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vdw.c
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vdw.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"error.h"
#include"params.h"
#include"vector.h"
#include"rotation.h"
#include"aadict.h"
#include"peptide.h"
#include"vdw.h"
/***********************************************************/
/**** CONSTANTS ****/
/***********************************************************/
//const int skip_14_vdw=0;
/***********************************************************/
/**** ENERGY CONTRIBUTIONS ****/
/***********************************************************/
/* hard cutoff potential:
Energy contribution of vdW repulsion
E = 10.4 (RT) * 0.95 p^2 / dist^2, if dist2 > 0.95 p^2
E = 0.0 (RT) otherwise
r1: position of atom1
r2: position of atom2
Rmin: minimum separation between the two atoms, typically sum of covalent radii */
inline double vdw_hard_cutoff(vector r1, vector r2, double Rmin, double depth, double vdw_rel_cutoff, double energy_shift, double clash_energy_at_hard_cutoff) {
double p = Rmin;
double dis2, sqp;
dis2 = distance(r1,r2);
sqp = 0.95 * p * p; // arbitrary adjustment
//return (dis2 < sqp) ? 10.4 * sqp / dis2 : 0.0;
//clash_energy_at_hard_cutoff = 6.5;
return (dis2 < sqp) ? clash_energy_at_hard_cutoff * sqp / dis2 : 0.0;
}
/* Lennard-Jones potential:
Energy contribution of vdW interaction
E = max{ clash_energy_at_hard_cutoff ; 4 * depth * ( (Rmin/|r1-r2|)^12 - (Rmin/|r1-r2|)^6 ) }, if dist2 < (0.4 * Rmin^2)
E = depth * ( (Rmin/|r1-r2|)^12 - (Rmin/|r1-r2|)^6 ), if dist2 > (Rmin * vdw_rel_cutoff)^2
E = 0.0 (RT) otherwise
r1: position of atom1
r2: position of atom2
Rmin: the minimum energy separation of the two atoms
depth: the energy at the minimum energy separation, that is the depth of the potential well
vdw_rel_cutoff: the cutoff of the potential is (Rmin * vdw_rel_cutoff)
energy_shift: the energy at the cutoff, to be subtracted to have continuous a function */
inline double vdw_lj(vector r1, vector r2, double Rmin, double depth, double vdw_rel_cutoff, double energy_shift, double clash_energy_at_hard_cutoff) {
double dis2, p6;// p12;
int clashing = 0;
dis2 = distance(r1,r2);
double Rmin2 = Rmin * Rmin;
// apply cutoff
//fprintf(stderr,"vdw_rel_cutoff: %g",vdw_rel_cutoff);
//fprintf(stderr,"Rmin2: %g",Rmin2);
//fprintf(stderr,"vector atom1: %g",r1[0]);
//fprintf(stderr," %g",r1[1]);
//fprintf(stderr," %g",r1[2]);
//fprintf(stderr,"vector atom2: %g",r2[0]);
//fprintf(stderr," %g",r2[1]);
//fprintf(stderr," %g",r2[2]);
//fprintf(stderr," dis2: %g\n",dis2);
if(dis2 > (vdw_rel_cutoff * vdw_rel_cutoff * Rmin2)) {
// fprintf(stderr,"return 0 dis2 %g\n",dis2);
return 0.0;
// } else {
// fprintf(stderr,"return non0 dis2 %g\n",dis2);
}
// set a max energy at an inner cutoff
if(dis2 < 0.4 * Rmin2) {
// return clash value
clashing = 1; //return clash_energy_at_hard_cutoff;
dis2 = 0.4 * Rmin2;
}
// calculate energy, with energy shifted to 0 at the cutoff
p6 = Rmin2 / dis2;
p6 *= (p6 * p6);
double ans = depth * p6 * (p6 - 2.0) - energy_shift;
if (clashing) {
if (ans > clash_energy_at_hard_cutoff)
return ans;
else
return clash_energy_at_hard_cutoff;
} else {
return ans;
}
}
/* vdW energy contribution within the atoms of 1 amino acid */
/* Only calculate contributions between atoms separated by >=4 bonds */
/* Revised by Csilla, 2011-10-28 */
double clash(AA *a, model_params *mod_params)
{
double erg = 0.0;
double rg;
double depth = 0;
double erg_tmp = 0.0;
//Assign function pointer to the vdW model
double (*vdw_fn) (vector r1, vector r2, double Rmin, double depth, double vdw_rel_cutoff, double energy_shift, double clash_energy_at_hard_cutoff) = NULL;
if (mod_params->vdw_potential == HARD_CUTOFF_VDW_POTENTIAL) {
vdw_fn = vdw_hard_cutoff;
} else if (mod_params->vdw_potential == LJ_VDW_POTENTIAL) {
vdw_fn = vdw_lj;
} else {
stop("Clash cannot be calculated without a valid vdW potential.");
}
// /* CB_ -- O__*/
// if (a->etc & CB_ && a->etc & O__ && mod_params->ro > 0.0 && mod_params->rcb > 0.0) {
// erg_tmp = vdw_fn(a->cb, a->o, mod_params->rcb + mod_params->ro,mod_params->vdw_depth_cb_o, mod_params->rel_vdw_cutoff, mod_params->vdw_Eshift_cb_o, mod_params->vdw_clash_energy_at_hard_cutoff);
// if (erg_tmp > 5.) fprintf(stderr,"Clash within residue %d CB_-O__.\n",a->num);
// erg += erg_tmp;
// }
if (mod_params->use_gamma_atoms != NO_GAMMA) {
if (a->etc & G__) {
if ((rg = sidechain_vdw_radius(a->id,1,mod_params->sidechain_properties)) < 0.0) {
fprintf(stderr,"Negative vdw radius for amino acid %c\n",a->id);
//exit(EXIT_FAILURE);
} else {
/* G__ -- O__ */
if (a->etc & O__ && mod_params->ro > 0.0) {
depth = sidechain_vdw_depth_sqrt(a->id,1,mod_params->sidechain_properties)*mod_params->vdw_depth_o_sqrt;
erg_tmp = vdw_fn(a->g, a->o, rg + mod_params->ro,depth, mod_params->rel_vdw_cutoff, mod_params->vdw_shift*depth, mod_params->vdw_clash_energy_at_hard_cutoff);
// if (erg_tmp > 5.) fprintf(stderr,"Clash within residue %d G__-O__.\n",a->num);
erg += erg_tmp;
}
// /* G__ -- C__ */
// if (a->etc & C__ && mod_params->rc > 0.0) {
// depth = sidechain_vdw_depth_sqrt(a->id,1,mod_params->sidechain_properties)*mod_params->vdw_depth_c_sqrt;
// erg_tmp = vdw_fn(a->g, a->c, rg + mod_params->rc,depth, mod_params->rel_vdw_cutoff, mod_params->vdw_shift*depth, mod_params->vdw_clash_energy_at_hard_cutoff);
// if (erg_tmp > 5.) fprintf(stderr,"Clash within residue %d G__-C__.\n",a->num);
// erg += erg_tmp;
// }
}
}
if (a->etc & G2_) { /* I, V, T */
if ((rg = sidechain_vdw_radius(a->id,2,mod_params->sidechain_properties)) < 0.0) {
fprintf(stderr,"Negative vdw radius for amino acid %c\n",a->id);
//exit(EXIT_FAILURE);
