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<title>[129475] trunk/dports/science/pymol</title>
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<dl class="meta">
<dt>Revision</dt> <dd><a href="https://trac.macports.org/changeset/129475">129475</a></dd>
<dt>Author</dt> <dd>ryandesign@macports.org</dd>
<dt>Date</dt> <dd>2014-12-13 14:12:42 -0800 (Sat, 13 Dec 2014)</dd>
</dl>
<h3>Log Message</h3>
<pre>pymol: update to 1.7.4.0 (maintainer, #46218)</pre>
<h3>Modified Paths</h3>
<ul>
<li><a href="#trunkdportssciencepymolPortfile">trunk/dports/science/pymol/Portfile</a></li>
<li><a href="#trunkdportssciencepymolfilespmg_tk_platformpatch">trunk/dports/science/pymol/files/pmg_tk_platform.patch</a></li>
<li><a href="#trunkdportssciencepymolfilespymolclangdiff">trunk/dports/science/pymol/files/pymol-clang.diff</a></li>
<li><a href="#trunkdportssciencepymolfilessetup_pydiff">trunk/dports/science/pymol/files/setup_py.diff</a></li>
</ul>
<h3>Added Paths</h3>
<ul>
<li><a href="#trunkdportssciencepymolfilespymoluseglkitdiff">trunk/dports/science/pymol/files/pymol-use-glkit.diff</a></li>
</ul>
<h3>Removed Paths</h3>
<ul>
<li><a href="#trunkdportssciencepymolfilesapbs_tkinterpatch">trunk/dports/science/pymol/files/apbs_tkinter.patch</a></li>
</ul>
</div>
<div id="patch">
<h3>Diff</h3>
<a id="trunkdportssciencepymolPortfile"></a>
<div class="modfile"><h4>Modified: trunk/dports/science/pymol/Portfile (129474 => 129475)</h4>
<pre class="diff"><span>
<span class="info">--- trunk/dports/science/pymol/Portfile 2014-12-13 20:40:58 UTC (rev 129474)
+++ trunk/dports/science/pymol/Portfile 2014-12-13 22:12:42 UTC (rev 129475)
</span><span class="lines">@@ -6,7 +6,7 @@
</span><span class="cx"> PortGroup active_variants 1.1
</span><span class="cx">
</span><span class="cx"> name pymol
</span><del>-version 1.7.2.1
</del><ins>+version 1.7.4.0
</ins><span class="cx"> categories science chemistry
</span><span class="cx"> license PSF
</span><span class="cx"> maintainers gmail.com:howarth.at.macports
</span><span class="lines">@@ -22,7 +22,7 @@
</span><span class="cx"> master_sites sourceforge
</span><span class="cx"> fetch.type svn
</span><span class="cx"> svn.url https://svn.code.sf.net/p/pymol/code/trunk/pymol
</span><del>-svn.revision 4087
</del><ins>+svn.revision 4107
</ins><span class="cx"> worksrcdir pymol
</span><span class="cx">
</span><span class="cx"> python.default_version 27
</span><span class="lines">@@ -46,9 +46,12 @@
</span><span class="cx"> pymol_shell.diff \
</span><span class="cx"> pmg_tk_platform.patch \
</span><span class="cx"> apbs-psize.patch \
</span><del>- apbs_tkinter.patch \
- pymol-clang.diff
</del><ins>+ pymol-clang.diff
</ins><span class="cx">
</span><ins>+if {${os.platform} eq "darwin" && ${os.major} >= 12} {
+ patchfiles-append pymol-use-glkit.diff
+}
+
</ins><span class="cx"> require_active_variants tcl "" corefoundation
</span><span class="cx"> require_active_variants tk "" quartz
</span><span class="cx">
</span></span></pre></div>
<a id="trunkdportssciencepymolfilesapbs_tkinterpatch"></a>
<div class="delfile"><h4>Deleted: trunk/dports/science/pymol/files/apbs_tkinter.patch (129474 => 129475)</h4>
<pre class="diff"><span>
<span class="info">--- trunk/dports/science/pymol/files/apbs_tkinter.patch 2014-12-13 20:40:58 UTC (rev 129474)
+++ trunk/dports/science/pymol/files/apbs_tkinter.patch 2014-12-13 22:12:42 UTC (rev 129475)
</span><span class="lines">@@ -1,196 +0,0 @@
</span><del>---- modules/pmg_tk/startup/apbs_tools.py.orig
-+++ modules/pmg_tk/startup/apbs_tools.py
-@@ -612,7 +612,8 @@
- # Set up the Main page
- page = self.notebook.add('Main')
- group = Pmw.Group(page,tag_text='Main options')
-- group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
-+ #group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
-+ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
- self.selection = Pmw.EntryField(group.interior(),
- labelpos='w',
- label_text='Selection to use: ',
-@@ -658,7 +659,8 @@
- page = self.notebook.add('Configuration')
-
- group = Pmw.Group(page,tag_text='Dielectric Constants')
-- group.pack(fill = 'both', expand = 1, padx = 4, pady = 5)
-+ #group.pack(fill = 'both', expand = 1, padx = 4, pady = 5)
-+ group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
- group.grid(column=0, row=0)
- self.interior_dielectric = Pmw.EntryField(group.interior(),labelpos='w',
- label_text = 'Protein Dielectric:',
-@@ -677,7 +679,8 @@
- #entry.pack(side='left',fill='both',expand=1,padx=4) # side-by-side
- entry.pack(fill='x',expand=1,padx=4,pady=1) # vertical
- group = Pmw.Group(page,tag_text='Other')
-- group.pack(fill='both',expand=1, padx=4, pady=5)
-+ #group.pack(fill='both',expand=1, padx=4, pady=5)
-+ group.grid(padx=4, pady=5, sticky=(N, S, E, W))
- group.grid(column=1, row=1,columnspan=4)
- self.max_mem_allowed = Pmw.EntryField(group.interior(),labelpos='w',
- label_text = 'Maximum Memory Allowed (MB):',
-@@ -735,7 +738,8 @@
-
-
- group = Pmw.Group(page,tag_text='Ions')
-- group.pack(fill='both',expand=1, padx=4, pady=5)
-+ #group.pack(fill='both',expand=1, padx=4, pady=5)
-+ group.grid(padx=4, pady=5, sticky=(N, S, E, W))
- group.grid(column=0, row=1, )
- self.ion_plus_one_conc = Pmw.EntryField(group.interior(),
- labelpos='w',
-@@ -794,7 +798,8 @@
- entry.pack(fill='x',expand=1,padx=4)
-
- group = Pmw.Group(page,tag_text = 'Coarse Mesh Length')
-- group.pack(fill = 'both', expand = 1, padx = 4, pady = 5)
-+ #group.pack(fill = 'both', expand = 1, padx = 4, pady = 5)
-+ group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
- group.grid(column = 1, row = 0)
- for coord in 'x y z'.split():
- setattr(self,'grid_coarse_%s'%coord,Pmw.EntryField(group.interior(),
-@@ -809,7 +814,8 @@
-
-
- group = Pmw.Group(page,tag_text = 'Fine Mesh Length')
-- group.pack(fill = 'both', expand = 1, padx = 4, pady = 5)
-+ #group.pack(fill = 'both', expand = 1, padx = 4, pady = 5)
-+ group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
- group.grid(column = 2, row = 0)
- for coord in 'x y z'.split():
- setattr(self,'grid_fine_%s'%coord,Pmw.EntryField(group.interior(),
-@@ -824,7 +830,8 @@
-
-
- group = Pmw.Group(page,tag_text = 'Grid Center')
-- group.pack(fill = 'both', expand = 1, padx = 4, pady = 5)
-+ #group.pack(fill = 'both', expand = 1, padx = 4, pady = 5)
-+ group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
- group.grid(column = 3, row = 0)
- for coord in 'x y z'.split():
- setattr(self,'grid_center_%s'%coord,Pmw.EntryField(group.interior(),
-@@ -838,7 +845,8 @@
- getattr(self,'grid_center_%s'%coord).pack(fill='x', expand=1, padx=4, pady=1)
-
- group = Pmw.Group(page,tag_text = 'Grid Points')
-- group.pack(fill = 'both', expand = 1, padx = 4, pady = 5)
-+ #group.pack(fill = 'both', expand = 1, padx = 4, pady = 5)
-+ group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
- group.grid(column = 4, row = 0)
- for coord in 'x y z'.split():
- setattr(self,'grid_points_%s'%coord,Pmw.EntryField(group.interior(),
-@@ -856,7 +864,8 @@
- page.grid_columnconfigure(5,weight=1)
- page = self.notebook.add('Program Locations')
- group = Pmw.Group(page,tag_text='Locations')
-- group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
-+ #group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
-+ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
- def quickFileValidation(s):
- if s == '': return Pmw.PARTIAL
- elif os.path.isfile(s): return Pmw.OK
-@@ -955,7 +964,8 @@
-
- page = self.notebook.add('Temp File Locations')
- group = Pmw.Group(page,tag_text='Locations')
-- group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
-+ #group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
-+ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
- self.pymol_generated_pqr_filename = Pmw.EntryField(group.interior(),
- labelpos = 'w',
- label_pyclass = FileDialogButtonClassFactory.get(self.setPymolGeneratedPqrFilename),
-@@ -1003,17 +1013,20 @@
- page = self.notebook.add('Visualization (1)')
- group = VisualizationGroup(page,tag_text='Visualization',visgroup_num=1)
- self.visualization_group_1 = group
-- group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
-+ #group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
-+ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
-
- page = self.notebook.add('Visualization (2)')
- group = VisualizationGroup(page,tag_text='Visualization',visgroup_num=2)
- self.visualization_group_2 = group
-- group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
-+ #group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
-+ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
-
- # Create a couple of other empty pages
- page = self.notebook.add('About')
- group = Pmw.Group(page, tag_text='About PyMOL APBS Tools')
-- group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
-+ #group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
-+ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
- text = """This plugin integrates PyMOL (http://PyMOL.org/) with APBS (http://www.poissonboltzmann.org/apbs/).
