diff options
Diffstat (limited to 'sci-chemistry/shiftx2/files/shiftx2-1.07_p20120106-system.patch')
| -rw-r--r-- | sci-chemistry/shiftx2/files/shiftx2-1.07_p20120106-system.patch | 231 |
1 files changed, 0 insertions, 231 deletions
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 |