sci-chemistry/molmol: Add patch from fink, enhances code style and fixes OGL bug, #429974

Package-Manager: portage-2.2.0_alpha120/cvs/Linux x86_64

5 files changed, 473 insertions, 23 deletions

diff --git a/sci-chemistry/molmol/ChangeLog b/sci-chemistry/molmol/ChangeLog
index 3d5ab53a1297..23520d18a78a 100644
--- a/sci-chemistry/molmol/ChangeLog
+++ b/sci-chemistry/molmol/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-chemistry/molmol
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/molmol/ChangeLog,v 1.30 2012/02/17 09:24:23 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/molmol/ChangeLog,v 1.31 2012/08/05 12:38:45 jlec Exp $
+
+*molmol-2k_p2-r3 (05 Aug 2012)
+
+  05 Aug 2012; Justin Lecher <jlec@gentoo.org> molmol-2k_p2-r2.ebuild,
+  +molmol-2k_p2-r3.ebuild, +files/molmol-2k_p2-fink.patch:
+  Add patch from fink, enhances code style and fixes OGL bug, #429974
 
   17 Feb 2012; Justin Lecher <jlec@gentoo.org> molmol-2k_p2-r2.ebuild:
   Add altenative dependency on libGLw
diff --git a/sci-chemistry/molmol/Manifest b/sci-chemistry/molmol/Manifest
index a7a2553f02d3..bfad7bcfb594 100644
--- a/sci-chemistry/molmol/Manifest
+++ b/sci-chemistry/molmol/Manifest
@@ -1,20 +1,23 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA512
+Hash: SHA256
 
