__.py
+++ /dev/null
@@ -1,19 +0,0 @@
-#------------------------------------------------------------------------------
-# This file is part of the OpenStructure project <www.openstructure.org>
-#
-# Copyright (C) 2008-2011 by the OpenStructure authors
-#
-# This library is free software; you can redistribute it and/or modify it under
-# the terms of the GNU Lesser General Public License as published by the Free
-# Software Foundation; either version 3.0 of the License, or (at your option)
-# any later version.
-# This library is distributed in the hope that it will be useful, but WITHOUT
-# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-# FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with this library; if not, write to the Free Software Foundation, Inc.,
-# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
-#------------------------------------------------------------------------------
-from _qa import *
\ No newline at end of file
diff --git a/modules/qa/pymod/export_interaction.cc b/modules/qa/pymod/export_interaction.cc
deleted file mode 100644
index 47f8a1c9ba1f8e543bda4772ec9527b2bd949fc5..0000000000000000000000000000000000000000
--- a/modules/qa/pymod/export_interaction.cc
+++ /dev/null
@@ -1,269 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2011 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
-//------------------------------------------------------------------------------
-#include <boost/python.hpp>
-using namespace boost::python;
-
-#include <ost/qa/interaction_statistics.hh>
-#include <ost/qa/all_atom_potential.hh>
-#include <boost/python/register_ptr_to_python.hpp>
-using namespace ost::qa;
-using namespace ost;
-
-namespace {
-typedef uint64_t(InteractionStatistics::*F1)(Real) const;
-typedef uint64_t(InteractionStatistics::*F2)(atom::ChemType,
- atom::ChemType, Real) const;
-F1 f1=&InteractionStatistics::GetCount;
-F2 f2=&InteractionStatistics::GetCount;
-
-
-
-typedef float (AllAtomPotential::*oneArg)(mol::EntityView,
- std::string);
-typedef float (AllAtomPotential::*twoArgs)(mol::EntityView,
- mol::EntityView,
- std::string);
-
-typedef float (AllAtomPotential::*threeArgs)(atom::ChemType,
- atom::ChemType, float);
-
-oneArg one_arg =&AllAtomPotential::GetTotalEnergy;
-twoArgs two_args =&AllAtomPotential::GetTotalEnergy;
-threeArgs three_args =&AllAtomPotential::GetEnergy;
-}
-
-void export_Interaction()
-{
- enum_<atom::ChemType>("ChemType")
- .value("O_GLY", atom::O_GLY)
- .value("N_GLY", atom::N_GLY)
- .value("C_GLY", atom::C_GLY)
- .value("C_GLY_A", atom::C_GLY_A)
-
- .value("O_ALA", atom::O_ALA)
- .value("N_ALA", atom::N_ALA)
- .value("C_ALA", atom::C_ALA)
- .value("C_ALA_A", atom::C_ALA_A)
- .value("C_ALA_B", atom::C_ALA_B)
-
- .value("O_VAL", atom::O_VAL)
- .value("N_VAL", atom::N_VAL)
- .value("C_VAL", atom::C_VAL)
- .value("C_VAL_A", atom::C_VAL_A)
- .value("C_VAL_B", atom::C_VAL_B)
- .value("C_VAL_G", atom::C_VAL_G)
-
- .value("O_LEU", atom::O_LEU)
- .value("N_LEU", atom::N_LEU)
- .value("C_LEU", atom::C_LEU)
- .value("C_LEU_A", atom::C_LEU_A)
- .value("C_LEU_B", atom::C_LEU_B)
- .value("C_LEU_G", atom::C_LEU_G)
- .value("C_LEU_D", atom::C_LEU_D)
-
- .value("O_ILE", atom::O_ILE)
- .value("N_ILE", atom::N_ILE)
- .value("C_ILE", atom::C_ILE)
- .value("C_ILE_A", atom::C_ILE_A)
- .value("C_ILE_B", atom::C_ILE_B)
- .value("C_ILE_G1", atom::C_ILE_G1)
- .value("C_ILE_G2", atom::C_ILE_G2)
- .value("C_ILE_D1", atom::C_ILE_D1)
-
- .value("O_THR", atom::O_THR)
- .value("N_THR", atom::N_THR)
- .value("C_THR", atom::C_THR)
- .value("C_THR_A", atom::C_THR_A)
- .value("C_THR_B", atom::C_THR_B)
- .value("O_THR_G1", atom::O_THR_G1)
- .value("C_THR_G2", atom::C_THR_G2)
-
- .value("O_SER", atom::O_SER)
- .value("N_SER", atom::N_SER)
- .value("C_SER", atom::C_SER)
- .value("C_SER_A", atom::C_SER_A)
- .value("C_SER_B", atom::C_SER_B)
- .value("O_SER_G", atom::O_SER_G)
-
- .value("O_CYS", atom::O_CYS)
- .value("N_CYS", atom::N_CYS)
- .value("C_CYS", atom::C_CYS)
- .value("C_CYS_A", atom::C_CYS_A)
- .value("C_CYS_B", atom::C_CYS_B)
- .value("S_CYS_G", atom::S_CYS_G)
-
- .value("O_MET", atom::O_MET)
- .value("N_MET", atom::N_MET)
- .value("C_MET", atom::C_MET)
- .value("C_MET_A", atom::C_MET_A)
- .value("C_MET_B", atom::C_MET_B)
- .value("C_MET_G", atom::C_MET_G)
- .value("S_MET_D", atom::S_MET_D)
- .value("C_MET_E", atom::C_MET_E)
-
- .value("O_ASP", atom::O_ASP)
- .value("N_ASP", atom::N_ASP)
- .value("C_ASP", atom::C_ASP)
- .value("C_ASP_A", atom::C_ASP_A)
- .value("C_ASP_B", atom::C_ASP_B)
- .value("C_ASP_G", atom::C_ASP_G)
- .value("O_ASP_D", atom::O_ASP_D)
-
- .value("O_GLU", atom::O_GLU)
- .value("N_GLU", atom::N_GLU)
- .value("C_GLU", atom::C_GLU)
- .value("C_GLU_A", atom::C_GLU_A)
- .value("C_GLU_B", atom::C_GLU_B)
- .value("C_GLU_G", atom::C_GLU_G)
- .value("C_GLU_D", atom::C_GLU_D)
- .value("O_GLU_E", atom::O_GLU_E)
-
- .value("O_ASN", atom::O_ASN)
- .value("N_ASN", atom::N_ASN)
- .value("C_ASN", atom::C_ASN)
- .value("C_ASN_A", atom::C_ASN_A)
- .value("C_ASN_B", atom::C_ASN_B)
- .value("C_ASN_G", atom::C_ASN_G)
- .value("O_ASN_D", atom::O_ASN_D)
- .value("N_ASN_D", atom::N_ASN_D)
-
- .value("O_GLN", atom::O_GLN)
- .value("N_GLN", atom::N_GLN)
- .value("C_GLN", atom::C_GLN)
- .value("C_GLN_A", atom::C_GLN_A)
- .value("C_GLN_B", atom::C_GLN_B)
- .value("C_GLN_G", atom::C_GLN_G)
- .value("C_GLN_D", atom::C_GLN_D)
- .value("O_GLN_E", atom::O_GLN_E)
- .value("N_GLN_E", atom::N_GLN_E)
-
- .value("O_LYS", atom::O_LYS)
- .value("N_LYS", atom::N_LYS)
- .value("C_LYS", atom::C_LYS)
- .value("C_LYS_A", atom::C_LYS_A)
- .value("C_LYS_B", atom::C_LYS_B)
- .value("C_LYS_G", atom::C_LYS_G)
- .value("C_LYS_D", atom::C_LYS_D)
- .value("C_LYS_E", atom::C_LYS_E)
- .value("N_LYS_Z", atom::N_LYS_Z)
-
- .value("O_ARG", atom::O_ARG)
- .value("N_ARG", atom::N_ARG)
- .value("C_ARG", atom::C_ARG)
- .value("C_ARG_A", atom::C_ARG_A)
- .value("C_ARG_B", atom::C_ARG_B)
- .value("C_ARG_G", atom::C_ARG_G)
- .value("C_ARG_D", atom::C_ARG_D)
- .value("N_ARG_E", atom::N_ARG_E)
- .value("C_ARG_Z", atom::C_ARG_Z)
- .value("N_ARG_H", atom::N_ARG_H)
-
- .value("O_TYR", atom::O_TYR)
- .value("N_TYR", atom::N_TYR)
- .value("C_TYR", atom::C_TYR)
- .value("C_TYR_A", atom::C_TYR_A)
- .value("C_TYR_B", atom::C_TYR_B)
- .value("C_TYR_G", atom::C_TYR_G)
- .value("C_TYR_D", atom::C_TYR_D)
- .value("C_TYR_E", atom::C_TYR_E)
- .value("C_TYR_Z", atom::C_TYR_Z)
- .value("O_TYR_H", atom::O_TYR_H)
-
- .value("O_PHE", atom::O_PHE)
- .value("N_PHE", atom::N_PHE)
- .value("C_PHE", atom::C_PHE)
- .value("C_PHE_A", atom::C_PHE_A)
- .value("C_PHE_B", atom::C_PHE_B)
- .value("C_PHE_G", atom::C_PHE_G)
- .value("C_PHE_D", atom::C_PHE_D)
- .value("C_PHE_E", atom::C_PHE_E)
- .value("C_PHE_Z", atom::C_PHE_Z)
-
- .value("O_HIS", atom::O_HIS)
- .value("N_HIS", atom::N_HIS)
- .value("C_HIS", atom::C_HIS)
- .value("C_HIS_A", atom::C_HIS_A)
- .value("C_HIS_B", atom::C_HIS_B)
- .value("C_HIS_G", atom::C_HIS_G)
- .value("N_HIS_D1", atom::N_HIS_D1)
- .value("C_HIS_D2", atom::C_HIS_D2)
- .value("C_HIS_E1", atom::C_HIS_E1)
- .value("N_HIS_E2", atom::N_HIS_E2)
-
- .value("O_TRP", atom::O_TRP)
- .value("N_TRP", atom::N_TRP)
- .value("C_TRP", atom::C_TRP)
- .value("C_TRP_A", atom::C_TRP_A)
- .value("C_TRP_B", atom::C_TRP_B)
- .value("C_TRP_G", atom::C_TRP_G)
- .value("C_TRP_D1", atom::C_TRP_D1)
- .value("C_TRP_D2", atom::C_TRP_D2)
- .value("N_TRP_E1", atom::N_TRP_E1)
- .value("C_TRP_E2", atom::C_TRP_E2)
- .value("C_TRP_E3", atom::C_TRP_E3)
- .value("C_TRP_Z2", atom::C_TRP_Z2)
- .value("C_TRP_Z3", atom::C_TRP_Z3)
- .value("C_TRP_H2", atom::C_TRP_H2)
-
- .value("O_PRO", atom::O_PRO)
- .value("N_PRO", atom::N_PRO)
- .value("C_PRO", atom::C_PRO)
- .value("C_PRO_A", atom::C_PRO_A)
- .value("C_PRO_B", atom::C_PRO_B)
- .value("C_PRO_G", atom::C_PRO_G)
- .value("C_PRO_D", atom::C_PRO_D)
- ;
-
- class_<InteractionStatistics>("InteractionStatistics",
- init<Real, Real, Real, int>(args("lower_cutoff","upper_cutoff",
- "bucket_size", "sequence_sep")))
- .def("Extract", &InteractionStatistics::Extract, args("view"))
- .def("GetCount", f1, args("distance"))
- .def("GetCount", f2, args("partner1", "partner2", "distance"))
- .def("SaveToFile", &InteractionStatistics::SaveToFile, args("file_name"))
- .def("LoadFromFile", &InteractionStatistics::LoadFromFile).staticmethod("LoadFromFile")
- ;
-
- class_<AllAtomPotentialOpts>("AllAtomPotentialOpts", init<>())
- .def(init<float,float,float,int,float>((arg("lower_cutoff"),
- arg("upper_cutoff"), arg("dist_bin_size"),
- arg("sequence_sep"), arg("sigma")=0.02)))
- .def_readwrite("LowerCutoff", &AllAtomPotentialOpts::lower_cutoff)
- .def_readwrite("UpperCutoff", &AllAtomPotentialOpts::upper_cutoff)
- .def_readwrite("DistanceBucketSize",
- &AllAtomPotentialOpts::distance_bucket_size)
- .def_readwrite("SequenceSeparation", &AllAtomPotentialOpts::sequence_sep)
- .def_readwrite("Sigma", &AllAtomPotentialOpts::sigma)
- ;
- class_<AllAtomPotential>("AllAtomPotential", no_init)
- .def("Create", &AllAtomPotential::Create).staticmethod("Create")
- .def("Repair", &AllAtomPotential::Repair).staticmethod("Repair")
- .def("LoadFromFile",
- &AllAtomPotential::LoadFromFile).staticmethod("LoadFromFile")
- .def("GetTotalEnergy", one_arg, args("view"))
- .def("GetTotalEnergy", two_args, args("view", "target_view"))
- .def("GetEnergyCounts", &AllAtomPotential::GetEnergyCounts)
- .def("GetEnergy", three_args, args("atom_type_1", "atom_type_1", "distance"))
- .def("SaveToFile", &AllAtomPotential::SaveToFile)
- .add_property("options", make_function(&AllAtomPotential::GetOptions, return_value_policy<copy_const_reference>()))
- .def("SetSequenceSeparation", &AllAtomPotential::SetSequenceSeparation)
- ;
- register_ptr_to_python<AllAtomPotentialPtr>();
- register_ptr_to_python<InteractionStatisticsPtr>();
-}
diff --git a/modules/qa/pymod/export_packing.cc b/modules/qa/pymod/export_packing.cc
deleted file mode 100644
index 607d0618250f66575756a469d13b7ebcc75f7cb7..0000000000000000000000000000000000000000
--- a/modules/qa/pymod/export_packing.cc
+++ /dev/null
@@ -1,63 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2011 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
-//------------------------------------------------------------------------------
-#include <boost/python.hpp>
-using namespace boost::python;
-#include <boost/python/register_ptr_to_python.hpp>
-#include <ost/qa/packing_statistics.hh>
-#include <ost/qa/packing_potential.hh>
-using namespace ost::qa;
-using namespace ost;
-
-namespace {
- typedef uint64_t (PackingStatistics::*F1)(AminoAcid) const;
- typedef uint64_t (PackingStatistics::*F2)(AminoAcid, int) const;
- F1 f1=&PackingStatistics::GetCount;
- F2 f2=&PackingStatistics::GetCount;
-}
-
-void export_Packing()
-{
- class_<PackingStatistics>("PackingStatistics",
- init<Real,int,int>())
- .def(init<>())
- .def("Extract", &PackingStatistics::Extract, arg("model"))
- .def("GetCount", f1,
- arg("amino_acid"))
- .def("GetCount", f2,
- arg("amino_acid"), arg("count"))
- .def("LoadFromFile", &PackingStatistics::LoadFromFile).staticmethod("LoadFromFile")
- .def("SaveToFile", &PackingStatistics::SaveToFile)
- ;
- register_ptr_to_python<PackingStatisticsPtr>();
-
- class_<PackingPotentialOpts>("PackingPotentialOpts", init<>())
- .def_readwrite("MaxCounts", &PackingPotentialOpts::max_counts)
- .def_readwrite("Sigma", &PackingPotentialOpts::sigma)
- .def_readwrite("Cutoff", &PackingPotentialOpts::cutoff)
- .def_readwrite("BucketSize", &PackingPotentialOpts::bucket_size)
- ;
- class_<PackingPotential>("PackingPotential", no_init)
- .def("Create", &PackingPotential::Create).staticmethod("Create")
- .def("LoadFromFile", &PackingPotential::LoadFromFile).staticmethod("LoadFromFile")
- .def("GetTotalEnergy", &PackingPotential::GetTotalEnergy)
- .def("GetEnergyCounts", &PackingPotential::GetEnergyCounts)
- .def("SaveToFile", &PackingPotential::SaveToFile)
- ;
- register_ptr_to_python<PackingPotentialPtr>();
-}
diff --git a/modules/qa/pymod/export_reduced.cc b/modules/qa/pymod/export_reduced.cc
deleted file mode 100644
index 14f9d546532e6456cee32cd23ffb60e26cfeb8f7..0000000000000000000000000000000000000000
--- a/modules/qa/pymod/export_reduced.cc
+++ /dev/null
@@ -1,73 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2011 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
-//------------------------------------------------------------------------------
-
-#include <boost/python.hpp>
-#include <ost/mol/mol.hh>
-#include <ost/qa/reduced_statistics.hh>
-#include <ost/qa/reduced_potential.hh>
-
-using namespace ost::qa;
-using namespace ost::mol;
-using namespace boost::python;
-
-uint64_t (ReducedStatistics::*get_count)(AminoAcid,
- AminoAcid,
- int,int)=&ReducedStatistics::GetCount;
-void (ReducedStatistics::*ex_h)(EntityHandle)=&ReducedStatistics::Extract;
-void (ReducedStatistics::*ex_v)(EntityView)=&ReducedStatistics::Extract;
-
-Real (ReducedPotential::*get_h)(EntityHandle,bool)=&ReducedPotential::GetTotalEnergy;
-Real (ReducedPotential::*get_v)(EntityView,bool)=&ReducedPotential::GetTotalEnergy;
-void export_Reduced()
-{
- class_<ReducedStatOptions>("ReducedStatOptions", init<>())
- .def(init<Real,Real,uint,uint,uint>((arg("l_cutoff"), arg("d_cutoff"),
- arg("num_ang_bins"), arg("num_dist_bins"), arg("sequence_sep"))))
- .def_readwrite("lower_cutoff", &ReducedStatOptions::lower_cutoff)
- .def_readwrite("upper_cutoff", &ReducedStatOptions::upper_cutoff)
- .def_readwrite("num_angular_bins", &ReducedStatOptions::num_angular_bins)
- .def_readwrite("num_dist_bins", &ReducedStatOptions::num_dist_bins)
- .def_readwrite("sequence_sep", &ReducedStatOptions::sequence_sep)
- ;
-
-
- class_<ReducedStatistics, ReducedStatisticsPtr>("ReducedStatistics", no_init)
- .def(init<Real,Real,uint,uint,uint>((arg("l_cutoff"), arg("u_cutoff"),
- arg("num_ang_bins"), arg("num_dist_bins"), arg("sequence_sep"))))
- .def("Extract", ex_h, arg("ent"))
- .def("Extract", ex_v, arg("ent"))
- .add_property("options", make_function(&ReducedStatistics::GetOptions,
- return_value_policy<copy_const_reference>()))
- .def("Save", &ReducedStatistics::Save)
- .def("Load", &ReducedStatistics::Load).staticmethod("Load")
- .def("GetCount", get_count)
- ;
- class_<ReducedPotential, ReducedPotentialPtr>("ReducedPotential", no_init)
- .def("Load", &ReducedPotential::Load).staticmethod("Load")
- .def("Create", &ReducedPotential::Create).staticmethod("Create")
- .def("Save", &ReducedPotential::Save)
- .def("GetEnergy", &ReducedPotential::GetEnergy)
- .def("GetTotalEnergy", get_h,
- (arg("ent"), arg("normalize")=true))
- .def("GetTotalEnergy", get_v,
- (arg("ent"), arg("normalize")=true))
- .add_property("options", make_function(&ReducedPotential::GetOptions,
- return_value_policy<copy_const_reference>()))
- ;
-}
\ No newline at end of file
diff --git a/modules/qa/pymod/export_torsion.cc b/modules/qa/pymod/export_torsion.cc
deleted file mode 100644
index 77d76a0d5c860848c470b8f8d47f2b4a9fdf7c59..0000000000000000000000000000000000000000
--- a/modules/qa/pymod/export_torsion.cc
+++ /dev/null
@@ -1,182 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2011 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
-//------------------------------------------------------------------------------
-#include <boost/python.hpp>
-using namespace boost::python;
-
-#include <ost/qa/solis_torsion_statistics.hh>
-#include <ost/qa/torsion_statistics.hh>
-#include <ost/mol/mol.hh>
-#include <boost/python/suite/indexing/vector_indexing_suite.hpp>
-#include <boost/python/register_ptr_to_python.hpp>
-#include <ost/qa/solis_torsion_potential.hh>
-#include <ost/qa/torsion_potential.hh>
-
-using namespace ost::qa;
-using namespace ost;
-
-
-namespace {
- typedef Real (TorsionStatisticsSolis::*ADDMethod)(AminoAcid,
- Real, Real) const;
- typedef Real (TorsionStatisticsSolis::*DDMethod)(Real, Real) const;
- typedef void (TorsionStatisticsSolis::*CMethod)(mol::EntityView);
- typedef void (TorsionStatisticsSolis::*EMethod)(mol::EntityHandle);
- ADDMethod GetF1 = &TorsionStatisticsSolis::GetFrequency;
- DDMethod GetF2 = &TorsionStatisticsSolis::GetFrequency;
- CMethod Extract1 = &TorsionStatisticsSolis::Extract;
- EMethod Extract2 = &TorsionStatisticsSolis::Extract;
-
-Real (TorsionPotentialSolis::*total_en_view_solis)(mol::EntityView)=
- &TorsionPotentialSolis::GetTotalEnergy;
-Real (TorsionPotentialSolis::*total_en_handl_solis)(mol::EntityHandle)=
- &TorsionPotentialSolis::GetTotalEnergy;
-
-
-
- typedef void (TorsionStatistics::*XMethod)(mol::EntityView);
- typedef void (TorsionStatistics::*YMethod)(mol::EntityHandle);
- XMethod Extract3 = &TorsionStatistics::Extract;
- YMethod Extract4 = &TorsionStatistics::Extract;
-
-Real (TorsionPotential::*total_en_view)(mol::EntityView)=
- &TorsionPotential::GetTotalEnergy;
-Real (TorsionPotential::*total_en_handl)(mol::EntityHandle)=
- &TorsionPotential::GetTotalEnergy;
-}
-
-void export_Torsion()
-{
-
- enum_<AminoAcid>("AminoAcid")
- .value("Ala", Ala)
- .value("Arg", Arg)
- .value("Asn", Asn)
- .value("Asp", Asp)
- .value("Gln", Gln)
- .value("Glu", Glu)
- .value("Lys", Lys)
- .value("Ser", Ser)
- .value("Cys", Cys)
- .value("Tyr", Tyr)
- .value("Thr", Thr)
- .value("Val", Val)
- .value("Ile", Ile)
- .value("Leu", Leu)
- .value("Gly", Gly)
- .value("Pro", Pro)
- .value("Met", Met)
- .value("His", His)
- .value("Phe", Phe)
- .value("Trp", Trp)
- .export_values()
- ;
-
- class_<AminoAcidSet>("AminoAcidSet", init<>())
- .def("Add", &AminoAcidSet::Add)
- .def("Remove", &AminoAcidSet::Remove)
- .def("Contains", &AminoAcidSet::Contains)
- .def("Empty", &AminoAcidSet::Empty)
- .def("CreatePolarSet",
- &AminoAcidSet::CreatePolarSet).staticmethod("CreatePolarSet")
- .def("CreateApolarSet",
- &AminoAcidSet::CreateApolarSet).staticmethod("CreateApolarSet")
- .def("CreateAromaticSet",
- &AminoAcidSet::CreateAromaticSet).staticmethod("CreateAromaticSet")
- .def("CreateThreeStateSet",
- &AminoAcidSet::CreateThreeStateSet).staticmethod("CreateThreeStateSet")
- .def("CreatePseudoSet",
- &AminoAcidSet::CreatePseudoSet).staticmethod("CreatePseudoSet")
- .def("CreateCompleteSet",
- &AminoAcidSet::CreateCompleteSet).staticmethod("CreateCompleteSet")
- .def("CreateSet", &AminoAcidSet::CreateSet).staticmethod("CreateSet")
- .def(self_ns::str(self))
- ;
-
- class_<AminoAcidAlphabet>("AminoAcidAlphabet", init<>())
- .def(vector_indexing_suite<AminoAcidAlphabet>())
- ;
-
-
- class_<TorsionPotentialOptsSolis>("TorsionPotentialOptsSolis", init<>())
- .def_readwrite("AngularBucketSize",
- &TorsionPotentialOptsSolis::angular_bucket_size)
- .def_readwrite("OuterAlphabet", &TorsionPotentialOptsSolis::outer_alphabet)
- .def_readwrite("InnerAlphabet", &TorsionPotentialOptsSolis::inner_alphabet)
- ;
-
- class_<TorsionPotentialOpts>("TorsionPotentialOpts", init<>())
- .def_readwrite("PrevAngularBucketSize",
- &TorsionPotentialOpts::prev_angular_bucket_size)
- .def_readwrite("CentralAngularBucketSize",
- &TorsionPotentialOpts::central_angular_bucket_size)
- .def_readwrite("NextAngularBucketSize",
- &TorsionPotentialOpts::next_angular_bucket_size)
- .def_readwrite("Alphabet", &TorsionPotentialOpts::alphabet)
- ;
-
-
- class_<TorsionPotentialSolis, boost::noncopyable>("TorsionPotentialSolis", no_init)
- .def("Create", &TorsionPotentialSolis::Create).staticmethod("Create")
- .def("LoadFromFile", &TorsionPotentialSolis::LoadFromFile).staticmethod("LoadFromFile")
- .def("SaveToFile", &TorsionPotentialSolis::SaveToFile)
- .def("GetEnergyCounts", &TorsionPotentialSolis::GetEnergyCounts)
- .def("GetTotalEnergy", total_en_view_solis)
- .def("GetTotalEnergy", total_en_handl_solis)
- ;
-
- class_<TorsionPotential, boost::noncopyable>("TorsionPotential", no_init)
- .def("Create", &TorsionPotential::Create).staticmethod("Create")
- .def("LoadFromFile", &TorsionPotential::LoadFromFile).staticmethod("LoadFromFile")
- .def("SaveToFile", &TorsionPotential::SaveToFile)
- .def("GetEnergyCounts", &TorsionPotential::GetEnergyCounts)
- .def("GetTotalEnergy", total_en_view)
- .def("GetTotalEnergy", total_en_handl)
- ;
-
-
- register_ptr_to_python<TorsionPotentialSolisPtr>();
- register_ptr_to_python<TorsionStatisticsSolisPtr>();
- class_<TorsionStatisticsSolis>("TorsionStatisticsSolis", init<>())
- .def(init<int>(args("torsion_bucket_size")))
- .def("Extract", Extract2, args("model"))
- .def("Extract", Extract1, args("chain"))
- .def("GetFrequency", GetF1,
- arg("amino_acid"), arg("phi_angle"), arg("psi_angle"))
- .def("GetFrequency", GetF2,
- arg("phi_angle"), arg("psi_angle"))
- .def("SaveToFile", &TorsionStatisticsSolis::SaveToFile, arg("file_name"))
- .def("LoadFromFile",
- &TorsionStatisticsSolis::LoadFromFile,
- arg("file_name")).staticmethod("LoadFromFile")
- ;
-
- register_ptr_to_python<TorsionPotentialPtr>();
- register_ptr_to_python<TorsionStatisticsPtr>();
- class_<TorsionStatistics>("TorsionStatistics", init<>())
- .def(init<int,int,int>(args("prev_torsion_bucket_size",
- "central_torsion_bucket_size",
- "next_torsion_bucket_size")))
- .def("Extract", Extract4, args("model"))
- .def("Extract", Extract3, args("chain"))
- .def("SaveToFile", &TorsionStatistics::SaveToFile, arg("file_name"))
- .def("LoadFromFile",
- &TorsionStatistics::LoadFromFile,
- arg("file_name")).staticmethod("LoadFromFile")
- ;
-}
diff --git a/modules/qa/pymod/export_utilities.cc b/modules/qa/pymod/export_utilities.cc
deleted file mode 100644
index 31a6f2ab8d5bd954b75c9f2829a8753b2840fbc5..0000000000000000000000000000000000000000
--- a/modules/qa/pymod/export_utilities.cc
+++ /dev/null
@@ -1,34 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2011 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
-//------------------------------------------------------------------------------
-#include <boost/python.hpp>
-#include <ost/qa/amino_acids.hh>
-using namespace boost::python;
-using namespace ost::qa;
-
-
-void export_Utilties()
-{
-
- def ("ResidueToAminoAcid",&ResidueToAminoAcid);
- def ("AminoAcidToResidueName",&AminoAcidToResidueName);
- def ("OneLetterCodeToResidueName",&OneLetterCodeToResidueName);
- def ("ResidueNameToOneLetterCode",&ResidueNameToOneLetterCode);
- def ("OneLetterCodeToAminoAcid",&OneLetterCodeToAminoAcid);
-
-}
\ No newline at end of file
diff --git a/modules/qa/pymod/pdbtools.py b/modules/qa/pymod/pdbtools.py
deleted file mode 100644
index d53d213a74df50c5382971cc5945930a6baec13d..0000000000000000000000000000000000000000
--- a/modules/qa/pymod/pdbtools.py
+++ /dev/null
@@ -1,59 +0,0 @@
-#------------------------------------------------------------------------------
-# This file is part of the OpenStructure project <www.openstructure.org>
-#
-# Copyright (C) 2008-2011 by the OpenStructure authors
-#
-# This library is free software; you can redistribute it and/or modify it under
-# the terms of the GNU Lesser General Public License as published by the Free
-# Software Foundation; either version 3.0 of the License, or (at your option)
-# any later version.
