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energy.c
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/*
** This is an implementation of model interactions between two amino acids
** as well within a single amino acid. This is a rather simple force-field.
**
** Copyright (c) 2004 - 2010 Alexei Podtelezhnikov
** Copyright (c) 2007 - 2013 Nikolas Burkoff, Csilla Varnai and David Wild
*/
#include<stdlib.h>
#include<stdio.h>
#include<string.h>
#include<float.h>
#include<math.h>
#include"canonicalAA.h"
#include"error.h"
#include"params.h"
#include"vector.h"
#include"rotation.h"
#include"aadict.h"
#include"peptide.h"
#include"vdw.h"
#include"energy.h"
#ifndef max
#define max(a,b) (((a) > (b)) ? (a) : (b))
#define min(a,b) (((a) < (b)) ? (a) : (b))
#endif
//#define NaN 0.0 / 0.0
#define Erg(I,J) erg[(I) * chain->NAA + (J)]
//#define Ergt(I,J) ergt[(I - start) * chain->NAA + (J)]
#define Ergt(I,J) ergt[(I) * chain->NAA + (J)]
/* contact map and associated stream */
#define Distb(I,J) biasmap->distb[(I) * biasmap->NAA + (J)]
/***********************************************************/
/**** CONSTANTS ****/
/***********************************************************/
/* CA-CA distance cutoff for Hbond interactions */
const double hbond_cutoff = 49.;
extern struct _ILE ILE;
extern struct _LEU LEU;
extern struct _PRO PRO;
extern struct _VAL VAL;
extern struct _PHE PHE;
extern struct _TRP TRP;
extern struct _TYR TYR;
extern struct _ASP ASP;
extern struct _GLU GLU;
extern struct _ARG ARG;
extern struct _HIS HIS;
extern struct _LYS LYS;
extern struct _SER SER;
extern struct _THR THR;
extern struct _CYS CYS;
extern struct _MET MET;
extern struct _ASN ASN;
extern struct _GLN GLN;
/***********************************************************/
/**** ENERGY MATRIX AND BIASMAP OPERATIONS ****/
/***********************************************************/
/* Initialize the energy matrix of a chain, that is,
fill the already allocated matrix with the amino acid
interaction energies. In the diagonal the intraresidual
energies go, and into (0,0), the global energy */
void energy_matrix_calculate(Chain *chain, Biasmap *biasmap, model_params *mod_params) {
int i, j;
//fprintf(stderr,"first row %g %g", chain->Erg(0, 0), chain->Erg(1, 0));
/* (0,*) and (*,0) */
for (i = 1; i < chain->NAA; i++){
chain->Erg(0, i) = chain->Erg(i, 0) = 0.;
fprintf(stderr,"%g ",chain->Erg(0,i));
}
//fprintf(stderr,"\n");
/* (0,0) */
chain->Erg(0, 0) = 0.0;
if (mod_params->external_potential_type == 5){
double ADenergies[chain->NAA-1];
ADenergyNoClash(ADenergies, 1, chain->NAA-1, chain, NULL, mod_params, 0);
for (i = 1; i < chain->NAA; i++) {
chain->Erg(0, i) = ADenergies[i-1];
fprintf(stderr," aaa %d %g \n",i, chain->Erg(0,i));
//chain->Erg(0, i) = ADenergy(chain->aa + i, mod_params);
chain->Erg(0, 0) += chain->Erg(0, i);
}
//free(ADenergies);
//chain->Erg(0, 0) = global_energy(0,0,chain, NULL,biasmap, mod_params);
}
fprintf(stderr,"SS Energy ");
chain->Erg(chain->NAA - 1, 0) = global_energy(0, 0,chain, NULL,biasmap, mod_params);
if (mod_params->external_potential_type2 == 4) chain->Erg(1, 0) = cyclic_energy((chain->aa) + 1, (chain->aa) + chain->NAA - 1, 0);
/* diagonal */
fprintf(stderr,"diag ");
//fprintf(stderr,"ENERGY1 START\n");
for (i = 1; i < chain->NAA; i++){
chain->Erg(i, i) = energy1((chain->aa) + i, mod_params);
// fprintf(stderr,"%g ",chain->Erg(i,i));
}
//fprintf(stderr,"\n");
//fprintf(stderr,"ENERGY1 END\n");
for (i = 2; i < chain->NAA - 1; i++){
chain->Erg(i, i) += ramabias((chain->aa)+i-1, (chain->aa) + i, (chain->aa) +i+1);
}
/* offdiagonal */
fprintf(stderr,"offdiag ");
for (i = 1; i < chain->NAA; i++){
for (j = 1; j < i; j++){
chain->Erg(i, j) = chain->Erg(j, i) = energy2(biasmap,(chain->aa) + i, (chain->aa) + j, mod_params);
// fprintf(stderr,"%g ",chain->Erg(i,j));
}
//fprintf(stderr,"\n");
}
if (mod_params->external_potential_type2 == 4)
chain->Erg(1, chain->NAA-1) = chain->Erg(chain->NAA-1, 1) = energy2cyclic(biasmap,(chain->aa) + 1, (chain->aa) + chain->NAA-1, mod_params);
