Consegna Progetto Sovrapposizione Strutturale - Filippo Gamberoni

Biopool/APPS/Makefile

@@ -1,58 +1,62 @@
-#--*- makefile -*--------------------------------------------------------------
-#
-#   Standard makefile
-#
-#------------------------------------------------------------------------------
-
-# Path to project directory.
-UPDIR = ../..
-# Path to subdirectories.
-SUBDIR=
-# Path to directory for binaries:
-BINPATH = ../../bin
-
-
-#
-# Libraries and paths (which are not defined globally).
-#
-
-LIBS =  -lEnergy -lTorsion -lBiopool  -ltools
-
-LIB_PATH = -L.
-
-INC_PATH = -I. -I../../tools/ -I../../Biopool/Sources -I../../Energy/Sources -I../../Energy/Sources/TorsionPotential
-
-#
-# Objects and headers
-#
-
-SOURCES =   PdbCorrector.cc PdbSecondary.cc PdbEditor.cc Pdb2Seq.cc pdb2secondary.cc pdbshifter.cc \
-	pdbMover.cc
-
-OBJECTS =   PdbCorrector.o PdbSecondary.o PdbEditor.o Pdb2Seq.o pdb2secondary.o pdbshifter.o \
-	pdbMover.o
-
-TARGETS = PdbCorrector PdbSecondary PdbEditor Pdb2Seq pdb2secondary pdbshifter \
-	pdbMover
-
-EXECS = PdbCorrector PdbSecondary PdbEditor Pdb2Seq pdb2secondary pdbshifter \
-	pdbMover
-
-LIBRARY = APPSlibBiopool.a
-
-#
-# Install rule
-#
-
-compile: all
-
-all: install
-install: $(LIBRARY) $(TARGETS)
-	mv $(EXECS) $(UPDIR)/bin/
-	mv $(LIBRARY) $(UPDIR)/lib/
-
-#
-# Call global Makefile to do the job.
-#
-
-include ../../Makefile.global
+#--*- makefile -*--------------------------------------------------------------
+#
+#   Standard makefile
+#
+#------------------------------------------------------------------------------
+
+# Path to project directory.
+UPDIR = ../..
+# Path to subdirectories.
+SUBDIR=
+# Path to directory for binaries:
+BINPATH = ../../bin
+
+
+#
+# Libraries and paths (which are not defined globally).
+#
+
+LIBS =  -lEnergy -lTorsion -lBiopool  -ltools
+
+LIB_PATH = -L.
+
+INC_PATH = -I. -I../../tools/ -I../../Biopool/Sources -I../../Energy/Sources -I../../Energy/Sources/TorsionPotential
+
+#
+# Objects and headers
+#
+
+SOURCES =   PdbCorrector.cc PdbSecondary.cc PdbEditor.cc Pdb2Seq.cc pdb2secondary.cc pdbshifter.cc \
+	pdbMover.cc \
+	PdbSuperimposition.cc
+
+OBJECTS =   PdbCorrector.o PdbSecondary.o PdbEditor.o Pdb2Seq.o pdb2secondary.o pdbshifter.o \
+	pdbMover.o \
+	PdbSuperimposition.o
+
+TARGETS = PdbCorrector PdbSecondary PdbEditor Pdb2Seq pdb2secondary pdbshifter \
+	pdbMover \
+	PdbSuperimposition
+
+EXECS = PdbCorrector PdbSecondary PdbEditor Pdb2Seq pdb2secondary pdbshifter \
+	pdbMover \
+	PdbSuperimposition
+
+LIBRARY = APPSlibBiopool.a
+
+#
+# Install rule
+#
+
+compile: all
+
+all: install
+install: $(LIBRARY) $(TARGETS)
+	mv $(EXECS) $(UPDIR)/bin/
+	mv $(LIBRARY) $(UPDIR)/lib/
+
+#
+# Call global Makefile to do the job.
+#
+
+include ../../Makefile.global

