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mm2_params
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mm2.site_parameters,
mm2_params.c,
mm2_params.make,
posting,
readme.mm2_params,
thiophene.mm2,
thiophene.para,
thiophene_mm2.out,
utility.c,
utility.h,
|
|
|
/*============================================================================*/
/* FILENAME: MM2_PARAMS.C (MM2_PARAMS)
/* USAGE: MM2_PARAMS [-A] [-D] {MM2/MM3 OUTPUT FILE WITH ERRORS}
/* -A AUTOMATICALLY TAKE ALL DERIVED PARAMETERS.
/* -D PRINTS OUT DEBUGGING INFO AS TO HOW PARAMETERS ARE DERIVED.
/* PURPOSE: SIFT THROUGH MM2/MM3 OUTPUT FILE FOR ERRORS REGARDING MISSING
/* PARAMETERS AND DERIVE THOSE PARAMETERS BASED ON SIMILARITIES
/* BETWEEN THE INVOLVED ATOM TYPES AND EXISTING PARAMETERS FOR OTHER
/* ATOM TYPES (OR BY ASKING USER IF NO SIMILAR CASES EXIST).
/* NOTE THAT THERE ARE SIGNIFICANT DIFFERENCES IN THE DETAILS OF HANDLING
/* MM2 VERSUS MM3 OUTPUT FILES (DIFFERENT BUILTIN PARAMETER FILE FORMATS,
/* DIFFERENT SITE PARAMETER FILES, DIFFERENT FILENAMES, DIFFERENT ERROR
/* MESSAGE FORMATS, ETC).
/* REFERENCE: JOURNAL OF COMPUTATIONAL CHEMISTRY, VOLUME 12, NUMBER 7,
/* 844-849 (1991) DORA SCHNUR, MARK GRIESHABER, J. PHILLIP BOWEN,
/* "DEVELOPMENT OF AN INTERNAL SEARCHING ALGORITHM FOR PARAMETERIZATION
/* OF THE MM2/MM3 FORCE FIELDS".
/* COPYRIGHT 1992 MONSANTO COMPANY
/* WRITTEN: M.V.GRIESHABER + D.M.SCHNUR
/* LAST MODIFICATION: 6 APRIL 1992 MVG (ADDED COPYRIGHT NOTICE)
/*============================================================================*/
#include "utility.h"
#define MAX_TORSION_ERRORS 100 /* MAX ALLOWED TORSION ERRORS. */
#define MAX_BOND_ERRORS 100 /* MAX ALLOWED BOND ERRORS. */
#define MAX_ANGLE_ERRORS 100 /* MAX ALLOWED (2D) ANGLE ERRORS. */
#define MAX_OUTOFPLANE_ERRORS 100 /* MAX ALLOWED OUT-OF-PLANE ERRORS. */
#define MAX_TORSION_PARAMS_NORMAL 900 /* MAX ALLOWED NORMAL TORSION PARAMETERS. */
#define MAX_TORSION_PARAMS_4RING 200 /* MAX ALLOWED 4 MEMBERED RING TORSION PARAMETERS. */
#define MAX_TORSION_PARAMS_ALLENE 20 /* MAX ALLOWED ALLENE TORSION PARAMETERS. */
#define MAX_BOND_PARAMS 400 /* MAX ALLOWED BOND PARAMETERS. */
#define MAX_ANGLE_PARAMS_NORMAL 600 /* MAX ALLOWED NORMAL (2D) ANGLE PARAMETERS. */
#define MAX_ANGLE_PARAMS_4RING 100 /* MAX ALLOWED 4 MEMBERED RING (2D) ANGLE PARAMETERS. */
#define MAX_ANGLE_PARAMS_3RING 100 /* MAX ALLOWED 3 MEMBERED RING (2D) ANGLE PARAMETERS. */
#define MAX_OUTOFPLANE_PARAMS 200 /* MAX ALLOWED OUT-OF-PLANE PARAMETERS. */
#define MAX_ATOM_TYPES 60 /* MAX MM2/MM3 ATOM TYPES. */
#define MAX_TRANSFORMS 3 /* MAX TRANSFORMATIONS FOR ANY ATOM TYPE. */
#define MAX_ATOMS 256 /* MAX ATOMS IN MOLECULE STRUCTURE. */
#define MAX_BONDS_PER_ATOM 8 /* MAX BONDS TO ONE ATOM. */
#define MM3_END_OF_SECTION '9' /* END OF MM3 PARAMETER SECTION FLAG. */
#define NORMAL 1 /* NORMAL (DEFAULT) ENVIRONMENT. */
#define ALLENE 2 /* ALLENE ENVIRONMENT. */
#define THREE_RING 3 /* 3-MEMBERED RING ENVIRONMENT. */
#define FOUR_RING 4 /* 4-MEMBERED RING ENVIRONMENT. */
#define NO_MATCH 1 /* NO SIMILAR PARAMETER FOUND. */
#define EXACT_MATCH 2 /* EXACT PARAMETER FOUND. */
#define SIMILAR_MATCH 3 /* SIMILAR PARAMETER FOUND. */
#define READ_ACCESS 4 /* FLAG FOR ACCESS ROUTINE. */
#define ATOM_TYPE 0 /* ARRAY INDEX FOR NEW ATOM TYPE. */
#define COST 1 /* ARRAY INDEX FOR COST. */
struct torsion_data
{
int atom_types[4]; /* ATOM TYPES IN TORSION. */
int atom_numbers[4]; /* ATOM NUMBERS IN TORSION (ERRORS ONLY). */
double v1; /* ONE-FOLD TORSIONAL CONSTANT. */
double v2; /* TWO-FOLD TORSIONAL CONSTANT. */