}
/* Calculate the total energy by adding up the energy matrix. */
double totenergy(Chain *chain)
{
int i, j;
double toten = 0.0;
//fprintf(stderr, "tote... %g\n", chain->Erg(0,0));
for (i = 0; i < chain->NAA; i++)
for (j = 0; j <= i; j++) {
toten += chain->Erg(i, j);
// fprintf(stderr, "%g ", chain->Erg(i,j));
}
// fprintf(stderr,"\n");
return toten;
}
/* Calculate the local energy by adding up the diagonal of the energy matrix. */
double locenergy(Chain *chain)
{
int i;
double toten = 0.;
for (i = 1; i < chain->NAA; i++)
toten += chain->Erg(i, i);
return toten;
}
/* Return the external energy. */
double extenergy(Chain *chain)
{
return chain->Erg(0, 0) + chain->Erg(1, 0);
}
/* Return the energy between first and last energy. */
double firstlastenergy(Chain *chain)
{
return chain->Erg(1, chain->NAA - 1);
//return chain->Erg(0, 0);
}
/* Print the energy matrix of a chain */
void energy_matrix_print(Chain *chain, Biasmap *biasmap, model_params *mod_params) {
int i, j;
for (i = 0; i < chain->NAA; i++)
fprintf(stderr,"%g ",chain->Erg(0, i));
fprintf(stderr,"\n");
for (i = 0; i < chain->NAA; i++){
for (j = 0; j <= i; j++){
fprintf(stderr,"%g ",chain->Erg(i, j));
}
fprintf(stderr,"\n");
}
}
/* Initialize matrix of Go-type contacts from a contact map file, unless
NULL is given as the contact map filename (return a zero contact map).
CAUTION! The diagonal contains the secondary structure information
of the amino acids. If the amino acid one letter codes are in the
diagonal, the contact map is meaningless. */
void biasmap_initialise(Chain *chain, Biasmap *biasmap, model_params *mod_params)
{
int i, j, k;
double val;
FILE *fin = NULL;
//fprintf(stderr,"Opening contact map file %s\n",mod_params->contact_map_file);
fin = fopen(mod_params->contact_map_file,"r");
int abort = 0;
if (fin == NULL) { // no file opened beforehand
if (mod_params->contact_map_file==NULL) {
fprintf(stderr, "ERROR: Invalid Go-type bias: %s.", mod_params->contact_map_file);
fprintf(stderr, " No contact map file specified.\n");
abort=1;
} else if ((fin = fopen(mod_params->contact_map_file, "r")) == NULL && strcmp(mod_params->contact_map_file,"NULL")!=0) { // nonexisting file and not NULL given
fprintf(stderr, "ERROR: Invalid Go-type bias: %s.", mod_params->contact_map_file);
fprintf(stderr, " Could not open file (missing?).\n");
abort = 1;
}
}
if (abort) {
stop("Contact map file has to be either an existing file or 'NULL' for no bias (see -p _B=... option).");
}
//if the biasmap has been already initialised (e.g. nested sampling), do not reread it
if((biasmap)->distb != NULL) {
if (fin) {
fclose(fin);
//fprintf(stderr,"Closing contact map file %s\n",mod_params->contact_map_file);
}
return; //when nested sampling - this is only to be done once
}
// allocate memory
(biasmap)->distb = (double *) realloc((biasmap)->distb, chain->NAA * chain->NAA * sizeof(double));
(biasmap)->NAA = chain->NAA;
if ((biasmap)->distb == NULL) {
stop("biasmap_initialise: Insufficient memory");
}
// if no biasmap, zero it
if (strcmp(mod_params->contact_map_file,"NULL")==0) {
fprintf(stderr,"WARNING! Contact map file 'NULL' given, so no bias interactions will be calculated.\n");
for (i = 1; i < chain->NAA; i++) {
for (j = 1; j < chain->NAA; j++) {
(biasmap)->distb[i * (biasmap)->NAA + j] = 0.0;
}
}
if (fin) {
fclose(fin);
//fprintf(stderr,"Closing contact map file %s\n",mod_params->contact_map_file);
}
return;
}
// otherwise read in contact map
for (i = 1; i < chain->NAA; i++)
for (j = 1; j < chain->NAA; j++) {
/* the fscanf consumes whitespaces, numbers,
decimal points, signs, but not most letters
so XOUZ is a good alphabet for symbolic maps */
k = fscanf(fin, "%lf", &val); /* read in actual number 0, 1 or -1 */
if (k == 0) { /* symbols used, not numbers */
switch (fgetc(fin) & 0x3) { /* character code % 4 */
case 0: /* X */
val = 1.0;
break;
case 1: /* U */
val = 1.0;
break;
case 2: /* Z */
val = -1.0;
