BioComputingUP · ozymandias89 · Jul 1, 2015 · Jul 1, 2015 · Jul 1, 2015 · Jul 2, 2015
diff --git a/.cproject b/.cproject
@@ -0,0 +1,60 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<?fileVersion 4.0.0?><cproject storage_type_id="org.eclipse.cdt.core.XmlProjectDescriptionStorage">
+	<storageModule moduleId="org.eclipse.cdt.core.settings">
+		<cconfiguration id="cdt.managedbuild.toolchain.gnu.cross.base.679775953">
+			<storageModule buildSystemId="org.eclipse.cdt.managedbuilder.core.configurationDataProvider" id="cdt.managedbuild.toolchain.gnu.cross.base.679775953" moduleId="org.eclipse.cdt.core.settings" name="Default">
+				<externalSettings/>
+				<extensions>
+					<extension id="org.eclipse.cdt.core.GmakeErrorParser" point="org.eclipse.cdt.core.ErrorParser"/>
+					<extension id="org.eclipse.cdt.core.CWDLocator" point="org.eclipse.cdt.core.ErrorParser"/>
+					<extension id="org.eclipse.cdt.core.GCCErrorParser" point="org.eclipse.cdt.core.ErrorParser"/>
+					<extension id="org.eclipse.cdt.core.GASErrorParser" point="org.eclipse.cdt.core.ErrorParser"/>
+					<extension id="org.eclipse.cdt.core.GLDErrorParser" point="org.eclipse.cdt.core.ErrorParser"/>
+					<extension id="org.eclipse.cdt.core.ELF" point="org.eclipse.cdt.core.BinaryParser"/>
+				</extensions>
+			</storageModule>
+			<storageModule moduleId="cdtBuildSystem" version="4.0.0">
+				<configuration buildProperties="" description="" id="cdt.managedbuild.toolchain.gnu.cross.base.679775953" name="Default" parent="org.eclipse.cdt.build.core.emptycfg">
+					<folderInfo id="cdt.managedbuild.toolchain.gnu.cross.base.679775953.1817176364" name="/" resourcePath="">
+						<toolChain id="cdt.managedbuild.toolchain.gnu.cross.base.1114783033" name="Cross GCC" superClass="cdt.managedbuild.toolchain.gnu.cross.base">
+							<option id="cdt.managedbuild.option.gnu.cross.prefix.258209284" name="Prefix" superClass="cdt.managedbuild.option.gnu.cross.prefix"/>
+							<option id="cdt.managedbuild.option.gnu.cross.path.509310917" name="Path" superClass="cdt.managedbuild.option.gnu.cross.path"/>
+							<targetPlatform archList="all" binaryParser="org.eclipse.cdt.core.ELF" id="cdt.managedbuild.targetPlatform.gnu.cross.265199028" isAbstract="false" osList="all" superClass="cdt.managedbuild.targetPlatform.gnu.cross"/>
+							<builder arguments="-f Makefile" command="make" id="cdt.managedbuild.builder.gnu.cross.926951898" incrementalBuildTarget="install" keepEnvironmentInBuildfile="false" managedBuildOn="false" name="Gnu Make Builder" parallelBuildOn="true" parallelizationNumber="optimal" superClass="cdt.managedbuild.builder.gnu.cross"/>
+							<tool id="cdt.managedbuild.tool.gnu.cross.c.compiler.933527225" name="Cross GCC Compiler" superClass="cdt.managedbuild.tool.gnu.cross.c.compiler">
+								<inputType id="cdt.managedbuild.tool.gnu.c.compiler.input.1818742666" superClass="cdt.managedbuild.tool.gnu.c.compiler.input"/>
+							</tool>
+							<tool id="cdt.managedbuild.tool.gnu.cross.cpp.compiler.2056037131" name="Cross G++ Compiler" superClass="cdt.managedbuild.tool.gnu.cross.cpp.compiler">
+								<inputType id="cdt.managedbuild.tool.gnu.cpp.compiler.input.1189602384" superClass="cdt.managedbuild.tool.gnu.cpp.compiler.input"/>
+							</tool>
+							<tool id="cdt.managedbuild.tool.gnu.cross.c.linker.1387695238" name="Cross GCC Linker" superClass="cdt.managedbuild.tool.gnu.cross.c.linker"/>
+							<tool id="cdt.managedbuild.tool.gnu.cross.cpp.linker.2007520852" name="Cross G++ Linker" superClass="cdt.managedbuild.tool.gnu.cross.cpp.linker">
+								<inputType id="cdt.managedbuild.tool.gnu.cpp.linker.input.1458424534" superClass="cdt.managedbuild.tool.gnu.cpp.linker.input">