double v3; /* THREE-FOLD TORSIONAL CONSTANT. */
int orig_env; /* ORIGINAL ENVIRONMENT OF TORSION (ERRORS ONLY). */
int save_param; /* FLAG; SAVE THIS PARAMETER (ERRORS ONLY). */
};
struct bond_data
{
int atom_types[2]; /* ATOM TYPES IN BOND. */
double s; /* STRETCHING CONSTANT. */
double l0; /* MINIMUM ENERGY BOND LENGTH. */
double slps; /* SLOPE OF BOND-ORDER STRETCHING EQUATION. */
double slpt; /* SLOPE OF BOND-ORDER LENGTH EQUATION. */
double bmom; /* BOND MOMENT. */
int save_param; /* FLAG; SAVE THIS PARAMETER (ERRORS ONLY). */
};
struct angle_data
{
int atom_types[3]; /* ATOM TYPES IN ANGLE. */
int atom_numbers[3]; /* ATOM NUMBERS IN ANGLE (ERRORS ONLY). */
double b; /* BENDING CONSTANT. */
double t; /* MINIMUM ENERGY BOND ANGLE (ALL ENVIRONMENTS). */
int orig_env; /* ORIGINAL ENVIRONMENT OF ANGLE (ERRORS ONLY). */
int save_param; /* FLAG; SAVE THIS PARAMETER (ERRORS ONLY). */
};
struct outofplane_data
{
int atom_types[3]; /* ATOM TYPES IN OUT OF PLANE. */
double b; /* BENDING CONSTANT. */
int save_param; /* FLAG; SAVE THIS PARAMETER (ERRORS ONLY). */
};
/* REMEMBER EACH ERROR FOUND IN THE MM2 OUTPUT FILE. */
struct torsion_data torsion_errors[MAX_TORSION_ERRORS];
struct bond_data bond_errors[MAX_BOND_ERRORS];
struct angle_data angle_errors[MAX_ANGLE_ERRORS];
struct outofplane_data outofplane_errors[MAX_OUTOFPLANE_ERRORS];
int ntorsion_errors; /* NUMBER OF TORSION (DIHEDRAL) ERRORS. */
int nbond_errors; /* NUMBER OF BOND ERRORS. */
int nangle_errors; /* NUMBER OF (2D) ANGLE ERRORS. */
int noutofplane_errors; /* NUMBER OF OUT-OF-PLANE ERRORS. */
/* REMEMBER ALL KNOWN PARAMETERS FOR COMPARISONS (TORSION AND ANGLE DATA IS */
/* SPECIFIC FOR THE STRUCTURAL ENVIRONMENT). */
/* NOTE: USAGE OF TORSION_PARAMS_ALLENE IS *NOT* CURRENTLY IMPLEMENTED SINCE */
/* THERE IS A BUG IN MM2 SUCH THAT THE ALLENE PARAMETERS DO NOT WORK; HOWEVER */
/* WE LEAVE THE DATA STRUCTURE HERE FOR FUTURE ACTIVATION. */
struct torsion_data torsion_params_normal[MAX_TORSION_PARAMS_NORMAL];
struct torsion_data torsion_params_4ring[MAX_TORSION_PARAMS_4RING];
struct torsion_data torsion_params_allene[MAX_TORSION_PARAMS_ALLENE];
struct bond_data bond_params[MAX_BOND_PARAMS];
struct angle_data angle_params_normal[MAX_ANGLE_PARAMS_NORMAL];
struct angle_data angle_params_4ring[MAX_ANGLE_PARAMS_4RING];
struct angle_data angle_params_3ring[MAX_ANGLE_PARAMS_3RING];
struct outofplane_data outofplane_params[MAX_OUTOFPLANE_PARAMS];
int ntorsion_params_normal; /* NUMBER OF NORMAL TORSION PARAMETERS. */
int ntorsion_params_4ring; /* NUMBER OF 4 MEMBER RING TORSION PARAMETERS. */
int ntorsion_params_allene; /* NUMBER OF ALLENE TORSION PARAMETERS. */
int nbond_params; /* NUMBER OF BOND PARAMETERS. */
int nangle_params_normal; /* NUMBER OF NORMAL (2D) ANGLE PARAMETERS. */
int nangle_params_4ring; /* NUMBER OF 4 MEMBERED RING (2D) ANGLE PARAMETERS. */
int nangle_params_3ring; /* NUMBER OF 3 MEMBERED RING (2D) ANGLE PARAMETERS. */
int noutofplane_params; /* NUMBER OF OUT-OF-PLANE PARAMETERS. */
int debug_on; /* FLAG; EXTRA DEBUGGING INFORMATION PRINTED. */
int auto_take; /* FLAG; AUTOMATICALLY TAKE ALL DEFAULTS. */
struct /* MOLECULE STRUCTURE, CONNECTIVITY ONLY. */
{
int nbonds; /* NUMBER OF BONDS TO THIS ATOM. */
int bonds[MAX_BONDS_PER_ATOM]; /* ATOMS BONDED TO THIS ATOM. */
} connect[MAX_ATOMS];
int natoms; /* NUMBER OF ATOMS IN MOLECULE STRUCTURE. */
int main(argc,argv)
/*============================================================================*/
/* PURPOSE: CREATE MISSING MM2/MM3 PARAMETERS BASED ON SIMILARITY TO OTHER
/* (KNOWN) PARAMETERS.
