Consegna progetto bioinformatica 2 - CIF parser - Pezzutti Marco 1084411

Biopool/APPS/Cif2Secondary.cc

@@ -0,0 +1,115 @@
+/*  This file is part of Victor.
+
+    Victor is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    Victor 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 General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with Victor.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#include <string>
+#include <GetArg.h>
+#include <Spacer.h>
+#include <CifLoader.h>
+#include <IoTools.h>
+
+using namespace Victor;
+using namespace Victor::Biopool;
+
+void sShowHelp() {
+    cout << "Cif 2 Secondary Structure converter\n"
+	    << "\t H = helix, \t E = extended (strand, sheet), \t . = other.\n"
+	    << "   Options: \n"
+	    << "\t-i <filename> \t\t Input file for CIF structure\n"
+	    << "\n";
+}
+
+int main(int argc, char** argv) {
+
+    if (getArg("h", argc, argv)) {
+	sShowHelp();
+	return 1;
+    };
+    vector<char> allCh;
+    string chainID = "!";
+    string inputFile;
+    getArg("i", inputFile, argc, argv, "!");
+
+    if (inputFile == "!") {
+	cout << "Missing file specification. Aborting. (-h for help)" << endl;
+	return -1;
+    }
+
+    ifstream inFile(inputFile.c_str());
+    if (!inFile) {
+	ERROR("File not found.", exception);
+    }
+
+    CifLoader il(inFile);
+    il.setNoHAtoms();
+    allCh = il.getAllChains();
+
+    for (unsigned int i = 0; i < allCh.size(); i++) {
+	cout << "\t," << allCh[i] << ",";
+    }
+    cout << "\n";
+
+    /*check on validity of chain: 
+    if user select a chain then check validity
+     else select first valid one by default*/
+    if (chainID != "!") {
+	bool validChain = false;
+	for (unsigned int i = 0; i < allCh.size(); i++) {
+	    if (allCh[i] == chainID[0]) {
+		il.setChain(chainID[0]);
+		cout << "Loading chain " << chainID << "\n";
+		validChain = true;
+		break;
+	    }
+	}
+	if (!validChain) {
+	    cout << "Chain " << chainID << " is not available\n";
+	    return -1;
+	}
+
+    } else {
+	chainID[0] = allCh[0];
+	cout << "Using chain " << chainID << "\n";
+    }
+
+    Protein prot;
+    prot.load(il);
+    Spacer *sp;
+    sp = prot.getSpacer(chainID[0]);
+
+    allCh = il.getAllChains();
+    cout << ">" << inputFile << "\n";
+
+    inFile.close();
+
+    for (unsigned int i = 0; i < sp->sizeAmino(); i++) {
+	switch (sp->getAmino(i).getState()) {
+	    case HELIX:
+		cout << "H";
+		break;
+	    case STRAND:
+		cout << "E";
+		break;
+	    default:
+		cout << ".";
+	};
+	if ((i + 1) % 60 == 0)
+	    cout << "\n";
+    }
+    cout << "\n";
+
+    return 0;
+}
+

