diff options
author | Horea Christian <chr@chymera.eu> | 2020-09-28 04:45:07 -0400 |
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committer | Horea Christian <chr@chymera.eu> | 2020-09-28 04:45:07 -0400 |
commit | 0c41dce4e820d00f5ec7ada1bd8a796c9849c2f4 (patch) | |
tree | d97c9f686f659cf2bbef21581ef39d265438ebfb /sci-chemistry | |
parent | sci-chemistry/nwchem: removed unmaintained package with broken distfiles (diff) | |
download | sci-0c41dce4e820d00f5ec7ada1bd8a796c9849c2f4.tar.gz sci-0c41dce4e820d00f5ec7ada1bd8a796c9849c2f4.tar.bz2 sci-0c41dce4e820d00f5ec7ada1bd8a796c9849c2f4.zip |
sci-chemistry/shiftx2: removed discontinued package
Package-Manager: Portage-3.0.8, Repoman-3.0.1
Signed-off-by: Horea Christian <chr@chymera.eu>
Diffstat (limited to 'sci-chemistry')
7 files changed, 0 insertions, 672 deletions
diff --git a/sci-chemistry/shiftx2/Manifest b/sci-chemistry/shiftx2/Manifest deleted file mode 100644 index 45150380b..000000000 --- a/sci-chemistry/shiftx2/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST shiftx2-v107-linux-20120106.tgz 114164215 BLAKE2B 33615b7e739acb2711b1946c0db84becf68ebd4e77dc773c5c3c672174d5e1932c4f88bfec1e38a24957bb0d7838ee4fa9c24e95462d620f06b38b895b934a93 SHA512 b1fa6ce19e988a938e6645fdbd14f7903b4db13754a476c67da0bf74909675e07b7cec4df63be30d7190ea645e8822eef551e6dd26625172e585da279f1f7396 diff --git a/sci-chemistry/shiftx2/files/shiftx2-1.07_p20120106-format-security.patch b/sci-chemistry/shiftx2/files/shiftx2-1.07_p20120106-format-security.patch deleted file mode 100644 index fc4a61eb5..000000000 --- a/sci-chemistry/shiftx2/files/shiftx2-1.07_p20120106-format-security.patch +++ /dev/null @@ -1,16 +0,0 @@ - modules/resmf/libc/misc.lib.c | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/modules/resmf/libc/misc.lib.c b/modules/resmf/libc/misc.lib.c -index 0ef12a4..1e22424 100755 ---- a/modules/resmf/libc/misc.lib.c -+++ b/modules/resmf/libc/misc.lib.c -@@ -71,7 +71,7 @@ void show_msg(msg) - char *msg; - { - -- fprintf(stdout, msg); -+ fprintf(stdout, "%s", msg); - - } /* show_msg */ - diff --git a/sci-chemistry/shiftx2/files/shiftx2-1.07_p20120106-internal-name.patch b/sci-chemistry/shiftx2/files/shiftx2-1.07_p20120106-internal-name.patch deleted file mode 100644 index 4fa5447db..000000000 --- a/sci-chemistry/shiftx2/files/shiftx2-1.07_p20120106-internal-name.patch +++ /dev/null @@ -1,25 +0,0 @@ - modules/resmf/hydropho_cal.c | 4 ++-- - 1 file changed, 2 insertions(+), 2 deletions(-) - -diff --git a/modules/resmf/hydropho_cal.c b/modules/resmf/hydropho_cal.c -index 1fde394..a889d08 100755 ---- a/modules/resmf/hydropho_cal.c -+++ b/modules/resmf/hydropho_cal.c -@@ -184,7 +184,7 @@ float hydroscore(Hydroscale *scale, char residue){ - } - - /* function for copying string */ --char * strndup (const char *s, size_t n) -+char * new_strndup (const char *s, size_t n) - { - char *result; - size_t len = strlen (s); -@@ -206,7 +206,7 @@ char* substring(const char* str, size_t begin, size_t len) - { - if (str == 0 || strlen(str) == 0 || strlen(str) < begin || strlen(str) < (begin+len)) - return 0; -- return (char *) strndup(str + begin, len); -+ return (char *) new_strndup(str + begin, len); - } - - /* calculate the average value from begin to end in the given array */ 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."); diff --git a/sci-chemistry/shiftx2/files/shiftx2-1.07_p20120106-system.patch b/sci-chemistry/shiftx2/files/shiftx2-1.07_p20120106-system.patch deleted file mode 100644 index 7625f7442..000000000 --- a/sci-chemistry/shiftx2/files/shiftx2-1.07_p20120106-system.patch +++ /dev/null @@ -1,231 +0,0 @@ - natsorted.py | 1 - - script/combine_cs.py | 2 +- - shiftx2.py | 39 +++++++++++++++++++-------------------- - shiftx2_util.py | 3 +-- - shifty3/shifty3.py | 2 +- - 5 files changed, 22 insertions(+), 25 deletions(-) - -diff --git a/natsorted.py b/natsorted.py -index 415b393..6fc909e 100755 ---- a/natsorted.py -+++ b/natsorted.py -@@ -1,4 +1,3 @@ --#!/usr/bin/env python - ############################################################ - # functions for performing natural sort - ############################################################ -diff --git a/script/combine_cs.py b/script/combine_cs.py -index 4d1dd4f..5182958 100755 ---- a/script/combine_cs.py -+++ b/script/combine_cs.py -@@ -9,7 +9,7 @@ - # last updated: Jan 06st, 2012 (by Beomsoo Han) - ################################################################################# - import sys, re, os --from natsorted import * -+from shiftx2.natsorted import * - from math import exp ## add for new combine rule - # from numpy import * - tablerows = {} # a hash table for all rows in the table, mapping from residue number to table entry object -diff --git a/shiftx2.py b/shiftx2.py -index 0a171c8..72ecbfe 100755 ---- a/shiftx2.py -+++ b/shiftx2.py -@@ -14,7 +14,7 @@ - ####################################################################### - import os, sys, getopt, re, fnmatch - from optparse import OptionParser --from shiftx2_util import * -+from shiftx2.shiftx2util import * - - DEUTERATED = None - NOSHIFTY = None -@@ -26,7 +26,7 @@ CHAINID = None - EXPLICIT = None - SHIFTTYPE = None - --SHIFTX2ROOT = "" -+SHIFTX2ROOT = "@GENTOO_PORTAGE_EPREFIX@/opt/shiftx2" - - # temporary file name - -@@ -136,8 +136,7 @@ def batch_mode(pattern_str): - print "## Running SHIFTX+ modules ..." ## Add by B HAN - - ## switch os.path.abspath("") with SHIFTX2ROOT (set from sys.path[0]) by B HAN -- cmd_prefix = "java -cp " + SHIFTX2ROOT + "/bin:" + SHIFTX2ROOT + \ -- "/lib/weka.jar ShiftXp -b " + "'" + BATCH + "'" + " -atoms " + options.atoms + \ -+ cmd_prefix = "jshiftx2" + " -b " + "'" + BATCH + "'" + " -atoms " + options.atoms + \ - " -ph " + str(options.ph) + " -temp " + str(options.temp) - if DEUTERATED: - cmd_prefix = cmd_prefix + " -d TRUE" -@@ -154,14 +153,14 @@ def batch_mode(pattern_str): - for infile in pdb_list: - # run SHIFTX - ## cmd_prefix = "modules/shiftx/shiftx 1 " + os.path.abspath("") + "/" + \ -- cmd_prefix = SHIFTX2ROOT + "/modules/shiftx/shiftx 1 " + infile + " " + infile + ".sx" -+ cmd_prefix = "shiftx 1 " + infile + " " + infile + ".sx" - os.system(cmd_prefix) - if VERBOSE: - print cmd_prefix - # convert from table format to CSV - ## cmd_prefix = "python script/shiftx2shiftxp.py " + os.path.abspath("") + "/" + \ - ## infile + ".sx " + os.path.abspath("") + "/" + infile + ".sxp" -- cmd_prefix = "python "+ SHIFTX2ROOT +"/script/shiftx2shiftxp.py " + \ -+ cmd_prefix = "shiftx2shiftxp.py " + \ - infile + ".sx " + infile + ".sxp" - ## switched by B HAN - ## infile + ".sx " + os.path.abspath("") + "/" + infile.split('.')[0] + ".sxp" -@@ -180,7 +179,7 @@ def batch_mode(pattern_str): - ## os.chdir(os.path.abspath("shifty3")) - sys.path.append(SHIFTX2ROOT+"/shifty3") - os.chdir(SHIFTX2ROOT+"/shifty3") -- shifty_cmd = "python shifty3.py -i " + \ -+ shifty_cmd = "shifty3 -i " + \ - infile + " -o " + infile + ".shifty -c 40 " - if DEUTERATED: - shifty_cmd = shifty_cmd + " -d" -@@ -207,7 +206,7 @@ def batch_mode(pattern_str): - errmsg = "Error: SHIFTX+ cannot make a prediction file." - return errmsg - -- combine_cmd = "python " + SHIFTX2ROOT +"/script/combine_cs.py " + sx_outfile + " " + infile + ".shifty " -+ combine_cmd = "combine_cs.py " + sx_outfile + " " + infile + ".shifty " - if not options.outfile: - combine_cmd = combine_cmd + infile + ".cs" - else: -@@ -248,7 +247,7 @@ def model_batch(pattern_str): - # run shiftx1 or shiftx+ - if not SHIFTX1: - # run SHIFTX+ -- cmd_prefix = "java -cp " + SHIFTX2ROOT + "/bin:" + SHIFTX2ROOT + "/lib/weka.jar ShiftXp -b " + \ -+ cmd_prefix = "jshiftx2 -b " + \ - "'" + pattern_str + "'" + " -atoms " + options.atoms + \ - " -ph " + str(options.ph) + " -temp " + str(options.temp) - if DEUTERATED: -@@ -263,14 +262,14 @@ def model_batch(pattern_str): - else: - for infile in pdb_list: - # run SHIFTX -- cmd_prefix = SHIFTX2ROOT + "/modules/shiftx/shiftx 1 " + infile + \ -+ cmd_prefix = "shiftx 1 " + infile + \ - " " + infile + ".sx" - os.system(cmd_prefix) - if VERBOSE: - print cmd_prefix - - # convert from table format to CSV -- cmd_prefix = "python "+ SHIFTX2ROOT +"/script/shiftx2shiftxp.py " + \ -+ cmd_prefix = "shiftx2shiftxp.py " + \ - infile + ".sx " + infile + ".sxp" - - os.system(cmd_prefix) -@@ -328,7 +327,7 @@ def nmr_mode(infile, obs_cs): - if not NOSHIFTY: - sys.path.append( SHIFTX2ROOT + "/shifty3") - os.chdir(SHIFTX2ROOT + "/shifty3") -- shifty_cmd = "python shifty3.py -i " + infile + \ -+ shifty_cmd = "shifty3 -i " + infile + \ - " -o " + infile + ".shifty -c 40 " - if DEUTERATED: - shifty_cmd = shifty_cmd + " -d" -@@ -350,7 +349,7 @@ def nmr_mode(infile, obs_cs): - return errmsg - - # combine result -- combine_cmd = "python "+ SHIFTX2ROOT + "/script/combine_cs.py " + infile_prefix + ".sxp " + infile + ".shifty " -+ combine_cmd = "combine_cs.py " + infile_prefix + ".sxp " + infile + ".shifty " - if not options.outfile: - combine_cmd = combine_cmd + infile + ".cs" - ## add by B HAN; if it does not exist, error message will occur -@@ -367,7 +366,7 @@ def nmr_mode(infile, obs_cs): - # should be accomplished in a function - if obs_cs!