+									<additionalInput kind="additionalinputdependency" paths="$(USER_OBJS)"/>
+									<additionalInput kind="additionalinput" paths="$(LIBS)"/>
+								</inputType>
+							</tool>
+							<tool id="cdt.managedbuild.tool.gnu.cross.archiver.31449503" name="Cross GCC Archiver" superClass="cdt.managedbuild.tool.gnu.cross.archiver"/>
+							<tool id="cdt.managedbuild.tool.gnu.cross.assembler.339030466" name="Cross GCC Assembler" superClass="cdt.managedbuild.tool.gnu.cross.assembler">
+								<inputType id="cdt.managedbuild.tool.gnu.assembler.input.1385081327" superClass="cdt.managedbuild.tool.gnu.assembler.input"/>
+							</tool>
+						</toolChain>
+					</folderInfo>
+				</configuration>
+			</storageModule>
+			<storageModule moduleId="org.eclipse.cdt.core.externalSettings"/>
+		</cconfiguration>
+	</storageModule>
+	<storageModule moduleId="cdtBuildSystem" version="4.0.0">
+		<project id="Mobi.null.747390746" name="Mobi"/>
+	</storageModule>
+	<storageModule moduleId="scannerConfiguration">
+		<autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId=""/>
+	</storageModule>
+	<storageModule moduleId="org.eclipse.cdt.core.LanguageSettingsProviders"/>
+	<storageModule moduleId="refreshScope" versionNumber="2">
+		<configuration configurationName="Default">
+			<resource resourceType="PROJECT" workspacePath="/Mobi"/>
+		</configuration>
+	</storageModule>
+</cproject>
diff --git a/.project b/.project
@@ -0,0 +1,27 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>Mobi</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.cdt.managedbuilder.core.genmakebuilder</name>
+			<triggers>clean,full,incremental,</triggers>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.cdt.managedbuilder.core.ScannerConfigBuilder</name>
+			<triggers>full,incremental,</triggers>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.eclipse.cdt.core.cnature</nature>
+		<nature>org.eclipse.cdt.core.ccnature</nature>
+		<nature>org.eclipse.cdt.managedbuilder.core.managedBuildNature</nature>
+		<nature>org.eclipse.cdt.managedbuilder.core.ScannerConfigNature</nature>
+	</natures>
+</projectDescription>
diff --git a/.settings/language.settings.xml b/.settings/language.settings.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<project>
+	<configuration id="cdt.managedbuild.toolchain.gnu.cross.base.679775953" name="Default">
+		<extension point="org.eclipse.cdt.core.LanguageSettingsProvider">
+			<provider copy-of="extension" id="org.eclipse.cdt.ui.UserLanguageSettingsProvider"/>
+			<provider-reference id="org.eclipse.cdt.core.ReferencedProjectsLanguageSettingsProvider" ref="shared-provider"/>
+			<provider class="org.eclipse.cdt.managedbuilder.language.settings.providers.GCCBuildCommandParser" id="org.eclipse.cdt.managedbuilder.core.GCCBuildCommandParser" keep-relative-paths="false" name="CDT GCC Build Output Parser" parameter="(gcc)|([gc]\+\+)|(clang)" prefer-non-shared="true"/>
+			<provider class="org.eclipse.cdt.internal.build.crossgcc.CrossGCCBuiltinSpecsDetector" console="false" env-hash="1323490044467186284" id="org.eclipse.cdt.build.crossgcc.CrossGCCBuiltinSpecsDetector" keep-relative-paths="false" name="CDT Cross GCC Built-in Compiler Settings" parameter="${COMMAND} ${FLAGS} -E -P -v -dD &quot;${INPUTS}&quot;" prefer-non-shared="true">
+				<language-scope id="org.eclipse.cdt.core.gcc"/>
+				<language-scope id="org.eclipse.cdt.core.g++"/>
+			</provider>
+			<provider-reference id="org.eclipse.cdt.managedbuilder.core.MBSLanguageSettingsProvider" ref="shared-provider"/>
+		</extension>
+	</configuration>
+</project>
diff --git a/Biopool/APPS/pdb2secondary.cc b/Biopool/APPS/pdb2secondary.cc
@@ -14,8 +14,11 @@
     along with Victor.  If not, see <http://www.gnu.org/licenses/>.
  */
 /**  
+
+
 @Description */
 
