* [gentoo-commits] proj/sci:master commit in: sci-chemistry/shiftx2/, sci-chemistry/shiftx2/files/
@ 2015-10-23 10:32 Justin Lecher
0 siblings, 0 replies; 3+ messages in thread
From: Justin Lecher @ 2015-10-23 10:32 UTC (permalink / raw
To: gentoo-commits
commit: 5923310384f4106c3980b94e82fb9e90e96ea3c0
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Oct 23 10:32:52 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Oct 23 10:32:52 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=59233103
sci-chemistry/shiftx2: Fix for using glibc internal namings and format-security
Package-Manager: portage-2.2.23
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
.../shiftx2-1.07_p20120106-format-security.patch | 16 ++++++++++++++
.../shiftx2-1.07_p20120106-internal-name.patch | 25 ++++++++++++++++++++++
.../shiftx2/shiftx2-1.07_p20120106.ebuild | 6 ++++--
3 files changed, 45 insertions(+), 2 deletions(-)
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
new file mode 100644
index 0000000..fc4a61e
--- /dev/null
+++ b/sci-chemistry/shiftx2/files/shiftx2-1.07_p20120106-format-security.patch
@@ -0,0 +1,16 @@
+ 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
new file mode 100644
index 0000000..4fa5447
--- /dev/null
+++ b/sci-chemistry/shiftx2/files/shiftx2-1.07_p20120106-internal-name.patch
@@ -0,0 +1,25 @@
+ 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/shiftx2-1.07_p20120106.ebuild b/sci-chemistry/shiftx2/shiftx2-1.07_p20120106.ebuild
index 9baabd4..b56d269 100644
--- a/sci-chemistry/shiftx2/shiftx2-1.07_p20120106.ebuild
+++ b/sci-chemistry/shiftx2/shiftx2-1.07_p20120106.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
@@ -41,7 +41,9 @@ QA_PREBUILT="/opt/.*"
src_prepare() {
epatch \
"${FILESDIR}"/${P}-java.patch \
- "${FILESDIR}"/${P}-system.patch
+ "${FILESDIR}"/${P}-system.patch \
+ "${FILESDIR}"/${P}-internal-name.patch \
+ "${FILESDIR}"/${P}-format-security.patch
rm "${S}"/src/FeatureRanges.java || die
^ permalink raw reply related [flat|nested] 3+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-chemistry/shiftx2/, sci-chemistry/shiftx2/files/
@ 2020-09-28 8:58 Horea Christian
0 siblings, 0 replies; 3+ messages in thread
From: Horea Christian @ 2020-09-28 8:58 UTC (permalink / raw
To: gentoo-commits
commit: 0c41dce4e820d00f5ec7ada1bd8a796c9849c2f4
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Mon Sep 28 08:45:07 2020 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Mon Sep 28 08:45:07 2020 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=0c41dce4
sci-chemistry/shiftx2: removed discontinued package
Package-Manager: Portage-3.0.8, Repoman-3.0.1
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
.../shiftx2-1.07_p20120106-format-security.patch | 16 --
.../shiftx2-1.07_p20120106-internal-name.patch | 25 ---
.../files/shiftx2-1.07_p20120106-java.patch | 227 --------------------
.../files/shiftx2-1.07_p20120106-system.patch | 231 ---------------------
sci-chemistry/shiftx2/metadata.xml | 42 ----
.../shiftx2/shiftx2-1.07_p20120106.ebuild | 130 ------------
6 files changed, 671 deletions(-)
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
-}
^ permalink raw reply related [flat|nested] 3+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-chemistry/shiftx2/, sci-chemistry/shiftx2/files/
@ 2013-06-16 17:23 Justin Lecher
0 siblings, 0 replies; 3+ messages in thread
From: Justin Lecher @ 2013-06-16 17:23 UTC (permalink / raw
To: gentoo-commits
commit: a5dea0ab4d52cd3e3c205d4bdb9ad1e8fe48f662
Author: Johann Schmitz <johann <AT> j-schmitz <DOT> net>
AuthorDate: Sun Jun 16 16:55:30 2013 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Jun 16 16:55:30 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a5dea0ab
Enhanced the sci-chemistry/shiftx ebuild. Still needs some love for the emake part
(portage complains about LDFLAGS not respected), but should work.
