Directory UMM :wiley:Public:journals:jcc:suppmat:21:
Molecular Mechanics-Based Measures of Steric Effects: Customized Code to
Compute Ligand Repulsive Energies
Robert J. Bubela, Warthen Douglass, and David P. White*b
Department of Chemistry, University of North Carolina at Wilmington, 601 South
College Road, Wilmington, NC 28403-3297
a
Undergraduate student from the State University of New York at New Paltz
b
Email address: whitedp@uncwil.edu
1
Supplementary Material: ERCODE.CPP
#include
#include
#include
#include
#include
#define TRUE 1
#define FALSE 0
/**********************GLOBAL VARIABLES*******************************/
struct nodetag
{
// each atom or LP in the molecule has one of
int number;
// these structures dedicated to them
float x, y, z;
// coordinates
char type[10];
// forcefield type
float r0, d0;
// constants from parameter file
int side;
// parameter indicating side ligand side = 0
//
fragment side = 1
struct nodetag *next;
};
typedef nodetag *nodeptr;
nodeptr bgf_list;
// global pointer to beginning of data
char rlist[230][100];
// 2d char array of parameter file
int cons[100][25];
// replica of connectivity table in interger form
int m[100][100];
// this is the binary array, may want to make it
// bigger in case of molecules with more than
// 99 atoms
float unitx, unity, unitz; // unit vector of re bond
float re;
// length of re bond
/***********************END GLOBAL VARIABLES*******************************/
void init_ref(void)
// opens the parameter file and stores the constants in the rlist
{
int i=0;
int j=0;
2
char buf[45]="Forcefields
(R0 / D0)\n";
FILE *stream;
stream=fopen("param_r.set","rt");
//open parameter file
if (!stream)
{printf("File not opened! \n");
exit(1);
//program will not work
}
do
{ fgets(rlist[i], 100, stream);
// useless info(top of file)
i++;
}
while(strcmp(buf, rlist[i-1]));
// until we get to first line
do
{ fgets(rlist[j], 100, stream);
// save these data to rlist
//
j++;
}while(rlist[j-1][0] != 'E');
// ends at END
}/*end init_ref*/
/*****************************************************************/
void menu(void)
{
printf( "==========================================================\n"
"Available commands are:\n"
"
calculate for *.bgf(start or continue)\n"
"
quit
\n"
"=========================================================\n");
}/*end menu*/
/**********************************************************************/
void getcomm(int &command)
{
printf("Enter command:
scanf("%d",&command);
");
// get the command
}/*end getcomm
/******************************************************************/
void connections(char conect[], int cons[])
//receives one line of chars from connectivity table translates it to ints
{
int i, j , k, l;
l=0;
k=9;
char cx[6];
//store 1 char # translated into int
i = strlen(conect);
3
do{
j=0;
do{
cx[j]=conect[k];
k++; j++;
}while (jwhich atoms make up ligand side? fragment side?
// returns a 1 on success, returns 0 if numbers given by user are bad
{
int side_array[100];
int lig, frag, i;
nodeptr t;
int number;
number = bgf_list->number;
// number of atoms on list
printf("Which atom number is on"
" the ligand side of the re bond (donor atom):
scanf("%d", &lig);
");
// prompt user for atom #'s
printf("Which atom number is on the fragment side of the re bond:
");
scanf("%d", &frag);
if (lig>numatoms || frag>numatoms)
{
printf("You have entered one of the numbers incorrectly! \n");
return 0;
}
// too high a number
// prevents program from crashing
else
if (!connected(lig-1, frag))
{
// checks to see if atoms are connected
printf("These atoms are not connected! \n");
6
return 0;
}
else
{
for(i=0; iside == 1)
{
coord1[0] = (factor*unitx) + t1->x; //if the atom is on the fragment
coord1[1] = (factor*unity) + t1->y; //side->move it by move it along