-# This library is distributed in the hope that it will be useful, but WITHOUT
-# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-# FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-# details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with this library; if not, write to the Free Software Foundation, Inc.,
-# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
-#------------------------------------------------------------------------------
-import httplib
-import os.path
-import types
-def GetModelsFromPISCES(pisces_list, skip_header=True):
- """
- generator function to iterate over models and chains listed in a PISCES
- file.
- """
- pisces=open(pisces_list)
- if skip_header:
- pisces.readline()
- for line in pisces:
- if line=='':
- continue
- pdb_id_and_chain=line.split(' ')[0]
- yield pdb_id_and_chain[:4], pdb_id_and_chain[4:]
- pisces.close()
-
-def RetrieveModels(models, output_dir, file_pattern='pdb%s.ent'):
- """
- Retrieve one or more pdb models from the pdb.org server.
-
- models must be a pdb id or list of pdb ids
- """
- is_tuple=isinstance(models, types.TupleType)
- is_list=isinstance(models, types.ListType)
- is_generator=isinstance(models, types.GeneratorType)
- if not (is_list or is_tuple or is_generator):
- models=[models]
- conn=httplib.HTTPConnection('www.pdb.org')
- for model_id, chain in models:
- print 'getting file for model with id=%s...' % model_id.lower(),
- conn.request('GET', '/pdb/files/%s.pdb' % model_id )
- response=conn.getresponse()
- print response.reason
- if response.status==200:
- data=response.read()
- f=open(os.path.join(output_dir, file_pattern % model_id), 'w+')
- f.write(data)
- f.close()
- conn.close()
\ No newline at end of file
diff --git a/modules/qa/pymod/wrap_qa.cc b/modules/qa/pymod/wrap_qa.cc
deleted file mode 100644
index 14c66d90e3b2ebce817671682f49dc93bea624b0..0000000000000000000000000000000000000000
--- a/modules/qa/pymod/wrap_qa.cc
+++ /dev/null
@@ -1,36 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2011 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
-//------------------------------------------------------------------------------
-#include <boost/python.hpp>
-
-
-void export_Torsion();
-void export_Interaction();
-void export_Packing();
-void export_Clash();
-void export_Reduced();
-void export_Utilties();
-BOOST_PYTHON_MODULE(_qa)
-{
- export_Torsion();
- export_Interaction();
- export_Packing();
- export_Clash();
- export_Reduced();
- export_Utilties();
-}
diff --git a/modules/qa/src/CMakeLists.txt b/modules/qa/src/CMakeLists.txt
deleted file mode 100644
index fee79e13a73d1c7a582c68ce7df81a4c5563f1a6..0000000000000000000000000000000000000000
--- a/modules/qa/src/CMakeLists.txt
+++ /dev/null
@@ -1,42 +0,0 @@
-set(OST_QA_HEADERS
-histogram.hh
-index.hh
-multi_classifier.hh
-amino_acids.hh
-torsion_statistics.hh
-torsion_potential.hh
-solis_torsion_statistics.hh
-solis_torsion_potential.hh
-interaction_statistics.hh
-all_atom_potential.hh
-packing_statistics.hh
-atom_types.hh
-packing_potential.hh
-clash_score.hh
-reduced_statistics.hh
-reduced_potential.hh
-module_config.hh
-)
-
-set(OST_QA_SOURCES
-reduced_statistics.cc
-reduced_potential.cc
-torsion_statistics.cc
-torsion_potential.cc
-solis_torsion_statistics.cc
-solis_torsion_potential.cc
-interaction_statistics.cc
-packing_statistics.cc
-amino_acids.cc
-atom_types.cc
-all_atom_potential.cc
-packing_potential.cc
-clash_score.cc
-impl/reduced_impl.cc
-)
-
-
-module(NAME qa SOURCES ${OST_QA_SOURCES}
- HEADERS reduced_impl.hh IN_DIR impl ${OST_QA_HEADERS}
- DEPENDS_ON io mol_alg)
-
diff --git a/modules/qa/src/all_atom_potential.cc b/modules/qa/src/all_atom_potential.cc
deleted file mode 100644
index 0de014227eee5a568a3cff0826e24b965f485000..0000000000000000000000000000000000000000
--- a/modules/qa/src/all_atom_potential.cc
+++ /dev/null
@@ -1,334 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2011 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
-//------------------------------------------------------------------------------
-#include "all_atom_potential.hh"
-#include <ost/mol/mol.hh>
-#include <ost/io/binary_data_source.hh>
-#include <ost/io/binary_data_sink.hh>
-#include <ost/io/container_serialization.hh>
-#include <boost/filesystem/convenience.hpp>
-#include <ost/message.hh>
-#include <ost/io/io_exception.hh>
-
-/*
- Author: Marco Biasini, Pascal Benkert
- */
-
-namespace ost { namespace qa {
-
-namespace {
-
-class AllAtomPotentialCalculator : public mol::EntityVisitor {
-public:
- AllAtomPotentialCalculator(AllAtomPotential::AllAtomEnergies& energies,
- AllAtomPotentialOpts& opts,
- mol::EntityView target_view,
- int s):
- energies_(energies),
- options_(opts),
- energy_(0.0),
- target_view_(target_view),
- interaction_counts_(0),
- interaction_counts_vector_(std::vector<int>(s, 0)),
- score_vector_(std::vector<float>(s, 0.0)),
- pos_counter(0)
- {
- }
-
- virtual bool VisitResidue(const mol::ResidueHandle& residue)
- {
- if(curr_aa_!=Xxx) pos_counter++;
- curr_aa_=ResidueToAminoAcid(residue);
-// std::cout << residue_energy_ << " " << interaction_counts_ << std::endl;
- return curr_aa_!=Xxx;
- }
-
- virtual bool VisitAtom(const mol::AtomHandle& atom_handle)
- {
- atom::ChemType type_a=GetAtomTypeByName(curr_aa_, atom_handle.GetName());
- if (type_a!=atom::UNKNOWN) {
- mol::AtomViewList nearby_atoms=target_view_.FindWithin(atom_handle.GetPos(),
- options_.upper_cutoff);
- for (mol::AtomViewList::iterator i=nearby_atoms.begin(),
- e=nearby_atoms.end(); i!=e; ++i) {
- mol::AtomView a=*i;
- AminoAcid aa_b=ResidueToAminoAcid(a.GetHandle().GetResidue());
- if (aa_b==Xxx)
- continue;
- atom::ChemType type_b=GetAtomTypeByName(aa_b, a.GetName());
- if (type_b!=atom::UNKNOWN) {
-
- float d=geom::Distance(atom_handle.GetPos(),
- a.GetPos());
-
- // avoid rounding problems: distances very close to the cut-off may
- // be rounded up the to cut-off and lead to an overflow in container
- // energies_
- d=d-0.0001; //used to prevent overflow if distance == upper_cutoff
- if (d<0) d=0.0;
-
- if (d>options_.lower_cutoff) {
- // GetHandle() necessary to retriev original index of the view (as
- // compared to index in the view):
- int abs_sep=abs(atom_handle.GetResidue().GetIndex()-
- a.GetResidue().GetHandle().GetIndex());
- if (abs_sep<options_.sequence_sep) {
- continue;
- }
- energy_+=energies_.Get(type_a, type_b, d);
- interaction_counts_vector_[pos_counter-1]++;
- score_vector_[pos_counter-1]+=energies_.Get(type_a, type_b, d);
- interaction_counts_++;
- }
- }
- }
- }
- return false;
- }
-
- float GetEnergy() const
- {
- return energy_;
- }
-
- int GetEnergyCounts() const
- {
- return interaction_counts_;
- }
-
- std::vector<float> GetResidueEnergyVector() const
- {
- return score_vector_;
- }
-
- std::vector<int> GetResidueCountsVector() const
- {
- return interaction_counts_vector_;
- ;
- }
-
-private:
- AllAtomPotential::AllAtomEnergies& energies_;
- AllAtomPotentialOpts options_;
- AminoAcid curr_aa_;
- float energy_;
- mol::EntityView target_view_;
- int interaction_counts_;
- std::vector<int> interaction_counts_vector_;
- std::vector<float> score_vector_;
- int pos_counter;
-};
-
-}
-
-AllAtomPotentialPtr AllAtomPotential::Create(const InteractionStatisticsPtr& s,
- const AllAtomPotentialOpts & o)
-{
-
- AllAtomPotentialPtr p(new AllAtomPotential);
- p->options_=o;
- int num=int((o.upper_cutoff-o.lower_cutoff)/o.distance_bucket_size);
- p->energies_=AllAtomEnergies(0.0, IntegralClassifier(atom::UNKNOWN, 0),
- IntegralClassifier(atom::UNKNOWN, 0),
- ContinuousClassifier(num, o.lower_cutoff,
- o.upper_cutoff));
- p->Fill(s);
- return p;
-}
-
-
-void AllAtomPotential::SaveToFile(const String& filename)
-{
- std::ofstream stream(filename.c_str(), std::ios_base::binary);
- io::BinaryDataSink ds(stream);
- ds << *this;
-}
-
-AllAtomPotentialPtr AllAtomPotential::LoadFromFile(const String& filename)
-{
- if (!boost::filesystem::exists(filename)) {
- std::stringstream ss;
- ss << "Could not open interaction potential. File '"
- << filename << "' does not exist";
- throw io::IOException(ss.str());
- }
-
-
- std::ifstream stream(filename.c_str(), std::ios_base::binary);
- io::BinaryDataSource ds(stream);
- AllAtomPotentialPtr all_atom_p(new AllAtomPotential);
- ds >> *all_atom_p.get();
- return all_atom_p;
-}
-
-float AllAtomPotential::GetTotalEnergy(mol::EntityView view,
- mol::EntityView target_view, std::string property_identifier="")
-{
- mol::EntityHandle e=view.GetHandle();
- int res_count=view.GetResidueList().size();
- AllAtomPotentialCalculator c(energies_, options_, target_view, res_count);
- view.Apply(c);
- interaction_counts_=c.GetEnergyCounts();
-
- std::vector<float> rev=c.GetResidueEnergyVector();
- std::vector<int> rcv=c.GetResidueCountsVector();
-
- if(property_identifier!="") {
- for(int i=0;i<res_count;++i) {
- view.GetResidueList()[i].SetFloatProp(property_identifier, rev[i]);
- view.GetResidueList()[i].SetIntProp(property_identifier+"_counts", rcv[i]);
- }
- }
- return c.GetEnergy();
-}
-
-float AllAtomPotential::GetTotalEnergy(mol::EntityView view, std::string property_identifier="")
-{
- mol::EntityHandle e=view.GetHandle();
- int res_count=view.GetResidueList().size();
- AllAtomPotentialCalculator c(energies_, options_, view, res_count);
- view.Apply(c);
- interaction_counts_=c.GetEnergyCounts();
- std::string a="";
- std::vector<float> rev=c.GetResidueEnergyVector();
- std::vector<int> rcv=c.GetResidueCountsVector();
-
- if(property_identifier!="") {
- for(int i=0;i<res_count;++i) {
- view.GetResidueList()[i].SetFloatProp(property_identifier, rev[i]);
- view.GetResidueList()[i].SetIntProp(property_identifier+"_counts", rcv[i]);
- }
- }
- return c.GetEnergy();
-}
-
-void AllAtomPotential::SetSequenceSeparation(int seq_sep) {
- options_.sequence_sep=seq_sep;
-}
-
-
-AllAtomPotentialOpts::AllAtomPotentialOpts():
- sigma(0.02), lower_cutoff(3.0), upper_cutoff(20.0), distance_bucket_size(1.0),
- sequence_sep(8)
-{
-}
-
-AllAtomPotentialOpts::AllAtomPotentialOpts(float lc, float uc,
- float dbs, int sp, float s):
- sigma(s), lower_cutoff(lc), upper_cutoff(uc), distance_bucket_size(dbs),
- sequence_sep(sp)
-{
-
-}
-
-template <typename DS>
-void AllAtomPotential::Serialize(DS& ds)
-{
- ds & options_;
- ds & energies_;
-}
-
-template <typename DS>
-void AllAtomPotentialOpts::Serialize(DS& ds)
-{
- ds & lower_cutoff;
- ds & upper_cutoff;
- ds & sigma;
- ds & sequence_sep;
- ds & distance_bucket_size;
-}
-
-void AllAtomPotential::Repair()
-{
- // for C-apha (backbone only) models fill Calpha interactions with corresponding Cbeta values
- typedef AllAtomPotential::AllAtomEnergies::IndexType Index;
- int num=int((options_.upper_cutoff-
- options_.lower_cutoff)/options_.distance_bucket_size);
-
- for (int i=0; i<atom::UNKNOWN-1; ++i) {
- for (int j=0; j<atom::UNKNOWN-1; ++j) {
-
- for (int k=0; k<num; ++k) {
- float e=energies_.Get(Index(i, j, k));
-
- //check if Cbeta (has counts) and not Glycin-Calpha
- if(i==0 or j==0){ //mysteriously needed for one case of j=0 (TODO: check later, perhaps in RepairCbetaStatistics())
- continue;
- }
- if (e!= 0 and i==3 and energies_.Get(Index(i, j+1, k))==0) {
- energies_.Set(Index(i, j-1, k), e);
-// std::cout << e << " ";
- }
- else if (e!= 0 and j==3 and energies_.Get(Index(i+1, j, k))==0) {
- energies_.Set(Index(i-1, j, k), e);
-// std::cout << e << " ";
- }
- else {
- if(e!= 0 and energies_.Get(Index(i, j+1, k))==0 and energies_.Get(Index(i+1, j, k))==0) {
-// std::cout << e << " ";
-
- energies_.Set(Index(i-1, j, k), e);
- energies_.Set(Index(i, j-1, k), e);
- energies_.Set(Index(i-1, j-1, k), e);
- }
- }
-
- }
- }
-
- }
-}
-
-void AllAtomPotential::Fill(const InteractionStatisticsPtr& stats)
-{
- typedef AllAtomPotential::AllAtomEnergies::IndexType Index;
- int num=int((options_.upper_cutoff-
- options_.lower_cutoff)/options_.distance_bucket_size);
-
- uint64_t total_counts = 0;
- for (int k=0; k<num; ++k) {
- total_counts = total_counts+stats->GetCount(options_.distance_bucket_size*k+
- options_.lower_cutoff+
- options_.distance_bucket_size*0.5);
- }
-
- for (int i=0; i<atom::UNKNOWN; ++i) {
- for (int j=0; j<atom::UNKNOWN; ++j) {
- uint64_t t2=stats->GetCount(atom::ChemType(i), atom::ChemType(j));
-
- for (int k=0; k<num; ++k) {
- uint64_t t3=stats->GetCount(atom::ChemType(i), atom::ChemType(j),
- options_.distance_bucket_size*k+
- options_.lower_cutoff+
- Real(options_.distance_bucket_size*0.5));
- // could be moved outside of the loop and cached...
- uint64_t t4=stats->GetCount(options_.distance_bucket_size*k+
- options_.lower_cutoff+
- options_.distance_bucket_size*0.5);
- float f1=t2 > 0 ?(float(t3)/float(t2)) : 0.0;
- float f2=total_counts > 0 ? (float(t4)/float(total_counts)) : 0.0;
- float d = f2>0.000000001 ? f1/f2: 0.0;
- // prop = (Nd_xy / Nxy) / (Nd / Ntot)
- float e=0.582*log(1+options_.sigma*t2)-0.582*log(1+options_.sigma*t2*d);
- energies_.Set(Index(i, j, k), e);
- }
- }
- }
-}
-
-}}
diff --git a/modules/qa/src/all_atom_potential.hh b/modules/qa/src/all_atom_potential.hh
deleted file mode 100644
index 9381e702474f7b36c6ea85d487bb9d67c604450a..0000000000000000000000000000000000000000
--- a/modules/qa/src/all_atom_potential.hh
+++ /dev/null
@@ -1,116 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2011 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
-//------------------------------------------------------------------------------
-#ifndef OST_QA_ALL_ATOM_POTENTIAL_HH
-#define OST_QA_ALL_ATOM_POTENTIAL_HH
-/*
- Author: Marco Biasini
- */
-
-#include <boost/shared_ptr.hpp>
-#include <ost/qa/module_config.hh>
-#include <ost/qa/interaction_statistics.hh>
-
-
-namespace ost { namespace qa {
-
-class AllAtomPotential;
-typedef boost::shared_ptr<AllAtomPotential> AllAtomPotentialPtr;
-
-/// \brief interaction statistics options
-struct DLLEXPORT_OST_QA AllAtomPotentialOpts {
-
- AllAtomPotentialOpts();
-
- AllAtomPotentialOpts(float lower_cutoff, float upper_cutoff,
- float distance_bucket_size, int sequence_sep,
- float sigma=0.02);
-
- public:
- /// \brief weight factor
- float sigma;
- /// \brief atoms that are closer than the lower cutoff are not considered
- float lower_cutoff;
- /// \brief atoms that are further apart than the upper cutoff are ignored
- float upper_cutoff;
-
- /// \brief distance bucket size
- float distance_bucket_size;
- /// \brief sequence separation
- int sequence_sep;
-
- template <typename DS>
- void Serialize(DS& ds);
-};
-
-
-
-class DLLEXPORT_OST_QA AllAtomPotential {
-public:
- /// \brief calculate new statistical potential from the given statistics
- /// and options
- static AllAtomPotentialPtr Create(const InteractionStatisticsPtr& s,
- const AllAtomPotentialOpts& o);
-
- /// \brief load interaction potential from file
- static AllAtomPotentialPtr LoadFromFile(const String& filename);
-
- /// \brief save interaction potential to file
- void SaveToFile(const String& filename);
-
- /// \brief calculate all-atom interaction score for whole entity
- float GetTotalEnergy(mol::EntityView view, std::string property_identifier);
-
- /// \brief extract energy of a specific interaction
- /// (for plotting pseudo Lennard-Jones potential).
- float GetEnergy(atom::ChemType type_a, atom::ChemType type_b,
- float distance)
- {
- return energies_.Get(type_a, type_b, distance);
- }
- /// \brief calculate all-atom interaction between two entities.
- /// Two entities need to be provided:
- /// the atoms for which the energy should be derived and
- /// the atoms with respect to which the energy should be calculted.
- float GetTotalEnergy(mol::EntityView view, mol::EntityView target_view, std::string property_identifier);
-
- /// \brief retrieve total number of interactions (for normalisation)
- int GetEnergyCounts() const { return interaction_counts_; }
-
- /// \brief set different seqeunce separation than used for training
- void SetSequenceSeparation(int seq_sep);
-
- const AllAtomPotentialOpts& GetOptions() const { return options_; }
- template <typename DS>
- void Serialize(DS& ds);
-public:
- void Repair();
- void Fill(const InteractionStatisticsPtr& stats);
-
- /// parameters: atom type one, atom type two, distance
- typedef MultiClassifier<float, int, int, float> AllAtomEnergies;
-private:
- AllAtomPotentialOpts options_;
- AllAtomEnergies energies_;
- mol::EntityView target_view_;
- int interaction_counts_;
-};
-
-}}
-
-#endif
diff --git a/modules/qa/src/atom_types.cc b/modules/qa/src/atom_types.cc
deleted file mode 100644
index 7933e93d6de590e9fcdc3fffb6af42fba56bde13..0000000000000000000000000000000000000000
--- a/modules/qa/src/atom_types.cc
+++ /dev/null
@@ -1,241 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2011 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
-//------------------------------------------------------------------------------
-#include <boost/version.hpp>
-#if BOOST_VERSION>=103800
-#define BOOST_SPIRIT_USE_OLD_NAMESPACE
-#include <boost/spirit/include/classic_symbols.hpp>
-#else
-#include <boost/spirit/symbols.hpp>
-#endif
-
-#include <map>
-#include "atom_types.hh"
-
-namespace ost { namespace qa {
-
-using namespace boost::spirit;
-
-
-// let's have a little bit of syntactic sugar to define the atom name to
-// atom type mapping.
