Merge remote-tracking branch 'refs/remotes/origin/gtk3' into gtk3

pemsley · Feb 5, 2022 · 050e7dd · 050e7dd
2 parents 7ca58cc + 18202fe
commit 050e7dd
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Showing 14 changed files with 23 additions and 42 deletions.
diff --git a/geometry/dict-utils.cc b/geometry/dict-utils.cc
@@ -954,7 +954,6 @@ coot::dictionary_residue_restraints_t::make_graph(bool use_hydrogens) const {
    // This contains the atom indices of of atom_info (0-indexed).  An
    // mmdb graph is 1-indexed.
    // 
-   int vertex_indexing[atom_info.size()];
 
    mmdb::math::Graph *graph = new mmdb::math::Graph;
    int i_atom = 0;
@@ -981,11 +980,11 @@ coot::dictionary_residue_restraints_t::make_graph(bool use_hydrogens) const {
 
 	 if (it_1 == name_map.end()) {
 	    if (use_hydrogens || !is_hydrogen(br.atom_id_1_4c()))
-	       std::cout << "Not found in name map atom 1 :" << br.atom_id_1() << ":" << std::endl;
+	       std::cout << "WARNING:: Not found in name map atom 1 :" << br.atom_id_1() << ":" << std::endl;
 	 } else { 
 	    if (it_2 == name_map.end()) {
 	       if (use_hydrogens || !is_hydrogen(br.atom_id_2_4c()))
-		  std::cout << "Not found in name map atom 2 :" << br.atom_id_2() << ":" << std::endl;
+		  std::cout << "WARNING:: Not found in name map atom 2 :" << br.atom_id_2() << ":" << std::endl;
 	    } else {
 
 	       if (use_hydrogens || (!is_hydrogen(br.atom_id_1_4c()) &&

diff --git a/python/coot_gui.py b/python/coot_gui.py
@@ -5795,7 +5795,7 @@ def pukka_puckers_qm(imol):
     import types
 
     residue_list = []
-    crit_d = 3.0  # Richardson's grup value to partition C2'-endo from C3'-endo
+    crit_d = 3.0  # Richardson's group value to partition C2'-endo from C3'-endo
 
     def add_questionable(r):
         residue_list.append(r)

diff --git a/src/c-interface-gui.cc b/src/c-interface-gui.cc
@@ -3222,7 +3222,6 @@ GtkWidget *wrapped_create_model_fit_refine_dialog() {
 void
 update_model_fit_refine_dialog_menu(GtkWidget *dialog) {
 
-#if (GTK_MAJOR_VERSION > 1)
    GtkWidget *menu_item;
    // update the menu for the rot/trans menu
    if (graphics_info_t::rot_trans_object_type == ROT_TRANS_TYPE_CHAIN) {
@@ -3237,7 +3236,6 @@ update_model_fit_refine_dialog_menu(GtkWidget *dialog) {
        gtk_check_menu_item_set_active(GTK_CHECK_MENU_ITEM(menu_item), TRUE);
      }
    }
-#endif
 }
 
 // function to update button labels (currently rot/trans only)

diff --git a/src/c-interface-pisa-gui.cc b/src/c-interface-pisa-gui.cc
@@ -40,7 +40,6 @@
 void
 coot::pisa_interfaces_gui(const std::vector<coot::pisa_interface_t> &gui_info) {
 
-#if (GTK_MAJOR_VERSION > 1)
    if (graphics_info_t::use_graphics_interface_flag) {
       GtkWidget *w = create_pisa_interfaces_dialog();
       gtk_widget_show(w);
@@ -95,10 +94,8 @@ coot::pisa_interfaces_gui(const std::vector<coot::pisa_interface_t> &gui_info) {
 		       gui_info_copy);
    }
 
-#endif   
 }
 
-#if (GTK_MAJOR_VERSION > 1)
 void
 coot::add_pisa_interfaces_cell_renderer(GtkTreeView *tree_view,
 					const std::string &column_title,
@@ -114,11 +111,9 @@ coot::add_pisa_interfaces_cell_renderer(GtkTreeView *tree_view,
    gtk_tree_view_column_set_sort_column_id(column, pos);   
    g_object_set_data (G_OBJECT (cell_renderer), "column", GINT_TO_POINTER (pos));
 }
-#endif
 
 
 
-#if (GTK_MAJOR_VERSION > 1)
 void
 coot::on_pisa_interfaces_seletion_changed(GtkTreeSelection *treeselection,
 					 gpointer          user_data) {
@@ -167,4 +162,3 @@ coot::on_pisa_interfaces_seletion_changed(GtkTreeSelection *treeselection,
 