break;
case 3: /* O */
val = 0.0;
break;
}
} else if (k == EOF)
goto out;
/* use 0s in the diagonal, if in the diagonal of the contact map the amino acid letters are printed,
otherwise they take a value according to the 1 letter code of the amino acid */
//if (i==j) val=0.0;
(biasmap)->distb[i * (biasmap)->NAA + j] = val;
}
out:
if (fin) {
fclose(fin);
//fprintf(stderr,"Closing contact map file %s\n",mod_params->contact_map_file);
}
fprintf(stderr, "Go-type bias: %dx%d\n", i - 1, chain->NAA - 1);
/* use 0s in the diagonal, if in the diagonal of the contact map the amino acid letters are printed,
otherwise they take a value according to the 1 letter code of the amino acid */
//fprintf(stderr,"WARNING: If the one-letter amino acid codes are in the diagonal, the bias potential's energy contribution will be meaningless! Check your contact map.\n");
/* special treatment for glycine */
if (mod_params->prt != 0.0)
for (i = 1; i < chain->NAA; i++)
if (chain->aa[i].id == 'G') {
//fprintf(stderr,"Gly %d (%d)",i,biasmap->NAA);
for (j = 1; j < chain->NAA; j++)
if (abs(i - j) > 1) {
//fprintf(stderr," %d",j);
(biasmap)->distb[i * (biasmap)->NAA + j] = (biasmap)->distb[j * (biasmap)->NAA + i] = 0.0;
}
//fprintf(stderr,"\n");
}
/* check if the biasing matrix is symmetric */
/* possible reasons for this are:
the contact map is lopsided
the contact contains spaces, which are skipped by fscanf
the one-letter amino acid codes are used in the diagonal, and there was a problem parsing N or I (on francesca) */
int lopsided = 0;
for (i = 1; i < chain->NAA; i++) {
for (j = 1; j < i; j++) {
if ((biasmap)->distb[i * (biasmap)->NAA + j] != (biasmap)->distb[j * (biasmap)->NAA + i]) {
fprintf(stderr, "Lopsided bias: %d %d valued %g %g\n", i, j, (biasmap)->distb[i * (biasmap)->NAA + j], (biasmap)->distb[j * (biasmap)->NAA + i]);
lopsided = 1;
}
}
}
if (lopsided) stop("Lopsided bias map!");
}
/* finalize matrix of Go-type contacts from contact map file
close input file */
void biasmap_finalise(Biasmap *biasmap){
if(biasmap){
if (biasmap->distb) free(biasmap->distb);
free(biasmap);
}
}
/*make energy grid map smoother*/
double lower_gridenergy(double E) {
//return E;
if (E > 2.718) {
//return log10f(E) + 9;
return log(E) + 1.718;
}
//if (E > 10) {
// //return log10f(E) + 9;
// return log(E-9) + 10;
//}
return E;
}
/*init the size and center and spacing of AD gridbox*/
void gridbox_initialise() {
FILE *gridmap = NULL;
gridmap = fopen("rigidReceptor.C.map", "r");
char line[256];
int i = 0, j = 0;
while (fgets(line, sizeof(line), gridmap)) {
if (i < 3) {
//printf("%s", line);
i++;
continue;
}
char * pch;
pch = strtok(line, " ");
j = 0;
while (pch != NULL)
{
if (i == 3 && j == 1) {
spacing = atof(pch);
}
else if (i == 4 && j == 1) {
NX = atoi(pch) + 1;
}
else if (i == 4 && j == 2) {
NY = atoi(pch) + 1;
}
else if (i == 4 && j == 3) {
NZ = atoi(pch) + 1;
}
else if (i == 5 && j == 1) {
centerX = atof(pch);
}
else if (i == 5 && j == 2) {
centerY = atof(pch);
}
else if (i == 5 && j == 3) {
centerZ = atof(pch);
}
pch = strtok(NULL, " ");
j++;
}
i++;
if (i > 5) break;
}
printf("grid box initialise succuss %i %i %i \n", NX, NY, NZ);
fclose(gridmap);
}
/* initialise the grip maps from the file, elements are 0:C, 1:N, 2:O, 3:H, 4:S, 5:CA, 6:NA*/
void gridmap_initialise(char *filename, int atype) {
FILE *gridmap_file = NULL;
gridmap_file = fopen(filename, "r");
if (gridmap_file == NULL) {
stop("Missing gridmap_file.map file.");
}
char line[256];
int i = 0;
double *curr_gridmap_values = malloc(NX*NY*NZ * sizeof(double));
while (fgets(line, sizeof(line), gridmap_file)) {
if (i < 6) {
i++;
continue;
}
curr_gridmap_values[i - 6] = lower_gridenergy(atof(line));
i++;
}
fclose(gridmap_file);
gridmapvalues[atype] = curr_gridmap_values;
}
/* initialise the tranpoints from the file, if no transpoints found, add the box center */
void transpts_initialise() {
FILE *transpts_file = NULL;
transpts_file = fopen("transpoints", "r");
char line[256];
