diff --git a/biology/molden/files/patch-makefile b/biology/molden/files/patch-makefile new file mode 100644 index 000000000000..4a086a6fdd57 --- /dev/null +++ b/biology/molden/files/patch-makefile @@ -0,0 +1,41 @@ +- pass supplied FFLAGS to the build + +--- makefile.orig 2021-01-28 14:05:10 UTC ++++ makefile +@@ -107,7 +107,7 @@ ifneq ($(comgcc), $(empty)) + EXTRAZ = -Wno-implicit-function-declaration + EXT = ${EXTRAZ} + endif +-FFLAGS = -g ${AFLAG} ++FFLAGS += -g ${AFLAG} + LIBS = -L/usr/X11R6/lib -lX11 -lm + ifeq ($(AFLAG),"-m64") + LIBS = -L/usr/X11R6/lib64 -lX11 -lm +@@ -132,11 +132,11 @@ ifeq ($(uname), Darwin) + # + CC=cc + CFLAGS= -std=gnu89 -Wno-return-type -DDARWIN -I/usr/X11R6/include -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0 -Wno-logical-op-parentheses +-FFLAGS=-O3 -funroll-loops ++FFLAGS+=-O3 -funroll-loops + LIBS = -L/usr/X11R6/lib -lX11 -lm + LIBSG = -L/usr/X11R6/lib -lGLU "-Wl,-dylib_file,/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib:/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib" -lGL -lXmu -lX11 -lm + EXT= -std=gnu89 -Wno-return-type -DDARWIN ${EXTRAZ} +-FFLAGS=-O3 -funroll-loops ++FFLAGS+=-O3 -funroll-loops + LIBS = -L/usr/X11R6/lib -lX11 -lm + LIBSG = -L/usr/X11R6/lib -lGLU "-Wl,-dylib_file,/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib:/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib" -lGL -lXmu -lX11 -lm + CFLAGS= -g -std=gnu89 -Wno-return-type -DDARWIN -I/usr/X11R6/include -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0 -Wno-logical-op-parentheses -Wno-implicit-function-declaration -Wno-tautological-pointer-compare -Wno-tautological-constant-out-of-range-compare +@@ -306,11 +306,11 @@ gmolden: $(OBJS) src/mpdum.o src/xwingl.o + mv gmolden bin/gmolden + + ambfor/ambfor: src/ambfor/*.f src/ambfor/*.c +- $(MAKE) -C src/ambfor FC=${FC} LDR="${LDR}" EXT="${EXT}" ++ $(MAKE) -C src/ambfor FC=${FC} LDR="${LDR}" EXT="${EXT}" FFLAGS="$(FFLAGS)" + mv src/ambfor/ambfor bin/ambfor + + ambfor/ambmd: src/ambfor/*.f src/ambfor/*.c +- $(MAKE) -C src/ambfor ambmd FC=${FC} LDR="${LDR}" EXT="${EXT}" ++ $(MAKE) -C src/ambfor ambmd FC=${FC} LDR="${LDR}" EXT="${EXT}" FFLAGS="$(FFLAGS)" FFLAGS="$(FFLAGS)" + mv src/ambfor/ambmd bin/ambmd + + surf/surf: src/surf/*.h src/surf/*.c diff --git a/biology/molden/files/patch-src_surf_Makefile b/biology/molden/files/patch-src_surf_Makefile new file mode 100644 index 000000000000..ca1673d9c3cf --- /dev/null +++ b/biology/molden/files/patch-src_surf_Makefile @@ -0,0 +1,13 @@ +- disable ex: it breaks the build, not sure why is it there + +--- src/surf/Makefile.orig 2022-07-15 23:19:54 UTC ++++ src/surf/Makefile +@@ -58,7 +58,7 @@ depend: $(DEPEND) + @ echo '$$r makedep' >>eddep + @ echo 'w' >>eddep + @ cp Makefile Makefile.bak +- @ ex - Makefile < eddep ++ #@ ex - Makefile < eddep + @ rm eddep makedep + @ echo ' ' >> Makefile + @ echo '# DEPENDENCIES MUST END AT END OF FILE' >> Makefile diff --git a/biology/molden/files/patch-src_surf_utils.c b/biology/molden/files/patch-src_surf_utils.c new file mode 100644 index 000000000000..bc05318375f8 --- /dev/null +++ b/biology/molden/files/patch-src_surf_utils.c @@ -0,0 +1,21 @@ +- fix return statements in the function the returns int + +--- src/surf/utils.c.orig 2022-07-15 23:20:39 UTC ++++ src/surf/utils.c +@@ -91,7 +91,7 @@ float radius; + disc = radius*radius - DOTPROD3(EO, EO); + if (FP_EQ_EPS(disc, 0, GP_EPS*GP_EPS)) + { VEC3_ASN_OP(int_point, =, ray_pt); +- return; ++ return -1; + } + + one_by_sq_dir_mag = 1.0/DOTPROD3(ray_dir, ray_dir); +@@ -107,6 +107,7 @@ float radius; + { t = v*one_by_sq_dir_mag - sqrt(disc*one_by_sq_dir_mag); + VEC3_V_OP_V_OP_S(int_point, ray_pt, +, ray_dir, *, t); + } ++ return -1; + } + + /*---------------------------------------------------------------------------------- diff --git a/biology/molden/files/patch-src_xwin.c b/biology/molden/files/patch-src_xwin.c new file mode 100644 index 000000000000..b16dab11bff8 --- /dev/null +++ b/biology/molden/files/patch-src_xwin.c @@ -0,0 +1,10 @@ +- disable GLIBC symbols specific to linux + +--- src/xwin.c.orig 2022-07-15 23:09:11 UTC ++++ src/xwin.c +@@ -1,4 +1,4 @@ +-#ifndef DARWIN ++#if !defined(DARWIN) && !defined(__FreeBSD__) + __asm__(".symver memcpy,memcpy@GLIBC_2.2.5"); + __asm__(".symver memmove,memmove@GLIBC_2.2.5"); + __asm__(".symver log,log@GLIBC_2.2.5"); diff --git a/biology/molden/pkg-descr b/biology/molden/pkg-descr index 45612201a3c7..2b20fa8c9f98 100644 --- a/biology/molden/pkg-descr +++ b/biology/molden/pkg-descr @@ -1,24 +1,24 @@ Molden is a package for displaying Molecular Density from the Ab Initio packages GAMESS-UK, GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac, it also supports a number of other programs via the Molden Format. Molden reads all the required information from the GAMESS / GAUSSIAN outputfile. Molden is capable of displaying Molecular Orbitals, the electron density and the Molecular minus Atomic density. Either the spherically averaged atomic density or the oriented ground state atomic density can be subtracted for a number of standard basis sets. Molden supports contour plots, 3-d grid plots with hidden lines and a combination of both. It can write a variety of graphics instructions; postscript, XWindows, VRML, povray, OpenGL, tekronix4014, hpgl, hp2392 and Figure. Both Xwindows and OpenGL versions of Molden are also capable of importing and displaying of chemx, PDB, and a variety of mopac/ampac files and lots of other formats. Molden also can animate reaction paths and molecular vibrations. It can calculate and display the true or Multipole Derived Electrostatic Potential and atomic charges can be fitted to the Electrostatic Potential calculated on a Connolly surface. Molden also features an stand alone forcefield program ambfor, which can optimise geometries with the combined Amber (protein) and GAFF (small molecules) force fields. Atom typing can be done automatically and interactively from within Molden, as well as firing optimisation jobs. Molden has a powerful Z-matrix editor which give full control over the geometry and allows you to build molecules from scratch, including polypeptides. -WWW: http://cheminf.cmbi.ru.nl/molden/ +WWW: https://www.theochem.ru.nl/molden/