*/
int argc;
char* argv[];
{
char program[10]; /* NAME OF PROGRAM USED (MM2 OR MM3). */
char error_filename[100]; /* NAME OF MM2 OUTPUT FILE CONTAINING ERRORS. */
char param_filename[100]; /* NAME OF CREATED NEW PARAMETER FILE. */
int initialize(); /* VERIFY INPUTS, READ KNOWN PARAMETERS. */
void digest_mm2_errors(); /* COLLECT ERRORS FROM MM2 .OUT FILE. */
void digest_mm3_errors(); /* COLLECT ERRORS FROM MM3 .OUT FILE. */
int make_parameters(); /* GENERATE MISSING PARAMETERS. */
void write_parameters(); /* CREATE THE MM2 ADDITIONAL PARAMETER FILE. */
/* VALIDATE INPUT AND READ KNOWN PARAMETERS FOR LATER COMPARISON. */
if (!initialize(argc,argv,program,error_filename,param_filename)) return(PROGRAM_FAILED);
/* PICK THE ERRORS OUT OF THE MM2/MM3 OUTPUT FILE. */
if (strcmp(program,"mm2")==0)
digest_mm2_errors(error_filename);
else
digest_mm3_errors(error_filename);
/* CREATE THE MISSING PARAMETERS BY SIMILARITY OR DIRECT USER QUERY AND */
/* WRITE OUT THE CORRECTLY FORMATTED MM2 ADDITIONAL INPUT PARAMETER FILE. */
if (make_parameters())
{
write_parameters(param_filename);
}
return(PROGRAM_SUCCEEDED);
}
int initialize(argc,argv,program,error_filename,param_filename)
/*============================================================================*/
/* PURPOSE: VERIFY INPUTS AND FILE EXISTENCE, AND READ KNOWN PARAMETERS
/* FOR LATER COMPARISONS.
*/
int argc;
char* argv[];
char program[]; /* NAME OF PROGRAM USED (MM2 OR MM3). */
char error_filename[]; /* NAME OF MM2 OUTPUT FILE CONTAINING ERRORS. */
char param_filename[]; /* NAME OF CREATED NEW PARAMETER FILE. */
{
char struct_filename[100]; /* NAME OF MOLECULE STRUCTURE FILE. */
char builtin_filename[100]; /* NAME OF BUILTIN DEFAULT PARAMETER FILE. */
char site_filename[100]; /* NAME OF LOCAL SITE PARAMETER FILE. */
int option; /* OPTION CHARACTER. */
extern int optind; /* ARGV INDEX OF NEXT OPTION TO PROCESS. */
extern int opterr; /* ERROR CONTROL FOR OPTION PROCESSING. */
extern char *optarg; /* OPTION ARGUMENT. */
int getopt(); /* GET OPTION LETTER FROM ARGUMENT VECTOR. */
char* getenv(); /* GET ENVIRONMENT NAME VALUE. */
/* CHECK PROPER USAGE. */
if (argc>4 || argc<2)
{
printf("Usage: mm2_params [-a] [-d] {mm2/mm3 output file containing errors}\n");
printf(" -a = automatically take all parameters found.\n");
printf(" -d = debug printing on.\n");
return(FALSE);
}
opterr=0; /* DISABLE ERROR MESSAGE ON BAD OPTION (SIMPLY IGNORE). */
debug_on=auto_take=FALSE;
while ((option=getopt(argc,argv,"ad")) != -1)
{
if (option=='a') auto_take=TRUE;
else if (option=='d') debug_on=TRUE;
}
/* FORM THE NAME OF THE MM2/MM3 OUTPUT FILE (WHICH CONTAINS THE ERRORS), */
/* AND DETERMINE THE NAME OF THE ORIGINATING PROGRAM. */
strcpy(error_filename,argv[optind]);
new_extension(error_filename,".out");
if (strstr(error_filename,"_mm2")!=NULL) strcpy(program,"mm2");
else if (strstr(error_filename,"_mm3")!=NULL) strcpy(program,"mm3");
else
{
printf("Error: Illegal MM2/MM3 output file name \"%s\".\n",error_filename);
return(FALSE);
}
if (access(error_filename,READ_ACCESS)!=0)
{
printf("Error: Cannot read MM2/MM3 output file \"%s\".\n",error_filename);
return(FALSE);
}
/* GET THE MOLECULE STRUCTURE FROM THE ORIGINAL MM2/MM3 INPUT FILE. */
strcpy(struct_filename,error_filename);
*strrchr(struct_filename,'_')=0; /* TRUNCATE "_MM2.OUT". */
if (strcmp(program,"mm2")==0)
new_extension(struct_filename,".mm2");
else
new_extension(struct_filename,".mm3");
if (!read_mm2_input(struct_filename)) return(FALSE);
/* READ THE BUILTIN DEFAULT (CAME WITH MM2 PROGRAM) PARAMETERS. */
strcpy(builtin_filename,getenv("LOCAL_DATA"));
if (strcmp(program,"mm2")==0)
{
strcat(builtin_filename,"/mm2.builtin_parameters");
if (!read_default_mm2_params(builtin_filename)) return(FALSE);
}
else
{
strcat(builtin_filename,"/KONST89.MM3");
if (!read_default_mm3_params(builtin_filename)) return(FALSE);
}
/* READ THE LOCAL SITE (LOCALLY OPTIMIZED) PARAMETERS. */
strcpy(site_filename,getenv("LOCAL_DATA"));
if (strcmp(program,"mm2")==0)
strcat(site_filename,"/mm2.site_parameters");
else
strcat(site_filename,"/mm3.site_parameters");
if (!read_local_params(site_filename)) return(FALSE);
/* FORM THE NAME OF THE NEW INPUT PARAMETER FILE TO BE CREATED. */
strcpy(param_filename,error_filename);
*strrchr(param_filename,'_')=0; /* TRUNCATE "_MM2.OUT". */
new_extension(param_filename,".para");
return(TRUE);
}
int read_mm2_input(struct_filename)
/*============================================================================*/
/* PURPOSE: READ IN MOLECULE STRUCTURE (CONNECTIVITY) FROM AN MM2 INPUT FILE.