} else {
/* G2_ -- O__ */
if (a->etc & O__ && mod_params->ro > 0.0) {
depth = sidechain_vdw_depth_sqrt(a->id,2,mod_params->sidechain_properties)*mod_params->vdw_depth_o_sqrt;
erg_tmp = vdw_fn(a->g2, a->o, rg + mod_params->ro,depth, mod_params->rel_vdw_cutoff, mod_params->vdw_shift*depth, mod_params->vdw_clash_energy_at_hard_cutoff);
// if (erg_tmp > 5.) fprintf(stderr,"Clash within residue %d G2_-O__.\n",a->num);
erg += erg_tmp;
}
// /* G2_ -- C__ */
// if (a->etc & C__ && mod_params->rc > 0.0) {
// depth = sidechain_vdw_depth_sqrt(a->id,2,mod_params->sidechain_properties)*mod_params->vdw_depth_c_sqrt;
// erg_tmp = vdw_fn(a->g2, a->c, rg + mod_params->rc,depth, mod_params->rel_vdw_cutoff, mod_params->vdw_shift*depth, mod_params->vdw_clash_energy_at_hard_cutoff);
// if (erg_tmp > 5.) fprintf(stderr,"Clash within residue %d G2_-C__.\n",a->num);
// erg += erg_tmp;
// }
}
}
}
return erg;
}
double HHvDW(AA *a, AA *b)
{
//return 0.0;
double HHradii = 2.6;
double HHstrength = 0.1;
if (a->id == 'P' || b->id == 'P') return 0.;
double distHH = distance(a->h, b->h);
if (distHH >= 9) return 0.;
double p6 = (HHradii*HHradii/distHH) * (HHradii*HHradii/distHH) *(HHradii*HHradii/distHH);
double erg=0.;
if (a->id != 'P' && b->id != 'P' && distHH<9) {
erg = 1/sqrt(distHH) + HHstrength * (p6*p6-2*p6) - 0.2665;
//fprintf(stderr, "close exN HH %g\n", erg);
}
return erg;
}
#ifdef LJ_NEIGHBOUR_HARD
/* Energy contribution of all vdW interaction between 2 neighbouring residues */
/* order of neighbors matter, b follows a in the chain */
/* Only calculate contributions between atoms separated by >=4 bonds */
/* Only hard cutoff interactions */
double exclude_neighbor(AA *a, AA *b, model_params *mod_params)
{
double erg = 0.0;
double rg_a, rg2_a, rg_b, rg2_b;
rg_a = rg2_a = rg_b = rg2_b = 0.0;
//Assign function pointer to the vdW model
double (*vdw_fn) (vector r1, vector r2, double Rmin, double depth, double vdw_rel_cutoff, double energy_shift, double clash_energy_at_hard_cutoff) = NULL;
if (mod_params->vdw_potential == HARD_CUTOFF_VDW_POTENTIAL) {
vdw_fn = vdw_hard_cutoff;
} else if (mod_params->vdw_potential == LJ_VDW_POTENTIAL) {
vdw_fn = vdw_lj;
} else {
stop("Clash cannot be calculated without a valid vdW potential.");
}
erg += HHvDW(a, b);
/* collect G__ and G2_ vdW parameters */
if (mod_params->use_gamma_atoms != NO_GAMMA) {
if (a->etc & G__) {
if ((rg_a = sidechain_vdw_radius(a->id,1,mod_params->sidechain_properties)) > 0.0);
}
if (a->etc & G2_) {
if ((rg2_a = sidechain_vdw_radius(a->id,2,mod_params->sidechain_properties)) > 0.0);
}
if (b->etc & G__) {
if ((rg_b = sidechain_vdw_radius(b->id,1,mod_params->sidechain_properties)) > 0.0);
}
if (b->etc & G2_) {
if ((rg2_b = sidechain_vdw_radius(b->id,2,mod_params->sidechain_properties)) > 0.0);
}
}
/* these should not be counted in, since 1-4 interactions */
// if (mod_params->rn > 0.0 && mod_params->rn > 0.0 && skip_14_vdw==0) erg += vdw_fn(a->n, b->n, mod_params->rn + mod_params->rn,mod_params->vdw_depth_n_n, mod_params->rel_vdw_cutoff, mod_params->vdw_Eshift_n_n, mod_params->vdw_clash_energy_at_hard_cutoff);
// if (mod_params->rc > 0.0 && mod_params->rc > 0.0 && skip_14_vdw==0) erg += vdw_fn(a->c, b->c, mod_params->rc + mod_params->rc,mod_params->vdw_depth_c_c, mod_params->rel_vdw_cutoff, mod_params->vdw_Eshift_c_c, mod_params->vdw_clash_energy_at_hard_cutoff);
// if (mod_params->rc > 0.0 && mod_params->rcb > 0.0 && skip_14_vdw==0) erg += vdw_fn(a->c, b->cb, mod_params->rc + mod_params->rcb,mod_params->vdw_depth_cb_c, mod_params->rel_vdw_cutoff, mod_params->vdw_Eshift_cb_c, mod_params->vdw_clash_energy_at_hard_cutoff);
// if (mod_params->rcb > 0.0 && mod_params->rn > 0.0 && skip_14_vdw==0) erg += vdw_fn(a->cb, b->n, mod_params->rcb + mod_params->rn,mod_params->vdw_depth_cb_n, mod_params->rel_vdw_cutoff, mod_params->vdw_Eshift_cb_n, mod_params->vdw_clash_energy_at_hard_cutoff);
/* All distances will be counted in, since the LJ vdW potential is long ranged */
//
/* (a) C__ -- (b) O__ */
if (mod_params->rc > 0.0 && mod_params->ro > 0.0) erg += vdw_fn(a->c, b->o, mod_params->rc + mod_params->ro,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
//
/* (a) O__ -- (b) CB_ */
if (mod_params->ro > 0.0 && mod_params->rcb > 0.0 && b->id != 'G') erg += vdw_fn(a->o, b->cb, mod_params->ro + mod_params->rcb,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
/* (a) O__ -- (b) C__ */
if (mod_params->ro > 0.0 && mod_params->rc > 0.0) erg += vdw_fn(a->o, b->c, mod_params->ro + mod_params->rc,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
/* (a) O__ -- (b) O__ */
if (mod_params->ro > 0.0 && mod_params->ro > 0.0) erg += vdw_fn(a->o, b->o, mod_params->ro + mod_params->ro,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
/* (a) CA_ -- (b) CB_ */
if (mod_params->rca > 0.0 && mod_params->rcb > 0.0 && b->id != 'G') erg += vdw_fn(a->ca, b->cb, mod_params->rca + mod_params->rcb,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
/* (a) CA_ -- (b) C__ */
if (mod_params->rca > 0.0 && mod_params->rc > 0.0) erg += vdw_fn(a->ca, b->c, mod_params->rca + mod_params->rc,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
/* (a) CA_ -- (b) O__ */
if (mod_params->rca > 0.0 && mod_params->ro > 0.0) erg += vdw_fn(a->ca, b->o, mod_params->rca + mod_params->ro,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
/* (a) CB_ -- (b) CA_ */
if (mod_params->rcb > 0.0 && mod_params->rca > 0.0 && a->id != 'G') erg += vdw_fn(a->cb, b->ca, mod_params->rcb + mod_params->rca,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
/* (a) CB_ -- (b) CB_ */
