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metropolis.c
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/*
** This is a core of Metropolis Monte Carlo sampling procedure for
** simplified polypeptides. It contains the simulation procedure
** as well as the setup of initial conformation based on provided PDB
** or simplified sequence-structure input.
**
** Copyright (c) 2004 - 2010 Alexei Podtelezhnikov
** Copyright (c) 2007 - 2013 Nikolas Burkoff, Csilla Varnai and David Wild
*/
#include<stdlib.h> /* rand() */
#include<stdio.h>
#include<string.h>
#include<math.h>
#include<float.h>
#include"error.h"
#include"params.h"
#include"aadict.h"
#include"vector.h"
#include"rotation.h"
#include"peptide.h"
#include"vdw.h"
#include"energy.h"
#include"metropolis.h"
#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)]
/***********************************************************/
/**** MOVES AND METROPOLIS CRITERIA ****/
/***********************************************************/
/* Modulo a number to range(1..mod)
reModNum(6,6)=6;
reModNum(1,6)=1
reModNum(7,6)=6;
reModNum(0,6)=6
*/
static int reModNum(int a, int mod) {
return ((a-1)%mod)+1;
}
static int indMoved(int ind, int start, int end){
if (start>=end){
if (ind>end && ind<start)
return 0;
else
return 1;
} else {
if (ind>=start && ind<=end)
return 1;
else
return 0;
}
}
/* Check if the proposed move (saved in chaint) is allowed
by applying the Metropolis criteria on the energy change.
If the move is allowed, update the coordinates and the
energy matrix. */
static int allowed(Chain *chain, Chaint *chaint, Biasmap* biasmap, int start, int end, double logLstar, double *currE, simulation_params *sim_params)
{
int i, j;
double q, loss = 0.0;
int linked = 0;
//get the AD energy first as it will set position for gamma atoms
double externalloss = 0.0;
double ADEnergy_Chaint[end-start+1];
//double* ADEnergy_Chaint;
if (sim_params->protein_model.external_potential_type == 5){ // AD potential enabled
ADenergyNoClash(ADEnergy_Chaint,start,end,chain,chaint,&(sim_params->protein_model), 0);
//ADEnergy_Chaint = ADenergyNoClash(start,end,chain,chaint,&(sim_params->protein_model), 0);
for (i = start; i <= end; i++){
//ADEnergy_Chaint[i-start] = chaint->Ergt(0, i);
externalloss += chain->Erg(0, reModNum(i, chain->NAA-1)) - ADEnergy_Chaint[i-start];
}
}
if (end>chain->NAA-1) linked=1;
for (i = start; i <= end; i++){
for (j = 1; j < chain->NAA; j++) {
if (j == reModNum(i, chain->NAA-1)){
q = energy1(chaint->aat + j, &(sim_params->protein_model));
if ( ( j==1 || j==chain->NAA-1)){
if (sim_params->protein_model.external_potential_type2 != 4)
q += 0;
else if (j==1 && indMoved(2,start,reModNum(end,chain->NAA-1)) && linked)
q += ramabias(chaint->aat + chain->NAA - 1, chaint->aat + 1, chaint->aat + 2);
else if (j==1 && linked)
q += ramabias(chaint->aat + chain->NAA - 1, chaint->aat + 1, chain->aa + 2);
else if (j==1)
q += ramabias(chain->aa + chain->NAA - 1, chaint->aat + 1, chaint->aat + 2);
else if (j==chain->NAA-1 && indMoved(chain->NAA-1,start,reModNum(end,chain->NAA-1)) && linked)
q += ramabias(chaint->aat + j - 1, chaint->aat + j, chaint->aat +1);
else if (j==chain->NAA-1 && linked)
q += ramabias(chain->aa + j - 1, chaint->aat + j, chaint->aat +1);
else
q += ramabias(chaint->aat + j - 1, chaint->aat + j, chain->aa +1);
} else if (i == start)
q += ramabias(chain->aa + reModNum(i-1, chain->NAA-1), chaint->aat + reModNum(i, chain->NAA-1), chaint->aat + reModNum(i+1, chain->NAA-1));
else if (i == end)
q += ramabias(chaint->aat + reModNum(i-1, chain->NAA-1), chaint->aat + reModNum(i, chain->NAA-1), chain->aa + reModNum(i+1, chain->NAA-1));
else
q += ramabias(chaint->aat + reModNum(i-1, chain->NAA-1), chaint->aat + reModNum(i, chain->NAA-1), chaint->aat + reModNum(i+1, chain->NAA-1));
}
else if (indMoved(j,start,reModNum(end,chain->NAA-1))){
if ((reModNum(i, chain->NAA-1) == 1 && j == chain->NAA-1 && sim_params->protein_model.external_potential_type2 == 4)) {
q = energy2cyclic(biasmap,chaint->aat + 1, chaint->aat + chain->NAA - 1, &(sim_params->protein_model));
chaint->Ergt(j, reModNum(i, chain->NAA-1)) = q;
} else if(j > reModNum(i, chain->NAA-1)) {
//fprintf(stderr,"MC move q = %d %d, loss = %d %d haha %d %d,",i,j,start,end,indMoved(j,start,reModNum(end,chain->NAA-1)),linked);
q = energy2(biasmap,(chaint->aat) + reModNum(i, chain->NAA-1), (chaint->aat) + j, &(sim_params->protein_model));
if (j < start && linked) {