*/
char struct_filename[]; /* NAME OF MM2 INPUT (STRUCTURE) FILE. */
{
FILE* struct_file; /* OPENED MM2 INPUT FILE. */
char line[130]; /* RAW LINE FROM MM2 INPUT FILE. */
int method; /* FLAG; WHETHER PI SYSTEM INFO PRESENT. */
int nconnected_atom_lists; /* NUMBER OF CONNECTED ATOM LISTS. */
int nattached_atoms; /* NUMBER OF ATTACHED ATOMS. */
int i; /* LOOP INDEX. */
/* OPEN THE SPECIFIED MM2 INPUT STRUCTURE FILE. */
if ((struct_file=fopen(struct_filename,"r"))==NULL)
{
printf("Error: Cannot read MM2/MM3 input file \"%s\".\n",struct_filename);
return(FALSE);
}
/* GET THE METHOD AND NUMBER OF ATOMS. */
if (fgets(line,sizeof line,struct_file)==NULL)
return(errmsg("Reading MM2/MM3 input file (number of atoms)",FALSE));
sscanf(&line[60],"%1d%4d",&method,&natoms);
/* SKIP THE AROMATIC FLAGS (THIS MAY CONTINUE ACROSS MULTIPLE CARDS). */
if (method)
{
do
{
if (fgets(line,sizeof line,struct_file)==NULL)
return(errmsg("Reading MM2/MM3 input file (aromatic flags)",FALSE));
} while (line[79]=='1');
}
/* GET NUMBER OF CONNECTED ATOM LISTS AND NUMBER OF ATTACHED ATOMS. */
if (fgets(line,sizeof line,struct_file)==NULL)
return(errmsg("Reading MM2/MM3 input file (number of atom lists)",FALSE));
sscanf(line,"%5d %*f %5d",&nconnected_atom_lists,&nattached_atoms);
/* BUILD THE BONDS BY READING IN THE CONNECTED AND ATTACHED ATOM LISTS. */
for (i=0; i=MAX_BONDS_PER_ATOM || connect[second_atom].nbonds>=MAX_BONDS_PER_ATOM)
return(errmsg("Too many bonds to a single atom",FALSE));
connect[first_atom].bonds[connect[first_atom].nbonds++] = second_atom;
connect[second_atom].bonds[connect[second_atom].nbonds++] = first_atom;
}
return(TRUE);
}
int process_attached_atom_list(line)
/*============================================================================*/
/* PURPOSE: PROCESS AN MM2 ATTACHED ATOM LIST INTO THE INDIVIDUAL BONDS.
/* NOTE THAT EACH PAIR IS COMPLETELY INDEPENDENT.
*/
char line[]; /* RAW ATTACHED ATOM LIST FROM MM2 INPUT FILE. */
{
int i; /* INDEX OF FIRST ATOM OF PAIR IN LINE. */
int first_atom; /* FIRST ATOM OF VALID PAIR. */
int second_atom; /* SECOND ATOM OF VALID PAIR. */
/* TAKE APART AN ATTACHED ATOM LIST AN ATOM PAIR AT A TIME. */
i=0;
while (i<15 && atoi(&line[i*5])!=0)
{
/* GET THE VALID ATOM PAIR. */
sscanf(&line[i*5],"%5d%5d",&first_atom,&second_atom);
first_atom--; /* ADJUST TO INDEX FROM 0 (MM2 COUNTS FROM 1). */
second_atom--;
i+=2; /* FINISHED THIS PAIR, MOVE AHEAD TO NEXT. */
/* ADD THE BONDS TO EACH ATOM'S RESPECTIVE BOND LIST. */
if (connect[first_atom].nbonds>=MAX_BONDS_PER_ATOM || connect[second_atom].nbonds>=MAX_BONDS_PER_ATOM)
return(errmsg("Too many bonds to a single atom",FALSE));
connect[first_atom].bonds[connect[first_atom].nbonds++] = second_atom;
connect[second_atom].bonds[connect[second_atom].nbonds++] = first_atom;
}
return(TRUE);
}
int read_default_mm2_params(builtin_filename)
/*============================================================================*/
/* PURPOSE: READ IN ALL NEEDED DEFAULT PARAMETERS FOR MM2.
