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freebsd-ports/biology/molden/files/patch-surf-Makefile
Kurt Jaeger d997d56941 biology/molden: 5.0.7 -> 5.4
Changes:
- Missing hydrogens atoms of HETATM molecules (pdb files) are stored locally.
- Pdb files can now be clipped.
- Fixes missing residues. Introduces an alternative way of generating rotamers,
  without using z-matrices. This potentially a faster algorithm.
- Supports Movie making through avconv/ffmpeg.
- calculates the Electron Localization Function (ELF).
- Updated code of ambfor/ambmd to speed up optimisations/MD of proteins
  solvated in water (Jan, 2014).

PR:		204341
2016-01-18 19:32:37 +00:00

790 lines
47 KiB
Plaintext

--- surf/Makefile.orig 2015-05-02 19:48:48 UTC
+++ surf/Makefile
@@ -1,12 +1,8 @@
# Compilation flags
-#CC = cc
-CC = cc
INCLUDE = -I.
#LINCLUDE = -lcurses -ltermcap -lm
LINCLUDE = -lm
-OPT_CFLAGS = -O2 $(FLAGS) $(INCLUDE)
#CFLAGS = -g $(FLAGS) $(INCLUDE)
-CFLAGS = -O2 $(FLAGS) $(INCLUDE) ${EXT}
ifeq ($(uname), Darwin)
#
@@ -73,670 +69,117 @@ depend: $(DEPEND)
# DO NOT DELETE
surf.o: surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h
-surf.o: /usr/include/sys/_symbol_aliasing.h
-surf.o: /usr/include/sys/_posix_availability.h /usr/include/Availability.h
-surf.o: /usr/include/AvailabilityInternal.h /usr/include/_types.h
-surf.o: /usr/include/sys/_types.h /usr/include/machine/_types.h
-surf.o: /usr/include/i386/_types.h /usr/include/sys/_pthread/_pthread_types.h
-surf.o: /usr/include/sys/_types/_va_list.h /usr/include/sys/_types/_size_t.h
-surf.o: /usr/include/sys/_types/_null.h /usr/include/sys/stdio.h
-surf.o: /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h
-surf.o: /usr/include/secure/_stdio.h /usr/include/secure/_common.h
-surf.o: /usr/include/math.h /usr/include/stdlib.h /usr/include/sys/wait.h
-surf.o: /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h
-surf.o: /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h
-surf.o: /usr/include/machine/signal.h /usr/include/i386/signal.h
-surf.o: /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h
-surf.o: /usr/include/mach/i386/_structs.h
-surf.o: /usr/include/sys/_pthread/_pthread_attr_t.h
-surf.o: /usr/include/sys/_types/_sigaltstack.h
-surf.o: /usr/include/sys/_types/_ucontext.h
-surf.o: /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h
-surf.o: /usr/include/sys/resource.h /usr/include/stdint.h
-surf.o: /usr/include/sys/_types/_int8_t.h /usr/include/sys/_types/_int16_t.h
-surf.o: /usr/include/sys/_types/_int32_t.h /usr/include/sys/_types/_int64_t.h
-surf.o: /usr/include/_types/_uint8_t.h /usr/include/_types/_uint16_t.h
-surf.o: /usr/include/_types/_uint32_t.h /usr/include/_types/_uint64_t.h
-surf.o: /usr/include/sys/_types/_intptr_t.h
-surf.o: /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h
-surf.o: /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h
-surf.o: /usr/include/machine/endian.h /usr/include/i386/endian.h
-surf.o: /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h
-surf.o: /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h
-surf.o: /usr/include/sys/_types/_ct_rune_t.h
-surf.o: /usr/include/sys/_types/_rune_t.h /usr/include/sys/_types/_wchar_t.h
-surf.o: /usr/include/machine/types.h /usr/include/i386/types.h
-surf.o: /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h
-surf.o: /usr/include/string.h /usr/include/sys/_types/_rsize_t.h
-surf.o: /usr/include/sys/_types/_errno_t.h /usr/include/strings.h
-surf.o: /usr/include/secure/_string.h /usr/include/sys/time.h
-surf.o: /usr/include/sys/_types/_fd_def.h /usr/include/sys/_types/_timespec.h
-surf.o: /usr/include/sys/_types/_time_t.h
