Release-0.8.7

pemsley · Nov 8, 2016 · 35659f9 · 35659f9
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commit 35659f9
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diff --git a/ChangeLog b/ChangeLog
@@ -1,3 +1,7 @@
+2016-11-07  Paul Emsley  <pemsley at mrc dash lmb dot ac dot uk>
+
+	* Release 0.8.7
+
 2016-08-18  Paul Emsley  <pemsley at mrc dash lmb dot ac dot uk>
 
 	* Release 0.8.6

diff --git a/RELEASE-NOTES b/RELEASE-NOTES
@@ -1,9 +1,12 @@
 
-  Pre-Release 0.8.7
+------
+------
+
+  Release 0.8.7
 
   o FEATURE: Lidia now has canvas scaling
 
-  o FEATURE: Lidia now has CH3 superatoms
+  o FEATURE: Lidia now has CH3 superatoms, atom name and index display modes
 
   o FEATURE: Atom renaming to reference comp_id now has a place on the
              Ligand menu
@@ -14,14 +17,21 @@
 
   o CHANGE:  File -> SMILES has been removed
 
+  o CHANGE:  Additional parameters available in the ligand-fitting dialog
+
   o CHANGE:  Non-bonded contact restraints calculation speed up
 
+  o BUG-FIX: Fix side-chain plane restraints for sphere-refined residues with 
+             alt confs
+
   o BUG-FIX: MSE atoms are HETATMs after mutation [Sivasankar Putta]
 
   o BUG-FIX: CD bump exception in HYP NBC across link [Jens Kaiser]
 
   o BUG-FIX: Bond-dragging in Lidia now cleaned up
 
+  o BUG-FIX: Correct bonds to W in WO4.
+
 
 ------
 

diff --git a/build-it b/build-it
@@ -2833,6 +2833,7 @@ if test -n "$build_python" ; then
 
    echo INFO:: ./configure $generic_prefix $python_spec_flags $python_lib_flags for python
    # 
+   # do we also need to use --with-threads=dir?
    if ./configure $generic_prefix --enable-shared $python_spec_flags $python_lib_flags ; then
      echo INFO:: make for python
      if $MAKE ; then
@@ -4001,10 +4002,13 @@ if [ "$run_tests" = true ] ; then
 	          # only copy over the binary files if they are not there
 	          # already (checked by publish executable).
 	          #
+                  # reading the git logs adding $BINARY_TAR_DEST_DIR seems to have fixed something. 
+                  # Now, the transfer-to-web-server.sh scripts take the second arg 
+                  # and munge it to be the correct directory for the binary (and .txt) files.
 	          echo $publish $bin_tar_file $BINARY_TAR_DEST_DIR
-	          $publish $bin_tar_file $BINARY_TAR_DEST_DIR
+	          $publish      $bin_tar_file $BINARY_TAR_DEST_DIR
 	          echo $publish $bin_tar_file.md5sum $BINARY_TAR_DEST_DIR
-	          $publish $bin_tar_file.md5sum $BINARY_TAR_DEST_DIR
+	          $publish      $bin_tar_file.md5sum $BINARY_TAR_DEST_DIR
 	          # echo $publish $binary_type_latest
 	          # publish $binary_type_latest
 	          echo $publish --no-server-check ChangeLog

diff --git a/configure.ac b/configure.ac
@@ -25,7 +25,7 @@ dnl implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
 dnl
 dnl Process this file with autoconf to produce a configure script.
 
-AC_INIT(coot, 0.8.7-pre)
+AC_INIT(coot, 0.8.7)
 AC_CONFIG_SRCDIR(src/main.cc)
 AM_INIT_AUTOMAKE
 

diff --git a/coot-gtk2.glade b/coot-gtk2.glade
@@ -25162,7 +25162,7 @@ programs to which you may be more accustomed.
   <child>
     <widget class="GtkImage" id="image10854">
       <property name="visible">True</property>
-      <property name="pixbuf">coot-0.8.7-pre.png</property>
+      <property name="pixbuf">coot-0.8.7.png</property>
       <property name="xalign">0.5</property>
       <property name="yalign">0.5</property>
       <property name="xpad">0</property>

diff --git a/pixmaps/Makefile.am b/pixmaps/Makefile.am
@@ -28,7 +28,7 @@ cootpixmapdir = $(pkgdatadir)/pixmaps
 # no longer use xpms.
 
 dist_cootpixmap_DATA = \
-coot-0.8.7-pre.png \
+coot-0.8.7.png \
 add-alt-conf.png      dna.svg			   probe-clash.svg                \
 add-alt-conf.svg      edit-backbone.svg		   radacina_handcuffs-small.svg   \
 add-peptide-1.png     edit-chi.png		   ramachandran.png               \

diff --git a/protein_db/protein_db.h b/protein_db/protein_db.h
@@ -64,8 +64,8 @@ class Residue {
  private:
   static const int ntype = 22;
   static const char rtype1[ntype], rtype3[ntype][4];
-  static void unpack_float( const char* d, float& f ) { const short s = ((short(d[0])<<8)&0xFF00) | ((short(d[1]))&0x00FF); f = float(s)/100.0; }
-  static void pack_float( char* d, const float& f ) { const short s = rint(100.0*f); d[0] = char((s>>8)&0x00FF); d[1] = char((s)&0x00FF); }
+  static void unpack_float( const char* d, float& f ) { short s = ((short(d[0])<<8)&0xFF00) | ((short(d[1]))&0x00FF); f = float(s)/100.0; }
+  static void pack_float( char* d, const float& f ) { short s = lrint(100.0*f); d[0] = char((s>>8)&0x00FF); d[1] = char((s)&0x00FF); }
   float nnx, nny, nnz, cax, cay, caz, ccx, ccy, ccz;
   char typ, flg;
 };

diff --git a/rel-todo b/rel-todo
@@ -1,13 +1,29 @@
 
+   For 0.8.7
+
+   o The mtz button on the refmac dialog
+
+* Done.
+
+   o New EDS Location [John Berrisford]
+
+* Done.
+
+   o PDBe files sfs cif location
+
+* seems OK, problem with python interface.
+
+
    For Release 0.8.8
 
    o if the chain has a TER and we add NCS residues, then the
    old/current TER should be deleted.
 
+   o enable mol2 reading to pyrogen
+
    o Ligand Builder -> Open [cif dictionary] Failures
      110 (butyl carboxylic acid - Oxygen formal charge)
 
-
    o Fix make check on test chemical features
 
 * Done.

diff --git a/src/gtk2-interface.c b/src/gtk2-interface.c
@@ -14236,7 +14236,7 @@ create_splash_screen_window (void)
   gtk_window_set_position (GTK_WINDOW (splash_screen_window), GTK_WIN_POS_CENTER);
   gtk_window_set_type_hint (GTK_WINDOW (splash_screen_window), GDK_WINDOW_TYPE_HINT_SPLASHSCREEN);
 
-  image10854 = create_pixmap (splash_screen_window, "coot-0.8.7-pre.png");
+  image10854 = create_pixmap (splash_screen_window, "coot-0.8.7.png");
   gtk_widget_set_name (image10854, "image10854");
   gtk_widget_show (image10854);
   gtk_container_add (GTK_CONTAINER (splash_screen_window), image10854);