int i = 0, j = 0;
fgets(line, sizeof(line), transpts_file);
transPtsCount = atoi(line);
if (transPtsCount == 0 || transpts_file == NULL) {
printf("no transpoints found \n");
Xpts = malloc(1 * sizeof(double));
Ypts = malloc(1 * sizeof(double));
Zpts = malloc(1 * sizeof(double));
Xpts[0] = centerX;
Ypts[0] = centerY;
Zpts[0] = centerZ;
transPtsCount = 1;
fclose(transpts_file);
return;
}
Xpts = malloc(transPtsCount * sizeof(double));
Ypts = malloc(transPtsCount * sizeof(double));
Zpts = malloc(transPtsCount * sizeof(double));
while (fgets(line, sizeof(line), transpts_file)) {
char * pch;
pch = strtok(line, " ");
j = 0;
while (pch != NULL)
{
if (j == 0) {
Xpts[i] = atof(pch);
}
else if (j == 1) {
Ypts[i] = atof(pch);
}
else if (j == 2) {
Zpts[i] = atof(pch);
}
pch = strtok(NULL, " ");
j++;
}
i++;
}
printf("transpoints initialise success with %i transpoints \n", transPtsCount);
fclose(transpts_file);
}
/*initialise the ramachandra probability from ramaprob.data file*/
void ramaprob_initialise() {
FILE *ramaprob_file = NULL;
ramaprob_file = fopen("ramaprob.data", "r");
if (ramaprob_file == NULL) {
stop("Missing ramaprob.data file.");
}
char line[256];
int i = 0, j = 0;
ramaprob = malloc(32400 * sizeof(double));
alaprob = malloc(32400 * sizeof(double));
glyprob = malloc(32400 * sizeof(double));
while (fgets(line, sizeof(line), ramaprob_file)) {
char * pch;
pch = strtok(line, " ");
j = 0;
while (pch != NULL)
{
if (j == 1) {
ramaprob[i] = atof(pch);
}
else if (j == 2) {
alaprob[i] = atof(pch);
}
else if (j == 3) {
glyprob[i] = atof(pch);
}
pch = strtok(NULL, " ");
j++;
}
i++;
}
printf("ramaprob initialise success \n");
fclose(ramaprob_file);
}
/***********************************************************/
/**** ENERGY CONTRIBUTIONS ****/
/***********************************************************/
/* Low level routine to calculate the intensity of a linearly decaying function
from a maximum value to zero beyond a cutoff function:
strength_____.
.\
. \
0 . . . . . . .\._________
|<->|-decay width
|
|-cutoff
*/
inline double linear_decay(double distance, /* distance of the 2 atoms */
double contact_cutoff, /* upto which sum of their contact radii */
//double strength, /* the maximum value taken below the cutoff */
double decay_width /* the width of the linear decay */ ) {
if (distance > contact_cutoff + decay_width) return 0.0;
if (distance < contact_cutoff) return 1.0;
return 1.0 - (distance - contact_cutoff) / decay_width;
}
/* Energy contribution of proline phi dihedral angles
E = 30.0 (RT) * (phi - phi_0)^2
phi_0: equilibrium value, -PI/3 */
/* proline B restraints its phi angle with preceding A */
double proline(AA *a, AA *b)
{
double phi;
if (b->id != 'P')
return 0.0;
phi = dihedral_4(a->c, b->n, b->ca, b->c) + M_PI_3;
return 30. * phi * phi; /* RMSD by Ho et al. (2004) */
}
/* Bending energy contribution (internal stress)
E = 150 (RT) * ( angle(n,ca,c) - arccos(-1/3) )^2 */
double stress(AA *a, model_params *mod_params)
{
vector nca, cac; /* N-Ca and Ca-C bonds */
double beta, erg = 0.0;
subtract(nca, a->ca, a->n);
subtract(cac, a->c, a->ca);
/* ground-state angle is 180 - 111 = 69 (EH2001) */
beta = angle(nca, cac) - mod_params->stress_angle; //1.20427718387608740808;
erg += mod_params->stress_k * beta * beta; /* softer than Engh and Huber (2001) */
//if (a->id == 1) erg = erg * 200;
return erg;
}
/*translate rama probability into energy*/
double ramabias(AA *prevaa, AA *a, AA *nextaa)
{
//return 0.0;
double phi = 0.0, psi = 0.0;
double energy = 0.0;
int segphi = 0;
int segpsi = 0;
phi = dihedral_rama(prevaa->c, a->n, a->ca, a->c, 1.46);
psi = dihedral_rama(a->n, a->ca, a->c, nextaa->n, 1.53);
//double anglephi = phi * M_180_PI;
//double anglepsi = psi * M_180_PI;
//int sig = (anglephi>0)? 1:-1;
//int segphi = 2 * int(anglephi/2)+sig;
//sig = (anglepsi>0)? 1:-1;
//int segpsi = 2 * int(anglepsi/2)+sig;
segphi = (int) ((phi + M_PI)/(2*M_PI_180));
segpsi = (int) ((psi + M_PI)/(2*M_PI_180));
int ind = segphi * 180 + segpsi;