    }
 }
-#endif
diff --git a/src/graphics-info-defines.cc b/src/graphics-info-defines.cc
@@ -147,11 +147,7 @@ graphics_info_t::model_fit_refine_button_name_list() {
    std::vector<std::string> names;
    names.push_back("model_refine_dialog_refine_params_button");
    names.push_back("model_refine_dialog_map_select_button");
-#if (GTK_MAJOR_VERSION >1)
    names.push_back("model_refine_dialog_fixed_atoms_button");
-#else
-   names.push_back("model_refine_dialog_fix_atoms_button");
-#endif
 //   names.push_back("model_refine_dialog_find_waters_button");
    names.push_back("model_refine_dialog_add_alt_conf_button");
    names.push_back("model_refine_dialog_pointer_atom_button");

diff --git a/src/graphics-info-draw.cc b/src/graphics-info-draw.cc
@@ -3728,6 +3728,10 @@ void
 graphics_info_t::reset_frame_buffers(int width, int height) {
 
    if (use_framebuffers) {
+
+
+      // 20220108-PE note to self. Try using the framebuffer::reset() function instead
+
       unsigned int sf = framebuffer_scale;
       unsigned int index_offset = 0;
 
@@ -5005,6 +5009,7 @@ graphics_info_t::fullscreen() {
 //static
 void
 graphics_info_t::unfullscreen() {
+
    GtkWidget *window = widget_from_builder("main_window");
    if (GTK_IS_WINDOW(window)) {
       gtk_window_unfullscreen(GTK_WINDOW(window));
@@ -5016,7 +5021,8 @@ graphics_info_t::unfullscreen() {
       GtkWidget *status_bar = widget_from_builder("main_window_statusbar");
       GtkWidget *tool_bar   = widget_from_builder("main_window_toolbar");
       GtkWidget *menu_bar   = widget_from_builder("main_window_menubar");
-#if 0
+
+#if (GTK_MAJOR_VERSION > 3)
       gtk_overlay_remove_overlay(GTK_OVERLAY(overlay), tool_bar);
       gtk_container_add(GTK_CONTAINER(vbox), tool_bar);
 

diff --git a/src/graphics-info-refmac.cc b/src/graphics-info-refmac.cc
@@ -1116,14 +1116,8 @@ graphics_info_t::update_refmac_column_labels_frame(GtkWidget *map_optionmenu,
     // if given mtz file: get the parameters from coot::refmac::saved_refmac_parameters
     std::string file_mtz_filename;
     GtkWidget *twin_mtz_label = lookup_widget(map_optionmenu, "run_refmac_mtz_file_label");
-#if (GTK_MAJOR_VERSION > 1)
     const gchar *mtz_filename = gtk_label_get_text(GTK_LABEL(twin_mtz_label));
     file_mtz_filename = mtz_filename;
-#else
-    gchar **mtz_filename = 0;
-    gtk_label_get(GTK_LABEL(twin_mtz_label), mtz_filename);
-    file_mtz_filename = (char *)mtz_filename;
-#endif // GTK
     std::string tmp_mtz;
     for (int i=0; i<n_molecules(); i++) {
       if (molecules[i].Refmac_file_mtz_filename().size() > 0) {

diff --git a/src/lbg-interface.cc b/src/lbg-interface.cc
@@ -23,13 +23,11 @@
 #endif
 
 #include "compat/coot-sysdep.h"
+#define ENABLE_NLS // 20220126-PE Charles says this is needed to fix dcgettext() problems
+                   // when including libintl.h - move it up above graphics-info.h
 #include "graphics-info.h"
 
-
 #include <cstring>
-#define ENABLE_NLS // fix dcgettext() header problems on including
-		   // libintl.h (via RDKitBase.h etc (including boost
-		   // stuff).
 
 #ifdef MAKE_ENHANCED_LIGAND_TOOLS
 #include "lidia-core/rdkit-interface.hh"

diff --git a/src/model-as-mesh.shader b/src/model-as-mesh.shader
@@ -2,6 +2,8 @@
 
 #version 330 core
 
+// this is for an instanced Mesh.
+
 layout(location = 0) in vec3 position;
 layout(location = 1) in vec3 normal;
 layout(location = 2) in vec4 colour; // instanced. For instanced objects, the colour is set

diff --git a/src/molecular-mesh-generator-mol-tris.cc b/src/molecular-mesh-generator-mol-tris.cc
@@ -210,7 +210,7 @@ molecular_mesh_generator_t::get_molecular_triangles_mesh(mmdb::Manager *mol,
 