-class ResidueMap : public std::map<AminoAcid, atom::ChemType> {
-public:
- ResidueMap(AminoAcid amino_acid, atom::ChemType type) {
- this->operator()(amino_acid, type);
- }
- ResidueMap& operator()(AminoAcid amino_acid, atom::ChemType type) {
- this->insert(std::make_pair(amino_acid, type));
- return *this;
- }
- atom::ChemType Get(AminoAcid amino_acid) {
- assert(amino_acid!=Xxx);
- std::map<AminoAcid, atom::ChemType>::const_iterator i;
- i=this->find(amino_acid);
- if (i!=this->end())
- return i->second;
- return atom::UNKNOWN;
- }
-};
-typedef ResidueMap R;
-
-
-struct AtomNames : public symbols<R> {
- AtomNames() {
- add
- ("C", R(Ala, atom::C_ALA)
- (Arg, atom::C_ARG)
- (Asn, atom::C_ASN)
- (Asp, atom::C_ASP)
- (Gln, atom::C_GLN)
- (Glu, atom::C_GLU)
- (Lys, atom::C_LYS)
- (Ser, atom::C_SER)
- (Cys, atom::C_CYS)
- (Met, atom::C_MET)
- (Trp, atom::C_TRP)
- (Tyr, atom::C_TYR)
- (Thr, atom::C_THR)
- (Val, atom::C_VAL)
- (Ile, atom::C_ILE)
- (Leu, atom::C_LEU)
- (Gly, atom::C_GLY)
- (Pro, atom::C_PRO)
- (His, atom::C_HIS)
- (Phe, atom::C_PHE))
- ("N", R(Ala, atom::N_ALA)
- (Arg, atom::N_ARG)
- (Asn, atom::N_ASN)
- (Asp, atom::N_ASP)
- (Gln, atom::N_GLN)
- (Glu, atom::N_GLU)
- (Lys, atom::N_LYS)
- (Ser, atom::N_SER)
- (Cys, atom::N_CYS)
- (Met, atom::N_MET)
- (Trp, atom::N_TRP)
- (Tyr, atom::N_TYR)
- (Thr, atom::N_THR)
- (Val, atom::N_VAL)
- (Ile, atom::N_ILE)
- (Leu, atom::N_LEU)
- (Gly, atom::N_GLY)
- (Pro, atom::N_PRO)
- (His, atom::N_HIS)
- (Phe, atom::N_PHE))
- ("O", R(Ala, atom::O_ALA)
- (Arg, atom::O_ARG)
- (Asn, atom::O_ASN)
- (Asp, atom::O_ASP)
- (Gln, atom::O_GLN)
- (Glu, atom::O_GLU)
- (Lys, atom::O_LYS)
- (Ser, atom::O_SER)
- (Cys, atom::O_CYS)
- (Met, atom::O_MET)
- (Trp, atom::O_TRP)
- (Tyr, atom::O_TYR)
- (Thr, atom::O_THR)
- (Val, atom::O_VAL)
- (Ile, atom::O_ILE)
- (Leu, atom::O_LEU)
- (Gly, atom::O_GLY)
- (Pro, atom::O_PRO)
- (His, atom::O_HIS)
- (Phe, atom::O_PHE))
- ("CA", R(Ala, atom::C_ALA_A)
- (Arg, atom::C_ARG_A)
- (Asn, atom::C_ASN_A)
- (Asp, atom::C_ASP_A)
- (Gln, atom::C_GLN_A)
- (Glu, atom::C_GLU_A)
- (Lys, atom::C_LYS_A)
- (Ser, atom::C_SER_A)
- (Cys, atom::C_CYS_A)
- (Met, atom::C_MET_A)
- (Trp, atom::C_TRP_A)
- (Tyr, atom::C_TYR_A)
- (Thr, atom::C_THR_A)
- (Val, atom::C_VAL_A)
- (Gly, atom::C_GLY_A)
- (Ile, atom::C_ILE_A)
- (Leu, atom::C_LEU_A)
- (Pro, atom::C_PRO_A)
- (His, atom::C_HIS_A)
- (Phe, atom::C_PHE_A))
- ("CB", R(Ala, atom::C_ALA_B)
- (Arg, atom::C_ARG_B)
- (Asn, atom::C_ASN_B)
- (Asp, atom::C_ASP_B)
- (Gln, atom::C_GLN_B)
- (Glu, atom::C_GLU_B)
- (Lys, atom::C_LYS_B)
- (Ser, atom::C_SER_B)
- (Cys, atom::C_CYS_B)
- (Met, atom::C_MET_B)
- (Trp, atom::C_TRP_B)
- (Tyr, atom::C_TYR_B)
- (Thr, atom::C_THR_B)
- (Val, atom::C_VAL_B)
- (Ile, atom::C_ILE_B)
- (Leu, atom::C_LEU_B)
- (Pro, atom::C_PRO_B)
- (His, atom::C_HIS_B)
- (Phe, atom::C_PHE_B))
- ("CG", R(Arg, atom::C_ARG_G)
- (Asn, atom::C_ASN_G)
- (Asp, atom::C_ASP_G)
- (Gln, atom::C_GLN_G)
- (Glu, atom::C_GLU_G)
- (Lys, atom::C_LYS_G)
- (Met, atom::C_MET_G)
- (Trp, atom::C_TRP_G)
- (Leu, atom::C_LEU_G)
- (Pro, atom::C_PRO_G)
- (Phe, atom::C_PHE_G)
- (Tyr, atom::C_TYR_G)
- (His, atom::C_HIS_G))
- ("CG1", R(Ile, atom::C_ILE_G1)
- (Val, atom::C_VAL_G))
- ("CG2", R(Ile, atom::C_ILE_G2)
- (Thr, atom::C_THR_G2)
- (Val, atom::C_VAL_G))
- ("CD", R(Glu, atom::C_GLU_D)
- (Ile, atom::C_GLN_D)
- (Lys, atom::C_LYS_D)
- (Pro, atom::C_PRO_D)
- (Gln, atom::C_GLN_D)
- (Glu, atom::C_GLU_D)
- (Arg, atom::C_ARG_D))
- ("CD1", R(Trp, atom::C_TRP_D1)
- (Tyr, atom::C_TYR_D)
- (Phe, atom::C_PHE_D)
- (Leu, atom::C_LEU_D)
- (Ile, atom::C_ILE_D1))
- ("CD2", R(Trp, atom::C_TRP_D2)
- (Tyr, atom::C_TYR_D)
- (Phe, atom::C_PHE_D)
- (Leu, atom::C_LEU_D)
- (His, atom::C_HIS_D2))
- ("CE", R(Lys, atom::C_LYS_E))
- ("CE1", R(Phe, atom::C_PHE_E)
- (Tyr, atom::C_TYR_E)
- (His, atom::C_HIS_E1))
- ("CE2", R(Phe, atom::C_PHE_E)
- (Tyr, atom::C_TYR_E))
- ("CE3", R(Trp, atom::C_TRP_E3))
- ("CZ", R(Arg, atom::C_ARG_Z)
- (Phe, atom::C_PHE_Z)
- (Tyr, atom::C_TYR_Z))
- ("CZ3", R(Trp, atom::C_TRP_Z3))
- ("OG", R(Ser, atom::O_SER_G))
- ("OG1", R(Thr, atom::O_THR_G1))
- ("SG", R(Cys, atom::S_CYS_G))
- ("SD", R(Met, atom::S_MET_D))
- ("OD1", R(Asp, atom::O_ASP_D)
- (Asn, atom::O_ASN_D))
- ("OD2", R(Asp, atom::O_ASP_D))
- ("OE1", R(Glu, atom::O_GLU_E)
- (Gln, atom::O_GLN_E))
- ("OE2", R(Glu, atom::O_GLU_E))
- ("ND1", R(His, atom::N_HIS_D1))
- ("ND2", R(Asn, atom::N_ASN_D))
- ("NE", R(Arg, atom::N_ARG_E))
- ("NE1", R(Arg, atom::N_ARG_E))
- ("NE2", R(Gln, atom::N_GLN_E)
- (His, atom::N_HIS_E2))
- ("NH1", R(Arg, atom::N_ARG_H))
- ("NH2", R(Arg, atom::N_ARG_H))
- ("NZ", R(Lys, atom::N_LYS_Z))
- ("OH", R(Tyr, atom::O_TYR_H))
- ;
- }
-};
-
-atom::ChemType GetAtomTypeByName(AminoAcid amino_acid, const String& aname) {
-
- static AtomNames aa_name_symbols;
- R* m=find(aa_name_symbols, aname.c_str());
- if (m) {
- atom::ChemType t=m->Get(amino_acid);
- return t;
- }
- return atom::UNKNOWN;
-
-}
-}}
diff --git a/modules/qa/src/atom_types.hh b/modules/qa/src/atom_types.hh
deleted file mode 100644
index 733edb00449008e3aa8b39e922a773eac8aeb207..0000000000000000000000000000000000000000
--- a/modules/qa/src/atom_types.hh
+++ /dev/null
@@ -1,217 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2011 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
-//------------------------------------------------------------------------------
-#ifndef OST_QA_ATOM_TYPES_HH
-#define OST_QA_ATOM_TYPES_HH
-
-#include <ost/qa/amino_acids.hh>
-
-namespace ost { namespace qa {
-
-namespace atom {
-
- // list of chemically distinguishable atoms.
- typedef enum {
- O_GLY = 0,
- N_GLY,
- C_GLY,
- C_GLY_A,
-
- O_ALA,
- N_ALA,
- C_ALA,
- C_ALA_A,
- C_ALA_B,
-
- O_VAL,
- N_VAL,
- C_VAL,
- C_VAL_A,
- C_VAL_B,
- C_VAL_G,
-
- O_LEU,
- N_LEU,
- C_LEU,
- C_LEU_A,
- C_LEU_B,
- C_LEU_G,
- C_LEU_D,
-
- O_ILE,
- N_ILE,
- C_ILE,
- C_ILE_A,
- C_ILE_B,
- C_ILE_G1,
- C_ILE_G2,
- C_ILE_D1,
-
- O_THR,
- N_THR,
- C_THR,
- C_THR_A,
- C_THR_B,
- O_THR_G1,
- C_THR_G2,
-
- O_SER,
- N_SER,
- C_SER,
- C_SER_A,
- C_SER_B,
- O_SER_G,
-
- O_CYS,
- N_CYS,
- C_CYS,
- C_CYS_A,
- C_CYS_B,
- S_CYS_G,
-
- O_MET,
- N_MET,
- C_MET,
- C_MET_A,
- C_MET_B,
- C_MET_G,
- S_MET_D,
- C_MET_E,
-
- O_ASP,
- N_ASP,
- C_ASP,
- C_ASP_A,
- C_ASP_B,
- C_ASP_G,
- O_ASP_D,
-
- O_GLU,
- N_GLU,
- C_GLU,
- C_GLU_A,
- C_GLU_B,
- C_GLU_G,
- C_GLU_D,
- O_GLU_E,
-
- O_ASN,
- N_ASN,
- C_ASN,
- C_ASN_A,
- C_ASN_B,
- C_ASN_G,
- O_ASN_D,
- N_ASN_D,
-
- O_GLN,
- N_GLN,
- C_GLN,
- C_GLN_A,
- C_GLN_B,
- C_GLN_G,
- C_GLN_D,
- O_GLN_E,
- N_GLN_E,
-
- O_LYS,
- N_LYS,
- C_LYS,
- C_LYS_A,
- C_LYS_B,
- C_LYS_G,
- C_LYS_D,
- C_LYS_E,
- N_LYS_Z,
-
- O_ARG,
- N_ARG,
- C_ARG,
- C_ARG_A,
- C_ARG_B,
- C_ARG_G,
- C_ARG_D,
- N_ARG_E,
- C_ARG_Z,
- N_ARG_H,
-
- O_TYR,
- N_TYR,
- C_TYR,
- C_TYR_A,
- C_TYR_B,
- C_TYR_G,
- C_TYR_D, //D1 AND D2
- C_TYR_E, //E1 and E2
- C_TYR_Z,
- O_TYR_H,
-
- O_PHE,
- N_PHE,
- C_PHE,
- C_PHE_A,
- C_PHE_B,
- C_PHE_G,
- C_PHE_D, //D1 AND D2
- C_PHE_E, //E1 AND E2
- C_PHE_Z,
-
- O_HIS,
- N_HIS,
- C_HIS,
- C_HIS_A,
- C_HIS_B,
- C_HIS_G,
- N_HIS_D1,
- C_HIS_D2,
- C_HIS_E1,
- N_HIS_E2,
-
- O_TRP,
- N_TRP,
- C_TRP,
- C_TRP_A,
- C_TRP_B,
- C_TRP_G,
- C_TRP_D1,
- C_TRP_D2,
- N_TRP_E1,
- C_TRP_E2,
- C_TRP_E3,
- C_TRP_Z2,
- C_TRP_Z3,
- C_TRP_H2,
-
- O_PRO,
- N_PRO,
- C_PRO,
- C_PRO_A,
- C_PRO_B,
- C_PRO_G,
- C_PRO_D,
- UNKNOWN
- } ChemType;
-}
-
-
-DLLEXPORT_OST_QA atom::ChemType GetAtomTypeByName(AminoAcid amino_acid,
- const String& aname);
-
-}}
-
-#endif
diff --git a/modules/qa/src/histogram.hh b/modules/qa/src/histogram.hh
deleted file mode 100644
index e8abb8ff9d894960d36ea5290b2d51be034794cd..0000000000000000000000000000000000000000
--- a/modules/qa/src/histogram.hh
+++ /dev/null
@@ -1,78 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2011 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
-//------------------------------------------------------------------------------
-#ifndef OST_QA_HISTOGRAM_HH
-#define OST_QA_HISTOGRAM_HH
-/*
- Author: Marco Biasini
- */
-#include <ost/stdint.hh>
-
-#include <ost/qa/module_config.hh>
-#include <ost/qa/multi_classifier.hh>
-
-namespace ost { namespace qa {
-
-/// \brief histogram specialization for multi classifier
-template <typename T1,
- typename T2=impl::NullType,
- typename T3=impl::NullType,
- typename T4=impl::NullType,
- typename T5=impl::NullType,
- typename T6=impl::NullType,
- typename T7=impl::NullType>
-class Histogram : public MultiClassifier<uint32_t, T1, T2, T3, T4, T5, T6, T7>
-{
-public:
- typedef Classifier<T1> C1;
- typedef Classifier<T2> C2;
- typedef Classifier<T3> C3;
- typedef Classifier<T4> C4;
- typedef Classifier<T5> C5;
- typedef Classifier<T6> C6;
- typedef Classifier<T7> C7;
-#ifdef _MSC_VER
- Histogram(typename C1::ConstRefType c1,
- typename C2::ConstRefType c2=C2::Type(),
- typename C3::ConstRefType c3=C3::Type(),
- typename C4::ConstRefType c4=C4::Type(),
- typename C5::ConstRefType c5=C5::Type(),
- typename C6::ConstRefType c6=C6::Type(),
- typename C7::ConstRefType c7=C7::Type())
-#else
- Histogram(typename C1::ConstRefType c1,
- typename C2::ConstRefType c2=typename C2::Type(),
- typename C3::ConstRefType c3=typename C3::Type(),
- typename C4::ConstRefType c4=typename C4::Type(),
- typename C5::ConstRefType c5=typename C5::Type(),
- typename C6::ConstRefType c6=typename C6::Type(),
- typename C7::ConstRefType c7=typename C7::Type())
-#endif
- : MultiClassifier<uint32_t, T1, T2, T3, T4,
- T5, T6, T7>(0, c1, c2, c3, c4, c5, c6, c7) {
- }
-
- Histogram():
- MultiClassifier<uint32_t, T1, T2, T3, T4, T5, T6, T7>()
- {
- }
-};
-
-}} // ost::qa
-
-#endif
diff --git a/modules/qa/src/impl/reduced_impl.cc b/modules/qa/src/impl/reduced_impl.cc
deleted file mode 100644
index 59e8c02095a9e1bce00c5afc019b39f9b219b15a..0000000000000000000000000000000000000000
--- a/modules/qa/src/impl/reduced_impl.cc
+++ /dev/null
@@ -1,113 +0,0 @@
-#include <ost/log.hh>
-#include <ost/mol/residue_handle.hh>
-#include <ost/mol/atom_handle.hh>
-#include <ost/mol/atom_view.hh>
-#include <ost/mol/alg/construct_cbeta.hh>
-#include "reduced_impl.hh"
-
-
-namespace ost { namespace qa { namespace impl {
-
-bool ReducedPotentialImpl::VisitResidue(const mol::ResidueHandle& res)
-{
- if (!res.IsPeptideLinking()) {
- return false;
- }
- AminoAcid aa_one=OneLetterCodeToAminoAcid(res.GetOneLetterCode());
- if (aa_one==Xxx) {
- return false;
- }
- geom::Vec3 ca_pos_one;
- geom::Vec3 cb_pos_one;
- uint index=res.GetIndex();
- if (!this->GetCAlphaCBetaPos(res, ca_pos_one, cb_pos_one)) {
- return false;
- }
-
- if (ent_) {
- // we got a full entity handle.
- mol::AtomHandleList within=ent_.FindWithin(ca_pos_one,
- opts_.upper_cutoff-0.00001);
- for (mol::AtomHandleList::const_iterator
- i=within.begin(), e=within.end(); i!=e; ++i) {
- if (i->GetName()=="CA") {
- this->HandleResidue(aa_one, ca_pos_one, cb_pos_one, index, *i);
- }
-
- }
- return false;
- }
- mol::AtomViewList within=view_.FindWithin(ca_pos_one,
- opts_.upper_cutoff-0.00001);
- for (mol::AtomViewList::const_iterator
- i=within.begin(), e=within.end(); i!=e; ++i) {
- if (i->GetName()=="CA") {
- this->HandleResidue(aa_one, ca_pos_one, cb_pos_one, index, i->GetHandle());
- }
-
- }
- return false;
-}
-
-void ReducedPotentialImpl::HandleResidue(AminoAcid aa_one,
- const geom::Vec3& ca_pos_one,
- const geom::Vec3& cb_pos_one,
- uint index_one,
- const mol::AtomHandle& ca_two)
-{
-
- mol::ResidueHandle res_two=ca_two.GetResidue();
- if (res_two.GetIndex()-index_one<opts_.sequence_sep) {
- return;
- }
- if (!res_two.IsPeptideLinking()) {
- return;
- }
-
-
- AminoAcid aa_two=OneLetterCodeToAminoAcid(res_two.GetOneLetterCode());
- if (aa_two==Xxx) {
- return;
- }
- geom::Vec3 ca_pos_two;
- geom::Vec3 cb_pos_two;
- if (!this->GetCAlphaCBetaPos(res_two, ca_pos_two, cb_pos_two)) {
- return;
- }
-
- Real dist=geom::Length(ca_pos_one-ca_pos_two);
- if (dist<opts_.lower_cutoff) {
- return;
- }
- Real angle=geom::Angle(cb_pos_one-ca_pos_one, cb_pos_two-ca_pos_two);
-
- this->OnInteraction(aa_one, aa_two, dist, angle);
-}
-
-bool ReducedPotentialImpl::GetCAlphaCBetaPos(const mol::ResidueHandle& res,
- geom::Vec3& ca_pos,
- geom::Vec3& cb_pos)
-{
- mol::AtomHandle ca=res.FindAtom("CA");
- if (!ca.IsValid()) {
- return false;
- }
- ca_pos=ca.GetPos();
- mol::AtomHandle cb=res.FindAtom("CB");
- if (cb.IsValid()) {
- cb_pos=cb.GetPos();
- return true;
- }
- mol::AtomHandle n=res.FindAtom("N");
- mol::AtomHandle c=res.FindAtom("C");
- if (!(ca.IsValid() && c.IsValid() && n.IsValid())) {
- LOG_WARNING("residue " << res.GetQualifiedName()
- << " doesn't have enough atoms to reconstruct Cbeta position");
- return false;
- }
- cb_pos=mol::alg::CBetaPosition(n.GetPos(), ca.GetPos(), c.GetPos());
- return true;
-}
-
-}}}
-
diff --git a/modules/qa/src/impl/reduced_impl.hh b/modules/qa/src/impl/reduced_impl.hh
deleted file mode 100644
index 1d1157228733a2157681e3d8bcb46a368d1bd085..0000000000000000000000000000000000000000
--- a/modules/qa/src/impl/reduced_impl.hh
+++ /dev/null
@@ -1,63 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2011 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
-//------------------------------------------------------------------------------
-
-#ifndef OST_QA_IMPL_REDUCED_HH
-#define OST_QA_IMPL_REDUCED_HH
-
-
-#include <ost/mol/entity_visitor.hh>
-#include <ost/mol/entity_handle.hh>
-#include <ost/mol/entity_view.hh>
-#include <ost/qa/module_config.hh>
-#include <ost/qa/amino_acids.hh>
-#include <ost/qa/reduced_statistics.hh>
-
-namespace ost { namespace qa { namespace impl {
-
-class DLLEXPORT_OST_QA ReducedPotentialImpl : public mol::EntityVisitor {
-public:
-
- ReducedPotentialImpl(const ReducedStatOptions& opts, mol::EntityHandle ent):
- opts_(opts), ent_(ent)
- { }
-
- ReducedPotentialImpl(const ReducedStatOptions& opts, mol::EntityView ent):
- opts_(opts), view_(ent)
- { }
-
- virtual bool VisitResidue(const mol::ResidueHandle& res);
-
- static bool GetCAlphaCBetaPos(const mol::ResidueHandle& res,
- geom::Vec3& ca_pos,
- geom::Vec3& cb_pos);
-
- virtual void OnInteraction(AminoAcid aa_one, AminoAcid aa_two,
- Real dist, Real angle)=0;
-private:
- void HandleResidue(AminoAcid aa_one, const geom::Vec3& ca_pos_one,
- const geom::Vec3& cb_pos_one,
- uint index_one, const mol::AtomHandle& ca_two);
- ReducedStatOptions opts_;
- mol::EntityHandle ent_;
- mol::EntityView view_;
-};
-
-}}}
-
-#endif
diff --git a/modules/qa/src/index.hh b/modules/qa/src/index.hh
deleted file mode 100644
index 8ae741851125060775b8afbd9a8b6eee8db51163..0000000000000000000000000000000000000000
--- a/modules/qa/src/index.hh
+++ /dev/null
@@ -1,185 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2011 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
-//------------------------------------------------------------------------------
-#ifndef OST_QA_INDEX_HH
-#define OST_QA_INDEX_HH
-
-/*
- Author: Marco Biasini
- */
-
-#include <ost/stdint.hh>
-
-#include <cstring>
-#include <boost/shared_ptr.hpp>
-#include <ost/qa/module_config.hh>
-
-namespace ost { namespace qa {
-
-namespace impl {
-template <uint32_t D>
-class IndexBase {
-public:
- enum { Dimension = D };
- IndexBase(const IndexBase& rhs) {
- memcpy(data_, rhs.data_, sizeof(uint32_t[D]));
- }
- IndexBase() {
- memset(data_, 0, sizeof(uint32_t[D]));
- }
- IndexBase& operator=(const IndexBase& rhs) {
- memcpy(data_, rhs.data_, sizeof(uint32_t[D]));
- return *this;
- }
- uint32_t operator[](uint32_t idx) const {
- assert(idx <= D);
- return data_[idx];
- }
- uint32_t& operator[](uint32_t idx) {
- assert(idx <= D);
- return data_[idx];
- }
-private:
- uint32_t data_[D];
-};
-
-} // namespace impl
-
-template <uint32_t D>
-class Index;
-
-template <>
-class Index<1> : public impl::IndexBase<1> {
-public:
- Index() : impl::IndexBase<1>() {}
- Index(uint32_t a) {
- (*this)[0]=a;
- }
-};
-template <>
-class Index<2> : public impl::IndexBase<2> {
-public:
- Index() : impl::IndexBase<2>() {}
- Index(uint32_t a, uint32_t b) {
- (*this)[0]=a;
- (*this)[1]=b;
- }
-};
-
-template <>
-class Index<3> : public impl::IndexBase<3> {
-public:
- Index() : impl::IndexBase<3>() {}
- Index(uint32_t a, uint32_t b, uint32_t c) {
- (*this)[0]=a;
- (*this)[1]=b;
- (*this)[2]=c;
- }
-};
-
-template <>
-class Index<4> : public impl::IndexBase<4> {
-public:
- Index() : impl::IndexBase<4>() {}
- Index(uint32_t a, uint32_t b, uint32_t c, uint32_t d) {
- (*this)[0]=a;
- (*this)[1]=b;
- (*this)[2]=c;
- (*this)[3]=d;
- }
-};
-
-template <>
-class Index<5> : public impl::IndexBase<5> {
-public:
- Index() : impl::IndexBase<5>() {}
- Index(uint32_t a, uint32_t b, uint32_t c, uint32_t d, uint32_t e) {
- (*this)[0]=a;
- (*this)[1]=b;
- (*this)[2]=c;
- (*this)[3]=d;
- (*this)[4]=e;
- }
-};
-
-template <>
-class Index<6> : public impl::IndexBase<6> {
-public:
- Index() : impl::IndexBase<6>() {}
- Index(uint32_t a, uint32_t b, uint32_t c, uint32_t d, uint32_t e, uint32_t f) {
- (*this)[0]=a;
- (*this)[1]=b;
- (*this)[2]=c;
- (*this)[3]=d;
- (*this)[4]=e;
- (*this)[5]=f;
- }
-};
-
-template <>
-class Index<7> : public impl::IndexBase<7> {
-public:
- Index() : impl::IndexBase<7>() {}
- Index(uint32_t a, uint32_t b, uint32_t c, uint32_t d, uint32_t e, uint32_t f, uint32_t g) {
- (*this)[0]=a;
- (*this)[1]=b;
- (*this)[2]=c;
- (*this)[3]=d;
- (*this)[4]=e;
- (*this)[5]=f;
- (*this)[6]=g;
- }
-};
-
-template<uint32_t D>
-class IndexIterator {
-public:
- typedef Index<D> IndexType;
- IndexIterator(const IndexType& s, const IndexType& e)
- : start_(s), end_(e), current_(s) {
-
- }
-
- IndexIterator<D>& operator++() {
- uint32_t current_it=0;
- while (++current_[current_it] > end_[current_it]) {
- current_it++;
- if (current_it < D) {
- current_[current_it-1] = start_[current_it-1];
- } else {
- break;
- }
- }
- return *this;
- }
- const IndexType& operator *() const {
- return current_;
- }
- bool AtEnd() {
- return current_[D-1] > end_[D-1];
- }
-private:
- IndexType start_;
- IndexType end_;
- IndexType current_;
-
-};
-
-}}
-
-#endif
diff --git a/modules/qa/src/interaction_statistics.cc b/modules/qa/src/interaction_statistics.cc
deleted file mode 100644
index c30fcf132999e9df487a133a8ba4ddd47128ba41..0000000000000000000000000000000000000000
--- a/modules/qa/src/interaction_statistics.cc
+++ /dev/null
@@ -1,194 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2011 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
-//------------------------------------------------------------------------------
-#include "interaction_statistics.hh"
-#include <ost/mol/atom_view.hh>
-#include <ost/mol/residue_view.hh>
-#include <ost/io/binary_data_source.hh>
-#include <ost/io/binary_data_sink.hh>
-#include <ost/io/container_serialization.hh>
-
-using namespace ost::mol::impl;
-
-namespace ost { namespace qa {