switch (a->id) {
case 'A':
energy = alaprob[ind];
break;
case 'G':
energy = glyprob[ind];
break;
default:
energy = ramaprob[ind];
break;
}
//fprintf(stderr,"aaa num %d id %c ind %d energy %g segphi %d segpsi %d phi %g psi %g \n",a->num, a->id, ind, -energy, segphi, segpsi, anglephi, anglepsi);
//energy = energy < -3.91 ? energy + 3.91 : 0.0;
return -energy; // RT * 0.59219 = kcal/mol
}
/* Csilla: energy contribution of Go-type potential
E = kappa * C_ij * r_ij^2 for |i-j|>1
E = eta * cos(gamma_ij) for i-j=1
kappa: force constant (different for alpha-helix and beta-sheet)
C_ij:
r_ij: C_beta distances
eta: force constant (different for alpha-helix(positive) and beta-sheet(negative))
gamma_ij: C_beta,i-C_alpha,i-C_alpha,j-C_beta,j dihedral angle
a, b: i-th and j-th amino acids
*/
/* Go-type biasing potentials that stabilize alpha-helices and beta-sheets */
double bias(Biasmap *biasmap, AA *a, AA *b, model_params *mod_params)
{
int i = a->num, j = b->num;
double bb, dst2;
double r = 0;
double rs = 2.15; /* rs */
double bs = -0.25; /*kappa s */
if (biasmap->distb == NULL) {
stop("Contact matrix is not initialised. Perhaps missing contact map?");
}
/* works for multi-chain proteins */
switch ( max(abs(i - j), 1000 * abs(a->chainid - b->chainid)) ) {
case 0:
return 0.0;
case 1:
if (Distb(i, j) < 0.) {
bb = mod_params->bias_eta_beta; /* beta-strand twist */ /* eta_beta */
} else {
bb = mod_params->bias_eta_alpha; /* alpha-helix twist */ /* eta_alpha */
}
break;
case 3:
if(Distb(i, j) < 0){
/*Cys bond */
bb = bs;
r = rs;
}
else if (Distb(i, i) > 0. && Distb(j, j) > 0.){
bb = mod_params->bias_kappa_alpha_3; /* alpha-helix elasticity */ /* kappa_alpha */
r = mod_params->bias_r_alpha;
}
else{
if (rand() < Distb(i, j)*RAND_MAX) {
bb = mod_params->bias_kappa_beta; /* kappa_beta */
} else {
bb = 0;
}
r = mod_params->bias_r_beta;
}
break;
case 4:
if(Distb(i, j) < 0){
/*Cys bond */
bb = bs;
r = rs;
}
else if (Distb(i, i) > 0. && Distb(j, j) > 0.){
bb = mod_params->bias_kappa_alpha_4; /* alpha-helix elasticity */ /* kappa_alpha */
r = mod_params->bias_r_alpha;
}
else{
if (rand() < Distb(i, j)*RAND_MAX) {
bb = mod_params->bias_kappa_beta; /* kappa_beta */
} else {
bb = 0;
}
r = mod_params->bias_r_beta;
}
break;
default:
if(Distb(i, j) < 0){
/*Cys bond */
bb = bs;
r = rs;
}
else{
bb = mod_params->bias_kappa_beta; /* beta-sheet elasticity */ /* kappa_beta */
r = mod_params->bias_r_beta;
}
}
/* works for multi-chain proteins */
if ( max(abs(i - j), 1000 * abs(a->chainid - b->chainid)) > 1 ) {
vector x, y;
lincomb(x, 1. - mod_params->prt, a->ca, mod_params->prt, a->cb);
lincomb(y, 1. - mod_params->prt, b->ca, mod_params->prt, b->cb);
dst2 = distance(x, y);
dst2 = dst2 - 2*sqrt(dst2)*r + r*r;
} else { /* neighbouring amino acids */
vector x, y, z;
if (i > j) { /* reorder */
AA *temp;
temp = a;
a = b;
b = temp;
}
/* either baab or naac pseudo-dihedral is suitable */
subtract(x, a->ca, a->n);
subtract(y, b->ca, a->ca);
subtract(z, b->c, b->ca);
//set helix eta alpha phase shift
if (Distb(i, j) > 0.) dst2 = -phasindihedral(x,y,z, 0.13917, 0.99);
else dst2 = -cosdihedral(x, y, z);
//dst2 = -phasindihedral(x,y,z, 0.985,0.174); //strand
}
return Distb(i, j) * bb * dst2;
}
/* Energy contribution of hydrogen bonds
E = num_hb * hbs
num_hb: number of H-bonds between the two amino acids
hbs: H-bond strength (default: 2.2 (RT))
*/
double hbond(Biasmap *biasmap, AA *a, AA *b, model_params *mod_params)
{
//return -hbs * (hdonor(a, b) + hdonor(b, a));
double fact = 1.0;
int i = a->num; int j = b->num;
if (abs(i-j) == 4)
fact = 1.0;
else if (abs(i-j) == 3)
fact = 1.0;
else
fact = 1.0;
// Gary hack to put more internal Hbond with cyclic CYS-CYS
if(mod_params->Sbond_strength != 0) fact = 1.0;
// if( Distb( i, i ) * Distb( j, j ) == 0) fact /= 3.0;
//fprintf(stderr,"hbond %d %c",a->num,a->id);
//fprintf(stderr," N: %g",a->n[0]);
//fprintf(stderr," %g",a->n[1]);
//fprintf(stderr," %g",a->n[2]);
//fprintf(stderr," H: %g",a->h[0]);