if (mod_params->rcb > 0.0 && mod_params->rcb > 0.0 && a->id != 'G' && b->id != 'G') erg += vdw_fn(a->cb, b->cb, mod_params->rcb + mod_params->rcb,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
/* (a) CB_ -- (b) C__ */
if (mod_params->rcb > 0.0 && mod_params->rc > 0.0 && a->id != 'G') erg += vdw_fn(a->cb, b->c, mod_params->rcb + mod_params->rc,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
/* (a) CB_ -- (b) O__ */
if (mod_params->rcb > 0.0 && mod_params->ro > 0.0 && a->id != 'G') erg += vdw_fn(a->cb, b->o, mod_params->rcb + mod_params->ro,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
/* (a) N__ -- (b) CA_ */
if (mod_params->rn > 0.0 && mod_params->rca > 0.0) erg += vdw_fn(a->n, b->ca, mod_params->rn + mod_params->rca,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
/* (a) N__ -- (b) CB_ */
if (mod_params->rn > 0.0 && mod_params->rcb > 0.0 && b->id != 'G') erg += vdw_fn(a->n, b->cb, mod_params->rn + mod_params->rcb,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
/* (a) N__ -- (b) C__ */
if (mod_params->rn > 0.0 && mod_params->rc > 0.0) erg += vdw_fn(a->n, b->c, mod_params->rn + mod_params->rc,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
/* (a) N__ -- (b) O__ */
if (mod_params->rn > 0.0 && mod_params->ro > 0.0) erg += vdw_fn(a->n, b->o, mod_params->rn + mod_params->ro,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
/* vdW contribution of gamma atoms */
if (mod_params->use_gamma_atoms != NO_GAMMA) {
if (rg_b > 0.0) {
/* (a) C__ -- (b) G__ */
if (mod_params->rc > 0.0) {
erg += vdw_fn(a->c, b->g, mod_params->rc + rg_b,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
}
/* (a) O__ -- (b) G__ */
if (mod_params->ro > 0.0) {
erg += vdw_fn(a->o, b->g, mod_params->ro + rg_b,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
}
/* (a) CA_ -- (b) G__ */
if (mod_params->rca > 0.0) {
erg += vdw_fn(a->ca, b->g, mod_params->rca + rg_b,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
}
/* (a) CB_ -- (b) G__ */
if (rg_b != 0.0 && mod_params->rcb > 0.0 && a->id != 'G') {
erg += vdw_fn(a->cb, b->g, mod_params->rcb + rg_b,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
}
/* (a) N__ -- (b) G__ */
if (rg_b != 0.0 && mod_params->rn > 0.0) {
erg += vdw_fn(a->n, b->g, mod_params->rn + rg_b,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
}
}
if (rg2_b > 0.0) {
/* (a) C__ -- (b) G__ */
if (rg2_b != 0.0 && mod_params->rc > 0.0) {
erg += vdw_fn(a->c, b->g2, mod_params->rc + rg2_b,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
}
/* (a) O__ -- (b) G__ */
if (rg2_b != 0.0 && mod_params->ro > 0.0) {
erg += vdw_fn(a->o, b->g2, mod_params->ro + rg2_b,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
}
/* (a) CA_ -- (b) G__ */
if (mod_params->rca > 0.0) {
erg += vdw_fn(a->ca, b->g2, mod_params->rca + rg2_b,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
}
/* (a) CB_ -- (b) G__ */
if (rg2_b != 0.0 && mod_params->rcb > 0.0 && a->id != 'G') {
erg += vdw_fn(a->cb, b->g2, mod_params->rcb + rg2_b,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
}
/* (a) N__ -- (b) G__ */
if (rg2_b != 0.0 && mod_params->rn > 0.0) {
erg += vdw_fn(a->n, b->g2, mod_params->rn + rg2_b,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
}
}
if (rg_a != 0.0) {
/* (a) G__ -- (b) CA_ */
if (mod_params->rca > 0.0) {
erg += vdw_fn(a->g, b->ca, rg_a + mod_params->rca,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
}
/* (a) G__ -- (b) C__ */
if (mod_params->rc > 0.0) {
erg += vdw_fn(a->g, b->c, rg_a + mod_params->rc,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
}
/* (a) G__ -- (b) O__ */
if (mod_params->ro > 0.0) {
erg += vdw_fn(a->g, b->o, rg_a + mod_params->ro,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
}
/* (a) G__ -- (b) CB_ */
if (mod_params->rcb > 0.0 && b->id != 'G') {
erg += vdw_fn(a->g, b->cb, rg_a + mod_params->rcb,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
}
/* (a) G__ -- (b) N__ */
if (mod_params->rn > 0.0) {
erg += vdw_fn(a->g, b->n, rg_a + mod_params->rn,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
}
/* (a) G__ -- (b) G__ */
if (rg_b != 0.0) {
erg += vdw_fn(a->g, b->g, rg_a + rg_b,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
}
if (rg2_b != 0.0) {
erg += vdw_fn(a->g, b->g2, rg_a + rg2_b,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
}
}
if (rg2_a != 0.0) {
/* (a) G__ -- (b) CA_ */
if (mod_params->rca > 0.0) {
erg += vdw_fn(a->g2, b->ca, rg2_a + mod_params->rca,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
}
/* (a) G__ -- (b) C__ */
if (mod_params->rc > 0.0) {
erg += vdw_fn(a->g2, b->c, rg2_a + mod_params->rc,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
}
/* (a) G__ -- (b) O__ */
if (mod_params->ro > 0.0) {
erg += vdw_fn(a->g2, b->o, rg2_a + mod_params->ro,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
}
/* (a) G__ -- (b) CB_ */
if (mod_params->rcb > 0.0 && b->id != 'G') {
erg += vdw_fn(a->g2, b->cb, rg2_a + mod_params->rcb,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
}
/* (a) G__ -- (b) N__ */
if (mod_params->rn > 0.0) {
erg += vdw_fn(a->g2, b->n, rg2_a + mod_params->rn,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
}
/* (a) G__ -- (b) G__ */
if (rg_b != 0.0) {
erg += vdw_fn(a->g2, b->g, rg2_a + rg_b,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
}
if (rg2_b != 0.0) {
erg += vdw_fn(a->g2, b->g2, rg2_a + rg2_b,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
}
}
}
return erg;
}
#else
/* Energy contribution of all vdW interaction between 2 neighbouring residues */
/* order of neighbors matter, b follows a in the chain */
/* Only calculate contributions between atoms separated by >=4 bonds */
double exclude_neighbor(AA *a, AA *b, model_params *mod_params)
{
