Thread: Re: [Apbs-users] multivalue.c: a modified version of value.c for multiple coordiante evaluations
Biomolecular electrostatics software
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From: Nathan B. <ba...@cc...> - 2006-12-02 13:42:34
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Hi Adrian -- This is great; we'll work on incorporating it into the source tree. Thanks! -- Nathan On Dec 1, 2006, at 8:34 PM, Adrian Kaats wrote: > Dear APBS users, > > Attached is a copy of the source for a routine called multivalue.c =20 > which will be included as part of an upcoming release of APBS as well. > > Multivalue is a minor modification to Nathan Baker's value.c - in =20 > fact, it is almost entirely the same except that: > > 1) It accepts a CSV-like-formatted coordinate file, a DX-formatted =20 > grid, and the name of an output file to write to. > 2) The lines of the CSV file contain coordinates at which you would =20= > like to get values from the DX-formatted grid. > 3) The result is output to the console, and also to the specified =20 > output file. The output file is formatted like, and contains =20 > exactly the same data as the input file, but includes an extra =20 > column at the end containing the calculated value at each coordinate. > 4) None of the curvature, gradient, etc... as in the original =20 > value.c are computed, JUST the value (if someone wants the other =20 > evaluation to be implemented, let me know). > > Compiling this may prove difficult, particularly if you are working =20= > with one of the RPM installations of APBS and/or Maloc. So, here =20 > is a modified version of the instructions, graciously provided by =20 > David Gohara, that I used to compile multivalue.c: > > A) Create a temporary directory somewhere on your system, we will =20 > call it 'programs' here. So everywhere 'programs' is written, =20 > replace it with the path to actual directory you have created. > > B) Install MALOC from source: > > 1) Downloaded a copy of MALOC 0.1-2 into programs and untar it. > 2) cd into the maloc directory > 3) ./configure --prefix=3D/programs > 4) make ; make install > > C) Install APBS from source: > > 1) Downloaded a copy of APBS 0.4.0 into programs and untar it. > 2) cd into the apbs directory > 3) ./configure --prefix=3D/programs > 4) make ; make install > > D) Build multivalue.c: > > 1) cd to wherever you placed multivalue.c > 2) gcc -o multivalue =96I/programs/include =96I/programs/apbs-0.4.0/src/= =20 > aaa_inc -I/programs/include multivalue.c =96L/programs/lib/XXXX -=20 > lapbs -lmaloc -lm -lreadline =96lncurses > > NOTE XXXX =3D possible sub directory where APBS and Maloc libraries =20= > were placed. Also note that the above is and only works as one =20 > glorious line > > I hope all this works for you. If not, I have very limited =20 > knowledge of compiling =96 you can ask me, but I may not (actually =20 > will likely not) have the answers... but I=92ll try. If there are =20 > problems with the code, please let me know. > > Sincerely, > > Adrian Kaats > Graduate Student > Department of Biomedical Engineering > McGill University > Montreal, Quebec, Canada > > Be smarter than spam. See how smart SpamGuard is at giving junk =20 > email the boot with the All-new Yahoo! Mail > <multivalue.c> > ----------------------------------------------------------------------=20= > --- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to =20 > share your > opinions on IT & business topics through brief surveys - and earn cash > http://www.techsay.com/default.php?=20 > page=3Djoin.php&p=3Dsourceforge&CID=3DDEVDEV____________________________= ____=20 > _______________ > apbs-users mailing list > apb...@li... > https://lists.sourceforge.net/lists/listinfo/apbs-users -- Associate Professor, Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/ |