//fprintf(stderr," %g",a->h[1]);
//fprintf(stderr," %g",a->h[2]);
//fprintf(stderr," , %d %c",b->num,b->id);
//fprintf(stderr," O: %g",b->o[0]);
//fprintf(stderr," %g",b->o[1]);
//fprintf(stderr," %g",b->o[2]);
//fprintf(stderr," C: %g",b->c[0]);
//fprintf(stderr," %g",b->c[1]);
//fprintf(stderr," %g\n",b->c[2]);
if (a->id == 'P') {
if (b->id == 'P') // no a->H, no b->H
return 0.0;
else // no a->H
return fact*-mod_params->hbs * hstrength(b->n, b->h, a->o, a->c, mod_params);
}
else {
if (b->id == 'P') // no b->H
return fact*-mod_params->hbs * hstrength(a->n, a->h, b->o, b->c, mod_params);
else
return fact*-mod_params->hbs * (hstrength(a->n, a->h, b->o, b->c, mod_params) + hstrength(b->n, b->h, a->o, a->c, mod_params));
}
}
/* The scaling factor of hydrophobic interaction between a and b
R. Srinivasan, ProtSFG 22, 81--99 (1995)
R. Srinivasan et al., PNAS 96(25), 14258--14263 (1999)
2 if both amino acids are hydrophobic,
1 if one amino acid is hydrophobic, and the other one is amphipathic,
0 otherwise */
inline int hydrophobic_interaction_intensity(AA *a, AA *b, model_params *mod_params) {
/* works for multi-chain proteins */
if ( ( abs(a->num - b->num) < mod_params->hydrophobic_min_separation ) && ( a->chainid == b->chainid ) ) return 0;
/* hydrophobic -- hydrophobic */
if ( (a->etc & HYDROPHOBIC) && (b->etc & HYDROPHOBIC) ) return 2;
if ( (a->etc & HYDROPHOBIC) && (b->etc & AMPHIPATHIC) ) return 1;
if ( (a->etc & AMPHIPATHIC) && (b->etc & HYDROPHOBIC) ) return 1;
/* hydrophobic -- polar */
/* this accounts for the fewer polar -- polar interactions */
if (a->etc & HYDROPHOBIC) return -2;
if (b->etc & HYDROPHOBIC) return -2;
return 0;
}
/* Low level routine to calculate 2 atoms hydrophobic energy contribution
E = -k_h * f(d(a,b)) * intensity, if a and b are in contact
k_h is the hydrophobicity parameter (in RT)
d(a,b) is the distance between the respective atoms of a and b
f(d(a,b)) = d(a,b)^-1 */
/* inline double hydrophobic_low_recip(double distance,
double contact_cutoff,
model_params *mod_params) {
if (distance > mod_params->hydrophobic_max_cutoff) return 0.0;
if (distance < mod_params->hydrophobic_min_cutoff) distance = mod_params->hydrophobic_min_cutoff;
//fprintf(stderr," calc %g\n",(1.0/distance) - mod_params->hydrophobic_max_Eshift);
return (1.0/distance) - mod_params->hydrophobic_max_Eshift;
} */
/* Low level routine to calculate 2 atoms hydrophobic energy contribution using a spline potential
E = -k_h * f(d(a,b)) * intensity, if a and b are in contact
k_h is the hydrophobicity parameter (in RT)
d(a,b) is the distance between the respective atoms of a and b
f(d(a,b)) is a beta spline going from 1 to 0 between min_cutoff and max_cutoff */
/* inline double hydrophobic_low_spline(double distance,
double contact_cutoff,
model_params *mod_params) {
if (distance > mod_params->hydrophobic_r + mod_params->hydrophobic_half_delta) return 0.0;
if (distance < mod_params->hydrophobic_r - mod_params->hydrophobic_half_delta) distance = mod_params->hydrophobic_r - mod_params->hydrophobic_half_delta;
return (distance - mod_params->hydrophobic_r - mod_params->hydrophobic_half_delta)
* (distance - mod_params->hydrophobic_r - mod_params->hydrophobic_half_delta)
* (mod_params->hydrophobic_r - 2.0 * mod_params->hydrophobic_half_delta - distance)
/ (4.0 * mod_params->hydrophobic_half_delta * mod_params->hydrophobic_half_delta * mod_params->hydrophobic_half_delta) ;
} */
/* Low level routine to calculate 2 atoms hydrophobic energy contribution */
/* R. Srinivasan et al., PNAS 96(25), 14258--14263 (1999) */
inline double hydrophobic_low(double distance /* distance of the 2 atoms */,
double contact_cutoff /* sum of their contact radii */,
model_params *mod_params) {
if (distance > contact_cutoff + mod_params->hydrophobic_cutoff_range) return 0.0;
if (distance < contact_cutoff) return 1.0;
return (distance - contact_cutoff) / mod_params->hydrophobic_cutoff_range;
}
/* Energy contribution of hydrophobic interaction between a and b
