undocumented beta release tested with beta tests

cbcrg · Dec 18, 2020 · 7d7e789 · 7d7e789
1 parent 7d81f5b
commit 7d7e789
Show file tree

Hide file tree

Showing 14 changed files with 24 additions and 16 deletions.
diff --git a/binaries/macosx/t_coffee b/binaries/macosx/t_coffee
diff --git a/build/web-readme.txt b/build/web-readme.txt
@@ -1,6 +1,6 @@
 T-Coffee distribution 
 =====================
-Version_13.45.31.11e8510 #_#UPDATE_VERSION -- Populated by edit_version.pl
+Version_13.45.32.7d81f5b #_#UPDATE_VERSION -- Populated by edit_version.pl
 The version ID is organized as follows: <Major Release>.<Latest Stable>.<Latest Beta>.<Github version tag>
 Content of this directory: 
 Linux Installation:

diff --git a/docs/.html/.buildinfo b/docs/.html/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 48b1608771a6f507e39a943ceaa9476b
+config: 99b8ce404b73fc8dc4d4822bc63651dd
 tags: 33eac41acc08762151beb8f3b7b86c8f
diff --git a/docs/.html/.doctrees/environment.pickle b/docs/.html/.doctrees/environment.pickle
diff --git a/docs/.html/_static/documentation_options.js b/docs/.html/_static/documentation_options.js
@@ -1,6 +1,6 @@
 var DOCUMENTATION_OPTIONS = {
     URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: 'Version_13.45.31.11e8510',
+    VERSION: 'Version_13.45.32.7d81f5b',
     LANGUAGE: 'None',
     COLLAPSE_INDEX: false,
     FILE_SUFFIX: '.html',

diff --git a/docs/.html/index.html b/docs/.html/index.html
@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>T-Coffee Version_13.45.31.11e8510 documentation</title>
+  <title>T-Coffee Version_13.45.32.7d81f5b documentation</title>
 
 
 
@@ -58,7 +58,7 @@
 
 
               <div class="version">
-                Version_13.45.31.11e8510
+                Version_13.45.32.7d81f5b
               </div>
 
 
@@ -716,7 +716,7 @@
 
       <li><a href="index.html#document-index">Docs</a> &raquo;</li>
 
-      <li>T-Coffee Version_13.45.31.11e8510 documentation</li>
+      <li>T-Coffee Version_13.45.32.7d81f5b documentation</li>
 
 
       <li class="wy-breadcrumbs-aside">

diff --git a/docs/.html/objects.inv b/docs/.html/objects.inv
diff --git a/docs/conf.py b/docs/conf.py
@@ -54,9 +54,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = u'Version_13.45.31.11e8510' #_#UPDATE_VERSION_TAG1 -- Populated by edit_version.pl
+version = u'Version_13.45.32.7d81f5b' #_#UPDATE_VERSION_TAG1 -- Populated by edit_version.pl
 # The full version, including alpha/beta/rc tags.
-release = u'Version_13.45.31.11e8510' #_#UPDATE_VERSION_TAG2 -- Populated by edit_version.pl
+release = u'Version_13.45.32.7d81f5b' #_#UPDATE_VERSION_TAG2 -- Populated by edit_version.pl
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

diff --git a/lib/perl/lib/scripts/extract_from_pdb b/lib/perl/lib/scripts/extract_from_pdb
@@ -217,7 +217,7 @@ else
 #  Netaddress for pdb
 
 # $netaddress="http://www.rcsb.org/pdb/cgi/export.cgi/%%.pdb.gz?format=PDB&pdbId=%%&compression=gz";
-$netaddress="http://www.rcsb.org/pdb/files/%%.pdb.gz";
+$netaddress="https://files.rcsb.org/download/%%.pdb.gz";
 $netcompression_pg="gunzip";
 $netcompression="gz";
 
@@ -1934,8 +1934,10 @@ sub url2file
 
     if (!$CONFIGURATION){&check_configuration ("wget", "INTERNET", "gzip");$CONFIGURATION=1;}
 
-    if (&pg_is_installed ("wget"))   {$pg="wget"; $flag="-O";$arg=$wget_arg;}
-    elsif (&pg_is_installed ("curl")){$pg="curl"; $flag="-o";$arg=$curl_arg;}
+
+    if (&pg_is_installed ("curl")){$pg="curl"; $flag="-o";$arg=$curl_arg;}
+    elsif (&pg_is_installed ("wget"))   {$pg="wget"; $flag="-O";$arg=$wget_arg;}
+
     return safe_system ("$pg $flag$out $address >/dev/null 2>/dev/null");
 
 }

diff --git a/lib/t_coffee_lib/t_coffee.c b/lib/t_coffee_lib/t_coffee.c
@@ -4522,8 +4522,14 @@ get_cl_param(\
 		   if ( list_file[a][0]=='P' && !check_file_exists(list_file[a]))
 		     {
 		       char buf[1000];
+		       char *b2;
 		       sprintf(buf, "%s", list_file[a]+1);
-		       sprintf(list_file[a], "P%s",is_pdb_struc (buf));
+		       b2=is_pdb_struc (buf);
+		       if (b2)sprintf(list_file[a], "P%s",b2);
+		       else 
+			 {
+			   myexit(fprintf_error (stderr, "\nERROR: Could not find PDB structure %s [FATAL:%s]",list_file[a], PROGRAM));
+			 }
 		     }
 		 }
 

diff --git a/lib/util_lib/reformat.c b/lib/util_lib/reformat.c
@@ -1956,7 +1956,6 @@ char **identify_list_format ( char **list, int n)
 	   char mode;
 
 
-
 	   declare_name (name);
 	   for ( a=0; a< n; a++)
 	       {
@@ -2234,6 +2233,7 @@ char*  is_pdb_struc_strict ( char *name)
      if (is_pdb_file(name)){r=name;}
      else if (is_pdb_name (name))
        {
+	 HERE ("extract_from_pdb -netfile \'%s\' > %s/%s 2>/dev/null",name, get_cache_dir(),name);
 	 printf_system ("extract_from_pdb -netfile \'%s\' > %s/%s 2>/dev/null",name, get_cache_dir(),name);
 	 if ( is_pdb_file(name))r=name;
 	 else r=NULL;

diff --git a/lib/version/build_version.version b/lib/version/build_version.version
@@ -1 +1 @@
-31
+32
diff --git a/lib/version/github.version b/lib/version/github.version
@@ -1 +1 @@
-* master 11e8510 [ahead 1] undocumented beta release tested with beta tests
+* master 7d81f5b undocumented beta release tested with beta tests
diff --git a/lib/version/version_number.version b/lib/version/version_number.version
@@ -1 +1 @@
-Version_13.45.31.11e8510
+Version_13.45.32.7d81f5b