diff options
Diffstat (limited to 'sci-chemistry/molmol')
| -rw-r--r-- | sci-chemistry/molmol/Manifest | 1 | ||||
| -rw-r--r-- | sci-chemistry/molmol/files/cast.patch | 21 | ||||
| -rw-r--r-- | sci-chemistry/molmol/files/ldflags.patch | 13 | ||||
| -rw-r--r-- | sci-chemistry/molmol/files/libpng15.patch | 32 | ||||
| -rw-r--r-- | sci-chemistry/molmol/files/molmol-2k_p2-fink.patch | 356 | ||||
| -rw-r--r-- | sci-chemistry/molmol/files/opengl.patch | 96 | ||||
| -rw-r--r-- | sci-chemistry/molmol/files/pjf_RH9_molmol2k2.diff | 103 | ||||
| -rw-r--r-- | sci-chemistry/molmol/files/prefix.patch | 22 | ||||
| -rw-r--r-- | sci-chemistry/molmol/files/wild.patch | 1866 | ||||
| -rw-r--r-- | sci-chemistry/molmol/molmol-2k_p2-r2.ebuild | 15 | ||||
| -rw-r--r-- | sci-chemistry/molmol/molmol-2k_p2-r3.ebuild | 17 | ||||
| -rw-r--r-- | sci-chemistry/molmol/molmol-2k_p2-r4.ebuild | 17 | ||||
| -rw-r--r-- | sci-chemistry/molmol/molmol-2k_p2-r5.ebuild | 17 |
13 files changed, 36 insertions, 2540 deletions
diff --git a/sci-chemistry/molmol/Manifest b/sci-chemistry/molmol/Manifest index 3b9280e4b834..aed5ea92035b 100644 --- a/sci-chemistry/molmol/Manifest +++ b/sci-chemistry/molmol/Manifest @@ -1,2 +1,3 @@ DIST molmol-2k.2.0-doc.tar.gz 1062297 SHA256 07e1c3fd04ffe7c9e9d91eaefa0bf72e6d0913a981eec3bf0879bfc65537a6be SHA512 131f747a5762859398ebe9b676a07df56c82c8864ecc035ec914f1dea74dafcd67f87993421dfe5899c640470c7e1e1ef03ae262b04a9b360ae329eb19a331fe WHIRLPOOL b74f47149c4dce8199722075fda17c9cbe22263eec57b647ef543b15386d53b267ee85d5a2c44a4fda7e533fd6ccdafb82fbbbd71e671ec4e1fd58e07363677c DIST molmol-2k.2.0-src.tar.gz 1088805 SHA256 1104dcb1b2517581c7d6b1695ff2e92f4076ad34afc48dd896eec38e5acf2287 SHA512 6ab01a6fd3d19752634a2cf22919a20e43d195768bd4bdacd5f0bbe016c3058c94915bad4c7fa64dcd86576be39cad0ae112cb62f5e69ffb10041518101e7a9b WHIRLPOOL e258ede83ac4a8fe9b4a9274588ced7e1294415d864c909ed83e3e56d36512e1388e6f77e45da614bc19992a265d32b739c54aace7faa28971c61a01bba27541 +DIST molmol-patches.tbz2 17528 SHA256 5c3b867762e563c91583e3c965c956e4004edc5532e84a33dce244e0140f596c SHA512 bd94baf0a378f40f854f396963edd9b9e4afc5c56462ee6f8b68889290afdb4c5d9b10878aa5619d0a70153453fe6ee8e7540064522c6db0291ae9162bba9287 WHIRLPOOL 6ebe6ee4142e9c10c5960a0defd3d3b4a7841281b42f865e7777d5f28d878202500442e6afa21e3bd64e691d4ed903712baffe5488abd8dcdec99cb616004380 diff --git a/sci-chemistry/molmol/files/cast.patch b/sci-chemistry/molmol/files/cast.patch deleted file mode 100644 index 16ac411c76e5..000000000000 --- a/sci-chemistry/molmol/files/cast.patch +++ /dev/null @@ -1,21 +0,0 @@ -diff --git a/src/data/DataDist.c b/src/data/DataDist.c -index 7f7121f..18eef33 100644 ---- a/src/data/DataDist.c -+++ b/src/data/DataDist.c -@@ -27,6 +27,7 @@ - - #include <stdio.h> - #include <stdlib.h> -+#include <stdint.h> - - #include <hashtab.h> - -@@ -89,7 +90,7 @@ hashInter(void *p, unsigned size) - { - TabEntryInter *entryP = p; - -- return ((unsigned) entryP->atom1P + (unsigned) entryP->atom2P) % size; -+ return ((unsigned)(uintptr_t) entryP->atom1P + (unsigned)(uintptr_t) entryP->atom2P) % size; - } - - static int diff --git a/sci-chemistry/molmol/files/ldflags.patch b/sci-chemistry/molmol/files/ldflags.patch deleted file mode 100644 index ff6e06ef490c..000000000000 --- a/sci-chemistry/molmol/files/ldflags.patch +++ /dev/null @@ -1,13 +0,0 @@ -diff --git a/src/main/Makefile b/src/main/Makefile -index 74530fa..102d1b7 100644 ---- a/src/main/Makefile -+++ b/src/main/Makefile -@@ -22,7 +22,7 @@ SRC = $(OBJ:.o=.c) - default: $(PROGRAM) - - $(PROGRAM): $(OBJ) $(LIBS) $(SGLIB) $(TOOLSLIB) -- $(CC) -o $@ $(CFLAGS) $(OBJ) $(LIBS) $(SGLIB) $(TOOLSLIB) $(SYSLIB) -+ $(CC) $(CFLAGS) ${LDFLAGS} -o $@ $(OBJ) $(LIBS) $(SGLIB) $(TOOLSLIB) $(SYSLIB) - - clean: - rm -f $(OBJ) $(PROGRAM) core *.ps diff --git a/sci-chemistry/molmol/files/libpng15.patch b/sci-chemistry/molmol/files/libpng15.patch deleted file mode 100644 index cd27e4906608..000000000000 --- a/sci-chemistry/molmol/files/libpng15.patch +++ /dev/null @@ -1,32 +0,0 @@ ---- src/motogl/MotOGLDump.c -+++ src/motogl/MotOGLDump.c -@@ -248,7 +248,7 @@ - pngErrHand(png_structp pngStrucP, char *errMsg) - { - IORaiseError(errMsg); -- longjmp(pngStrucP->jmpbuf, 1); -+ longjmp(png_jmpbuf(pngStrucP), 1); - } - #endif - -@@ -357,7 +357,7 @@ - return IO_RES_ERR; - } - -- if (setjmp(pngStrucP->jmpbuf)) { -+ if (setjmp(png_jmpbuf(pngStrucP))) { - if (cBuf != NULL) - free(cBuf); - if (fBuf != NULL) -@@ -368,10 +368,7 @@ - - png_init_io(pngStrucP, ImgFileP); - -- pngInfoP->width = imgW; -- pngInfoP->height = imgH; -- pngInfoP->bit_depth = 8; -- pngInfoP->color_type = PNG_COLOR_TYPE_RGB; -+ png_set_IHDR(pngStrucP, pngInfoP, imgW, imgH, 8, PNG_COLOR_TYPE_RGB, 0, PNG_COMPRESSION_TYPE_DEFAULT, PNG_FILTER_TYPE_DEFAULT); - png_write_info(pngStrucP, pngInfoP); - } - #endif diff --git a/sci-chemistry/molmol/files/molmol-2k_p2-fink.patch b/sci-chemistry/molmol/files/molmol-2k_p2-fink.patch deleted file mode 100644 index 14cc83b63e9e..000000000000 --- a/sci-chemistry/molmol/files/molmol-2k_p2-fink.patch +++ /dev/null @@ -1,356 +0,0 @@ - src/calc/CalcRmsd.c | 8 ++++---- - src/cmdfig/FigUtil.c | 46 +++++++++++++++++++++++----------------------- - src/cmdio/ExWriteSec.c | 6 +++--- - src/data/DataDist.c | 2 +- - src/data/DataHand.c | 8 ++++---- - src/expr/ExprScan.c | 2 +- - src/iodev/IODev.c | 2 -- - src/motif/MotifDial.c | 2 +- - src/motif/MotifMainW.c | 4 ++-- - src/os/GFile.c | 2 +- - src/prim/PrimDraw.c | 2 +- - src/prim/RibbonCalc.c | 12 ++++++------ - src/pudev/PuMainW.c | 2 +- - src/tty/TTY.c | 2 +- - tools/src/IsoSurface.c | 22 +++++++++++----------- - 15 files changed, 60 insertions(+), 62 deletions(-) - -diff --git a/src/calc/CalcRmsd.c b/src/calc/CalcRmsd.c -index 0e4629e..ed99e76 100644 ---- a/src/calc/CalcRmsd.c -+++ b/src/calc/CalcRmsd.c -@@ -1025,10 +1025,10 @@ CalcRmsd(BOOL fitPairs, char *range, char *glob1, char *glob2, - } - - for (propI = 0; propI < 2; propI++) { -- if (groupNo == 0 || propI == 0 && ! calc1) -+ if (groupNo == 0 || (propI == 0 && ! calc1)) - continue; - -- if (groupNo == 0 || propI == 1 && ! calc2) -+ if (groupNo == 0 || (propI == 1 && ! calc2)) - continue; - - Report("\nAverage RMSD, dev., min. and max of "); -@@ -1052,8 +1052,8 @@ CalcRmsd(BOOL fitPairs, char *range, char *glob1, char *glob2, - Report(" "); - - for (groupI2 = 0; groupI2 < groupNo; groupI2++) { -- if (groupI1 < groupI2 && -- groupInfoP[groupI1].membNo != groupInfoP[groupI2].membNo || -+ if (((groupI1 < groupI2) && -+ (groupInfoP[groupI1].membNo != groupInfoP[groupI2].membNo)) || - groupInfoP[groupI1].membNo == 0 || - groupInfoP[groupI2].membNo == 0) { - groupInfoP[groupI2].stat.avg = 0.0f; -diff --git a/src/cmdfig/FigUtil.c b/src/cmdfig/FigUtil.c -index 20d403a..b8dc3a6 100644 ---- a/src/cmdfig/FigUtil.c -+++ b/src/cmdfig/FigUtil.c -@@ -44,29 +44,29 @@ typedef struct { - } TabEntry; - - static TabEntry GreekTab[] = { -- "ALPHA", 'a', -- "BETA", 'b', -- "CHI", 'c', -- "DELTA", 'd', -- "EPSILON", 'e', -- "PHI" , 'f', -- "GAMMA", 'g', -- "ETA", 'h', -- "IOTA", 'i', -- "KAPPA", 'k', -- "LAMBDA", 'l', -- "MU", 'm', -- "NU", 'n', -- "PI", 'p', -- "THETA", 'q', -- "RHO", 'r', -- "SIGMA", 's', -- "TAU", 't', -- "UPSILON", 'u', -- "OMEGA", 'w', -- "XI", 'x', -- "PSI", 'y', -- "ZETA", 'z' -+ {"ALPHA", 'a'}, -+ {"BETA", 'b'}, -+ {"CHI", 'c'}, -+ {"DELTA", 'd'}, -+ {"EPSILON", 'e'}, -+ {"PHI" , 'f'}, -+ {"GAMMA", 'g'}, -+ {"ETA", 'h'}, -+ {"IOTA", 'i'}, -+ {"KAPPA", 'k'}, -+ {"LAMBDA", 'l'}, -+ {"MU", 'm'}, -+ {"NU", 'n'}, -+ {"PI", 'p'}, -+ {"THETA", 'q'}, -+ {"RHO", 'r'}, -+ {"SIGMA", 's'}, -+ {"TAU", 't'}, -+ {"UPSILON", 'u'}, -+ {"OMEGA", 'w'}, -+ {"XI", 'x'}, -+ {"PSI", 'y'}, -+ {"ZETA", 'z'} - }; - - int -diff --git a/src/cmdio/ExWriteSec.c b/src/cmdio/ExWriteSec.c -index 7f705d4..8da8336 100644 ---- a/src/cmdio/ExWriteSec.c -+++ b/src/cmdio/ExWriteSec.c -@@ -250,9 +250,9 @@ writeSecondary(DhResP *resPA, int resNo) - - if (neighLStart != NO_RES) { - if (num != neighLEnd + 1 || -- neighNum != neighREnd + 1 && neighNum != neighREnd - 1 || -- neighREnd > neighRStart && neighNum != neighREnd + 1 || -- neighREnd < neighRStart && neighNum != neighREnd - 1) { -+ (neighNum != neighREnd + 1 && neighNum != neighREnd - 1) || -+ (neighREnd > neighRStart && neighNum != neighREnd + 1) || -+ (neighREnd < neighRStart && neighNum != neighREnd - 1)) { - writeNeigh(neighLStart, neighLEnd, neighRStart, neighREnd); - neighLStart = NO_RES; - } else { -diff --git a/src/data/DataDist.c b/src/data/DataDist.c -index 18eef33..c683f9e 100644 ---- a/src/data/DataDist.c -+++ b/src/data/DataDist.c -@@ -117,7 +117,7 @@ fillIntra(TabEntryIntra *entryP, DhAtomP atom1P, DhAtomP atom2P) - entryP->atom2I = DhAtomGetNumber(atom2P); - - if (entryP->res1I > entryP->res2I || -- entryP->res1I == entryP->res2I && entryP->atom1I > entryP->atom2I) { -+ (entryP->res1I == entryP->res2I && entryP->atom1I > entryP->atom2I)) { - t = entryP->res1I; - entryP->res1I = entryP->res2I; - entryP->res2I = t; -diff --git a/src/data/DataHand.c b/src/data/DataHand.c -index b20e29c..368aad3 100644 ---- a/src/data/DataHand.c -+++ b/src/data/DataHand.c -@@ -2043,8 +2043,8 @@ applyBondList(PropRefP refP, LINLIST bondL, int groupNum, - groupNum1 = getGroupNum(bondAddP->res1P->molP); - groupNum2 = getGroupNum(bondAddP->res2P->molP); - if (atom1P->state == AS_VALID && atom2P->state == AS_VALID && -- (groupNum1 == groupNum && groupNum2 == groupNum || -- groupNum < 0 && groupNum1 != groupNum2)) -+ ((groupNum1 == groupNum && groupNum2 == groupNum) || -+ (groupNum < 0 && groupNum1 != groupNum2))) - applyF(bondP, atom1P, atom2P, clientData); - } - bondAddP = nextBondAddP; -@@ -2367,8 +2367,8 @@ callDistApply(PropRefP refP, DhDistP distP, int groupNum, - groupNum1 = getGroupNum(distP->res1P->molP); - groupNum2 = getGroupNum(distP->res2P->molP); - if (atom1P->state == AS_VALID && atom2P->state == AS_VALID && -- (groupNum1 == groupNum && groupNum2 == groupNum || -- groupNum < 0 && groupNum1 != groupNum2)) -+ ((groupNum1 == groupNum && groupNum2 == groupNum) || -+ (groupNum < 0 && groupNum1 != groupNum2))) - applyF(distP, atom1P, atom2P, clientData); - } - } -diff --git a/src/expr/ExprScan.c b/src/expr/ExprScan.c -index dcef69e..6266b4d 100644 ---- a/src/expr/ExprScan.c -+++ b/src/expr/ExprScan.c -@@ -221,7 +221,7 @@ ExprScanGetSym(void) - for (;;) { - if (isdigit(ch)) { - DStrAppChar(StrVal, ch); -- } else if (ch == '.' && ExprStr[1] != '.' || -+ } else if ((ch == '.' && ExprStr[1] != '.') || - ch == 'e' || ch == 'E') { - DStrAppChar(StrVal, ch); - isFloat = TRUE; -diff --git a/src/iodev/IODev.c b/src/iodev/IODev.c -index 9c04ce8..aa4f9a7 100644 ---- a/src/iodev/IODev.c -+++ b/src/iodev/IODev.c -@@ -44,7 +44,6 @@ extern void IOMotifGLDSetDev(void); - #endif - #ifdef IO_DEV_MOTIF_OGL - extern void IOMotifOGLSetDev(void); --extern void IOMotifOGLDSetDev(void); - #endif - #ifdef IO_DEV_MOTIF_XGL - extern void IOMotifXGLSetDev(void); -@@ -76,7 +75,6 @@ static DevListEntry DevList[] = { - #endif - #ifdef IO_DEV_MOTIF_OGL - {"Motif/OpenGL", IOMotifOGLSetDev}, -- {"Motif/OpenGLD", IOMotifOGLDSetDev}, - #endif - #ifdef IO_DEV_MOTIF_XGL - {"Motif/XGL", IOMotifXGLSetDev}, -diff --git a/src/motif/MotifDial.c b/src/motif/MotifDial.c -index 2514549..6e3bfd7 100644 ---- a/src/motif/MotifDial.c -+++ b/src/motif/MotifDial.c -@@ -1323,7 +1323,7 @@ PuMotifAddGizmoCB(PuGizmo gizmo, PuGizmoCBType type, - - switch (type) { - case PU_CT_ACTIVATE: -- if (gType == GIZMO_TEXT_FIELD || GIZMO_TEXT) -+ if (gType == (GIZMO_TEXT_FIELD | GIZMO_TEXT)) - XtAddCallback(gizmo, XmNactivateCallback, textActivateCB, infoP); - else if (gType == GIZMO_BUTTON) - XtAddCallback(gizmo, XmNactivateCallback, gizmoGenCB, infoP); -diff --git a/src/motif/MotifMainW.c b/src/motif/MotifMainW.c -index abbb444..77ce8fd 100644 ---- a/src/motif/MotifMainW.c -+++ b/src/motif/MotifMainW.c -@@ -80,8 +80,8 @@ checkPressOrExpose(Display *dpy, XEvent *eventP, XPointer arg) - { - Window *winP = (Window *) arg; - -- return eventP->type == ButtonPress && eventP->xbutton.window == *winP || -- eventP->type == Expose && eventP->xexpose.window == *winP; -+ return (eventP->type == ButtonPress && eventP->xbutton.window == *winP) || -+ (eventP->type == Expose && eventP->xexpose.window == *winP); - } - - static void -diff --git a/src/os/GFile.c b/src/os/GFile.c -index d0d63b6..08d48c7 100644 ---- a/src/os/GFile.c -+++ b/src/os/GFile.c -@@ -385,7 +385,7 @@ GFileEOF(GFile gf) - { - if (gf->format == GF_FORMAT_MEMORY) - return gf->currP == NULL || -- gf->currP->nextP == NULL && gf->currPos == gf->currP->len; -+ (gf->currP->nextP == NULL && gf->currPos == gf->currP->len); - else - return feof(gf->fp); - } -diff --git a/src/prim/PrimDraw.c b/src/prim/PrimDraw.c -index 32bd593..ba89c57 100644 ---- a/src/prim/PrimDraw.c -+++ b/src/prim/PrimDraw.c -@@ -461,7 +461,7 @@ drawRibbon(PrimObjP primP) - } - - if (partP->paint == RP_ATOM || -- partP->paint == RP_ATOM_SMOOTH && partP->polyNo > 0) -+ (partP->paint == RP_ATOM_SMOOTH && partP->polyNo > 0)) - SgSetColor(attrP->colR, attrP->colG, attrP->colB); - - if (partP->paint == RP_ATOM_SMOOTH) -diff --git a/src/prim/RibbonCalc.c b/src/prim/RibbonCalc.c -index 09874cf..0849d03 100644 ---- a/src/prim/RibbonCalc.c -+++ b/src/prim/RibbonCalc.c -@@ -907,7 +907,7 @@ calcStrips(PrimObjP primP, PrimObjP prevP) - getSplinePoints(partP, ribbonP, ePar, partP->endPar, ePNo + 1, - parA + sPNo + mPNo - 1, xA + sPNo + mPNo - 1, dzA + sPNo + mPNo - 1); - -- if (partP->style == RS_ROUND && partP->midRad == 0.0f || -+ if ((partP->style == RS_ROUND && partP->midRad == 0.0f) || - BreakInterrupted()) { - /* draw only one line */ - partP->traceNo = 1; -@@ -1128,15 +1128,15 @@ calcStrips(PrimObjP primP, PrimObjP prevP) - Vec3Copy(partP->traceA[traceI].nvA[pointI], nv); - } - -- if (pointI == 0 && partP->startStyle == RE_SHARP || -- pointI == pointNo - ePNo && partP->endStyle == RE_ARROW) -+ if ((pointI == 0 && partP->startStyle == RE_SHARP) || -+ (pointI == pointNo - ePNo && partP->endStyle == RE_ARROW)) - Vec3Copy(partP->polyA[polyI].xA[traceNo - 1 - traceI], x); - else if (pointI == pointNo - 1 && partP->endStyle == RE_SHARP) - Vec3Copy(partP->polyA[polyI].xA[traceI], x); - } - -- if (pointI == 0 && partP->startStyle == RE_SHARP || -- pointI == pointNo - ePNo && partP->endStyle == RE_ARROW) { -+ if ((pointI == 0 && partP->startStyle == RE_SHARP) || -+ (pointI == pointNo - ePNo && partP->endStyle == RE_ARROW)) { - Vec3Copy(x, dy); - Vec3Cross(x, dx); - Vec3Copy(partP->polyA[polyI].nv, x); -@@ -1327,7 +1327,7 @@ RibbonCalc(PrimObjP primP) - - if (! partP->pointValid || prec != partP->prec || - startRad != partP->startRad || -- partP->style == RS_ROUND && midRad != partP->midRad || -+ (partP->style == RS_ROUND && midRad != partP->midRad) || - endRad != partP->endRad || radChanged) { - for (i = 0; i < partP->traceNo; i++) { - free(partP->traceA[i].xA); -diff --git a/src/pudev/PuMainW.c b/src/pudev/PuMainW.c -index 73d183b..d287345 100644 ---- a/src/pudev/PuMainW.c -+++ b/src/pudev/PuMainW.c -@@ -57,7 +57,7 @@ PuSetTextField(PuTextFieldChoice fieldChoice, char *text) - if (text[0] != LOCK_CHAR) - return; - text++; -- if (text[0] == '\0' || text[0] == ' ' && text[1] == '\0') { -+ if (text[0] == '\0' || (text[0] == ' ' && text[1] == '\0')) { - StatusLocked = FALSE; - text = " "; - } -diff --git a/src/tty/TTY.c b/src/tty/TTY.c -index 0090f75..22adfef 100644 ---- a/src/tty/TTY.c -+++ b/src/tty/TTY.c -@@ -164,7 +164,7 @@ PuTTYSwitchFullscreen(BOOL onOff) - void - PuTTYSetTextField(PuTextFieldChoice fieldChoice, char *text) - { -- if (text[0] == '\0' || text[0] == ' ' && text[1] == '\0') -+ if (text[0] == '\0' || (text[0] == ' ' && text[1] == '\0')) - return; - - switch (fieldChoice) { -diff --git a/tools/src/IsoSurface.c b/tools/src/IsoSurface.c -index 5e11a98..09f89d0 100644 ---- a/tools/src/IsoSurface.c -+++ b/tools/src/IsoSurface.c -@@ -104,19 +104,19 @@ typedef struct { - } Strip; - - static CubeDesc CubeEven = { -- 0, 3, 5, 6, {{D_0, 1}, {D_0, 2}, {D_0, 3}, {D_0, 4}}, -- 3, 0, 5, 1, {{D_0, 0}, {D_MZ, 4}, {D_MY, 1}, {D_PX, 2}}, -- 0, 3, 6, 2, {{D_0, 0}, {D_MZ, 3}, {D_PY, 2}, {D_MX, 1}}, -- 3, 5, 6, 7, {{D_0, 0}, {D_PX, 3}, {D_PZ, 1}, {D_PY, 4}}, -- 5, 0, 6, 4, {{D_0, 0}, {D_MY, 3}, {D_MX, 4}, {D_PZ, 2}} -+ {{0, 3, 5, 6, {{D_0, 1}, {D_0, 2}, {D_0, 3}, {D_0, 4}}}, -+ {3, 0, 5, 1, {{D_0, 0}, {D_MZ, 4}, {D_MY, 1}, {D_PX, 2}}}, -+ {0, 3, 6, 2, {{D_0, 0}, {D_MZ, 3}, {D_PY, 2}, {D_MX, 1}}}, -+ {3, 5, 6, 7, {{D_0, 0}, {D_PX, 3}, {D_PZ, 1}, {D_PY, 4}}}, -+ {5, 0, 6, 4, {{D_0, 0}, {D_MY, 3}, {D_MX, 4}, {D_PZ, 2}}}} - }; - - static CubeDesc CubeOdd = { -- 1, 2, 7, 4, {{D_0, 1}, {D_0, 2}, {D_0, 3}, {D_0, 4}}, -- 2, 1, 7, 3, {{D_0, 0}, {D_MZ, 3}, {D_PX, 2}, {D_PY, 1}}, -- 1, 2, 4, 0, {{D_0, 0}, {D_MZ, 4}, {D_MX, 1}, {D_MY, 2}}, -- 2, 7, 4, 6, {{D_0, 0}, {D_PY, 4}, {D_PZ, 2}, {D_MX, 3}}, -- 7, 1, 4, 5, {{D_0, 0}, {D_PX, 4}, {D_MY, 3}, {D_PZ, 1}} -+ {{1, 2, 7, 4, {{D_0, 1}, {D_0, 2}, {D_0, 3}, {D_0, 4}}}, -+ {2, 1, 7, 3, {{D_0, 0}, {D_MZ, 3}, {D_PX, 2}, {D_PY, 1}}}, -+ {1, 2, 4, 0, {{D_0, 0}, {D_MZ, 4}, {D_MX, 1}, {D_MY, 2}}}, -+ {2, 7, 4, 6, {{D_0, 0}, {D_PY, 4}, {D_PZ, 2}, {D_MX, 3}}}, -+ {7, 1, 4, 5, {{D_0, 0}, {D_PX, 4}, {D_MY, 3}, {D_PZ, 1}}}} - }; - - static BOOL Initialized = FALSE; -@@ -158,7 +158,7 @@ fillFaces(TetDesc *tetP) - static BOOL - equalPair(int i00, int i01, int i10, int i11) - { -- return i00 == i10 && i01 == i11 || i00 == i11 && i01 == i10; -+ return (i00 == i10 && i01 == i11) || (i00 == i11 && i01 == i10); - } - - static int diff --git a/sci-chemistry/molmol/files/opengl.patch b/sci-chemistry/molmol/files/opengl.patch deleted file mode 100644 index c1db35d9013d..000000000000 --- a/sci-chemistry/molmol/files/opengl.patch +++ /dev/null @@ -1,96 +0,0 @@ - molmol | 65 +++++++++-------------------------------------------------------- - 1 file changed, 9 insertions(+), 56 deletions(-) - -diff --git a/molmol b/molmol -index 7863225..b6c75ce 100755 ---- a/molmol -+++ b/molmol -@@ -11,55 +11,8 @@ ostype=`uname` - osrel=`uname -r` - osmaj=`echo $osrel | awk -F. '{print $1}'` - osmin=`echo $osrel | awk -F. '{print $2}'` --localdev= --glxdev= -- --if [ $ostype = "IRIX" -o $ostype = "IRIX64" ]; then -- if [ $osmaj -eq 6 -a $osmin -ge 2 -o $osmaj -gt 6 ]; then -- arch=sgi6 -- localdev=Motif/OpenGL -- glxdev=Motif/OpenGL -- elif [ $osmaj -eq 5 -a $osmin -ge 3 -o $osmaj -gt 5 ]; then -- arch=sgi5 -- localdev=Motif/OpenGL -- glxdev=Motif/OpenGL -- else -- arch=sgi4 -- localdev=Motif/GL -- fi -- MONITOR=72HZ; export MONITOR --elif [ $ostype = "AIX" ]; then -- arch=aix -- localdev=Motif/OpenGL --elif [ $ostype = "HP-UX" ]; then -- arch=hp -- localdev=Motif/OpenGL -- glxdev=Motif/OpenGL --elif [ $ostype = "OSF1" ]; then -- arch=dec -- localdev=Motif/OpenGL --elif [ $ostype = "Linux" ]; then -- arch=lnx -- localdev=Motif/OpenGL --elif [ $ostype = "SunOS" ]; then -- if [ $osmaj -eq 5 -a $osmin -ge 4 -o $osmaj -gt 5 ]; then -- arch=sol -- localdev=Motif/OpenGL -- else -- arch=sun -- fi --else -- arch=unknown --fi -- --if [ $ostype = "SunOS" ]; then -- xdpy=/usr/openwin/bin/xdpyinfo --elif [ $ostype = "HP-UX" ]; then -- xdpy=/usr/contrib/bin/X11/xdpyinfo --else -- xdpy=/usr/bin/X11/xdpyinfo --fi -- -+localdev=Motif/OpenGL -+glxdev=Motif/OpenGL - printUsage () { - echo "Usage: molmol -ht2as [-o dev] [-r range] [-f macro] files" - echo "" -@@ -121,15 +74,15 @@ done - - magictmp=/tmp/molmol_magic$$ - --if [ ! -d $HOME/molmol ]; then -- mkdir $HOME/molmol -+if [ ! -d $HOME/.molmol ]; then -+ mkdir $HOME/.molmol - fi --startmacro=$HOME/molmol/options.mac -+startmacro=$HOME/.molmol/options.mac - cp /dev/null $startmacro - - if [ -n "$*" ]; then -- if [ -f $HOME/molmol/dump ]; then -- mv -f $HOME/molmol/dump $HOME/molmol/dump.old -+ if [ -f $HOME/.molmol/dump ]; then -+ mv -f $HOME/.molmol/dump $HOME/.molmol/dump.old - fi - echo "0 long 0x3b7a12f9 MOLMOL" > $magictmp - echo "0 long 0xf9127a3b MOLMOL" >> $magictmp -@@ -209,7 +162,7 @@ elif [ -x $xdpy ]; then - fi - - if [ "$input" = "-" -o -n "$nograph" ]; then -- $MOLMOLHOME/molmol.