-
-InteractionStatistics::InteractionStatistics()
-{
-
-}
-
-void InteractionStatistics::Extract(mol::EntityView view_a, mol::EntityView view_b) {
- view_a_=view_a;
- view_b_=view_b;
- view_a.Apply(*this);
-}
-
-bool InteractionStatistics::VisitResidue(const mol::ResidueHandle& r) {
- amino_acid_=ResidueToAminoAcid(r);
- return amino_acid_!=Xxx;
-}
-
-bool InteractionStatistics::VisitAtom(const mol::AtomHandle& atom) {
- atom::ChemType atype=GetAtomTypeByName(amino_acid_, atom.GetName());
- mol::ResidueHandle my_res=atom.GetResidue();
- if (atype!=atom::UNKNOWN) {
- mol::AtomViewList atoms_in_reach=view_b_.FindWithin(atom.GetPos(),
- upper_cutoff_);
- for (mol::AtomViewList::iterator i=atoms_in_reach.begin(),
- e=atoms_in_reach.end(); i!=e; ++i) {
- mol::AtomView other=*i;
- // avoid rounding problems: distances very close to the cut-off may
- // be rounded up the to cut-off and lead to an overflow in histogram_
- Real dist_sqr=geom::Length2(other.GetPos()-atom.GetPos())-0.0001;
- if (dist_sqr<lower_sqr_) {
- continue;
- }
- mol::ResidueView other_res=other.GetResidue();
- AminoAcid other_aa=ResidueToAminoAcid(other_res.GetHandle());
- if (other_aa==Xxx) {
- continue;
- }
- if (abs(other_res.GetNumber().GetNum()-my_res.GetNumber().GetNum())<sequence_sep_) {
- continue;
- }
- atom::ChemType btype=GetAtomTypeByName(other_aa, other.GetName());
- if (btype==atom::UNKNOWN) {
- continue;
- }
- histogram_.Add(1, atype, btype, sqrt(dist_sqr));
- }
- }
- return true;
-}
-
-InteractionStatistics::InteractionStatistics(Real lower_cutoff,
- Real upper_cutoff,
- Real bucket_size,
- int sequence_sep)
- : lower_cutoff_(lower_cutoff), upper_cutoff_(upper_cutoff),
- bucket_size_(bucket_size),
- sequence_sep_(sequence_sep),
- histogram_(IntegralClassifier(atom::UNKNOWN, 0),
- IntegralClassifier(atom::UNKNOWN, 0),
- ContinuousClassifier(int((upper_cutoff_-lower_cutoff_)/bucket_size),
- lower_cutoff_, upper_cutoff_))
-{
- upper_sqr_=upper_cutoff_*upper_cutoff_;
- lower_sqr_=lower_cutoff_*lower_cutoff_;
-}
-
-int InteractionStatistics::GetSequenceSeparation() const
-{
- return sequence_sep_;
-}
-
-Real InteractionStatistics::GetUpperCutoff() const
-{
- return upper_cutoff_;
-}
-
-Real InteractionStatistics::GetLowerCutoff() const
-{
- return lower_cutoff_;
-}
-
-void InteractionStatistics::SaveToFile(const String& file_name) const
-{
- std::ofstream stream(file_name.c_str(), std::ios_base::binary);
- io::BinaryDataSink ds(stream);
- ds << *this;
-}
-
-Real InteractionStatistics::GetDistanceBucketSize() const
-{
- return bucket_size_;
-}
-
-uint64_t InteractionStatistics::GetCount(Real distance) const
-{
- uint64_t total=0;
- for (uint64_t i=0; i<atom::UNKNOWN; ++i) {
- for (uint64_t j=0; j<atom::UNKNOWN; ++j) {
- total+=histogram_.Get(i, j, distance);
- }
- }
- return total;
-}
-
-uint64_t InteractionStatistics::GetCount(atom::ChemType a,
- atom::ChemType b,
- Real distance) const
-{
- return histogram_.Get(a, b, distance);
-}
-
-
-uint64_t InteractionStatistics::GetCount(atom::ChemType a,
- atom::ChemType b,
- int distance_bin) const
-{
- typedef InteractionHistogram::IndexType Index;
-
- return histogram_.Get(Index(a, b, distance_bin));
-}
-
-
-
-uint64_t InteractionStatistics::GetCount(atom::ChemType a,
- atom::ChemType b) const
-{
- typedef InteractionHistogram::IndexType Index;
- uint64_t num=uint64_t((upper_cutoff_-lower_cutoff_)/bucket_size_);
- uint64_t total=0;
- for (uint64_t k=0; k<num; ++k) {
- total+=histogram_.Get(Index(a, b, k));
- }
- return total;
-}
-
-void InteractionStatistics::Set(atom::ChemType a, atom::ChemType b,
- int distance_bin, int counts) {
- typedef InteractionHistogram::IndexType Index;
- histogram_.Set(Index(a, b, distance_bin), counts);
-}
-
-
-template <typename DS>
-void InteractionStatistics::Serialize(DS& ds)
-{
- ds & lower_cutoff_;
- ds & upper_cutoff_;
- ds & bucket_size_;
- ds & sequence_sep_;
- if (ds.IsSource()) {
- upper_sqr_=upper_cutoff_*upper_cutoff_;
- lower_sqr_=lower_cutoff_*lower_cutoff_;
- }
- ds & histogram_;
-}
-
-InteractionStatisticsPtr InteractionStatistics::LoadFromFile(const String& fn)
-{
- std::ifstream stream(fn.c_str(), std::ios_base::binary);
- io::BinaryDataSource ds(stream);
- InteractionStatisticsPtr p(new InteractionStatistics);
- ds >> *p.get();
- return p;
-}
-
-}}
diff --git a/modules/qa/src/interaction_statistics.hh b/modules/qa/src/interaction_statistics.hh
deleted file mode 100644
index 046a24cc4fe02f5df5c14e0fb4b9910de1138f2b..0000000000000000000000000000000000000000
--- a/modules/qa/src/interaction_statistics.hh
+++ /dev/null
@@ -1,122 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2011 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
-//------------------------------------------------------------------------------
-#ifndef OST_QA_INTERACTION_STATISTICS_HH
-#define OST_QA_INTERACTION_STATISTICS_HH
-/*
- Author: Marco Biasini
- */
-#include <ost/mol/entity_view.hh>
-#include <ost/mol/entity_visitor.hh>
-#include <ost/qa/module_config.hh>
-#include <ost/qa/amino_acids.hh>
-#include <ost/qa/histogram.hh>
-#include <ost/qa/atom_types.hh>
-
-
-
-namespace ost { namespace qa {
-
-/// \brief histogram for interaction histogram
-///
-/// the meaning of the dimensions is: type of first interaction partner, type
-/// of second interaction partner, distance between the two paterns.
-typedef Histogram<int, int, Real> InteractionHistogram;
-class InteractionStatistics;
-typedef boost::shared_ptr<InteractionStatistics> InteractionStatisticsPtr;
-
-class DLLEXPORT_OST_QA InteractionStatistics : public mol::EntityVisitor {
-public:
- /// \brief construct new interaction statistics.
- ///
- /// \param lower_cutoff only interaction parters that are further apart than
- /// this cutoff are taken into account.
- /// \param upper_cutoff only interaction partners below the cutoff are taken
- /// into account
- /// \param bucket_size size of distance bins in Angstroem.
- /// \param sequence_sep residues that are closer than sequence_sep in
- /// sequence are not considered.
- InteractionStatistics(Real lower_cutoff,
- Real upper_cutoff,
- Real bucket_size,
- int sequence_sep);
-
- /// \brief load interaction statistics from file
- static InteractionStatisticsPtr LoadFromFile(const String& file_name);
-
-
- /// Extract the interaction potential from the given entity view.
- void Extract(mol::EntityView a, mol::EntityView b);
-
- void SaveToFile(const String& file_name) const;
-
-
- /// \brief Get distance bucket size
- Real GetDistanceBucketSize() const;
-
- int GetSequenceSeparation() const;
-
- Real GetUpperCutoff() const;
-
- Real GetLowerCutoff() const;
-
- /// \brief Get number of atoms at the given distance regardless of their atom
- /// type.
- uint64_t GetCount(Real distance) const;
-
- /// \brief get number of atoms at given distance by taking their type into
- /// account.
- uint64_t GetCount(atom::ChemType a, atom::ChemType b, Real distance) const;
-
- /// \brief get number of atoms in given distance-bin by taking their type into
- /// account.
- uint64_t GetCount(atom::ChemType a, atom::ChemType b, int distance_bin) const;
-
- /// \brief get number of atoms at given distance by taking their type into
- /// account.
- uint64_t GetCount(atom::ChemType a, atom::ChemType b) const;
-
- /// \brief get number of atoms at given distance by taking their type into
- /// account.
- void Set(atom::ChemType a, atom::ChemType b, int distance_bin, int counts);
-
- /// \internal
- template <typename DS>
- void Serialize(DS& ds);
-public:
- virtual bool VisitResidue(const mol::ResidueHandle& r);
- virtual bool VisitAtom(const mol::AtomHandle& a);
-
-private:
- InteractionStatistics();
-
- Real lower_cutoff_;
- Real lower_sqr_;
- Real upper_cutoff_;
- Real upper_sqr_;
-
- Real bucket_size_;
- int sequence_sep_;
- mol::EntityView view_a_;
- mol::EntityView view_b_;
- AminoAcid amino_acid_;
- InteractionHistogram histogram_;
-};
-
-}}
-#endif
diff --git a/modules/qa/src/module_config.hh b/modules/qa/src/module_config.hh
deleted file mode 100644
index 1d07f3dd7c95819cb2e4c4315c2eae5302e59722..0000000000000000000000000000000000000000
--- a/modules/qa/src/module_config.hh
+++ /dev/null
@@ -1,30 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2011 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
-//------------------------------------------------------------------------------
-#ifndef OST_QA_MODULE_CONFIG_HH
-#define OST_QA_MODULE_CONFIG_HH
-
-#include <ost/qa/module_config.hh>
-
-#if defined(OST_MODULE_OST_QA)
-# define DLLEXPORT_OST_QA DLLEXPORT
-#else
-# define DLLEXPORT_OST_QA DLLIMPORT
-#endif
-
-#endif
diff --git a/modules/qa/src/multi_classifier.hh b/modules/qa/src/multi_classifier.hh
deleted file mode 100644
index 846fdddecbadd99b92093482bcd1024923d6797a..0000000000000000000000000000000000000000
--- a/modules/qa/src/multi_classifier.hh
+++ /dev/null
@@ -1,455 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2011 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
-//------------------------------------------------------------------------------
-#ifndef OST_QA_MULTI_CLASSIFIER_HH
-#define OST_QA_MULTI_CLASSIFIER_HH
-
-#include <ost/stdint.hh>
-#include <vector>
-#include <cassert>
-#include <fstream>
-#include <ost/message.hh>
-#include <iostream>
-
-#include <boost/shared_ptr.hpp>
-
-#include "index.hh"
-#include <ost/config.hh>
-
-namespace ost { namespace qa {
-
-namespace impl {
- // Determine length of a typelist, i.e. the number of template arguments
- // different from NullType. The length can be accessed over the Value
- // member.
- // usage example:
- // int length=LengthOf<int, int>::Value;
- struct NullType {
- template <typename DS>
- void Serialize(DS&) {}
- };
- template <typename T1,
- typename T2,
- typename T3,
- typename T4,
- typename T5,
- typename T6,
- typename T7>
- struct LengthOf;
-
- template <typename T1,
- typename T2,
- typename T3,
- typename T4,
- typename T5,
- typename T6,
- typename T7>
- struct LengthOf {
- enum { Value = 1+LengthOf<T2, T3, T4, T5, T6, T7, NullType>::Value };
- };
- template <>
- struct LengthOf<NullType, NullType, NullType, NullType, NullType, NullType,
- NullType>
- {
- enum { Value = 0 };
- };
-
- //! compile time if statement. If<C, T, F>::Type is set to T if C is true
- // and set to F otherwise.
- template <bool C,
- typename T,
- typename F>
- struct If;
-
- template <typename T,
- typename F>
- struct If<true, T, F> {
- typedef T Type;
- };
-
- template <typename T,
- typename F>
- struct If<false, T, F> {
- typedef F Type;
- };
-
- //! Compile-time check for identity of two types. IsEqual<T1,T2>::Value
- // is true if T1 and T2 are identical, and false otherwise.
- template <typename T1,
- typename T2>
- struct IsEqual;
- template <typename T1,
- typename T2>
- struct IsEqual {
- enum { Value = false };
- };
- template <typename T>
- struct IsEqual<T,T> {
- enum { Value = true };
- };
-
- // Compile-time selector statement to execute conditional statement based
- // on the identity of \c C. If C is identical to the NullType
- // then IfNull<...>::Type is a typedef of T, otherwise, IfNull<...>::Type is a
- // typedef for F.
- template <typename C, typename T, typename F>
- struct IfNull;
-
- template <typename C,
- typename T,
- typename F>
- struct IfNull {
- typedef typename If<IsEqual<NullType, C>::Value, T, F>::Type Type;
- };
-
-}
-
-//! Base class for classifiers.
-class DLLEXPORT_OST_QA ClassifierBase {
-public:
- ClassifierBase(uint32_t number_of_classes)
- : number_of_classes_(number_of_classes) {
- }
- ClassifierBase()
- : number_of_classes_(0) {}
- virtual ~ClassifierBase() {}
- uint32_t GetNumberOfClasses() const {
- return number_of_classes_;
- }
-protected:
- uint32_t number_of_classes_;
-};
-
-//! Classifier for integral classes.
-class DLLEXPORT_OST_QA IntegralClassifier : public ClassifierBase {
-public:
- IntegralClassifier(uint32_t number_of_classes,
- int lower_bound)
- : ClassifierBase(number_of_classes),
- lower_bound_(lower_bound) {
- }
- uint32_t GetIndexOf(int value) const {
- uint32_t idx=(value-lower_bound_);
- assert(this->GetNumberOfClasses()>idx);
- return idx;
- }
- IntegralClassifier()
- : ClassifierBase(0),
- lower_bound_(0) {
- }
-
- template <typename DS>
- void Serialize(DS& ds)
- {
- ds & number_of_classes_;
- ds & lower_bound_;
- }
-private:
- int32_t lower_bound_;
-};
-
-//! Classifier for real valued classes.
-class DLLEXPORT_OST_QA ContinuousClassifier : public ClassifierBase {
-public:
- ContinuousClassifier(uint32_t number_of_classes,
- Real lower_bound,
- Real upper_bound)
- : ClassifierBase(number_of_classes),
- lower_bound_(lower_bound),
- upper_bound_(upper_bound) {
- }
- uint32_t GetIndexOf(Real value) const {
- Real factor=(value-lower_bound_)/(upper_bound_-lower_bound_);
- uint32_t idx=uint32_t(floor(this->GetNumberOfClasses()*factor));
-// std::cout << value << " " << factor << std::endl;
- assert(this->GetNumberOfClasses()>idx);
- return idx;
- }
- ContinuousClassifier()
- : ClassifierBase(1),
- lower_bound_(0), upper_bound_(1) {
- }
- template <typename DS>
- void Serialize(DS& ds)
- {
- ds & number_of_classes_;
- ds & lower_bound_;
- ds & upper_bound_;
- }
-private:
- Real lower_bound_;
- Real upper_bound_;
-};
-
-
-template <typename T>
-struct Classifier;
-
-template <>
-struct DLLEXPORT_OST_QA Classifier<int> {
- typedef IntegralClassifier Type;
- typedef const IntegralClassifier& ConstRefType;
- typedef IntegralClassifier& RefType;
-};
-template <>
-struct DLLEXPORT_OST_QA Classifier<Real> {
- typedef ContinuousClassifier Type;
- typedef const ContinuousClassifier& ConstRefType;
- typedef ContinuousClassifier& RefType;
-};
-#if OST_DOUBLE_PRECISION
-template <>
-struct DLLEXPORT_OST_QA Classifier<float> {
- typedef ContinuousClassifier Type;
- typedef const ContinuousClassifier& ConstRefType;
- typedef ContinuousClassifier& RefType;
-};
-#endif
-template <>
-struct DLLEXPORT_OST_QA Classifier<impl::NullType> {
- typedef impl::NullType Type;
- typedef const impl::NullType& ConstRefType;
- typedef impl::NullType& RefType;
-};
-
-template <typename I>
-struct DLLEXPORT_OST_QA NullFind {
- NullFind(const ClassifierBase&,uint32_t,const impl::NullType&,I&) {};
-};
-template <typename C, typename T, typename I>
-struct IndexFind;
-
-template <typename C, typename I>
-struct DLLEXPORT_OST_QA IndexFind<C,impl::NullType,I> {
- IndexFind(const C&,
- uint32_t,
- const impl::NullType&, I&) {
- }
-};
-
-template <typename C, typename T, typename I>
-struct DLLEXPORT_OST_QA IndexFind {
- IndexFind(const C& classifier, uint32_t i, const T& value, I& index) {
- index[i]=classifier.GetIndexOf(value);
- }
-};
-template <typename T>
-struct NumberOfClasses;
-
-
-template <>
-struct DLLEXPORT_OST_QA NumberOfClasses<impl::NullType> {
- uint32_t operator ()(const impl::NullType& t) {
- return 1;
- }
-};
-
-template <typename T>
-struct DLLEXPORT_OST_QA NumberOfClasses {
- uint32_t operator ()(const T& t) {
- return t.GetNumberOfClasses();
- }
-};
-
-//! \brief generic n-dimensional classifier
-template <typename V, typename T1,
- typename T2=impl::NullType,
- typename T3=impl::NullType,
- typename T4=impl::NullType,
- typename T5=impl::NullType,
- typename T6=impl::NullType,
- typename T7=impl::NullType>
-class DLLEXPORT_OST_QA MultiClassifier {
-public:
- enum { Dimension = impl::LengthOf<T1, T2, T3, T4, T5, T6, T7>::Value };
- typedef V ValueType;
- typedef Index<MultiClassifier::Dimension> IndexType;
- typedef IndexIterator<Dimension> Iterator;
- typedef Classifier<T1> C1;
- typedef Classifier<T2> C2;
- typedef Classifier<T3> C3;
- typedef Classifier<T4> C4;
- typedef Classifier<T5> C5;
- typedef Classifier<T6> C6;
- typedef Classifier<T7> C7;
-#if WIN32
- MultiClassifier(const V& initial_value,
- typename C1::ConstRefType c1,
- typename C2::ConstRefType c2=C2::Type(),
- typename C3::ConstRefType c3=C3::Type(),
- typename C4::ConstRefType c4=C4::Type(),
- typename C5::ConstRefType c5=C5::Type(),
- typename C6::ConstRefType c6=C6::Type(),
- typename C7::ConstRefType c7=C7::Type())
-#else
- MultiClassifier(const V& initial_value,
- typename C1::ConstRefType c1,
- typename C2::ConstRefType c2=typename C2::Type(),
- typename C3::ConstRefType c3=typename C3::Type(),
- typename C4::ConstRefType c4=typename C4::Type(),
- typename C5::ConstRefType c5=typename C5::Type(),
- typename C6::ConstRefType c6=typename C6::Type(),
- typename C7::ConstRefType c7=typename C7::Type())
-#endif
- : classifier1_(c1), classifier2_(c2), classifier3_(c3),
- classifier4_(c4), classifier5_(c5), classifier6_(c6),
- classifier7_(c7) {
- this->ExtractNumberOfClasses();
- // allocate enough memory for all the buckets
- uint32_t total=this->CalculateNumberOfBuckets();
- buckets_.resize(total, initial_value);
- }
-
- MultiClassifier()
- {
- memset(number_of_classes_, 0, sizeof(number_of_classes_));
- }
-
- template <typename DS>
- void Serialize(DS& ds)
- {
- ds & classifier1_;
- ds & classifier2_;
- ds & classifier3_;
- ds & classifier4_;
- ds & classifier5_;
- ds & classifier6_;
- ds & classifier7_;
- if (ds.IsSource()) {
- this->ExtractNumberOfClasses();
- }
- ds & buckets_;
- }
-
- MultiClassifier(const MultiClassifier& rhs)
- : classifier1_(rhs.classifier1_), classifier2_(rhs.classifier2_),
- classifier3_(rhs.classifier3_), classifier4_(rhs.classifier4_),
- classifier5_(rhs.classifier5_), classifier6_(rhs.classifier6_),
- classifier7_(rhs.classifier7_) {
- this->ExtractNumberOfClasses();
- uint32_t total=this->CalculateNumberOfBuckets();
- buckets_.resize(total);
- memcpy(&buckets_.front(), &rhs.buckets_.front(), sizeof(V)*total);
- }
-
- uint32_t GetBucketCount() const {
- return static_cast<uint32_t>(buckets_.size());
- }
-
- void Add(const ValueType& value,
- T1 x1=T1(), T2 x2=T2(),
- T3 x3=T3(), T4 x4=T4(),
- T5 x5=T5(), T6 x6=T6(),
- T7 x7=T7()) {
- IndexType index=this->FindBucket(x1, x2, x3, x4, x5, x6, x7);
- uint32_t linear_index=this->LinearizeBucketIndex(index);
- buckets_[linear_index]+=value;
- }
-
- const ValueType& Get(T1 x1=T1(), T2 x2=T2(),
- T3 x3=T3(), T4 x4=T4(),
- T5 x5=T5(), T6 x6=T6(), T7 x7=T7()) const {
- IndexType index=this->FindBucket(x1, x2, x3, x4, x5, x6, x7);
- uint32_t linear_index=this->LinearizeBucketIndex(index);
- return buckets_[linear_index];
- }
-
- const ValueType& Get(const IndexType& index) const
- {
- return buckets_[this->LinearizeBucketIndex(index)];
- }
-
- void Set(const IndexType& index, const ValueType& value)
- {
- buckets_[this->LinearizeBucketIndex(index)]=value;
- }
- //TODO Make sure that FindBucket is called with the correct number of
- // arguments. Can be done over a wrapper type around T1..T6 that only
- // provides a default c'tor when T is equal to NullType.