---
sci-chemistry/shiftx2/files/gentoo-fixes.patch | 194 +++++++++++++++++++++
sci-chemistry/shiftx2/metadata.xml | 57 +++---
.../shiftx2/shiftx2-1.07_p20120106.ebuild | 56 ++++--
3 files changed, 271 insertions(+), 36 deletions(-)
diff --git a/sci-chemistry/shiftx2/files/gentoo-fixes.patch b/sci-chemistry/shiftx2/files/gentoo-fixes.patch
new file mode 100644
index 0000000..2baa443
--- /dev/null
+++ b/sci-chemistry/shiftx2/files/gentoo-fixes.patch
@@ -0,0 +1,194 @@
+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();
+@@ -140,8 +140,7 @@ 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() ) ) {
++ if (!new File(SHIFTX2_DIR + "/shiftx2.py").exists()) {
+
+ System.err.println("\n********************************************************************************");
+ System.err.println("[Error]\t Required: When the SHIFTX2 execute on other directory,\n"
diff --git a/sci-chemistry/shiftx2/metadata.xml b/sci-chemistry/shiftx2/metadata.xml
index 8fb55f2..947e346 100644
--- a/sci-chemistry/shiftx2/metadata.xml
+++ b/sci-chemistry/shiftx2/metadata.xml
@@ -1,28 +1,39 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
-<herd>sci</herd>
-<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.
+ <herd>sci</herd>
+ <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>
+ 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
index b13677b..e9cb4c7 100644
--- a/sci-chemistry/shiftx2/shiftx2-1.07_p20120106.ebuild
+++ b/sci-chemistry/shiftx2/shiftx2-1.07_p20120106.ebuild
@@ -19,7 +19,7 @@ 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=""
+IUSE="debug"
CDEPEND="dev-util/weka"
@@ -31,44 +31,74 @@ DEPEND="${CDEPEND}
S="${WORKDIR}"/${MY_P}
+src_prepare() {
+ epatch "${FILESDIR}/gentoo-fixes.patch"
+ rm "${S}"/src/FeatureRanges.java || die
+
+ shared=$(echo "/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 '/-o/s:$: -lm:g' -i "${S}/modules/resmf/Makefile" || die
+}
+
src_compile() {
mkdir "${S}"/build || die
- ejavac -classpath "$(java-pkg_getjars weka)" -nowarn -d "${S}"/build $(find src/ -name "*.java")
+ ejavac -classpath "$(java-pkg_getjars weka)" -nowarn \
+ -d "${S}"/build $(find src/ -name "*.java")
jar cf "${PN}.jar" -C "${S}"/build . || die
- ejavac -cp $(java-pkg_getjars weka):. -Xlint ShiftXp.java
-
+ einfo "Building module angles"
cd "${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="${CFLAGS}" GCC=$(tc-getCC) LINK="${LDFLAGS}" all
}
src_install() {
- java-pkg_dolauncher ${PN} --main "ShiftXp"
+ java-pkg_dojar "${PN}.jar"
+ java-pkg_dolauncher ${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/${PN}"
dodoc README 1UBQ.pdb
- python_parallel_foreach_impl python_doscript *py
+ python_parallel_foreach_impl python_doscript "${S}"/*py
# modules/angles
cd "${S}"/modules/angles || die
dobin get_angles phipsi
+ # other modules
+ dobin "${S}"/modules/resmf/resmf "${S}"/modules/effects/caleffect
# script
python_scriptinto ${instdir}/script
- python_parallel_foreach_impl python_doscript script/*py
+ python_parallel_foreach_impl python_doscript "${S}"/script/*py
exeinto ${instdir}/script
- doexe script/*.r
-
+ doexe "${S}"/script/*.r
# shifty3
- insinto ${instdir}
- doins -r shifty3
python_scriptinto ${instdir}/shifty3
- python_parallel_foreach_impl python_doscript shifty3/*py
+ python_parallel_foreach_impl python_doscript "${S}"/shifty3/*py
exeinto ${instdir}/shifty3
- doexe shifty3/xalign_x
+ doexe "${S}"/shifty3/xalign_x
}
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2015-10-23 10:32 [gentoo-commits] proj/sci:master commit in: sci-chemistry/shiftx2/, sci-chemistry/shiftx2/files/ Justin Lecher
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2020-09-28 8:58 Horea Christian
2013-06-16 17:23 Justin Lecher
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