src/gmxlib/copyrite.c

   1 /*
   2  * $Id$
   3  *
   4  *                This source code is part of
   5  *
   6  *                 G   R   O   M   A   C   S
   7  *
   8  *          GROningen MAchine for Chemical Simulations
   9  *
  10  *                        VERSION 3.2.0
  11  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  12  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  13  * Copyright (c) 2001-2004, The GROMACS development team,
  14  * check out http://www.gromacs.org for more information.
  15
  16  * This program is free software; you can redistribute it and/or
  17  * modify it under the terms of the GNU General Public License
  18  * as published by the Free Software Foundation; either version 2
  19  * of the License, or (at your option) any later version.
  20  *
  21  * If you want to redistribute modifications, please consider that
  22  * scientific software is very special. Version control is crucial -
  23  * bugs must be traceable. We will be happy to consider code for
  24  * inclusion in the official distribution, but derived work must not
  25  * be called official GROMACS. Details are found in the README & COPYING
  26  * files - if they are missing, get the official version at www.gromacs.org.
  27  *
  28  * To help us fund GROMACS development, we humbly ask that you cite
  29  * the papers on the package - you can find them in the top README file.
  30  *
  31  * For more info, check our website at http://www.gromacs.org
  32  *
  33  * And Hey:
  34  * GROningen Mixture of Alchemy and Childrens' Stories
  35  */
  36 #ifdef HAVE_CONFIG_H
  37 #include <config.h>
  38 #endif
  39
  40 #ifdef USE_THREADS
  41 #include <pthread.h>
  42 #endif
  43 /* This file is completely threadsafe - keep it that way! */
  44
  45 #include <string.h>
  46 #include <ctype.h>
  47 #include "sysstuff.h"
  48 #include "smalloc.h"
  49 #include "string2.h"
  50 #include "macros.h"
  51 #include "time.h"
  52 #include "random.h"
  53 #include "statutil.h"
  54 #include "copyrite.h"
  55 #include "strdb.h"
  56 #include "futil.h"
  57
  58 static void pr_two(FILE *out,int c,int i)
  59 {
  60   if (i < 10)
  61     fprintf(out,"%c0%1d",c,i);
  62   else
  63     fprintf(out,"%c%2d",c,i);
  64 }
  65
  66 void pr_difftime(FILE *out,double dt)
  67 {
  68   int    ndays,nhours,nmins,nsecs;
  69   bool   bPrint,bPrinted;
  70
  71   ndays = dt/(24*3600);
  72   dt    = dt-24*3600*ndays;
  73   nhours= dt/3600;
  74   dt    = dt-3600*nhours;
  75   nmins = dt/60;
  76   dt    = dt-nmins*60;
  77   nsecs = dt;
  78   bPrint= (ndays > 0);
  79   bPrinted=bPrint;
  80   if (bPrint)
  81     fprintf(out,"%d",ndays);
  82   bPrint=bPrint || (nhours > 0);
  83   if (bPrint) {
  84     if (bPrinted)
  85       pr_two(out,'d',nhours);
  86     else
  87       fprintf(out,"%d",nhours);
  88   }
  89   bPrinted=bPrinted || bPrint;
  90   bPrint=bPrint || (nmins > 0);
  91   if (bPrint) {
  92     if (bPrinted)
  93       pr_two(out,'h',nmins);
  94     else
  95       fprintf(out,"%d",nmins);
  96   }
  97   bPrinted=bPrinted || bPrint;
  98   if (bPrinted)
  99     pr_two(out,':',nsecs);
 100   else
 101     fprintf(out,"%ds",nsecs);
 102   fprintf(out,"\n");
 103 }
 104
 105
 106 bool be_cool(void)
 107 {
 108   int cool=-1;
 109   char *envptr;
 110
 111   /* Yes, it is bad to check the environment variable every call,
 112    * but we dont call this routine often, and it avoids using
 113    * a mutex for locking the variable...