Biopool/APPS/Cif2Seq.cc

@@ -0,0 +1,133 @@
+/*  This file is part of Victor.
+
+    Victor is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    Victor 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 General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with Victor.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#include <Protein.h>
+#include <CifLoader.h>
+#include <SeqSaver.h>
+#include <IoTools.h>
+#include <GetArg.h>
+
+using namespace Victor;
+using namespace Victor::Biopool;
+
+void sShowHelp() {
+    cout << "Cif 2 Seq $Revision: 0.1 $ -- converts a CIF file into SEQ\n"
+            << "(torsion angles) protein structure backbone torsion angles\n"
+            << " Options: \n"
+            << "\t-i <filename> \t Input CIF file\n"
+            << "\t-o <filename> \t Output to file (default stdout)\n"
+            << "\t-c <id>       \t Chain identifier to read\n"
+            << "\t--all         \t All chains\n"
+            << "\t-m <number>   \t Model number to read (NMR only, default is first model)\n"
+            << "\t--chi         \t Write Chi angles (default false)\n"
+            << "\t-v            \t verbose output\n\n"
+            << "\tIf both -c and --all are missing, only the first chain is processed.\n\n";
+
+}
+
+int main(int argc, char** argv) {
+
+    if (getArg("h", argc, argv)) {
+        sShowHelp();
+        return 1;
+    }
+
+    string inputFile, outputFile, chainID;
+    unsigned int modelNum;
+    bool chi, all;
+
+    getArg("i", inputFile, argc, argv, "!");
+    getArg("o", outputFile, argc, argv, "!");
+    getArg("c", chainID, argc, argv, "!");
+    getArg("m", modelNum, argc, argv, 999);
+    all = getArg("-all", argc, argv);
+    chi = getArg("-chi", argc, argv);
+
+    // Check input file
+    if (inputFile == "!") {
+        cout << "Missing input file specification. Aborting. (-h for help)" << endl;
+        return -1;
+    }
+    ifstream inFile(inputFile.c_str());
+    if (!inFile)
+        ERROR("Input file not found.", exception);
+
+
+    CifLoader cl(inFile);
+
+    // Set PdbLoader variables
+    cl.setModel(modelNum);
+    cl.setNoHAtoms();
+    cl.setNoHetAtoms();
+    cl.setNoSecondary();
+    if (!getArg("v", argc, argv)) {
+        cl.setNoVerbose();
+    }
+
+
+    // Check chain args
+    if ((chainID != "!") && all) {
+        ERROR("You can use --all or -c, not both", error);
+    }
+    // User selected chain
+    if (chainID != "!") {
+        if (chainID.size() > 1)
+            ERROR("You can choose only 1 chain", error);
+        cl.setChain(chainID[0]);
+    }// All chains
+    else if (all) {
+        cl.setAllChains();
+    }// First chain
+    else {
+        cl.setChain(cl.getAllChains()[0]);
+    }
+
+    // Load the protein object
+    Protein prot;
+    prot.load(cl);
+
+    inFile.close();
+
+    // Open the proper output stream (file or stdout)
+    std::ostream* os = &cout;
+    std::ofstream fout;
+    if (outputFile != "!") {
+        fout.open(outputFile.c_str());
+        if (!fout) {
+            ERROR("Could not open file for writing.", exception);
+        } else {
+            os = &fout;
+        }
+    }
+
+
+    Spacer* sp;
+    for (unsigned int i = 0; i < prot.sizeProtein(); i++) {
+
+        sp = prot.getSpacer(i);
+
+        // Write the sequence
+        SeqSaver ss(*os);
+        if (!chi)
+            ss.setWriteChi(false);
+        sp->save(ss);
+    }
+
+    fout.close();
+
+    return 0;
+}
+

Biopool/APPS/CifCorrector.cc

@@ -0,0 +1,71 @@
+/*  This file is part of Victor.
+
+    Victor is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    Victor 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 General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with Victor.  If not, see <http://www.gnu.org/licenses/>.
+ */
+
+#include <Spacer.h>
+#include <Group.h>
+#include <SideChain.h>
+#include <vector3.h>
+#include <CifLoader.h>
+#include <CifSaver.h>
+#include <XyzSaver.h>
+#include <SeqSaver.h>
+#include <IoTools.h>
+#include <IntCoordConverter.h>
+#include <IntSaver.h>
+
+using namespace Victor;
+using namespace Victor::Biopool;
+
+/*
+ * 
+ */
+int main(int argc, char** argv) {
+
+    if (argc != 2) {
+        cout << "Cif Corrector $Revision: 0.1 $ -- adds missing oxygen atoms to "
+                << "protein structure backbones" << endl;
+        cout << "  Usage: \t\t CifCorrector <filename> \n";
+        return 1;
+    };
+
+    ifstream inFile(argv[1]);
+    if (!inFile)
+        ERROR("File not found.", exception);
+
+    CifLoader il(inFile);
+    Protein prot;
+    prot.load(il);
+    unsigned int zero = 0;
+    Spacer sp = *(prot.getSpacer(zero));
+
+    for (unsigned int i = 0; i < sp.sizeAmino(); i++)
+        sp.getAmino(i).addMissingO();
+
+    inFile.close();
+
+    ofstream outFile(argv[1]);
+
+    if (!outFile)
+        ERROR("Couldn't write file.", exception);
+
+    CifSaver pss(outFile);
+    sp.save(pss);
+
+    outFile.close();
+
+    return 0;
+}
+