- IndexType FindBucket(T1 x1=T1(), T2 x2=T2(), T3 x3=T3(),
- T4 x4=T4(), T5 x5=T5(), T6 x6=T6(),
- T7 x7=T7()) const {
- // determine indices for parameters whose type is not equal to
- // NullType
- IndexType index;
- IndexFind<typename C1::Type, T1,
- IndexType> find_index_1(classifier1_, 0, x1, index);
- IndexFind<typename C2::Type, T2,
- IndexType> find_index_2(classifier2_, 1, x2, index);
- IndexFind<typename C3::Type, T3,
- IndexType> find_index_3(classifier3_, 2, x3, index);
- IndexFind<typename C4::Type, T4,
- IndexType> find_index_4(classifier4_, 3, x4, index);
- IndexFind<typename C5::Type, T5,
- IndexType> find_index_5(classifier5_, 4, x5, index);
- IndexFind<typename C6::Type, T6,
- IndexType> find_index_6(classifier6_, 5, x6, index);
- IndexFind<typename C7::Type, T7,
- IndexType> find_index_7(classifier7_, 6, x7, index);
- return index;
- }
-
- void Add(const ValueType& value, const IndexType& index)
- {
- buckets_[this->LinearizeBucketIndex(index)]+=value;
- }
-private:
- void ExtractNumberOfClasses()
- {
- number_of_classes_[0]=NumberOfClasses<typename C1::Type>()(classifier1_);
- number_of_classes_[1]=NumberOfClasses<typename C2::Type>()(classifier2_);
- number_of_classes_[2]=NumberOfClasses<typename C3::Type>()(classifier3_);
- number_of_classes_[3]=NumberOfClasses<typename C4::Type>()(classifier4_);
- number_of_classes_[4]=NumberOfClasses<typename C5::Type>()(classifier5_);
- number_of_classes_[5]=NumberOfClasses<typename C6::Type>()(classifier6_);
- number_of_classes_[6]=NumberOfClasses<typename C7::Type>()(classifier7_);
- }
-
- uint32_t LinearizeBucketIndex(const IndexType& index) const
- {
- uint32_t factor=1;
- uint32_t linear_index=0;
- for (uint32_t i=0; i<MultiClassifier::Dimension; ++i) {
- linear_index+=factor*index[i];
- factor*=number_of_classes_[i];
- }
- return linear_index;
- }
-
- uint32_t CalculateNumberOfBuckets() const
- {
- uint32_t total=1;
- for (uint32_t i=0; i<MultiClassifier::Dimension; ++i) {
- total*=number_of_classes_[i];
- }
- return total;
- }
- typename C1::Type classifier1_;
- typename C2::Type classifier2_;
- typename C3::Type classifier3_;
- typename C4::Type classifier4_;
- typename C5::Type classifier5_;
- typename C6::Type classifier6_;
- typename C7::Type classifier7_;
- uint32_t number_of_classes_[7];
- std::vector<ValueType> buckets_;
-};
-
-}}
-
-#endif
diff --git a/modules/qa/src/packing_potential.cc b/modules/qa/src/packing_potential.cc
deleted file mode 100644
index b64ab96d0c05742cc6736be5fca87edf882962fb..0000000000000000000000000000000000000000
--- a/modules/qa/src/packing_potential.cc
+++ /dev/null
@@ -1,200 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2011 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
-//------------------------------------------------------------------------------
-#include "packing_potential.hh"
-#include <ost/io/binary_data_source.hh>
-#include <ost/io/binary_data_sink.hh>
-#include <ost/io/container_serialization.hh>
-#include <boost/filesystem/convenience.hpp>
-#include <ost/message.hh>
-#include <sstream>
-#include <ost/mol/atom_view.hh>
-#include <ost/io/io_exception.hh>
-#include <ost/integrity_error.hh>
-
-/*
- Authors: Marco Biasini, Pascal Benkert
- */
-
-namespace ost { namespace qa {
-
-
-PackingPotentialOpts::PackingPotentialOpts():
- sigma(0.02), cutoff(10.0), bucket_size(1), max_counts(25)
-{
-
-}
-
-
-PackingPotentialOpts::PackingPotentialOpts(int b, int m, Real c, Real s):
- sigma(s), cutoff(c), bucket_size(b), max_counts(m)
-{
-
-}
-
-template <typename DS>
-void PackingPotentialOpts::Serialize(DS& ds)
-{
- ds & sigma;
- ds & cutoff;
- ds & bucket_size;
- ds & max_counts;
-}
-
-
-PackingPotential::PackingPotential()
-{
-
-}
-
-void PackingPotential::Fill(const PackingStatisticsPtr& stat, bool calculate_average_energy_flag)
-{
- typedef PackingEnergies::IndexType Index;
- int buckets=(options_.max_counts/options_.bucket_size)+1; // +1 since zero counts are in the first bin
- uint64_t M=stat->GetTotalCount();
- for (int i=0; i < Xxx; ++i) {
- uint64_t Mi=stat->GetCount(AminoAcid(i));
-
- if (calculate_average_energy_flag==1) std::cout << AminoAcid(i) << " " << float(Mi)/M << " ";
- Real per_aa_energy = 0; // for average energy
-
- for (int j=0; j<buckets; ++j) {
- uint64_t fxi=stat->GetCount(AminoAcid(i), j*options_.bucket_size);
- // could be moved out of the loop and cached for more speed. at the
- // moment I just don't care...
- uint64_t fx=stat->GetCount(j*options_.bucket_size);
-
- // propensity = (fxi/Mi)/(fx/M)
- Real propensity=0.0;
- //avoid division by zero:
- if (fx != 0 && Mi != 0 && M != 0) {
- propensity=Real(Real(fxi)/Mi)/(Real(fx)/M);
- }
-
- Real e=log(1+options_.sigma*Mi)-
- log(1+options_.sigma*Mi*propensity);
-
- per_aa_energy=per_aa_energy+fxi*e; // for average energy
-
- energies_.Set(Index(i, j), e);
- }
- if (calculate_average_energy_flag==1) std::cout << per_aa_energy/Mi << std::endl;
- }
-}
-
-PackingPotentialPtr PackingPotential::Create(const PackingStatisticsPtr& stat,
- const PackingPotentialOpts& opts,
- bool calculate_average_energy_flag)
-{
-// stat->bucket_size_=opts.bucket_size;
-// stat->max_counts_=opts.max_counts;
-// stat->cutoff_=opts.cutoff;
-
- if (stat->GetBucketSize() != opts.bucket_size) {
- std::stringstream error_message;
- error_message << "BucketSize limit specified in opts does not agree with those of the statistics file: " << opts.bucket_size << " vs " << stat->GetBucketSize();
- throw IntegrityError(error_message.str());
- }
-
- if (stat->GetMaxCounts() != opts.max_counts) {
- std::stringstream error_message;
- error_message << "MaxCounts limit specified in opts does not agree with those of the statistics file: " << opts.max_counts << " vs " << stat->GetMaxCounts();
- throw IntegrityError(error_message.str());
- }
-
- if (stat->GetCutoffDistance() != opts.cutoff) {
- std::stringstream error_message;
- error_message << "CutoffDistance limit specified in opts does not agree with those of the statistics file: " << opts.cutoff << " vs " << stat->GetCutoffDistance();
- throw IntegrityError(error_message.str());
- }
-
- PackingPotentialPtr p(new PackingPotential);
- p->options_=opts;
-
- p->options_.cutoff=opts.cutoff;
- p->options_.bucket_size=opts.bucket_size;
- p->options_.max_counts=opts.max_counts;
- IntegralClassifier counts((opts.max_counts/opts.bucket_size)+1, 0); // +1 since zero counts are in the first bin
- p->energies_=PackingEnergies(0.0, IntegralClassifier(Xxx, 0), counts);
- p->Fill(stat, calculate_average_energy_flag);
- return p;
-}
-
-PackingPotentialPtr PackingPotential::LoadFromFile(const String& filename)
-{
- if(!boost::filesystem::exists(filename))
- throw io::IOException("Could not open packing potential data file.\nFile does not exist at: "+filename);
-
- PackingPotentialPtr p(new PackingPotential);
- std::ifstream stream(filename.c_str(), std::ios_base::binary);
- io::BinaryDataSource ds(stream);
- ds >> *p.get();
- return p;
-}
-
-void PackingPotential::SaveToFile(const String& filename)
-{
- std::ofstream stream(filename.c_str(), std::ios_base::binary);
- io::BinaryDataSink ds(stream);
- ds << *this;
-}
-
-template <typename DS>
-void PackingPotential::Serialize(DS& ds)
-{
- ds & options_;
- ds & energies_;
-}
-
-
-Real PackingPotential::GetTotalEnergy(const mol::EntityView& view,
- const mol::EntityViewList& views)
-{
- view_=view;
- views_=views;
- energy_=0.0;
- energy_counts_=0;
- view_.Apply(*this);
- return energy_;
-}
-
-int PackingPotential::GetEnergyCounts()
-{
- return energy_counts_;
-}
-
-bool PackingPotential::VisitAtom(const mol::AtomHandle& atom)
-{
- AminoAcid aa=ResidueToAminoAcid(atom.GetResidue());
- if (aa==Xxx) {
- atom.GetResidue().SetFloatProp("solvation_energy",0);
- return false;
- }
- int count=0;
- for (mol::EntityViewList::iterator i=views_.begin(),
- e=views_.end(); i!=e; ++i) {
- count+=i->FindWithin(atom.GetPos(), options_.cutoff).size();
- }
- float local_energy=this->GetPackingEnergy(aa, count);
- atom.GetResidue().SetFloatProp("solvation_energy",local_energy);
- energy_+=local_energy;
- energy_counts_++;
- return false;
-}
-
-}}
diff --git a/modules/qa/src/packing_potential.hh b/modules/qa/src/packing_potential.hh
deleted file mode 100644
index 00c3229f6ea55b5e39d6c2b495baee7796bbe87b..0000000000000000000000000000000000000000
--- a/modules/qa/src/packing_potential.hh
+++ /dev/null
@@ -1,126 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2011 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
-//------------------------------------------------------------------------------
-#ifndef OST_QA_PACKING_POTENTIAL_HH
-#define OST_QA_PACKING_POTENTIAL_HH
-
-/*
- Author: Marco Biasini
- */
-
-
-#include <boost/shared_ptr.hpp>
-
-#include <ost/mol/entity_visitor.hh>
-
-#include "packing_statistics.hh"
-#include "multi_classifier.hh"
-
-namespace ost { namespace qa {
-
-struct DLLEXPORT_OST_QA PackingPotentialOpts {
- /// \brief initialise with sigma 0.02 and bucket_size 1 distance cutoff
- /// 2.0 and max_counts 100.
- PackingPotentialOpts();
-
- /// \brief initialise with specified bucket size, max count and sigma
- PackingPotentialOpts(int bucket_size, int max_count, Real cutoff,
- Real sigma=0.02);
- /// \brief sigma for smoothing, after Sippl, 1990. Usually set to 0.02
- Real sigma;
- /// \brief upper distance cutoff
- Real cutoff;
- /// \brief bin size for counts.
- int bucket_size;
- /// \brief maximal number of atoms
- int max_counts;
-
- template <typename DS>
- void Serialize(DS& ds);
-};
-
-class PackingPotential;
-typedef boost::shared_ptr<PackingPotential> PackingPotentialPtr;
-
-
-/// \brief packing (solvent accessibility) potential
-///
-/// Not thread safe
-class DLLEXPORT_OST_QA PackingPotential : public mol::EntityVisitor {
-public:
- typedef MultiClassifier<float, int, int> PackingEnergies;
-public:
- PackingPotential();
-
- /// \brief create new solvation potential with the given solvation statistics
- /// and options
- /// If the flag ist set the average energy per is calculated
- /// and shown on stdout. May be used to correct compositional bias in
- /// scoring functions (e.g. Pro and Gly have on average lower torsion energies).
- static PackingPotentialPtr Create(const PackingStatisticsPtr& stat,
- const PackingPotentialOpts& opts,
- bool calculate_average_energy_flag=0);
-
- static PackingPotentialPtr LoadFromFile(const String& filename);
-
- void SaveToFile(const String& filename);
-
- /// \brief extract packing statistics of entity view.
- ///
- /// See documentation for PackingStatistics::Extract()
- Real GetTotalEnergy(const mol::EntityView& view,
- const mol::EntityViewList& views);
-
- int GetEnergyCounts();
-
-
- Real GetPackingEnergy(AminoAcid aa, int count) const
- {
- count=count>options_.max_counts ? options_.max_counts : count;
- return energies_.Get(aa, count/options_.bucket_size);
- }
- const PackingPotentialOpts& GetOptions() const { return options_; }
- template <typename DS>
- void Serialize(DS& ds);
-
-public:
- /// \internal
- virtual bool VisitAtom(const mol::AtomHandle& atom);
-private:
- /// \brief potenials are calculated based on the derived statistics
- ///
- /// If the flag ist set the average energy per is calculated
- /// and shown on stdout. May be used to correct compositional bias in
- /// scoring functions (e.g. Pro and Gly have on average lower torsion energies).
- void Fill(const PackingStatisticsPtr& stat,
- bool calculate_average_energy_flag=0);
-
- PackingPotentialOpts options_;
- PackingEnergies energies_;
-
- // used to calculate total energy...
- mol::EntityView view_;
- mol::EntityViewList views_;
- Real energy_;
- int energy_counts_;
-};
-
-}}
-
-#endif
-
diff --git a/modules/qa/src/packing_statistics.cc b/modules/qa/src/packing_statistics.cc
deleted file mode 100644
index d557931ca9ec23af1b7cd81a5cf792a71230eabc..0000000000000000000000000000000000000000
--- a/modules/qa/src/packing_statistics.cc
+++ /dev/null
@@ -1,143 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2011 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
-//------------------------------------------------------------------------------
-#include "packing_statistics.hh"
-
-#include <ost/log.hh>
-#include <ost/geom/geom.hh>
-#include <ost/mol/atom_handle.hh>
-#include <ost/mol/residue_handle.hh>
-#include <ost/mol/atom_view.hh>
-#include <ost/io/binary_data_source.hh>
-#include <ost/io/binary_data_sink.hh>
-#include <ost/io/container_serialization.hh>
-
-namespace ost { namespace qa {
-
-PackingStatistics::PackingStatistics(Real cutoff,
- int max_counts,
- int bucket_size)
- : cutoff_(cutoff),
- max_counts_(max_counts),
- bucket_size_(bucket_size),
- histogram_(IntegralClassifier(Xxx, 0), // Xxx is the last object in enum and therefore corresponds to the total number of atom types
- IntegralClassifier((max_counts/bucket_size)+1, 0)) { // since zero counts is possible, we have n+1 bins
- if (max_counts%bucket_size!=0) {
- LOG_INFO("initialising packing statistics with max_count="
- << max_counts << "which is not divisible by bucket_size="
- << bucket_size << "without remainder. Will continue anyway.");
- }
-}
-
-
-PackingStatistics::PackingStatistics():
- cutoff_(0.0),
- max_counts_(0),
- bucket_size_(0),
- histogram_()
-{
-}
-
-
-void PackingStatistics::Extract(mol::EntityView view, const mol::EntityViewList& views)
-{
- view_=view;
- views_=views;
- view.Apply(*this);
-}
-
-bool PackingStatistics::VisitAtom(const mol::AtomHandle& atom) {
- AminoAcid aa=ResidueToAminoAcid(atom.GetResidue());
- if (aa==Xxx)
- return false;
- int count=0;
- for (mol::EntityViewList::iterator i=views_.begin(),
- e=views_.end(); i!=e; ++i) {
- count+=i->FindWithin(atom.GetPos(), cutoff_).size();
- }
- count=count>=max_counts_ ? max_counts_ : count; // if more counts observed than maximum expected -> set to maximum
- histogram_.Add(1, aa, count/bucket_size_);
- return false;
-}
-
-int PackingStatistics::GetBucketSize() const {
- return bucket_size_;
-}
-
-int PackingStatistics::GetMaxCounts() const {
- return max_counts_;
-}
-
-//! \brief Get cutoff radius of sphere around CB.
-Real PackingStatistics::GetCutoffDistance() const {
- return cutoff_;
-}
-
-uint64_t PackingStatistics::GetCount(AminoAcid aa, int counts) const {
- return histogram_.Get(aa, counts/bucket_size_);
-}
-
-uint64_t PackingStatistics::GetCount(AminoAcid aa) const {
- uint64_t b=(max_counts_/bucket_size_)+1;
- uint64_t total=0;
- for (uint64_t i=0; i<b;++i) {
- total+=histogram_.Get(aa, i);
- }
- return total;
-}
-
-PackingStatisticsPtr PackingStatistics::LoadFromFile(const String& filename)
-{
- std::ifstream stream(filename.c_str(), std::ios_base::binary);
- io::BinaryDataSource ds(stream);
- PackingStatisticsPtr ptr(new PackingStatistics);
- ds >> *ptr.get();
- return ptr;
-}
-
-void PackingStatistics::SaveToFile(const String& filename)
-{
- std::ofstream stream(filename.c_str(), std::ios_base::binary);
- io::BinaryDataSink ds(stream);
- ds << *this;
-}
-
-uint64_t PackingStatistics::GetTotalCount() const
-{
- uint64_t b=(max_counts_/bucket_size_)+1;
- uint64_t total=0;
- for (uint64_t i=0; i<Xxx; ++i) {
- for (uint64_t j=0; j<b;++j) {
- total+=histogram_.Get(i, j);
- }
- }
- return total;
-}
-
-uint64_t PackingStatistics::GetCount(int count) const
-{
- uint64_t total=0;
- for (uint64_t i=0; i<Xxx; ++i) {
- total+=histogram_.Get(i, count/bucket_size_);
- }
- return total;
-}
-
-
-
-}}
diff --git a/modules/qa/src/packing_statistics.hh b/modules/qa/src/packing_statistics.hh
deleted file mode 100644
index 68e4e616c5d37d35f1b5ab4c9b8798772276861e..0000000000000000000000000000000000000000
--- a/modules/qa/src/packing_statistics.hh
+++ /dev/null
@@ -1,90 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2011 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
-//------------------------------------------------------------------------------
-#ifndef OST_QA_PACKING_STATISTICS_HH
-#define OST_QA_PACKING_STATISTICS_HH
-
-#include <ost/mol/entity_visitor.hh>
-#include <ost/qa/histogram.hh>
-#include <ost/qa/amino_acids.hh>
-#include <ost/mol/entity_view.hh>
-
-namespace ost { namespace qa {
-
-/// \brief two dimensional histogram
-/// the meaning of the histogram axes is: amino acid type, number of
-/// atoms inside of cutoff radius.
-typedef Histogram<int, int> PackingHistogram;
-class PackingStatistics;
-typedef boost::shared_ptr<PackingStatistics> PackingStatisticsPtr;
-class DLLEXPORT_OST_QA PackingStatistics : public mol::EntityVisitor {
-public:
- PackingStatistics(Real cutoff, int max_counts, int bucket_size);
- PackingStatistics();
-
- /// \brief Get bucket size for counts, i.e. 2 indicates that a residue with
- /// 6 and 7 seven CB within the cutoff radius have the same packing.
- int GetBucketSize() const;
-
- /// \brief Get maximal count of CB atoms inside cutoff distance. larger
- /// values are truncated.
- int GetMaxCounts() const;
-
- /// \brief Get cutoff radius of sphere around CB.
- Real GetCutoffDistance() const;
-
- /// \brief extract packing statistics of entity view.
- ///
- /// For each peptide residue in view, the total number of CB (CA for glycine)
- /// in views are counted.
- void Extract(mol::EntityView view, const mol::EntityViewList& views);
-
- static PackingStatisticsPtr LoadFromFile(const String& filename);
-
- void SaveToFile(const String& filename);
-
- virtual bool VisitAtom(const mol::AtomHandle& atom);
-
- uint64_t GetCount(AminoAcid aa) const;
- uint64_t GetCount(AminoAcid aa, int count) const;
-
- uint64_t GetTotalCount() const;
- uint64_t GetCount(int count) const;
-
- template <typename DS>
- void Serialize(DS& ds)
- {
- ds & cutoff_;
- ds & max_counts_;
- ds & bucket_size_;
- ds & histogram_;
- }
-
- Real cutoff_;
- int max_counts_;
- int bucket_size_;
-
-private:
- mol::EntityView view_;
- mol::EntityViewList views_;
- PackingHistogram histogram_;
-};
-
-}}
-
-#endif
diff --git a/modules/qa/src/rapdf.cc b/modules/qa/src/rapdf.cc
deleted file mode 100644
index d530c27b12d23c991233f324cdf96487d0618e04..0000000000000000000000000000000000000000
--- a/modules/qa/src/rapdf.cc
+++ /dev/null
@@ -1,95 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2011 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
-//------------------------------------------------------------------------------
-#include "rapdf.hh"
-#include <ost/mol/mol.hh>
-#include <ost/geom/geom.hh>
-namespace ost { namespace qa {
-
-
-RAPDF::RAPDF(const String& file) {
- energies_.reset(new InteractionEnergies(file));
-}
-
-RAPDF::RAPDF(InteractionStatisticsPtr statistics, Real sigma) {
- typedef InteractionEnergies::IndexType Index;
- Real upper=statistics->GetUpperCutoff();
- Real lower=statistics->GetLowerCutoff();
- Real bucket_size=statistics->GetDistanceBucketSize();
- uint32_t distance_buckets=uint32_t((upper-lower)/bucket_size);
- ContinuousClassifier distance_classifier(distance_buckets, lower, upper);
- energies_.reset(new InteractionEnergies(0.0,
- IntegralClassifier(atom::UNKNOWN, 0),
- IntegralClassifier(atom::UNKNOWN, 0),
- distance_classifier));
- // loop over all distance buckets and calculate energies for all atom pairs.
- for (uint32_t i=0; i<distance_buckets;++i) {
- Index start(0, 0, i), end(atom::UNKNOWN-1, atom::UNKNOWN-1, i);
- Real radius=i*bucket_size+bucket_size/2;
- uint32_t total=statistics->GetCount(radius);
- for (uint32_t j=0; j<atom::UNKNOWN; ++j) {
- for (uint32_t k=0; k<atom::UNKNOWN;++k) {
- uint32_t lc=statistics->GetCount(atom::ChemType(j),
- atom::ChemType(k), radius);
- Real frequency=lc/Real(total);
- Real energy=log((1+lc*sigma)/(1+lc*sigma*frequency));
- energies_->Set(Index(j, k, i), energy);
- }
- }
- }
-}
-
-Real RAPDF::GetTotalEnergy(mol::EntityView entity) {
- tmp_energy_=0.0;
- entity.Apply(*this);
- return tmp_energy_;
-}
-
-RAPDF::RAPDF(const RAPDF& rhs) {
- energies_.reset(new InteractionEnergies(*rhs.energies_.get()));
-}
-
-bool RAPDF::VisitAtom(const mol::AtomHandle& atom) {
- mol::EntityHandle e=atom.GetResidue().GetChain().GetEntity();
- atom::ChemType atype=GetAtomTypeByName(amino_acid_, atom.GetName());
- //FIXME: do not hard-code the distance cutoff here.
- mol::AtomHandleList atoms=e.FindWithin(atom.GetPos(), 20.0);
- mol::AtomHandleList::iterator i;
- for(i=atoms.begin(); i!=atoms.end(); ++i) {
- mol::AtomHandle& a=*i;
- if (abs(a.GetResidue().GetNumber().GetNum()-rnumber_)<3)
- continue;
- AminoAcid b=ResidueToAminoAcid(a.GetResidue());
- if (b==Xxx)
- continue;
- atom::ChemType btype=GetAtomTypeByName(b, a.GetName());
- if (btype==atom::UNKNOWN)
- continue;
- Real d=Length(a.GetPos()-atom.GetPos());
- tmp_energy_+=energies_->Get(atype, btype, d);
- }
- return true;
-}
-
-bool RAPDF::VisitResidue(const mol::ResidueHandle& residue) {
- amino_acid_=ResidueToAminoAcid(residue);
- rnumber_=residue.GetNumber().GetNum();
- return amino_acid_!=Xxx;
-}
-
-}}
diff --git a/modules/qa/src/rapdf.hh b/modules/qa/src/rapdf.hh
deleted file mode 100644
index ae69b054e33210992f1ca532960a013ef7989565..0000000000000000000000000000000000000000
--- a/modules/qa/src/rapdf.hh
+++ /dev/null
@@ -1,64 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2011 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
-//------------------------------------------------------------------------------
-#ifndef OST_QA_RAPDF_HH
-#define OST_QA_RAPDF_HH
-
-#include <ost/mol/entity_view.hh>
-#include <boost/shared_ptr.hpp>
-#include <boost/scoped_ptr.hpp>
-#include <ost/mol/entity_visitor.hh>
-#include <ost/qa/interaction_statistics.hh>
-
-namespace ost { namespace qa {
-
-typedef MultiClassifier<Real, int, int, Real> InteractionEnergies;
-class RAPDF;
-
-typedef boost::shared_ptr<RAPDF> RAPDFPtr;
-
-/// \brief RAPDF after (Samudrala & Moult, 1998)
-class DLLEXPORT_OST_QA RAPDF : public EntityVisitor {
-public:
- /// load RAPDF potential from file.
- RAPDF(const String& file);
- RAPDF(const RAPDF& rhs);
- /// create new interaction potential from interaction statistics
- /// \param statistics interaction statistics
- /// \param sigma mixing parameter (see Sippl et al., 1990)
- RAPDF(InteractionStatisticsPtr statistics, Real sigma=50.0);
-
- /// calculate all-atom interaction score for entity. all atoms of the
- /// entity are taken into account, but only energies from atoms in the
- /// view contribute to the energy.