 114    */
 115   if (cool == -1) {
 116     envptr=getenv("IAMCOOL");
 117
 118     if ((envptr!=NULL) && (!strcmp(envptr,"no") || !strcmp(envptr,"NO")))
 119       cool=0;
 120     else
 121       cool=1;
 122   }
 123
 124   return cool;
 125 }
 126
 127 void space(FILE *out, int n)
 128 {
 129   fprintf(out,"%*s",n,"");
 130 }
 131
 132 void f(char *a){int i;for(i=0;i<(int)strlen(a);i++)a[i]=~a[i]; }
 133
 134 static void sp_print(FILE *out,const char *s)
 135 {
 136   int slen;
 137
 138   slen=strlen(s);
 139   space(out,(80-slen)/2);
 140   fprintf(out,"%s\n",s);
 141 }
 142
 143 static void ster_print(FILE *out,const char *s)
 144 {
 145   int  slen;
 146   char buf[128];
 147
 148   sprintf(buf,":-)  %s  (-:",s);
 149   slen=strlen(buf);
 150   space(out,(80-slen)/2);
 151   fprintf(out,"%s\n",buf);
 152 }
 153
 154
 155 static char *pukeit(char *db,char *defstring, char *retstring,
 156                     int retsize, int *cqnum)
 157 {
 158   FILE *fp;
 159   char **help;
 160   int  i,nhlp;
 161   int  seed;
 162
 163   if (!be_cool())
 164     return defstring;
 165   else if ((fp = low_libopen(db,FALSE)) != NULL) {
 166     nhlp=fget_lines(fp,&help);
 167     fclose(fp);
 168     seed=time(NULL);
 169     *cqnum=nhlp*rando(&seed);
 170     if (strlen(help[*cqnum]) >= STRLEN)
 171       help[*cqnum][STRLEN-1] = '\0';
 172     strncpy(retstring,help[*cqnum],retsize);
 173     f(retstring);
 174     for(i=0; (i<nhlp); i++)
 175       sfree(help[i]);
 176     sfree(help);
 177     return retstring;
 178   }
 179   else
 180     return defstring;
 181 }
 182
 183
 184 char *bromacs(char *retstring, int retsize)
 185 {
 186   int dum;
 187
 188   return pukeit("bromacs.dat",
 189                 "Groningen Machine for Chemical Simulation",
 190                 retstring,retsize,&dum);
 191 }
 192
 193
 194 char *cool_quote(char *retstring, int retsize, int *cqnum)
 195 {
 196   char tmpstr[1024];
 197   char *s,*ptr;
 198   int tmpcq,*p;
 199
 200   if(cqnum!=NULL)
 201     p=cqnum;
 202   else
 203     p=&tmpcq;
 204
 205   /* protect audience from explicit lyrics */
 206   pukeit("gurgle.dat","Thanx for Using GROMACS - Have a Nice Day",
 207          tmpstr,1024,p);
 208
 209   if (be_cool() && ((ptr=strchr(tmpstr,'_')) != NULL)) {
 210     *ptr='\0';
 211     ptr++;
 212     sprintf(retstring,"\"%s\" %s",tmpstr,ptr);
 213   }
 214   else {
 215     strncpy(retstring,tmpstr,1023);
 216   }
 217
 218   return retstring;
 219 }
 220
 221 void CopyRight(FILE *out,char *szProgram)
 222 {
 223   /* Dont change szProgram arbitrarily - it must be argv[0], i.e. the
 224    * name of a file. Otherwise, we won't be able to find the library dir.