-surf.o: /usr/include/sys/_types/_suseconds_t.h
-surf.o: /usr/include/sys/_types/_fd_setsize.h
-surf.o: /usr/include/sys/_types/_fd_set.h /usr/include/sys/_types/_fd_clr.h
-surf.o: /usr/include/sys/_types/_fd_isset.h
-surf.o: /usr/include/sys/_types/_fd_zero.h /usr/include/sys/_types/_fd_copy.h
-surf.o: /usr/include/time.h /usr/include/sys/_types/_clock_t.h
-surf.o: /usr/include/sys/_select.h linalg.h
+surf.o: /usr/include/sys/_null.h /usr/include/sys/_types.h
+surf.o: /usr/include/machine/_types.h /usr/include/math.h
+surf.o: /usr/include/machine/_limits.h /usr/include/stdlib.h
+surf.o: /usr/include/string.h /usr/include/strings.h /usr/include/sys/time.h
+surf.o: /usr/include/sys/_timeval.h /usr/include/sys/types.h
+surf.o: /usr/include/machine/endian.h /usr/include/sys/_pthreadtypes.h
+surf.o: /usr/include/sys/select.h /usr/include/sys/_sigset.h
+surf.o: /usr/include/sys/timespec.h /usr/include/time.h linalg.h
io.o: surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h
-io.o: /usr/include/sys/_symbol_aliasing.h
-io.o: /usr/include/sys/_posix_availability.h /usr/include/Availability.h
-io.o: /usr/include/AvailabilityInternal.h /usr/include/_types.h
-io.o: /usr/include/sys/_types.h /usr/include/machine/_types.h
-io.o: /usr/include/i386/_types.h /usr/include/sys/_pthread/_pthread_types.h
-io.o: /usr/include/sys/_types/_va_list.h /usr/include/sys/_types/_size_t.h
-io.o: /usr/include/sys/_types/_null.h /usr/include/sys/stdio.h
-io.o: /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h
-io.o: /usr/include/secure/_stdio.h /usr/include/secure/_common.h
-io.o: /usr/include/math.h /usr/include/stdlib.h /usr/include/sys/wait.h
-io.o: /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h
-io.o: /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h
-io.o: /usr/include/machine/signal.h /usr/include/i386/signal.h
-io.o: /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h
-io.o: /usr/include/mach/i386/_structs.h
-io.o: /usr/include/sys/_pthread/_pthread_attr_t.h
-io.o: /usr/include/sys/_types/_sigaltstack.h
-io.o: /usr/include/sys/_types/_ucontext.h /usr/include/sys/_types/_sigset_t.h
-io.o: /usr/include/sys/_types/_uid_t.h /usr/include/sys/resource.h
-io.o: /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h
-io.o: /usr/include/sys/_types/_int16_t.h /usr/include/sys/_types/_int32_t.h
-io.o: /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h
-io.o: /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h
-io.o: /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h
-io.o: /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h
-io.o: /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h
-io.o: /usr/include/machine/endian.h /usr/include/i386/endian.h
-io.o: /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h
-io.o: /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h
-io.o: /usr/include/sys/_types/_ct_rune_t.h /usr/include/sys/_types/_rune_t.h
-io.o: /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h
-io.o: /usr/include/i386/types.h /usr/include/sys/_types/_dev_t.h
-io.o: /usr/include/sys/_types/_mode_t.h /usr/include/string.h
-io.o: /usr/include/sys/_types/_rsize_t.h /usr/include/sys/_types/_errno_t.h
-io.o: /usr/include/strings.h /usr/include/secure/_string.h
-io.o: /usr/include/sys/time.h /usr/include/sys/_types/_fd_def.h
-io.o: /usr/include/sys/_types/_timespec.h /usr/include/sys/_types/_time_t.h
-io.o: /usr/include/sys/_types/_suseconds_t.h
-io.o: /usr/include/sys/_types/_fd_setsize.h /usr/include/sys/_types/_fd_set.h
-io.o: /usr/include/sys/_types/_fd_clr.h /usr/include/sys/_types/_fd_isset.h
-io.o: /usr/include/sys/_types/_fd_zero.h /usr/include/sys/_types/_fd_copy.h