coord1[2] = (factor*unitz) + t1->z; //unit vector a distace of factor
}
else
{
coord1[0] = t1->x;
coord1[1] = t1->y;
// then it is on the ligand side so
// we use the same coordinates
coord1[2] = t1->z;
}
if(t2->side == 1)
{
coord2[0] = (factor*unitx) + t2->x;
coord2[1] = (factor*unity) + t2->y;
coord2[2] = (factor*unitz) + t2->z;
}
else
{
coord2[0] = t2->x;
coord2[1] = t2->y;
coord2[2] = t2->z;
}
dis=dist_form(coord1[0], coord1[1], coord1[2],
coord2[0], coord2[1], coord2[2]);
vander_out = (d0 * exp(12.5*(1 - (dis/r0))));
// get distance
// EvdW,R formula
return vander_out;
}/*end vander*/
/*************************************************************************/
void vdw_formula(nodeptr p, int atom1, int atom2, float vdw[])
// receive two atom #'s, lookup info on them calculate 7 different Evdw,R
// for the pair, add it to the total
{
float d0, r0;
nodeptr t1=p, t2=p;
while(t1->number != atom1)
// look up info on each atom
t1 = t1->next;
while(t2->number != atom2)
t2 = t2->next;
d0 = sqrt(t1->d0 * t2->d0);
// D0-geometric mean of both constants
r0 = (t1->r0 + t2->r0)/2;
// R0-arithmetic mean of "
10
"
vdw[0] = vdw[0] + vander(t1, t2, 0, r0, d0);
// EvdW,R with no change
// in re bond length
vdw[1] = vdw[1] + vander(t1, t2, .01, r0, d0);
// EvdW,R with bond lenth
// increased by .01 angstroms
vdw[2] = vdw[2] + vander(t1, t2, -.01, r0, d0); // EvdW,R with bond lenth
// decreased by .01 angstroms
vdw[3] = vdw[3] + vander(t1, t2, .02, r0, d0);
// increased .02
vdw[4] = vdw[4] + vander(t1, t2, -.02, r0, d0); // decreased .02
vdw[5] = vdw[5] + vander(t1, t2, .03, r0, d0);
vdw[6] = vdw[6] + vander(t1, t2, -.03, r0, d0);
}/*end vdw_formula*/
/******************************************************************/
void vanderwahls(nodeptr p, float vdw[])
// examines binary array searching for 1's, sends two atom #'s
// for which seven Evdw,R values are going to be calculated
{
int number, i, j;
number = p->number;
// last atom number
i=0; j=0;
while(inumber;
atom2 = cons[atom1-1][1];
// if it finds one identify the H
// and the C
while(t2->number != atom2)
t2 = t2->next;
//lookup info about C atom
distance = dist_form(t1->x, t1->y, t1->z, t2->x, t2->y, t2->z);
ux = ((t1->x - t2->x)/distance);
uy = ((t1->y - t2->y)/distance); // find unit vector from C to H
uz = ((t1->z - t2->z)/distance);
n_distance = distance * .915;
// decrease distance by 0.915
t1->x = n_distance*ux + t2->x;
t1->y = n_distance*uy + t2->y;
// add new vector to C coordinates
t1->z = n_distance*uz + t2->z;
}
t1 = t1->next;
// go on looking for more
t2 = bgf_list;
}
}/*end bond_shrinkage*/
/*************************************************************************/
void find_er(float vdw[], char filename[], FILE *out)
//calculates Ligand Repulsive Energy
{
float sxx, sxy, slope, er, avg;
avg = (vdw[0] + vdw[1] + vdw[2] + vdw[3] + vdw[4] + vdw[5] + vdw[6])/7;
sxx = .0028;
sxy = (.01*(vdw[1]-avg))+(-.01*(vdw[2]-avg))+(.02*(vdw[3]-avg))+
(-.02*(vdw[4]-avg))+(.03*(vdw[5]-avg))+(-.03*(vdw[6]-avg));
slope = sxy/sxx;
// average slope formula
er = re*slope;
fprintf(out,"%s
", filename);
// sends filename to outfile
fprintf(out,"%f
\n", er);
// sends Er to outfile
}/*end find_er*/
/*********************************************************************/
void free_mem(void)
// traverses through list deleting all nodes to get mem back
{
nodeptr t1,t2;
t1=bgf_list;
t2=bgf_list->next;
while(t2->next != NULL)
{ free (t1);
t1 = t2;
12
t2 = t2->next;
}
}/*end free_mem*/
/********************************************************************/
void adjust_filename(char filename[])
// receives user input file name, checks and adds *.bgf extension
{
int len;
len = strlen(filename);
if (toupper(filename[len-1]) == 'F' &&
//if user entered file extension
toupper(filename[len-2]) == 'G' &&
toupper(filename[len-3]) == 'B' &&
filename[len-4] == '.')