 225    */
 226 #define NCR (int)asize(CopyrightText)
 227 #define NGPL (int)asize(GPLText)
 228
 229   char buf[256],tmpstr[1024];
 230
 231   char *ptr;
 232
 233   int i;
 234
 235   set_program_name(szProgram);
 236
 237   ster_print(out,"G  R  O  M  A  C  S");
 238   fprintf(out,"\n");
 239
 240   ptr=bromacs(tmpstr,1023);
 241   sp_print(out,ptr);
 242   fprintf(out,"\n");
 243
 244   ster_print(out,GromacsVersion());
 245   fprintf(out,"\n\n");
 246
 247   /* fprintf(out,"\n");*/
 248
 249   /* sp_print(out,"PLEASE NOTE: THIS IS A BETA VERSION\n");
 250
 251   fprintf(out,"\n"); */
 252
 253   for(i=0; (i<NCR); i++)
 254     sp_print(out,CopyrightText[i]);
 255   for(i=0; (i<NGPL); i++)
 256     sp_print(out,GPLText[i]);
 257
 258   fprintf(out,"\n");
 259
 260   sprintf(buf,"%s",Program());
 261 #ifdef DOUBLE
 262   strcat(buf," (double precision)");
 263 #endif
 264   ster_print(out,buf);
 265   fprintf(out,"\n");
 266 }
 267
 268
 269 void thanx(FILE *fp)
 270 {
 271   char tmpbuf[1024];
 272   char *cq,*c;
 273   int cqnum;
 274
 275   /* protect the audience from suggestive discussions */
 276   cq=cool_quote(tmpbuf,1023,&cqnum);
 277
 278   if (be_cool()) {
 279     snew(c,strlen(cq)+20);
 280
 281     sprintf(c,"gcq#%d: %s\n",cqnum,cq);
 282
 283     fprintf(fp,"\n%s\n",c);
 284     sfree(c);
 285   }
 286   else
 287     fprintf(fp,"\n%s\n",cq);
 288 }
 289
 290 typedef struct {
 291   char *key;
 292   char *author;
 293   char *title;
 294   char *journal;
 295   int volume,year,p0,p1;
 296 } t_citerec;
 297
 298 void please_cite(FILE *fp,char *key)
 299 {
 300   static t_citerec citedb[] = {
 301     { "Berendsen95a",
 302       "H. J. C. Berendsen, D. van der Spoel and R. van Drunen",
 303       "GROMACS: A message-passing parallel molecular dynamics implementation",
 304       "Comp. Phys. Comm.",
 305       91, 1995, 43, 56 },
 306     { "Berendsen84a",
 307       "H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak",
 308       "Molecular dynamics with coupling to an external bath",
 309       "J. Chem. Phys.",
 310       81, 1984, 3684, 3690 },
 311     { "Ryckaert77a",
 312       "J. P. Ryckaert and G. Ciccotti and H. J. C. Berendsen",
 313       "Numerical Integration of the Cartesian Equations of Motion of a System with Constraints; Molecular Dynamics of n-Alkanes",
 314       "J. Comp. Phys.",
 315       23, 1977, 327, 341 },
 316     { "Miyamoto92a",
 317       "S. Miyamoto and P. A. Kollman",
 318       "SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid Water Models",
 319       "J. Comp. Chem.",
 320       13, 1992, 952, 962 },
 321     { "Barth95a",
 322       "E. Barth and K. Kuczera and B. Leimkuhler and R. D. Skeel",
 323       "Algorithms for Constrained Molecular Dynamics",
 324       "J. Comp. Chem.",
 325       16, 1995, 1192, 1209 },
 326     { "Essman95a",
 327       "U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen ",
 328       "A smooth particle mesh Ewald method",
 329       "J. Chem. Phys.",
 330       103, 1995, 8577, 8592 },
 331     { "Torda89a",
 332       "A. E. Torda and R. M. Scheek and W. F. van Gunsteren",
 333       "Time-dependent distance restraints in molecular dynamics simulations",
 334       "Chem. Phys. Lett.",
 335       157, 1989, 289, 294 },
 336     { "Tironi95a",
 337       "I. G. Tironi and R. Sperb and P. E. Smith and W. F. van Gunsteren",
 338       "Generalized reaction field method for molecular dynamics simulations",
 339       "J. Chem. Phys",
 340       102, 1995, 5451, 5459 },
 341     { "Hess97a",
 342       "B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije",
 343       "LINCS: A Linear Constraint Solver for molecular simulations",
 344       "J. Comp. Chem.",
 345       18, 1997, 1463, 1472 },
 346     { "In-Chul99a",
 347       "Y. In-Chul and M. L. Berkowitz",
 348       "Ewald summation for systems with slab geometry",
 349       "J. Chem. Phys.",
 350       111, 1999, 3155, 3162 },
 351     { "DeGroot97a",