-io.o: /usr/include/time.h /usr/include/sys/_types/_clock_t.h
-io.o: /usr/include/sys/_select.h linalg.h
+io.o: /usr/include/sys/_null.h /usr/include/sys/_types.h
+io.o: /usr/include/machine/_types.h /usr/include/math.h
+io.o: /usr/include/machine/_limits.h /usr/include/stdlib.h
+io.o: /usr/include/string.h /usr/include/strings.h /usr/include/sys/time.h
+io.o: /usr/include/sys/_timeval.h /usr/include/sys/types.h
+io.o: /usr/include/machine/endian.h /usr/include/sys/_pthreadtypes.h
+io.o: /usr/include/sys/select.h /usr/include/sys/_sigset.h
+io.o: /usr/include/sys/timespec.h /usr/include/time.h linalg.h
compute.o: surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h
-compute.o: /usr/include/sys/_symbol_aliasing.h
-compute.o: /usr/include/sys/_posix_availability.h /usr/include/Availability.h
-compute.o: /usr/include/AvailabilityInternal.h /usr/include/_types.h
-compute.o: /usr/include/sys/_types.h /usr/include/machine/_types.h
-compute.o: /usr/include/i386/_types.h
-compute.o: /usr/include/sys/_pthread/_pthread_types.h
-compute.o: /usr/include/sys/_types/_va_list.h
-compute.o: /usr/include/sys/_types/_size_t.h /usr/include/sys/_types/_null.h
-compute.o: /usr/include/sys/stdio.h /usr/include/sys/_types/_off_t.h
-compute.o: /usr/include/sys/_types/_ssize_t.h /usr/include/secure/_stdio.h
-compute.o: /usr/include/secure/_common.h /usr/include/math.h
-compute.o: /usr/include/stdlib.h /usr/include/sys/wait.h
-compute.o: /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h
-compute.o: /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h
-compute.o: /usr/include/machine/signal.h /usr/include/i386/signal.h
-compute.o: /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h
-compute.o: /usr/include/mach/i386/_structs.h
-compute.o: /usr/include/sys/_pthread/_pthread_attr_t.h
-compute.o: /usr/include/sys/_types/_sigaltstack.h
-compute.o: /usr/include/sys/_types/_ucontext.h
-compute.o: /usr/include/sys/_types/_sigset_t.h
-compute.o: /usr/include/sys/_types/_uid_t.h /usr/include/sys/resource.h
-compute.o: /usr/include/stdint.h /usr/include/sys/_types/_int8_t.h
-compute.o: /usr/include/sys/_types/_int16_t.h
-compute.o: /usr/include/sys/_types/_int32_t.h
-compute.o: /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h
-compute.o: /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h
-compute.o: /usr/include/_types/_uint64_t.h
-compute.o: /usr/include/sys/_types/_intptr_t.h
-compute.o: /usr/include/sys/_types/_uintptr_t.h
-compute.o: /usr/include/_types/_intmax_t.h /usr/include/_types/_uintmax_t.h
-compute.o: /usr/include/sys/_types/_timeval.h /usr/include/machine/endian.h
-compute.o: /usr/include/i386/endian.h /usr/include/sys/_endian.h
-compute.o: /usr/include/libkern/_OSByteOrder.h
-compute.o: /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h
-compute.o: /usr/include/sys/_types/_ct_rune_t.h
-compute.o: /usr/include/sys/_types/_rune_t.h
-compute.o: /usr/include/sys/_types/_wchar_t.h /usr/include/machine/types.h
-compute.o: /usr/include/i386/types.h /usr/include/sys/_types/_dev_t.h
-compute.o: /usr/include/sys/_types/_mode_t.h /usr/include/string.h
-compute.o: /usr/include/sys/_types/_rsize_t.h
-compute.o: /usr/include/sys/_types/_errno_t.h /usr/include/strings.h
-compute.o: /usr/include/secure/_string.h /usr/include/sys/time.h
-compute.o: /usr/include/sys/_types/_fd_def.h
-compute.o: /usr/include/sys/_types/_timespec.h
-compute.o: /usr/include/sys/_types/_time_t.h
-compute.o: /usr/include/sys/_types/_suseconds_t.h
-compute.o: /usr/include/sys/_types/_fd_setsize.h
-compute.o: /usr/include/sys/_types/_fd_set.h
-compute.o: /usr/include/sys/_types/_fd_clr.h