+// Includes:
 #include <string>
 #include <GetArg.h>
 #include <Spacer.h>

diff --git a/Biopool/Sources/Atom.h b/Biopool/Sources/Atom.h
@@ -45,6 +45,8 @@ namespace Victor { namespace Biopool {
         virtual ~Atom();
 
         // PREDICATES:
+
+
         AtomCode getCode() const;
         unsigned long getNumber() const;
 
@@ -130,17 +132,30 @@ namespace Victor { namespace Biopool {
     // -----------------x-------------------x-------------------x-----------------
 
     // PREDICATES:
-
+    /**
+            *   Return the code of the Atom
+            * @param none
+            * @return AtomCode
+            */
     inline AtomCode
     Atom::getCode() const {
         return type;
     }
-
+    /**
+            *   Return the number of the Atom in the model
+            * @param none
+            * @return id, id of atom
+            */
     inline unsigned long
     Atom::getNumber() const {
         return id;
     }
 
+    /**
+            *   Return 3D vector with coordinate 3D of the Atom
+            * @param none
+            * @return vgVector3<double>
+            */
     inline vgVector3<double>
     Atom::getCoords() {
         if (!inSync())

diff --git a/Biopool/Sources/PdbLoader.h b/Biopool/Sources/PdbLoader.h
@@ -92,19 +92,35 @@ namespace Victor { namespace Biopool {
         void setNonPermissive() {
             permissive = false;
         }
-
+        /**
+        	 You can chose if you want verbose output from this class
+        	 @param  none
+        	 @return void
+        	 */
         void setVerbose() {
             verbose = true;
         }
-
+        /**
+        	 You can chose if you want not verbose output from this class
+        	 @param  none
+        	 @return void
+        	 */
         void setNoVerbose() {
             verbose = false;
         }
-
+	/**
+	 Set the chain that do you want load
+	 @param  char
+	 @return void
+	 */
         void setChain(char _ch) {
             chain = _ch;
         }
-
+     /**
+       set the Model that do you want load
+       @param  unsigned int
+       @return void
+     */
         void setModel(unsigned int _mod) {
             model = _mod;
         }

diff --git a/Biopool/Sources/PdbSaver.h b/Biopool/Sources/PdbSaver.h
@@ -56,6 +56,11 @@ namespace Victor { namespace Biopool {
 
         // PREDICATES:
 
+        /**
+        	 close the output file
+         	 @param  none
+        	 @return void
+        */
         void endFile() {
             output << "END\n";
         }
@@ -103,8 +108,6 @@ namespace Victor { namespace Biopool {
 
     protected:
 