- /// not thread-safe (just factor out visitor to make thread-safe)
- Real GetTotalEnergy(mol::EntityView entity);
-
- virtual bool VisitAtom(const mol::AtomHandle& atom);
- virtual bool VisitResidue(const mol::ResidueHandle& residue);
-
-private:
- boost::scoped_ptr<InteractionEnergies> energies_;
- AminoAcid amino_acid_;
- int rnumber_;
- Real tmp_energy_;
-};
-
-}}
-
-#endif
diff --git a/modules/qa/src/reduced_potential.cc b/modules/qa/src/reduced_potential.cc
deleted file mode 100644
index 3963fc132f0880ae94f715057af0beda3dfaf2b9..0000000000000000000000000000000000000000
--- a/modules/qa/src/reduced_potential.cc
+++ /dev/null
@@ -1,153 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2011 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
-//------------------------------------------------------------------------------
-
-#include <ost/io/binary_data_source.hh>
-#include <ost/io/binary_data_sink.hh>
-#include <ost/io/container_serialization.hh>
-#include "reduced_potential.hh"
-#include "impl/reduced_impl.hh"
-namespace ost { namespace qa {
-
-
-namespace {
-
-class ReducedEnergiesCalc : public impl::ReducedPotentialImpl {
-public:
-
- ReducedEnergiesCalc(const ReducedStatOptions& opts, ReducedEnergies& energies,
- mol::EntityHandle ent, bool norm):
- impl::ReducedPotentialImpl(opts, ent),
- energies_(energies), energy_(0.0), norm_(norm), count_(0)
- { }
- ReducedEnergiesCalc(const ReducedStatOptions& opts, ReducedEnergies& energies,
- mol::EntityView ent, bool norm):
- impl::ReducedPotentialImpl(opts, ent),
- energies_(energies), energy_(0.0), norm_(norm), count_(0)
- { }
- virtual void OnInteraction(AminoAcid aa_one, AminoAcid aa_two,
- Real dist, Real angle)
- {
- //std::cout << aa_one << " " << aa_two << " " << dist << " " << angle << std::endl;
- energy_+=energies_.Get(aa_one, aa_two, dist, angle);
- count_+=1;
- }
-
- Real GetEnergy() const
- {
- if (norm_) {
- return count_ > 0 ? energy_ /count_ : 0.0;
- }
- return energy_;
- }
-private:
- ReducedEnergies& energies_;
- Real energy_;
- bool norm_;
- uint64_t count_;
-};
-
-
-}
-
-bool ReducedPotential::GetCAlphaCBetaPos(const mol::ResidueHandle& res,
- geom::Vec3& ca_pos,
- geom::Vec3& cb_pos)
-{
- return impl::ReducedPotentialImpl::GetCAlphaCBetaPos(res, ca_pos, cb_pos);
-}
-
-ReducedPotentialPtr ReducedPotential::Load(const String& filename)
-{
- std::ifstream stream(filename.c_str(), std::ios_base::binary);
- io::BinaryDataSource ds(stream);
- ReducedPotentialPtr p(new ReducedPotential);
- ds >> *p.get();
- return p;
-}
-
-
-ReducedPotentialPtr ReducedPotential::Create(const ReducedStatisticsPtr& stat)
-{
- ReducedPotentialPtr pot(new ReducedPotential);
- pot->opts_=stat->GetOptions();
- pot->energies_=ReducedEnergies(0.0, IntegralClassifier(20, 0),
- IntegralClassifier(20, 0),
- ContinuousClassifier(pot->opts_.num_dist_bins,
- pot->opts_.lower_cutoff,
- pot->opts_.upper_cutoff),
- ContinuousClassifier(pot->opts_.num_angular_bins,
- 0.0, M_PI));
- pot->InitFromStats(stat);
- return pot;
-}
-
-void ReducedPotential::InitFromStats(const ReducedStatisticsPtr& stats)
-{
- typedef ReducedEnergies::IndexType Index;
- uint64_t total_count=stats->GetTotalCount();
- for (size_t i=0; i<Xxx; ++i) {
- for (size_t j=0; j<Xxx; ++j) {
- uint64_t t2=stats->GetCount(AminoAcid(i), AminoAcid(j));
- for (size_t k=0; k<opts_.num_dist_bins; ++k) {
- for (size_t l=0; l<opts_.num_angular_bins; ++l) {
- uint64_t t3=stats->GetCount(AminoAcid(i), AminoAcid(j), k, l);
- // could be moved outside of the loop and cached...
- uint64_t t4=stats->GetCount(k, l);
- float f1=t2 > 0 ?(float(t3)/float(t2)) : 0.0;
- float f2=total_count > 0 ? (float(t4)/float(total_count)) : 0.0;
- float d = f2>1e-10 ? f1/f2: 0.0;
- float e=0.582*(log(1+0.02*t2)-log(1+0.02*t2*d));
- energies_.Set(Index(i, j, k, l), e);
- }
- }
- }
- }
-}
-
-void ReducedPotential::Save(const String& filename)
-{
- std::ofstream stream(filename.c_str(), std::ios_base::binary);
- io::BinaryDataSink ds(stream);
- ds << *this;
-}
-
-
-template <typename DS>
-void ReducedPotential::Serialize(DS& ds)
-{
- ds & opts_;
- ds & energies_;
-}
-
-Real ReducedPotential::GetTotalEnergy(ost::mol::EntityHandle ent, bool norm)
-{
- ReducedEnergiesCalc calc(opts_, energies_, ent, norm);
- ent.Apply(calc);
- return calc.GetEnergy();
-}
-
-Real ReducedPotential::GetTotalEnergy(ost::mol::EntityView ent, bool norm)
-{
- ReducedEnergiesCalc calc(opts_, energies_, ent.GetHandle(), norm);
- ent.Apply(calc);
- return calc.GetEnergy();
-}
-
-
-}}
diff --git a/modules/qa/src/reduced_potential.hh b/modules/qa/src/reduced_potential.hh
deleted file mode 100644
index e2d600b7f1f01d58197225ada94ed3ec298f4b22..0000000000000000000000000000000000000000
--- a/modules/qa/src/reduced_potential.hh
+++ /dev/null
@@ -1,78 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2011 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
-//------------------------------------------------------------------------------
-#ifndef OST_QA_REDUCED_POTENTIAL_HH
-#define OST_QA_REDUCED_POTENTIAL_HH
-
-#include <ost/qa/reduced_statistics.hh>
-
-
-namespace ost { namespace qa {
-
-
-class ReducedPotential;
-
-typedef boost::shared_ptr<ReducedPotential> ReducedPotentialPtr;
-
-typedef MultiClassifier<float, int, int, float, float> ReducedEnergies;
-/// \brief reduced model statistical potential operating on the residue level
-class DLLEXPORT_OST_QA ReducedPotential {
-public:
-
-
-
- static ReducedPotentialPtr Create(const ReducedStatisticsPtr& stats);
- static ReducedPotentialPtr Load(const String& filename);
-
- void Save(const String& filename);
-
-
- template <typename DS>
- void Serialize(DS& ds);
-
- const ReducedStatOptions& GetOptions() const { return opts_; }
-
- Real GetTotalEnergy(ost::mol::EntityHandle ent, bool normalize=true);
-
- Real GetTotalEnergy(ost::mol::EntityView ent, bool normalize=true);
- static bool GetCAlphaCBetaPos(const mol::ResidueHandle& res,
- geom::Vec3& ca_pos,
- geom::Vec3& cb_pos);
-
- Real GetEnergy(AminoAcid aa_one, AminoAcid aa_two,
- Real ca_dist, Real angle) const
- {
- if (aa_one==Xxx || aa_two==Xxx) { return 0.0; }
- if (ca_dist<opts_.lower_cutoff || ca_dist>=opts_.upper_cutoff) {
- return 0.0;
- }
- if (angle<0.0 || angle>M_PI) { return 0.0; }
- return energies_.Get(aa_one, aa_two, ca_dist, angle);
- }
-private:
- void InitFromStats(const ReducedStatisticsPtr& stats);
- ReducedPotential() { }
-
- ReducedStatOptions opts_;
- ReducedEnergies energies_;
-};
-
-
-}}
-
-#endif
diff --git a/modules/qa/src/reduced_statistics.cc b/modules/qa/src/reduced_statistics.cc
deleted file mode 100644
index 403153e8b295055ee4b1e8fea606dc8f30b14451..0000000000000000000000000000000000000000
--- a/modules/qa/src/reduced_statistics.cc
+++ /dev/null
@@ -1,152 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2011 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
-//------------------------------------------------------------------------------
-
-#include <ost/log.hh>
-#include <ost/mol/mol.hh>
-#include "amino_acids.hh"
-#include "reduced_statistics.hh"
-#include "impl/reduced_impl.hh"
-
-#include <ost/io/binary_data_source.hh>
-#include <ost/io/binary_data_sink.hh>
-#include <ost/io/container_serialization.hh>
-
-namespace ost { namespace qa {
-
-
-namespace {
-
-class ReducedStatExtractor : public impl::ReducedPotentialImpl {
-public:
-
- ReducedStatExtractor(const ReducedStatOptions& opts, ReducedHistogram& histo,
- mol::EntityHandle ent):
- impl::ReducedPotentialImpl(opts, ent),
- histo_(histo)
- { }
-
- ReducedStatExtractor(const ReducedStatOptions& opts, ReducedHistogram& histo,
- mol::EntityView ent):
- impl::ReducedPotentialImpl(opts, ent),
- histo_(histo)
- { }
-
- virtual void OnInteraction(AminoAcid aa_one, AminoAcid aa_two,
- Real dist, Real angle)
- {
- histo_.Add(1, aa_one, aa_two, dist, angle);
- }
-private:
- ReducedHistogram& histo_;
-};
-
-
-}
-
-uint64_t ReducedStatistics::GetTotalCount() const
-{
- typedef ReducedHistogram::IndexType Index;
- uint64_t count=0;
- for (size_t i=0; i<Xxx; ++i) {
- for (size_t j=0; j<Xxx; ++j) {
- for (size_t k=0; k<opts_.num_dist_bins; ++k) {
- for (size_t l=0; l<opts_.num_angular_bins; ++l) {
- count+=histo_.Get(Index(i, j, k, l));
- }
- }
- }
- }
- return count;
-}
-
-uint64_t ReducedStatistics::GetCount(AminoAcid aa_one, AminoAcid aa_two) const
-{
- typedef ReducedHistogram::IndexType Index;
- uint64_t count=0;
- for (size_t k=0; k<opts_.num_dist_bins; ++k) {
- for (size_t l=0; l<opts_.num_angular_bins; ++l) {
- count+=histo_.Get(Index(aa_one, aa_two, k, l));
- }
- }
- return count;
-}
-
-uint64_t ReducedStatistics::GetCount(int dist_bin, int ang_bin) const
-{
- typedef ReducedHistogram::IndexType Index;
- uint64_t count=0;
- for (size_t i=0; i<Xxx; ++i) {
- for (size_t j=0; j<Xxx; ++j) {
- count+=histo_.Get(Index(i, j, dist_bin, ang_bin));
- }
- }
- return count;
-}
-
-void ReducedStatistics::Save(const String& filename)
-{
- std::ofstream stream(filename.c_str(), std::ios_base::binary);
- io::BinaryDataSink ds(stream);
- ds << *this;
-}
-
-
-ReducedStatisticsPtr ReducedStatistics::Load(const String& filename)
-{
- std::ifstream stream(filename.c_str(), std::ios_base::binary);
- io::BinaryDataSource ds(stream);
- ReducedStatisticsPtr p(new ReducedStatistics);
- ds >> *p.get();
- return p;
-}
-
-template <typename DS>
-void ReducedStatistics::Serialize(DS& ds)
-{
- ds & opts_;
- ds & histo_;
-}
-
-
-void ReducedStatistics::Extract(mol::EntityHandle ent)
-{
- if (ent.GetChainCount()!=1) {
- std::stringstream ss;
- ss << "Expected exactly one chain, but entity has "
- << ent.GetChainCount() << " chains";
- throw std::runtime_error(ss.str());
- }
- ReducedStatExtractor extractor(opts_, histo_, ent);
- ent.Apply(extractor);
-}
-
-void ReducedStatistics::Extract(mol::EntityView ent)
-{
- if (ent.GetChainCount()!=1) {
- std::stringstream ss;
- ss << "Expected exactly one chain, but entity has "
- << ent.GetChainCount() << " chains";
- throw std::runtime_error(ss.str());
- }
- ReducedStatExtractor extractor(opts_, histo_, ent.GetHandle());
- ent.Apply(extractor);
-}
-
-
-}}
\ No newline at end of file
diff --git a/modules/qa/src/reduced_statistics.hh b/modules/qa/src/reduced_statistics.hh
deleted file mode 100644
index 1f1ab2426abf419e1b2e05a02998cb390320567a..0000000000000000000000000000000000000000
--- a/modules/qa/src/reduced_statistics.hh
+++ /dev/null
@@ -1,123 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2011 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
-//------------------------------------------------------------------------------
-#ifndef OST_QA_REDUCED_STATISTICS_HH
-#define OST_QA_REDUCED_STATISTICS_HH
-
-#include <ost/qa/histogram.hh>
-#include <ost/qa/amino_acids.hh>
-namespace ost {
-
-namespace mol {
-
-class EntityHandle;
-
-}
-namespace qa {
-
-/// \brief aggregates the option for the reduced model statistics
-struct DLLEXPORT_OST_QA ReducedStatOptions {
- ReducedStatOptions(): lower_cutoff(0), upper_cutoff(0),
- num_angular_bins(0), num_dist_bins(0),
- sequence_sep(0)
- { }
-
- ReducedStatOptions(Real l_cutoff, Real u_cutoff, uint n_ang_bins,
- uint n_dist_bins, uint ssep):
- lower_cutoff(l_cutoff), upper_cutoff(u_cutoff),
- num_angular_bins(n_ang_bins), num_dist_bins(n_dist_bins),
- sequence_sep(ssep)
- { }
- Real lower_cutoff;
- Real upper_cutoff;
- uint num_angular_bins;
- uint num_dist_bins;
- uint sequence_sep;
-
-
- template <typename DS>
- void Serialize(DS& ds)
- {
- ds & lower_cutoff;
- ds & upper_cutoff;
- ds & num_angular_bins;
- ds & num_dist_bins;
- ds & sequence_sep;
- }
-};
-
-
-class ReducedStatistics;
-typedef boost::shared_ptr<ReducedStatistics> ReducedStatisticsPtr;
-
-
-// parametrized as first amino acid, second amino acid,
-// calpha-calpha distance, angle
-typedef Histogram<int, int, float, float> ReducedHistogram;
-
-class DLLEXPORT_OST_QA ReducedStatistics {
-public:
- ReducedStatistics(Real l_cutoff, Real u_cutoff, uint num_ang_bins,
- uint num_dist_bins, uint ssep):
- opts_(l_cutoff, u_cutoff, num_ang_bins, num_dist_bins, ssep),
- histo_(IntegralClassifier(20, 0), IntegralClassifier(20, 0),
- ContinuousClassifier(num_dist_bins, l_cutoff, u_cutoff),
- ContinuousClassifier(num_ang_bins, 0.0, M_PI))
- { }
-
- const ReducedStatOptions& GetOptions() const { return opts_; }
-
- /// \brief extract the statistics from the given entity (handle)
- void Extract(mol::EntityHandle ent);
-
- /// \brief extract statistics from given entity (view)
- void Extract(mol::EntityView ent);
-
- void Save(const String& filename);
-
-
- static ReducedStatisticsPtr Load(const String& filename);
- /// \internal
- template <typename DS>
- void Serialize(DS& ds);
-
- uint64_t GetTotalCount() const;
-
- uint64_t GetCount(AminoAcid aa_one, AminoAcid aa_two) const;
-
-
- uint64_t GetCount(AminoAcid aa_one, AminoAcid aa_two, int dist_bin,
- int ang_bin)
- {
- return histo_.Get(ReducedHistogram::IndexType(aa_one, aa_two, dist_bin,
- ang_bin));
- }
-
- uint64_t GetCount(int dist_bin, int ang_bin) const;
-private:
- ReducedStatistics(): opts_(), histo_() {}
- ReducedStatOptions opts_;
- ReducedHistogram histo_;
-};
-
-
-
-}}
-
-
-#endif
diff --git a/modules/qa/src/solis_torsion_potential.cc b/modules/qa/src/solis_torsion_potential.cc
deleted file mode 100644
index 3c463ac00da97ca91994ae6cbd1b1dd7fb901dc0..0000000000000000000000000000000000000000
--- a/modules/qa/src/solis_torsion_potential.cc
+++ /dev/null
@@ -1,266 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2011 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
-//------------------------------------------------------------------------------
-#include "solis_torsion_potential.hh"
-#include "amino_acids.hh"
-
-#include <ost/mol/mol.hh>
-#include <ost/log.hh>
-#include <ost/io/binary_data_source.hh>
-#include <ost/io/binary_data_sink.hh>
-#include <ost/io/container_serialization.hh>
-#include <ost/integrity_error.hh>
-#include <boost/filesystem/convenience.hpp>
-#include <ost/message.hh>
-#include <ost/io/io_exception.hh>
-
-namespace ost { namespace qa {
-
-namespace {
-
-class SolisTorsionEnergyCalc : public mol::EntityVisitor {
-public:
- SolisTorsionEnergyCalc(TorsionPotentialSolis::TorsionEnergies& energies,
- TorsionPotentialOptsSolis opts):
- energies_(energies), prev_(Xxx), center_(Xxx), energy_(0.0),
- opts_(opts), num_torsions_(0)
- {
- }
-
- virtual bool VisitResidue(const mol::ResidueHandle& rh)
- {
- AminoAcid c=ResidueToAminoAcid(rh);
-
- if (prev_==Xxx || center_==Xxx || c==Xxx) {
- prev_=center_;
- center_=c;
- cr_=rh;
- return false;
- }
- mol::TorsionHandle phit=cr_.GetPhiTorsion();
- mol::TorsionHandle psit=cr_.GetPsiTorsion();
- if (!phit || !psit) {
- prev_=center_;
- center_=c;
- cr_=rh;
- return false;
- }
- Real phi=phit.GetAngle()*180/M_PI - 0.000000001;
- Real psi=psit.GetAngle()*180/M_PI - 0.000000001;
- int ibefore=this->GetOuterAAIndex(prev_);
- int iafter=this->GetOuterAAIndex(c);
- int icenter=this->GetInnerAAIndex(center_);
-
-
- if (iafter>-1 && icenter >-1 && ibefore>-1) {
- energy_+=energies_.Get(ibefore, icenter, iafter, phi, psi);
- num_torsions_++;
- }
- else {
- LOG_INFO("Amino acid not found in alphabets...");
- }
- prev_=center_;
- center_=c;
- cr_=rh;
- return false;
- }
-
- Real GetEnergy() const {
- return energy_;
- //return num_torsions_==0?0:energy_/num_torsions_;
- }
- int GetEnergyCounts() const {
- return num_torsions_;
- }
-private:
- int GetOuterAAIndex(AminoAcid aa)
- {
- return this->GetIndex(aa, opts_.outer_alphabet);
- }
-
- int GetInnerAAIndex(AminoAcid aa)
- {
- return this->GetIndex(aa, opts_.inner_alphabet);
- }
-
- int GetIndex(AminoAcid aa, AminoAcidAlphabet& alpha) {
- AminoAcidAlphabet::iterator i=alpha.begin();
- for (int index=0; i!=alpha.end(); ++i, ++index) {
- if ((*i).Contains(aa)) {
- return index;
- }
-
- }
- return -1;
- }
-private:
- TorsionPotentialSolis::TorsionEnergies& energies_;
- AminoAcid prev_;
- AminoAcid center_;
- mol::ResidueHandle cr_;
- Real energy_;
- TorsionPotentialOptsSolis opts_;
- int num_torsions_;
-};
-
-}
-
-template <typename DS>
-void TorsionPotentialOptsSolis::Serialize(DS& ds)
-{
- ds & angular_bucket_size;
- ds & outer_alphabet;
- ds & inner_alphabet;
- ds & sigma;
-}
-
-template <typename DS>
-void TorsionPotentialSolis::Serialize(DS& ds)
-{
- ds & options_;
- ds & energies_;
-}
-
-TorsionPotentialOptsSolis::TorsionPotentialOptsSolis():
- angular_bucket_size(30), sigma(0.02)
-{
-
-}
-
-
-TorsionPotentialSolisPtr TorsionPotentialSolis::Create(
- TorsionStatisticsSolisPtr statistics,
- const TorsionPotentialOptsSolis& opts)
-{
- typedef TorsionPotentialSolis::TorsionEnergies TorsionEnergies;
- int bucket_size=statistics->GetTorsionBucketSize();
-
- if ((opts.angular_bucket_size % bucket_size)!=0) {
- throw IntegrityError("Angular bucket size for torsion potential is not an "
- "integral multiple of the statistics bucket size");
- }
- int buckets=360/opts.angular_bucket_size;
- TorsionPotentialSolisPtr ptr(new TorsionPotentialSolis);
-
- ptr->options_.angular_bucket_size = opts.angular_bucket_size;
- ptr->options_.outer_alphabet = opts.outer_alphabet;
- ptr->options_.inner_alphabet = opts.inner_alphabet;
-
- uint32_t outer_s=ptr->options_.outer_alphabet.size();
- uint32_t inner_s=ptr->options_.inner_alphabet.size();
- ptr->energies_=TorsionEnergies(0.0, IntegralClassifier(outer_s, 0),
- IntegralClassifier(inner_s, 0),
- IntegralClassifier(outer_s, 0),
- ContinuousClassifier(buckets,-180,180),
- ContinuousClassifier(buckets,-180,180));
- ptr->FillAll(statistics);
- return ptr;
-}
-
-TorsionPotentialSolisPtr TorsionPotentialSolis::LoadFromFile(const String& path)
-{
- if(!boost::filesystem::exists(path))
- throw io::IOException("Could not open torsion potential data file.\nFile does not exist at: "+path);
-
- std::ifstream stream(path.c_str(), std::ios_base::binary);
- io::BinaryDataSource ds(stream);
- TorsionPotentialSolisPtr ptr(new TorsionPotentialSolis);
- ds >> *ptr.get();
- return ptr;
-}
-
-void TorsionPotentialSolis::SaveToFile(const String& path)
-{
- std::ofstream stream(path.c_str(), std::ios_base::binary);
- io::BinaryDataSink ds(stream);
- ds << *this;
-}
-
-Real TorsionPotentialSolis::GetTotalEnergy(mol::EntityHandle entity)
-{
- SolisTorsionEnergyCalc c(energies_, options_);
- entity.Apply(c);
- num_torsions_ = c.GetEnergyCounts();
- return c.GetEnergy();
-}
-
-Real TorsionPotentialSolis::GetTotalEnergy(mol::EntityView entity)
-{
- SolisTorsionEnergyCalc c(energies_, options_);
- entity.Apply(c);
- num_torsions_ = c.GetEnergyCounts();
- return c.GetEnergy();
-}
-
-int TorsionPotentialSolis::GetEnergyCounts() const {
- return num_torsions_;
-}
-
-
-void TorsionPotentialSolis::FillAll(const TorsionStatisticsSolisPtr& stat)
-{
- uint32_t total=stat->GetCount();
- int num_b=360/(options_.angular_bucket_size);
- int half_b=options_.angular_bucket_size/2;
- for (int phi=0; phi<num_b; ++phi) {
- for (int psi=0; psi<num_b; ++psi) {
- int phi_a=-180+options_.angular_bucket_size*phi+half_b;
- int psi_a=-180+options_.angular_bucket_size*psi+half_b;
- this->FillPhiPsi(stat, phi_a, psi_a, total);
- }
- }
-}
-
-void TorsionPotentialSolis::FillPhiPsi(const TorsionStatisticsSolisPtr& stat,
- int phi, int psi, uint32_t M)
-{
- // collect total counts for all amino acids first
- uint32_t fx=stat->GetCount(phi, psi);
- typedef AminoAcidAlphabet::const_iterator AAA;
- for (AAA i=options_.outer_alphabet.begin(),
- e1=options_.outer_alphabet.end(); i!=e1; ++i) {
- for (AAA j=options_.inner_alphabet.begin(),
- e2=options_.inner_alphabet.end(); j!=e2; ++j) {
- for (AAA k=options_.outer_alphabet.begin(),
- e3=options_.outer_alphabet.end(); k!=e3; ++k) {
-
- uint32_t fxi=stat->GetCount(*i, *j, *k, phi, psi);
- uint32_t Mi=stat->GetCount(*i, *j, *k);
-
- // propensity = (fxi/Mi)/(fx/M)
- Real propensity=0.0;
- //avoid division by zero:
- if (fx != 0 && Mi != 0 && M != 0) {
- propensity=Real(Real(fxi)/Mi)/(Real(fx)/M);
- }
-
- Real energy=log(1+options_.sigma*Mi)-
- log(1+options_.sigma*Mi*propensity);
-
- energies_.Add(energy,
- i-options_.outer_alphabet.begin(),
- j-options_.inner_alphabet.begin(),
- k-options_.outer_alphabet.begin(), phi, psi);
- }
- }
- }
-}
-
-
-
-}}
diff --git a/modules/qa/src/solis_torsion_potential.hh b/modules/qa/src/solis_torsion_potential.hh
deleted file mode 100644
index acfb2aed108e7d46f1673b37b68f1be5b9b20314..0000000000000000000000000000000000000000
--- a/modules/qa/src/solis_torsion_potential.hh
+++ /dev/null
@@ -1,121 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2011 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
-//------------------------------------------------------------------------------
-#ifndef OST_QA_SOLIS_TORSION_POTENTIAL_HH
-#define OST_QA_SOLIS_TORSION_POTENTIAL_HH
-/*
-
-
- Author: Marco Biasini, Pascal Benkert
- */
-#include <ost/qa/solis_torsion_statistics.hh>
-#include <boost/shared_ptr.hpp>
-#include <vector>
-#include <boost/scoped_ptr.hpp>
-
-namespace ost { namespace qa {
-
-typedef std::vector<AminoAcidSet> AminoAcidAlphabet;
-
-/// \brief torsion potential options
-///
-/// These options may be used to configure the different torsion potentials
-/// based on a sliding window of 3 amino acids.
