Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv7120
Modified Files:
pymol-py-clang.patch
Log Message:
update to pymol 1.6.0
Index: pymol-py-clang.patch
===================================================================
RCS file:
/cvsroot/fink/dists/10.4/stable/main/finkinfo/sci/pymol-py-clang.patch,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -d -r1.1 -r1.2
--- pymol-py-clang.patch 8 Jun 2013 01:31:32 -0000 1.1
+++ pymol-py-clang.patch 23 Aug 2013 20:34:22 -0000 1.2
@@ -1,6 +1,6 @@
--- pymol-1.5/layer0/Tetsurf.c.orig 2013-06-07 19:07:33.000000000 -0400
+++ pymol-1.5/layer0/Tetsurf.c 2013-06-07 19:08:35.000000000 -0400
-@@ -712,8 +712,7 @@
+@@ -679,8 +679,7 @@
if(I->Tri) {
VLAFreeP(I->Tri);
}
@@ -12,7 +12,7 @@
if(I->VertexCodes) {
--- pymol-1.5/layer1/P.c.orig 2013-06-07 19:19:20.000000000 -0400
+++ pymol-1.5/layer1/P.c 2013-06-07 19:19:39.000000000 -0400
-@@ -2618,7 +2618,7 @@
+@@ -2613,7 +2613,7 @@
/* don't run if we're currently banned */
char *buffer = 0;
int size, curSize = 0;
@@ -21,7 +21,7 @@
if (!curSize){
buffer = VLACalloc(char, size);
curSize = size;
-@@ -2662,7 +2662,7 @@
+@@ -2657,7 +2657,7 @@
int did_work = false;
char *buffer = 0;
int size, curSize = 0;
@@ -32,7 +32,7 @@
curSize = size;
--- pymol-1.5/layer1/Ortho.c.orig 2013-06-07 19:10:57.000000000 -0400
+++ pymol-1.5/layer1/Ortho.c 2013-06-07 19:16:16.000000000 -0400
-@@ -1088,7 +1088,7 @@
+@@ -1014,7 +1014,7 @@
curLine = I->CurLine & OrthoSaveLines;
if(I->PromptChar) {
strcpy(buffer, I->Line[curLine]);
@@ -43,7 +43,7 @@
break;
--- pymol-1.5/layer1/Control.c.orig 2013-06-07 19:20:31.000000000 -0400
+++ pymol-1.5/layer1/Control.c 2013-06-07 19:20:50.000000000 -0400
-@@ -709,7 +709,7 @@
+@@ -637,7 +637,7 @@
but_bottom = y - (cControlBoxSize - 1);
but_height = cControlBoxSize;
@@ -54,7 +54,7 @@
} else if(((but_num == 6) && ((int) SettingGet(G, cSetting_seq_view)))
||
--- pymol-1.5/layer1/Scene.c.orig 2013-06-07 19:22:02.000000000 -0400
+++ pymol-1.5/layer1/Scene.c 2013-06-07 19:41:53.000000000 -0400
-@@ -7686,7 +7686,7 @@
+@@ -7640,7 +7640,7 @@
/* update all gadgets first (single-threaded since they're
thread-unsafe) */
rec = NULL;
while(ListIterate(I->Obj, rec, next)) {
@@ -65,7 +65,7 @@
}
--- pymol-1.5/layer2/ObjectMolecule.c.orig 2013-06-07 19:42:56.000000000
-0400
+++ pymol-1.5/layer2/ObjectMolecule.c 2013-06-07 19:46:08.000000000 -0400
-@@ -1390,7 +1390,7 @@
+@@ -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;
@@ -74,7 +74,7 @@
int NEXTRA, IPOL = 0;
int wid, col;
float BETA;
-@@ -2018,7 +2018,7 @@
+@@ -2076,7 +2076,7 @@
if(IFBOX > 0) {
@@ -83,7 +83,7 @@
if(amber7) {
p = findflag(G, buffer, "SOLVENT_POINTERS", "3I8");
-@@ -10478,7 +10478,7 @@
+@@ -10539,7 +10539,7 @@
rms = MatrixFitRMSTTTf(G, op->nvv1, op->vv1, vt, NULL,
op->ttt);
else
rms = MatrixGetRMS(G, op->nvv1, op->vv1, vt, NULL);
@@ -92,46 +92,6 @@
ObjectMoleculeTransformTTTf(I, op->ttt, b);
if(op->i3) {
---- pymol-1.5/layer2/ObjectMolecule2.c.orig 2013-06-07 19:47:12.000000000
-0400
-+++ pymol-1.5/layer2/ObjectMolecule2.c 2013-06-07 19:47:49.000000000 -0400
-@@ -3624,7 +3624,7 @@
- #else
- int ok = true;
- ObjectMolecule *I = NULL;
-- int discrete_flag;
-+ int discrete_flag = 0;
- int ll;
- (*result) = NULL;
-
---- pymol-1.5/layer2/RepSurface.c.orig 2013-06-07 19:48:34.000000000 -0400
-+++ pymol-1.5/layer2/RepSurface.c 2013-06-07 19:49:43.000000000 -0400
-@@ -5653,7 +5653,7 @@
- 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;
-@@ -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 *v2 = coord + 3 * j;