-    private:
-
         // HELPERS:
         void writeSeqRes(Spacer& sp); // writes SEQRES entry
         void writeSecondary(Spacer& sp);

diff --git a/Biopool/Sources/Protein.cc b/Biopool/Sources/Protein.cc
@@ -18,9 +18,9 @@
 // Includes:
 #include <Protein.h>
 #include <iostream>
-using namespace std;
-using namespace Victor; using namespace Victor::Biopool;
 
+using namespace std;
+using namespace Victor;
 using namespace Victor::Biopool;
 
 // CONSTRUCTORS/DESTRUCTOR:

diff --git a/Biopool/Sources/Protein.h b/Biopool/Sources/Protein.h
@@ -68,7 +68,18 @@ namespace Victor { namespace Biopool {
         void deleteComponent(Component* c);
 
         void copy(const Protein& orig);
-        void load(Loader& l); // data loader                 
+
+        /**
+         * load one model by Loader object. Use after command PdbLoader.setModel(i) , PdbLoader.checkModel();
+         * @code
+         * 	Loader.setModel(i);
+			Loader.checkModel();
+			this->load(Loader);
+         * @endcode
+         * @param Loader& , loader object
+         * @return void
+         */
+        virtual void load(Loader& l); // data loader
 
         virtual Protein* clone();
 

diff --git a/Biopool/Sources/Spacer.cc b/Biopool/Sources/Spacer.cc
@@ -1664,25 +1664,29 @@ void Spacer::setDSSP(bool verbose) {
                 set<char> ::iterator it = ss[i].find(turns[l]);
                 if (it != ss[i].end()) { // found a n-turn
                     char pos_s = *it;
-                    int pos = atoi(&(pos_s));
-                    set<char> ::iterator it1 = ss[i + pos - 1].find(turns[l]);
-                    if (it1 != ss[i + pos - 1].end()) { // found the same n-turn after n-1 positions
-                        bool helixBreak = false;
-                        for (unsigned int m = i; m < (i + pos); m++) {
-                            set<char> ::iterator it2 = ss[m].find(turns[l]);
-                            if (it2 == ss[m].end()) {
-                                helixBreak = true;
-                            }
-                        }
-                        if (!helixBreak) {
-                            for (unsigned int m = i; m < (i + pos); m++) {
-                                ss[m].insert(helices[l]);
-                            }
-                        }
-                        break;
-                    }
-                }
-            }
+					int pos = atoi(&(pos_s));
+					if(i+pos-1 >= ss.size())
+						break;
+					set<char>::iterator it1 = ss[i + pos - 1].find(
+							turns[l]);
+					if (it1 != ss[i + pos - 1].end()) { // found the same n-turn after n-1 positions
+						bool helixBreak = false;
+						for (unsigned int m = i; m < (i + pos); m++) {
+							set<char>::iterator it2 = ss[m].find(turns[l]);
+							if (it2 == ss[m].end()) {
+								helixBreak = true;
+							}
+						}
+						if (!helixBreak) {
+							for (unsigned int m = i; m < (i + pos); m++) {
+								ss[m].insert(helices[l]);
+							}
+						}
+						break;
+					}
+
+				}
+			}
             // Set sheets (E)
             set<char> ::iterator it = ss[i].find('B');
             if (it != ss[i].end()) {

diff --git a/Biopool/Sources/Spacer.h b/Biopool/Sources/Spacer.h
@@ -160,6 +160,21 @@ namespace Victor { namespace Biopool {
         void setStateFromTorsionAngles();
         void setDSSP(bool verbose);
 