double erg = 0.0;
double rg_a, rg2_a, rg_b, rg2_b;
rg_a = rg2_a = rg_b = rg2_b = 0.0;
double eps_g_a_sqrt, eps_g2_a_sqrt, eps_g_b_sqrt, eps_g2_b_sqrt;
eps_g_a_sqrt = eps_g2_a_sqrt = eps_g_b_sqrt = eps_g2_b_sqrt = 0.0;
double depth = 0;
//Assign function pointer to the vdW model
double (*vdw_fn) (vector r1, vector r2, double Rmin, double depth, double vdw_rel_cutoff, double energy_shift, double clash_energy_at_hard_cutoff) = NULL;
if (mod_params->vdw_potential == HARD_CUTOFF_VDW_POTENTIAL) {
vdw_fn = vdw_hard_cutoff;
} else if (mod_params->vdw_potential == LJ_VDW_POTENTIAL) {
vdw_fn = vdw_lj;
} else {
stop("Clash cannot be calculated without a valid vdW potential.");
}
erg += HHvDW(a, b);
/* collect G__ and G2_ vdW parameters */
if (mod_params->use_gamma_atoms != NO_GAMMA) {
if (a->etc & G__) {
if ((rg_a = sidechain_vdw_radius(a->id,1,mod_params->sidechain_properties)) > 0.0)
eps_g_a_sqrt = sidechain_vdw_depth_sqrt(a->id,1,mod_params->sidechain_properties);
}
if (a->etc & G2_) {
if ((rg2_a = sidechain_vdw_radius(a->id,2,mod_params->sidechain_properties)) > 0.0)
eps_g2_a_sqrt = sidechain_vdw_depth_sqrt(a->id,2,mod_params->sidechain_properties);
}
if (b->etc & G__) {
if ((rg_b = sidechain_vdw_radius(b->id,1,mod_params->sidechain_properties)) > 0.0)
eps_g_b_sqrt = sidechain_vdw_depth_sqrt(b->id,1,mod_params->sidechain_properties);
}
if (b->etc & G2_) {
if ((rg2_b = sidechain_vdw_radius(b->id,2,mod_params->sidechain_properties)) > 0.0)
eps_g2_b_sqrt = sidechain_vdw_depth_sqrt(b->id,2,mod_params->sidechain_properties);
}
}
/* these should not be counted in, since 1-4 interactions */
// if (mod_params->rn > 0.0 && mod_params->rn > 0.0 && skip_14_vdw==0) erg += vdw_fn(a->n, b->n, mod_params->rn + mod_params->rn,mod_params->vdw_depth_n_n, mod_params->rel_vdw_cutoff, mod_params->vdw_Eshift_n_n, mod_params->vdw_clash_energy_at_hard_cutoff);
// if (mod_params->rc > 0.0 && mod_params->rc > 0.0 && skip_14_vdw==0) erg += vdw_fn(a->c, b->c, mod_params->rc + mod_params->rc,mod_params->vdw_depth_c_c, mod_params->rel_vdw_cutoff, mod_params->vdw_Eshift_c_c, mod_params->vdw_clash_energy_at_hard_cutoff);
// if (mod_params->rc > 0.0 && mod_params->rcb > 0.0 && skip_14_vdw==0) erg += vdw_fn(a->c, b->cb, mod_params->rc + mod_params->rcb,mod_params->vdw_depth_cb_c, mod_params->rel_vdw_cutoff, mod_params->vdw_Eshift_cb_c, mod_params->vdw_clash_energy_at_hard_cutoff);
// if (mod_params->rcb > 0.0 && mod_params->rn > 0.0 && skip_14_vdw==0) erg += vdw_fn(a->cb, b->n, mod_params->rcb + mod_params->rn,mod_params->vdw_depth_cb_n, mod_params->rel_vdw_cutoff, mod_params->vdw_Eshift_cb_n, mod_params->vdw_clash_energy_at_hard_cutoff);
/* All distances will be counted in, since the LJ vdW potential is long ranged */
//
/* (a) C__ -- (b) O__ */
if (mod_params->rc > 0.0 && mod_params->ro > 0.0) erg += vdw_fn(a->c, b->o, mod_params->rc + mod_params->ro,mod_params->vdw_depth_c_o, mod_params->rel_vdw_cutoff, mod_params->vdw_Eshift_c_o, mod_params->vdw_clash_energy_at_hard_cutoff);
//
/* (a) O__ -- (b) CB_ */
if (mod_params->ro > 0.0 && mod_params->rcb > 0.0 && b->id != 'G') erg += vdw_fn(a->o, b->cb, mod_params->ro + mod_params->rcb,mod_params->vdw_depth_cb_o, mod_params->rel_vdw_cutoff, mod_params->vdw_Eshift_cb_o, mod_params->vdw_clash_energy_at_hard_cutoff);
/* (a) O__ -- (b) C__ */
if (mod_params->ro > 0.0 && mod_params->rc > 0.0) erg += vdw_fn(a->o, b->c, mod_params->ro + mod_params->rc,mod_params->vdw_depth_c_o, mod_params->rel_vdw_cutoff, mod_params->vdw_Eshift_c_o, mod_params->vdw_clash_energy_at_hard_cutoff);
/* (a) O__ -- (b) O__ */
if (mod_params->ro > 0.0 && mod_params->ro > 0.0) erg += vdw_fn(a->o, b->o, mod_params->ro + mod_params->ro,mod_params->vdw_depth_o_o, mod_params->rel_vdw_cutoff, mod_params->vdw_Eshift_o_o, mod_params->vdw_clash_energy_at_hard_cutoff);
/* (a) CA_ -- (b) CB_ */
if (mod_params->rca > 0.0 && mod_params->rcb > 0.0 && b->id != 'G') erg += vdw_fn(a->ca, b->cb, mod_params->rca + mod_params->rcb,mod_params->vdw_depth_ca_cb, mod_params->rel_vdw_cutoff, mod_params->vdw_Eshift_ca_cb, mod_params->vdw_clash_energy_at_hard_cutoff);
/* (a) CA_ -- (b) C__ */
if (mod_params->rca > 0.0 && mod_params->rc > 0.0) erg += vdw_fn(a->ca, b->c, mod_params->rca + mod_params->rc,mod_params->vdw_depth_ca_c, mod_params->rel_vdw_cutoff, mod_params->vdw_Eshift_ca_c, mod_params->vdw_clash_energy_at_hard_cutoff);
/* (a) CA_ -- (b) O__ */
if (mod_params->rca > 0.0 && mod_params->ro > 0.0) erg += vdw_fn(a->ca, b->o, mod_params->rca + mod_params->ro,mod_params->vdw_depth_ca_o, mod_params->rel_vdw_cutoff, mod_params->vdw_Eshift_ca_o, mod_params->vdw_clash_energy_at_hard_cutoff);
/* (a) CB_ -- (b) CA_ */
if (mod_params->rcb > 0.0 && mod_params->rca > 0.0 && a->id != 'G') erg += vdw_fn(a->cb, b->ca, mod_params->rcb + mod_params->rca,mod_params->vdw_depth_ca_cb, mod_params->rel_vdw_cutoff, mod_params->vdw_Eshift_ca_cb, mod_params->vdw_clash_energy_at_hard_cutoff);
/* (a) CB_ -- (b) CB_ */
if (mod_params->rcb > 0.0 && mod_params->rcb > 0.0 && a->id != 'G' && b->id != 'G') erg += vdw_fn(a->cb, b->cb, mod_params->rcb + mod_params->rcb,mod_params->vdw_depth_cb_cb, mod_params->rel_vdw_cutoff, mod_params->vdw_Eshift_cb_cb, mod_params->vdw_clash_energy_at_hard_cutoff);
/* (a) CB_ -- (b) C__ */
if (mod_params->rcb > 0.0 && mod_params->rc > 0.0 && a->id != 'G') erg += vdw_fn(a->cb, b->c, mod_params->rcb + mod_params->rc,mod_params->vdw_depth_cb_c, mod_params->rel_vdw_cutoff, mod_params->vdw_Eshift_cb_c, mod_params->vdw_clash_energy_at_hard_cutoff);
/* (a) CB_ -- (b) O__ */
