diff --git a/shiftx2-v107-linux/src/LimitedCShift.java b/shiftx2-v107-linux/src/LimitedCShift.java index cd27fbf..9e72208 100755 --- a/shiftx2-v107-linux/src/LimitedCShift.java +++ b/shiftx2-v107-linux/src/LimitedCShift.java @@ -13,8 +13,8 @@ public class LimitedCShift { public void loadLimitedCShift () { // System.out.println("SHIFTX2_DIR: "+ShiftXp.SHIFTX2_DIR); - String filename = ShiftXp.SHIFTX2_DIR + "/lib/limitedcshift.dat"; - String objFilename = ShiftXp.SHIFTX2_DIR + "/lib/limitedcshift.osf"; + String filename = ShiftXp.GENTOO_SHARE_PATH + "/limitedcshift.dat"; + String objFilename = ShiftXp.GENTOO_SHARE_PATH + "/limitedcshift.osf"; File f = new File(objFilename); if (f.exists()) { @@ -44,7 +44,7 @@ public class LimitedCShift { br.close(); // save object into object file format for speed up - saveObjectFile(objFilename, limshift); + //saveObjectFile(objFilename, limshift); } catch(IOException ex){ ex.printStackTrace(); diff --git a/shiftx2-v107-linux/src/ModuleExecutor.java b/shiftx2-v107-linux/src/ModuleExecutor.java index 36cfeb1..704451f 100755 --- a/shiftx2-v107-linux/src/ModuleExecutor.java +++ b/shiftx2-v107-linux/src/ModuleExecutor.java @@ -22,12 +22,12 @@ public class ModuleExecutor { // private static final String WORKING_DIR = "./wkdir/"; private static String WORKING_DIR = ""; - private static final String RESMF_EXE = "/modules/resmf/resmf"; - private static final String EFFECTS_EXE = "/modules/effects/caleffect"; - private static final String ANGLES_EXE = "/modules/angles/get_angles"; - private static final String ANGLES_REDUCE_DIR = "/modules/angles"; + private static final String RESMF_EXE = "resmf"; + private static final String EFFECTS_EXE = "caleffect"; + private static final String ANGLES_EXE = "get_angles"; + private static final String ANGLES_REDUCE_DIR = "angles"; - private static String SHIFTXP_DIR = ShiftXp.SHIFTX2_DIR; +// private static String SHIFTXP_DIR = ShiftXp.SHIFTX2_DIR; private static final String REDUCE_FLAG = "1"; // 1 or 0 @@ -80,8 +80,8 @@ public class ModuleExecutor { if(DEBUG) System.out.println("> Processing [Major Features] with " + pdbfile); // Update: add pdbdir both input pdbfile and output result, pdbId (2011.03.17) // cmd = RESMF_EXE + " -f " + pdbdir +"/"+ pdbfile + " -o " + WORKING_DIR + pdbId + ".resmf"; - cmd = SHIFTXP_DIR + RESMF_EXE + " -f " + pdbdir + pdbfile + " -o " + WORKING_DIR + pdbId + ".resmf" - + " -d " + SHIFTXP_DIR + "/modules/resmf/lib"; + cmd = RESMF_EXE + " -f " + pdbdir + pdbfile + " -o " + WORKING_DIR + pdbId + ".resmf" + + " -d " + ShiftXp.GENTOO_SHARE_PATH + "/vader"; if(DEBUG){ System.out.println("\t"+cmd); } execCode = execute_command(cmd); @@ -93,7 +93,7 @@ public class ModuleExecutor { /* call effects for calculating ring current calculator */ if(DEBUG) System.out.println("> processing [Effects] with " + pdbfile); - cmd = SHIFTXP_DIR + EFFECTS_EXE + " 1 " + pdbdir + pdbfile + " " + WORKING_DIR + pdbfile + ".dummy"; + cmd = EFFECTS_EXE + " 1 " + pdbdir + pdbfile + " " + WORKING_DIR + pdbfile + ".dummy"; if(DEBUG){ System.out.println("\t"+cmd); } execCode = execute_command(cmd); @@ -106,7 +106,7 @@ public class ModuleExecutor { /* call angle calculator : output must be redirected to file using PrintStream */ if(DEBUG) System.out.println("> Processing [Angle] with " + pdbfile); // cmd = ANGLES_EXE + " " + ANGLES_REDUCE_DIR + " " + pdbfile ; - cmd = SHIFTXP_DIR + ANGLES_EXE + " " + SHIFTXP_DIR + ANGLES_REDUCE_DIR + " " + pdbdir + pdbfile + " "+ REDUCE_FLAG; + cmd = ANGLES_EXE + " " + ShiftXp.GENTOO_SHARE_PATH + " " + pdbdir + pdbfile + " "+ REDUCE_FLAG; String outpath = WORKING_DIR + pdbId + ".angles"; if(DEBUG){ System.out.println("\t"+cmd); } diff --git a/shiftx2-v107-linux/src/PredictionModels.java b/shiftx2-v107-linux/src/PredictionModels.java index a77d1cb..fb84666 100755 --- a/shiftx2-v107-linux/src/PredictionModels.java +++ b/shiftx2-v107-linux/src/PredictionModels.java @@ -13,9 +13,7 @@ public class PredictionModels { private final static String MODEL_FILE_SIDECHAIN_ONLY = "predmodels_sidechain.sobj"; private final static String OBJECT_MODEL_DIRECTORY = "/lib"; - private final static String MODEL_DIRECTORY = "/lib/predmodels"; - - private static String SHIFTXP_DIR = ShiftXp.SHIFTX2_DIR; + private final static String MODEL_DIRECTORY = "predmodels"; HashMap hsmap_predmodel = new HashMap(); @@ -36,7 +34,7 @@ public class PredictionModels { // System.out.println("SHIFTXP_DIR:" + SHIFTXP_DIR+"\n\n"); // System.out.println("SHIFTX2_DIR:" + ShiftXp.SHIFTX2_DIR+"\n\n"); - String headerfilename = ShiftXp.SHIFTX2_DIR + "/lib/data-header.arff"; + String headerfilename = ShiftXp.GENTOO_SHARE_PATH + "/data-header.arff"; try { // assigned instance header from data-header.arff @@ -150,7 +148,7 @@ public class PredictionModels { // if option is not sidechain only, put backbone models into modeling file if ( ! this.prediction_type.equals("SIDECHAIN") ) { for(int i=0; i < BACKBONE_MODEL_LENGTH; i++) { - ois = new ObjectInputStream( new BufferedInputStream( new FileInputStream( ShiftXp.SHIFTX2_DIR + MODEL_DIRECTORY + "/" + modelFileArray[i]) )); + ois = new ObjectInputStream( new BufferedInputStream( new FileInputStream( ShiftXp.GENTOO_SHARE_PATH + "/" + MODEL_DIRECTORY + "/" + modelFileArray[i]) )); classifier = (Classifier) ois.readObject(); hsmap_predmodel.put(atomNameArray[i],classifier); ois.close(); @@ -160,7 +158,7 @@ public class PredictionModels { // if option is not backbone only, put/append sidechain models into modeling file if ( ! this.prediction_type.equals("BACKBONE") ) { for(int i=BACKBONE_MODEL_LENGTH; i < (BACKBONE_MODEL_LENGTH + SIDECHAIN_MODEL_LENGTH); i++) { - ois = new ObjectInputStream( new BufferedInputStream( new FileInputStream( ShiftXp.SHIFTX2_DIR + MODEL_DIRECTORY + "/" + modelFileArray[i]) )); + ois = new ObjectInputStream( new BufferedInputStream( new FileInputStream( ShiftXp.GENTOO_SHARE_PATH + "/" + MODEL_DIRECTORY + "/" + modelFileArray[i]) )); classifier = (Classifier) ois.readObject(); hsmap_predmodel.put(atomNameArray[i], classifier); ois.close(); @@ -185,11 +183,11 @@ public class PredictionModels { */ if ( this.prediction_type.equals("ALL") == true) { - model_file = ShiftXp.SHIFTX2_DIR + OBJECT_MODEL_DIRECTORY + "/" + MODEL_FILE_ALLATOMS; + model_file = ShiftXp.GENTOO_SHARE_PATH + "/" + MODEL_FILE_ALLATOMS; } else if ( this.prediction_type.equals("BACKBONE") == true) { - model_file = ShiftXp.SHIFTX2_DIR + OBJECT_MODEL_DIRECTORY + "/" + MODEL_FILE_BACKBONE_ONLY; + model_file = ShiftXp.GENTOO_SHARE_PATH + "/" + MODEL_FILE_BACKBONE_ONLY; } else if ( this.prediction_type.equals("SIDECHAIN") == true) { - model_file = ShiftXp.SHIFTX2_DIR + OBJECT_MODEL_DIRECTORY + "/" + MODEL_FILE_SIDECHAIN_ONLY; + model_file = ShiftXp.GENTOO_SHARE_PATH + "/" + MODEL_FILE_SIDECHAIN_ONLY; } File f = new File( model_file ); @@ -198,7 +196,7 @@ public class PredictionModels { readHashObjectPredModelFile( model_file ); } else { setHashMap(); - saveHashObjectPredModelFile( model_file ); +// saveHashObjectPredModelFile( model_file ); } } diff --git a/shiftx2-v107-linux/src/RandomCoil.java b/shiftx2-v107-linux/src/RandomCoil.java index 25a8999..7442938 100755 --- a/shiftx2-v107-linux/src/RandomCoil.java +++ b/shiftx2-v107-linux/src/RandomCoil.java @@ -33,11 +33,9 @@ public class RandomCoil { public void loadRandomCoil() { // change path as absolute path - String SHIFTXP_DIR = ShiftXp.SHIFTX2_DIR; - - String filename = SHIFTXP_DIR + "/lib/RandomCoil.csv"; - String objFilename = SHIFTXP_DIR + "/lib/RandomCoil.osf"; - String objAtomListname = SHIFTXP_DIR + "/lib/RCoilAtomlist.osf"; + String filename = ShiftXp.GENTOO_SHARE_PATH + "/RandomCoil.csv"; + String objFilename = ShiftXp.GENTOO_SHARE_PATH + "/RandomCoil.osf"; + String objAtomListname = ShiftXp.GENTOO_SHARE_PATH + "/RCoilAtomlist.osf"; File f = new File(objFilename); @@ -85,8 +83,8 @@ public class RandomCoil { br.close(); // save object into object file format for speed up - saveObjectFile(objFilename, rcoil); - saveObjectFile(objAtomListname, restypeAtomStringList); +// saveObjectFile(objFilename, rcoil); +// saveObjectFile(objAtomListname, restypeAtomStringList); } catch(IOException ex){ ex.printStackTrace(); diff --git a/shiftx2-v107-linux/src/ShiftXp.java b/shiftx2-v107-linux/src/ShiftXp.java index 505a3f6..920f420 100755 --- a/shiftx2-v107-linux/src/ShiftXp.java +++ b/shiftx2-v107-linux/src/ShiftXp.java @@ -27,7 +27,7 @@ public class ShiftXp { static final boolean DEBUG = false; static boolean RCOIL_PRINTOUT = false; static String SHIFTX2_DIR = "."; // to support running on other directory - + public static final String GENTOO_SHARE_PATH = "PUT_GENTOO_SHARE_PATH_HERE"; // Loading only one time, that's why these are here static RandomCoil rcoil = new RandomCoil(); static LimitedCShift chkcshift = new LimitedCShift(); @@ -41,7 +41,7 @@ public class ShiftXp { buf.append("Detail information: http://www.shiftx2.ca or http://redpoll.pharmacy.ualberta.ca\n"); buf.append("--------------------------------------------------------------------------------\n\n"); - buf.append("SYNOPSIS\n\t java -Xmx1500m -cp /bin:/lib/weka.jar ShiftXp [options]\n"); + buf.append("SYNOPSIS\n\t jshiftx2 [options]\n"); buf.append("OPTIONS:\n"); buf.append("\t -i [ infile.pdb | ALLPDB]\n"); @@ -54,10 +54,10 @@ public class ShiftXp { buf.append("\t -temp Temperature, default=298\n"); buf.append("\t -d [TRUE | FALSE] Deuterated pdb, default=FALSE \n"); buf.append("\t -r [TRUE | FALSE] Print randon coild shift (only for CSV format), default=FALSE \n"); - buf.append("\t -dir The installed directory of SHIFTX+/SHIFTX2\n\n"); +// buf.append("\t -dir The installed directory of SHIFTX+/SHIFTX2\n\n"); buf.append("EXAMPLE:\n"); - buf.append("\t java -Xmx1500m -cp ~/shiftx2/bin:~/shiftx2/lib/weka.jar ShiftXp -i 1ubq.pdb\n\n"); + buf.append("\t jshiftx2 -i 1ubq.pdb\n\n"); buf.append("\n"); System.out.println( buf ); @@ -138,20 +138,6 @@ public class ShiftXp { } } - // check execute directory - // 2011.08.31 changed shiftx2_main.py --> shiftx2.py - if ( !( new File( SHIFTX2_DIR + "/shiftx2.py").exists() - && new File(SHIFTX2_DIR + "/lib/weka.jar").exists() ) ) { - - System.err.println("\n********************************************************************************"); - System.err.println("[Error]\t Required: When the SHIFTX2 execute on other directory,\n" - +"\t it should be set as a parameter. Use '-dir' option."); - System.err.println("> Current directory: "+System.getProperty("user.dir")); - System.err.println("********************************************************************************\n"); - - usage(); - } - if ( inPDBFile == null || inPDBFile.length() < 1) { System.err.println("\n********************************************************************************"); System.err.println("[Error] Required: There is no input PDB filename.");