= None: - # calculate correlation -- cmd = "python " + SHIFTX2ROOT +"/script/model_corr.py " + obs_cs + " " + infile_prefix + ".modelcorr " + ' '.join(model_outfiles) -+ cmd = "model_corr.py " + obs_cs + " " + infile_prefix + ".modelcorr " + ' '.join(model_outfiles) - os.system(cmd) - - # plot correlation graphs, plot line graph but no barplots -@@ -456,7 +455,7 @@ def single_mode(infile, outfile): - - if not SHIFTX1: - # run SHIFTX+ -- cmd_prefix = "java -cp " + SHIFTX2ROOT + "/bin:" + SHIFTX2ROOT + "/lib/weka.jar ShiftXp -i " + inputfile \ -+ cmd_prefix = "jshiftx2 -i " + inputfile \ - + " -atoms " + options.atoms + " -ph " + str(options.ph) + " -temp " + str(options.temp) - if DEUTERATED: - cmd_prefix = cmd_prefix + " -d TRUE" -@@ -476,12 +475,12 @@ def single_mode(infile, outfile): - sys.exit(-1) - else: - # run SHIFTX -- cmd_prefix = SHIFTX2ROOT + "/modules/shiftx/shiftx 1 " + inputfile + " " + sx1_outfile -+ cmd_prefix = "shiftx 1 " + inputfile + " " + sx1_outfile - os.system(cmd_prefix) - if VERBOSE: - print cmd_prefix - # convert from table format to CSV -- cmd_prefix = "python " + SHIFTX2ROOT + "/script/shiftx2shiftxp.py " + sx1_outfile + " " + sxp_outfile -+ cmd_prefix = "shiftx2shiftxp.py " + sx1_outfile + " " + sxp_outfile - os.system(cmd_prefix) - if VERBOSE: - print cmd_prefix -@@ -490,7 +489,7 @@ def single_mode(infile, outfile): - if not NOSHIFTY: - sys.path.append(SHIFTX2ROOT + "/shifty3") - os.chdir(SHIFTX2ROOT +"/shifty3") -- shifty_cmd = "python shifty3.py -i " + inputfile + " -o " + sy_outfile + " -c 40 " -+ shifty_cmd = "shifty3 -i " + inputfile + " -o " + sy_outfile + " -c 40 " - if DEUTERATED: - shifty_cmd = shifty_cmd + " -d" - if VERBOSE: -@@ -513,7 +512,7 @@ def single_mode(infile, outfile): - return errmsg - - # combine result -- combine_cmd = "python script/combine_cs.py " + sxp_outfile + " " + sy_outfile + " " -+ combine_cmd = "combine_cs.py " + sxp_outfile + " " + sy_outfile + " " - combine_cmd = combine_cmd + outfile # specify output file name - - combine_cmd = add_atom_format_option(combine_cmd) -@@ -543,7 +542,7 @@ def cleanup_tempfiles(files): - if __name__ == '__main__': - print "## SHIFTX2 Ver 1.07 (Released 4 Jan. 2012) ##" - -- SHIFTX2ROOT = sys.path[0] -+ #SHIFTX2ROOT = sys.path[0] - - #if len(sys.argv)<3: - # print "Usage: python shiftx2_main.py [input.pdb] [-atoms: all]" -diff --git a/shiftx2_util.py b/shiftx2_util.py -index d357a8e..6ce5e6c 100755 ---- a/shiftx2_util.py -+++ b/shiftx2_util.py -@@ -1,4 +1,3 @@ --#!/usr/bin/env python - #################################################################### - # shiftx2_util.py: utility functions supporting shiftx2_main.py - # -@@ -6,7 +5,7 @@ - # date: April 13th, 2011 - #################################################################### - import sys, os --from natsorted import * -+from shiftx2.natsorted import * - - # FUNCTIONS FOR SPLITING PDB FILE WITH MULTIPLE NMR MODELS - -diff --git a/shifty3/shifty3.py b/shifty3/shifty3.py -index 796af32..9360b87 100755 ---- a/shifty3/shifty3.py -+++ b/shifty3/shifty3.py -@@ -12,7 +12,7 @@ import