E = -k_h * f(d(a,b)) * intensity, if a and b are in contact
k_h is the hydrophobicity parameter (in RT)
d(a,b) is the distance between the respective atoms of a and b
intensity depends on the hydrophobicity of the amino acids (see hydrophobic_intensity) */
/* Default: f(d(a,b)) = 1 */
double hydrophobic(Biasmap *biasmap, AA *a, AA *b, model_params *mod_params) {
/* return 0 if 0 */
if (mod_params->kauzmann_param == 0.0) return 0.0;
int intensity;
if ((intensity = hydrophobic_interaction_intensity(a,b,mod_params)) == 0) return 0.0;
/* calc hydrophobic contact radii */
double r_cb_a=0, r_g_a=0, r_g2_a=0;
double r_cb_b=0, r_g_b=0, r_g2_b=0;
if (a->etc & CB_) r_cb_a = hydrophobic_contact_radius(a->id, CB_, mod_params->sidechain_properties);
if (a->etc & G__) r_g_a = hydrophobic_contact_radius(a->id, G__, mod_params->sidechain_properties);
if (a->etc & G2_) r_g2_a = hydrophobic_contact_radius(a->id, G2_, mod_params->sidechain_properties);
if (b->etc & CB_) r_cb_b = hydrophobic_contact_radius(b->id, CB_, mod_params->sidechain_properties);
if (b->etc & G__) r_g_b = hydrophobic_contact_radius(b->id, G__, mod_params->sidechain_properties);
if (b->etc & G2_) r_g2_b = hydrophobic_contact_radius(b->id, G2_, mod_params->sidechain_properties);
double energy = 0;
if (mod_params->use_gamma_atoms != NO_GAMMA) {
/* all side chain contributions */
/* peptide should have been fixed by now, so no missing coordinates */
if ( (a->etc & CB_) && (b->etc & CB_) && r_cb_a > 0. && r_cb_b > 0. ) { /* CB -- CB */
energy += hydrophobic_low(sqrt(distance(a->cb, b->cb)), r_cb_a + r_cb_b, mod_params);
}
if ( (a->etc & CB_) && (b->etc & G__) && r_cb_a > 0. && r_g_b > 0. ) { /* CB -- G1 */
energy += hydrophobic_low(sqrt(distance(a->cb, b->g )), r_cb_a + r_g_b , mod_params);
}
if ( (a->etc & CB_) && (b->etc & G2_) && r_cb_a > 0. && r_g2_b > 0. ) { /* CB -- G2 */
energy += hydrophobic_low(sqrt(distance(a->cb, b->g2)), r_cb_a + r_g2_b, mod_params);
}
if ( (a->etc & G__) && (b->etc & CB_) && r_g_a > 0. && r_cb_b > 0. ) { /* G1 -- CB */
energy += hydrophobic_low(sqrt(distance(a->g , b->cb)), r_g_a + r_cb_b, mod_params);
}
if ( (a->etc & G__) && (b->etc & G__) && r_g_a > 0. && r_g_b > 0. ) { /* G1 -- G1 */
energy += hydrophobic_low(sqrt(distance(a->g , b->g )), r_g_a + r_g_b , mod_params);
}
if ( (a->etc & G__) && (b->etc & G2_) && r_g_a > 0. && r_g2_b > 0. ) { /* G1 -- G2 */
energy += hydrophobic_low(sqrt(distance(a->g , b->g2)), r_g_a + r_g2_b, mod_params);
}
if ( (a->etc & G2_) && (b->etc & CB_) && r_g2_a > 0. && r_cb_b > 0. ) { /* G2 -- CB */
energy += hydrophobic_low(sqrt(distance(a->g2, b->cb)), r_g2_a + r_cb_b, mod_params);
}
if ( (a->etc & G2_) && (b->etc & G__) && r_g2_a > 0. && r_g_b > 0. ) { /* G2 -- G1 */
energy += hydrophobic_low(sqrt(distance(a->g2, b->g )), r_g2_a + r_g_b , mod_params);
}
if ( (a->etc & G2_) && (b->etc & G2_) && r_g2_a > 0. && r_g2_b > 0. ) { /* G2 -- G2 */
energy += hydrophobic_low(sqrt(distance(a->g2, b->g2)), r_g2_a + r_g2_b, mod_params);
}
//fprintf(stderr,"%d %d %f ",a->num,b->num, energy);
return -mod_params->kauzmann_param * energy * (double) intensity;
} else {
/* OLD VERSION */
if (contact(a,b, mod_params)) {
return (-mod_params->kauzmann_param * ((double) intensity));
} else {
return 0.0;
}
}
}
double sidechain_hbond(Biasmap *biasmap, AA *a, AA *b, model_params *mod_params)
{
double intensity;
double erg = 0.0;
double hbond_distance;
double cos_goc_angle;
/* only from i, i+X */
/* works for multi-chain proteins */
if ( ( abs(a->num - b->num) < mod_params->sidechain_hbond_min_separation ) && ( a->chainid == b->chainid ) ) return 0.0;
/* side chain donor - backbone acceptor */
if (a->etc &G__ && b->etc &C__ && hbond_donor(a->id,G__, mod_params->sidechain_properties)) {
// check G--C distance
hbond_distance = sqrt(distance(a->g,b->c));
if (hbond_distance < sidechain_hbond_donor_radius(a->id,mod_params->sidechain_properties) + BACKBONE_ACCEPTOR_RADIUS + mod_params->sidechain_hbond_decay_width) {