+
+        /**
+         *
+         *  Return a vector of set, each set correspond whit one amino acid.
+         *  Use this command after setDSSP(boool verbose) command.
+         *  Each set contain many information about secondary structure of one amino acid.
+         *  The first letter of the set is the secondary structure.
+         *  @code
+         *  Spacer.setDSSP(false);
+		 *	vector<set<char> > = Spacer.getDSSP();
+         *  @endcode
+         *
+         *	@param none
+         *	@return  vector<set<char> > , a vector of set
+         */
         vector< set<char> > getDSSP() {
             return ss;
         };

diff --git a/Makefile b/Makefile
@@ -7,7 +7,7 @@
 # Path to project directory.
 UPDIR = .
 # Path to subdirectories.
-SUBDIRS =  tools Energy/Sources   Biopool/Sources  Align2/Sources Energy/Sources/TorsionPotential  Lobo/Sources Lobo/APPS Energy/APPS   Biopool/APPS   Align2/APPS
+SUBDIRS =  tools Energy/Sources   Biopool/Sources  Align2/Sources Energy/Sources/TorsionPotential  Lobo/Sources Lobo/APPS	Energy/APPS	Biopool/APPS	Align2/APPS	Mobi/Sources	Mobi/APPS
 
 #
 # Libraries and paths (which are not defined globally).
@@ -27,8 +27,8 @@ BINPATH = bin
 
 SOURCES =
 OBJECTS =
-EXECS =
-TARGET  =
+EXECS	=
+TARGET 	=
 LIBRARY =
 
 #

diff --git a/Makefile.global b/Makefile.global
@@ -77,7 +77,7 @@ ifeq ($(verbose), 3)
   USERFLAGS += -DVERBOSE=3
 endif
 
-CFLAGS = $(USERFLAGS) 
+CFLAGS = $(USERFLAGS)
 
 #
 # Tools 
@@ -106,11 +106,13 @@ SUBDIRS += _dummy_
 
 LIB_PATH += -L$(UPDIR)/lib
 
-INC_PATH += -I$(UPDIR)/tools -I$(UPDIR)/Energy/Sources   -I$(UPDIR)/Biopool/Sources -I$(UPDIR)/Energy/Sources/TorsionPotential     -I$(UPDIR)/Lobo/Sources  -I$(UPDIR)/Align2/Sources  -I$(UPDIR)/Biopool/APPS -I$(UPDIR)/Energy/APPS -I$(UPDIR)/Align2/APPS  -I$(UPDIR)/Lobo/APPS
+### MODIFIED BY MOBI - ***LUCA DEMO***
+INC_PATH += -I$(UPDIR)/tools -I$(UPDIR)/Energy/Sources   -I$(UPDIR)/Biopool/Sources -I$(UPDIR)/Energy/Sources/TorsionPotential  -I$(UPDIR)/Lobo/Sources  -I$(UPDIR)/Align2/Sources  -I$(UPDIR)/Mobi/Sources -I$(UPDIR)/Biopool/APPS -I$(UPDIR)/Energy/APPS -I$(UPDIR)/Align2/APPS  -I$(UPDIR)/Lobo/APPS  -I$(UPDIR)/Mobi/APPS
 
+### MODIFIED BY MOBI - ***LUCA DEMO***
 ifdef test
-  INC_PATH += -I$(UPDIR)/Biopool/Tests -I$(UPDIR)/Energy/Tests -I$(UPDIR)/Align2/Tests -I$(UPDIR)/Lobo/Tests
-  SUBDIRS =  Biopool/Tests Energy/Tests Align2/Tests Lobo/Tests
+  INC_PATH += -I$(UPDIR)/Biopool/Tests -I$(UPDIR)/Energy/Tests -I$(UPDIR)/Align2/Tests -I$(UPDIR)/Lobo/Tests -I$(UPDIR)/Mobi/Tests
+  SUBDIRS =  Biopool/Tests Energy/Tests Align2/Tests Lobo/Tests Mobi/Tests
 endif
 
 ####### Implicit rules
@@ -175,6 +177,8 @@ subclean:
 	$(RM) -fr ./Energy/data
 	$(RM) -fr ./Lobo/data
 	$(RM) -fr ./Biopool/data
+	$(RM) -fr ./Mobi/data
+	$(RM) -fr ./Mobi/data/*