-
- Documentation may be found at
-@@ -2267,7 +2280,8 @@
- self.update_buttonbox = Pmw.ButtonBox(self.mm_group.interior(), padx=0)
- self.update_buttonbox.pack(side=LEFT)
- self.update_buttonbox.add('Update',command=self.refresh)
-- self.mm_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=TOP)
-+ #self.mm_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=TOP)
-+ self.mm_group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
-
- self.ms_group = Pmw.Group(self.interior(),tag_text='Molecular Surface')
- self.ms_buttonbox = Pmw.ButtonBox(self.ms_group.interior(), padx=0)
-@@ -2317,8 +2331,9 @@
- )
- bars = (self.mol_surf_low,self.mol_surf_middle,self.mol_surf_high)
- Pmw.alignlabels(bars)
-- for bar in bars: bar.pack(side=LEFT)
-- self.ms_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT)
-+ for bar in bars: bar.pack(expand = 1, side=LEFT)
-+ #self.ms_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT)
-+ self.ms_group.grid(column=0, row=1, padx = 4, pady = 5, rowspan = 2, sticky=(N, S, E, W))
-
- self.fl_group = Pmw.Group(self.interior(),tag_text='Field Lines')
- self.fl_buttonbox = Pmw.ButtonBox(self.fl_group.interior(), padx=0)
-@@ -2333,11 +2348,13 @@
- text = """Follows same coloring as surface.""",
- )
- label.pack()
-- self.fl_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=TOP)
-+ #self.fl_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=TOP)
-+ self.fl_group.grid(column = 1, row=0, padx = 4, pady = 5)
-
- self.pi_group = Pmw.Group(self.interior(),tag_text='Positive Isosurface')
- self.pi_buttonbox = Pmw.ButtonBox(self.pi_group.interior(), padx=0)
-- self.pi_buttonbox.pack()
-+ #self.pi_buttonbox.pack()
-+ self.pi_buttonbox.grid()
- self.pi_buttonbox.add('Show',command=self.showPosSurface)
- self.pi_buttonbox.add('Hide',command=self.hidePosSurface)
- self.pi_buttonbox.add('Update',command=self.updatePosSurface)
-@@ -2351,12 +2368,15 @@
- datatype = 'real',
- entryfield_validate = {'validator' : 'real', 'min':0}
- )
-- self.pos_surf_val.pack(side=LEFT)
-- self.pi_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT)
-+ #self.pos_surf_val.pack(side=LEFT)
-+ self.pos_surf_val.grid()
-+ #self.pi_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT)
-+ self.pi_group.grid(column = 1, row = 1, padx = 4, pady = 5, sticky=(N, S, E, W))
-
- self.ni_group = Pmw.Group(self.interior(),tag_text='Negative Isosurface')
- self.ni_buttonbox = Pmw.ButtonBox(self.ni_group.interior(), padx=0)
-- self.ni_buttonbox.pack()
-+ #self.ni_buttonbox.pack()
-+ self.ni_buttonbox.grid()
- self.ni_buttonbox.add('Show',command=self.showNegSurface)
- self.ni_buttonbox.add('Hide',command=self.hideNegSurface)
- self.ni_buttonbox.add('Update',command=self.updateNegSurface)
-@@ -2370,8 +2390,10 @@
- datatype = 'real',
- entryfield_validate = {'validator' : 'real', 'max':0}
- )
-- self.neg_surf_val.pack(side=LEFT)
-- self.ni_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT)
-+ #self.neg_surf_val.pack(side=LEFT)
-+ self.neg_surf_val.grid()
-+ #self.ni_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT)
-+ self.ni_group.grid(column = 1, row=2, padx = 4, pady = 5, sticky=(N, S, E, W))
-
-
-
</del></span></pre></div>
<a id="trunkdportssciencepymolfilespmg_tk_platformpatch"></a>
<div class="modfile"><h4>Modified: trunk/dports/science/pymol/files/pmg_tk_platform.patch (129474 => 129475)</h4>
<pre class="diff"><span>
<span class="info">--- trunk/dports/science/pymol/files/pmg_tk_platform.patch 2014-12-13 20:40:58 UTC (rev 129474)
+++ trunk/dports/science/pymol/files/pmg_tk_platform.patch 2014-12-13 22:12:42 UTC (rev 129475)
</span><span class="lines">@@ -1,6 +1,30 @@
</span><del>---- modules/pmg_tk/skins/normal/__init__.py.orig
-+++ modules/pmg_tk/skins/normal/__init__.py
-@@ -236,7 +236,7 @@
</del><ins>+Index: modules/pmg_tk/PMGApp.py
+===================================================================
+--- modules/pmg_tk/PMGApp.py (revision 4106)
++++ modules/pmg_tk/PMGApp.py (working copy)
+@@ -210,7 +210,7 @@ class PMGApp(Pmw.MegaWidget):
+ self.fifo.put(cmmd)
+
+ def my_show(self,win,center=1):
+- if sys.platform!='linux2':
++ if (sys.platform!='linux2') and (sys.platform!='darwin'):
+ win.show()
+ else: # autocenter, deiconify, and run mainloop
+ # this is a workaround for a bug in the
+@@ -228,7 +228,7 @@ class PMGApp(Pmw.MegaWidget):
+ win.deiconify()
+
+ def my_withdraw(self,win):
+- if sys.platform!='linux2':
++ if (sys.platform!='linux2') or (sys.platform!='darwin'):
+ win.withdraw()
+ else:
+ win.destroy()
+Index: modules/pmg_tk/skins/normal/__init__.py
+===================================================================
+--- modules/pmg_tk/skins/normal/__init__.py (revision 4106)
++++ modules/pmg_tk/skins/normal/__init__.py (working copy)
+@@ -271,7 +271,7 @@ class Normal(PMGSkin):
</ins><span class="cx"> self.buttonArea.destroy()
</span><span class="cx">
</span><span class="cx"> def my_show(self,win,center=1):
</span><span class="lines">@@ -9,7 +33,7 @@
</span><span class="cx"> win.show()
</span><span class="cx"> else: # autocenter, deiconify, and run mainloop
</span><span class="cx"> # this is a workaround for a bug in the
</span><del>-@@ -255,13 +255,13 @@
</del><ins>+@@ -290,13 +290,13 @@ class Normal(PMGSkin):
</ins><span class="cx"> # win.show()
</span><span class="cx">
</span><span class="cx"> def my_withdraw(self,win):
</span><span class="lines">@@ -25,7 +49,7 @@
</span><span class="cx"> win.activate()
</span><span class="cx"> else: # autocenter, deiconify, and run mainloop
</span><span class="cx"> # this is a workaround for a bug in the
</span><del>-@@ -282,7 +282,7 @@
</del><ins>+@@ -317,7 +317,7 @@ class Normal(PMGSkin):
</ins><span class="cx"> win.mainloop()
</span><span class="cx">
</span><span class="cx"> def my_deactivate(self,win):
</span><span class="lines">@@ -34,23 +58,3 @@
</span><span class="cx"> win.deactivate()
</span><span class="cx"> else: # autocenter, deiconify, and run mainloop
</span><span class="cx"> win.destroy()
</span><del>---- modules/pmg_tk/PMGApp.py.orig
-+++ modules/pmg_tk/PMGApp.py
-@@ -184,7 +184,7 @@
- self.fifo.put(cmmd)
-
- def my_show(self,win,center=1):
-- if sys.platform!='linux2':
-+ if (sys.platform!='linux2') and (sys.platform!='darwin'):
- win.show()
- else: # autocenter, deiconify, and run mainloop
- # this is a workaround for a bug in the
-@@ -202,7 +202,7 @@
- win.deiconify()
-
- def my_withdraw(self,win):
-- if sys.platform!='linux2':