*/
char builtin_filename[]; /* NAME OF THE BUILTIN PARAMETER FILE. */
{
FILE* builtin_file; /* FILE DESCRIPTOR FOR KNOWN PARAMETER FILE. */
char line[100]; /* RAW LINE FROM PARAMETER FILE. */
builtin_file=fopen(builtin_filename,"r");
/* FIND THE START OF THE REGULAR (NON SPECIAL) TORSIONAL PARAMETERS, */
/* THEN SUCK UP REGULAR TORSION PARAMETERS UNTIL END OF SECTION. */
find_line(builtin_file,"TORSIONAL PARAMETERS",line,sizeof line);
find_line(builtin_file,"ANGLE V1",line,sizeof line);
while (!find_string(fgets(line,sizeof line,builtin_file),"4-MEMBERED RING"))
{
/* SKIP BLANK, FORTRAN CONTROL, AND EXTRA COLUMN HEADER LINES. */
if (strlen(line)>1 && line[0]!='+' && line[0]!='1' && line[0]!='0' && !find_string(line,"ANGLE"))
{
sscanf(line,"%*d %d-%d-%d-%d %lf %lf %lf",
&torsion_params_normal[ntorsion_params_normal].atom_types[0],
&torsion_params_normal[ntorsion_params_normal].atom_types[1],
&torsion_params_normal[ntorsion_params_normal].atom_types[2],
&torsion_params_normal[ntorsion_params_normal].atom_types[3],
&torsion_params_normal[ntorsion_params_normal].v1,
&torsion_params_normal[ntorsion_params_normal].v2,
&torsion_params_normal[ntorsion_params_normal].v3);
ntorsion_params_normal++;
}
}
/* NOW AT START OF 4 MEMBERED RING TORSION PARAMETERS, SKIP TO DATA, */
/* THEN SUCK UP 4 MEMBER TORSIONAL PARAMETERS UNTIL END OF SECTION. */
find_line(builtin_file,"ANGLE V1",line,sizeof line);
while (!find_string(fgets(line,sizeof line,builtin_file),"ALLENES"))
{
/* SKIP BLANK, FORTRAN CONTROL, AND EXTRA COLUMN HEADER LINES. */
if (strlen(line)>1 && line[0]!='+' && line[0]!='1' && line[0]!='0' && !find_string(line,"ANGLE"))
{
sscanf(line,"%*d %d-%d-%d-%d %lf %lf %lf",
&torsion_params_4ring[ntorsion_params_4ring].atom_types[0],
&torsion_params_4ring[ntorsion_params_4ring].atom_types[1],
&torsion_params_4ring[ntorsion_params_4ring].atom_types[2],
&torsion_params_4ring[ntorsion_params_4ring].atom_types[3],
&torsion_params_4ring[ntorsion_params_4ring].v1,
&torsion_params_4ring[ntorsion_params_4ring].v2,
&torsion_params_4ring[ntorsion_params_4ring].v3);
ntorsion_params_4ring++;
}
}
/* NOW AT START OF ALLENES TORSION PARAMETERS, SKIP TO DATA, THEN */
/* SUCK UP ALLENES TORSIONAL PARAMETERS UNTIL END OF SECTION. */
find_line(builtin_file,"ANGLE V1",line,sizeof line);
while (!find_string(fgets(line,sizeof line,builtin_file),"MM2 (1987)"))
{
/* SKIP BLANK, FORTRAN CONTROL, AND EXTRA COLUMN HEADER LINES. */
if (strlen(line)>1 && line[0]!='+' && line[0]!='1' && line[0]!='0' && !find_string(line,"ANGLE"))
{
sscanf(line,"%*d %d-%d-%d-%d %lf %lf %lf",
&torsion_params_allene[ntorsion_params_allene].atom_types[0],
&torsion_params_allene[ntorsion_params_allene].atom_types[1],
&torsion_params_allene[ntorsion_params_allene].atom_types[2],
&torsion_params_allene[ntorsion_params_allene].atom_types[3],
&torsion_params_allene[ntorsion_params_allene].v1,
&torsion_params_allene[ntorsion_params_allene].v2,
&torsion_params_allene[ntorsion_params_allene].v3);
ntorsion_params_allene++;
}
}
/* FIND THE START OF THE BOND PARAMETERS, THEN */
/* SUCK UP BOND PARAMETERS UNTIL END OF SECTION. */
find_line(builtin_file,"STRETCHING PARAMETERS",line,sizeof line);
find_line(builtin_file,"BOND KS",line,sizeof line);
while (!find_string(fgets(line,sizeof line,builtin_file),"4-MEMBERED RING"))
{
/* SKIP BLANK, FORTRAN CONTROL, AND EXTRA COLUMN HEADER LINES. */
if (strlen(line)>1 && line[0]!='+' && line[0]!='1' && line[0]!='0' && !find_string(line,"BOND"))
{
sscanf(line,"%*d %d-%d %lf %lf %lf %lf %lf",
&bond_params[nbond_params].atom_types[0],
&bond_params[nbond_params].atom_types[1],
&bond_params[nbond_params].s,
&bond_params[nbond_params].l0,
&bond_params[nbond_params].bmom,
&bond_params[nbond_params].slps,
&bond_params[nbond_params].slpt);
/* BONDS MARKED WITH 999 ARE PLACE HOLDERS AND ARE INVALID. */
if (bond_params[nbond_params].s < 999.0) nbond_params++;
}
}
/* FIND THE START OF THE REGULAR (NON SPECIAL) ANGLE PARAMETERS, THEN */
/* SUCK UP ANGLE PARAMETERS UNTIL END OF SECTION. */
find_line(builtin_file,"BENDING PARAMETERS",line,sizeof line);
find_line(builtin_file,"ANGLE KS",line,sizeof line);
find_line(builtin_file,"(-CR2-)",line,sizeof line);
while (!find_string(fgets(line,sizeof line,builtin_file),"TYPE-2 BENDING KS"))
{
/* SKIP BLANK, FORTRAN CONTROL, AND EXTRA COLUMN HEADER LINES. */
if (strlen(line)>1 && line[0]!='+' && line[0]!='1' && line[0]!='0' &&