;
// do nothing
else
{
char end[4] = ".bgf";
strncat(filename, end, 4);
// attach .bgf to end if filename
}
}/*end adjust_filename*/
/********************************************************************/
void bfg(FILE *out, int on_off)
// essentially bgf file driver
{
int done=0;
while(!done)
// this while loop allows user to calc
// several files without having to go
// back to menu
{
char filename[50];
char buf[30]="FORMAT CONECT (a6,12i6)\n";// when to stop reading
char input[100];
// holds data temporarily
int numatoms;
int i;
float vdw[7];
// to find Er we need seven different
// values for Evdw
for(i=0; inext = bgf_list;
bgf_list = p;
// bgf_list is the real list we use
}
}while(strcmp(buf, input));
numatoms = bgf_list->number;
find_connections(stream);
//function uses connectivity table to
// create binary array
if(find_side(numatoms))
// this function is used to tell which
// side of the re each atom is on
{
if (on_off == 1)
bond_shrinkage();//allows for C__H bond shrinkage
vanderwahls(bgf_list, vdw);
// simultaneously solves
// for seven values of repulsive
// vanderwahls energy by
// adjusting xyz coordinates of
// individual atoms
find_er(vdw, filename, out);// calculates Er and sends it to ouput
// file along with file name
}
free_mem();
//clears up memory so we can do it again
fclose(stream);
//close the current input file stream
}
}
}/*end bfg()*/
14
void driver()
// gets the ouput filename, options...
{
int done;
//finish flag
int command;
int on_off = -1;
char shrink[1];
char outfile[20];
// file for data output
printf("Please enter a filename for the data:
");
scanf("%s",outfile);
FILE *out;
if ((out = fopen(outfile, "wt"))
== NULL)
{
fprintf(stderr, "Cannot open output file.\n");
exit(1);
}
done = FALSE;
do {
printf("Do you want SHRINK_CH_BONDS on? (y/n) \n");
scanf("%s",&shrink);
if(toupper(shrink[0]) == 'Y')
on_off = 1;
else
if(toupper(shrink[0]) == 'N')
on_off =0;
}while (on_off == -1);
menu();
while (!done)
{
getcomm (command);
if (command == 1)
{ bfg(out, on_off);
}
else
if (command == 0)
done = TRUE;
menu();
}
fclose(out);
}/*end driver*/
/*********************************************************************/
void main()
15
{
printf("ERCODE. \n"
"When using this work, please reference \n"
"Robert J. Bubel \n"
"T. Warthen Douglass
and \n"
"David P. White \n"
"Journal of Computational Chemistry \n"
"submitted for publication, 1999 \n");
init_ref();//this fills up char rlist[155][100] with information in
//parameter file
driver();
//this is the main part of the program
printf("Bye ! \n");
}
16
Compute Ligand Repulsive Energies
Robert J. Bubela, Warthen Douglass, and David P. White*b
Department of Chemistry, University of North Carolina at Wilmington, 601 South
College Road, Wilmington, NC 28403-3297
a
Undergraduate student from the State University of New York at New Paltz
b
Email address: whitedp@uncwil.edu
1
Supplementary Material: ERCODE.CPP
#include
#include
#include
#include
#include
#define TRUE 1
#define FALSE 0
/**********************GLOBAL VARIABLES*******************************/
struct nodetag
{
// each atom or LP in the molecule has one of
int number;
// these structures dedicated to them
float x, y, z;
// coordinates
char type[10];
// forcefield type
float r0, d0;
// constants from parameter file
int side;
// parameter indicating side ligand side = 0
//
fragment side = 1
struct nodetag *next;
};
typedef nodetag *nodeptr;
nodeptr bgf_list;
// global pointer to beginning of data
char rlist[230][100];
// 2d char array of parameter file
int cons[100][25];
// replica of connectivity table in interger form
int m[100][100];
// this is the binary array, may want to make it
// bigger in case of molecules with more than
// 99 atoms
float unitx, unity, unitz; // unit vector of re bond
float re;
// length of re bond
/***********************END GLOBAL VARIABLES*******************************/
void init_ref(void)
// opens the parameter file and stores the constants in the rlist
{
int i=0;
int j=0;
2
char buf[45]="Forcefields
(R0 / D0)\n";
FILE *stream;
stream=fopen("param_r.set","rt");
//open parameter file
if (!stream)
{printf("File not opened! \n");
exit(1);
//program will not work
}
do
{ fgets(rlist[i], 100, stream);
// useless info(top of file)
i++;
}
while(strcmp(buf, rlist[i-1]));
// until we get to first line
do
{ fgets(rlist[j], 100, stream);
// save these data to rlist
//
j++;
}while(rlist[j-1][0] != 'E');
// ends at END
}/*end init_ref*/
/*****************************************************************/
void menu(void)
{
printf( "==========================================================\n"
"Available commands are:\n"
"
calculate for *.bgf(start or continue)\n"
"
quit
\n"
"=========================================================\n");
}/*end menu*/
/**********************************************************************/
void getcomm(int &command)
{
printf("Enter command:
scanf("%d",&command);
");
// get the command
}/*end getcomm
/******************************************************************/
void connections(char conect[], int cons[])
//receives one line of chars from connectivity table translates it to ints
{
int i, j , k, l;
l=0;
k=9;
char cx[6];
//store 1 char # translated into int
i = strlen(conect);
3
do{
j=0;
do{
cx[j]=conect[k];
k++; j++;
}while (jwhich atoms make up ligand side? fragment side?