-+ if (sys.platform!='linux2') or (sys.platform!='darwin'):
- win.withdraw()
- else:
- win.destroy()
</del></span></pre></div>
<a id="trunkdportssciencepymolfilespymolclangdiff"></a>
<div class="modfile"><h4>Modified: trunk/dports/science/pymol/files/pymol-clang.diff (129474 => 129475)</h4>
<pre class="diff"><span>
<span class="info">--- trunk/dports/science/pymol/files/pymol-clang.diff 2014-12-13 20:40:58 UTC (rev 129474)
+++ trunk/dports/science/pymol/files/pymol-clang.diff 2014-12-13 22:12:42 UTC (rev 129475)
</span><span class="lines">@@ -1,815 +1,113 @@
</span><del>-Index: layer0/ShaderMgr.c
</del><ins>+Index: layer0/ShaderMgr.cpp
</ins><span class="cx"> ===================================================================
</span><del>---- layer0/ShaderMgr.c (revision 4074)
-+++ layer0/ShaderMgr.c (working copy)
-@@ -151,7 +151,7 @@
- while (replaceStrings[i]){
- slen = strlen(replaceStrings[i]);
- rlen = strlen(replaceStrings[i+1]);
-- while(rstr=strstr(dest_line, replaceStrings[i])){
-+ while((rstr=strstr(dest_line, replaceStrings[i]))){
- strcpy(tmp_line, rstr + slen);
- strcpy(rstr, replaceStrings[i+1]);
- strcpy(rstr+rlen, tmp_line);
-@@ -499,15 +499,15 @@
- if (I){
- GLenum err ;
- glBindAttribLocation(I->id, VERTEX_POS, "a_Vertex");
-- if (err = glGetError()){
-+ if ((err = glGetError())){
- PRINTFB(G, FB_ShaderMgr, FB_Warnings) "GLERROR: a_Vertex: %d\n", err ENDFB(G);
- }
- glBindAttribLocation(I->id, VERTEX_NORMAL, "a_Normal");
-- if (err = glGetError()){
-+ if ((err = glGetError())){
- PRINTFB(G, FB_ShaderMgr, FB_Warnings) "GLERROR: a_Normal: %d\n", err ENDFB(G);
- }
- glBindAttribLocation(I->id, VERTEX_COLOR, "a_Color");
-- if (err = glGetError()){
-+ if ((err = glGetError())){
- PRINTFB(G, FB_ShaderMgr, FB_Warnings) "GLERROR: a_Color: %d\n", err ENDFB(G);
- }
- CShaderPrg_Link(I);
-@@ -538,19 +538,19 @@
- if (I){
- GLenum err ;
- glBindAttribLocation(I->id, CYLINDER_ORIGIN, "attr_origin");
-- if (err = glGetError()){
-+ if ((err = glGetError())){
- PRINTFB(G, FB_ShaderMgr, FB_Warnings) "GLERROR: attr_origin: %d\n", err ENDFB(G);
- }
- glBindAttribLocation(I->id, CYLINDER_AXIS, "attr_axis");
-- if (err = glGetError()){
-+ if ((err = glGetError())){
- PRINTFB(G, FB_ShaderMgr, FB_Warnings) "GLERROR: attr_axis: %d\n", err ENDFB(G);
- }
- glBindAttribLocation(I->id, CYLINDER_COLOR, "attr_color");
-- if (err = glGetError()){
-+ if ((err = glGetError())){
- PRINTFB(G, FB_ShaderMgr, FB_Warnings) "GLERROR: attr_color: %d\n", err ENDFB(G);
- }
- glBindAttribLocation(I->id, CYLINDER_COLOR2, "attr_color2");
-- if (err = glGetError()){
-+ if ((err = glGetError())){
- PRINTFB(G, FB_ShaderMgr, FB_Warnings) "GLERROR: attr_color2: %d\n", err ENDFB(G);
- }
- CShaderPrg_Link(I);
-@@ -873,11 +873,11 @@
- if (indicatorShader){
- GLenum err ;
- glBindAttribLocation(indicatorShader->id, VERTEX_POS, "a_Vertex");
-- if (err = glGetError()){
-+ if ((err = glGetError())){
- PRINTFB(G, FB_ShaderMgr, FB_Warnings) "GLERROR: a_Vertex: %d\n", err ENDFB(G);
- }
- glBindAttribLocation(indicatorShader->id, VERTEX_COLOR, "a_Color");
-- if (err = glGetError()){
-+ if ((err = glGetError())){
- PRINTFB(G, FB_ShaderMgr, FB_Warnings) "GLERROR: a_Color: %d\n", err ENDFB(G);
- }
- CShaderPrg_Link(indicatorShader);
-Index: layer0/Map.c
-===================================================================
---- layer0/Map.c (revision 4074)
-+++ layer0/Map.c (working copy)
-@@ -588,7 +588,7 @@
- register int *link = I->Link;
- register int st, flag;
- register int *i_ptr3, *i_ptr4, *i_ptr5;
-- register int *e_list;
-+ register int *e_list = NULL;
- #ifdef _MemoryCache_ON
- register int block_offset = I->block_base + cCache_map_elist_offset;
- register int group_id = I->group_id;
-Index: layer1/Basis.c
-===================================================================
---- layer1/Basis.c (revision 4074)
-+++ layer1/Basis.c (working copy)
-@@ -2868,11 +2868,11 @@
- float ll;
- CPrimitive *prm;
- register int i;
-- register int *tempRef;
-- int n, h, q, x, y, z, j, k, l, e;
-+ register int *tempRef = NULL;
-+ int n = 0, h, q, x, y, z, j, k, l, e;
- int extra_vert = 0;
- float p[3], dd[3], *d1, *d2, vd[3], cx[3], cy[3];
-- float *tempVertex;
-+ float *tempVertex = NULL;
- float xs, ys;
- int remapMode = true; /* remap mode means that some objects will span more
- * than one voxel, so we have to worry about populating
-Index: layer1/CGO.c
-===================================================================
---- layer1/CGO.c (revision 4074)
-+++ layer1/CGO.c (working copy)
-@@ -47,7 +47,7 @@
- #define CLIP_NORMAL_VALUE(cv) ((cv>1.f) ? 127 : (cv < -1.f) ? -128 : pymol_roundf(((cv + 1.f)/2.f) * 255) - 128 )
</del><ins>+--- layer0/ShaderMgr.cpp (revision 4107)
++++ layer0/ShaderMgr.cpp (working copy)
+@@ -665,7 +665,7 @@ void CShaderPrg_Update_Shaders_For_Backg
+ }
</ins><span class="cx">
</span><del>- #define CHECK_GL_ERROR_OK(printstr) \
-- if (err = glGetError()){ \
-+ if ((err = glGetError())){ \
- PRINTFB(I->G, FB_CGO, FB_Errors) printstr, err ENDFB(I->G); \
- }
-
-@@ -2310,7 +2310,7 @@
- *num_total_vertices = 0;
- *num_total_indexes = 0;
-
-- while(op = (CGO_MASK & CGO_read_int(pc))) {
-+ while((op = (CGO_MASK & CGO_read_int(pc)))) {
- save_pc = pc;
- err = 0;
- switch (op) {
-@@ -4368,7 +4368,7 @@
- GL_C_INT_TYPE *indexVals = 0;
- int tot = 4 * 4 * 3 * num_total_cylinders;
- short copyToLeftOver, copyColorToLeftOver, copyPickColorToLeftOver, copyAlphaToLeftOver, copyToReturnCGO ;
-- float *org_originVals;
-+ float *org_originVals= NULL;
- float *org_axisVals;
- float *org_colorVals;
- float *org_color2Vals = NULL;
-@@ -7135,7 +7135,7 @@
- int texture_id = CGO_get_int(*pc);
- float worldPos[4], screenMin[3], screenMax[3], textExtent[4];
- CShaderPrg * shaderPrg;
-- int buf1, buf2, attr_worldpos, attr_screenoffset, attr_texcoords;
-+ int buf1 = 0, buf2 = 0, attr_worldpos, attr_screenoffset, attr_texcoords;
- copy3f(*pc, worldPos); worldPos[3] = 1.f;
- copy3f(*pc+3, screenMin);
- copy3f(*pc+6, screenMax);
-@@ -7176,7 +7176,7 @@
- int texture_id = CGO_get_int(*pc);
- float worldPos[4], screenMin[3], screenMax[3], textExtent[4];
- CShaderPrg * shaderPrg;
-- int buf1, buf2, attr_worldpos, attr_screenoffset, attr_texcoords;
-+ int buf1 = 0, buf2 = 0, attr_worldpos, attr_screenoffset, attr_texcoords;
- copy3f(*pc, worldPos); worldPos[3] = 1.f;
- copy3f(*pc+3, screenMin);
- copy3f(*pc+6, screenMax);
-@@ -9564,7 +9564,7 @@
- int CGOChangeShadersTo(CGO *I, int frommode, int tomode){
- register float *pc = I->op;