Biopool/APPS/PdbSuperimposition.cc

@@ -0,0 +1,172 @@
+#include <PdbLoader.h>
+#include <Protein.h>
+#include <iostream>
+#include <Eigen/Geometry> 
+#include <StructuralSuperimposition.h>
+
+using namespace Victor::Biopool;
+using namespace Victor; 
+using namespace std;
+
+
+
+int main( int argc, char* argv[] ) 
+{
+	double d0= 3.5; //algorithm threshold
+	int L=4; //algorithm seeds size
+	string inputFile1, inputFile2, outputFile, score;
+
+	// Check the number of parameters
+    if (argc < 5)
+    {
+        // Tell the user how to run the program
+        cout<<endl<<endl;
+        cout<<"STRUCTURAL SUPERIMPOSITION utility:"<<endl;
+        cout<<"This program evaluates the optimal rigid superimposition of two sequence equivalent proteic structures."<<endl;
+        cout<<"It uses an heuristic iterative algorithm (Siew, Elofsson, Rychlewski, Fischer) to find the largest subset "<<endl;
+        cout<<"of model (A) residues that best superimpose with their corresponding residues in the experimental structure (B)"<<endl;
+        cout<<"From the resulting subset it's possible to select which superimposition quality score to view."<<endl;
+        cout<<"The avaiable score are: RMSD, GDT_TS, TM-Score, MaxSub."<<endl<<endl<<endl;
+        cout<<"Usage: "<<endl<<endl;
+        cout<<"\t"<<argv[0]<<"\t<in_file1>\t<in_file2>\t<out_file>\t<seed_size>\t<score>\t[OPTIONS]"<<endl<<endl;
+        cout<<"Files required:"<<endl<<endl;
+        cout<<"\tin_file1\t PDB file of the first protein structure (the \"native\" structure)"<<endl;
+        cout<<"\tin_file2\t PDB file of the second protein structure (the \"experimental\" structure)"<<endl;
+        cout<<"\tout_file\t PDB file of the experimental structure optimally superimposed"<<endl<<endl;
+        cout<<"Seed: "<<endl<<endl;
+        cout<<"\t<integer>\t Select the initial seed matches size (must be >=4, default is 4)."<<endl<<endl;
+        cout<<"Scores: "<<endl<<endl;
+        cout<<"\t[-r <double>]\tUse RMSD score with custom d0 threshold (default is 3.5 A)"<<endl;
+        cout<<"\t[-t]\t\tUse TM-Score"<<endl;
+        cout<<"\t[-m <double>]\tUse MaxSub score with custom d0 threshold (default is 3.5 A)"<<endl;
+        cout<<"\t[-g]\t\tUse GDT-TS score"<<endl;
+        cout<<"\t[-a]\t\tAll"<<endl<<endl;
+
+        return 1;
+    }
+    else
+    {
+    	//argument parsing 
+    	inputFile1 = argv[1];
+    	inputFile2 = argv[2];
+    	outputFile = argv[3];
+    	L= strtol(argv[4],NULL,10);
+    	score = argv[5];
+
+    	if(L<4)
+    	{
+    		cout<<"\nError on parsing seed_size: input must be >= 4."<<endl;
+    		return 1;
+    	}
+
+    	//options parsing
+	    if(argc > 6)
+	    {
+		    d0 = strtod (argv[6], NULL);
+		    if(d0 <= 0.0)
+		    {
+		    	cout<<"\nError on parsing the d0 threshold: input is not a number and can't be <= 0"<<endl;
+		    	return 1;
+		    }
+	    }
+
+
+    	if(score=="-r" || score=="-t" || score=="-m" || score=="-g" || score=="-a")
+	    {
+
+	    	ifstream inFile1(inputFile1.c_str());
+			ifstream inFile2(inputFile2.c_str());
+
+			Protein prot1, prot2;   
+			Spacer *sp1, *sp2;
+
+
+		    PdbLoader pl1(inFile1);
+		    PdbLoader pl2(inFile2);
+
+		    pl1.setNoHAtoms();
+		    pl2.setNoHAtoms();
+
+			cout<<"Loading protein A ("<<inputFile1<<")"<<endl;
+			prot1.load(pl1);       
+			cout<<endl<<endl<<"Loading protein B ("<<inputFile2<<")"<<endl;
+			prot2.load(pl2);       
+			cout<<endl<<endl;
+
+
+			vector<char> chain1 = prot1.getAllChains();
+			vector<char> chain2 = prot2.getAllChains();
+
+			sp1=prot1.getSpacer(chain1[0]);
+			sp2=prot2.getSpacer(chain2[0]);
+
+			StructuralSuperimposition s1, s2= StructuralSuperimposition();
+
+			Eigen::Matrix<double,Eigen::Dynamic,Eigen::Dynamic> A=StructuralSuperimposition::convertSpacerToEigen(sp1);
+
+			Eigen::Matrix<double,Eigen::Dynamic,Eigen::Dynamic> B=StructuralSuperimposition::convertSpacerToEigen(sp2);
+
+			if(L>A.rows() || L>B.rows())
+    		{
+    			cout<<"\nError: L is bigger than the protein size ("<<A.rows()<<")"<<endl;
+    			return 1;
+    		}
+
+			StructuralSuperimposition ssi= StructuralSuperimposition();
+
+	    	if(score=="-r")
+	    	{
+	    		double rmsdscore= ssi.getRmsdScore(A,B,L,d0);
+	    		cout<<"RMSD score: "<<rmsdscore<<endl;
+	    		ssi.printPDBFile(outputFile.c_str(),*sp1,*sp2, A);
+	    	}
+
+	    	if(score=="-t")
+	    	{
+				double tmscore= ssi.getTMScore(A, B, L);
+				cout<<"TM-score: "<<tmscore<<endl;
+				ssi.printPDBFile(outputFile.c_str(),*sp1,*sp2, A);
+	    	}
+	    	if(score=="-m")
+	    	{
+	    		double msscore= ssi.getMaxSubScore(A, B, L, d0);
+	    		cout<<"MaxSub score: "<<msscore<<endl;
+	    		ssi.printPDBFile(outputFile.c_str(),*sp1,*sp2, A);
+	    	}
+
+	    	if(score=="-g")
+	    	{
+	    		double gdttsscore= ssi.getGDTTSScore(A,B,L);
+				cout<<"GDT-TS score: "<<gdttsscore<<endl;
+				ssi.printPDBFile(outputFile.c_str(),*sp1,*sp2, A);
+	    	}
+
+	    	if(score=="-a")
+	    	{
+	    		double rmsdscore= ssi.getRmsdScore(A,B,L,d0);
+	    		cout<<"\nRMSD score: "<<rmsdscore<<endl<<endl;
+
+	    		ssi.printPDBFile((outputFile+".RMSD.pdb").c_str(),*sp1,*sp2, A);
+
+	    		double tmscore= ssi.getTMScore(A, B, L);
+	    		cout<<"TM-score: "<<tmscore<<endl<<endl;
+	    		ssi.printPDBFile( (outputFile+".TMS.pdb").c_str(),*sp1,*sp2, A);
+
+	    		double msscore= ssi.getMaxSubScore(A, B, L, d0);
+	    		cout<<"MaxSub score: "<<msscore<<endl<<endl;
+
+	    		ssi.printPDBFile( (outputFile+".MSS.pdb").c_str(),*sp1,*sp2, A);
+
+	    		double gdttsscore= ssi.getGDTTSScore(A,B,L);
+				cout<<"GDT-TS score: "<<gdttsscore<<endl<<endl;
+				ssi.printPDBFile( (outputFile+".GDTTS.pdb").c_str(),*sp1,*sp2, A);
+	    	}
+	    }
+		else
+		{
+			cout<<"\nInvalid score selection, the valid ones are: -r (RMSD), -t (TM-Score), -m (MaxSub), -g (GDT-TS)."<<endl;
+			return 1;
+		}
+	}	
+	cout<<endl<<endl;
+}