-struct DLLEXPORT_OST_QA TorsionPotentialOptsSolis {
- /// \brief initialize torsion potential with angular bucket size of 30 and
- /// sigma of 0.02
- ///
- /// The amino acid alphabets are empty.
- TorsionPotentialOptsSolis();
-
- /// angular bucket size, 360 % angular_bucket_size must be zero
- int angular_bucket_size;
- /// alphabet of residues before and after the central amino acids in the
- /// window. The amino acids in the set must be mutually exclusive
- AminoAcidAlphabet outer_alphabet;
- /// alphabet of the central amino acid. The amino acid sets must be
- /// mutually exclusive
- AminoAcidAlphabet inner_alphabet;
- /// weighting factor after (Sippl et al., 1990), usually 0.02
- Real sigma;
- /// \internal
- template <typename DS>
- void Serialize(DS& ds);
-};
-
-class TorsionPotentialSolis;
-typedef boost::shared_ptr<TorsionPotentialSolis> TorsionPotentialSolisPtr;
-
-/// \brief Torsion potential
-///
-/// The torsion potential class is parametrisable by TorsionPotentialOptsSolis.
-///
-/// This implementation of the torsion angle potential combines 1 torsion angle
-/// pair with up to 3 residues in analogy to the potential described by:
-/// Armando D. Solis, S. Rackovsky
-/// Optimally informative backbone structural propensities in proteins Proteins,
-/// 2002 The ordinary trosion angle potential (1 angle-pair, 1 residue) is
-/// covered as well.
-class DLLEXPORT_OST_QA TorsionPotentialSolis {
-public:
- /// \brief create new torsion potential with the given torsion statistics
- /// and options
- static TorsionPotentialSolisPtr Create(TorsionStatisticsSolisPtr statistics,
- const TorsionPotentialOptsSolis& opts);
- /// \brief Load potential from file.
- static TorsionPotentialSolisPtr LoadFromFile(const String& path);
-
- /// \brief Calculate energy for entity.
- Real GetTotalEnergy(mol::EntityHandle entity);
-
- /// \brief Calculate energy for entity view. Only residues in the view are
- /// considered.
- Real GetTotalEnergy(mol::EntityView view);
-
- /// \brief retrieve total number of energy local (i.e. valid residues)
- int GetEnergyCounts() const;
-
- /// \brief save torsion potential
- ///
- /// The output is in a non-portable binary form.
- void SaveToFile(const String& path);
-
- /// \internal
- template <typename DS>
- void Serialize(DS& ds);
-
-
-public:
- /// Meaning of parameters: AA before AA center AA after,
- /// phi torsion angle, psi torsion angle
- typedef MultiClassifier<float, int, int,
- int, Real, Real> TorsionEnergies;
-private:
- void FillAll(const TorsionStatisticsSolisPtr& stat);
-
- void FillPhiPsi(const TorsionStatisticsSolisPtr& stat, int phi, int psi,
- uint32_t total);
- TorsionPotentialOptsSolis options_;
- TorsionEnergies energies_;
- int num_torsions_;
-};
-
-
-}}
-
-#endif
diff --git a/modules/qa/src/solis_torsion_statistics.cc b/modules/qa/src/solis_torsion_statistics.cc
deleted file mode 100644
index ed2c6ac1683e15d9bcfaa5d76d261d2425543aec..0000000000000000000000000000000000000000
--- a/modules/qa/src/solis_torsion_statistics.cc
+++ /dev/null
@@ -1,261 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2011 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
-//------------------------------------------------------------------------------
-#include "solis_torsion_statistics.hh"
-#include "amino_acids.hh"
-#include <ost/log.hh>
-#include <ost/mol/mol.hh>
-#include <fstream>
-#include <ost/message.hh>
-#include <ost/io/binary_data_source.hh>
-#include <ost/io/binary_data_sink.hh>
-#include <ost/io/container_serialization.hh>
-
-/*
- Author: Marco Biasini, Pascal Benkert
- */
-namespace ost { namespace qa {
-
-
-namespace {
-
-class TorsionStatSolis : public mol::EntityVisitor {
-public:
- TorsionStatSolis(TorsionStatisticsSolis::TorsionHistogram& histo):
- histo_(histo)
- {}
-
- virtual bool VisitResidue(const mol::ResidueHandle& residue) {
-
- mol::ResidueHandle prev=residue.GetPrev();
- mol::ResidueHandle next=residue.GetNext();
- if (!(next && prev && next.IsPeptideLinking() &&
- prev.IsPeptideLinking() && residue.IsPeptideLinking())) {
- return false;
- }
-
- AminoAcid pa=ResidueToAminoAcid(prev);
- AminoAcid na=ResidueToAminoAcid(next);
- AminoAcid ca=ResidueToAminoAcid(residue);
-
- if (pa==Xxx || na==Xxx || ca==Xxx)
- return false;
- mol::TorsionHandle phit=residue.GetPhiTorsion();
- mol::TorsionHandle psit=residue.GetPsiTorsion();
- if (!phit || !psit)
- return false;
- Real phi=phit.GetAngle()*180/M_PI - 0.000000001;
- Real psi=psit.GetAngle()*180/M_PI - 0.000000001;
- histo_.Add(1, pa, ca, na, phi, psi);
- return false;
- }
-private:
- TorsionStatisticsSolis::TorsionHistogram& histo_;
-};
-
-}
-
-// initialise with 0 or 1 (1 better for combined potentials)
-TorsionStatisticsSolis::TorsionStatisticsSolis(int torsion_bucket_size)
- : histogram_(1,IntegralClassifier(20, 0),
- IntegralClassifier(20, 0),
- IntegralClassifier(20, 0),
- ContinuousClassifier(int(360/torsion_bucket_size), -180, 180),
- ContinuousClassifier(int(360/torsion_bucket_size), -180, 180)),
- torsion_bucket_size_(torsion_bucket_size)
-{
-
-}
-
-uint32_t TorsionStatisticsSolis::GetTorsionBucketCount() const
-{
- return uint32_t(360/torsion_bucket_size_);
-}
-
-int TorsionStatisticsSolis::GetTorsionBucketSize() const
-{
- return torsion_bucket_size_;
-}
-
-void TorsionStatisticsSolis::Extract(mol::EntityView view)
-{
- TorsionStatSolis stat(histogram_);
- view.Apply(stat);
-}
-
-void TorsionStatisticsSolis::Extract(mol::EntityHandle entity)
-{
- TorsionStatSolis stat(histogram_);
- entity.Apply(stat);
-}
-
-TorsionStatisticsSolisPtr TorsionStatisticsSolis::LoadFromFile(const String& file_name)
-{
- std::ifstream stream(file_name.c_str(), std::ios_base::binary);
- TorsionStatisticsSolisPtr ptr(new TorsionStatisticsSolis);
- io::BinaryDataSource ds(stream);
- ds >> *ptr.get();
- return ptr;
-}
-
-void TorsionStatisticsSolis::SaveToFile(const String& file_name) const
-{
- std::ofstream stream(file_name.c_str(), std::ios_base::binary);
- io::BinaryDataSink ds(stream);
- ds << *this;
-}
-
-uint32_t TorsionStatisticsSolis::GetCount(const AminoAcidSet& prev_aa,
- const AminoAcidSet& central_aa,
- const AminoAcidSet& next_aa,
- Real phi_angle, Real psi_angle) const
-{
- uint32_t count=0;
- uint32_t phi_bucket=this->IndexForAngle(phi_angle);
- uint32_t psi_bucket=this->IndexForAngle(psi_angle);
- for (AminoAcidSet::Iterator i=prev_aa.Begin(), e1=prev_aa.End(); i!=e1; ++i) {
- for (AminoAcidSet::Iterator j=central_aa.Begin(),
- e2=central_aa.End(); j!=e2; ++j) {
- for (AminoAcidSet::Iterator k=next_aa.Begin(),
- e3=next_aa.End(); k!=e3; ++k) {
- TorsionHistogram::IndexType start(*i, *j, *k, phi_bucket, psi_bucket),
- end(*i, *j, *k, phi_bucket, psi_bucket);
- count+=this->Accumulate(start, end);
- }
- }
- }
- return count;
-}
-
-uint32_t TorsionStatisticsSolis::GetCount(const AminoAcidSet& prev_aa,
- const AminoAcidSet& central_aa,
- const AminoAcidSet& next_aa) const
-{
- uint32_t count=0;
- uint32_t torsion_buckets=uint32_t(360.0/torsion_bucket_size_);
- for (AminoAcidSet::Iterator i=prev_aa.Begin(), e1=prev_aa.End(); i!=e1; ++i) {
- for (AminoAcidSet::Iterator j=central_aa.Begin(),
- e2=central_aa.End(); j!=e2; ++j) {
- for (AminoAcidSet::Iterator k=next_aa.Begin(),
- e3=next_aa.End(); k!=e3; ++k) {
- TorsionHistogram::IndexType start(*i, *j, *k, 0, 0),
- end(*i, *j, *k, torsion_buckets-1,
- torsion_buckets-1);
- count+=this->Accumulate(start, end);
- }
- }
- }
- return count;
-}
-
-
-uint32_t TorsionStatisticsSolis::GetCount(Real phi_angle, Real psi_angle) const
-{
- uint32_t phi_bucket=this->IndexForAngle(phi_angle);
- uint32_t psi_bucket=this->IndexForAngle(psi_angle);
- TorsionHistogram::IndexType start(0,0,0, phi_bucket, psi_bucket),
- end(Xxx-1, Xxx-1, Xxx-1, phi_bucket, psi_bucket);
- return this->Accumulate(start, end);
-}
-
-uint32_t TorsionStatisticsSolis::Accumulate(const IndexType& start,
- const IndexType& end) const
-{
- uint32_t total=0;
- for (TorsionHistogram::Iterator i(start, end); !i.AtEnd(); ++i) {
- total+=histogram_.Get(*i);
- }
- return total;
-}
-
-
-uint32_t TorsionStatisticsSolis::IndexForAngle(Real angle) const
-{
- return (histogram_.FindBucket(0,0,0,angle,0))[3];
-}
-
-uint32_t TorsionStatisticsSolis::GetCount(AminoAcid central_aa,
- Real phi_angle, Real psi_angle) const
-{
- uint32_t phi_bucket=this->IndexForAngle(phi_angle);
- uint32_t psi_bucket=this->IndexForAngle(psi_angle);
- TorsionHistogram::IndexType start(0,central_aa,0, phi_bucket, psi_bucket),
- end(Xxx-1, central_aa, Xxx-1,
- phi_bucket, psi_bucket);
- return this->Accumulate(start, end);
-}
-
-
-Real TorsionStatisticsSolis::GetFrequency(AminoAcid aa, Real phi_angle,
- Real psi_angle) const
-{
- uint32_t phi_bucket=this->IndexForAngle(phi_angle);
- uint32_t psi_bucket=this->IndexForAngle(psi_angle);
- uint32_t local_count=0, total_count=0;
- uint32_t torsion_buckets=uint32_t(360.0/torsion_bucket_size_);
- for (uint32_t phi=0; phi<torsion_buckets; ++phi) {
- for (uint32_t psi=0; psi<torsion_buckets; ++psi) {
- TorsionHistogram::IndexType start(0, aa, 0, phi, psi),
- end(Xxx-1, aa, Xxx-1, phi, psi);
- uint32_t phi_psi_count=this->Accumulate(start, end);
- if (phi==phi_bucket && psi==psi_bucket) {
- local_count+=phi_psi_count;
- }
- total_count+=phi_psi_count;
- }
- }
- return Real(local_count)/Real(total_count);
-}
-
-Real TorsionStatisticsSolis::GetFrequency(Real phi_angle,
- Real psi_angle) const
-{
- uint32_t phi_bucket=this->IndexForAngle(phi_angle);
- uint32_t psi_bucket=this->IndexForAngle(psi_angle);
- uint32_t local_count=0, total_count=0;
- uint32_t torsion_buckets=uint32_t(360.0/torsion_bucket_size_);
- for (uint32_t phi=0; phi<torsion_buckets; ++phi) {
- for (uint32_t psi=0; psi<torsion_buckets; ++psi) {
- TorsionHistogram::IndexType start(0, 0, 0, phi, psi),
- end(Xxx-1, Xxx-1, Xxx-1, phi, psi);
- uint32_t phi_psi_count=this->Accumulate(start, end);
- if (phi==phi_bucket && psi==psi_bucket) {
- local_count+=phi_psi_count;
- }
- total_count+=phi_psi_count;
- }
- }
- return Real(local_count)/Real(total_count);
-}
-
-int TorsionStatisticsSolis::GetCount() const
-{
- uint32_t torsion_buckets=uint32_t(360/torsion_bucket_size_);
- TorsionHistogram::IndexType start(0, 0, 0, 0, 0),
- end(Xxx-1, Xxx-1, Xxx-1, torsion_buckets-1,
- torsion_buckets-1);
- return this->Accumulate(start, end);
-}
-
-
-TorsionStatisticsSolis::TorsionStatisticsSolis():
- torsion_bucket_size_(0)
-{
-}
-
-}}
diff --git a/modules/qa/src/solis_torsion_statistics.hh b/modules/qa/src/solis_torsion_statistics.hh
deleted file mode 100644
index 5c189595b2aa88c2e6e76d89752fc945881d1302..0000000000000000000000000000000000000000
--- a/modules/qa/src/solis_torsion_statistics.hh
+++ /dev/null
@@ -1,127 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2011 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
-//------------------------------------------------------------------------------
-#ifndef OST_QA_SOLIS_TORSION_STATISTICS_HH
-#define OST_QA_SOLIS_TORSION_STATISTICS_HH
-/*
- This implementation of the torsion angle potential combines 1
- torsion angle pair with up to 3 residues in analogy to the
- potential described by:
- Armando D. Solis, S. Rackovsky
- Optimally informative backbone structural propensities in proteins
- Protei
- The ordinary trosion angle potential (1 angle-pair, 1 residue) is covered
- as well.
-
- Author: Marco Biasini, Pascal Benkert
- */
-#include <ost/mol/entity_handle.hh>
-#include <ost/qa/module_config.hh>
-#include <ost/qa/histogram.hh>
-#include <ost/qa/amino_acids.hh>
-#include <boost/shared_ptr.hpp>
-
-namespace ost { namespace qa {
-
-class TorsionStatisticsSolis;
-typedef boost::shared_ptr<TorsionStatisticsSolis> TorsionStatisticsSolisPtr;
-
-/// \brief sequence dependent torsion statistics
-class DLLEXPORT_OST_QA TorsionStatisticsSolis {
-public:
- /// construct new torsion statistics. In order to get something useful
- /// you need to either extract statistics from a set of PDBs or the
- /// statistics from file.
- ///
- /// \param torsion_bucket_size is the histogram bucket size for torsion
- /// angles.
- TorsionStatisticsSolis(int torsion_bucket_size);
- TorsionStatisticsSolis();
- /// \brief extract torsion counts from whole entity.
- void Extract(mol::EntityHandle entity);
-
- /// \brief extract torsion counts from (filtered) entity
- void Extract(mol::EntityView view);
-
- /// \brief load torsion statistics from file
- static TorsionStatisticsSolisPtr LoadFromFile(const String& file_name);
-
- void SaveToFile(const String& file_name) const;
-
- /// \brief Get count of phi/psi torsions with the specified torsion
- /// bucket size away conditional on the central, previous
- /// and next amino acid.
- uint32_t GetCount(const AminoAcidSet& prev_aa,
- const AminoAcidSet& central_aa,
- const AminoAcidSet& next_aa,
- Real phi_angle, Real psi_angle) const;
-
- uint32_t GetCount(const AminoAcidSet& prev_aa,
- const AminoAcidSet& central_aa,
- const AminoAcidSet& next_aa) const;
-
- /// \brief Get count of amino acids with the given phi/psi angle.
- uint32_t GetCount(Real phi_angle, Real psi_angle) const;
-
- /// \brief Get count of amino acids with the given phi/psi angle
- /// conditional on the central residue.
- uint32_t GetCount(AminoAcid central_aa,
- Real phi_angle, Real psi_angle) const;
-
- /// \brief Get frequency of phi/psi angle in bucket phi_angle/psi_angle when
- /// the amino acid is aa.
- /// \return frequency in the range of [0, 1]
- Real GetFrequency(AminoAcid aa, Real phi_angle, Real psi_angle) const;
-
- /// \brief Get frequency of phi/psi angle in bucket phi_angle/psi_angle
- /// regardless of the amino acid type.
- /// \return frequency in the range of [0, 1]
- Real GetFrequency(Real phi_angle, Real psi_angle) const;
-
- /// \brief get the number of torsion buckets for every of the torsion
- /// angles.
- uint32_t GetTorsionBucketCount() const;
- int GetTorsionBucketSize() const;
-
- int GetCount() const;
- /// \internal
- template <typename DS>
- void Serialize(DS& ds)
- {
- ds & torsion_bucket_size_;
- ds & histogram_;
- }
-public:
- typedef MultiClassifier<int, int, int, int, Real, Real> TorsionHistogram;
- typedef TorsionHistogram::IndexType IndexType;
-private:
- /// \brief Convenience function to add counts in the inclusive range
- /// [start, end]
- uint32_t Accumulate(const IndexType& start, const IndexType& end) const;
-
- uint32_t IndexForAngle(Real angle) const;
-
-
- TorsionHistogram histogram_;
- int torsion_bucket_size_;
-};
-}}
-
-#endif
-
-
diff --git a/modules/qa/src/torsion_potential.cc b/modules/qa/src/torsion_potential.cc
deleted file mode 100644
index d3fd7bcd81f5aea49b5bc6d6aa4c1a071a996cb8..0000000000000000000000000000000000000000
--- a/modules/qa/src/torsion_potential.cc
+++ /dev/null
@@ -1,321 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2011 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
-//------------------------------------------------------------------------------
-
-#include "torsion_potential.hh"
-#include "amino_acids.hh"
-
-#include <ost/log.hh>
-#include <ost/io/binary_data_source.hh>
-#include <ost/io/binary_data_sink.hh>
-#include <ost/io/container_serialization.hh>
-#include <ost/integrity_error.hh>
-#include <ost/mol/mol.hh>
-#include <boost/filesystem/convenience.hpp>
-#include <ost/message.hh>
-#include <ost/io/io_exception.hh>
-
-/*
- Authors: Marco Biasini, Pascal Benkert
- */
-
-namespace ost { namespace qa {
-
-namespace {
-
-class TorsionEnergyCalc : public mol::EntityVisitor {
-public:
- TorsionEnergyCalc(const TorsionPotentialPtr& pot,
- TorsionPotentialOpts opts, int length):
- pot_(pot), energy_(0.0), num_torsions_(0), score_vector_(std::vector<float>(length, 0.0)),
- pos_counter_(0)
- {
- }
-
- virtual bool VisitResidue(const mol::ResidueHandle& rh)
- {
- pos_counter_++;
- mol::ResidueHandle prev=rh.GetPrev();
- mol::ResidueHandle next=rh.GetNext();
- if (!(next && prev && next.IsPeptideLinking() &&
- prev.IsPeptideLinking() && rh.IsPeptideLinking())) {
- return false;
- }
-
- AminoAcid ca=ResidueToAminoAcid(rh);
- if (ca==Xxx)
- return false;
-
- mol::TorsionHandle prev_phit=prev.GetPhiTorsion();
- mol::TorsionHandle prev_psit=prev.GetPsiTorsion();
- mol::TorsionHandle central_phit=rh.GetPhiTorsion();
- mol::TorsionHandle central_psit=rh.GetPsiTorsion();
- mol::TorsionHandle next_phit=next.GetPhiTorsion();
- mol::TorsionHandle next_psit=next.GetPsiTorsion();
- if (!prev_phit || !prev_psit || !central_phit || !central_psit ||
- !next_phit || !next_psit)
- return false;
- Real prev_phi=prev_phit.GetAngle()*180/M_PI - 0.001; if (prev_phi<-180) prev_phi=-180;
- Real prev_psi=prev_psit.GetAngle()*180/M_PI - 0.001; if (prev_psi<-180) prev_psi=-180;
- Real central_phi=central_phit.GetAngle()*180/M_PI - 0.001; if (central_phi<-180) central_phi=-180;
- Real central_psi=central_psit.GetAngle()*180/M_PI - 0.001; if (central_psi<-180) central_psi=-180;
- Real next_phi=next_phit.GetAngle()*180/M_PI - 0.001; if (next_phi<-180) next_phi=-180;
- Real next_psi=next_psit.GetAngle()*180/M_PI - 0.001; if (next_psi<-180) next_psi=-180;
-
-
- // calculate position of the amino acid in the alphabet
- float local_energy=pot_->GetTorsionEnergy(ca, prev_phi, prev_psi, central_phi,
- central_psi, next_phi, next_psi);
- energy_+=local_energy;
-
- score_vector_[pos_counter_-1]=local_energy;
- ++num_torsions_;
- return false;
- }
-
- Real GetEnergy() const {
- return energy_;
- }
-
- int GetEnergyCounts() const {
- return num_torsions_;
- }
-
- std::vector<float> GetResidueEnergyVector() const {
- return score_vector_;
- }
-
-private:
- TorsionPotentialPtr pot_;
- AminoAcid prev_;
- AminoAcid center_;
- mol::ResidueHandle cr_;
- Real energy_;
- int num_torsions_;
- std::vector<float> score_vector_;
- int pos_counter_;
-};
-
-}
-
-template <typename DS>
-void TorsionPotentialOpts::Serialize(DS& ds)
-{
- ds & prev_angular_bucket_size;
- ds & central_angular_bucket_size;
- ds & next_angular_bucket_size;
- ds & alphabet;
- ds & sigma;
-}
-
-template <typename DS>
-void TorsionPotential::Serialize(DS& ds)
-{
- ds & options_;
- ds & energies_;
-}
-
-TorsionPotentialOpts::TorsionPotentialOpts():
- prev_angular_bucket_size(90), central_angular_bucket_size(45),
- next_angular_bucket_size(90), sigma(0.0005)
-{
-
-}
-
-
-int TorsionPotential::GetAAIndex(AminoAcid aa) const
-{
- AminoAcidAlphabet::const_iterator i=options_.alphabet.begin();
- for (int index=0; i!=options_.alphabet.end(); ++i, ++index) {
- if ((*i).Contains(aa)) {
- return index;
- }
- }
- return -1;
-}
-
-
-TorsionPotentialPtr TorsionPotential::Create(TorsionStatisticsPtr statistics,
- const TorsionPotentialOpts& opts,
- bool calculate_average_energy_flag)
-{
-
- typedef TorsionPotential::TorsionEnergies TorsionEnergies;
- int prev_bucket_size=statistics->GetTorsionBucketSizePrev();
- int central_bucket_size=statistics->GetTorsionBucketSizeCentral();
- int next_bucket_size=statistics->GetTorsionBucketSizeNext();
-
- //std::cout << prev_bucket_size << " " << central_bucket_size << " " << next_bucket_size << std::endl;
-
- if (prev_bucket_size == 0 || central_bucket_size == 0 || next_bucket_size == 0) {
- throw IntegrityError("Torsion angle statistics does not exist. Re-extract counts.");
- }
-
- if ((opts.prev_angular_bucket_size % prev_bucket_size)!=0) {
- throw IntegrityError("Previous angular bucket size for torsion potential is not an "
- "integral multiple of the statistics bucket size");
- }
- if ((opts.central_angular_bucket_size % central_bucket_size)!=0) {
- throw IntegrityError("Central angular bucket size for torsion potential is not an "
- "integral multiple of the statistics bucket size");
- }
- if ((opts.next_angular_bucket_size % next_bucket_size)!=0) {
- throw IntegrityError("Next angular bucket size for torsion potential is not an "
- "integral multiple of the statistics bucket size");
- }
- int prev_buckets=360/opts.prev_angular_bucket_size;
- int central_buckets=360/opts.central_angular_bucket_size;
- int next_buckets=360/opts.next_angular_bucket_size;
- TorsionPotentialPtr ptr(new TorsionPotential);
-
- ptr->options_.prev_angular_bucket_size = opts.prev_angular_bucket_size;
- ptr->options_.central_angular_bucket_size = opts.central_angular_bucket_size;
- ptr->options_.next_angular_bucket_size = opts.next_angular_bucket_size;
-
- ptr->options_.alphabet = opts.alphabet;
- uint64_t alphabet_size=ptr->options_.alphabet.size();
-
- ptr->energies_=TorsionEnergies(0.0, IntegralClassifier(alphabet_size, 0),
- ContinuousClassifier(prev_buckets,-180,180),
- ContinuousClassifier(prev_buckets,-180,180),
- ContinuousClassifier(central_buckets,-180,180),
- ContinuousClassifier(central_buckets,-180,180),
- ContinuousClassifier(next_buckets,-180,180),
- ContinuousClassifier(next_buckets,-180,180));
- ptr->Fill(statistics, calculate_average_energy_flag);
- return ptr;
-}
-
-TorsionPotentialPtr TorsionPotential::LoadFromFile(const String& path)
-{
- if(!boost::filesystem::exists(path))
- throw io::IOException("Could not open torsion potential data file.\nFile does not exist at: "+path);
-
- std::ifstream stream(path.c_str(), std::ios_base::binary);
- io::BinaryDataSource ds(stream);
- TorsionPotentialPtr ptr(new TorsionPotential);
- ds >> *ptr.get();
- return ptr;
-}
-
-void TorsionPotential::SaveToFile(const String& path)
-{
- std::ofstream stream(path.c_str(), std::ios_base::binary);
- io::BinaryDataSink ds(stream);
- ds << *this;
-}
-
-Real TorsionPotential::GetTotalEnergy(mol::EntityHandle entity)
-{
- int res_count=entity.GetResidueList().size();
- TorsionEnergyCalc c(this->shared_from_this(), options_, res_count);
- entity.Apply(c);
- num_torsions_ = c.GetEnergyCounts();
- std::vector<float> rev=c.GetResidueEnergyVector();
- for(int i=0;i<res_count;++i) {
- entity.GetResidueList()[i].SetFloatProp("torsion_energy", rev[i]);
- }
- return c.GetEnergy();
-}
-
-Real TorsionPotential::GetTotalEnergy(mol::EntityView entity)
-{
- int res_count=entity.GetResidueList().size();
- TorsionEnergyCalc c(this->shared_from_this(), options_, res_count);
- entity.Apply(c);
- num_torsions_ = c.GetEnergyCounts();
- std::vector<float> rev=c.GetResidueEnergyVector();
- for(int i=0;i<res_count;++i) {
- entity.GetResidueList()[i].SetFloatProp("torsion_energy", rev[i]);
- }
- return c.GetEnergy();
-}
-
-int TorsionPotential::GetEnergyCounts() const {
- return num_torsions_;
-}
-
-void TorsionPotential::Fill(const TorsionStatisticsPtr& stat, bool calculate_average_energy_flag)
-{
- int prev_num_b=360/(options_.prev_angular_bucket_size);
- int central_num_b=360/(options_.central_angular_bucket_size);
- int next_num_b=360/(options_.next_angular_bucket_size);
-
- int prev_half_b=options_.prev_angular_bucket_size/2;
- int central_half_b=options_.central_angular_bucket_size/2;
- int next_half_b=options_.next_angular_bucket_size/2;
-
- uint64_t M=stat->GetCount();
- //std::cout << "total counts: " << M << std::endl;
-
- typedef AminoAcidAlphabet::const_iterator AAA;
- for (AAA i=options_.alphabet.begin(),
- e1=options_.alphabet.end(); i!=e1; ++i) {
-
- uint64_t Mi=stat->GetCount(*i);
- if (calculate_average_energy_flag==1) std::cout << *i << " " << float(Mi)/M << " ";
- Real per_aa_energy = 0; // for average energy
-
-
- for (int prev_phi=0; prev_phi<prev_num_b; ++prev_phi) {
- for (int prev_psi=0; prev_psi<prev_num_b; ++prev_psi) {
- int prev_phi_a=-180+options_.prev_angular_bucket_size*prev_phi+prev_half_b;
- int prev_psi_a=-180+options_.prev_angular_bucket_size*prev_psi+prev_half_b;
-
- for (int central_phi=0; central_phi<central_num_b; ++central_phi) {
- for (int central_psi=0; central_psi<central_num_b; ++central_psi) {
- int central_phi_a=-180+options_.central_angular_bucket_size*central_phi+central_half_b;
- int central_psi_a=-180+options_.central_angular_bucket_size*central_psi+central_half_b;
-
- for (int next_phi=0; next_phi<next_num_b; ++next_phi) {
- for (int next_psi=0; next_psi<next_num_b; ++next_psi) {
- int next_phi_a=-180+options_.next_angular_bucket_size*next_phi+next_half_b;
- int next_psi_a=-180+options_.next_angular_bucket_size*next_psi+next_half_b;
-
- uint64_t fxi=stat->GetCount(*i, prev_phi_a, prev_psi_a, central_phi_a, central_psi_a, next_phi_a, next_psi_a);
- uint64_t fx=stat->GetCount(prev_phi_a, prev_psi_a, central_phi_a, central_psi_a, next_phi_a, next_psi_a);
-
- // propensity = (fxi/Mi)/(fx/M)
- Real propensity=0.0;
- Real energy=0.0;
- //avoid division by zero:
- if (fx != 0 && Mi != 0 && M != 0) {
- propensity=Real(Real(fxi)/Mi)/(Real(fx)/M);
- }
-
- energy=log(1+options_.sigma*Mi)-
- log(1+options_.sigma*Mi*propensity);
-
- per_aa_energy=per_aa_energy+fxi*energy; // for average energy
-
-
- energies_.Add(energy,
- i-options_.alphabet.begin(),
- prev_phi_a, prev_psi_a, central_phi_a, central_psi_a, next_phi_a, next_psi_a);
- }
- }
-
- }
- }
-
- }
- }
- if (calculate_average_energy_flag==1) std::cout << per_aa_energy/Mi << std::endl;
-}
-}
-}}
diff --git a/modules/qa/src/torsion_potential.hh b/modules/qa/src/torsion_potential.hh
deleted file mode 100644
index 91b5407db4a9877460c033e31f78b36b0db82aa5..0000000000000000000000000000000000000000
--- a/modules/qa/src/torsion_potential.hh
+++ /dev/null
@@ -1,137 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2011 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
-//------------------------------------------------------------------------------
-#ifndef OST_QA_TORSION_POTENTIAL_HH
-#define OST_QA_TORSION_POTENTIAL_HH
-/*
- This implementation of the torsion angle potential combines 3
- torsion angle pairs with 1 residues in analogy to the combined
- potential described by:
- Pascal Benkert, Silvio C. E. Tosatto, Dietmar Schomburg
- QMEAN: A comprehensive scoring function for model quality assessment
- Proteins, 2008
-
- Author: Pascal, Benkert, Marco Biasini
-*/
-#include <ost/qa/torsion_statistics.hh>
-#include <boost/shared_ptr.hpp>
-#include <boost/enable_shared_from_this.hpp>
-#include <vector>
-#include <boost/scoped_ptr.hpp>
-
-namespace ost { namespace qa {
-
-typedef std::vector<AminoAcidSet> AminoAcidAlphabet;
-
-/// \brief torsion potential options
-///
-/// These options may be used to configure the different torsion potentials
-/// based on a sliding window of 3 amino acids.