- int op = 0, totops = 0;
-- while(op = (CGO_MASK & CGO_read_int(pc))) {
-+ while((op = (CGO_MASK & CGO_read_int(pc)))) {
- totops++;
- switch (op) {
- case CGO_ENABLE:
-Index: layer1/Ortho.c
</del><ins>+ int CShaderPrg_Reload(PyMOLGlobals * G, char *name, char *v, char *f){
+- int status, howLong, needAttach = 0;
++ int status, howLong;
+ CShaderPrg * I = CShaderMgr_GetShaderPrg_NoSet(G->ShaderMgr, name);
+ if (!I){
+ CShaderMgr *SM = G->ShaderMgr;
+Index: layer0/Sphere.cpp
</ins><span class="cx"> ===================================================================
</span><del>---- layer1/Ortho.c (revision 4074)
-+++ layer1/Ortho.c (working copy)
-@@ -1020,7 +1020,7 @@
- curLine = I->CurLine & OrthoSaveLines;
- if(I->PromptChar) {
- strcpy(buffer, I->Line[curLine]);
-- if(PComplete(G, buffer + I->PromptChar, sizeof(OrthoLineType) - I->PromptChar)); /* just print, don't complete */
-+ PComplete(G, buffer + I->PromptChar, sizeof(OrthoLineType) - I->PromptChar); /* just print, don't complete */
- }
- }
- break;
-@@ -1400,7 +1400,7 @@
</del><ins>+--- layer0/Sphere.cpp (revision 4107)
++++ layer0/Sphere.cpp (working copy)
+@@ -32,6 +32,9 @@ Z* -------------------------------------
+ #define tau 0.8506508084F /* t=(1+sqrt(5))/2, tau=t/sqrt(1+t^2) */
+ #define one 0.5257311121F /* one=1/sqrt(1+t^2) , unit sphere */
</ins><span class="cx">
</span><del>- {
- if (!I->bgCGO) {
-- CGO *cgo = CGONew(G), *cgo2;
-+ CGO *cgo = CGONew(G), *cgo2 = NULL;
- ok &= CGOBegin(cgo, GL_TRIANGLE_STRIP);
- if (ok)
- ok &= CGOVertex(cgo, -1.f, -1.f, 0.98f);
-Index: layer1/P.c
-===================================================================
---- layer1/P.c (revision 4074)
-+++ layer1/P.c (working copy)
-@@ -1464,7 +1464,7 @@
- void PUnlockAPIAsGlut(PyMOLGlobals * G)
- { /* must call with unblocked interpreter */
- PRINTFD(G, FB_Threads)
-- " PUnlockAPIAsGlut-DEBUG: entered as thread 0x%x\n", PyThread_get_thread_ident()
-+ " PUnlockAPIAsGlut-DEBUG: entered as thread 0x%lx\n", PyThread_get_thread_ident()
- ENDFD;
- PBlock(G);
- PXDecRef(PyObject_CallFunction(G->P_inst->unlock, "iO", 0, G->P_inst->cmd)); /* NOTE this may flush the command buffer! */
-@@ -1478,7 +1478,7 @@
- void PUnlockAPIAsGlutNoFlush(PyMOLGlobals * G)
- { /* must call with unblocked interpreter */
- PRINTFD(G, FB_Threads)
-- " PUnlockAPIAsGlut-DEBUG: entered as thread 0x%x\n", PyThread_get_thread_ident()
-+ " PUnlockAPIAsGlut-DEBUG: entered as thread 0x%lx\n", PyThread_get_thread_ident()
- ENDFD;
- PBlock(G);
- PXDecRef(PyObject_CallFunction(G->P_inst->unlock, "iO", -1, G->P_inst->cmd)); /* prevents flushing of the buffer */
-@@ -1529,7 +1529,7 @@
- int PLockAPIAsGlut(PyMOLGlobals * G, int block_if_busy)
- {
- PRINTFD(G, FB_Threads)
-- "*PLockAPIAsGlut-DEBUG: entered as thread 0x%x\n", PyThread_get_thread_ident()
-+ "*PLockAPIAsGlut-DEBUG: entered as thread 0x%lx\n", PyThread_get_thread_ident()
- ENDFD;
</del><ins>++#define FAST_SPHERE_INIT
++
++#ifndef FAST_SPHERE_INIT
+ static const float start_points[13][3] = {
+ {tau, one, 0},
+ {-tau, one, 0},
+@@ -69,6 +72,7 @@ static const int icosahedron[21][3] = {
+ {7, 2, 9},
+ {6, 10, 2}
+ };
++#endif
</ins><span class="cx">
</span><del>- PBlock(G);
-@@ -1541,7 +1541,7 @@
- PUnlockStatus(G);
</del><ins>+ static const int mesh[30][2] = {
+ {0, 3},
+@@ -103,8 +107,6 @@ static const int mesh[30][2] = {
+ {9, 10}
+ };
</ins><span class="cx">
</span><del>- PRINTFD(G, FB_Threads)
-- "#PLockAPIAsGlut-DEBUG: acquiring lock as thread 0x%x\n", PyThread_get_thread_ident()
-+ "#PLockAPIAsGlut-DEBUG: acquiring lock as thread 0x%lx\n", PyThread_get_thread_ident()
- ENDFD;
</del><ins>+-#define FAST_SPHERE_INIT
+-
+ #ifdef FAST_SPHERE_INIT
+ #include"SphereData.h"
</ins><span class="cx">
</span><del>- if(!get_api_lock(G, block_if_busy)) {
-@@ -1559,7 +1559,7 @@
- holding the API lock, therefore it is safe even through increment
- isn't atomic. */
- PRINTFD(G, FB_Threads)
-- "-PLockAPIAsGlut-DEBUG: glut_thread_keep_out 0x%x\n", PyThread_get_thread_ident()
-+ "-PLockAPIAsGlut-DEBUG: glut_thread_keep_out 0x%lx\n", PyThread_get_thread_ident()
- ENDFD;
-
- PXDecRef(PyObject_CallFunction(G->P_inst->unlock, "iO", -1, G->P_inst->cmd)); /* prevent buffer flushing */
-@@ -2632,7 +2632,7 @@
- /* don't run if we're currently banned */
- char *buffer = 0;
- int size, curSize = 0;
-- while(size = OrthoCommandOutSize(G)){
-+ while((size = OrthoCommandOutSize(G))){
- if (!curSize){
- buffer = VLACalloc(char, size);
- curSize = size;
-@@ -2676,7 +2676,7 @@
- int did_work = false;
- char *buffer = 0;
- int size, curSize = 0;
-- while(size = OrthoCommandOutSize(G)){
-+ while((size = OrthoCommandOutSize(G))){
- if (!curSize){
- buffer = VLACalloc(char, size);
- curSize = size;
-@@ -2688,7 +2688,7 @@
- OrthoCommandNest(G, 1);
- did_work = true;
- PRINTFD(G, FB_Threads)
-- " PFlushFast-DEBUG: executing '%s' as thread 0x%x\n", buffer,
-+ " PFlushFast-DEBUG: executing '%s' as thread 0x%lx\n", buffer,
- PyThread_get_thread_ident()
- ENDFD;
- if(PyErr_Occurred()) {
-@@ -2784,7 +2784,7 @@
- PXDecRef(PyObject_CallFunction(G->P_inst->unlock_c, "O", G->P_inst->cmd));
-
- PRINTFD(G, FB_Threads)
-- " PAutoBlock-DEBUG: blocked 0x%x (0x%x, 0x%x, 0x%x)\n",
-+ " PAutoBlock-DEBUG: blocked 0x%lx (0x%x, 0x%x, 0x%x)\n",
- PyThread_get_thread_ident(), SavedThread[MAX_SAVED_THREAD - 1].id,
- SavedThread[MAX_SAVED_THREAD - 2].id, SavedThread[MAX_SAVED_THREAD - 3].id ENDFD;
-
-@@ -2793,7 +2793,7 @@
- a--;
- }
- PRINTFD(G, FB_Threads)
-- " PAutoBlock-DEBUG: 0x%x not found, thus already blocked.\n",
-+ " PAutoBlock-DEBUG: 0x%lx not found, thus already blocked.\n",
- PyThread_get_thread_ident()
- ENDFD;
- return 0;
-@@ -2814,7 +2814,7 @@
- SavedThreadRec *SavedThread = G->P_inst->savedThread;
- /* NOTE: ASSUMES a locked API */
- PRINTFD(G, FB_Threads)
-- " PUnblock-DEBUG: entered as thread 0x%x\n", PyThread_get_thread_ident()
-+ " PUnblock-DEBUG: entered as thread 0x%lx\n", PyThread_get_thread_ident()
- ENDFD;
-
- /* reserve a space while we have a lock */
-Index: layer1/Extrude.c
</del><ins>+Index: layer2/RepNonbonded.cpp
</ins><span class="cx"> ===================================================================
</span><del>---- layer1/Extrude.c (revision 4074)
-+++ layer1/Extrude.c (working copy)
-@@ -687,7 +687,7 @@
- float *v;
- float *n;
- float *c;
-- float *sv, *sn, *tv, *tn, *tv1, *tn1, *TV, *TN;
-+ float *sv, *sn, *tv, *tn, *tv1, *tn1, *TV, *TN = NULL;
- float v0[3];
- int start, stop;