 352       "B. L. de Groot and D. M. F. van Aalten and R. M. Scheek and A. Amadei and G. Vriend and H. J. C. Berendsen",
 353       "Prediction of Protein Conformational Freedom From Distance Constrains",
 354       "Proteins",
 355       29, 1997, 240, 251 },
 356     { "Spoel98a",
 357       "D. van der Spoel and P. J. van Maaren and H. J. C. Berendsen",
 358       "A systematic study of water models for molecular simulation. Derivation of models optimized for use with a reaction-field.",
 359       "J. Chem. Phys.",
 360       108, 1998, 10220, 10230 },
 361     { "Wishart98a",
 362       "D. S. Wishart and A. M. Nip",
 363       "Protein Chemical Shift Analysis: A Practical Guide",
 364       "Biochem. Cell Biol.",
 365       76, 1998, 153, 163 },
 366     { "Maiorov95",
 367       "V. N. Maiorov and G. M. Crippen",
 368       "Size-Independent Comparison of Protein Three-Dimensional Structures",
 369       "PROTEINS: Struct. Funct. Gen.",
 370       22, 1995, 273, 283 },
 371     { "Feenstra99",
 372       "K. A. Feenstra and B. Hess and H. J. C. Berendsen",
 373       "Improving Efficiency of Large Time-scale Molecular Dynamics Simulations of Hydrogen-rich Systems",
 374       "J. Comput. Chem.",
 375       20, 1999, 786, 798 },
 376     { "Lindahl2001a",
 377       "E. Lindahl and B. Hess and D. van der Spoel",
 378       "GROMACS 3.0: A package for molecular simulation and trajectory analysis",
 379       "J. Mol. Mod.",
 380       7, 2001, 306, 317 },
 381     { "Wang2001a",
 382       "J. Wang and W. Wang and S. Huo and M. Lee and P. A. Kollman",
 383       "Solvation model based on weighted solvent accessible surface area",
 384       "J. Phys. Chem. B",
 385       105, 2001, 5055, 5067 },
 386     { "Eisenberg86a",
 387       "D. Eisenberg and A. D. McLachlan",
 388       "Solvation energy in protein folding and binding",
 389       "Nature",
 390       319, 1986, 199, 203 },
 391     { "Eisenhaber95",
 392       "Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and Michael Scharf",
 393       "The Double Cube Lattice Method: Efficient Approaches to Numerical Integration of Surface Area and Volume and to Dot Surface Contouring of Molecular Assemblies",
 394       "J. Comp. Chem.",
 395       16, 1995, 273, 284 },
 396     { "Hetenyi2002b",
 397       "Csaba Hetenyi and David van der Spoel",
 398       "Efficient docking of peptides to proteins without prior knowledge of the binding site.",
 399       "Prot. Sci.",
 400       11, 2002, 1729, 1737 }
 401   };
 402 #define NSTR (int)asize(citedb)
 403
 404   int  j,index;
 405   char *author;
 406   char *title;
 407 #define LINE_WIDTH 79
 408
 409   for(index=0; (index<NSTR) && (strcmp(citedb[index].key,key) != 0); index++)
 410     ;
 411
 412   fprintf(fp,"\n++++++++ PLEASE CITE THE FOLLOWING REFERENCE ++++++++\n");
 413   if (index < NSTR) {
 414     /* Insert newlines */
 415     author = wrap_lines(citedb[index].author,LINE_WIDTH,0,FALSE);
 416     title  = wrap_lines(citedb[index].title,LINE_WIDTH,0,FALSE);
 417     fprintf(fp,"%s\n%s\n%s %d (%d) pp. %d-%d\n",
 418             author,title,citedb[index].journal,
 419             citedb[index].volume,citedb[index].year,
 420             citedb[index].p0,citedb[index].p1);
 421     sfree(author);
 422     sfree(title);
 423   }
 424   else {
 425     fprintf(fp,"Entry %s not found in citation database\n",key);
 426   }
 427   fprintf(fp,"-------- -------- --- Thank You --- -------- --------\n\n");
 428   fflush(fp);
 429 }
 430
 431 /* This routine only returns a static (constant) string, so we use a
 432  * mutex to initialize it. Since the string is only written to the
 433  * first time, there is no risk with multiple calls overwriting the
 434  * output for each other.
 435  */
 436 const char *GromacsVersion()
 437 {
 438
 439   /* Concatenate the version info during preprocessing */
 440   static const char ver_string[]="VERSION " VERSION;
 441
 442   return ver_string;
 443 }