sys, os, re, datetime, time - ############################################################### - # path for xalign and blast executibles and blast databases - XALIGN_EXE = "xalign_x" # executable for xalign --BLASTP_EXE = "./blast/bin/blastall -p blastp" # executable for blast -+BLASTP_EXE = "blastall -p blastp" # executable for blast - - BLASTDB = "blastdb" # folder containing the blast database - SHIFTDB = "refdb" # folder containing the BMRB shift database diff --git a/sci-chemistry/shiftx2/metadata.xml b/sci-chemistry/shiftx2/metadata.xml deleted file mode 100644 index e35d2bc02..000000000 --- a/sci-chemistry/shiftx2/metadata.xml +++ /dev/null @@ -1,42 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-chemistry@gentoo.org</email> - <name>Gentoo Chemistry Project</name> - </maintainer> - <longdescription> -SHIFTX2 predicts both the backbone and side chain 1H, 13C and 15N chemical -shifts for proteins using their structural (PDB) coordinates as input. -SHIFTX2 combines ensemble machine learning methods with sequence -alignment-based methods to calculate protein chemical shifts for -backbone -and side chain atoms. SHIFTX2 has been trained on a carefully selected -set of -197 proteins and tested on a separate set of 61 proteins. Both the -training -and testing sets consisted of high resolution X-ray structures (less -2.1A) -with carefully verified chemical shifts assignments. SHIFTX2 is able to -attain -correlation coefficients between experimentally observed and predicted -backbone chemical shifts of 0.9800 (15N), 0.9959 (13CA), 0.9992 (13CB), -0.9676 (13CO), 0.9714 (1HN), 0.9744 (1HA) and RMS errors of 1.1169, 0.4412, -0.5163, 0.5330, 0.1711, and 0.1231 ppm, respectively. Comparisons to -other -chemical shift predictors using the same testing data set indicates that -SHIFTX2 is substantially more accurate (up to 26% better by -correlation -coefficient with an RMS error that is up to 3.3X smaller) than any other -program. - -Please cite the following: Beomsoo Han, Yifeng Liu, Simon Ginzinger, and -David Wishart. (2011) SHIFTX2: significantly improved protein chemical -shift -prediction. Journal of Biomolecular NMR, Volume 50, Number 1, 43-57. -doi: 10.1007/s10858-011-9478-4. -</longdescription> - <use> - <flag name="debug">Enables debug output in the shiftx2 java part</flag> - </use> -</pkgmetadata> diff --git a/sci-chemistry/shiftx2/shiftx2-1.07_p20120106.ebuild b/sci-chemistry/shiftx2/shiftx2-1.07_p20120106.ebuild deleted file mode 100644 index 2b7a478af..000000000 --- a/sci-chemistry/shiftx2/shiftx2-1.07_p20120106.ebuild +++ /dev/null @@ -1,130 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) - -inherit java-pkg-2 java-pkg-simple prefix python-r1 versionator - -MY_PV="$(delete_all_version_separators $(get_version_component_range 1-2))" -MY_PATCH="20120106" -MY_P="${PN}-v${MY_PV}-linux" - -DESCRIPTION="Predicts of backbone and side chain 1H, 13C and 15N CS for proteins" -HOMEPAGE="http://shiftx2.wishartlab.com/" -SRC_URI="http://shiftx2.wishartlab.com/download/${MY_P}-${MY_PATCH}.tgz" - -SLOT="0" -LICENSE="all-rights-reserved" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="debug" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -CDEPEND="dev-util/weka ${PYTHON_DEPS}" - -RDEPEND="${CDEPEND} - ${PYTHON_DEPS} - dev-lang/R - sci-biology/ncbi-tools - sci-chemistry/reduce - >=virtual/jre-1.5" -DEPEND="${CDEPEND} - >=virtual/jdk-1.5" - -S="${WORKDIR}"/${MY_P} - -QA_PREBUILT="/opt/.