</del><ins>+--- layer2/RepNonbonded.cpp (revision 4107)
++++ layer2/RepNonbonded.cpp (working copy)
+@@ -199,7 +199,7 @@ static void RepNonbondedRender(RepNonbon
</ins><span class="cx"> int ok = true;
</span><del>-@@ -1387,7 +1387,7 @@
- float *v;
- float *n;
- float *c;
-- float *sv, *sn, *tv, *tn, *tv1, *tn1, *TV, *TN;
-+ float *sv, *sn, *tv, *tn, *tv1, *tn1, *TV, *TN = NULL;
- float v0[3];
- int ok = true;
</del><ins>+ // 0.018f is found by trial and error
+ // TODO: this is not sufficient to solve the problem of disappearing cylinders
+- float scale_bound = SettingGetGlobal_f(G, cSetting_field_of_view) * cPI / 180.0f * 0.018f;
++ // float scale_bound = SettingGetGlobal_f(G, cSetting_field_of_view) * cPI / 180.0f * 0.018f;
</ins><span class="cx">
</span><del>-@@ -1705,7 +1705,7 @@
- float *v;
- float *n;
- float *c;
-- float *sv, *sn, *tv, *tn, *tv1, *tn1, *TV, *TN;
-+ float *sv, *sn, *tv, *tn, *tv1, *tn1, *TV, *TN = NULL;
- float v0[3], n0[3], s0[3], z[3] = { 1.0, 0.0, 1.0 };
- int subN;
- int ok = true;
-Index: layer1/Scene.c
-===================================================================
---- layer1/Scene.c (revision 4074)
-+++ layer1/Scene.c (working copy)
-@@ -7623,7 +7623,7 @@
- /* update all gadgets first (single-threaded since they're thread-unsafe) */
- rec = NULL;
- while(ListIterate(I->Obj, rec, next)) {
-- if((rec->obj->type == cObjectGadget)) {
-+ if(rec->obj->type == cObjectGadget) {
- if(rec->obj->fUpdate)
- rec->obj->fUpdate(rec->obj);
- }
-Index: layer1/Control.c
-===================================================================
---- layer1/Control.c (revision 4074)
-+++ layer1/Control.c (working copy)
-@@ -637,7 +637,7 @@
- but_bottom = y - (cControlBoxSize - 1);
- but_height = cControlBoxSize;
</del><ins>+ alpha =
+ SettingGet_f(G, I->R.cs->Setting, I->R.obj->Setting, cSetting_nonbonded_transparency);
+@@ -208,7 +208,6 @@ static void RepNonbondedRender(RepNonbon
+ alpha = 1.0F;
+ if(ray) {
+ float radius;
+- float pixel_radius = ray->PixelRadius;
+ ray->transparentf(1.0F - alpha);
</ins><span class="cx">
</span><del>-- if((but_num == I->Active)) {
-+ if(but_num == I->Active) {
- draw_button(but_left, but_bottom,
- but_width, but_height, lightEdge, darkEdge, pushed ORTHOCGOARGVAR);
- } else if(((but_num == 6) && (SettingGetGlobal_b(G, cSetting_seq_view))) ||
-Index: layer2/RepSphere.c
</del><ins>+ if(I->Radius == 0.0F) {
+@@ -360,7 +359,6 @@ static void RepNonbondedRender(RepNonbon
+ CShaderPrg *shaderPrg;
+ if (nonbonded_as_cylinders){
+ // vertex scale is bound so that cylinders cannot disappear when it gets too low
+- float vertex_scale = info->vertex_scale;
+ float pixel_scale_value = SettingGetGlobal_f(G, cSetting_ray_pixel_scale);
+ if(pixel_scale_value < 0)
+ pixel_scale_value = 1.0F;
+@@ -596,7 +594,6 @@ static void RepNonbondedRender(RepNonbon
+ CShaderPrg *shaderPrg;
+ if (nonbonded_as_cylinders){
+ // vertex scale is bound so that cylinders cannot disappear when it gets too low
+- float vertex_scale = info->vertex_scale;
+ float pixel_scale_value = SettingGetGlobal_f(G, cSetting_ray_pixel_scale);
+ if(pixel_scale_value < 0)
+ pixel_scale_value = 1.0F;
+Index: layer2/RepWireBond.cpp
</ins><span class="cx"> ===================================================================
</span><del>---- layer2/RepSphere.c (revision 4074)
-+++ layer2/RepSphere.c (working copy)
-@@ -2204,8 +2204,8 @@
- int c = I->N;
- SphereRec *sp = I->SP;
- float alpha;
-- int n_quad_verts;
-- float radius;
-+ int n_quad_verts = 0;
-+ float radius = 0.0;
- int ok = true;
- short use_shader = SettingGetGlobal_b(G, cSetting_sphere_use_shader) &
- SettingGetGlobal_b(G, cSetting_use_shaders);
-Index: layer2/ObjectMolecule2.c
</del><ins>+--- layer2/RepWireBond.cpp (revision 4107)
++++ layer2/RepWireBond.cpp (working copy)
+@@ -779,7 +779,6 @@ static void RepWireBondRender(RepWireBon
+ CShaderPrg *shaderPrg;
+ if (line_as_cylinders){
+ // vertex scale is bound so that cylinders cannot disappear when it gets too low
+- float vertex_scale = info->vertex_scale;
+ float pixel_scale_value = SettingGetGlobal_f(G, cSetting_ray_pixel_scale);
+ if(pixel_scale_value < 0)
+ pixel_scale_value = 1.0F;
+@@ -973,7 +972,6 @@ static void RepWireBondRender(RepWireBon
+ CShaderPrg *shaderPrg;
+ if (line_as_cylinders){
+ // vertex scale is bound so that cylinders cannot disappear when it gets too low
+- float vertex_scale = info->vertex_scale;
+ float pixel_scale_value = SettingGetGlobal_f(G, cSetting_ray_pixel_scale);
+ if(pixel_scale_value < 0)
+ pixel_scale_value = 1.0F;
+Index: layer3/Executive.cpp
</ins><span class="cx"> ===================================================================
</span><del>---- layer2/ObjectMolecule2.c (revision 4074)
-+++ layer2/ObjectMolecule2.c (working copy)
-@@ -3678,7 +3678,7 @@
- #else
- int ok = true;
- ObjectMolecule *I = NULL;
-- int discrete_flag;
-+ int discrete_flag = 0;
- int ll;
- (*result) = NULL;
</del><ins>+--- layer3/Executive.cpp (revision 4107)
++++ layer3/Executive.cpp (working copy)
+@@ -13978,7 +13978,6 @@ void ExecutiveFullScreen(PyMOLGlobals *
</ins><span class="cx">
</span><del>-@@ -4305,7 +4305,7 @@
- register int a, b;
- CoordSet *cs, **dcs;
- AtomInfoType *atInfo;
-- int *dAtmToIdx;
-+ int *dAtmToIdx = NULL;
- int ok = true;
- if(!I->DiscreteFlag) { /* currently, discrete objects are never sorted */
- int n_bytes = sizeof(int) * I->NAtom;
-Index: layer2/RepDot.c
-===================================================================
---- layer2/RepDot.c (revision 4074)
-+++ layer2/RepDot.c (working copy)
-@@ -192,7 +192,7 @@
- ok &= CGOColorv(cgo, v);
- v += 3;
- }
-- /* if(normals) /* NORMALS do not get set for points
-+ /* if(normals) NORMALS do not get set for points
- CGONormalv(cgo, v);*/
- v += 3;
- if (ok)
-@@ -210,7 +210,7 @@
- I->shaderCGO = CGOOptimizeSpheresToVBONonIndexed(cgo, CGO_BOUNDING_BOX_SZ + CGO_DRAW_SPHERE_BUFFERS_SZ);
- CHECKOK(ok, I->shaderCGO);
- } else {
-- CGO *convertcgo = CGOCombineBeginEnd(cgo, 0), *tmpCGO;
-+ CGO *convertcgo = CGOCombineBeginEnd(cgo, 0), *tmpCGO = NULL;
- CHECKOK(ok, convertcgo);
- if (ok)
- tmpCGO = CGOOptimizeToVBONotIndexed(convertcgo, CGO_BOUNDING_BOX_SZ + I->N * 3 + 7);
-@@ -344,7 +344,7 @@
- float *countPtr = NULL;
- int colorCnt, lastColor;
- Vector3f v1;
-- MapType *map;
-+ MapType *map = NULL;
- SphereRec *sp = G->Sphere->Sphere[0];
- int ds;
- float max_vdw = MAX_VDW;
-Index: layer2/RepSurface.c
-===================================================================