!find_string(line,"ANGLE") && !find_string(line,"(-CR2-)"))
{
sscanf(line,"%*d %d-%d-%d %lf %lf",
&angle_params_normal[nangle_params_normal].atom_types[0],
&angle_params_normal[nangle_params_normal].atom_types[1],
&angle_params_normal[nangle_params_normal].atom_types[2],
&angle_params_normal[nangle_params_normal].b,
&angle_params_normal[nangle_params_normal].t);
/* ANGLES MARKED WITH 99 ARE PLACE HOLDERS AND ARE INVALID. */
if (angle_params_normal[nangle_params_normal].b < 99.0) nangle_params_normal++;
}
}
/* FIND THE START OF THE 4-MEMBERED RING ANGLE PARAMETERS, THEN */
/* SUCK UP 4-MEMBERED RING ANGLE PARAMETERS UNTIL END OF SECTION. */
find_line(builtin_file,"4-MEMBERED RING",line,sizeof line);
find_line(builtin_file,"ANGLE KS",line,sizeof line);
find_line(builtin_file,"(-CR2-)",line,sizeof line);
while (!find_string(fgets(line,sizeof line,builtin_file),"TYPE-2 BENDING KS"))
{
/* SKIP BLANK, FORTRAN CONTROL, AND EXTRA COLUMN HEADER LINES. */
if (strlen(line)>1 && line[0]!='+' && line[0]!='1' && line[0]!='0' &&
!find_string(line,"ANGLE") && !find_string(line,"(-CR2-)"))
{
sscanf(line,"%*d %d-%d-%d %lf %lf",
&angle_params_4ring[nangle_params_4ring].atom_types[0],
&angle_params_4ring[nangle_params_4ring].atom_types[1],
&angle_params_4ring[nangle_params_4ring].atom_types[2],
&angle_params_4ring[nangle_params_4ring].b,
&angle_params_4ring[nangle_params_4ring].t);
nangle_params_4ring++;
}
}
/* FIND THE START OF THE 3-MEMBERED RING ANGLE PARAMETERS, THEN */
/* SUCK UP 3-MEMBERED RING ANGLE PARAMETERS UNTIL END OF SECTION. */
find_line(builtin_file,"3-MEMBERED RING",line,sizeof line);
while (!find_string(fgets(line,sizeof line,builtin_file),"TYPE-2 BENDING KS"))
{
/* SKIP BLANK, FORTRAN CONTROL, AND EXTRA COLUMN HEADER LINES. */
if (strlen(line)>1 && line[0]!='+' && line[0]!='1' && line[0]!='0' &&
!find_string(line,"ANGLE") && !find_string(line,"(-CR2-)"))
{
sscanf(line,"%*d %d-%d-%d %lf %lf",
&angle_params_3ring[nangle_params_3ring].atom_types[0],
&angle_params_3ring[nangle_params_3ring].atom_types[1],
&angle_params_3ring[nangle_params_3ring].atom_types[2],
&angle_params_3ring[nangle_params_3ring].b,
&angle_params_3ring[nangle_params_3ring].t);
nangle_params_3ring++;
}
}
/* FIND THE START OF THE OUT OF PLANE PARAMETERS, THEN */
/* SUCK UP OUT OF PLANE PARAMETERS UNTIL END OF SECTION. */
find_line(builtin_file,"OUT-OF-PLANE BENDING PARAMETERS",line,sizeof line);
while (!find_string(fgets(line,sizeof line,builtin_file),"STRETCH-BEND"))
{
/* SKIP BLANK AND FORTRAN CONTROL LINES. */
if (strlen(line)>1 && line[0]!='+' && line[0]!='1' && line[0]!='0')
{
outofplane_params[noutofplane_params].atom_types[0]=0;
sscanf(line,"%*d %d-%d %lf",
&outofplane_params[noutofplane_params].atom_types[1],
&outofplane_params[noutofplane_params].atom_types[2],
&outofplane_params[noutofplane_params].b);
noutofplane_params++;
}
}
/* DONE READING BUILT IN DEFAULT PARAMETERS, CLOSE THE FILE AND RETURN. */
fclose(builtin_file);
return(TRUE);
}
int read_default_mm3_params(builtin_filename)
/*============================================================================*/
/* PURPOSE: READ IN ALL NEEDED DEFAULT PARAMETERS FOR MM3. NOTE SLIGHT
/* TRICKERY WITH ATOM TYPES - THEY ARE PACKED ########, BUT THE FIRST
/* DIGIT MAY BE BLANK (WHICH PRECLUDES USING SSCANF DIRECTLY).
*/
char builtin_filename[]; /* NAME OF THE BUILTIN PARAMETER FILE. */
{
FILE* builtin_file; /* FILE DESCRIPTOR FOR KNOWN PARAMETER FILE. */
char line[100]; /* RAW LINE FROM PARAMETER FILE. */
char packed_atom_types[20]; /* ATOM TYPES PACKED AS ########. */
char tmp_str[20]; /* TEMP STRING FOR STRNCPY. */
builtin_file=fopen(builtin_filename,"r");
/* FIND THE START OF THE REGULAR (NON SPECIAL) TORSIONAL PARAMETERS, */
/* THEN SUCK UP REGULAR TORSION PARAMETERS UNTIL END OF SECTION. */
find_line(builtin_file,"TORSIONAL PARAMETERS",line,sizeof line);
find_line(builtin_file,"--------------------",line,sizeof line);
find_line(builtin_file,"--------------------",line,sizeof line);
while (fgets(line,sizeof line,builtin_file) && line[0]!=MM3_END_OF_SECTION)
{
sscanf(line,"%*d %8c %lf %lf %lf",
packed_atom_types,
&torsion_params_normal[ntorsion_params_normal].v1,
&torsion_params_normal[ntorsion_params_normal].v2,
&torsion_params_normal[ntorsion_params_normal].v3);
torsion_params_normal[ntorsion_params_normal].atom_types[0]=atoi(strncpy(tmp_str,packed_atom_types,2));