*" - -src_prepare() { - epatch \ - "${FILESDIR}"/${P}-java.patch \ - "${FILESDIR}"/${P}-system.patch \ - "${FILESDIR}"/${P}-internal-name.patch \ - "${FILESDIR}"/${P}-format-security.patch - - rm "${S}"/src/FeatureRanges.java || die - - shared=$(echo "${EPREFIX}/usr/share/${PN}" | sed -e 's/\//\\\//g') - sed -i -e "s/PUT_GENTOO_SHARE_PATH_HERE/${shared}/g" "${S}/src/ShiftXp.java" || die - - if use debug; then - sed -i -e 's/DEBUG = false/DEBUG = true/g' "${S}/src/ShiftXp.java" || die - fi - - # hack alert! - sed \ - -e '/-o/s:$(GCC):$(GCC) $(LDFLAGS):g' \ - -e '/-o/s:$(CC):$(CC) $(LDFLAGS):g' \ - -i modules/*/Makefile || die - - sed -e '/-o/s:$: -lm:g' -i "${S}/modules/resmf/Makefile" || die - - eprefixify ${PN}.py -} - -src_compile() { - mkdir "${S}"/build || die - ejavac -classpath "$(java-pkg_getjars weka)" -nowarn \ - -d "${S}"/build $(find src/ -name "*.java") - jar cf "${PN}.jar" -C "${S}"/build . || die - - einfo "Building module angles" - cd "${S}"/modules/angles || die - emake clean - emake CFLAGS="${CFLAGS}" GCC=$(tc-getCC) LINK="${LDFLAGS}" get_angles phipsi - - einfo "Building module resmf" - cd "${S}"/modules/resmf || die - emake clean - emake CFLAGS="${CFLAGS}" GCC=$(tc-getCC) LINK="${LDFLAGS}" resmf - - einfo "Building module effects" - cd "${S}"/modules/effects || die - emake clean - emake CFLAGS="${CFLAGS}" CC=$(tc-getCC) LINK="${LDFLAGS}" all -} - -src_install() { - java-pkg_dojar "${PN}.jar" - java-pkg_dolauncher j${PN} --main "ShiftXp" --pkg_args "-dir ${EPREFIX}/usr/bin" - - insinto /usr/share/${PN} - doins "${S}"/lib/{limitedcshift.dat,RandomCoil.csv,data-header.arff} - doins -r "${S}"/lib/predmodels - - insinto /usr/share/${PN}/vader - doins -r "${S}"/modules/resmf/lib/* - - local instdir="/opt/${PN}" - dodoc README 1UBQ.pdb - python_foreach_impl python_newscript ${PN}.py ${PN} - mv shiftx2_util.py shiftx2util.py || die - python_moduleinto ${PN} - touch __init__.py - python_foreach_impl python_domodule natsorted.py shiftx2util.py __init__.py - - # other modules - dobin \ - "${S}"/modules/angles/{get_angles,phipsi} \ - "${S}"/modules/resmf/resmf \ - "${S}"/modules/effects/caleffect - - # script - python_foreach_impl python_doscript "${S}"/script/*py - exeinto ${instdir}/script - doexe "${S}"/script/*.r - - # shifty3 - python_foreach_impl python_newscript "${S}"/shifty3/*py shifty3 - exeinto ${instdir}/shifty3 - doexe "${S}"/shifty3/xalign_x - dosym ../${PN}/shifty3/xalign_x /opt/bin/xalign_x - - insinto ${instdir}/shifty3 - doins -r "${S}"/shifty3/{blastdb,refdb,xalign.parms,wt.rbo} - - python_foreach_impl python_doscript "${S}"/shifty3/utils/*py - dobin "${S}"/shifty3/utils/create_blastdb.sh -} |