---- layer2/RepSurface.c (revision 4074)
-+++ layer2/RepSurface.c (working copy)
-@@ -3304,7 +3304,7 @@
- if (ok)
- convertcgo->use_shader = true;
- } else if (I->Type == 2) {
-- CGO *convertcgo2, *simple;
-+ CGO *convertcgo2, *simple = NULL;
- convertcgo2 = CGOConvertLinesToShaderCylinders(I->shaderCGO, 0);
- CHECKOK(ok, convertcgo2);
- if (ok)
-@@ -4503,7 +4503,7 @@
- }
- ok &= !G->Interrupt;
- if(ok) {
-- MapType *map, *solv_map;
-+ MapType *map, *solv_map = NULL;
- map = MapNewFlagged(G, I->maxVdw + probe_rad_more,
- I->coord, VLAGetSize(I->coord) / 3, NULL, NULL);
- CHECKOK(ok, map);
-@@ -5747,7 +5747,7 @@
- SurfaceJobAtomInfo *j_atom_info = atom_info + j;
- if(j > a) /* only check if this is atom trails */
- if((!present) || present[j]) {
-- if((j_atom_info->vdw == a_atom_info->vdw)) { /* handle singularities */
-+ if(j_atom_info->vdw == a_atom_info->vdw) { /* handle singularities */
- float *v1 = coord + 3 * j;
- if((v0[0] == v1[0]) && (v0[1] == v1[1]) && (v0[2] == v1[2]))
- skip_flag = true;
-@@ -5842,7 +5842,7 @@
- SurfaceJobAtomInfo *j_atom_info = atom_info + j;
- if(j > a) /* only check if this is atom trails */
- if((!present) || present[j]) {
-- if((j_atom_info->vdw == a_atom_info->vdw)) { /* handle singularities */
-+ if(j_atom_info->vdw == a_atom_info->vdw) { /* handle singularities */
- float *v2 = coord + 3 * j;
- if((v0[0] == v2[0]) && (v0[1] == v2[1]) && (v0[2] == v2[2]))
- skip_flag = true;
-@@ -6002,7 +6002,7 @@
- SurfaceJobAtomInfo *j_atom_info = atom_info + j;
- if(j > a) /* only check if this is atom trails */
- if((!present) || present[j]) {
-- if((j_atom_info->vdw == a_atom_info->vdw)) { /* handle singularities */
-+ if(j_atom_info->vdw == a_atom_info->vdw) { /* handle singularities */
- float *v1 = coord + 3 * j;
- if((v0[0] == v1[0]) && (v0[1] == v1[1]) && (v0[2] == v1[2]))
- skip_flag = true;
-Index: layer2/RepCartoon.c
-===================================================================
---- layer2/RepCartoon.c (revision 4074)
-+++ layer2/RepCartoon.c (working copy)
-@@ -2615,7 +2615,7 @@
-
- #ifdef _PYMOL_CGO_DRAWARRAYS
- int nverts = nAt * 4, pl = 0;
-- float *vertexVals, *tmp_ptr;
-+ float *vertexVals = NULL, *tmp_ptr;
- if (ok)
- vertexVals = CGODrawArrays(cgo, GL_LINES, CGO_VERTEX_ARRAY, nverts);
- CHECKOK(ok, vertexVals);
-Index: layer2/ObjectMolecule.c
-===================================================================
---- layer2/ObjectMolecule.c (revision 4074)
-+++ layer2/ObjectMolecule.c (working copy)
-@@ -1448,7 +1448,7 @@
- int NPHIH, MPHIA, NHPARM, NPARM, NNB, NRES;
- int NBONA, NTHETA, NPHIA, NUMBND, NUMANG, NPTRA;
- int NATYP, NPHB, IFPERT, NBPER, NGPER, NDPER;
-- int MBPER, MGPER, MDPER, IFBOX, NMXRS, IFCAP;
-+ int MBPER, MGPER, MDPER, IFBOX = 0, NMXRS, IFCAP;
- int NEXTRA, IPOL = 0;
- int wid, col;
- float BETA;
-@@ -2076,7 +2076,7 @@
-
- if(IFBOX > 0) {
-
-- int IPTRES, NSPM, NSPSOL;
-+ int IPTRES, NSPM = 0, NSPSOL;
-
- if(amber7) {
- p = findflag(G, buffer, "SOLVENT_POINTERS", "3I8");
-@@ -4431,7 +4431,7 @@
- AtomInfoType *ai;
- int n, nn;
- float v[3], v0[3], d;
-- CoordSet *cs;
-+ CoordSet *cs = NULL;
- int ok = true;
-
- ok &= ObjectMoleculeUpdateNeighbors(I);
-@@ -9767,7 +9767,7 @@
- CoordSet * cs, int bondSearchFlag, int aic_mask, int invalidate)
- {
- PyMOLGlobals *G = I->Obj.G;
-- int *index, *outdex, *a2i, *i2a;
-+ int *index, *outdex, *a2i, *i2a = NULL;
- BondType *bond = NULL;
- register int a, b, lb = 0, ac;
- int c, nb, a1, a2;
-@@ -10551,7 +10551,7 @@
- rms = MatrixFitRMSTTTf(G, op->nvv1, op->vv1, vt, NULL, op->ttt);
- else
- rms = MatrixGetRMS(G, op->nvv1, op->vv1, vt, NULL);
-- if((op->i1 == 2)) {
-+ if(op->i1 == 2) {
- ObjectMoleculeTransformTTTf(I, op->ttt, b);
-
- if(op->i3) {
-Index: layer3/Selector.c
-===================================================================
---- layer3/Selector.c (revision 4074)
-+++ layer3/Selector.c (working copy)
-@@ -8658,11 +8658,11 @@
- for(a = cNDummyAtoms; a < I->NAtom; a++) {
- b = i_obj[i_table[a].model]->AtomInfo[i_table[a].atom].protons;
- base[0].sele[a] = (
-- b > 2 && b < 5 ||
-- b > 10 && b < 14 ||
-- b > 18 && b < 32 ||
-- b > 36 && b < 51 ||
-- b > 54 && b < 85 ||
-+ (b > 2 && b < 5) ||
-+ (b > 10 && b < 14) ||
-+ (b > 18 && b < 32) ||
-+ (b > 36 && b < 51) ||
-+ (b > 54 && b < 85) ||
- b > 86);
- }
- break;
-Index: layer3/Executive.c
-===================================================================
---- layer3/Executive.c (revision 4074)
-+++ layer3/Executive.c (working copy)
-@@ -15928,7 +15928,7 @@
- ExecutiveSpecSetVisibility(G, rec, true, mod, false);
- I->LastChanged = rec;
- }
-- if((mod == (cOrthoSHIFT | cOrthoCTRL))) {
-+ if(mod == (cOrthoSHIFT | cOrthoCTRL)) {
- if(rec != I->LastZoomed)
- ExecutiveWindowZoom(G, rec->name, 0.0F, -1, false, -1.0F,
- true);
-Index: layer3/PlugIOManager.c
-===================================================================
---- layer3/PlugIOManager.c (revision 4074)
-+++ layer3/PlugIOManager.c (working copy)
-@@ -229,7 +229,7 @@
- ENDFB(G);
- }
-
-- if(stop > 0 && cnt >= stop || max > 0 && ncnt >= max) {
-+ if((stop > 0 && cnt >= stop) || (max > 0 && ncnt >= max)) {
- cs = NULL;
- break;
- }
-Index: layer4/Cmd.c
-===================================================================
---- layer4/Cmd.c (revision 4074)
-+++ layer4/Cmd.c (working copy)
-@@ -128,7 +128,7 @@
- static void APIEnter(PyMOLGlobals * G)
- { /* assumes API is locked */
- PRINTFD(G, FB_API)
-- " APIEnter-DEBUG: as thread 0x%x.\n", PyThread_get_thread_ident()
-+ " APIEnter-DEBUG: as thread 0x%lx.\n", PyThread_get_thread_ident()
- ENDFD;
-
- if(G->Terminating) { /* try to bail */
-@@ -163,7 +163,7 @@
- { /* assumes API is locked */
-
- PRINTFD(G, FB_API)
-- " APIEnterBlocked-DEBUG: as thread 0x%x.\n", PyThread_get_thread_ident()
-+ " APIEnterBlocked-DEBUG: as thread 0x%lx.\n", PyThread_get_thread_ident()
- ENDFD;
-
- if(G->Terminating) { /* try to bail */
-@@ -199,7 +199,7 @@
- if(!PIsGlutThread())
- G->P_inst->glut_thread_keep_out--;
- PRINTFD(G, FB_API)
-- " APIExit-DEBUG: as thread 0x%x.\n", PyThread_get_thread_ident()
-+ " APIExit-DEBUG: as thread 0x%lx.\n", PyThread_get_thread_ident()
- ENDFD;
- }
-
-@@ -209,7 +209,7 @@
- if(!PIsGlutThread())
- G->P_inst->glut_thread_keep_out--;
- PRINTFD(G, FB_API)
-- " APIExitBlocked-DEBUG: as thread 0x%x.\n", PyThread_get_thread_ident()
-+ " APIExitBlocked-DEBUG: as thread 0x%lx.\n", PyThread_get_thread_ident()
- ENDFD;
- }
-
-@@ -1853,7 +1853,7 @@