-AUX cast.patch 519 RMD160 3ce926dbda9345a380b7e9da9dd062db7b5f4b78 SHA1 2f1bfefbc5a146665cf90cf3a7147387ee3d7eb8 SHA256 25acec7df7e5739e2e4664672e979636ccd13c68b2ce5d26e555b3d619be0e77
-AUX ldflags.patch 435 RMD160 17c6cfc1539c0d774531c950d82f1fb28f366aea SHA1 e9e736664e773b32f2ae861f65fc0670d3625998 SHA256 cbae8934e2be43ceac0f541ed14e843ed76baf86219e0f669eab0af6d5714c64
-AUX libpng15.patch 826 RMD160 3ae336cba8937bfde272a4384103efa6e15f0c5d SHA1 d2baa71a5055638d1c5f6b90e7f8020a29ae573a SHA256 656a088b11f0ce171ab666aed8de36e3eeac3576322055ab0036794b02c370ed
-AUX pjf_RH9_molmol2k2.diff 3138 RMD160 1792aa433a21c2f64880b244d11b6bbd2552c95b SHA1 e654f3105d496538af42a8282f1d55c272ff3d4d SHA256 5b7c3ede5714b123824cc0b8533f679d22d1c5219bf88e8d6a4cebe8e245aeb9
-AUX prefix.patch 513 RMD160 23239041256a23c6223daab56e1aa59b5e911afa SHA1 5f3707fec532b15579020b5f21112d3fa2d41924 SHA256 efcb5d3fa7258cf88f02b63d1df3100eb0b73848c0ebabb59c84cb9ea082d8e7
-DIST molmol-2k.2.0-doc.tar.gz 1062297 RMD160 08b3e21ab6eb7c9044e59373334181ff91ca8a53 SHA1 b47551283fa19f57f4d5edcbd52f725055d80b7f SHA256 07e1c3fd04ffe7c9e9d91eaefa0bf72e6d0913a981eec3bf0879bfc65537a6be
-DIST molmol-2k.2.0-src.tar.gz 1088805 RMD160 b1de89953631dd9b11928751d7853cb511bf45f0 SHA1 09482a1dea601563ca64e773dc0ec47019e22c63 SHA256 1104dcb1b2517581c7d6b1695ff2e92f4076ad34afc48dd896eec38e5acf2287
-EBUILD molmol-2k_p2-r2.ebuild 1782 RMD160 8c6a9079e568059dfac5c77ea59c0ca31286449e SHA1 3f1e9c1914fd3acab7f8cb26b5fb6b50007a3061 SHA256 997582e74b2c788942cad885c05ab75b8392fc4c563518a670551f7d36acda78
-MISC ChangeLog 4206 RMD160 c063a102904495f4a8060d4a7a422f4a4b509885 SHA1 1806432fd44af477ba41dc9afe7c935006556d98 SHA256 7a8349c9db65479b076953c737e6521b5d73ecce9c502e346cfbe928a827c2d4
-MISC metadata.xml 167 RMD160 ea4003a55d6e2079381a540c441fc59cde29025a SHA1 3bc6dc4dd68f7de22828138e62aa117387b1765d SHA256 f313eeec4ebffac500b57a98a225e32c77489fc826a50494749b6cdeec28e3e8
+AUX cast.patch 519 SHA256 25acec7df7e5739e2e4664672e979636ccd13c68b2ce5d26e555b3d619be0e77 SHA512 4c57ee9b61a81c8e3b43527914bb3bb16e53083cafacb65fa77e3dd630ec76289e0dbbac62a013b6245c6a5460e0fb40d515af1e5273f8088165e272caecbe17 WHIRLPOOL 38637d00c9d30f71ac23ce6cfc1936dd42837e2d484a083f8324d71ef021d8bc5e13c6ceee006602b75386a24e57d9ff5aa09ae73dd319ca18158e2496b7c608
+AUX ldflags.patch 435 SHA256 cbae8934e2be43ceac0f541ed14e843ed76baf86219e0f669eab0af6d5714c64 SHA512 32c266444bf4341bf2db3fb3330c240729f7a538750c0962ee6b128947c5895fa84425a380a9f0897dacfe95bdc8d395e56e62a44c070513274000d5a493e0e3 WHIRLPOOL 39e7ec799e81a814e8f75e33b9996f82f0ecfde31cb4d0d02a01a98b1ac93cdd57879b58c57941b86ae67047f7d235af18844370474f9409c09397ff11f4d2c0
+AUX libpng15.patch 826 SHA256 656a088b11f0ce171ab666aed8de36e3eeac3576322055ab0036794b02c370ed SHA512 df973c637f09225d3f193bb6f977df515b9d475fb47d3a5e6288daaf1cea79afc1fe022803f9cbc1331b373c6ac1e52056e1fbb8e909562065347cf1ae87a205 WHIRLPOOL 54ba85edd7481a6532cba1ffbf007ec408d27965aa19a8ca358140b137ffee2a69237443ad25698b9ab1ce2bc36cd71914af62889c4be219a2584411ddfcba41