if (mod_params->rcb > 0.0 && mod_params->ro > 0.0 && a->id != 'G') erg += vdw_fn(a->cb, b->o, mod_params->rcb + mod_params->ro,mod_params->vdw_depth_cb_o, mod_params->rel_vdw_cutoff, mod_params->vdw_Eshift_cb_o, mod_params->vdw_clash_energy_at_hard_cutoff);
/* (a) N__ -- (b) CA_ */
if (mod_params->rn > 0.0 && mod_params->rca > 0.0) erg += vdw_fn(a->n, b->ca, mod_params->rn + mod_params->rca,mod_params->vdw_depth_ca_n, mod_params->rel_vdw_cutoff, mod_params->vdw_Eshift_ca_n, mod_params->vdw_clash_energy_at_hard_cutoff);
/* (a) N__ -- (b) CB_ */
if (mod_params->rn > 0.0 && mod_params->rcb > 0.0 && b->id != 'G') erg += vdw_fn(a->n, b->cb, mod_params->rn + mod_params->rcb,mod_params->vdw_depth_cb_n, mod_params->rel_vdw_cutoff, mod_params->vdw_Eshift_cb_n, mod_params->vdw_clash_energy_at_hard_cutoff);
/* (a) N__ -- (b) C__ */
if (mod_params->rn > 0.0 && mod_params->rc > 0.0) erg += vdw_fn(a->n, b->c, mod_params->rn + mod_params->rc,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
/* (a) N__ -- (b) O__ */
if (mod_params->rn > 0.0 && mod_params->ro > 0.0) erg += vdw_fn(a->n, b->o, mod_params->rn + mod_params->ro,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
/* vdW contribution of gamma atoms */
if (mod_params->use_gamma_atoms != NO_GAMMA) {
if (rg_b > 0.0) {
/* (a) C__ -- (b) G__ */
if (mod_params->rc > 0.0) {
depth = eps_g_b_sqrt*mod_params->vdw_depth_c_sqrt;
erg += vdw_fn(a->c, b->g, mod_params->rc + rg_b,depth, mod_params->rel_vdw_cutoff, mod_params->vdw_shift*depth, mod_params->vdw_clash_energy_at_hard_cutoff);
}
/* (a) O__ -- (b) G__ */
if (mod_params->ro > 0.0) {
depth = eps_g_b_sqrt*mod_params->vdw_depth_o_sqrt;
erg += vdw_fn(a->o, b->g, mod_params->ro + rg_b,depth, mod_params->rel_vdw_cutoff, mod_params->vdw_shift*depth, mod_params->vdw_clash_energy_at_hard_cutoff);
}
/* (a) CA_ -- (b) G__ */
if (mod_params->rca > 0.0) {
depth = eps_g_b_sqrt*mod_params->vdw_depth_ca_sqrt;
erg += vdw_fn(a->ca, b->g, mod_params->rca + rg_b,depth, mod_params->rel_vdw_cutoff, mod_params->vdw_shift*depth, mod_params->vdw_clash_energy_at_hard_cutoff);
}
/* (a) CB_ -- (b) G__ */
if (rg_b != 0.0 && mod_params->rcb > 0.0 && a->id != 'G') {
depth = eps_g_b_sqrt*mod_params->vdw_depth_cb_sqrt;
erg += vdw_fn(a->cb, b->g, mod_params->rcb + rg_b,depth, mod_params->rel_vdw_cutoff, mod_params->vdw_shift*depth, mod_params->vdw_clash_energy_at_hard_cutoff);
}
/* (a) N__ -- (b) G__ */
if (rg_b != 0.0 && mod_params->rn > 0.0) {
depth = eps_g_b_sqrt*mod_params->vdw_depth_n_sqrt;
erg += vdw_fn(a->n, b->g, mod_params->rn + rg_b,depth, mod_params->rel_vdw_cutoff, mod_params->vdw_shift*depth, mod_params->vdw_clash_energy_at_hard_cutoff);
}
}
if (rg2_b > 0.0) {
/* (a) C__ -- (b) G__ */
if (rg2_b != 0.0 && mod_params->rc > 0.0) {
depth = eps_g2_b_sqrt*mod_params->vdw_depth_c_sqrt;
erg += vdw_fn(a->c, b->g2, mod_params->rc + rg2_b,depth, mod_params->rel_vdw_cutoff, mod_params->vdw_shift*depth, mod_params->vdw_clash_energy_at_hard_cutoff);
}
/* (a) O__ -- (b) G__ */
if (rg2_b != 0.0 && mod_params->ro > 0.0) {
depth = eps_g2_b_sqrt*mod_params->vdw_depth_o_sqrt;
erg += vdw_fn(a->o, b->g2, mod_params->ro + rg2_b,depth, mod_params->rel_vdw_cutoff, mod_params->vdw_shift*depth, mod_params->vdw_clash_energy_at_hard_cutoff);
}
/* (a) CA_ -- (b) G__ */
if (mod_params->rca > 0.0) {
depth = eps_g2_b_sqrt*mod_params->vdw_depth_ca_sqrt;
erg += vdw_fn(a->ca, b->g2, mod_params->rca + rg2_b,depth, mod_params->rel_vdw_cutoff, mod_params->vdw_shift*depth, mod_params->vdw_clash_energy_at_hard_cutoff);
}
/* (a) CB_ -- (b) G__ */
if (rg2_b != 0.0 && mod_params->rcb > 0.0 && a->id != 'G') {
depth = eps_g2_b_sqrt*mod_params->vdw_depth_cb_sqrt;
erg += vdw_fn(a->cb, b->g2, mod_params->rcb + rg2_b,depth, mod_params->rel_vdw_cutoff, mod_params->vdw_shift*depth, mod_params->vdw_clash_energy_at_hard_cutoff);
}
/* (a) N__ -- (b) G__ */
if (rg2_b != 0.0 && mod_params->rn > 0.0) {
depth = eps_g2_b_sqrt*mod_params->vdw_depth_n_sqrt;
erg += vdw_fn(a->n, b->g2, mod_params->rn + rg2_b,depth, mod_params->rel_vdw_cutoff, mod_params->vdw_shift*depth, mod_params->vdw_clash_energy_at_hard_cutoff);
}
}
if (rg_a != 0.0) {
/* (a) G__ -- (b) CA_ */
if (mod_params->rca > 0.0) {
depth = eps_g_a_sqrt*mod_params->vdw_depth_ca_sqrt;
erg += vdw_fn(a->g, b->ca, rg_a + mod_params->rca,depth, mod_params->rel_vdw_cutoff, mod_params->vdw_shift*depth, mod_params->vdw_clash_energy_at_hard_cutoff);
}
/* (a) G__ -- (b) C__ */
if (mod_params->rc > 0.0) {
depth = eps_g_a_sqrt*mod_params->vdw_depth_c_sqrt;
erg += vdw_fn(a->g, b->c, rg_a + mod_params->rc,depth, mod_params->rel_vdw_cutoff, mod_params->vdw_shift*depth, mod_params->vdw_clash_energy_at_hard_cutoff);
}
/* (a) G__ -- (b) O__ */
if (mod_params->ro > 0.0) {
depth = eps_g_a_sqrt*mod_params->vdw_depth_o_sqrt;
erg += vdw_fn(a->g, b->o, rg_a + mod_params->ro,depth, mod_params->rel_vdw_cutoff, mod_params->vdw_shift*depth, mod_params->vdw_clash_energy_at_hard_cutoff);
}
/* (a) G__ -- (b) CB_ */
if (mod_params->rcb > 0.0 && b->id != 'G') {
depth = eps_g_a_sqrt*mod_params->vdw_depth_cb_sqrt;
erg += vdw_fn(a->g, b->cb, rg_a + mod_params->rcb,depth, mod_params->rel_vdw_cutoff, mod_params->vdw_shift*depth, mod_params->vdw_clash_energy_at_hard_cutoff);
}
/* (a) G__ -- (b) N__ */
if (mod_params->rn > 0.0) {
depth = eps_g_a_sqrt*mod_params->vdw_depth_n_sqrt;
erg += vdw_fn(a->g, b->n, rg_a + mod_params->rn,depth, mod_params->rel_vdw_cutoff, mod_params->vdw_shift*depth, mod_params->vdw_clash_energy_at_hard_cutoff);
}
/* (a) G__ -- (b) G__ */
if (rg_b != 0.0) {
depth = eps_g_a_sqrt*eps_g_b_sqrt;
erg += vdw_fn(a->g, b->g, rg_a + rg_b,depth, mod_params->rel_vdw_cutoff, mod_params->vdw_shift*depth, mod_params->vdw_clash_energy_at_hard_cutoff);
}
if (rg2_b != 0.0) {
depth = eps_g_a_sqrt*eps_g2_b_sqrt;