       if (colour_scheme == "colorRampChainsScheme" || colour_scheme == "Ramp") {
 
-         std::cout << "here with colorRampChainsScheme" << std::endl;
+         std::cout << "debug:: in get_molecular_triangles_mesh() with colorRampChainsScheme" << std::endl;
          for(int imod = 1; imod<=mol->GetNumberOfModels(); imod++) {
             mmdb::Model *model_inner_p = mol->GetModel(imod);
             if (model_p) {
@@ -244,7 +244,7 @@ molecular_mesh_generator_t::get_molecular_triangles_mesh(mmdb::Manager *mol,
       r->redraw();
       std::vector<std::shared_ptr<DisplayPrimitive> > vdp = r->getDisplayPrimitives();
       auto displayPrimitiveIter = vdp.begin();
-      int i=0;
+      // int i=0;
       std::vector<s_generic_vertex> vertices;
       std::vector<g_triangle> triangles;
 
@@ -270,7 +270,7 @@ molecular_mesh_generator_t::get_molecular_triangles_mesh(mmdb::Manager *mol,
 #endif
 
       unsigned int idx = 0;
-      for (displayPrimitiveIter=vdp.begin(); displayPrimitiveIter != vdp.end(); displayPrimitiveIter++, idx++) {
+      for (displayPrimitiveIter=vdp.begin(); displayPrimitiveIter != vdp.end(); displayPrimitiveIter++, ++idx) {
 
          molecular_triangles_mesh_t current_primitives;
 
@@ -300,7 +300,7 @@ molecular_mesh_generator_t::get_molecular_triangles_mesh(mmdb::Manager *mol,
                // BoxSectionPrimitive have not had their colours scaled for some reason.
                if (displayPrimitive.type() == DisplayPrimitive::PrimitiveType::BoxSectionPrimitive) {
                   // std::cout << "vertex iVertex " << iVertex << " " << glm::to_string(gv.color) << std::endl;
-                  for (int i=0; i<3; i++) gv.color[i] /= 255.0;
+                  for (int ii=0; ii<3; ii++) gv.color[ii] /= 255.0;
                }
             }
 

diff --git a/src/molecule-class-info.h b/src/molecule-class-info.h
@@ -3425,9 +3425,7 @@ class molecule_class_info_t {
 
 
 #ifdef USE_MOLECULES_TO_TRIANGLES
-#ifdef HAVE_CXX11
    std::vector<std::shared_ptr<MolecularRepresentationInstance> > molrepinsts;
-#endif
 #endif // USE_MOLECULES_TO_TRIANGLES
 
    // return the index in the molrepinsts vector (can be negative for failure)

diff --git a/src/moleculestotriangles.shader b/src/moleculestotriangles.shader
@@ -95,6 +95,7 @@ void main() {
             specular_strength = 0.0;
          dp = clamp(dp, 0.1, 1.0); // no negative dot products for diffuse
 
+         // why don't I use the light source?
          vec4 lsa = vec4(0.4, 0.4, 0.4, 1.0);
          vec4 lsd = vec4(0.6, 0.6, 0.6, 1.0);
          vec4 ambient = colour_transfer * lsa * 0.1;

diff --git a/src/restraints-editor.cc b/src/restraints-editor.cc
@@ -36,8 +36,6 @@
 #include <string.h>  // strcpy
 #include <gtk/gtk.h>
 
-#if (GTK_MAJOR_VERSION > 1)
-
 #include "interface.h"
 #include "support.h"
 
@@ -228,8 +226,8 @@ coot::restraints_editor::get_column_type(int tree_type, int column_number, int m
 	 break;
       default:
 	 r = G_TYPE_STRING;
-      } 
-   } 
+      }
+   }
    if (tree_type == coot::restraints_editor::TREE_TYPE_CHIRALS) {
       switch(column_number) {
       case(5):
@@ -1470,4 +1468,3 @@ coot::restraints_editor::get_tree_view_by_notebook_page(gint current_page_index)
    return tree_view;
 }
 
-#endif // (GTK_MAJOR_VERSION > 1)
diff --git a/src/sdf-interface.cc b/src/sdf-interface.cc
@@ -25,6 +25,8 @@
 
 // We need this high so that dcgettext() so we don't get expected unqualified-id before 'const'
 // errors when we read libintl from rdkit-interface.hh
+#define ENABLE_NLS // 20220126-PE Charles says this is needed to fix dcgettext() problems
+                   // when including libintl.h - hmm!
 #include "graphics-info.h"
 #ifdef MAKE_ENHANCED_LIGAND_TOOLS
 #include <libintl.h>
@@ -34,10 +36,6 @@
 
 #include <cstring>
 
-#define ENABLE_NLS // fix dcgettext() header problems on including
-		   // libintl.h (via RDKitBase.h etc (including boost
-		   // stuff).
-
 #include <iostream> // for istream?
 #include <istream> // for istream?