- if((v0[0] == v2[0]) && (v0[1] == v2[1]) && (v0[2] ==
v2[2]))
- skip_flag = true;
-@@ -5917,7 +5917,7 @@
- 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;
--- pymol-1.5/modules/cealign/src/tnt/tnt_array1d.h.orig 2013-06-07
19:51:46.000000000 -0400
+++ pymol-1.5/modules/cealign/src/tnt/tnt_array1d.h 2013-06-07
19:52:08.000000000 -0400
@@ -258,7 +258,7 @@
@@ -156,7 +116,7 @@
X.n_ = i1-i0+1;
--- pymol-1.5/layer3/Executive.c.orig 2013-06-07 19:55:06.000000000 -0400
+++ pymol-1.5/layer3/Executive.c 2013-06-07 19:56:00.000000000 -0400
-@@ -17137,7 +17137,7 @@
+@@ -15915,7 +15915,7 @@
ExecutiveSpecSetVisibility(G, rec, true, mod,
false);
I->LastChanged = rec;
}
@@ -189,7 +149,7 @@
char keystring[20];
--- pymol-1.5/layer4/Cmd.c.orig 2013-06-07 20:01:48.000000000 -0400
+++ pymol-1.5/layer4/Cmd.c 2013-06-07 20:03:00.000000000 -0400
-@@ -1881,7 +1881,7 @@
+@@ -1846,7 +1846,7 @@
static PyObject *CmdGetRenderer(PyObject * self, PyObject * args)
{
PyMOLGlobals *G = NULL;
@@ -316,3 +276,394 @@
vtf_error("could not get altloc in atom record", line);
return MOLFILE_ERROR;
}
+--- pymol-1.6.0/layer0/ShaderMgr.c.orig 2013-08-23 08:40:42.000000000
-0400
++++ pymol-1.6.0/layer0/ShaderMgr.c 2013-08-23 08:48:53.000000000 -0400
+@@ -150,7 +150,7 @@
+ 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);
+@@ -488,15 +488,15 @@
+ 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);
+@@ -510,19 +510,19 @@
+ 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);
+@@ -842,11 +842,11 @@
+ 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);
+--- pymol-1.6.0/layer1/Extrude.c.orig 2013-08-23 10:11:35.000000000 -0400
++++ pymol-1.6.0/layer1/Extrude.c 2013-08-23 10:13:25.000000000 -0400
+@@ -753,7 +753,7 @@
+ 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;
+ int ok = true;
+@@ -1683,7 +1683,7 @@
+ 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;
+
+@@ -1737,7 +1737,7 @@
+ for(b = 0; ok && b < I->Ns; b += 2) {
+ #ifdef _PYMOL_CGO_DRAWARRAYS
+ int nverts = 2*I->N, pl = 0, plc = 0, damode = CGO_VERTEX_ARRAY |
CGO_NORMAL_ARRAY | CGO_PICK_COLOR_ARRAY, nxtn = 3;
+- float *vertexVals, *normalVals, *colorVals = 0, *nxtVals = 0, *tmp_ptr;
++ float *vertexVals = NULL, *normalVals, *colorVals = 0, *nxtVals = 0,
*tmp_ptr;
+ float *pickColorVals;
+ GLenum mode = GL_LINE_STRIP;
+ if(SettingGetGlobal_i(I->G, cSetting_cartoon_debug) < 1.5)
+@@ -2048,7 +2048,7 @@
+ i = I->i;
+ if (ok){
+ int nverts = 2*I->N, pl = 0, plc = 0, damode = CGO_VERTEX_ARRAY |
CGO_NORMAL_ARRAY | CGO_PICK_COLOR_ARRAY, nxtn = 3;
+- float *vertexVals, *normalVals, *colorVals = 0, *nxtVals = 0, *tmp_ptr;
++ float *vertexVals = NULL, *normalVals, *colorVals = 0, *nxtVals = 0,
*tmp_ptr;
+ float *pickColorVals;
+ if (color_override)
+ ok &= CGOColorv(cgo, color_override);
+@@ -2156,7 +2156,7 @@
+ 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;
+--- pymol-1.6.0/layer1/Basis.c.orig 2013-08-23 08:56:15.000000000 -0400
++++ pymol-1.6.0/layer1/Basis.c 2013-08-23 08:57:18.000000000 -0400
+@@ -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
+--- pymol-1.6.0/layer1/CGO.c.orig 2013-08-23 08:58:55.000000000 -0400
++++ pymol-1.6.0/layer1/CGO.c 2013-08-23 09:05:57.000000000 -0400
+@@ -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 )
+
+ #define CHECK_GL_ERROR_OK(printstr) \
+- if (err = glGetError()){ \
++ if ((err = glGetError())){ \
+ PRINTFB(I->G, FB_CGO, FB_Errors) printstr, err ENDFB(I->G); \
+ }
+
+@@ -2279,7 +2279,7 @@
+ *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) {
+@@ -4339,7 +4339,7 @@
