diff options
Diffstat (limited to 'sci-chemistry/shiftx2/files/shiftx2-1.07_p20120106-java.patch')
| -rw-r--r-- | sci-chemistry/shiftx2/files/shiftx2-1.07_p20120106-java.patch | 227 |
1 files changed, 0 insertions, 227 deletions
diff --git a/sci-chemistry/shiftx2/files/shiftx2-1.07_p20120106-java.patch b/sci-chemistry/shiftx2/files/shiftx2-1.07_p20120106-java.patch deleted file mode 100644 index ea64cea2d..000000000 --- a/sci-chemistry/shiftx2/files/shiftx2-1.07_p20120106-java.patch +++ /dev/null @@ -1,227 +0,0 @@ -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<String, Classifier> hsmap_predmodel = new HashMap<String, Classifier>(); - -@@ -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 <SHIFTX+ dir>/bin:<SHIFTX+ dir>/lib/weka.jar ShiftXp [options]\n"); -+ buf.append("SYNOPSIS\n\t jshiftx2 [options]\n"); - - buf.append("OPTIONS:\n"); - buf.append("\t -i [<directory/> infile.pdb | ALLPDB]\n"); -@@ -54,10 +54,10 @@ public class ShiftXp { - buf.append("\t -temp <number> 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 <SHIFTX+ directory> The installed directory of SHIFTX+/SHIFTX2\n\n"); -+// buf.append("\t -dir <SHIFTX+ directory> 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."); |