-compute.o: /usr/include/sys/_types/_fd_isset.h
-compute.o: /usr/include/sys/_types/_fd_zero.h
-compute.o: /usr/include/sys/_types/_fd_copy.h /usr/include/time.h
-compute.o: /usr/include/sys/_types/_clock_t.h /usr/include/sys/_select.h
-compute.o: linalg.h chull.h dual.h
+compute.o: /usr/include/sys/_null.h /usr/include/sys/_types.h
+compute.o: /usr/include/machine/_types.h /usr/include/math.h
+compute.o: /usr/include/machine/_limits.h /usr/include/stdlib.h
+compute.o: /usr/include/string.h /usr/include/strings.h
+compute.o: /usr/include/sys/time.h /usr/include/sys/_timeval.h
+compute.o: /usr/include/sys/types.h /usr/include/machine/endian.h
+compute.o: /usr/include/sys/_pthreadtypes.h /usr/include/sys/select.h
+compute.o: /usr/include/sys/_sigset.h /usr/include/sys/timespec.h
+compute.o: /usr/include/time.h linalg.h chull.h dual.h
dual.o: surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h
-dual.o: /usr/include/sys/_symbol_aliasing.h
-dual.o: /usr/include/sys/_posix_availability.h /usr/include/Availability.h
-dual.o: /usr/include/AvailabilityInternal.h /usr/include/_types.h
-dual.o: /usr/include/sys/_types.h /usr/include/machine/_types.h
-dual.o: /usr/include/i386/_types.h /usr/include/sys/_pthread/_pthread_types.h
-dual.o: /usr/include/sys/_types/_va_list.h /usr/include/sys/_types/_size_t.h
-dual.o: /usr/include/sys/_types/_null.h /usr/include/sys/stdio.h
-dual.o: /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h
-dual.o: /usr/include/secure/_stdio.h /usr/include/secure/_common.h
-dual.o: /usr/include/math.h /usr/include/stdlib.h /usr/include/sys/wait.h
-dual.o: /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h
-dual.o: /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h
-dual.o: /usr/include/machine/signal.h /usr/include/i386/signal.h
-dual.o: /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h
-dual.o: /usr/include/mach/i386/_structs.h
-dual.o: /usr/include/sys/_pthread/_pthread_attr_t.h
-dual.o: /usr/include/sys/_types/_sigaltstack.h
-dual.o: /usr/include/sys/_types/_ucontext.h
-dual.o: /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h
-dual.o: /usr/include/sys/resource.h /usr/include/stdint.h
-dual.o: /usr/include/sys/_types/_int8_t.h /usr/include/sys/_types/_int16_t.h
-dual.o: /usr/include/sys/_types/_int32_t.h /usr/include/sys/_types/_int64_t.h
-dual.o: /usr/include/_types/_uint8_t.h /usr/include/_types/_uint16_t.h
-dual.o: /usr/include/_types/_uint32_t.h /usr/include/_types/_uint64_t.h
-dual.o: /usr/include/sys/_types/_intptr_t.h
-dual.o: /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h
-dual.o: /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h
-dual.o: /usr/include/machine/endian.h /usr/include/i386/endian.h
-dual.o: /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h
-dual.o: /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h
-dual.o: /usr/include/sys/_types/_ct_rune_t.h
-dual.o: /usr/include/sys/_types/_rune_t.h /usr/include/sys/_types/_wchar_t.h
-dual.o: /usr/include/machine/types.h /usr/include/i386/types.h
-dual.o: /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h
-dual.o: /usr/include/string.h /usr/include/sys/_types/_rsize_t.h
-dual.o: /usr/include/sys/_types/_errno_t.h /usr/include/strings.h
-dual.o: /usr/include/secure/_string.h /usr/include/sys/time.h
-dual.o: /usr/include/sys/_types/_fd_def.h /usr/include/sys/_types/_timespec.h
-dual.o: /usr/include/sys/_types/_time_t.h
-dual.o: /usr/include/sys/_types/_suseconds_t.h
-dual.o: /usr/include/sys/_types/_fd_setsize.h
-dual.o: /usr/include/sys/_types/_fd_set.h /usr/include/sys/_types/_fd_clr.h
-dual.o: /usr/include/sys/_types/_fd_isset.h