// returns a 1 on success, returns 0 if numbers given by user are bad
{
int side_array[100];
int lig, frag, i;
nodeptr t;
int number;
number = bgf_list->number;
// number of atoms on list
printf("Which atom number is on"
" the ligand side of the re bond (donor atom):
scanf("%d", &lig);
");
// prompt user for atom #'s
printf("Which atom number is on the fragment side of the re bond:
");
scanf("%d", &frag);
if (lig>numatoms || frag>numatoms)
{
printf("You have entered one of the numbers incorrectly! \n");
return 0;
}
// too high a number
// prevents program from crashing
else
if (!connected(lig-1, frag))
{
// checks to see if atoms are connected
printf("These atoms are not connected! \n");
6
return 0;
}
else
{
for(i=0; iside == 1)
{
coord1[0] = (factor*unitx) + t1->x; //if the atom is on the fragment
coord1[1] = (factor*unity) + t1->y; //side->move it by move it along
coord1[2] = (factor*unitz) + t1->z; //unit vector a distace of factor
}
else
{
coord1[0] = t1->x;
coord1[1] = t1->y;
// then it is on the ligand side so
// we use the same coordinates
coord1[2] = t1->z;
}
if(t2->side == 1)
{
coord2[0] = (factor*unitx) + t2->x;
coord2[1] = (factor*unity) + t2->y;
coord2[2] = (factor*unitz) + t2->z;
}
else
{
coord2[0] = t2->x;
coord2[1] = t2->y;
coord2[2] = t2->z;
}
dis=dist_form(coord1[0], coord1[1], coord1[2],
coord2[0], coord2[1], coord2[2]);
vander_out = (d0 * exp(12.5*(1 - (dis/r0))));
// get distance
// EvdW,R formula
return vander_out;
}/*end vander*/
/*************************************************************************/
void vdw_formula(nodeptr p, int atom1, int atom2, float vdw[])
// receive two atom #'s, lookup info on them calculate 7 different Evdw,R
// for the pair, add it to the total
{
float d0, r0;
nodeptr t1=p, t2=p;
while(t1->number != atom1)
// look up info on each atom
t1 = t1->next;
while(t2->number != atom2)
t2 = t2->next;
d0 = sqrt(t1->d0 * t2->d0);
// D0-geometric mean of both constants
r0 = (t1->r0 + t2->r0)/2;
// R0-arithmetic mean of "
10
"
vdw[0] = vdw[0] + vander(t1, t2, 0, r0, d0);
// EvdW,R with no change
// in re bond length
vdw[1] = vdw[1] + vander(t1, t2, .01, r0, d0);
// EvdW,R with bond lenth
// increased by .01 angstroms
vdw[2] = vdw[2] + vander(t1, t2, -.01, r0, d0); // EvdW,R with bond lenth
// decreased by .01 angstroms
vdw[3] = vdw[3] + vander(t1, t2, .02, r0, d0);
// increased .02
vdw[4] = vdw[4] + vander(t1, t2, -.02, r0, d0); // decreased .02
vdw[5] = vdw[5] + vander(t1, t2, .03, r0, d0);
vdw[6] = vdw[6] + vander(t1, t2, -.03, r0, d0);
}/*end vdw_formula*/
/******************************************************************/
void vanderwahls(nodeptr p, float vdw[])
// examines binary array searching for 1's, sends two atom #'s
// for which seven Evdw,R values are going to be calculated
{
int number, i, j;
number = p->number;
// last atom number
i=0; j=0;
while(inumber;
atom2 = cons[atom1-1][1];
// if it finds one identify the H
// and the C
while(t2->number != atom2)
t2 = t2->next;
//lookup info about C atom
distance = dist_form(t1->x, t1->y, t1->z, t2->x, t2->y, t2->z);
ux = ((t1->x - t2->x)/distance);
uy = ((t1->y - t2->y)/distance); // find unit vector from C to H
uz = ((t1->z - t2->z)/distance);
n_distance = distance * .915;
// decrease distance by 0.915
t1->x = n_distance*ux + t2->x;
t1->y = n_distance*uy + t2->y;
// add new vector to C coordinates
t1->z = n_distance*uz + t2->z;
}
t1 = t1->next;
// go on looking for more
t2 = bgf_list;
}
}/*end bond_shrinkage*/
/*************************************************************************/
void find_er(float vdw[], char filename[], FILE *out)
//calculates Ligand Repulsive Energy
{
