ADL: Autodock MSVC

Jack Shultz js at drugdiscoveryathome.com
Tue Jun 30 09:25:47 PDT 2009


as i see it looks like autodock depends on this struct found in the
times.h header


/*  Get Process Times, P1003.1b-1993, p. 92 */
struct tms {
        clock_t tms_utime;              /* user time */
        clock_t tms_stime;              /* system time */
        clock_t tms_cutime;             /* user time, children */
        clock_t tms_cstime;             /* system time, children */
};

I ran a sed command to comment out all preprocessing references to times.h

$ make
make  all-am
make[1]: Entering directory `/home/jshultz/autodocksuite-4.2.1/src/autodock-v1'
g++ -DPACKAGE_NAME=\"autodock\" -DPACKAGE_TARNAME=\"autodock\"
-DPACKAGE_VERSION=\"4.2.1\" -DPACKAGE_STRING=\"autodock\ 4.2.1\"
-DPACKAGE_BUGREPORT=\"autodock at scripps.edu\" -DPACKAGE=\"autodock\"
-DVERSION=\"4.2.1\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1
-DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1
-DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1
-DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1
-DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_POW=1 -DHAVE_SQRT=1
-DHAVE_STRNCASECMP=1 -I.  -DNOSQRT -DUSE_8A_NBCUTOFF -DWRITEPDBQSTATE
-I./../acro/include   -Wall -O3   -MT clmode.o -MD -MP -MF
.deps/clmode.Tpo -c -o clmode.o clmode.cc
clmode.cc: In function `void clmode(int, Real, char*, clock_t, tms,
Boole, char*, Real (*)[3], Real*, Boole, char*)':
clmode.cc:56: error: `tms_jobStart' has incomplete type
timesyshms.h:38: error: forward declaration of `struct tms'
clmode.cc: In function `void clmode(int, Real, char*, clock_t, tms,
Boole, char*, Real (*)[3], Real*, Boole, char*)':
clmode.cc:103: error: invalid use of undefined type `struct tms'
timesyshms.h:38: error: forward declaration of `struct tms'
clmode.cc:103: error:   initializing argument 5 of `int
openFile(char*, char*, FILE**, clock_t, tms, Boole)'
clmode.cc:318: error: invalid use of undefined type `struct tms'
timesyshms.h:38: error: forward declaration of `struct tms'
clmode.cc:318: error:   initializing argument 3 of `void
success(char*, clock_t, tms)'
make[1]: *** [clmode.o] Error 1
make[1]: Leaving directory `/home/jshultz/autodocksuite-4.2.1/src/autodock-v1'
make: *** [all] Error 2

Is there a pre-defined struct in msvc or msys analogous to struct tms?
If so can we just replace any reference in the code with such a
struct. Otherwise how about defining a new struct tms?


On Tue, Jun 23, 2009 at 1:11 PM, Sargis Dallakyan<sargis at scripps.edu> wrote:
> Jack Shultz wrote:
>>
>> Hello,
>>
>> I'm trying to build autodock so it is compatible with the BOINC
>> libraries. Some boinc developers think it would be better to avoid
>> building this in cygwin. I tried this two years ago and gave up. I'm
>> making another attempt. This time I'm trying to build it in visual
>> studio c++. I am encountering many libraries and headers that are
>> incompatible so I am looking for the right code modifications that
>> will make this work. Has anyone else attempted this?
>
> I've tried this a couple of years ago too and managed to build autodock with
> MS compiler. I tried this again after your post on gpuautodock, since I
> couldn't use the Cygwin gcc with CUDA:
> http://forums.nvidia.com/index.php?showtopic=42906
>
> I haven't push gpuautodock too hard since OpenCL might become a better
> alternative to CUDA, and hopefully, more users will have CUDA or OpenCL
> enabled graphics card.
>
> Regarding building autodock with visual studio c++: I came across this page
> that discusses building OpenBabel with MinGW:
> http://www.bioinformatics.org/molekel/wiki/pmwiki.php/Main/OpenBabel
>
> The changes that needs to be done in autodock are similar to what is written
> in that page. However, I don't know Microsoft Visual Studio well enough to
> make a project that would handle both autodock and autogrid.
>
> Cheers,
> Sargis
>
>
> --
>
> Sargis Dallakyan, Ph.D. - Research Programmer III
> The Scripps Research Institute,
> Dept. Molecular Biology,  MB-5,
> 10550  North Torrey Pines Road,
> La Jolla,  CA 92037-1000
> Tel: (858) 784-9559
> http://mgltools.scripps.edu/Members/sargis
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>



-- 
Jack

http://drugdiscoveryathome.com
http://hydrogenathome.org



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