erg += vdw_fn(a->g, b->g2, rg_a + rg2_b,depth, mod_params->rel_vdw_cutoff, mod_params->vdw_shift*depth, mod_params->vdw_clash_energy_at_hard_cutoff);
}
}
if (rg2_a != 0.0) {
/* (a) G__ -- (b) CA_ */
if (mod_params->rca > 0.0) {
depth = eps_g2_a_sqrt*mod_params->vdw_depth_ca_sqrt;
erg += vdw_fn(a->g2, b->ca, rg2_a + mod_params->rca,depth, mod_params->rel_vdw_cutoff, mod_params->vdw_shift*depth, mod_params->vdw_clash_energy_at_hard_cutoff);
}
/* (a) G__ -- (b) C__ */
if (mod_params->rc > 0.0) {
depth = eps_g2_a_sqrt*mod_params->vdw_depth_c_sqrt;
erg += vdw_fn(a->g2, b->c, rg2_a + mod_params->rc,depth, mod_params->rel_vdw_cutoff, mod_params->vdw_shift*depth, mod_params->vdw_clash_energy_at_hard_cutoff);
}
/* (a) G__ -- (b) O__ */
if (mod_params->ro > 0.0) {
depth = eps_g2_a_sqrt*mod_params->vdw_depth_o_sqrt;
erg += vdw_fn(a->g2, b->o, rg2_a + mod_params->ro,depth, mod_params->rel_vdw_cutoff, mod_params->vdw_shift*depth, mod_params->vdw_clash_energy_at_hard_cutoff);
}
/* (a) G__ -- (b) CB_ */
if (mod_params->rcb > 0.0 && b->id != 'G') {
depth = eps_g2_a_sqrt*mod_params->vdw_depth_cb_sqrt;
erg += vdw_fn(a->g2, b->cb, rg2_a + mod_params->rcb,depth, mod_params->rel_vdw_cutoff, mod_params->vdw_shift*depth, mod_params->vdw_clash_energy_at_hard_cutoff);
}
/* (a) G__ -- (b) N__ */
if (mod_params->rn > 0.0) {
depth = eps_g2_a_sqrt*mod_params->vdw_depth_n_sqrt;
erg += vdw_fn(a->g2, b->n, rg2_a + mod_params->rn,depth, mod_params->rel_vdw_cutoff, mod_params->vdw_shift*depth, mod_params->vdw_clash_energy_at_hard_cutoff);
}
/* (a) G__ -- (b) G__ */
if (rg_b != 0.0) {
depth = eps_g2_a_sqrt*eps_g_b_sqrt;
erg += vdw_fn(a->g2, b->g, rg2_a + rg_b,depth, mod_params->rel_vdw_cutoff, mod_params->vdw_shift*depth, mod_params->vdw_clash_energy_at_hard_cutoff);
}
if (rg2_b != 0.0) {
depth = eps_g2_a_sqrt*eps_g2_b_sqrt;
erg += vdw_fn(a->g2, b->g2, rg2_a + rg2_b,depth, mod_params->rel_vdw_cutoff, mod_params->vdw_shift*depth, mod_params->vdw_clash_energy_at_hard_cutoff);
}
}
}
return erg;
}
#endif
#ifdef LJ_HBONDED_HARD
/* Energy contribution of all vdW interaction between 2 residues
a, b: amino acids
d2: squared distance of their alpha carbons
hbond_proxmity: if they or their neighbours connect these guys by H-bonds */
double exclude_hard(AA *a, AA *b, double d2, model_params *mod_params, int hbond_proximity)
{
double erg = 0.0;
double rg_a, rg2_a, rg_b, rg2_b;
rg_a = rg2_a = rg_b = rg2_b = 0.0;
double vdw_erg = 0;
const double backbone_constants[3] = { mod_params->vdw_backbone_cutoff, mod_params->vdw_backbone_cutoff, mod_params->vdw_backbone_cutoff };
//Assign function pointer to the vdW model
double (*vdw_fn) (vector r1, vector r2, double Rmin, double depth, double vdw_rel_cutoff, double energy_shift, double clash_energy_at_hard_cutoff) = NULL;
if (mod_params->vdw_potential == HARD_CUTOFF_VDW_POTENTIAL) {
vdw_fn = vdw_hard_cutoff;
} else if (mod_params->vdw_potential == LJ_VDW_POTENTIAL) {
vdw_fn = vdw_lj;
} else {
stop("Clash cannot be calculated without a valid vdW potential.");
}
erg += HHvDW(a, b);
/* Calculates the correct index for maxvdw_gamma_gamma
* note the other d2 > should be changed for maximum efficiency*/
int index = (a->id - '@') * 26 + (b->id - '@') -1;
if (mod_params->use_gamma_atoms != NO_GAMMA) {
/* 1. check maximum interaction distance: this is the G-G case */
if (d2 > (mod_params->vdw_gamma_gamma_cutoff)[index]) /* cg - cg */
return erg;
if (a->etc & G__) {
if ((rg_a = sidechain_vdw_radius(a->id,1,mod_params->sidechain_properties)) > 0.0);
}
if (a->etc & G2_) {
if ((rg2_a = sidechain_vdw_radius(a->id,2,mod_params->sidechain_properties)) > 0.0);
}
if (b->etc & G__) {
if ((rg_b = sidechain_vdw_radius(b->id,1,mod_params->sidechain_properties)) > 0.0);
}
if (b->etc & G2_) {
if ((rg2_b = sidechain_vdw_radius(b->id,2,mod_params->sidechain_properties)) > 0.0);
}
if (rg_a != 0.0) {
/* Skip CYS--CYS gamma-gamma interactions (should really only miss when they are S-S bonded!, but let's try this for now) */
if (rg_b != 0.0 && (a->id != 'C' || b->id != 'C')) { //&& (mod_params->Sbond_strength == 0 || a->id != 'C' || b->id != 'C' ))
vdw_erg = vdw_fn(a->g, b->g, rg_a + rg_b,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
erg += vdw_erg;
}
if (rg2_b != 0.0) {
vdw_erg = vdw_fn(a->g, b->g2, rg_a + rg2_b,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
erg += vdw_erg;
}
}
if (rg2_a != 0.0) {
if (rg_b != 0.0) {
vdw_erg = vdw_fn(a->g2, b->g, rg2_a + rg_b,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
erg += vdw_erg;
}
if (rg2_b != 0.0) {
vdw_erg = vdw_fn(a->g2, b->g2, rg2_a + rg2_b,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
erg += vdw_erg;
}
}
/* 2. check slightly closer: this is the G-nonG case */
if (d2 > (mod_params->vdw_gamma_nongamma_cutoff)[index]) /* cg - o */
return erg;
if (rg_a != 0.0 && mod_params->ro > 0.0) {
vdw_erg = vdw_fn(a->g, b->o, rg_a + mod_params->ro,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
erg += vdw_erg;
}
if (rg2_a != 0.0 && mod_params->ro > 0.0) {
vdw_erg = vdw_fn(a->g2, b->o, rg2_a + mod_params->ro,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
erg += vdw_erg;
}
if (rg_b != 0.0 && mod_params->ro > 0.0) {
vdw_erg = vdw_fn(b->g, a->o, rg_b + mod_params->ro,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
erg += vdw_erg;
}
if (rg2_b != 0.0 && mod_params->ro > 0.0) {
vdw_erg = vdw_fn(b->g2, a->o, rg2_b + mod_params->ro,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
erg += vdw_erg;
}
//if (d2 > 94.79) /* cg - cb */
// return erg;
/* Skip CYS--CYS beta-gamma interactions (should really only miss when they are S-S bonded!, but let's try this for now) */