- static PyObject *CmdGetRenderer(PyObject * self, PyObject * args)
- {
- PyMOLGlobals *G = NULL;
-- char *vendor, *renderer, *version;
-+ char *vendor = NULL, *renderer = NULL, *version = NULL;
- int ok = false;
- ok = PyArg_ParseTuple(args, "O", &self);
- if(ok) {
-Index: contrib/uiuc/plugins/molfile_plugin/src/pbeqplugin.cpp
-===================================================================
---- contrib/uiuc/plugins/molfile_plugin/src/pbeqplugin.cpp (revision 4074)
-+++ contrib/uiuc/plugins/molfile_plugin/src/pbeqplugin.cpp (working copy)
-@@ -259,7 +259,7 @@
- int addr = z*nclx*ncly + y*nclx + x;
- if (fread(datablock + addr, 4, 1, fd) != 1) {
- printf("pbeqplugin) Error reading potential map cell: %d,%d,%d\n", x, y, z);
-- printf("pbeqplugin) offset: %d\n", ftell(fd));
-+ printf("pbeqplugin) offset: %ld\n", ftell(fd));
- return MOLFILE_ERROR;
- }
- count++;
-Index: contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp
-===================================================================
---- contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp (revision 4074)
-+++ contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp (working copy)
-@@ -484,7 +484,7 @@
- /* constant frame size */
- if (keys[i].size() != m_framesize) {
- fprintf(stderr, "non-constant framesize at frame %ld\n", i);
-- printf("size %d framesize %d\n\n",
-+ printf("size %lld framesize %lld\n\n",
- keys[i].size(), m_framesize);
- return true;
- }
-@@ -1298,7 +1298,7 @@
- }
- Blob pos=blobs["POSITION"];
- if (pos.count != 3*natoms) {
-- fprintf(stderr, "ERROR, Expected %d elements in POSITION; got %ld\n",
-+ fprintf(stderr, "ERROR, Expected %d elements in POSITION; got %lld\n",
- 3*natoms, pos.count);
- return MOLFILE_ERROR;
- }
-@@ -1307,7 +1307,7 @@
- if (with_velocity && ts->velocities && blobs.find("VELOCITY")!=blobs.end()) {
- Blob vel=blobs["VELOCITY"];
- if (vel.count != 3*natoms) {
-- fprintf(stderr, "ERROR, Expected %d elements in VELOCITY; got %ld\n",
-+ fprintf(stderr, "ERROR, Expected %d elements in VELOCITY; got %lld\n",
- 3*natoms, vel.count);
- return MOLFILE_ERROR;
- }
-@@ -1569,7 +1569,7 @@
- // if required, get velocities
- if (ts->velocities && velblob.count > 0) {
- if (velblob.count != 3*natoms) {
-- fprintf(stderr, "VELOCITY field has %ld values; expected %d\n",
-+ fprintf(stderr, "VELOCITY field has %lld values; expected %d\n",
- velblob.count, 3*natoms);
- return MOLFILE_ERROR;
- }
-Index: contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c
-===================================================================
---- contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c (revision 4074)
-+++ contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c (working copy)
-@@ -99,7 +99,7 @@
- const char *filetype,
- int *natoms) {
- FILE *fd;
-- qmdata_t *data;
-+ qmdata_t *data = NULL;
- moldendata_t *moldendata;
- char buffer[1024];
- char keystring[20];
-Index: contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c
-===================================================================
---- contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c (revision 4074)
-+++ contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c (working copy)
-@@ -231,7 +231,7 @@
- switch (tolower(keyword[0])) {
- case 'n': {
- /* name */
-- if (sscanf(s, "%16s %n", &atom.name, &n) < 1) {
-+ if (sscanf(s, "%16s %n", (char *) &atom.name, &n) < 1) {
- vtf_error("could not get name in atom record", line);
- return MOLFILE_ERROR;
- }
-@@ -240,7 +240,7 @@
- }
- case 't': {
- /* type */
-- if (sscanf(s, "%16s %n", &atom.type, &n) < 1) {
-+ if (sscanf(s, "%16s %n", (char *) &atom.type, &n) < 1) {
- vtf_error("could not get type in atom record", line);
- return MOLFILE_ERROR;
- }
-@@ -266,7 +266,7 @@
- } else if (strcmp(keyword, "res") == 0 ||
- strcmp(keyword, "resname") == 0) {
- /* resname */
-- if (sscanf(s, "%8s %n", &atom.resname, &n) < 1) {
-+ if (sscanf(s, "%8s %n", (char *) &atom.resname, &n) < 1) {
- vtf_error("could not get resname in atom record", line);
- return MOLFILE_ERROR;
- }
-@@ -281,7 +281,7 @@
- }
- case 's': {
- /* segid */
-- if (sscanf(s, "%8s %n", &atom.segid, &n) < 1) {
-+ if (sscanf(s, "%8s %n", (char *) &atom.segid, &n) < 1) {
- vtf_error("could not get segid in atom record", line);
- return MOLFILE_ERROR;
- }
-@@ -290,7 +290,7 @@
- }
- case 'i': {
- /* insertion */
-- if (sscanf(s, "%2s %n", &atom.insertion, &n) < 1) {
-+ if (sscanf(s, "%2s %n", (char *) &atom.insertion, &n) < 1) {
- vtf_error("could not get insertion in atom record", line);
- return MOLFILE_ERROR;
- }
-@@ -302,7 +302,7 @@
- /* chain, charge */
- if (strlen(keyword) == 1 ||
- strcmp(keyword, "chain") == 0) {
-- if (sscanf(s, "%2s %n", &atom.chain, &n) < 1) {
-+ if (sscanf(s, "%2s %n", (char *) &atom.chain, &n) < 1) {
- vtf_error("could not get chain in atom record", line);
- return MOLFILE_ERROR;
- }
-@@ -336,7 +336,7 @@
- }
- d->optflags |= MOLFILE_ATOMICNUMBER;
- } else if (strcmp(keyword, "altloc")) {
-- if (sscanf(s, "%2s %n", &atom.altloc, &n) < 1) {
-+ if (sscanf(s, "%2s %n", (char *) &atom.altloc, &n) < 1) {
- vtf_error("could not get altloc in atom record", line);
- return MOLFILE_ERROR;
- }
-Index: contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c
-===================================================================
---- contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c (revision 4074)
-+++ contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c (working copy)
-@@ -375,7 +375,7 @@
- const char *filetype, int *natoms) {
-
- FILE *fd;
-- qmdata_t *data;
-+ qmdata_t *data = NULL;
- gmsdata *gms;
-
- /* open the input file */
-Index: contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp
-===================================================================
---- contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp (revision 4074)
-+++ contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp (working copy)
-@@ -1983,7 +1983,7 @@
- }
- }
- catch (std::exception &e) {
-- fprintf(stderr, e.what());
-+ fprintf(stderr, "%s", e.what());
- return MOLFILE_ERROR;
- }
- return MOLFILE_SUCCESS;
-Index: contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp
-===================================================================
---- contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp (revision 4074)
-+++ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp (working copy)
-@@ -104,7 +104,7 @@
-
- ///ojo aqui le quite el !