+ 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;
+@@ -7101,7 +7101,7 @@
+ 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);
+@@ -7142,7 +7142,7 @@
+ 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);
+@@ -9528,7 +9528,7 @@
+ 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:
+--- pymol-1.6.0/layer1/Ortho.c.orig 2013-08-23 09:08:11.000000000 -0400
++++ pymol-1.6.0/layer1/Ortho.c 2013-08-23 09:08:43.000000000 -0400
+@@ -1394,7 +1394,7 @@
+
+ {
+ 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);
+--- pymol-1.6.0/layer0/Map.c.orig 2013-08-23 09:09:51.000000000 -0400
++++ pymol-1.6.0/layer0/Map.c 2013-08-23 09:10:15.000000000 -0400
+@@ -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;
+--- pymol-1.6.0/layer2/RepDot.c.orig 2013-08-23 09:11:34.000000000 -0400
++++ pymol-1.6.0/layer2/RepDot.c 2013-08-23 09:14:10.000000000 -0400
+@@ -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;
+--- pymol-1.6.0/layer2/RepCartoon.c.orig 2013-08-23 09:15:13.000000000
-0400
++++ pymol-1.6.0/layer2/RepCartoon.c 2013-08-23 09:15:33.000000000 -0400
+@@ -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);
+--- pymol-1.6.0/layer2/ObjectMolecule.c.orig 2013-08-23 09:16:59.000000000
-0400
++++ pymol-1.6.0/layer2/ObjectMolecule.c 2013-08-23 09:17:39.000000000
-0400
+@@ -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);
+@@ -9755,7 +9755,7 @@
+ 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;
+--- pymol-1.6.0/layer3/PlugIOManager.c.orig 2013-08-23 09:18:58.000000000
-0400
++++ pymol-1.6.0/layer3/PlugIOManager.c 2013-08-23 09:21:05.000000000 -0400
+@@ -225,7 +225,7 @@
+ ENDFB(G);
+ }
+
+- if(stop > 0 && cnt >= stop || max > 0 && ncnt >= max) {
++ if((stop > 0 && cnt >= stop) || (max > 0 && ncnt >= max)) {
+ cs = NULL;
+ break;
+ }
+--- pymol-1.6.0/layer2/RepSphere.c.orig 2013-08-23 09:22:18.000000000
-0400
++++ pymol-1.6.0/layer2/RepSphere.c 2013-08-23 09:33:47.000000000 -0400
+@@ -1991,8 +1991,8 @@
+ int a;
+ 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);
+--- pymol-1.6.0/layer2/RepSurface.c.orig 2013-08-22 16:13:32.000000000
-0400
++++ pymol-1.6.0/layer2/RepSurface.c 2013-08-23 09:30:18.000000000 -0400
+@@ -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;
+--- pymol-1.6.0/layer3/Selector.c.orig 2013-08-23 09:37:29.000000000 -0400
++++ pymol-1.6.0/layer3/Selector.c 2013-08-23 09:38:53.000000000 -0400
+@@ -8615,11 +8615,11 @@
+ 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;
+--- pymol-1.6.0/layer2/ObjectMolecule2.c.orig 2013-08-22 16:13:32.000000000
-0400
++++ pymol-1.6.0/layer2/ObjectMolecule2.c 2013-08-23 09:44:20.000000000
-0400
+@@ -3678,7 +3678,7 @@
+ #else
+ int ok = true;
+ ObjectMolecule *I = NULL;
+- int discrete_flag;
++ int discrete_flag = 0;
+ int ll;
+ (*result) = NULL;
+
+@@ -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;
+--- pymol-1.6.0/layer2/RepCylBond.c.orig 2013-08-23 10:17:15.000000000
-0400
++++ pymol-1.6.0/layer2/RepCylBond.c 2013-08-23 10:17:43.000000000 -0400
+@@ -1998,7 +1998,7 @@
+ I->NSPC++;
+ }
+
+- if(s2 && (!marked[b2]) && (!stick_ball_filter_single_atoms || (ord==1
|| adjacent_atoms[a2] && adjacent_atoms[a2][0] > 1))) {
++ if(s2 && (!marked[b2]) && (!stick_ball_filter_single_atoms || (ord==1
|| (adjacent_atoms[a2] && adjacent_atoms[a2][0] > 1)))) {
+ /* just once for each atom..., if stick_ball_filter is on, then
only for atoms that have more than one adjacent atom */
+ float vdw =
+ stick_ball_ratio * ((ati2->protons == cAN_H) ? bd_radius :
bd_radius_full);
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