$arch $xopt -+ $MOLMOLHOME/molmol $xopt - else -- $MOLMOLHOME/molmol.$arch $xopt < /dev/null -+ $MOLMOLHOME/molmol $xopt < /dev/null - fi diff --git a/sci-chemistry/molmol/files/pjf_RH9_molmol2k2.diff b/sci-chemistry/molmol/files/pjf_RH9_molmol2k2.diff deleted file mode 100644 index 0ad57d93e107..000000000000 --- a/sci-chemistry/molmol/files/pjf_RH9_molmol2k2.diff +++ /dev/null @@ -1,103 +0,0 @@ -Only in molmol_rh9: makedef -diff -ru molmol_rh9_unpatched/makedef.lnx molmol_rh9/makedef.lnx ---- molmol_rh9_unpatched/makedef.lnx 2003-01-20 16:10:18.000000000 -0500 -+++ molmol_rh9/makedef.lnx 2003-05-06 10:40:08.000000000 -0400 -@@ -1,31 +1,38 @@ - # definitions for Linux - --MISSFUNC = -Dsqrtf=sqrt -Dexpf=exp -Dlogf=log -Dpowf=pow \ -- -Dsinf=sin -Dcosf=cos -Dtanf=tan \ -- -Dasinf=asin -Dacosf=acos -Datanf=atan -Datan2f=atan2 \ -- -Dfabsf=fabs -Dceilf=ceil --MCPPFLAGS = $(MISSFUNC) --MCFLAGS = -O2 -- --RANLIB = /bin/true --WAIT = /usr/bin/sleep 2 --SHELL = /bin/sh --CPP = /lib/cpp --CC = /usr/bin/gcc -+#TIFFDIR = $(TOP)/tiff-v3.4/libtiff -+#JPEGDIR = $(TOP)/../libjpeg/jpeg-6a -+#PNGDIR = $(TOP)/../libpng/libpng-0.89c -+#ZLIBDIR = $(TOP)/../libpng/zlib-1.0.2 -+ -+IMGDEF = -DTIFF_SUPPORT -DJPEG_SUPPORT -DPNG_SUPPORT -+IMGLIB = -ltiff -ljpeg -lpng -lz -+IMGINCL = # -I$(TIFFDIR) -I$(JPEGDIR) -I$(PNGDIR) -I$(ZLIBDIR) -+ -+XINCL = -I/usr/X11R6/include -+ -+CC=gcc -+MCPPFLAGS = -+MCFLAGS =-pipe -O3 -ffast-math -march=i686 -mcpu=i686 -+ -+RANLIB = /bin/true -+WAIT = sleep 2 -+SHELL = /bin/sh -+CPP = /lib/cpp - --SGDEVDIR = x11 no pov rib vrml1 vrml2 ps fm -- --SGDEVDEF = -DSG_DEV_X11 -DSG_DEV_NO -DSG_DEV_POV -DSG_DEV_RIB -DSG_DEV_VRML1 -DSG_DEV_VRML2 -DSG_DEV_PS -DSG_DEV_CPS -DSG_DEV_FM3 -DSG_DEV_FM4 -+SGDEVDIR = ogl x11 no pov rib vrml1 vrml2 ps fm -+SGDEVDEF = -DSG_DEV_OGL -DSG_DEV_X11 -DSG_DEV_NO -DSG_DEV_POV -DSG_DEV_RIB -DSG_DEV_VRML1 -DSG_DEV_VRML2 -DSG_DEV_PS -DSG_DEV_CPS -DSG_DEV_FM3 -DSG_DEV_FM4 - - PUDEVDIR = motif tty - PUDEVDEF = -DPU_DEV_MOTIF -DPU_DEV_TTY - --IODEVDIR = motx11 ttyno --IODEVDEF = -DIO_DEV_MOTIF_X11 -DIO_DEV_TTY_NO -+IODEVDIR = motogl motx11 ttyno -+IODEVDEF = -DIO_DEV_MOTIF_OGL -DIO_DEV_MOTIF_X11 -DIO_DEV_TTY_NO - -+OPENGLDEF = -DOPENGL_SGI_STEREO - MOTIFDEF = -DFUNCPROTO - --SYSLIB = -L/usr/X11R6/lib -lXm -lXt -lXpm -lX11 -lm -lc -lieee -+SYSLIB = -lGLw -lGLU -lGL -lXm -lXpm -lXt -lXext -lX11 -lm - - TOOLSDIR = $(TOP)/tools --SGDIR = $(TOP)/sg -+SGDIR = $(TOP)/sg -diff -ru molmol_rh9_unpatched/src/motogl/MotOGL.c molmol_rh9/src/motogl/MotOGL.c ---- molmol_rh9_unpatched/src/motogl/MotOGL.c 2000-05-29 12:31:51.000000000 -0400 -+++ molmol_rh9/src/motogl/MotOGL.c 2003-05-06 11:51:05.000000000 -0400 -@@ -31,7 +31,7 @@ - #include <Xm/XmStrDefs.h> - - #define BOOL MOTIF_BOOL /* hack to avoid naming conflict */ --#include <X11/GLw/GLwMDrawA.h> -+#include <GL/GLwMDrawA.h> - #undef BOOL - - #include <sg.h> -diff -ru molmol_rh9_unpatched/src/os/GFile.c molmol_rh9/src/os/GFile.c ---- molmol_rh9_unpatched/src/os/GFile.c 2001-06-17 14:59:17.000000000 -0400 -+++ molmol_rh9/src/os/GFile.c 2003-05-06 12:34:34.000000000 -0400 -@@ -30,6 +30,7 @@ - #include <string.h> - #include <memory.h> - #include <ctype.h> -+#include <errno.h> - - #include <linlist.h> - -@@ -38,7 +39,7 @@ - const INT32 GFMagic = 0x3b7a12f9; - - #ifndef __linux__ --extern char *sys_errlist[]; -+extern char *strerror(); - #endif - extern int errno; - -@@ -81,7 +82,7 @@ - { - if (msg == NULL) { - if (NextMsg == NULL) -- msg = sys_errlist[errno]; -+ msg = strerror(errno); - else - msg = NextMsg; - } diff --git a/sci-chemistry/molmol/files/prefix.patch b/sci-chemistry/molmol/files/prefix.patch deleted file mode 100644 index 89f17b2e984e..000000000000 --- a/sci-chemistry/molmol/files/prefix.patch +++ /dev/null @@ -1,22 +0,0 @@ -diff --git a/molmol b/molmol -index e774abf..9f10558 100755 ---- a/molmol -+++ b/molmol -@@ -57,7 +57,7 @@ if [ $ostype = "SunOS" ]; then - elif [ $ostype = "HP-UX" ]; then - xdpy=/usr/contrib/bin/X11/xdpyinfo - else -- xdpy=/usr/bin/X11/xdpyinfo -+ xdpy=@GENTOO_PORTAGE_EPREFIX@/usr/bin/xdpyinfo - fi - - printUsage () { -@@ -119,7 +119,7 @@ while [ -n "$*" ]; do - esac - done - --magictmp=/tmp/molmol_magic$$ -+magictmp=@GENTOO_PORTAGE_EPREFIX@/tmp/molmol_magic$$ - - if [ ! -d $HOME/molmol ]; then - mkdir $HOME/molmol diff --git a/sci-chemistry/molmol/files/wild.patch b/sci-chemistry/molmol/files/wild.patch deleted file mode 100644 index 8be9baf92203..000000000000 --- a/sci-chemistry/molmol/files/wild.patch +++ /dev/null @@ -1,1866 +0,0 @@ - include/cmd_dial.h | 1 + - include/cmd_io.h | 7 +- - include/cmd_struc.h | 1 + - include/curr_dir.h | 1 + - include/data_hand.h | 6 + - src/cip/cmd_tab.h | 3 + - src/cmddial/ExDialColor.c | 314 +++++++++++++++++++++++++++++++----------- - src/cmddial/ExDialRes.c | 340 ++++++++++++++++++++++++++++++++++++++++++++++ - src/cmddial/Makefile | 2 +- - src/cmdio/ExPdb.c | 70 +++++++++- - src/cmdstruc/ExBuild.c | 123 +++++++++++++++++ - src/data/DataHand.c | 114 +++++++++++++++- - src/iodev/IODev.c | 2 + - src/main/MolInit.c | 5 +- - src/main/MolMol.c | 2 +- - src/motif/MotifDial.c | 32 ++--- - src/motogl/MotOGLDump.c | 2 +- - src/os/CurrDir.c | 46 ++----- - src/os/ProgDir.c | 25 +++- - src/win/WinDial.c | 255 +++++++++++++++++----------------- - src/winogl/WinOGLDump.c | 7 +- - 21 files changed, 1073 insertions(+), 285 deletions(-) - -diff --git a/include/cmd_dial.h b/include/cmd_dial.h -index f60e918..47fb8f8 100644 ---- a/include/cmd_dial.h -+++ b/include/cmd_dial.h -@@ -29,6 +29,7 @@ extern ErrCode ExUserInterface(char *); - - extern ErrCode ExDialColor(char *); - extern ErrCode ExDialMol(char *); -+extern ErrCode ExDialRes(char *); - extern ErrCode ExDialMeasure(char *); - extern ErrCode ExDialRmsd(char *); - extern ErrCode ExDialSelect(char *); -diff --git a/include/cmd_io.h b/include/cmd_io.h -index 79b173c..9a7b12c 100644 ---- a/include/cmd_io.h -+++ b/include/cmd_io.h -@@ -30,15 +30,16 @@ extern ErrCode ExReadAng(char *); - extern ErrCode ExReadDg(char *); - extern ErrCode ExReadDump(char *); - extern ErrCode ExReadLib(char *); --extern ErrCode ExReadPdb(char *); --extern ErrCode ExReadSeq(char *); --extern ErrCode ExReadShift(char *); - extern ErrCode ExReadLimit(char *); - extern ErrCode ExReadListAng(char *); - extern ErrCode ExReadListDg(char *); - extern ErrCode ExReadListPdb(char *); -+extern ErrCode ExReadOldPdb(char *); - extern ErrCode ExReadOmap(char *); -+extern ErrCode ExReadPdb(char *); - extern ErrCode ExReadPot(char *); -+extern ErrCode ExReadSeq(char *); -+extern ErrCode ExReadShift(char *); - extern ErrCode ExReadSybyl(char *); - extern ErrCode ExReadXyz(char *); - extern ErrCode ExWriteAng(char *); -diff --git a/include/cmd_struc.h b/include/cmd_struc.h -index e0d729f..f4950b9 100644 ---- a/include/cmd_struc.h -+++ b/include/cmd_struc.h -@@ -33,6 +33,7 @@ extern ErrCode ExAddDist(char *); - extern ErrCode ExAddLimit(char *); - extern ErrCode ExAddPseudo(char *); - extern ErrCode ExAddRes(char *); -+extern ErrCode ExMakeMolCyclic(char *); - extern ErrCode ExChangeRes(char *); - extern ErrCode ExFirstMol(char *); - extern ErrCode ExFlipAtom(char *); -diff --git a/include/curr_dir.h b/include/curr_dir.h -index c7895c4..04e404d 100644 ---- a/include/curr_dir.h -+++ b/include/curr_dir.h -@@ -26,6 +26,7 @@ - #ifndef _CURR_DIR_H_ - #define _CURR_DIR_H_ - -+extern void CurrDirSet(char *dir); - extern char *CurrDirGet(void); - - #endif /* _CURR_DIR_H_ */ -diff --git a/include/data_hand.h b/include/data_hand.h -index 4462328..74a716a 100644 ---- a/include/data_hand.h -+++ b/include/data_hand.h -@@ -112,6 +112,7 @@ extern void DhMolMoveFirst(DhMolP); - extern void DhMolDestroy(DhMolP); - - extern DhResP DhResNew(DhMolP, DhResDefP, DhSeqPos); -+extern DhResP DhResNewCyclic(DhMolP, DhResDefP, DhSeqPos); - extern void DhResMutate(DhResP, DhResDefP, DhMutationKind); - extern void DhResSetNeigh(DhResP, DhNeighChoice, DhResP); - extern BOOL DhResDestroy(DhResP); -@@ -287,6 +288,7 @@ extern void DhMolGetTransVect(DhMolP, Vec3); - extern MolAttrP DhMolGetAttr(DhMolP); - - extern DSTR DhResGetName(DhResP); -+extern DhAtomP DhResGetAtomA(DhResP); - extern int DhResGetNumber(DhResP); - - extern DSTR DhAtomGetName(DhAtomP); -@@ -335,6 +337,10 @@ extern void DhResAnglesChanged(DhResP); - extern void DhResDockPrev(DhResP); - extern void DhResDockNext(DhResP); - extern void DhResCalcAtom(DhResP, DSTR); -+extern DhResP DhResPrev(DhResP resP); -+extern DhResP DhResNext(DhResP resP); -+extern DhResP DhResFirst(DhMolP molP); -+extern DhResP DhResLast(DhMolP molP); - - /* dump/undump */ - -diff --git a/src/cip/cmd_tab.h b/src/cip/cmd_tab.h -index 0b73f65..cf7bc2a 100644 ---- a/src/cip/cmd_tab.h -+++ b/src/cip/cmd_tab.h -@@ -108,6 +108,7 @@ static CmdTabEntry BuiltinCmdTab[] = { - {"DialColor", ExDialColor, US_NONE}, - {"DialMeasure", ExDialMeasure, US_NONE}, - {"DialMol", ExDialMol, US_NONE}, -+ {"DialRes", ExDialRes, US_NONE}, - {"DialRmsd", ExDialRmsd, US_NONE}, - {"DialSelect", ExDialSelect, US_NONE}, - {"DialStyle", ExDialStyle, US_NONE}, -@@ -164,6 +165,7 @@ static CmdTabEntry BuiltinCmdTab[] = { - {"ListSelectedDist", ExListSelected, US_NONE}, - {"ListSelectedMol", ExListSelected, US_NONE}, - {"ListSelectedRes", ExListSelected, US_NONE}, -+ {"MakeMolCyclic", ExMakeMolCyclic, US_ALL}, - {"MaterialAtom", ExMaterial, US_ALL}, - {"MaterialBond", ExMaterial, US_ALL}, - {"MaterialDist", ExMaterial, US_ALL}, -@@ -213,6 +215,7 @@ static CmdTabEntry BuiltinCmdTab[] = { - {"ReadListDg", ExReadListDg, US_ALL}, - {"ReadListPdb", ExReadListPdb, US_ALL}, - {"ReadLol", ExReadLimit, US_ALL}, -+ {"ReadOldPdb", ExReadOldPdb, US_ALL}, - {"ReadOmap", ExReadOmap, US_ALL}, - {"ReadPdb", ExReadPdb, US_ALL}, - {"ReadPot", ExReadPot, US_ALL}, -diff --git a/src/cmddial/ExDialColor.c b/src/cmddial/ExDialColor.c -index f960e1d..e827c4f 100644 ---- a/src/cmddial/ExDialColor.c -+++ b/src/cmddial/ExDialColor.c -@@ -43,6 +43,9 @@ - #define NAME_LEN 100 - #define NUM_LEN 6 - #define CMD_NO 7 -+#define MAXRGBVALUE 255 -+#define ICOLOR(c) (int) ((float)c * (float)MAXRGBVALUE) -+#define FCOLOR(c) (float) ((float)c / (float)MAXRGBVALUE) - - #define EPS ((float) 1.0e-5) - -@@ -56,8 +59,8 @@ typedef struct { - static ColorDesc *ColorList; - static int ColorNo = 0; - static BOOL DialOn = FALSE; --static PuGizmo DialGizmo = NULL, NameGizmo, RGizmo, GGizmo, BGizmo, ColGizmo; --static DSTR NameStr = NULL, RStr, GStr, BStr; -+static PuGizmo DialGizmo = NULL, NameGizmo, RGizmo, GGizmo, BGizmo, ColGizmo, rGizmo, gGizmo, bGizmo; -+static DSTR NameStr = NULL, RStr, GStr, BStr, rStr, gStr, bStr; - - static char *LabelList[] = { - "Back", -@@ -136,22 +139,50 @@ editCB(PuGizmo g, char *name, void *clientData, void *callData) - char *field = clientData; - PuTextCBStruc *callP = callData; - -- if (field[0] == 'N') -+ if (field[0] == 'N') { - DStrAssignStr(NameStr, callP->newText); -- else if (field[0] == 'R') -+ } -+ else if (field[0] == 'R') { - DStrAssignStr(RStr, callP->newText); -- else if (field[0] == 'G') -+ } -+ else if (field[0] == 'G') { - DStrAssignStr(GStr, callP->newText); -- else -+ } -+ else if (field[0] == 'B') { - DStrAssignStr(BStr, callP->newText); -+ } -+ else if (field[0] == 'r') { -+ DStrAssignStr(rStr, callP->newText); -+ } -+ else if (field[0] == 'g') { -+ DStrAssignStr(gStr, callP->newText); -+ } -+ else if (field[0] == 'b') { -+ DStrAssignStr(bStr, callP->newText); -+ } - } - - static void - updateFields(int colorI) - { -+ char buf[10]; -+ float f; -+ - PuSetStr(RGizmo, PU_SC_TEXT, ColorList[colorI].r); - PuSetStr(GGizmo, PU_SC_TEXT, ColorList[colorI].g); - PuSetStr(BGizmo, PU_SC_TEXT, ColorList[colorI].b); -+ -+ f = atof(ColorList[colorI].r); -+ (void) sprintf(buf, "%i", ICOLOR(f)); -+ PuSetStr(rGizmo, PU_SC_TEXT, buf); -+ -+ f = atof(ColorList[colorI].g); -+ (void) sprintf(buf, "%i", ICOLOR(f)); -+ PuSetStr(gGizmo, PU_SC_TEXT, buf); -+ -+ f = atof(ColorList[colorI].b); -+ (void) sprintf(buf, "%i", ICOLOR(f)); -+ PuSetStr(bGizmo, PU_SC_TEXT, buf); - } - - static void -@@ -190,17 +221,96 @@ activateCB(PuGizmo g, char *name, void *clientData, void *callData) - { - char *field = clientData; - int i; -+ float f; -+ char buf[10]; - - if (field[0] == 'N') { - for (i = 0; i < ColorNo; i++) - if (strcmp(ColorList[i].name, DStrToStr(NameStr)) == 0) { -- updateFields(i); -- break; -+ updateFields(i); -+ break; - } - } else { -+ if (field[0] == 'R') { -+ f = atof(DStrToStr(RStr)); -+ if (f>1.0) { -+ f=1.0; -+ i=MAXRGBVALUE; -+ sprintf(buf,"%1.3f", FCOLOR(i)); -+ DStrAssignStr(RStr, buf); -+ PuSetStr(RGizmo, PU_SC_TEXT, buf); -+ } -+ sprintf(buf,"%i", ICOLOR(f)); -+ DStrAssignStr(rStr, buf); -+ PuSetStr(rGizmo, PU_SC_TEXT, buf); -+ } -+ else if (field[0] == 'G') { -+ f = atof(DStrToStr(GStr)); -+ if (f>1.0) { -+ f=1.0; -+ i=MAXRGBVALUE; -+ sprintf(buf,"%1.3f", FCOLOR(i)); -+ DStrAssignStr(GStr, buf); -+ PuSetStr(GGizmo, PU_SC_TEXT, buf); -+ } -+ sprintf(buf,"%i", ICOLOR(f)); -+ DStrAssignStr(gStr, buf); -+ PuSetStr(gGizmo, PU_SC_TEXT, buf); -+ } -+ else if (field[0] == 'B') { -+ f = atof(DStrToStr(BStr)); -+ if (f>1.0) { -+ f=1.0; -+ i=MAXRGBVALUE; -+ sprintf(buf,"%1.3f", FCOLOR(i)); -+ DStrAssignStr(BStr, buf); -+ PuSetStr(BGizmo, PU_SC_TEXT, buf); -+ } -+ sprintf(buf,"%i", ICOLOR(f)); -+ DStrAssignStr(bStr, buf); -+ PuSetStr(bGizmo, PU_SC_TEXT, buf); -+ } -+ else if (field[0] == 'r') { -+ i = atoi(DStrToStr(rStr)); -+ if (i>MAXRGBVALUE) { -+ f=1.0; -+ i=MAXRGBVALUE; -+ sprintf(buf,"%i", ICOLOR(f)); -+ DStrAssignStr(rStr, buf); -+ PuSetStr(rGizmo, PU_SC_TEXT, buf); -+ } -+ sprintf(buf,"%1.3f", FCOLOR(i)); -+ DStrAssignStr(RStr, buf); -+ PuSetStr(RGizmo, PU_SC_TEXT, buf); -+ } -+ else if (field[0] == 'g') { -+ i = atoi(DStrToStr(gStr)); -+ if (i>MAXRGBVALUE) { -+ f=1.0; -+ i=MAXRGBVALUE; -+ sprintf(buf,"%i", ICOLOR(f)); -+ DStrAssignStr(gStr, buf); -+ PuSetStr(gGizmo, PU_SC_TEXT, buf); -+ } -+ sprintf(buf,"%1.3f", FCOLOR(i)); -+ DStrAssignStr(GStr, buf); -+ PuSetStr(GGizmo, PU_SC_TEXT, buf); -+ } -+ else if (field[0] == 'b') { -+ i = atoi(DStrToStr(bStr)); -+ if (i>MAXRGBVALUE) { -+ f=1.0; -+ i=MAXRGBVALUE; -+ sprintf(buf,"%i", ICOLOR(f)); -+ DStrAssignStr(bStr, buf); -+ PuSetStr(bGizmo, PU_SC_TEXT, buf); -+ } -+ sprintf(buf,"%1.3f", FCOLOR(i)); -+ DStrAssignStr(BStr, buf); -+ PuSetStr(BGizmo, PU_SC_TEXT, buf); -+ } - showName(); - } -- - showColor(); - } - -@@ -258,13 +368,20 @@ showAttr(AttrP attrP) - { - char buf[10]; - -- (void) sprintf(buf, "%5.3f", attrP->colR); -+ (void) sprintf(buf, "%1.3f", attrP->colR); - PuSetStr(RGizmo, PU_SC_TEXT, buf); -- (void) sprintf(buf, "%5.3f", attrP->colG); -+ (void) sprintf(buf, "%1.3f", attrP->colG); - PuSetStr(GGizmo, PU_SC_TEXT, buf); -- (void) sprintf(buf, "%5.3f", attrP->colB); -+ (void) sprintf(buf, "%1.3f", attrP->colB); - PuSetStr(BGizmo, PU_SC_TEXT, buf); - -+ (void) sprintf(buf, "%i", ICOLOR(attrP->colR)); -+ PuSetStr(rGizmo, PU_SC_TEXT, buf); -+ (void) sprintf(buf, "%i", ICOLOR(attrP->colG)); -+ PuSetStr(gGizmo, PU_SC_TEXT, buf); -+ (void) sprintf(buf, "%i", ICOLOR(attrP->colB)); -+ PuSetStr(bGizmo, PU_SC_TEXT, buf); -+ - showName(); - showColor(); - } -@@ -315,107 +432,152 @@ buildDial(void) - PuGizmo g; - PuConstraints con; - int i; -- -- DialGizmo = PuCreateDialog("Color Dialog", 7, 5); -- PuSetBool(DialGizmo, PU_BC_PLACE_OUTSIDE, TRUE); -- -- con.x = 0; -- con.w = 1; -- con.h = 1; -- -- g = PuCreateLabel(DialGizmo, "Name"); -- con.y = 0; -- PuSetConstraints(g, con); -- PuSwitchGizmo(g, TRUE); -- -- g = PuCreateLabel(DialGizmo, "Red"); -- con.y = 1; -- PuSetConstraints(g, con); -- PuSwitchGizmo(g, TRUE); -- -- g = PuCreateLabel(DialGizmo, "Green"); -- con.y = 2; -- PuSetConstraints(g, con); -- PuSwitchGizmo(g, TRUE); -- -- g = PuCreateLabel(DialGizmo, "Blue"); -- con.y = 3; -- PuSetConstraints(g, con); -- PuSwitchGizmo(g, TRUE); -- -- con.x = 1; -- con.w = 2; -- con.h = 1; -- - NameStr = DStrNew(); -+ - RStr = DStrNew(); - GStr = DStrNew(); - BStr = DStrNew(); -+ rStr = DStrNew(); -+ gStr = DStrNew(); -+ bStr = DStrNew(); -+ - DStrAssignStr(RStr, "0.0"); - DStrAssignStr(GStr, "0.0"); - DStrAssignStr(BStr, "0.0"); -+ DStrAssignStr(rStr, "0"); -+ DStrAssignStr(gStr, "0"); -+ DStrAssignStr(bStr, "0"); - -+ DialGizmo = PuCreateDialog("Color Dialog", 3, 20); -+ PuSetBool(DialGizmo, PU_BC_PLACE_OUTSIDE, TRUE); -+ -+ con.x = 1; -+ con.y = 0; -+ con.w = 2; -+ con.h = 3; -+ ColGizmo = PuCreateColorField(DialGizmo, "Color"); -+ PuSetConstraints(ColGizmo, con); -+ PuSetConstraints(ColGizmo, con); -+ showColor(); -+ PuSwitchGizmo(ColGizmo, TRUE); -+ -+ con.x = 0; -+ con.y = 4; -+ con.w = 1; -+ con.h = 1; -+ g = PuCreateLabel(DialGizmo, "Name"); -+ PuSetConstraints(g, con); -+ PuSwitchGizmo(g, TRUE); -+ con.x = 1; -+ con.w = 2; -+ con.h = 1; - NameGizmo = PuCreateTextField(DialGizmo, "Name", DStrToStr(NameStr)); -- con.y = 0; - PuSetConstraints(NameGizmo, con); -- PuSetInt(NameGizmo, PU_IC_TEXT_WIDTH, 13); -+ PuSetInt(NameGizmo, PU_IC_TEXT_WIDTH, 10); - PuAddGizmoCB(NameGizmo, PU_CT_MODIFY, editCB, "N", NULL); - PuAddGizmoCB(NameGizmo, PU_CT_ACTIVATE, activateCB, "N", NULL); - showName(); - PuSwitchGizmo(NameGizmo, TRUE); - -- RGizmo = PuCreateTextField(DialGizmo, "Red", DStrToStr(RStr)); -- con.y = 1; -+ con.x = 1; -+ con.y = 5; -+ con.w = 2; -+ con.h = 5; -+ g = PuCreateList(DialGizmo, "Color List"); -+ for (i = 0; i < ColorNo; i++) -+ PuAddListEntry(g, ColorList[i].name, FALSE); -+ PuSetConstraints(g, con); -+ PuSetBool(g, PU_BC_AUTO_DESEL, TRUE); -+ PuAddGizmoCB(g, PU_CT_SELECT, selectCB, NULL, NULL); -+ PuSwitchGizmo(g, TRUE); -+ -+ con.x = 1; -+ con.y = 11; -+ con.w = 1; -+ con.h = 1; -+ g = PuCreateLabel(DialGizmo, "Float"); -+ PuSetConstraints(g, con); -+ PuSwitchGizmo(g, TRUE); -+ con.x = 2; -+ con.y = 11; -+ g = PuCreateLabel(DialGizmo, "RGB"); -+ PuSetConstraints(g, con); -+ PuSwitchGizmo(g, TRUE); -+ -+ con.x = 0; -+ con.y = 12; -+ con.w = 1; -+ con.h = 1; -+ g = PuCreateLabel(DialGizmo, "Red"); -+ PuSetConstraints(g, con); -+ PuSwitchGizmo(g, TRUE); -+ con.x = 1; -+ RGizmo = PuCreateTextField(DialGizmo, "RED", DStrToStr(RStr)); - PuSetConstraints(RGizmo, con); - PuSetInt(RGizmo, PU_IC_TEXT_WIDTH, NUM_LEN); - PuAddGizmoCB(RGizmo, PU_CT_MODIFY, editCB, "R", NULL); - PuAddGizmoCB(RGizmo, PU_CT_ACTIVATE, activateCB, "R", NULL); - PuSwitchGizmo(RGizmo, TRUE); -+ con.x = 2; -+ rGizmo = PuCreateTextField(DialGizmo, "red", DStrToStr(rStr)); -+ PuSetConstraints(rGizmo, con); -+ PuSetInt(rGizmo, PU_IC_TEXT_WIDTH, NUM_LEN); -+ PuAddGizmoCB(rGizmo, PU_CT_MODIFY, editCB, "r", NULL); -+ PuAddGizmoCB(rGizmo, PU_CT_ACTIVATE, activateCB, "r", NULL); -+ PuSwitchGizmo(rGizmo, TRUE); - -- GGizmo = PuCreateTextField(DialGizmo, "Green", DStrToStr(GStr)); -- con.y = 2; -+ con.x = 0; -+ con.y = 13; -+ con.w = 1; -+ con.h = 1; -+ g = PuCreateLabel(DialGizmo, "Green"); -+ PuSetConstraints(g, con); -+ PuSwitchGizmo(g, TRUE); -+ con.x = 1; -+ GGizmo = PuCreateTextField(DialGizmo, "GREEN", DStrToStr(GStr)); - PuSetConstraints(GGizmo, con); - PuSetInt(GGizmo, PU_IC_TEXT_WIDTH, NUM_LEN); - PuAddGizmoCB(GGizmo, PU_CT_MODIFY, editCB, "G", NULL); - PuAddGizmoCB(GGizmo, PU_CT_ACTIVATE, activateCB, "G", NULL); - PuSwitchGizmo(GGizmo, TRUE); -+ con.x = 2; -+ gGizmo = PuCreateTextField(DialGizmo, "green", DStrToStr(gStr)); -+ PuSetConstraints(gGizmo, con); -+ PuSetInt(gGizmo, PU_IC_TEXT_WIDTH, NUM_LEN); -+ PuAddGizmoCB(gGizmo, PU_CT_MODIFY, editCB, "g", NULL); -+ PuAddGizmoCB(gGizmo, PU_CT_ACTIVATE, activateCB, "g", NULL); -+ PuSwitchGizmo(gGizmo, TRUE); - -- BGizmo = PuCreateTextField(DialGizmo, "Blue", DStrToStr(BStr)); -- con.y = 3; -+ con.x = 0; -+ con.y = 14; -+ con.w = 1; -+ con.h = 1; -+ g = PuCreateLabel(DialGizmo, "Blue"); -+ PuSetConstraints(g, con); -+ PuSwitchGizmo(g, TRUE); -+ con.x = 1; -+ BGizmo = PuCreateTextField(DialGizmo, "BLUE", DStrToStr(BStr)); - PuSetConstraints(BGizmo, con); - PuSetInt(BGizmo, PU_IC_TEXT_WIDTH, NUM_LEN); - PuAddGizmoCB(BGizmo, PU_CT_MODIFY, editCB, "B", NULL); - PuAddGizmoCB(BGizmo, PU_CT_ACTIVATE, activateCB, "B", NULL); - PuSwitchGizmo(BGizmo, TRUE); -+ con.x = 2; -+ bGizmo = PuCreateTextField(DialGizmo, "blue", DStrToStr(bStr)); -+ PuSetConstraints(bGizmo, con); -+ PuSetInt(bGizmo, PU_IC_TEXT_WIDTH, NUM_LEN); -+ PuAddGizmoCB(bGizmo, PU_CT_MODIFY, editCB, "b", NULL); -+ PuAddGizmoCB(bGizmo, PU_CT_ACTIVATE, activateCB, "b", NULL); -+ PuSwitchGizmo(bGizmo, TRUE); - -- ColGizmo = PuCreateColorField(DialGizmo, "Color"); -- con.x = 3; -- con.y = 0; -- con.w = 2; -- con.h = 4; -- PuSetConstraints(ColGizmo, con); -- showColor(); -- PuSwitchGizmo(ColGizmo, TRUE); -- -- g = PuCreateList(DialGizmo, "Color List"); -- for (i = 0; i < ColorNo; i++) -- PuAddListEntry(g, ColorList[i].name, FALSE); -- con.x = 5; -- con.y = 0; -- con.w = 2; -- con.h = 4; -- PuSetConstraints(g, con); -- PuSetBool(g, PU_BC_AUTO_DESEL, TRUE); -- PuAddGizmoCB(g, PU_CT_SELECT, selectCB, NULL, NULL); -- PuSwitchGizmo(g, TRUE); -- -- con.y = 4; -+ con.x = 0; -+ con.y = 15; - con.w = 1; - con.h = 1; -- - for (i = 0; i < CMD_NO; i++) { - g = PuCreateButton(DialGizmo, LabelList[i]); -- con.x = i; -+ con.x = i%3; -+ if (i%3 == 0) con.y++; - PuSetConstraints(g, con); - PuAddGizmoCB(g, PU_CT_ACTIVATE, cmdCB, NULL, NULL); - PuSwitchGizmo(g, TRUE); -diff --git a/src/cmddial/ExDialRes.c b/src/cmddial/ExDialRes.c -new file mode 100644 -index 0000000..06925ff ---- /dev/null -+++ b/src/cmddial/ExDialRes.c -@@ -0,0 +1,340 @@ -+/* -+************************************************************************ -+* -+* ExDialMol.c - DialMol command -+* -+* Copyright (c) 1994-98 -+* -+* ETH Zuerich -+* Institut fuer Molekularbiologie und Biophysik -+* ETH-Hoenggerberg -+* CH-8093 Zuerich -+* -+* SPECTROSPIN AG -+* Industriestr. 26 -+* CH-8117 Faellanden -+* -+* All Rights Reserved -+* -+* Date of last modification : 98/08/17 -+* Pathname of SCCS file : /tmp_mnt/net/sn/homeb/rkoradi/molmol-master/src/cmddial/SCCS/s.ExDialMol.c -+* SCCS identification : 1.10 -+* -+************************************************************************ -+*/ -+ -+#include <cmd_dial.h> -+ -+#include <stdio.h> -+#include <string.h> -+#include <stdlib.h> -+ -+#include <break.h> -+#include <pu.h> -+#include <arg.h> -+#include <cip.h> -+#include <data_hand.h> -+ -+#define PROP_NO 3 -+ -+typedef struct { -+ char *label; -+ char *propName; -+ char *cmd; -+} PropDesc; -+typedef struct { -+ char *name; -+ BOOL active; -+} Residue; -+ -+static BOOL DialOn = FALSE; -+static PuGizmo DialGizmo = NULL, ListGizmo; -+static int CurrProp; -+static PropRefP CurrRefP; -+static int MolNo, MolI; -+static BOOL *MolStateA; -+static BOOL SuppressUpdate = FALSE; -+static PropDesc PropTab[] = { -+ {"sel", PROP_SELECTED, "SelectRes"}, -+ {"disp", PROP_DISPLAYED, "DefPropRes 'displayed'"}, -+ {"move", PROP_MOVABLE, "DefProRes 'movable'"} -+}; -+static Residue ResidueTab[] = { -+ {"ARG", FALSE}, -+ {"CYS", FALSE}, -+ {"PRO", FALSE}, -+ {"ASP", FALSE}, -+ {"PHE", FALSE}, -+ {"LEU", FALSE}, -+ {"GLU", FALSE}, -+ {"PRO", FALSE}, -+ {"TYR", FALSE}, -+ {"GLY", FALSE}, -+ {"ASN", FALSE}, -+ {"ALA", FALSE}, -+ {"SER", FALSE}, -+ {"THR", FALSE}, -+ {"LYS", FALSE}, -+ {"ILE", FALSE} -+}; -+ -+static void -+countMol(DhResP molP, void *clientData) -+{ -+ MolNo++; -+} -+ -+ -+ -+static void -+addMol(DhResP molP, void *clientData) -+{ -+ -+ -+ DSTR name; -+ DSTR residue; -+ char buf[10]; -+ char buf2[5]; -+ BOOL propVal; -+ int j; -+ name = DStrNew(); -+ residue = DStrNew(); -+ -+ -+ j= DhResGetNumber(molP); -+ (void) sprintf(buf, "%5d " , j); -+ -+ DStrAssignStr(name, buf); -+ DStrAssignStr(residue, buf2); -+ DStrAppStr(name, " "); -+ -+ DStrAppDStr(residue, DhResGetName(molP)); -+ DStrAppDStr(name, DhResGetName(molP)); -+ propVal = DhResGetProp(CurrRefP, molP); -+ -+ -+ -+ if (! BreakCheck(10)){ -+ PuAddListEntry(ListGizmo, DStrToStr(name), propVal); -+ -+ } -+ -+ -+ -+ MolStateA[MolI] = propVal; -+ -+ DStrFree(name); -+ -+ MolI++; -+} -+ -+static void -+selectMolCB(PuGizmo g, char *name, void *clientData, void *callData) -+{ -+ PuSelectCBStruc *callP = callData; -+ DSTR cmd; -+ BOOL isFirst; -+ char buf[10]; -+ int num, startI, i; -+ -+ (void) sscanf(name, "%d", &num); -+ MolStateA[num - 1] = callP->onOff; -+ -+ if (! callP->last) -+ return; -+ -+ cmd = DStrNew(); -+ DStrAssignStr(cmd, PropTab[CurrProp].cmd); -+ isFirst = TRUE; -+ -+ for (i = 0; i < MolNo; i++) { -+ if (i == 0 || ! MolStateA[i - 1]) -+ startI = i; -+ if (MolStateA[i] && (i == MolNo - 1 || ! MolStateA[i + 1])) { -+ if (isFirst) -+ DStrAppStr(cmd, " 'num = "); -+ else -+ DStrAppStr(cmd, ","); -+ (void) sprintf(buf, "%d", startI + 1); -+ DStrAppStr(cmd, buf); -+ if (i > startI) { -+ DStrAppStr(cmd, ".."); -+ (void) sprintf(buf, "%d", i + 1); -+ DStrAppStr(cmd, buf); -+ } -+ -+ isFirst = FALSE; -+ } -+ } -+ -+ if (isFirst) -+ DStrAppStr(cmd, " '0'"); -+ else -+ DStrAppStr(cmd, "'"); -+ -+ SuppressUpdate = TRUE; -+ CipExecCmd(DStrToStr(cmd)); -+ SuppressUpdate = FALSE; -+ -+ DStrFree(cmd); -+} -+ -+static void -+buildList(void) -+{ -+ int lineNo; -+ -+ MolNo = 0; -+ DhApplyRes(PropGetRef(PROP_ALL, FALSE), countMol, NULL); -+ if (MolNo > 0) { -+ if (MolStateA == NULL) -+ MolStateA = malloc(MolNo * sizeof(*MolStateA)); -+ else -+ MolStateA = realloc(MolStateA, MolNo * sizeof(*MolStateA)); -+ lineNo = MolNo; -+ if (lineNo > 40) -+ lineNo = 40; -+ } else { -+ lineNo = 1; -+ } -+ -+ PuSetInt(ListGizmo, PU_IC_ENTRY_NO, lineNo); -+ -+ MolI = 0; -+ BreakActivate(TRUE); -+ DhApplyRes(PropGetRef(PROP_ALL, FALSE), addMol, NULL); -+ BreakActivate(FALSE); -+ -+ PuSwitchGizmo(ListGizmo, TRUE); -+} -+ -+static void -+updateList(void) -+{ -+ if (SuppressUpdate) -+ return; -+ -+ PuSwitchGizmo(ListGizmo, FALSE); -+ PuRemoveListEntries(ListGizmo, 0, MolNo); -+ buildList(); -+} -+ -+static void -+selectPropCB(PuGizmo g, char *name, void *clientData, void *callData) -+{ -+ PuSelectCBStruc *callP = callData; -+ PropRefP newPropP; -+ int i; -+ -+ if (! callP->onOff) -+ return; -+ -+ for (i = 0; i < PROP_NO; i++) -+ if (strcmp(name, PropTab[i].label) == 0) -+ break; -+ -+ newPropP = PropGetRef(PropTab[i].propName, FALSE); -+ -+ if (newPropP != CurrRefP) { -+ CurrRefP = newPropP; -+ CurrProp = i; -+ updateList(); -+ } -+} -+ -+static void -+popdownCB(PuGizmo g, char *name, void *clientData, void *callData) -+{ -+ PuSwitchGizmo(DialGizmo, FALSE); -+ DialOn = FALSE; -+} -+ -+static void -+listCB(void *clientData) -+{ -+ updateList(); -+} -+ -+static void -+helpCB(PuGizmo g, char *name, void *clientData, void *callData) -+{ -+ CipShowHelpFile(DialGizmo, "DialMol"); -+} -+ -+static void -+buildDial(void) -+{ -+ -+ PuGizmo g; -+ int i; -+ -+ CurrProp = 0; -+ CurrRefP = PropGetRef(PropTab[CurrProp].propName, FALSE); -+ -+ DialGizmo = PuCreateDialog("Residue Dialog", 0, 0); -+ PuSetBool(DialGizmo, PU_BC_PLACE_OUTSIDE, TRUE); -+ -+ g = PuCreateRadioBox(DialGizmo, "Property"); -+ for (i = 0; i < PROP_NO; i++) -+ PuAddToggle(g, PropTab[i].label, i == 0); -+ PuAddGizmoCB(g, PU_CT_SELECT, selectPropCB, NULL, NULL); -+ PuSwitchGizmo(g, TRUE); -+ -+ ListGizmo = PuCreateList(DialGizmo, "Molecules"); -+ PuAddGizmoCB(ListGizmo, PU_CT_SELECT, selectMolCB, NULL, NULL); -+ PuSetBool(ListGizmo, PU_BC_MULT_SEL, TRUE); -+ buildList(); -+ -+ PuAddGizmoCB(DialGizmo, PU_CT_CLOSE, popdownCB, NULL, NULL); -+ PuAddGizmoCB(DialGizmo, PU_CT_HELP, helpCB, NULL, NULL); -+ -+} -+ -+ErrCode -+ExDialRes(char *cmd) -+{ -+ ArgDescr arg; -+ EnumEntryDescr enumEntry[2]; -+ ErrCode errCode; -+ -+ arg.type = AT_ENUM; -+ -+ ArgInit(&arg, 1); -+ -+ arg.prompt = "Residue Dialog"; -+ arg.u.enumD.entryP = enumEntry; -+ arg.u.enumD.n = 2; -+ -+ enumEntry[0].str = "off"; -+ enumEntry[1].str = "on"; -+ -+ enumEntry[0].onOff = DialOn; -+ enumEntry[1].onOff = ! DialOn; -+ if (DialOn) -+ arg.v.intVal = 0; -+ else -+ arg.v.intVal = 1; -+ -+ errCode = ArgGet(&arg, 1); -+ if (errCode != EC_OK) { -+ ArgCleanup(&arg, 1); -+ return errCode; -+ } -+ -+ DialOn = (arg.v.intVal == 1); -+ -+ ArgCleanup(&arg, 1); -+ -+ if (DialOn) { -+ if (DialGizmo == NULL) { -+ buildDial(); -+ DhAddMolListCB(listCB, NULL); -+ } -+ PuSwitchGizmo(DialGizmo, TRUE); -+ } else { -+ if (DialGizmo != NULL) -+ PuSwitchGizmo(DialGizmo, FALSE); -+ } -+ -+ return EC_OK; -+} -\ No newline at end of file -diff --git a/src/cmddial/Makefile b/src/cmddial/Makefile -index d94609d..66fdea9 100644 ---- a/src/cmddial/Makefile -+++ b/src/cmddial/Makefile -@@ -8,7 +8,7 @@ CPPFLAGS = $(INCLUDES) $(MCPPFLAGS) - CFLAGS = $(CPPFLAGS) $(MCFLAGS) - - OBJ = ExDialColor.o ExDialSelect.o ExDialStyle.o ExDialMol.o ExDialMeas.o \ -- ExDialRmsd.o ExUserInterf.o ExRecordMac.o -+ ExDialRes.o ExDialRmsd.o ExUserInterf.o ExRecordMac.o - SRC = $(OBJ:.o=.c) - - default: $(LIBDIR)/libcmd.a -diff --git a/src/cmdio/ExPdb.c b/src/cmdio/ExPdb.c -index 8447c4c..fde9c73 100644 ---- a/src/cmdio/ExPdb.c -+++ b/src/cmdio/ExPdb.c -@@ -1,7 +1,7 @@ - /* - ************************************************************************ - * --* ExPdb.c - ReadPdb, ReadListPdb and WritePdb commands -+* ExPdb.c - ReadPdb, ReadOldPdb, ReadListPdb and WritePdb commands - * - * Copyright (c) 1994-98 - * -@@ -105,7 +105,7 @@ compFunc(void *p1, void *p2) - } - - static void --readTransTab(BOOL pdbToIntern) -+readTransTab(BOOL pdbToIntern, BOOL isNewNomenclature) - { - GFile gf; - GFileRes res; -@@ -114,7 +114,7 @@ readTransTab(BOOL pdbToIntern) - - TransTab = TreeOpen(sizeof(TransTabEntry), compFunc); - gf = SetupOpen(PN_PDB_ATOMS, "PdbAtoms", FALSE); -- if (gf == NULL) -+ if (gf == NULL || isNewNomenclature) - return; - - if (pdbToIntern) { -@@ -675,7 +675,7 @@ ExReadPdb(char *cmd) - return errCode; - } - -- readTransTab(TRUE); -+ readTransTab(TRUE, TRUE); - UnknownErrInit(); - - if (replace) { -@@ -755,7 +755,7 @@ ExReadListPdb(char *cmd) - - FileNamePath(fileName); - -- readTransTab(TRUE); -+ readTransTab(TRUE,TRUE); - UnknownErrInit(); - inName = DStrNew(); - pdbName = DStrNew(); -@@ -932,7 +932,7 @@ ExWritePdb(char *cmd) - if (gf == NULL) - return EC_ERROR; - -- readTransTab(FALSE); -+ readTransTab(FALSE,TRUE); - - CHECK_RES(GFileWriteStr(gf, "HEADER Structure from")); - CHECK_RES(GFileWriteStr(gf, PROG_NAME)); -@@ -987,3 +987,61 @@ ExWritePdb(char *cmd) - - return EC_OK; - } -+ -+ErrCode -+ExReadOldPdb(char *cmd) -+{ -+ BOOL replace; -+ DSTR name; -+ int molNo, readNo; -+ DhMolP *molPA; -+ ErrCode errCode; -+ DSTR errStr; -+ -+ replace = (strncmp(cmd, "Replace", 7) == 0); -+ -+ name = DStrNew(); -+ errCode = ArgGetFilename(name, CurrDirGet(), "*.pdb", TRUE); -+ if (errCode != EC_OK) { -+ DStrFree(name); -+ return errCode; -+ } -+ -+ readTransTab(TRUE, FALSE); -+ UnknownErrInit(); -+ -+ if (replace) { -+ molNo = SelMolGet(NULL, 0); -+ if (molNo > 0) { -+ molPA = malloc(molNo * sizeof(*molPA)); -+ (void) SelMolGet(molPA, molNo); -+ } -+ } else { -+ molNo = 0; -+ molPA = NULL; -+ } -+ -+ BreakActivate(TRUE); -+ errCode = readFile(molPA, molNo, name, &readNo); -+ BreakActivate(FALSE); -+ -+ DStrFree(name); -+ TreeClose(TransTab); -+ if (molNo > 0) -+ free(molPA); -+ -+ if (errCode != EC_OK) -+ return EC_ERROR; -+ -+ if (replace) -+ GraphMolChanged(PROP_SELECTED); -+ -+ errStr = UnknownErrGet(); -+ if (errStr != NULL) { -+ CipSetError(DStrToStr(errStr)); -+ DStrFree(errStr); -+ return EC_WARNING; -+ } -+ -+ return EC_OK; -+} -diff --git a/src/cmdstruc/ExBuild.c b/src/cmdstruc/ExBuild.c -index 32bc650..7f003b2 100644 ---- a/src/cmdstruc/ExBuild.c -+++ b/src/cmdstruc/ExBuild.c -@@ -31,11 +31,16 @@ - #include <data_hand.h> - #include <data_sel.h> - #include <graph_draw.h> -+#include <pu.h> - - #define ARG_NUM 1 - - static int CurrPos = 1; - static int CurrKind = 0; -+static PuTextWindow TextW; -+static DhMolP LastMolP=NULL; -+static BOOL messageWindowCreated=FALSE; -+static BOOL cyclicResidueFound=FALSE; - - ErrCode - ExNewMol(char *cmd) -@@ -206,3 +211,121 @@ ExChangeRes(char *cmd) - - return EC_OK; - } -+ -+static void -+writeInt(int num) -+{ -+ char buf[10]; -+ (void) sprintf(buf, "%5d ", num); -+ PuWriteStr(TextW, buf); -+} -+ -+static void -+checkMolCyclic(DhMolP molP, void *clientData) -+{ -+ DhResP resP; -+ DSTR resName = DStrNew(); -+ DStrAssignStr(resName, "XXX"); -+ -+ resP = DhResFirst(molP); -+ while (resP != NULL) { -+ if (DStrCmp(resName, DhResGetName(resP)) == 0) { -+ cyclicResidueFound=TRUE; -+ } -+ resP = DhResNext(resP); -+ } -+ -+ if (cyclicResidueFound && !messageWindowCreated) { -+ TextW = PuCreateTextWindow("MakeMolCyclic"); -+ PuWriteStr(TextW, "--------------------------------------------------\n"); -+ messageWindowCreated=TRUE; -+ } -+ if (cyclicResidueFound) { -+ PuWriteStr(TextW, "Error -"); -+ writeInt(DhMolGetNumber(molP) + 1); -+ PuWriteStr(TextW, DStrToStr(DhMolGetName(molP))); -+ PuWriteStr(TextW, " already made cyclic!\n"); -+ } -+} -+ -+static void -+makeMolCyclic(DhMolP molP, void *clientData) -+{ -+ DhResP xResP, yResP; -+ Vec3 firstCoord, lastCoord, midCoord; -+ DhResP firstResP, lastResP; -+ DhAtomP caAtomP; -+ DSTR atomName = DStrNew(); -+ DhResDefP resDefP = (DhResDefP) clientData; -+ -+ DStrAssignStr(atomName, "CA"); -+ -+ xResP = DhResNewCyclic(molP, resDefP, SP_FIRST); -+ DhResInit(xResP); -+ yResP = DhResNewCyclic(molP, resDefP, SP_LAST); -+ DhResInit(yResP); -+ -+ xResP = DhResFirst(molP); -+ -+ firstResP = DhResNext(xResP); -+ caAtomP = NULL; -+ while (caAtomP == NULL && firstResP != NULL) { -+ caAtomP = DhAtomFindName(firstResP, atomName, FALSE); -+ firstResP = DhResNext(firstResP); -+ } -+ if (caAtomP == NULL) { -+ return; -+ } -+ DhAtomGetCoord(caAtomP, firstCoord); -+ -+ yResP = DhResLast(molP); -+ lastResP = DhResPrev(yResP); -+ caAtomP = NULL; -+ while (caAtomP == NULL && lastResP != NULL) { -+ caAtomP = DhAtomFindName(lastResP, atomName, FALSE); -+ lastResP = DhResPrev(lastResP); -+ } -+ if (caAtomP == NULL) { -+ return; -+ } -+ -+ DhAtomGetCoord(caAtomP, lastCoord); -+ -+ midCoord[0] = (firstCoord[0]+lastCoord[0])/2; -+ midCoord[1] = (firstCoord[1]+lastCoord[1])/2; -+ midCoord[2] = (firstCoord[2]+lastCoord[2])/2; -+ -+ DhAtomSetCoord(DhResGetAtomA(xResP), midCoord); -+ DhAtomSetCoord(DhResGetAtomA(yResP), midCoord); -+} -+ -+ErrCode -+ExMakeMolCyclic(char *cmd) -+{ -+ int ind=0; -+ DhResDefP resDefP; -+ DSTR resName = DStrNew(); -+ -+ messageWindowCreated=FALSE; -+ cyclicResidueFound=FALSE; -+ DhApplyMol(PropGetRef(PROP_SELECTED, FALSE), checkMolCyclic, NULL); -+ if (cyclicResidueFound) { -+ DSTR msg = DStrNew(); -+ DStrAssignStr(msg, "Error cyclic molecules selected"); -+ PuSetTextField(PU_TF_STATUS, DStrToStr(msg)); -+ DStrFree(msg); -+ return EC_OK; -+ } -+ -+ DStrAssignStr(resName, "XXX"); -+ resDefP = DhResDefGet(resName); -+ if (resDefP == NULL) { -+ CipSetError("error cyclic marker residue 'XXX' not found in residue library"); -+ return EC_ERROR; -+ } -+ -+ DhApplyMol(PropGetRef(PROP_SELECTED, FALSE), makeMolCyclic, resDefP); -+ GraphMolChanged(PROP_SELECTED); -+ GraphRedrawNeeded(); -+ return EC_OK; -+} -diff --git a/src/data/DataHand.c b/src/data/DataHand.c -index 368aad3..d020c20 100644 ---- a/src/data/DataHand.c -+++ b/src/data/DataHand.c -@@ -994,9 +994,11 @@ BOOL - DhResDestroy(DhResP resP) - { - /* can only destroy first or last residue of molecule! */ -+ DhMolP molP; - if (resP == ListFirst(resP->molP->resL)) { -+ molP = resP->molP; - ListRemove(resP->molP->resL, resP); -- setEquivI(ListFirst(resP->molP->resL), NULL); -+ setEquivI((DhResP)ListFirst(molP->resL), NULL); - return TRUE; - } else if (resP == ListLast(resP->molP->resL)) { - ListRemove(resP->molP->resL, resP); -@@ -2842,6 +2844,18 @@ DhResGetName(DhResP resP) - return resP->defP->name; - } - -+DhAtomP -+DhResGetAtomA(DhResP resP) -+{ -+ return resP->atomA; -+} -+ -+DhResDefP -+DhResGetDefP(DhResP resP) -+{ -+ return resP->defP; -+} -+ - int - DhResGetNumber(DhResP resP) - { -@@ -3313,3 +3327,101 @@ DhAltCoordListGet(void) - { - return AltCoordList; - } -+ -+static void -+initResCyclic(DhResP resP) -+{ -+ DhResDefP defP; -+ DhResP prevResP, nextResP; -+ DhAtomP atomP, equivAtomP; -+ int i; -+ -+ defP = resP->defP; -+ -+ resP->neighLeftP = NULL; -+ resP->neighRightP = NULL; -+ -+ resP->atomA = malloc(defP->atomNo * sizeof(*resP->atomA)); -+ resP->bondA = malloc(defP->bondNo * sizeof(*resP->bondA)); -+ resP->angleA = malloc(defP->angleNo * sizeof(*resP->angleA)); -+ -+ for (i = 0; i < defP->atomNo; i++) -+ initAtom(resP->atomA + i, resP); -+ -+ for (i = defP->firstBondI; i <= defP->lastBondI; i++) -+ initBond(resP->bondA + i, resP); -+ -+ for (i = 0; i < defP->angleNo; i++) { -+ resP->angleA[i].resP = resP; -+ resP->angleA[i].val = 0.0f; -+ resP->angleA[i].minVal = DH_ANGLE_MIN; -+ resP->angleA[i].maxVal = DH_ANGLE_MAX; -+ resP->angleA[i].changed = FALSE; -+ resP->angleA[i].propTab = PropNewTab(FALSE); -+ } -+ -+ resP->propTab = PropNewTab(FALSE); -+ -+ for (i = 0; i < EQUIV_NO; i++) { -+ resP->equivI[i] = -1; -+ } -+ -+ prevResP = ListPrev(resP->molP->resL, resP); -+ nextResP = ListNext(resP->molP->resL, resP); -+} -+ -+DhResP -+DhResNewCyclic(DhMolP molP, DhResDefP defP, DhSeqPos pos) -+{ -+ struct DhResS resS; -+ DhResP resP, prevResP, nextResP; -+ -+ resS.molP = molP; -+ resS.defP = defP; -+ -+ if (pos == SP_FIRST) { -+ nextResP = ListFirst(molP->resL); -+ if (nextResP == NULL) -+ resS.num = 1; -+ else -+ resS.num = nextResP->num - 1; -+ -+ resP = ListInsertFirst(molP->resL, &resS); -+ } else { -+ prevResP = ListLast(molP->resL); -+ if (prevResP == NULL) -+ resS.num = 1; -+ else -+ resS.num = prevResP->num + 1; -+ -+ resP = ListInsertLast(molP->resL, &resS); -+ } -+ -+ initResCyclic(resP); -+ -+ return resP; -+} -+ -+DhResP -+DhResPrev(DhResP resP) -+{ -+ return (DhResP) ListPrev(resP->molP->resL, resP); -+} -+ -+DhResP -+DhResNext(DhResP resP) -+{ -+ return (DhResP) ListNext(resP->molP->resL, resP); -+} -+ -+DhResP -+DhResFirst(DhMolP molP) -+{ -+ return (DhResP) ListFirst(molP->resL); -+} -+ -+DhResP -+DhResLast(DhMolP molP) -+{ -+ return (DhResP) ListLast(molP->resL); -+} -diff --git a/src/iodev/IODev.c b/src/iodev/IODev.c -index aa4f9a7..9c04ce8 100644 ---- a/src/iodev/IODev.c -+++ b/src/iodev/IODev.c -@@ -44,6 +44,7 @@ extern void IOMotifGLDSetDev(void); - #endif - #ifdef IO_DEV_MOTIF_OGL - extern void IOMotifOGLSetDev(void); -+extern void IOMotifOGLDSetDev(void); - #endif - #ifdef IO_DEV_MOTIF_XGL - extern void IOMotifXGLSetDev(void); -@@ -75,6 +76,7 @@ static DevListEntry DevList[] = { - #endif - #ifdef IO_DEV_MOTIF_OGL - {"Motif/OpenGL", IOMotifOGLSetDev}, -+ {"Motif/OpenGLD", IOMotifOGLDSetDev}, - #endif - #ifdef IO_DEV_MOTIF_XGL - {"Motif/XGL", IOMotifXGLSetDev}, -diff --git a/src/main/MolInit.c b/src/main/MolInit.c -index a7c467a..fccccd3 100644 ---- a/src/main/MolInit.c -+++ b/src/main/MolInit.c -@@ -313,8 +313,9 @@ MolInit(char *defaultDev, int argc, char *argv[], char *macroName) - - SgSetDoubleBuffer(TRUE); - -- ProgDirSet("MOLMOLHOME", "/usr/molmol"); -+ ProgDirSet("MOLMOLHOME", argv[0]); - SetupSetDir("setup"); -+ CurrDirSet(getenv("HOME")); -- UserFileSetDir(CurrDirGet(), "molmol"); -+ UserFileSetDir(CurrDirGet(), ".molmol"); - GFileSetErrorHandler(handleFileError); - -@@ -326,7 +327,7 @@ MolInit(char *defaultDev, int argc, char *argv[], char *macroName) - IOSetErrorHandler(handleIOError); - - PuSetTextField(PU_TF_TITLE, -- "MOLMOL - MOLecule analysis and MOLecule display"); -+ "MOLMOL - MOLecule analysis and MOLecule display - JCU V1.0.8"); - - gf = UserFileOpenRead("par"); - if (gf != NULL) { -diff --git a/src/main/MolMol.c b/src/main/MolMol.c -index 6f825e8..902b50a 100644 ---- a/src/main/MolMol.c -+++ b/src/main/MolMol.c -@@ -30,5 +30,5 @@ - int - main(int argc, char *argv[]) - { -- return MolInit("Motif/X11", argc, argv, NULL); -+ return MolInit("Motif/OpenGL", argc, argv, NULL); - } -diff --git a/src/motif/MotifDial.c b/src/motif/MotifDial.c -index 6e3bfd7..8fe0c5a 100644 ---- a/src/motif/MotifDial.c -+++ b/src/motif/MotifDial.c -@@ -1115,26 +1115,24 @@ PuMotifSetStr(PuGizmo gizmo, PuStrChoice choice, char *val) - void - PuMotifSetColor(PuGizmo gizmo, float r, float g, float b) - { -- Display *dpy; -- int screen; -- Pixel pix; -- XColor col; -+ Display *display; -+ Pixel pixel; -+ XColor color; -+ Colormap colormap; - -- dpy = XtDisplay(gizmo); -- screen = DefaultScreen(dpy); -- XtVaGetValues(gizmo, -- XmNbackground, &pix, -- NULL); -+ display = XtDisplay(gizmo); -+ XtVaGetValues(gizmo, XmNbackground, &pixel, NULL); -+ colormap = DefaultColormapOfScreen(XtScreen(gizmo)); - -- if (pix == BlackPixel(dpy, screen)) -- return; -+ color.pixel = pixel; -+ color.red = FLOAT2SHORT(r); -+ color.green = FLOAT2SHORT(g); -+ color.blue = FLOAT2SHORT(b); -+ color.flags = DoRed | DoGreen | DoBlue; - -- col.pixel = pix; -- col.red = FLOAT2SHORT(r); -- col.green = FLOAT2SHORT(g); -- col.blue = FLOAT2SHORT(b); -- col.flags = DoRed | DoGreen | DoBlue; -- XStoreColor(dpy, DefaultColormap(dpy, screen), &col); -+ XFreeColors(display, colormap, &pixel, 1, 0); -+ XAllocColor(display, colormap, &color); -+ XtVaSetValues(gizmo, XmNbackground, color.pixel, NULL); - } - - void -diff --git a/src/motogl/MotOGLDump.c b/src/motogl/MotOGLDump.c -index 54a4222..3bc25cc 100644 ---- a/src/motogl/MotOGLDump.c -+++ b/src/motogl/MotOGLDump.c -@@ -302,7 +302,7 @@ writeImg(void) - TIFFSetField(tif, TIFFTAG_BITSPERSAMPLE, 8); - - if (Quality < 100) -- TIFFSetField(tif, TIFFTAG_COMPRESSION, COMPRESSION_PACKBITS); -+ TIFFSetField(tif, TIFFTAG_COMPRESSION, COMPRESSION_LZW); - else - TIFFSetField(tif, TIFFTAG_COMPRESSION, COMPRESSION_NONE); - -diff --git a/src/os/CurrDir.c b/src/os/CurrDir.c -index edee778..7d2b242 100644 ---- a/src/os/CurrDir.c -+++ b/src/os/CurrDir.c -@@ -26,9 +26,9 @@ - #include <curr_dir.h> - - #include <stdlib.h> --#ifdef WIN32 --#include <direct.h> - #include <string.h> -+#ifdef WIN32 -+#include <direct.h> - #else - #include <unistd.h> - #include <errno.h> -@@ -36,43 +36,15 @@ - - static char *CurrDir = NULL; - -+void -+CurrDirSet(char *dir) -+{ -+ CurrDir = malloc(strlen(dir) + 1); -+ (void) strcpy(CurrDir, dir); -+} -+ - char * - CurrDirGet(void) - { --#ifdef WIN32 -- int len, i; --#else -- int size = 10; --#endif -- -- if (CurrDir != NULL) -- return CurrDir; -- --#ifdef WIN32 -- CurrDir = _getcwd(NULL, 0); -- if (CurrDir != NULL) { -- len = strlen(CurrDir); -- for (i = 0; i < len; i++) -- if (CurrDir[i] == '\\') -- CurrDir[i] = '/'; -- return CurrDir; -- } --#else -- CurrDir = malloc(size); -- for (;;) { -- if (getcwd(CurrDir, size) != NULL) -- return CurrDir; -- if (errno != ERANGE) -- break; -- size *= 2; -- CurrDir = realloc(CurrDir, size); -- } --#endif -- -- /* cannot get current directory, return root directory */ -- CurrDir = realloc(CurrDir, 2); -- CurrDir[0] = '/'; -- CurrDir[1] = '\0'; -- - return CurrDir; - } -diff --git a/src/os/ProgDir.c b/src/os/ProgDir.c -index 7abb08d..79ede45 100644 ---- a/src/os/ProgDir.c -+++ b/src/os/ProgDir.c -@@ -45,10 +45,6 @@ ProgDirSet(char *envVar, char *defVal) - dir = getenv(envVar); - if (dir == NULL) { - len = GetModuleFileName(NULL, exePath, sizeof(exePath)); -- if (len == 0) { -- ProgDir = defVal; -- return; -- } - len--; - while (len > 0 && exePath[len] != '\\') - len--; -@@ -65,9 +61,24 @@ ProgDirSet(char *envVar, char *defVal) - if (ProgDir[i] == '\\') - ProgDir[i] = '/'; - #else -- ProgDir = getenv(envVar); -- if (ProgDir == NULL) -- ProgDir = defVal; -+ char *dir; -+ char *exePath; -+ int len; -+ dir = getenv(envVar); -+ if (dir == NULL) { -+ exePath = defVal; -+ len = strlen(exePath); -+ len--; -+ while (len > 0 && exePath[len] != '/') -+ len--; -+ dir = exePath; -+ } else { -+ len = strlen(dir); -+ } -+ -+ ProgDir = malloc(len + 1); -+ (void) strncpy(ProgDir, dir, len); -+ - #endif - } - -diff --git a/src/win/WinDial.c b/src/win/WinDial.c -index 61d6432..e880559 100644 ---- a/src/win/WinDial.c -+++ b/src/win/WinDial.c -@@ -1072,148 +1072,143 @@ dialProc(HWND w, UINT msgKind, WPARAM wParam, LPARAM lParam) - childP = (GizmoInfo *) GetWindowLong(childW, GWL_USERDATA); - - switch (notifyCode) { -- case BN_CLICKED: -- if (childId < infoP->u.dial.childNo) { -+ case BN_CLICKED: -+ if (childId < infoP->u.dial.childNo) { - childP = (GizmoInfo *) GetWindowLong(GetFocus(), GWL_USERDATA); -- if (childP->type == GIZMO_TOGGLE) { -- boxP = childP->u.toggle.boxP; -- if (boxP->type == GIZMO_RADIO_BOX) { -- for (i = 0; i < infoP->u.dial.childNo; i++) { -- cP = infoP->u.dial.childPA[i]; -- if (cP->type != GIZMO_TOGGLE) -- continue; -- if (cP->u.toggle.boxP != boxP) -- continue; -- onOff = SendMessage(cP->w, BM_GETCHECK, 0, 0); -- if (onOff && cP != childP) { -- cP->u.toggle.onOff = FALSE; -- SendMessage(cP->w, BM_SETCHECK, FALSE, 0); -- selectStruc.onOff = FALSE; -- callCB(boxP, PU_CT_SELECT, cP->name, &selectStruc); -- break; -- } -- } -- if (cP != childP) { -- childP->u.toggle.onOff = TRUE; -- SendMessage(childP->w, BM_SETCHECK, TRUE, 0); -- selectStruc.onOff = TRUE; -- callCB(boxP, PU_CT_SELECT, childP->name, &selectStruc); -- } -- } else { -- onOff = ! SendMessage(childP->w, BM_GETCHECK, 0, 0); -- childP->u.toggle.onOff = onOff; -- SendMessage(childP->w, BM_SETCHECK, onOff, 0); -- selectStruc.onOff = onOff; -- callCB(boxP, PU_CT_SELECT, childP->name, &selectStruc); -- } -- } else { -- callCB(childP, PU_CT_ACTIVATE, childP->name, NULL); -- if (childP->type == GIZMO_TEXT_FIELD && -- childP->u.text.historySize > 0) -- childP->u.text.firstMod = TRUE; -- } -- } else { -- buttonI = childId - infoP->u.dial.childNo; -- callCB(infoP, BUTTON_FIRST + buttonI, ButtonLabelA[buttonI], NULL); -- } -+ if (childP->type == GIZMO_TOGGLE) { -+ boxP = childP->u.toggle.boxP; -+ if (boxP->type == GIZMO_RADIO_BOX) { -+ for (i = 0; i < infoP->u.dial.childNo; i++) { -+ cP = infoP->u.dial.childPA[i]; -+ if (cP->type != GIZMO_TOGGLE) continue; -+ if (cP->u.toggle.boxP != boxP) continue; -+ onOff = SendMessage(cP->w, BM_GETCHECK, 0, 0); -+ if (onOff && cP != childP) { -+ cP->u.toggle.onOff = FALSE; -+ SendMessage(cP->w, BM_SETCHECK, FALSE, 0); -+ selectStruc.onOff = FALSE; -+ callCB(boxP, PU_CT_SELECT, cP->name, &selectStruc); -+ break; -+ } -+ } -+ if (cP != childP) { -+ childP->u.toggle.onOff = TRUE; -+ SendMessage(childP->w, BM_SETCHECK, TRUE, 0); -+ selectStruc.onOff = TRUE; -+ callCB(boxP, PU_CT_SELECT, childP->name, &selectStruc); -+ } -+ } else { -+ onOff = ! SendMessage(childP->w, BM_GETCHECK, 0, 0); -+ childP->u.toggle.onOff = onOff; -+ SendMessage(childP->w, BM_SETCHECK, onOff, 0); -+ selectStruc.onOff = onOff; -+ callCB(boxP, PU_CT_SELECT, childP->name, &selectStruc); -+ } -+ } else { -+ callCB(childP, PU_CT_ACTIVATE, childP->name, NULL); -+ if (childP->type == GIZMO_TEXT_FIELD && childP->u.text.historySize > 0) childP->u.text.firstMod = TRUE; -+ } -+ } else { -+ buttonI = childId - infoP->u.dial.childNo; -+ callCB(infoP, BUTTON_FIRST + buttonI, ButtonLabelA[buttonI], NULL); -+ } - return TRUE; -- case EN_UPDATE: -- textEdit(childP); -- return TRUE; -- case LBN_SELCHANGE: -- for (i = 0; i < childP->u.list.entryNo; i++) -- if (SendMessage(childW, LB_GETSEL, i, 0) != -- childP->u.list.entryA[i].onOff) -- lastI = i; - -- for (i = 0; i < childP->u.list.entryNo; i++) { -- onOff = SendMessage(childW, LB_GETSEL, i, 0); -- if (onOff != childP->u.list.entryA[i].onOff) { -- if (! childP->u.list.autoDesel) -+ case EN_UPDATE: -+ textEdit(childP); -+ return TRUE; -+ -+ case LBN_SELCHANGE: -+ for (i = 0; i < childP->u.list.entryNo; i++) -+ if (SendMessage(childW, LB_GETSEL, i, 0) != childP->u.list.entryA[i].onOff) -+ lastI = i; -+ -+ for (i = 0; i < childP->u.list.entryNo; i++) { -+ onOff = SendMessage(childW, LB_GETSEL, i, 0); -+ if (onOff != childP->u.list.entryA[i].onOff) { -+ if (! childP->u.list.autoDesel) - childP->u.list.entryA[i].onOff = onOff; -- selectStruc.onOff = onOff; -- selectStruc.last = (i == lastI); -- callCB(childP, PU_CT_SELECT, -- childP->u.list.entryA[i].str, &selectStruc); -- } -- } -- -- if (childP->u.list.autoDesel) -- SendMessage(childW, LB_SETCURSEL, -1, 0); -- -- return TRUE; -+ selectStruc.onOff = onOff; -+ selectStruc.last = (i == lastI); -+ callCB(childP, PU_CT_SELECT, -+ childP->u.list.entryA[i].str, &selectStruc); -+ } -+ } -+ if (childP->u.list.autoDesel) -+ SendMessage(childW, LB_SETCURSEL, -1, 0); -+ return TRUE; - } -+ break; - -- break; -- case WM_VSCROLL: -- childW = (HWND) lParam; -- childP = (GizmoInfo *) GetWindowLong(childW, GWL_USERDATA); -- scrollCode = LOWORD(wParam); -+ case WM_VSCROLL: -+ childW = (HWND) lParam; -+ childP = (GizmoInfo *) GetWindowLong(childW, GWL_USERDATA); -+ scrollCode = LOWORD(wParam); - -- if (scrollCode == SB_LINEUP) { -- upHistory(childP->u.scroll.textP); -- } else if (scrollCode == SB_LINEDOWN) { -- downHistory(childP->u.scroll.textP); -- } else { -- return FALSE; -- } -- return TRUE; -- case WM_HSCROLL: -- scrollCode = LOWORD(wParam); -- if (scrollCode != SB_THUMBPOSITION && scrollCode != SB_THUMBTRACK) -- return FALSE; -+ if (scrollCode == SB_LINEUP) { -+ upHistory(childP->u.scroll.textP); -+ } else if (scrollCode == SB_LINEDOWN) { -+ downHistory(childP->u.scroll.textP); -+ } else { -+ return FALSE; -+ } -+ return TRUE; -+ case WM_HSCROLL: -+ scrollCode = LOWORD(wParam); -+ if (scrollCode != SB_THUMBPOSITION && scrollCode != SB_THUMBTRACK) -+ return FALSE; - -- scrollPos = (int)(short)HIWORD(wParam); -- childW = (HWND) lParam; -- childP = (GizmoInfo *) GetWindowLong(childW, GWL_USERDATA); -+ scrollPos = (int)(short)HIWORD(wParam); -+ childW = (HWND) lParam; -+ childP = (GizmoInfo *) GetWindowLong(childW, GWL_USERDATA); - -- floatStruc.oldVal = childP->u.slider.val; -- childP->u.slider.val = scrollPos / childP->u.slider.factor; -- SetScrollPos(childW, SB_CTL, -- (int) (childP->u.slider.val * childP->u.slider.factor), -- TRUE); -+ floatStruc.oldVal = childP->u.slider.val; -+ childP->u.slider.val = scrollPos / childP->u.slider.factor; -+ SetScrollPos(childW, SB_CTL, -+ (int) (childP->u.slider.val * childP->u.slider.factor), TRUE); - -- if (childP->u.slider.valuatorCB == NULL) { -- floatStruc.newVal = childP->u.slider.val; -- callCB(childP, PU_CT_MODIFY, childP->name, &floatStruc); -- } else { -- valStruc.act = PU_MA_ACTIVATE; -- valStruc.name = childP->name; -- valStruc.val = childP->u.slider.val; -- childP->u.slider.valuatorCB(childP, childP->u.slider.clientData, &valStruc); -- } -+ if (childP->u.slider.valuatorCB == NULL) { -+ floatStruc.newVal = childP->u.slider.val; -+ callCB(childP, PU_CT_MODIFY, childP->name, &floatStruc); -+ } else { -+ valStruc.act = PU_MA_ACTIVATE; -+ valStruc.name = childP->name; -+ valStruc.val = childP->u.slider.val; -+ childP->u.slider.valuatorCB(childP, childP->u.slider.clientData, &valStruc); -+ } -+ return TRUE; - -- return TRUE; -- case WM_PAINT: -- for (childId = 0; childId < infoP->u.dial.childNo; childId++) { -- childP = infoP->u.dial.childPA[childId]; -- if (childP->type == GIZMO_COLOR_FIELD) -- paintColor(childP->w, -- childP->u.color.r, childP->u.color.g, childP->u.color.b); -- } -- break; -- case WM_MOVE: -- if (infoP->u.dial.outside) { -- WinPlaceChanged(infoP->w); -- return TRUE; -- } -- break; -- case WM_CLOSE: -- buttonNo = 0; -- for (i = 0; i < BUTTON_NO; i++) -- if (infoP->u.dial.buttonSwitchA[i]) -- buttonNo++; -- if (buttonNo == 0) -- ShowWindow(infoP->w, SW_HIDE); -- return TRUE; -- case WM_DESTROY: -- WinRemoveDialog(w); -- for (childId = 0; childId < infoP->u.dial.childNo; childId++) -- freeInfo(infoP->u.dial.childPA[childId]); -- freeInfo(infoP); -- return TRUE; -- } -+ case WM_PAINT: -+ for (childId = 0; childId < infoP->u.dial.childNo; childId++) { -+ childP = infoP->u.dial.childPA[childId]; -+ if (childP->type == GIZMO_COLOR_FIELD) -+ paintColor(childP->w, -+ childP->u.color.r, childP->u.color.g, childP->u.color.b); -+ } -+ break; - -+ case WM_MOVE: -+ if (infoP->u.dial.outside) { -+ WinPlaceChanged(infoP->w); -+ return TRUE; -+ } -+ break; -+ case WM_CLOSE: -+ buttonNo = 0; -+ for (i = 0; i < BUTTON_NO; i++) { -+ if (infoP->u.dial.buttonSwitchA[i]) buttonNo++; -+ if (buttonNo == 0) { -+ ShowWindow(infoP->w, SW_HIDE); -+ } -+ } -+ return TRUE; -+ case WM_DESTROY: -+ WinRemoveDialog(w); -+ for (childId = 0; childId < infoP->u.dial.childNo; childId++) -+ freeInfo(infoP->u.dial.childPA[childId]); -+ freeInfo(infoP); -+ return TRUE; -+ } - return FALSE; - } - -diff --git a/src/winogl/WinOGLDump.c b/src/winogl/WinOGLDump.c -index 0a7d61a..a8ce850 100644 ---- a/src/winogl/WinOGLDump.c -+++ b/src/winogl/WinOGLDump.c -@@ -44,6 +44,7 @@ - #endif - #ifdef PNG_SUPPORT - #include <png.h> -+#include <pngpriv.h> - #endif - - #include "winogl_int.h" -@@ -251,7 +252,7 @@ static void - pngErrHand(png_structp pngStrucP, char *errMsg) - { - IORaiseError(errMsg); -- longjmp(pngStrucP->jmpbuf, 1); -+ longjmp(pngStrucP->longjmp_buffer, 1); - } - #endif - -@@ -314,7 +315,7 @@ writeImg(void) - TIFFSetField(tif, TIFFTAG_BITSPERSAMPLE, 8); - - if (Quality < 100) -- TIFFSetField(tif, TIFFTAG_COMPRESSION, COMPRESSION_PACKBITS); -+ TIFFSetField(tif, TIFFTAG_COMPRESSION, COMPRESSION_LZW); - else - TIFFSetField(tif, TIFFTAG_COMPRESSION, COMPRESSION_NONE); - -@@ -369,7 +370,7 @@ writeImg(void) - return IO_RES_ERR; - } - -- if (setjmp(pngStrucP->jmpbuf)) { -+ if (setjmp(pngStrucP->longjmp_buffer)) { - if (cBuf != NULL) - free(cBuf); - if (fBuf != NULL) diff --git a/sci-chemistry/molmol/molmol-2k_p2-r2.ebuild b/sci-chemistry/molmol/molmol-2k_p2-r2.ebuild index 9fafb28a9e9f..888c738d4f15 100644 --- a/sci-chemistry/molmol/molmol-2k_p2-r2.ebuild +++ b/sci-chemistry/molmol/molmol-2k_p2-r2.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2013 Gentoo Foundation +# Copyright 1999-2017 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 EAPI=4 @@ -12,7 +12,8 @@ DESCRIPTION="Publication-quality molecular visualization package" HOMEPAGE="http://hugin.ethz.ch/wuthrich/software/molmol/index.html" SRC_URI=" ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-src.tar.gz - ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-doc.tar.gz" + ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-doc.tar.gz + https://dev.gentoo.org/~soap/distfiles/${PN}-patches.tbz2" LICENSE="molmol" SLOT="0" @@ -45,12 +46,12 @@ pkg_setup() { src_prepare() { rm -rf tiff* # Patch from http://pjf.net/science/molmol.html, where src.rpm is provided - epatch "${FILESDIR}"/pjf_RH9_molmol2k2.diff + epatch "${WORKDIR}"/patches/pjf_RH9_molmol2k2.diff - epatch "${FILESDIR}"/prefix.patch + epatch "${WORKDIR}"/patches/prefix.patch eprefixify molmol - epatch "${FILESDIR}"/ldflags.patch + epatch "${WORKDIR}"/patches/ldflags.patch ln -s makedef.lnx "${S}"/makedef || die @@ -63,8 +64,8 @@ src_prepare() { -e "s:^CC.*:CC = $(tc-getCC):" \ -i "${S}"/makedef || die - epatch "${FILESDIR}"/cast.patch - epatch "${FILESDIR}"/libpng15.patch + epatch "${WORKDIR}"/patches/cast.patch + epatch "${WORKDIR}"/patches/libpng15.patch } src_install() { diff --git a/sci-chemistry/molmol/molmol-2k_p2-r3.ebuild b/sci-chemistry/molmol/molmol-2k_p2-r3.ebuild index 318269562f26..22f3e6a03bdf 100644 --- a/sci-chemistry/molmol/molmol-2k_p2-r3.ebuild +++ b/sci-chemistry/molmol/molmol-2k_p2-r3.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2013 Gentoo Foundation +# Copyright 1999-2017 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 EAPI=4 @@ -12,7 +12,8 @@ DESCRIPTION="Publication-quality molecular visualization package" HOMEPAGE="http://hugin.ethz.ch/wuthrich/software/molmol/index.html" SRC_URI=" ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-src.tar.gz - ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-doc.tar.gz" + ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-doc.tar.gz + https://dev.gentoo.org/~soap/distfiles/${PN}-patches.tbz2" LICENSE="molmol" SLOT="0" @@ -45,12 +46,12 @@ pkg_setup() { src_prepare() { rm -rf tiff* # Patch from http://pjf.net/science/molmol.html, where src.rpm is provided - epatch "${FILESDIR}"/pjf_RH9_molmol2k2.diff + epatch "${WORKDIR}"/patches/pjf_RH9_molmol2k2.diff - epatch "${FILESDIR}"/prefix.patch + epatch "${WORKDIR}"/patches/prefix.patch eprefixify molmol - epatch "${FILESDIR}"/ldflags.patch + epatch "${WORKDIR}"/patches/ldflags.patch ln -s makedef.lnx "${S}"/makedef || die @@ -63,12 +64,12 @@ src_prepare() { -e "s:^CC.*:CC = $(tc-getCC):" \ -i "${S}"/makedef || die - epatch "${FILESDIR}"/cast.patch - epatch "${FILESDIR}"/libpng15.patch + epatch "${WORKDIR}"/patches/cast.patch + epatch "${WORKDIR}"/patches/libpng15.patch # patch from fink # fixes numerous bad bracings and hopefully the OGL bug 429974 - epatch "${FILESDIR}"/${P}-fink.patch + epatch "${WORKDIR}"/patches/${P}-fink.patch } src_install() { diff --git a/sci-chemistry/molmol/molmol-2k_p2-r4.ebuild b/sci-chemistry/molmol/molmol-2k_p2-r4.ebuild index d4034a9d63c5..26a294922182 100644 --- a/sci-chemistry/molmol/molmol-2k_p2-r4.ebuild +++ b/sci-chemistry/molmol/molmol-2k_p2-r4.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2017 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 EAPI=5 @@ -12,7 +12,8 @@ DESCRIPTION="Publication-quality molecular visualization package" HOMEPAGE="http://hugin.ethz.ch/wuthrich/software/molmol/index.html" SRC_URI=" ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-src.tar.gz - ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-doc.tar.gz" + ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-doc.tar.gz + https://dev.gentoo.org/~soap/distfiles/${PN}-patches.tbz2" LICENSE="molmol" SLOT="0" @@ -45,12 +46,12 @@ pkg_setup() { src_prepare() { rm -rf tiff* # Patch from http://pjf.net/science/molmol.html, where src.rpm is provided - epatch "${FILESDIR}"/pjf_RH9_molmol2k2.diff + epatch "${WORKDIR}"/patches/pjf_RH9_molmol2k2.diff - epatch "${FILESDIR}"/prefix.patch + epatch "${WORKDIR}"/patches/prefix.patch eprefixify molmol - epatch "${FILESDIR}"/ldflags.patch + epatch "${WORKDIR}"/patches/ldflags.patch ln -s makedef.lnx "${S}"/makedef || die @@ -63,12 +64,12 @@ src_prepare() { -e "s:^CC.*:CC = $(tc-getCC):" \ -i "${S}"/makedef || die - epatch "${FILESDIR}"/cast.patch - epatch "${FILESDIR}"/libpng15.patch + epatch "${WORKDIR}"/patches/cast.patch + epatch "${WORKDIR}"/patches/libpng15.patch # patch from fink # fixes numerous bad bracings and hopefully the OGL bug 429974 - epatch "${FILESDIR}"/${P}-fink.patch + epatch "${WORKDIR}"/patches/${P}-fink.patch tc-export AR } diff --git a/sci-chemistry/molmol/molmol-2k_p2-r5.ebuild b/sci-chemistry/molmol/molmol-2k_p2-r5.ebuild index 16e8b8553600..d788caa2005a 100644 --- a/sci-chemistry/molmol/molmol-2k_p2-r5.ebuild +++ b/sci-chemistry/molmol/molmol-2k_p2-r5.ebuild @@ -12,7 +12,8 @@ DESCRIPTION="Publication-quality molecular visualization package" HOMEPAGE="http://hugin.ethz.ch/wuthrich/software/molmol/index.html" SRC_URI=" ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-src.tar.gz - ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-doc.tar.gz" + ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-doc.tar.gz + https://dev.gentoo.org/~soap/distfiles/${PN}-patches.tbz2" LICENSE="molmol" SLOT="0" @@ -45,10 +46,10 @@ pkg_setup() { src_prepare() { rm -rf tiff* # Patch from http://pjf.net/science/molmol.html, where src.rpm is provided - epatch "${FILESDIR}"/pjf_RH9_molmol2k2.diff + epatch "${WORKDIR}"/patches/pjf_RH9_molmol2k2.diff - epatch "${FILESDIR}"/ldflags.patch - epatch "${FILESDIR}"/opengl.patch + epatch "${WORKDIR}"/patches/ldflags.patch + epatch "${WORKDIR}"/patches/opengl.patch ln -s makedef.lnx "${S}"/makedef || die @@ -61,14 +62,14 @@ src_prepare() { -e "s:^CC.*:CC = $(tc-getCC):" \ -i "${S}"/makedef || die - epatch "${FILESDIR}"/cast.patch - epatch "${FILESDIR}"/libpng15.patch + epatch "${WORKDIR}"/patches/cast.patch + epatch "${WORKDIR}"/patches/libpng15.patch # patch from fink # fixes numerous bad bracings and hopefully the OGL bug 429974 - epatch "${FILESDIR}"/${P}-fink.patch + epatch "${WORKDIR}"/patches/${P}-fink.patch - epatch "${FILESDIR}"/wild.patch + epatch "${WORKDIR}"/patches/wild.patch tc-export AR } |