- if ((grassp->flag)!=POTENTIALS) {
-- if (index >=0 && index <= 4)
-+ if (index <= 4)
- printf("graspplugin) No data available for '%s' option\n", name[index]);
- else
- printf("graspplugin) out of range property, flag: %d index: %d\n", grassp->flag, index);
-Index: modules/cealign/src/tnt/tnt_fortran_array1d.h
-===================================================================
---- modules/cealign/src/tnt/tnt_fortran_array1d.h (revision 4074)
-+++ modules/cealign/src/tnt/tnt_fortran_array1d.h (working copy)
-@@ -221,7 +221,7 @@
- #ifdef TNT_DEBUG
- std::cout << "entered subarray. \n";
- #endif
-- if ((i0 > 0) && (i1 < n_) || (i0 <= i1))
-+ if (((i0 > 0) && (i1 < n_)) || (i0 <= i1))
- {
- Fortran_Array1D<T> X(*this); /* create a new instance of this array. */
- X.n_ = i1-i0+1;
-Index: modules/cealign/src/tnt/tnt_array1d.h
-===================================================================
---- modules/cealign/src/tnt/tnt_array1d.h (revision 4074)
-+++ modules/cealign/src/tnt/tnt_array1d.h (working copy)
-@@ -258,7 +258,7 @@
- template <class T>
- inline Array1D<T> Array1D<T>::subarray(int i0, int i1)
- {
-- if ((i0 >= 0) && (i1 < n_) || (i0 <= i1))
-+ if (((i0 >= 0) && (i1 < n_)) || (i0 <= i1))
- {
- Array1D<T> X(*this); /* create a new instance of this array. */
- X.n_ = i1-i0+1;
</del><ins>+ #ifndef _PYMOL_NO_GLUT
+ if(G->HaveGUI && G->ValidContext) {
+- CExecutive *I = G->Executive;
+ if (flag) {
+ #ifndef GLUT_FULL_SCREEN
+ if(wm_flag < 1) {
</ins></span></pre></div>
<a id="trunkdportssciencepymolfilespymoluseglkitdiff"></a>
<div class="addfile"><h4>Added: trunk/dports/science/pymol/files/pymol-use-glkit.diff (0 => 129475)</h4>
<pre class="diff"><span>
<span class="info">--- trunk/dports/science/pymol/files/pymol-use-glkit.diff (rev 0)
+++ trunk/dports/science/pymol/files/pymol-use-glkit.diff 2014-12-13 22:12:42 UTC (rev 129475)
</span><span class="lines">@@ -0,0 +1,39 @@
</span><ins>+Index: layer1/Scene.cpp
+===================================================================
+--- layer1/Scene.cpp (revision 4106)
++++ layer1/Scene.cpp (working copy)
+@@ -57,6 +57,8 @@ Z* -------------------------------------
+ #include"ScrollBar.h"
+ #include "ShaderMgr.h"
+
++#include <GLKit/GLKMatrix4.h>
++
+ #ifdef _PYMOL_IP_EXTRAS
+ #include "IncentiveCopyToClipboard.h"
+ #endif
+@@ -9156,7 +9158,8 @@ void SceneRender(PyMOLGlobals * G, Picki
+ }
+ if(!SettingGetGlobal_b(G, cSetting_ortho)) {
+ float fov = SettingGetGlobal_f(G, cSetting_field_of_view);
+- gluPerspective(fov, aspRat, I->FrontSafe, I->BackSafe);
++ // gluPerspective(fov, aspRat, I->FrontSafe, I->BackSafe);
++ glMultMatrixf(GLKMatrix4MakePerspective(fov*PI/180., aspRat, I->FrontSafe, I->BackSafe).m);
+ } else {
+ height = fmax(R_SMALL4, -I->Pos[2]) * GetFovWidth(G) / 2.f;
+ width = height * aspRat;
+Index: setup.py
+===================================================================
+--- setup.py (revision 4106)
++++ setup.py (working copy)
+@@ -279,6 +279,11 @@ else: # unix style (linux, mac, ...)
+ glut = posix_find_lib(['glut', 'freeglut'], lib_dirs)
+ pyogl_libs += ["GL", "GLU", glut]
+
++ if sys.platform == 'darwin':
++ ext_link_args += [
++ "-framework", "GLKit",
++ ]
++
+ libs += ["GLEW"]
+ libs += pyogl_libs
+
</ins></span></pre></div>
<a id="trunkdportssciencepymolfilessetup_pydiff"></a>
<div class="modfile"><h4>Modified: trunk/dports/science/pymol/files/setup_py.diff (129474 => 129475)</h4>
<pre class="diff"><span>
<span class="info">--- trunk/dports/science/pymol/files/setup_py.diff 2014-12-13 20:40:58 UTC (rev 129474)
+++ trunk/dports/science/pymol/files/setup_py.diff 2014-12-13 22:12:42 UTC (rev 129475)
</span><span class="lines">@@ -1,25 +1,8 @@
</span><del>---- setup.py.orig 2014-05-24 16:55:05.000000000 -0400
-+++ setup.py 2014-05-24 17:00:43.000000000 -0400
-@@ -47,18 +47,6 @@
- pmap(_single_compile, objects)
- return objects
-
--# handle extra arguments
--class options:
-- osx_frameworks = False
--
--try:
-- import argparse
-- parser = argparse.ArgumentParser()
-- parser.add_argument('--osx-frameworks', action="store_true")
-- options, sys.argv[1:] = parser.parse_known_args(namespace=options)
--except ImportError:
-- print "argparse not available"
--
- jobs = int(os.getenv('JOBS', 0))
- pmap = map if jobs == 1 else multiprocessing.pool.ThreadPool(jobs or None).map
-
-@@ -242,22 +230,17 @@
</del><ins>+Index: setup.py
+===================================================================
+--- setup.py (revision 4106)
++++ setup.py (working copy)
+@@ -264,7 +264,7 @@ else: # unix style (linux, mac, ...)
</ins><span class="cx"> try:
</span><span class="cx"> prefix_path = os.environ['PREFIX_PATH'].split(os.pathsep)
</span><span class="cx"> except KeyError:
</span><span class="lines">@@ -27,22 +10,4 @@
</span><span class="cx"> + prefix_path = ["@PREFIX@", "/usr", "/usr/X11"]
</span><span class="cx">
</span><span class="cx"> for prefix in prefix_path:
</span><del>- inc_dirs += filter(os.path.isdir, [prefix + s for s in ["/include", "/include/freetype2"]])
- lib_dirs += filter(os.path.isdir, [prefix + s for s in ["/lib64", "/lib"]])
-
-- if sys.platform == 'darwin' and options.osx_frameworks:
-- ext_link_args += [
-- "-framework", "OpenGL",
-- "-framework", "GLUT",
-- ]
-- else:
-- glut = posix_find_lib(['glut', 'freeglut'], lib_dirs)
-- pyogl_libs += ["GL", "GLU", glut]
-+ glut = posix_find_lib(['glut', 'freeglut'], lib_dirs)
-
- libs += ["GLEW"]
-+ pyogl_libs += ["GL", "GLU", glut]
-+
- libs += pyogl_libs
-
- ext_comp_args += ["-ffast-math", "-funroll-loops", "-O3", "-fcommon"]
</del><ins>+ inc_dirs += filter(os.path.isdir, [prefix + s for s in ["/include", "/include/freetype2", "/include/libxml2"]])
</ins></span></pre>
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