-dual.o: /usr/include/sys/_types/_fd_zero.h /usr/include/sys/_types/_fd_copy.h
-dual.o: /usr/include/time.h /usr/include/sys/_types/_clock_t.h
-dual.o: /usr/include/sys/_select.h linalg.h dual.h chull.h
+dual.o: /usr/include/sys/_null.h /usr/include/sys/_types.h
+dual.o: /usr/include/machine/_types.h /usr/include/math.h
+dual.o: /usr/include/machine/_limits.h /usr/include/stdlib.h
+dual.o: /usr/include/string.h /usr/include/strings.h /usr/include/sys/time.h
+dual.o: /usr/include/sys/_timeval.h /usr/include/sys/types.h
+dual.o: /usr/include/machine/endian.h /usr/include/sys/_pthreadtypes.h
+dual.o: /usr/include/sys/select.h /usr/include/sys/_sigset.h
+dual.o: /usr/include/sys/timespec.h /usr/include/time.h linalg.h dual.h
+dual.o: chull.h
utils.o: surf.h /usr/include/stdio.h /usr/include/sys/cdefs.h
-utils.o: /usr/include/sys/_symbol_aliasing.h
-utils.o: /usr/include/sys/_posix_availability.h /usr/include/Availability.h
-utils.o: /usr/include/AvailabilityInternal.h /usr/include/_types.h
-utils.o: /usr/include/sys/_types.h /usr/include/machine/_types.h
-utils.o: /usr/include/i386/_types.h
-utils.o: /usr/include/sys/_pthread/_pthread_types.h
-utils.o: /usr/include/sys/_types/_va_list.h /usr/include/sys/_types/_size_t.h
-utils.o: /usr/include/sys/_types/_null.h /usr/include/sys/stdio.h
-utils.o: /usr/include/sys/_types/_off_t.h /usr/include/sys/_types/_ssize_t.h
-utils.o: /usr/include/secure/_stdio.h /usr/include/secure/_common.h
-utils.o: /usr/include/math.h /usr/include/stdlib.h /usr/include/sys/wait.h
-utils.o: /usr/include/sys/_types/_pid_t.h /usr/include/sys/_types/_id_t.h
-utils.o: /usr/include/sys/signal.h /usr/include/sys/appleapiopts.h
-utils.o: /usr/include/machine/signal.h /usr/include/i386/signal.h
-utils.o: /usr/include/machine/_mcontext.h /usr/include/i386/_mcontext.h
-utils.o: /usr/include/mach/i386/_structs.h
-utils.o: /usr/include/sys/_pthread/_pthread_attr_t.h
-utils.o: /usr/include/sys/_types/_sigaltstack.h
-utils.o: /usr/include/sys/_types/_ucontext.h
-utils.o: /usr/include/sys/_types/_sigset_t.h /usr/include/sys/_types/_uid_t.h
-utils.o: /usr/include/sys/resource.h /usr/include/stdint.h
-utils.o: /usr/include/sys/_types/_int8_t.h /usr/include/sys/_types/_int16_t.h
-utils.o: /usr/include/sys/_types/_int32_t.h
-utils.o: /usr/include/sys/_types/_int64_t.h /usr/include/_types/_uint8_t.h
-utils.o: /usr/include/_types/_uint16_t.h /usr/include/_types/_uint32_t.h
-utils.o: /usr/include/_types/_uint64_t.h /usr/include/sys/_types/_intptr_t.h
-utils.o: /usr/include/sys/_types/_uintptr_t.h /usr/include/_types/_intmax_t.h
-utils.o: /usr/include/_types/_uintmax_t.h /usr/include/sys/_types/_timeval.h
-utils.o: /usr/include/machine/endian.h /usr/include/i386/endian.h
-utils.o: /usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h
-utils.o: /usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h
-utils.o: /usr/include/sys/_types/_ct_rune_t.h
-utils.o: /usr/include/sys/_types/_rune_t.h /usr/include/sys/_types/_wchar_t.h
-utils.o: /usr/include/machine/types.h /usr/include/i386/types.h
-utils.o: /usr/include/sys/_types/_dev_t.h /usr/include/sys/_types/_mode_t.h
-utils.o: /usr/include/string.h /usr/include/sys/_types/_rsize_t.h
-utils.o: /usr/include/sys/_types/_errno_t.h /usr/include/strings.h
-utils.o: /usr/include/secure/_string.h /usr/include/sys/time.h
-utils.o: /usr/include/sys/_types/_fd_def.h
-utils.o: /usr/include/sys/_types/_timespec.h
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-# DEPENDENCIES MUST END AT END OF FILE
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-# see make depend above
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