Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv31570
Modified Files: pymol-py-clang.patch Log Message: update to 1.6.0 Index: pymol-py-clang.patch =================================================================== RCS file: /cvsroot/fink/dists/10.7/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 01:32:57 -0000 1.1 +++ pymol-py-clang.patch 23 Aug 2013 17:53:25 -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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