if (rg_a != 0.0 && mod_params->rcb > 0.0 && (a->id != 'C' || b->id != 'C') && b->id != 'G') {
vdw_erg = vdw_fn(a->g, b->cb, rg_a + mod_params->rcb,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
erg += vdw_erg;
}
if (rg2_a != 0.0 && mod_params->rcb > 0.0 && b->id != 'G') {
vdw_erg = vdw_fn(a->g2, b->cb, rg2_a + mod_params->rcb,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
erg += vdw_erg;
}
if (rg_b != 0.0 && mod_params->rcb > 0.0 && (a->id != 'C' || b->id != 'C') && a->id != 'G') {
vdw_erg = vdw_fn(b->g, a->cb, rg_b + mod_params->rcb,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
erg += vdw_erg;
}
if (rg2_b != 0.0 && mod_params->rcb > 0.0 && a->id != 'G') {
vdw_erg = vdw_fn(b->g2, a->cb, rg2_b + mod_params->rcb,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
erg += vdw_erg;
}
//if (d2 > 91.80) /* cg -- c */
// return erg;
if (rg_a != 0.0 && mod_params->rc > 0.0) {
vdw_erg = vdw_fn(a->g, b->c, rg_a + mod_params->rc,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
erg += vdw_erg;
}
if (rg2_a != 0.0 && mod_params->rc > 0.0) {
vdw_erg = vdw_fn(a->g2, b->c, rg2_a + mod_params->rc,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
erg += vdw_erg;
}
if (rg_b != 0.0 && mod_params->rc > 0.0) {
vdw_erg = vdw_fn(b->g, a->c, rg_b + mod_params->rc,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
erg += vdw_erg;
}
if (rg2_b != 0.0 && mod_params->rc > 0.0) {
vdw_erg = vdw_fn(b->g2, a->c, rg2_b + mod_params->rc,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
erg += vdw_erg;
}
//if (d2 > 88.06) /* cg -- n */
// return erg;
if (rg_a != 0.0 && mod_params->rn > 0.0) {
vdw_erg = vdw_fn(a->g, b->n, rg_a + mod_params->rn,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
erg += vdw_erg;
}
if (rg2_a != 0.0 && mod_params->rn > 0.0) {
vdw_erg = vdw_fn(a->g2, b->n, rg2_a + mod_params->rn,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
erg += vdw_erg;
}
if (rg_b != 0.0 && mod_params->rn > 0.0) {
vdw_erg = vdw_fn(b->g, a->n, rg_b + mod_params->rn,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
erg += vdw_erg;
}
if (rg2_b != 0.0 && mod_params->rn > 0.0) {
vdw_erg = vdw_fn(b->g2, a->n, rg2_b + mod_params->rn,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
erg += vdw_erg;
}
//if (d2 > 67.33) /* cg - ca */
// return erg;
if (rg_a != 0.0 && mod_params->rca > 0.0) {
vdw_erg = vdw_fn(a->g, b->ca, rg_a + mod_params->rca,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
erg += vdw_erg;
}
if (rg2_a != 0.0 && mod_params->rca > 0.0) {
vdw_erg = vdw_fn(a->g2, b->ca, rg2_a + mod_params->rca,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
erg += vdw_erg;
}
if (rg_b != 0.0 && mod_params->rca > 0.0) {
vdw_erg = vdw_fn(b->g, a->ca, rg_b + mod_params->rca,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
erg += vdw_erg;
}
if (rg2_b != 0.0 && mod_params->rca > 0.0) {
vdw_erg = vdw_fn(b->g2, a->ca, rg2_b + mod_params->rca,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
erg += vdw_erg;
}
}
/* 3. check even closer: this is the nonG-nonG case (CB-extended backbone) */
if (d2 > backbone_constants[0]) /* o-o, farthest */
/* 3.A O-else */
return erg;
/* o - o, o - n, o - c */
if (mod_params->ro > 0.0 && mod_params->ro > 0.0) {
vdw_erg = vdw_fn(a->o, b->o, mod_params->ro + mod_params->ro,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
erg += vdw_erg;
}
// only hard cutoff for N-O, the H-bond interactions will pull them in
if (mod_params->ro > 0.0 && mod_params->rn > 0.0) {
vdw_erg = vdw_fn(a->o, b->n, mod_params->ro + mod_params->rn,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
erg += vdw_erg;
}
if (mod_params->rn > 0.0 && mod_params->ro > 0.0) {
vdw_erg = vdw_fn(a->n, b->o, mod_params->rn + mod_params->ro,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
erg += vdw_erg;
}
if (mod_params->ro > 0.0 && mod_params->rc > 0.0) {
vdw_erg = vdw_fn(a->o, b->c, mod_params->ro + mod_params->rc,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
erg += vdw_erg;
}
if (mod_params->rc > 0.0 && mod_params->ro > 0.0) {
vdw_erg = vdw_fn(a->c, b->o, mod_params->rc + mod_params->ro,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
erg += vdw_erg;
}
if ( d2 > backbone_constants[1])
return erg;
/* 3.B any-any, within N-N, mostly N with others */
/* n - n, n - c, c - c, o - cb, o - ca, n - cb, c - cb */
if (mod_params->rn > 0.0 && mod_params->rn > 0.0) {
vdw_erg = vdw_fn(a->n, b->n, mod_params->rn + mod_params->rn,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
erg += vdw_erg;
}
if (mod_params->rn > 0.0 && mod_params->rc > 0.0) {
vdw_erg = vdw_fn(a->n, b->c, mod_params->rn + mod_params->rc,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
erg += vdw_erg;
}
if (mod_params->rc > 0.0 && mod_params->rn > 0.0) {
vdw_erg = vdw_fn(a->c, b->n, mod_params->rc + mod_params->rn,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
erg += vdw_erg;
}
if (mod_params->rc > 0.0 && mod_params->rc > 0.0) {
vdw_erg = vdw_fn(a->c, b->c, mod_params->rc + mod_params->rc,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
erg += vdw_erg;
}
if (mod_params->ro > 0.0 && mod_params->rcb > 0.0 && b->id != 'G') {
vdw_erg = vdw_fn(a->o, b->cb, mod_params->ro + mod_params->rcb,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
erg += vdw_erg;
}
if (mod_params->rcb > 0.0 && mod_params->ro > 0.0 && a->id != 'G') {
vdw_erg = vdw_fn(a->cb, b->o, mod_params->rcb + mod_params->ro,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
erg += vdw_erg;
}
if (mod_params->ro > 0.0 && mod_params->rca > 0.0) {
vdw_erg = vdw_fn(a->o, b->ca, mod_params->ro + mod_params->rca,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
erg += vdw_erg;
}