torsion_params_normal[ntorsion_params_normal].atom_types[1]=atoi(strncpy(tmp_str,&packed_atom_types[2],2));
torsion_params_normal[ntorsion_params_normal].atom_types[2]=atoi(strncpy(tmp_str,&packed_atom_types[4],2));
torsion_params_normal[ntorsion_params_normal].atom_types[3]=atoi(strncpy(tmp_str,&packed_atom_types[6],2));
ntorsion_params_normal++;
}
/* SKIP 5 MEMBERED RING SECTION TO GET TO THE START OF THE 4 MEMBERED RING */
/* TORSION PARAMETERS, SKIP TO DATA, THEN SUCK UP 4 MEMBER TORSIONAL */
/* PARAMETERS UNTIL END OF SECTION. */
find_line(builtin_file,"4-MEMBERED RING",line,sizeof line);
find_line(builtin_file,"--------------------",line,sizeof line);
while (fgets(line,sizeof line,builtin_file) && line[0]!=MM3_END_OF_SECTION)
{
sscanf(line,"%*d %8c %lf %lf %lf",
packed_atom_types,
&torsion_params_4ring[ntorsion_params_4ring].v1,
&torsion_params_4ring[ntorsion_params_4ring].v2,
&torsion_params_4ring[ntorsion_params_4ring].v3);
torsion_params_4ring[ntorsion_params_4ring].atom_types[0]=atoi(strncpy(tmp_str,packed_atom_types,2));
torsion_params_4ring[ntorsion_params_4ring].atom_types[1]=atoi(strncpy(tmp_str,&packed_atom_types[2],2));
torsion_params_4ring[ntorsion_params_4ring].atom_types[2]=atoi(strncpy(tmp_str,&packed_atom_types[4],2));
torsion_params_4ring[ntorsion_params_4ring].atom_types[3]=atoi(strncpy(tmp_str,&packed_atom_types[6],2));
ntorsion_params_4ring++;
}
/* FIND START OF ALLENES TORSION PARAMETERS, SKIP TO DATA, THEN */
/* SUCK UP ALLENES TORSIONAL PARAMETERS UNTIL END OF SECTION. */
find_line(builtin_file,"ALLENES",line,sizeof line);
find_line(builtin_file,"--------------------",line,sizeof line);
while (fgets(line,sizeof line,builtin_file) && line[0]!=MM3_END_OF_SECTION)
{
sscanf(line,"%*d %8c %lf %lf %lf",
packed_atom_types,
&torsion_params_allene[ntorsion_params_allene].v1,
&torsion_params_allene[ntorsion_params_allene].v2,
&torsion_params_allene[ntorsion_params_allene].v3);
torsion_params_allene[ntorsion_params_allene].atom_types[0]=atoi(strncpy(tmp_str,packed_atom_types,2));
torsion_params_allene[ntorsion_params_allene].atom_types[1]=atoi(strncpy(tmp_str,&packed_atom_types[2],2));
torsion_params_allene[ntorsion_params_allene].atom_types[2]=atoi(strncpy(tmp_str,&packed_atom_types[4],2));
torsion_params_allene[ntorsion_params_allene].atom_types[3]=atoi(strncpy(tmp_str,&packed_atom_types[6],2));
ntorsion_params_allene++;
}
/* FIND THE START OF THE BOND PARAMETERS, THEN */
/* SUCK UP BOND PARAMETERS UNTIL END OF SECTION. */
find_line(builtin_file,"BOND PARAMETERS",line,sizeof line);
find_line(builtin_file,"--------------------",line,sizeof line);
find_line(builtin_file,"--------------------",line,sizeof line);
while (fgets(line,sizeof line,builtin_file) && line[0]!=MM3_END_OF_SECTION)
{
sscanf(line,"%*d %4c %lf %lf %lf %lf %lf",
packed_atom_types,
&bond_params[nbond_params].s,
&bond_params[nbond_params].l0,
&bond_params[nbond_params].bmom,
&bond_params[nbond_params].slps,
&bond_params[nbond_params].slpt);
bond_params[nbond_params].atom_types[0]=atoi(strncpy(tmp_str,packed_atom_types,2));
bond_params[nbond_params].atom_types[1]=atoi(strncpy(tmp_str,&packed_atom_types[2],2));
/* BONDS MARKED WITH 999 ARE PLACE HOLDERS AND ARE INVALID. */
if (bond_params[nbond_params].s < 999.0) nbond_params++;
}
/* FIND THE START OF THE REGULAR (NON SPECIAL) ANGLE PARAMETERS, THEN */
/* SUCK UP ANGLE PARAMETERS UNTIL END OF SECTION. */
find_line(builtin_file,"BENDING PARAMETERS",line,sizeof line);
find_line(builtin_file,"--------------------",line,sizeof line);
find_line(builtin_file,"--------------------",line,sizeof line);
while (fgets(line,sizeof line,builtin_file) && line[0]!=MM3_END_OF_SECTION)
{
sscanf(line,"%*d %6c %lf %lf",
packed_atom_types,
&angle_params_normal[nangle_params_normal].b,
&angle_params_normal[nangle_params_normal].t);
angle_params_normal[nangle_params_normal].atom_types[0]=atoi(strncpy(tmp_str,packed_atom_types,2));
angle_params_normal[nangle_params_normal].atom_types[1]=atoi(strncpy(tmp_str,&packed_atom_types[2],2));
angle_params_normal[nangle_params_normal].atom_types[2]=atoi(strncpy(tmp_str,&packed_atom_types[4],2));
/* ANGLES MARKED WITH 99 ARE PLACE HOLDERS AND ARE INVALID. */
if (angle_params_normal[nangle_params_normal].b < 99.0) nangle_params_normal++;
}
/* FIND THE START OF THE 4-MEMBERED RING ANGLE PARAMETERS, THEN */
/* SUCK UP 4-MEMBERED RING ANGLE PARAMETERS UNTIL END OF SECTION. */