+AUX molmol-2k_p2-fink.patch 12821 SHA256 b7ddc4d48e6149f6ced7e287bf7b72b798394d17d01dee373d2615bf6407f04b SHA512 5646ae8f4801d53f1673c0656b3e5d152767a7cd6b85adec0d13fcb8e60a39e825ac733d18ed14ee1ef738d24841061f7fac2f6aa02cae78bead7f6b39a0a77f WHIRLPOOL 539b94c01fd7333b778b9c534bbc0c3c19c93331170c5afa8f2c4ea5e945a4398ab238fa5b988ff81f7d580b4f677e74e391174ab92f0de5986ceb6caba94c28
+AUX pjf_RH9_molmol2k2.diff 3138 SHA256 5b7c3ede5714b123824cc0b8533f679d22d1c5219bf88e8d6a4cebe8e245aeb9 SHA512 93b78202d7bb705e253f2111eeda64c44269e2662c44e2ad5e02a0db9eaa62a7ef3efa25463668a17be9dcc39c81ac1f1875ac7d1990ee537c3dcbd53258bece WHIRLPOOL 9b5a9f5576535e96f23046ca4ce5c9b3e34167818b8c8fa469c4fdf10549e33d75fb4a290547791bb37d7c7ad07e297fc63659bf1c87eafc468b6b2fca4b7b76
+AUX prefix.patch 513 SHA256 efcb5d3fa7258cf88f02b63d1df3100eb0b73848c0ebabb59c84cb9ea082d8e7 SHA512 5e566b80238a5caf1f1d6de4d14ce4088b38dd5f1263390afa4304853f2b8bd71285da21cd14bf56c44211781593686696571e283915f528cffa8d6d3b8f12a4 WHIRLPOOL ac502216971039b07e43596d545b05b52b8a94e32339883c3cfaa46264d8b0992f39beb149b7d5bbb650500cc6040876d0e0818317e34db7abf193813c5f0744
+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
+EBUILD molmol-2k_p2-r2.ebuild 1800 SHA256 1693f8e9ba8943403c67af754bd69e7984392e258325b2f60ae01674d751243f SHA512 b7a6b4793212aea593a7dcbf7b03a9f75e6aa69c30f5ab4b3cf4d1e93fc4e38773ccb53c9b33cb4e34cafc77a664836efbeb88f938241b7c251d75be32cb6aa5 WHIRLPOOL 09eaf131c1a5293e3008cade8a46f9541cee35ba7fe4bbc8bd9300c651fe2a3e1da03ef7082f9964117c99ad8a749d068a444d76b04b64ca9b7ba34a5484b499
+EBUILD molmol-2k_p2-r3.ebuild 1924 SHA256 7cc499cb1f3e55844d74b9504323558fe6f2ada25655d1b9af9c8b53441a4c3d SHA512 4a1ba130789ff89c1b08c52c2e9b7ca2de118a2123c1f22f8c235947f6514daa7fd441e2f150a9d6ad72f4630babf798d34757c2fb6cd469e52c91887f5b06c1 WHIRLPOOL b235a3e8068c9145b145c9fb0a907a8bfe49ad5bf4d93d48c6d5d59498175fb0cc5b7885e8139d76fbd0880eeb1066f1bad6080ff3f9a7b05b6bfef9bb29a15b
+MISC ChangeLog 4439 SHA256 41f3db6c6b0da8fb355f9ccc1736afad7c1d504d1fe67f98c8b1e2400ddc36bd SHA512 bdf4d7110827044209a608f5ff4df0b90b7e0381339ef02a70a7697db741e6e42662c4f84886611788aec5e9f11ee612e364ae26a81688e71bc618af0acad453 WHIRLPOOL 435490713b4b9712b53454b5264e8030109b483f3faa30a17c07e893c4ae48f8ee5987fb7ab79e47f2264ee29ee5292e29ebb6dcda9f550c2a6623c2d680b2a0
+MISC metadata.xml 167 SHA256 f313eeec4ebffac500b57a98a225e32c77489fc826a50494749b6cdeec28e3e8 SHA512 0f65f650c91edb15011884892b3e2447ec2342f207b6b71541ec25939fed33cd219b1fcd85dd06008b56a50622973febeb63c9c6158f62435c63c4fbd3ab93bd WHIRLPOOL 0823fd1d22e4aea50bcf78c359303d804128475e21e39514505ee6528c9c46376ceafc1f13bb1cc4e1143d434397fb4ef65dc028e924fdc831521947534fd93f
 -----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.18 (GNU/Linux)
+Version: GnuPG v2.0.19 (GNU/Linux)
+Comment: GPGTools - http://gpgtools.org
 