if (mod_params->rca > 0.0 && mod_params->ro > 0.0) {
vdw_erg = vdw_fn(a->ca, b->o, mod_params->rca + mod_params->ro,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
erg += vdw_erg;
}
if (mod_params->rn > 0.0 && mod_params->rcb > 0.0 && b->id != 'G') {
vdw_erg = vdw_fn(a->n, b->cb, mod_params->rn + mod_params->rcb,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
erg += vdw_erg;
}
if (mod_params->rcb > 0.0 && mod_params->rn > 0.0 && a->id != 'G') {
vdw_erg = vdw_fn(a->cb, b->n, mod_params->rcb + mod_params->rn,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
erg += vdw_erg;
}
if (mod_params->rc > 0.0 && mod_params->rcb > 0.0 && b->id != 'G') {
vdw_erg = vdw_fn(a->c, b->cb, mod_params->rc + mod_params->rcb,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
erg += vdw_erg;
}
if (mod_params->rcb > 0.0 && mod_params->rc > 0.0 && a->id != 'G') {
vdw_erg = vdw_fn(a->cb, b->c, mod_params->rcb + mod_params->rc,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
erg += vdw_erg;
}
if ( d2 > backbone_constants[2])
return erg;
/* 3.B rest, within N-CA, mostly ca with all others */
/* n - ca, c - ca, cb - ca, cb - cb, ca - ca */
if (mod_params->rca > 0.0 && mod_params->rn > 0.0) {
vdw_erg = vdw_fn(a->ca, b->n, mod_params->rca + mod_params->rn,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
erg += vdw_erg;
}
if (mod_params->rn > 0.0 && mod_params->rca > 0.0) {
vdw_erg = vdw_fn(a->n, b->ca, mod_params->rn + mod_params->rca,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
erg += vdw_erg;
}
if (mod_params->rc > 0.0 && mod_params->rca > 0.0) {
vdw_erg = vdw_fn(a->c, b->ca, mod_params->rc + mod_params->rca,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
erg += vdw_erg;
}
if (mod_params->rca > 0.0 && mod_params->rc > 0.0) {
vdw_erg = vdw_fn(a->ca, b->c, mod_params->rca + mod_params->rc,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
erg += vdw_erg;
}
if (mod_params->rcb > 0.0 && mod_params->rcb > 0.0 && a->id != 'G' && b->id != 'G') {
vdw_erg = vdw_fn(a->cb, b->cb, mod_params->rcb + mod_params->rcb,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
erg += vdw_erg;
}
if (mod_params->rca > 0.0 && mod_params->rcb > 0.0 && b->id != 'G') {
vdw_erg = vdw_fn(a->ca, b->cb, mod_params->rca + mod_params->rcb,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
erg += vdw_erg;
}
if (mod_params->rcb > 0.0 && mod_params->rca > 0.0 && a->id != 'G') {
vdw_erg = vdw_fn(a->cb, b->ca, mod_params->rcb + mod_params->rca,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
erg += vdw_erg;
}
if (mod_params->rca > 0.0 && mod_params->rca > 0.0) {
vdw_erg = vdw_fn(a->ca, b->ca, mod_params->rca + mod_params->rca,0, mod_params->rel_vdw_cutoff, 0, mod_params->vdw_clash_energy_at_hard_cutoff);
erg += vdw_erg;
}
return erg;
}
#endif
/* Energy contribution of all vdW interaction between 2 residues
a, b: amino acids
d2: squared distance of their alpha carbons */
double exclude(AA *a, AA *b, double d2, model_params *mod_params)
{
double erg = 0.0;
double rg_a, rg2_a, rg_b, rg2_b;
rg_a = rg2_a = rg_b = rg2_b = 0.0;
double eps_g_a_sqrt, eps_g2_a_sqrt, eps_g_b_sqrt, eps_g2_b_sqrt;
eps_g_a_sqrt = eps_g2_a_sqrt = eps_g_b_sqrt = eps_g2_b_sqrt = 0.0;
double depth = 0;
double vdw_erg = 0;
const double backbone_constants[3] = { mod_params->vdw_backbone_cutoff, mod_params->vdw_backbone_cutoff, mod_params->vdw_backbone_cutoff };
erg += HHvDW(a, b);
//Assign function pointer to the vdW model
double (*vdw_fn) (vector r1, vector r2, double Rmin, double depth, double vdw_rel_cutoff, double energy_shift, double clash_energy_at_hard_cutoff) = NULL;
if (mod_params->vdw_potential == HARD_CUTOFF_VDW_POTENTIAL) {
vdw_fn = vdw_hard_cutoff;
} else if (mod_params->vdw_potential == LJ_VDW_POTENTIAL) {
vdw_fn = vdw_lj;
} else {
stop("Clash cannot be calculated without a valid vdW potential.");
}
/* Calculates the correct index for maxvdw_gamma_gamma
* note the other d2 > should be changed for maximum efficiency*/
int index = (a->id - '@') * 26 + (b->id - '@') -1;
if (mod_params->use_gamma_atoms != NO_GAMMA) {
/* 1. check maximum interaction distance: this is the G-G case */
if (d2 > (mod_params->vdw_gamma_gamma_cutoff)[index]) /* cg - cg */
return erg;
if (a->etc & G__) {
if ((rg_a = sidechain_vdw_radius(a->id,1,mod_params->sidechain_properties)) > 0.0)
eps_g_a_sqrt = sidechain_vdw_depth_sqrt(a->id,1,mod_params->sidechain_properties);
}
if (a->etc & G2_) {
if ((rg2_a = sidechain_vdw_radius(a->id,2,mod_params->sidechain_properties)) > 0.0)
eps_g2_a_sqrt = sidechain_vdw_depth_sqrt(a->id,2,mod_params->sidechain_properties);
}
if (b->etc & G__) {
if ((rg_b = sidechain_vdw_radius(b->id,1,mod_params->sidechain_properties)) > 0.0)
eps_g_b_sqrt = sidechain_vdw_depth_sqrt(b->id,1,mod_params->sidechain_properties);
}
if (b->etc & G2_) {
if ((rg2_b = sidechain_vdw_radius(b->id,2,mod_params->sidechain_properties)) > 0.0)
eps_g2_b_sqrt = sidechain_vdw_depth_sqrt(b->id,2,mod_params->sidechain_properties);
}
if (rg_a != 0.0) {
/* Skip CYS--CYS gamma-gamma interactions (should really only miss when they are S-S bonded!, but let's try this for now) */
if (rg_b != 0.0 && (a->id != 'C' || b->id != 'C')) { //&& (mod_params->Sbond_strength == 0 || a->id != 'C' || b->id != 'C' ))
depth = eps_g_a_sqrt*eps_g_b_sqrt;
vdw_erg = vdw_fn(a->g, b->g, rg_a + rg_b,depth, mod_params->rel_vdw_cutoff, mod_params->vdw_shift*depth, mod_params->vdw_clash_energy_at_hard_cutoff);
erg += vdw_erg;
}
if (rg2_b != 0.0) {
depth = eps_g_a_sqrt*eps_g2_b_sqrt;
vdw_erg = vdw_fn(a->g, b->g2, rg_a + rg2_b,depth, mod_params->rel_vdw_cutoff, mod_params->vdw_shift*depth, mod_params->vdw_clash_energy_at_hard_cutoff);
erg += vdw_erg;
}