//fprintf(stderr,"%c%d %c%d G-C distance %g ,",a->id,a->num,b->id,b->num,hbond_distance);
// check C--O--G angle
cos_goc_angle = cosangle(a->g,b->o,b->c);
//fprintf(stderr,"cos_goc_angle %g\n",cos_goc_angle);
if (cos_goc_angle < mod_params->sidechain_hbond_angle_cutoff) {
if ( (intensity = linear_decay(hbond_distance, sidechain_hbond_donor_radius(a->id,mod_params->sidechain_properties) + BACKBONE_ACCEPTOR_RADIUS, mod_params->sidechain_hbond_decay_width )) > 0.0 ) {
// fprintf(stderr,"found hbond %c %d G__ >> %c %d C__ %g\n",a->id,a->num,b->id,b->num,distance(a->g,b->c));
erg += -mod_params->sidechain_hbond_strength_s2b * intensity;
}
}
}
}
if (b->etc &G__ && a->etc &C__ && hbond_donor(b->id,G__, mod_params->sidechain_properties)) {
// check G--C distance
hbond_distance = sqrt(distance(b->g,a->c));
if (hbond_distance < sidechain_hbond_donor_radius(b->id,mod_params->sidechain_properties) + BACKBONE_ACCEPTOR_RADIUS + mod_params->sidechain_hbond_decay_width) {
//fprintf(stderr,"%c%d %c%d G-C distance %g ,",a->id,a->num,b->id,b->num,hbond_distance);
// check C--O--G angle
cos_goc_angle = cosangle(b->g,a->o,a->c);
//fprintf(stderr,"cos_goc_angle %g\n",cos_goc_angle);
if (cos_goc_angle < mod_params->sidechain_hbond_angle_cutoff) {
if ( (intensity = linear_decay(hbond_distance, sidechain_hbond_donor_radius(b->id,mod_params->sidechain_properties) + BACKBONE_ACCEPTOR_RADIUS, mod_params->sidechain_hbond_decay_width )) > 0.0 ) {
// fprintf(stderr,"found hbond %c %d G__ >> %c %d C__ %g\n",a->id,a->num,b->id,b->num,distance(a->g,b->c));
erg += -mod_params->sidechain_hbond_strength_s2b * intensity;
}
}
}
}
/* side chain acceptor - backbone donor */
if (a->etc &G__ && b->etc &N__ && b->etc &H__ && hbond_acceptor(a->id,G__, mod_params->sidechain_properties)) {
// check G--N distance
hbond_distance = sqrt(distance(a->g,b->n));
//fprintf(stderr,"check %c %d %c %d G-N distance %g (%g) %g \n",a->id,a->num,b->id,b->num,hbond_distance,sidechain_hbond_acceptor_radius(a->id,mod_params->sidechain_properties) + BACKBONE_DONOR_RADIUS + sidechain_hbond_decay_width,sqrt(distance(a->g,b->h)));
if (hbond_distance < sidechain_hbond_acceptor_radius(a->id,mod_params->sidechain_properties) + BACKBONE_DONOR_RADIUS + mod_params->sidechain_hbond_decay_width) {
//fprintf(stderr,"found %c %d %c %d G-N distance %g (%g) %g \n",a->id,a->num,b->id,b->num,hbond_distance,sidechain_hbond_acceptor_radius(a->id,mod_params->sidechain_properties) + BACKBONE_DONOR_RADIUS + sidechain_hbond_decay_width,sqrt(distance(a->g,b->h)));
// check C--H--N angle
cos_goc_angle = cosangle(a->g,b->h,b->n);
//fprintf(stderr,"cos_ghn_angle %g\n",cos_goc_angle);
if (cos_goc_angle < mod_params->sidechain_hbond_angle_cutoff) {
if ( (intensity = linear_decay(hbond_distance, sidechain_hbond_acceptor_radius(a->id,mod_params->sidechain_properties) + BACKBONE_DONOR_RADIUS, mod_params->sidechain_hbond_decay_width )) > 0.0 ) {
// fprintf(stderr,"found hbond %c %d G__ >> %c %d N__ %g\n",a->id,a->num,b->id,b->num,distance(a->g,b->n));
erg += -mod_params->sidechain_hbond_strength_b2s * intensity;
}
}
}
}
if (b->etc &G__ && a->etc &N__ && a->etc &H__ && hbond_acceptor(b->id,G__, mod_params->sidechain_properties)) {
// check G--N distance
hbond_distance = sqrt(distance(b->g,a->n));
//fprintf(stderr,"check %c %d %c %d G-N distance %g (%g) %g\n",b->id,b->num,a->id,a->num,hbond_distance,sidechain_hbond_acceptor_radius(b->id,mod_params->sidechain_properties) + BACKBONE_DONOR_RADIUS + sidechain_hbond_decay_width,sqrt(distance(b->g,a->h)));
if (hbond_distance < sidechain_hbond_acceptor_radius(b->id,mod_params->sidechain_properties) + BACKBONE_DONOR_RADIUS + mod_params->sidechain_hbond_decay_width) {
//fprintf(stderr,"found %c %d %c %d G-N distance %g (%g) %g\n",b->id,b->num,a->id,a->num,hbond_distance,sidechain_hbond_acceptor_radius(b->id,mod_params->sidechain_properties) + BACKBONE_DONOR_RADIUS + sidechain_hbond_decay_width,sqrt(distance(b->g,a->h)));
// check C--H--N angle