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-=+JQg
+iEYEAREIAAYFAlAeaVoACgkQgAnW8HDreRbZtwCdFa/S0lnOTWhmYc3WaiLfB9r6
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diff --git a/sci-chemistry/molmol/files/molmol-2k_p2-fink.patch b/sci-chemistry/molmol/files/molmol-2k_p2-fink.patch
new file mode 100644
index 000000000000..14cc83b63e9e
--- /dev/null
+++ b/sci-chemistry/molmol/files/molmol-2k_p2-fink.patch
@@ -0,0 +1,356 @@
+ 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/molmol-2k_p2-r2.ebuild b/sci-chemistry/molmol/molmol-2k_p2-r2.ebuild
index d1ba46400aab..72e2633ae3d2 100644
--- a/sci-chemistry/molmol/molmol-2k_p2-r2.ebuild
+++ b/sci-chemistry/molmol/molmol-2k_p2-r2.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2012 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/molmol/molmol-2k_p2-r2.ebuild,v 1.11 2012/02/17 09:24:23 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/molmol/molmol-2k_p2-r2.ebuild,v 1.12 2012/08/05 12:38:45 jlec Exp $
 
 EAPI=4
 
@@ -22,24 +22,26 @@ IUSE=""
 
 DEPEND="
 	|| (
-		media-libs/mesa[motif]
 		(	media-libs/mesa
-			x11-libs/libGLw ) )
+			x11-libs/libGLw )
+		media-libs/mesa[motif] )
 	media-libs/libpng:0
 	media-libs/tiff:0
 	sys-libs/zlib
 	virtual/jpeg
 	x11-libs/libXpm
-	>=x11-libs/openmotif-2.3:0
+	x11-libs/openmotif:0
 	x11-apps/xdpyinfo"
 RDEPEND="${DEPEND}"
 
 S="${WORKDIR}"
 
-MMDIR="/usr/$(get_libdir)/molmol"
-
 MAKEOPTS="${MAKEOPTS} -j1"
 
+pkg_setup() {
+	MMDIR="/usr/$(get_libdir)/molmol"
+}
+
 src_prepare() {
 	rm -rf tiff*
 	# Patch from http://pjf.net/science/molmol.html, where src.rpm is provided
@@ -50,7 +52,7 @@ src_prepare() {
 
 	epatch "${FILESDIR}"/ldflags.patch
 
-	ln -s makedef.lnx "${S}"/makedef
+	ln -s makedef.lnx "${S}"/makedef || die
 
 	sed \
 		-e "s:/bin/ksh:${EPREFIX}/bin/sh:" \
diff --git a/sci-chemistry/molmol/molmol-2k_p2-r3.ebuild b/sci-chemistry/molmol/molmol-2k_p2-r3.ebuild
new file mode 100644
index 000000000000..aaae9fb21de8
--- /dev/null
+++ b/sci-chemistry/molmol/molmol-2k_p2-r3.ebuild
@@ -0,0 +1,83 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/molmol/molmol-2k_p2-r3.ebuild,v 1.1 2012/08/05 12:38:45 jlec Exp $
+
+EAPI=4
+
+inherit eutils multilib prefix toolchain-funcs
+
+MY_PV="${PV/_p/.}.0"
+MY_P="${PN}-${MY_PV}"
+
+DESCRIPTION="Publication-quality molecular visualization package"
+HOMEPAGE="http://hugin.ethz.ch/wuthrich/software/molmol/index.html"
+SRC_URI="
+	ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-src.tar.gz
+	ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-doc.tar.gz"
+
+LICENSE="molmol"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+DEPEND="
+	|| (
+		(	media-libs/mesa
+			x11-libs/libGLw )
+		media-libs/mesa[motif] )
+	media-libs/libpng:0
+	media-libs/tiff:0
+	sys-libs/zlib
+	virtual/jpeg
+	x11-libs/libXpm
+	x11-libs/openmotif:0
+	x11-apps/xdpyinfo"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"
+
+MAKEOPTS="${MAKEOPTS} -j1"
+
+pkg_setup() {
+	MMDIR="/usr/$(get_libdir)/molmol"
+}
+
+src_prepare() {
+	rm -rf tiff*
+	# Patch from http://pjf.net/science/molmol.html, where src.rpm is provided
+	epatch "${FILESDIR}"/pjf_RH9_molmol2k2.diff
+
+	epatch "${FILESDIR}"/prefix.patch
+	eprefixify molmol
+
+	epatch "${FILESDIR}"/ldflags.patch
+
+	ln -s makedef.lnx "${S}"/makedef || die
+
+	sed \
+		-e "s:/bin/ksh:${EPREFIX}/bin/sh:" \
+		-e "s:^MOLMOLHOME.*:MOLMOLHOME=${EPREFIX}/${MMDIR}:" \
+		-i "${S}"/molmol || die
+	sed \
+		-e "s:^MCFLAGS.*:MCFLAGS = ${CFLAGS}:" \
+		-e "s:^CC.*:CC = $(tc-getCC):" \
+		-i "${S}"/makedef || die
+
+	epatch "${FILESDIR}"/cast.patch
+	epatch "${FILESDIR}"/libpng15.patch
+
+	# patch from fink
+	# fixes numerous bad bracings and hopefully the OGL bug 429974
+	epatch "${FILESDIR}"/${P}-fink.patch
+}
+
+src_install() {
+	dobin molmol
+
+	exeinto ${MMDIR}
+	newexe src/main/molmol molmol.lnx
+	insinto ${MMDIR}
+	doins -r auxil help macros man setup tips
+
+	dodoc HISTORY README
+}