Biopool/Sources/Eigen/Array

@@ -0,0 +1,11 @@
+#ifndef EIGEN_ARRAY_MODULE_H
+#define EIGEN_ARRAY_MODULE_H
+
+// include Core first to handle Eigen2 support macros
+#include "Core"
+
+#ifndef EIGEN2_SUPPORT
+  #error The Eigen/Array header does no longer exist in Eigen3. All that functionality has moved to Eigen/Core.
+#endif
+
+#endif // EIGEN_ARRAY_MODULE_H

Biopool/Sources/Eigen/CMakeLists.txt

@@ -0,0 +1,19 @@
+include(RegexUtils)
+test_escape_string_as_regex()
+
+file(GLOB Eigen_directory_files "*")
+
+escape_string_as_regex(ESCAPED_CMAKE_CURRENT_SOURCE_DIR "${CMAKE_CURRENT_SOURCE_DIR}")
+
+foreach(f ${Eigen_directory_files})
+  if(NOT f MATCHES "\\.txt" AND NOT f MATCHES "${ESCAPED_CMAKE_CURRENT_SOURCE_DIR}/[.].+" AND NOT f MATCHES "${ESCAPED_CMAKE_CURRENT_SOURCE_DIR}/src")
+    list(APPEND Eigen_directory_files_to_install ${f})
+  endif()
+endforeach(f ${Eigen_directory_files})
+
+install(FILES
+  ${Eigen_directory_files_to_install}
+  DESTINATION ${INCLUDE_INSTALL_DIR}/Eigen COMPONENT Devel
+  )
+
+add_subdirectory(src)

Biopool/Sources/Eigen/Cholesky

@@ -0,0 +1,32 @@
+#ifndef EIGEN_CHOLESKY_MODULE_H
+#define EIGEN_CHOLESKY_MODULE_H
+
+#include "Core"
+
+#include "src/Core/util/DisableStupidWarnings.h"
+
+/** \defgroup Cholesky_Module Cholesky module
+  *
+  *
+  *
+  * This module provides two variants of the Cholesky decomposition for selfadjoint (hermitian) matrices.
+  * Those decompositions are accessible via the following MatrixBase methods:
+  *  - MatrixBase::llt(),
+  *  - MatrixBase::ldlt()
+  *
+  * \code
+  * #include <Eigen/Cholesky>
+  * \endcode
+  */
+
+#include "src/misc/Solve.h"
+#include "src/Cholesky/LLT.h"
+#include "src/Cholesky/LDLT.h"
+#ifdef EIGEN_USE_LAPACKE
+#include "src/Cholesky/LLT_MKL.h"
+#endif
+
+#include "src/Core/util/ReenableStupidWarnings.h"
+
+#endif // EIGEN_CHOLESKY_MODULE_H
+/* vim: set filetype=cpp et sw=2 ts=2 ai: */