float sxx, sxy, slope, er, avg;
avg = (vdw[0] + vdw[1] + vdw[2] + vdw[3] + vdw[4] + vdw[5] + vdw[6])/7;
sxx = .0028;
sxy = (.01*(vdw[1]-avg))+(-.01*(vdw[2]-avg))+(.02*(vdw[3]-avg))+
(-.02*(vdw[4]-avg))+(.03*(vdw[5]-avg))+(-.03*(vdw[6]-avg));
slope = sxy/sxx;
// average slope formula
er = re*slope;
fprintf(out,"%s
", filename);
// sends filename to outfile
fprintf(out,"%f
\n", er);
// sends Er to outfile
}/*end find_er*/
/*********************************************************************/
void free_mem(void)
// traverses through list deleting all nodes to get mem back
{
nodeptr t1,t2;
t1=bgf_list;
t2=bgf_list->next;
while(t2->next != NULL)
{ free (t1);
t1 = t2;
12
t2 = t2->next;
}
}/*end free_mem*/
/********************************************************************/
void adjust_filename(char filename[])
// receives user input file name, checks and adds *.bgf extension
{
int len;
len = strlen(filename);
if (toupper(filename[len-1]) == 'F' &&
//if user entered file extension
toupper(filename[len-2]) == 'G' &&
toupper(filename[len-3]) == 'B' &&
filename[len-4] == '.')
;
// do nothing
else
{
char end[4] = ".bgf";
strncat(filename, end, 4);
// attach .bgf to end if filename
}
}/*end adjust_filename*/
/********************************************************************/
void bfg(FILE *out, int on_off)
// essentially bgf file driver
{
int done=0;
while(!done)
// this while loop allows user to calc
// several files without having to go
// back to menu
{
char filename[50];
char buf[30]="FORMAT CONECT (a6,12i6)\n";// when to stop reading
char input[100];
// holds data temporarily
int numatoms;
int i;
float vdw[7];
// to find Er we need seven different
// values for Evdw
for(i=0; inext = bgf_list;
bgf_list = p;
// bgf_list is the real list we use
}
}while(strcmp(buf, input));
numatoms = bgf_list->number;
find_connections(stream);
//function uses connectivity table to
// create binary array
if(find_side(numatoms))
// this function is used to tell which
// side of the re each atom is on
{
if (on_off == 1)
bond_shrinkage();//allows for C__H bond shrinkage
vanderwahls(bgf_list, vdw);
// simultaneously solves
// for seven values of repulsive
// vanderwahls energy by
// adjusting xyz coordinates of
// individual atoms
find_er(vdw, filename, out);// calculates Er and sends it to ouput
// file along with file name
}
free_mem();
//clears up memory so we can do it again
fclose(stream);
//close the current input file stream
}
}
}/*end bfg()*/
14
void driver()
// gets the ouput filename, options...
{
int done;
//finish flag
int command;
int on_off = -1;
char shrink[1];
char outfile[20];
// file for data output
printf("Please enter a filename for the data:
");
scanf("%s",outfile);
FILE *out;
if ((out = fopen(outfile, "wt"))
== NULL)
{
fprintf(stderr, "Cannot open output file.\n");
exit(1);
}
done = FALSE;
do {
printf("Do you want SHRINK_CH_BONDS on? (y/n) \n");
scanf("%s",&shrink);
if(toupper(shrink[0]) == 'Y')
on_off = 1;
else
if(toupper(shrink[0]) == 'N')
on_off =0;
}while (on_off == -1);
menu();
while (!done)
{
getcomm (command);
if (command == 1)
{ bfg(out, on_off);
}
else
if (command == 0)
done = TRUE;
menu();
}
fclose(out);
}/*end driver*/
/*********************************************************************/
void main()
15
{
printf("ERCODE. \n"
"When using this work, please reference \n"
"Robert J. Bubel \n"
"T. Warthen Douglass
and \n"
"David P. White \n"
"Journal of Computational Chemistry \n"
"submitted for publication, 1999 \n");
init_ref();//this fills up char rlist[155][100] with information in
//parameter file
driver();
//this is the main part of the program
printf("Bye ! \n");
}
16