-struct DLLEXPORT_OST_QA TorsionPotentialOpts {
- /// \brief initialize torsion potential with angular bucket size of 30 and
- /// sigma of 0.02
- ///
- /// The amino acid alphabets are empty.
- TorsionPotentialOpts();
-
- /// angular bucket size, 360 % angular_bucket_size must be zero
- int prev_angular_bucket_size;
- int central_angular_bucket_size;
- int next_angular_bucket_size;
- /// alphabet of the central. The amino acids in the set must be mutually excl.
- AminoAcidAlphabet alphabet;
- /// weighting factor after (Sippl et al., 1990), usually 0.02
- Real sigma;
- /// \internal
- template <typename DS>
- void Serialize(DS& ds);
-};
-
-class TorsionPotential;
-typedef boost::shared_ptr<TorsionPotential> TorsionPotentialPtr;
-
-/// \brief Torsion potential
-///
-/// The torsion potential class is parametrisable by TorsionPotentialOpts.
-class DLLEXPORT_OST_QA TorsionPotential :
- public boost::enable_shared_from_this<TorsionPotential> {
-public:
- /// \brief create new torsion potential with the given torsion statistics
- /// and options
- /// If the flag ist set the average energy per is calculated
- /// and shown on stdout. May be used to correct compositional bias in
- /// scoring functions (e.g. Pro and Gly have on average lower torsion energies).
- static TorsionPotentialPtr Create(TorsionStatisticsPtr statistics,
- const TorsionPotentialOpts& opts,
- bool calculate_average_energy_flag);
- /// \brief Load potential from file.
- static TorsionPotentialPtr LoadFromFile(const String& path);
-
- /// \brief Calculate energy for entity.
- Real GetTotalEnergy(mol::EntityHandle entity);
-
- /// \brief Calculate energy for entity view. Only residues in the view are
- /// considered.
- Real GetTotalEnergy(mol::EntityView view);
-
- /// \brief retrieve total number of energy local (i.e. valid residues)
- int GetEnergyCounts() const;
-
-
-
- Real GetTorsionEnergy(AminoAcid central_aa, Real prev_phi, Real prev_psi,
- Real central_phi, Real central_psi,
- Real next_phi, Real next_psi) const {
- int icenter=this->GetAAIndex(central_aa);
- return energies_.Get(icenter, prev_phi, prev_psi,
- central_phi, central_psi,
- next_phi, next_psi);
- }
-
-
- /// \brief save torsion potential
- ///
- /// The output is in a non-portable binary form.
- void SaveToFile(const String& path);
-
- /// \internal
- template <typename DS>
- void Serialize(DS& ds);
-
-
-public:
- /// Meaning of parameters: AA before AA center AA after,
- /// phi torsion angle, psi torsion angle
- typedef MultiClassifier<float, int, Real, Real,
- Real, Real, Real, Real> TorsionEnergies;
-private:
-
- int GetAAIndex(AminoAcid aa) const;
-
- void Fill(const TorsionStatisticsPtr& stat,
- bool calculate_average_energy_flag);
-
- TorsionPotentialOpts options_;
- TorsionEnergies energies_;
- int num_torsions_;
-};
-
-
-}}
-
-#endif
diff --git a/modules/qa/src/torsion_statistics.cc b/modules/qa/src/torsion_statistics.cc
deleted file mode 100644
index fd67b7f864e1f99e92d58f84201573f3e50e3564..0000000000000000000000000000000000000000
--- a/modules/qa/src/torsion_statistics.cc
+++ /dev/null
@@ -1,271 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2011 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
-//------------------------------------------------------------------------------
-#include "torsion_statistics.hh"
-#include "amino_acids.hh"
-#include <ost/log.hh>
-#include <ost/mol/mol.hh>
-#include <fstream>
-#include <ost/message.hh>
-#include <ost/io/binary_data_source.hh>
-#include <ost/io/binary_data_sink.hh>
-#include <ost/io/container_serialization.hh>
-
-/*
- Author: Marco Biasini, Pascal Benkert
- */
-namespace ost { namespace qa {
-
-
-namespace {
-
-class TorsionStat : public mol::EntityVisitor {
-public:
- TorsionStat(TorsionStatistics::TorsionHistogram& histo):
- histo_(histo)
- {}
-
- virtual bool VisitResidue(const mol::ResidueHandle& residue) {
-
- mol::ResidueHandle prev=residue.GetPrev();
- mol::ResidueHandle next=residue.GetNext();
- if (!(next && prev && next.IsPeptideLinking() &&
- prev.IsPeptideLinking() && residue.IsPeptideLinking())) {
- return false;
- }
-
- AminoAcid ca=ResidueToAminoAcid(residue);
- if (ca==Xxx)
- return false;
-
- mol::TorsionHandle prev_phit=prev.GetPhiTorsion();
- mol::TorsionHandle prev_psit=prev.GetPsiTorsion();
- mol::TorsionHandle central_phit=residue.GetPhiTorsion();
- mol::TorsionHandle central_psit=residue.GetPsiTorsion();
- mol::TorsionHandle next_phit=next.GetPhiTorsion();
- mol::TorsionHandle next_psit=next.GetPsiTorsion();
- if (!prev_phit || !prev_psit || !central_phit || !central_psit ||
- !next_phit || !next_psit)
- return false;
- Real prev_phi=prev_phit.GetAngle()*180/M_PI - 0.001;
- Real prev_psi=prev_psit.GetAngle()*180/M_PI - 0.001;
- Real central_phi=central_phit.GetAngle()*180/M_PI - 0.001;
- Real central_psi=central_psit.GetAngle()*180/M_PI - 0.001;
- Real next_phi=next_phit.GetAngle()*180/M_PI - 0.001;
- Real next_psi=next_psit.GetAngle()*180/M_PI - 0.001;
-
- histo_.Add(1, ca, prev_phi, prev_psi, central_phi, central_psi, next_phi, next_psi);
- return false;
- }
-private:
- TorsionStatistics::TorsionHistogram& histo_;
-};
-
-}
-
-TorsionStatistics::TorsionStatistics(int prev_torsion_bucket_size,
- int central_torsion_bucket_size,
- int next_torsion_bucket_size)
- : histogram_(1, IntegralClassifier(20, 0),
- ContinuousClassifier(int(360/prev_torsion_bucket_size), -180, 180),
- ContinuousClassifier(int(360/prev_torsion_bucket_size), -180, 180),
- ContinuousClassifier(int(360/central_torsion_bucket_size), -180, 180),
- ContinuousClassifier(int(360/central_torsion_bucket_size), -180, 180),
- ContinuousClassifier(int(360/next_torsion_bucket_size), -180, 180),
- ContinuousClassifier(int(360/next_torsion_bucket_size), -180, 180)),
- prev_torsion_bucket_size_(prev_torsion_bucket_size),
- central_torsion_bucket_size_(central_torsion_bucket_size),
- next_torsion_bucket_size_(next_torsion_bucket_size)
-{
-
-}
-
-uint32_t TorsionStatistics::GetTorsionBucketCountPrev() const
-{
- return uint32_t(360/prev_torsion_bucket_size_);
-}
-
-uint32_t TorsionStatistics::GetTorsionBucketCountCentral() const
-{
- return uint32_t(360/central_torsion_bucket_size_);
-}
-
-uint32_t TorsionStatistics::GetTorsionBucketCountNext() const
-{
- return uint32_t(360/next_torsion_bucket_size_);
-}
-
-
-int TorsionStatistics::GetTorsionBucketSizePrev() const
-{
- return prev_torsion_bucket_size_;
-}
-
-int TorsionStatistics::GetTorsionBucketSizeCentral() const
-{
- return central_torsion_bucket_size_;
-}
-
-int TorsionStatistics::GetTorsionBucketSizeNext() const
-{
- return next_torsion_bucket_size_;
-}
-
-
-void TorsionStatistics::Extract(mol::EntityView view)
-{
- TorsionStat stat(histogram_);
- view.Apply(stat);
-}
-
-void TorsionStatistics::Extract(mol::EntityHandle entity)
-{
- TorsionStat stat(histogram_);
- entity.Apply(stat);
-}
-
-TorsionStatisticsPtr TorsionStatistics::LoadFromFile(const String& file_name)
-{
- std::ifstream stream(file_name.c_str(), std::ios_base::binary);
- TorsionStatisticsPtr ptr(new TorsionStatistics);
- io::BinaryDataSource ds(stream);
- ds >> *ptr.get();
- return ptr;
-}
-
-void TorsionStatistics::SaveToFile(const String& file_name) const
-{
- std::ofstream stream(file_name.c_str(), std::ios_base::binary);
- io::BinaryDataSink ds(stream);
- ds << *this;
-}
-
-
-uint64_t TorsionStatistics::GetCount(const AminoAcidSet& central_aa,
- Real prev_phi_angle, Real prev_psi_angle,
- Real central_phi_angle, Real central_psi_angle,
- Real next_phi_angle, Real next_psi_angle) const
-{
- uint64_t count=0;
- uint32_t prev_phi_bucket=this->IndexForAnglePrev(prev_phi_angle);
- uint32_t prev_psi_bucket=this->IndexForAnglePrev(prev_psi_angle);
- uint32_t central_phi_bucket=this->IndexForAngleCentral(central_phi_angle);
- uint32_t central_psi_bucket=this->IndexForAngleCentral(central_psi_angle);
- uint32_t next_phi_bucket=this->IndexForAngleNext(next_phi_angle);
- uint32_t next_psi_bucket=this->IndexForAngleNext(next_psi_angle);
- for (AminoAcidSet::Iterator i=central_aa.Begin(), e1=central_aa.End(); i!=e1; ++i) {
- TorsionHistogram::IndexType start(*i, prev_phi_bucket, prev_psi_bucket,
- central_phi_bucket, central_psi_bucket,
- next_phi_bucket, next_psi_bucket),
- end(*i, prev_phi_bucket, prev_psi_bucket,
- central_phi_bucket, central_psi_bucket,
- next_phi_bucket, next_psi_bucket);
- count+=this->Accumulate(start, end);
- }
- return count;
-}
-
-
-uint64_t TorsionStatistics::GetCount(Real prev_phi_angle, Real prev_psi_angle,
- Real central_phi_angle, Real central_psi_angle,
- Real next_phi_angle, Real next_psi_angle) const
-{
- uint32_t prev_phi_bucket=this->IndexForAnglePrev(prev_phi_angle);
- uint32_t prev_psi_bucket=this->IndexForAnglePrev(prev_psi_angle);
- uint32_t central_phi_bucket=this->IndexForAngleCentral(central_phi_angle);
- uint32_t central_psi_bucket=this->IndexForAngleCentral(central_psi_angle);
- uint32_t next_phi_bucket=this->IndexForAngleNext(next_phi_angle);
- uint32_t next_psi_bucket=this->IndexForAngleNext(next_psi_angle);
- TorsionHistogram::IndexType start(0, prev_phi_bucket, prev_psi_bucket,
- central_phi_bucket, central_psi_bucket,
- next_phi_bucket, next_psi_bucket),
- end(Xxx-1, prev_phi_bucket, prev_psi_bucket,
- central_phi_bucket, central_psi_bucket,
- next_phi_bucket, next_psi_bucket);
- return this->Accumulate(start, end);
-}
-
-
-uint64_t TorsionStatistics::GetCount(const AminoAcidSet& central_aa) const
-{
- uint64_t count=0;
- uint32_t prev_buckets=uint32_t(360.0/prev_torsion_bucket_size_);
- uint32_t central_buckets=uint32_t(360.0/central_torsion_bucket_size_);
- uint32_t next_buckets=uint32_t(360.0/next_torsion_bucket_size_);
-
- for (AminoAcidSet::Iterator i=central_aa.Begin(), e1=central_aa.End(); i!=e1; ++i) {
- TorsionHistogram::IndexType start(*i, 0, 0, 0, 0, 0, 0),
- end(*i, prev_buckets-1, prev_buckets-1,
- central_buckets-1, central_buckets-1,
- next_buckets-1, next_buckets-1);
- count+=this->Accumulate(start, end);
- }
- return count;
-}
-
-
-uint64_t TorsionStatistics::GetCount() const
-{
- uint32_t prev_buckets=uint32_t(360.0/prev_torsion_bucket_size_);
- uint32_t central_buckets=uint32_t(360.0/central_torsion_bucket_size_);
- uint32_t next_buckets=uint32_t(360.0/next_torsion_bucket_size_);
-
- TorsionHistogram::IndexType start(0, 0, 0, 0, 0, 0, 0),
- end(Xxx-1, prev_buckets-1, prev_buckets-1,
- central_buckets-1, central_buckets-1,
- next_buckets-1, next_buckets-1);
- return this->Accumulate(start, end);
-}
-
-
-uint64_t TorsionStatistics::Accumulate(const IndexType& start,
- const IndexType& end) const
-{
- uint64_t total=0;
- for (TorsionHistogram::Iterator i(start, end); !i.AtEnd(); ++i) {
- total+=histogram_.Get(*i);
- }
- return total;
-}
-
-
-uint32_t TorsionStatistics::IndexForAnglePrev(Real angle) const
-{
- return (histogram_.FindBucket(0,angle,0,0,0,0,0))[1];
-}
-
-uint32_t TorsionStatistics::IndexForAngleCentral(Real angle) const
-{
- return (histogram_.FindBucket(0,0,0,angle,0,0,0))[3];
-}
-
-uint32_t TorsionStatistics::IndexForAngleNext(Real angle) const
-{
- return (histogram_.FindBucket(0,0,0,0,0,angle,0))[5];
-}
-
-
-
-TorsionStatistics::TorsionStatistics():
- prev_torsion_bucket_size_(0),
- central_torsion_bucket_size_(0),
- next_torsion_bucket_size_(0)
-{
-}
-
-} }
diff --git a/modules/qa/src/torsion_statistics.hh b/modules/qa/src/torsion_statistics.hh
deleted file mode 100644
index 73105e6e5c0d7f2fd2e16740e7f6150f04191ebb..0000000000000000000000000000000000000000
--- a/modules/qa/src/torsion_statistics.hh
+++ /dev/null
@@ -1,129 +0,0 @@
-//------------------------------------------------------------------------------
-// This file is part of the OpenStructure project <www.openstructure.org>
-//
-// Copyright (C) 2008-2011 by the OpenStructure authors
-//
-// This library is free software; you can redistribute it and/or modify it under
-// the terms of the GNU Lesser General Public License as published by the Free
-// Software Foundation; either version 3.0 of the License, or (at your option)
-// any later version.
-// This library is distributed in the hope that it will be useful, but WITHOUT
-// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
-// details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with this library; if not, write to the Free Software Foundation, Inc.,
-// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
-//------------------------------------------------------------------------------
-#ifndef OST_QA_TORSION_STATISTICS_HH
-#define OST_QA_TORSION_STATISTICS_HH
-/*
- Author: Pascal, Benkert, Marco Biasini
-*/
-#include <ost/mol/entity_handle.hh>
-#include <ost/qa/histogram.hh>
-#include <ost/qa/amino_acids.hh>
-#include <boost/shared_ptr.hpp>
-
-namespace ost { namespace qa {
-
-class TorsionStatistics;
-typedef boost::shared_ptr<TorsionStatistics> TorsionStatisticsPtr;
-
-/// \brief sequence dependent torsion statistics
-///
-/// This implementation of the torsion angle potential combines 3 torsion angle
-/// pairs with 1 residues in analogy to the combined potential described by:
-/// Pascal Benkert, Silvio C. E. Tosatto, Dietmar Schomburg QMEAN: A
-/// comprehensive scoring function for model quality assessment Proteins, 2008
-class DLLEXPORT_OST_QA TorsionStatistics {
-public:
- /// construct new torsion statistics. In order to get something useful
- /// you need to either extract statistics from a set of PDBs or the
- /// statistics from file.
- ///
- /// \param prev_torsion_bucket_size is torsion bucket size for the first
- /// torsion
- /// \param central_torsion_bucket_size is the bucket size for the second
- /// torsion
- /// \param next_torsion_bucket_size is the bucket size for the third torsion
- TorsionStatistics(int prev_torsion_bucket_size, int central_torsion_bucket_size,
- int next_torsion_bucket_size);
- TorsionStatistics();
- /// \brief extract torsion counts from whole entity.
- void Extract(mol::EntityHandle entity);
-
- /// \brief extract torsion counts from (filtered) entity
- void Extract(mol::EntityView view);
-
- /// \brief load torsion statistics from file
- static TorsionStatisticsPtr LoadFromFile(const String& file_name);
-
- void SaveToFile(const String& file_name) const;
-
- /// \brief Get count of phi/psi torsions with the specified torsion
- /// bucket size away conditional on the central amino acid.
- uint64_t GetCount(const AminoAcidSet& central_aa,
- Real prev_phi_angle, Real prev_psi_angle,
- Real central_phi_angle, Real central_psi_angle,
- Real next_phi_angle, Real next_psi_angle) const;
-
- uint64_t GetCount(Real prev_phi_angle, Real prev_psi_angle,
- Real central_phi_angle, Real central_psi_angle,
- Real next_phi_angle, Real next_psi_angle) const;
-
- uint64_t GetCount(const AminoAcidSet& central_aa) const;
-
- uint64_t GetCount() const;
-
-// /// \brief Get frequency of the amino acid aa.
-// /// \return frequency in the range of [0, 1]
-// Real GetFrequency(AminoAcid aa) const;
-
-
- /// \brief get the number of torsion buckets for every of the torsion
- /// angles.
- uint32_t GetTorsionBucketCountPrev() const;
- int GetTorsionBucketSizePrev() const;
- uint32_t GetTorsionBucketCountCentral() const;
- int GetTorsionBucketSizeCentral() const;
- uint32_t GetTorsionBucketCountNext() const;
- int GetTorsionBucketSizeNext() const;
-
-
- /// \internal
- template <typename DS>
- void Serialize(DS& ds)
- {
- ds & prev_torsion_bucket_size_;
- ds & central_torsion_bucket_size_;
- ds & next_torsion_bucket_size_;
- ds & histogram_;
- }
-public:
-
- typedef MultiClassifier<uint32_t, int, Real, Real,
- Real, Real, Real, Real> TorsionHistogram;
- typedef TorsionHistogram::IndexType IndexType;
-
-
-private:
- /// \brief Convenience function to add counts in the inclusive range
- /// [start, end]
- uint64_t Accumulate(const IndexType& start, const IndexType& end) const;
-
- uint32_t IndexForAnglePrev(Real angle) const;
- uint32_t IndexForAngleCentral(Real angle) const;
- uint32_t IndexForAngleNext(Real angle) const;
-
- TorsionHistogram histogram_;
- int prev_torsion_bucket_size_;
- int central_torsion_bucket_size_;
- int next_torsion_bucket_size_;
-};
-}}
-
-#endif
-
-