find_line(builtin_file,"4-MEMBERED RING",line,sizeof line);
find_line(builtin_file,"--------------------",line,sizeof line);
while (fgets(line,sizeof line,builtin_file) && line[0]!=MM3_END_OF_SECTION)
{
sscanf(line,"%*d %6c %lf %lf",
packed_atom_types,
&angle_params_4ring[nangle_params_4ring].b,
&angle_params_4ring[nangle_params_4ring].t);
angle_params_4ring[nangle_params_4ring].atom_types[0]=atoi(strncpy(tmp_str,packed_atom_types,2));
angle_params_4ring[nangle_params_4ring].atom_types[1]=atoi(strncpy(tmp_str,&packed_atom_types[2],2));
angle_params_4ring[nangle_params_4ring].atom_types[2]=atoi(strncpy(tmp_str,&packed_atom_types[4],2));
nangle_params_4ring++;
}
/* FIND THE START OF THE 3-MEMBERED RING ANGLE PARAMETERS, THEN */
/* SUCK UP 3-MEMBERED RING ANGLE PARAMETERS UNTIL END OF SECTION. */
find_line(builtin_file,"3-MEMBERED RING",line,sizeof line);
find_line(builtin_file,"--------------------",line,sizeof line);
while (fgets(line,sizeof line,builtin_file) && line[0]!=MM3_END_OF_SECTION)
{
sscanf(line,"%*d %6c %lf %lf",
packed_atom_types,
&angle_params_3ring[nangle_params_3ring].b,
&angle_params_3ring[nangle_params_3ring].t);
angle_params_3ring[nangle_params_3ring].atom_types[0]=atoi(strncpy(tmp_str,packed_atom_types,2));
angle_params_3ring[nangle_params_3ring].atom_types[1]=atoi(strncpy(tmp_str,&packed_atom_types[2],2));
angle_params_3ring[nangle_params_3ring].atom_types[2]=atoi(strncpy(tmp_str,&packed_atom_types[4],2));
nangle_params_3ring++;
}
/* FIND THE START OF THE OUT OF PLANE PARAMETERS, THEN */
/* SUCK UP OUT OF PLANE PARAMETERS UNTIL END OF SECTION. */
find_line(builtin_file,"OUT OF PLANE BENDING PARAMETERS",line,sizeof line);
find_line(builtin_file,"--------------------",line,sizeof line);
find_line(builtin_file,"--------------------",line,sizeof line);
while (fgets(line,sizeof line,builtin_file) && line[0]!=MM3_END_OF_SECTION)
{
sscanf(line,"%*d %4c %lf",
packed_atom_types,
&outofplane_params[noutofplane_params].b);
outofplane_params[noutofplane_params].atom_types[0]=0;
outofplane_params[noutofplane_params].atom_types[1]=atoi(strncpy(tmp_str,packed_atom_types,2));
outofplane_params[noutofplane_params].atom_types[2]=atoi(strncpy(tmp_str,&packed_atom_types[2],2));
noutofplane_params++;
}
/* DONE READING BUILT IN DEFAULT PARAMETERS, CLOSE THE FILE AND RETURN. */
fclose(builtin_file);
return(TRUE);
}
int read_local_params(param_filename)
/*============================================================================*/
/* PURPOSE: READ IN LOCAL SITE PARAMETERS. THESE ARE PARAMETERS
/* THAT HAVE BEEN OPTIMIZED AT LOCAL SITE.
*/
char param_filename[]; /* NAME OF THE LOCAL PARAMETER FILE. */
{
FILE* param_file; /* FILE DESCRIPTOR FOR PARAMETER FILE. */
char line[100]; /* RAW LINE FROM PARAMETER FILE. */
int nparameters; /* NUMBER OF PARAMETERS IN EACH SECTION. */
int i; /* LOOP INDEX. */
/* PERFECTLY VALID NOT TO HAVE ANY LOCAL PARAMETER FILE. */
if ((param_file=fopen(param_filename,"r"))==NULL) return(TRUE);
/* READ NORMAL TORSION PARAMETERS. */
get_data_line(param_file,line,sizeof line);
sscanf(line,"%d",&nparameters);
for (i=0; i=MAX_TRANSFORMS || original_atom_type<1) return(FALSE);
else
{
/* VALID TRANSFORMATION REQUESTED; RETURN NEW TYPE AND COST IF DEFINED. */
*new_atom_type=similar[original_atom_type-1][*transform_level][ATOM_TYPE];
if (*new_atom_type==0) return(FALSE);
else
{
/* THIS IS A DEFINED TRANSFORMATION; GET THE COST AND INCREMENT THE LEVEL FOR NEXT TIME. */
*cost=similar[original_atom_type-1][*transform_level][COST];
(*transform_level)++;
return(TRUE);
}
}
}
void write_parameters(param_filename)
/*============================================================================*/
/* PURPOSE: WRITE A CORRECTLY FORMATTED MM2/MM3 PARAMETER FILE CONTAINING ALL
/* THE NEW PARAMETERS. LINE DESCRIPTIONS ARE VERBATIM FROM THE MM2(87)
/* QCPE PROGRAM MANUAL.
*/
char param_filename[]; /* NEW PARAMETER FILE NAME. */
{
FILE* param_file; /* NEW PARAMETER FILE. */
char env_flag; /* ORIGINAL ENVIRONMENT FLAG (LINES 9A,9F). */
int i; /* LOOP INDEX. */
param_file=fopen(param_filename,"w");
/* WRITE LINE 9 (CHANGED CONSTANTS). */
fprintf(param_file,"%5d%5d%2d%3d%5d%5d%5d%5d%5d\n",
ntorsion_errors,nbond_errors,0,0,nangle_errors+noutofplane_errors,nbond_errors,0,0,0);
/* WRITE LINES 9A (TORSIONAL CONSTANTS). */
for (i=0; i
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