//fprintf(stderr,"aaa move q = %d %d, loss = %d %d haha %d %d,\n",i,j,start,end,indMoved(j,start,reModNum(end,chain->NAA-1)),linked);
chaint->Ergt(j + chain->NAA-1, reModNum(i, chain->NAA-1)) = q;
} else {
//fprintf(stderr,"MC move q = %d %d, loss = %d %d haha %d %d,\n",i,j,start,end,indMoved(j,start,reModNum(end,chain->NAA-1)),linked);
chaint->Ergt(j, reModNum(i, chain->NAA-1)) = q;
}
} else {
//q = energy2(biasmap,(chaint->aat) + reModNum(i, chain->NAA-1), (chaint->aat) + j, &(sim_params->protein_model));
//chaint->Ergt(reModNum(i, chain->NAA-1), j) = chaint->Ergt(j, reModNum(i, chain->NAA-1));
continue;
}
} else {
if (j == 1 && i == chain->NAA-1 && sim_params->protein_model.external_potential_type2 == 4)
q = energy2cyclic(biasmap,chain->aa + 1, chaint->aat + chain->NAA - 1, &(sim_params->protein_model));
else if (i == 1 && j == chain->NAA-1 && sim_params->protein_model.external_potential_type2 == 4)
q = energy2cyclic(biasmap,chaint->aat + 1, chain->aa + chain->NAA - 1, &(sim_params->protein_model));
else
q = energy2(biasmap,chaint->aat + reModNum(i, chain->NAA-1), (chain->aa) + j, &(sim_params->protein_model));
}
chaint->Ergt(i, j) = q;
loss += (chain->Erg(reModNum(i, chain->NAA-1), j) - q);
//fprintf(stderr,"MC move i = %d, j = %d, %g\n",i,j,loss);
}
}
/*Also take into account the global_energy term */
double SSEnergy = global_energy(start,end,chain,chaint,biasmap,&(sim_params->protein_model));
double SSloss = 0.0;
SSloss = chain->Erg(chain->NAA - 1, 0) - SSEnergy;
//loss += (chain->Erg(0, 0) - q);
//fprintf(stderr,"MC move q = %g, loss = %g,",q,loss);
//double externalloss = (chain->Erg(0, 0) - q);
currTargetEnergy = sim_params->protein_model.opt_totE_weight*(totenergy(chain)-loss)
+ (sim_params->protein_model.opt_extE_weight+sim_params->protein_model.opt_totE_weight)*(extenergy(chain)-externalloss);
double internalloss = loss;
double external_k = 1.0;
if (sim_params->protein_model.external_potential_type == 5 || sim_params->protein_model.external_potential_type2 == 4) external_k = sim_params->protein_model.external_k[0];
//if (chain->Erg(0, 0) > 5 || currTargetEnergy - targetBest > 15) external_k = 0.5;
//if ((targetBest > 0 || currTargetEnergy - targetBest < 25.) && (externalloss < -10 || loss < -10 )) external_k = 0.05 * external_k;
//if (chain->Erg(0, 0) < 1000 && rand()%100<10) external_k = 0.05 * external_k;
//if (externalloss < -10 || loss < -10) external_k = 0.15 * external_k;
//if (chain->Erg(0, 0) > 20 ||chain->Erg(0, 0) > 50) external_k = 0.2 * external_k;
//if ((targetBest > 0 || currTargetEnergy - targetBest < 25.) && (externalloss < -10 || loss < -10 )) external_k = 0.05 * external_k;
//loss is negative!! if loss is negative, it's worse, bad
/* Metropolis criteria */
//loss += q - chain->Erg(0, 0);
//loss = loss/sqrt(chain->NAA) + externalloss;
//external_k = 0.05 * external_k;
double cyclicBondEnergy = 0.0;
/*special cyclic*/ // needs attention !!! sign might be wrong...!!!GARY HACK
if (sim_params->protein_model.external_potential_type2 == 4) {
if (linked)
cyclicBondEnergy = cyclic_energy((chaint->aat) + 1, (chaint->aat) + chain->NAA - 1, 0);
else if (start == 1)
cyclicBondEnergy = cyclic_energy((chaint->aat) + 1, (chain->aa) + chain->NAA - 1, 0);
else if (end == chain->NAA-1)
cyclicBondEnergy = cyclic_energy((chain->aa) + 1, (chaint->aat) + chain->NAA - 1, 0);
else
cyclicBondEnergy = cyclic_energy((chain->aa) + 1, (chain->aa) + chain->NAA - 1, 0);
externalloss += chain->Erg(1, 0) - cyclicBondEnergy;
}
loss = loss + SSloss + externalloss;
if (loss < -10) external_k = 0.15 * external_k;
//loss = 0.25 * (loss + SSloss) + externalloss;
//if (externalloss > 0.) loss = loss + externalloss;
//if (loss < 0.0 && !sim_params->NS && loss * RAND_MAX * external_k < -rand()) {
// return 0; /* disregard rejected changes */
//}
//if (loss < 0.0 ) {
//// //fprintf(stderr," rejected\n");
// return 0; /* disregard rejected changes */
//}
//if (loss < 0.0 && !sim_params->NS && exp(sim_params->thermobeta * loss) * RAND_MAX < rand()) {
// //fprintf(stderr," rejected\n", );
// return 0; /* disregard rejected changes */
//}
//
if (loss < 0.0 && !sim_params->NS && exp(sim_params->thermobeta * loss *external_k) * RAND_MAX < rand()) {
//fprintf(stderr," rejected\n", );
//if (sim_params->protein_model.external_potential_type == 5)
//free(ADEnergy_Chaint);
return 0; /* disregard rejected changes */
}
//if ((currTargetEnergy - targetBest > 5.) ) external_k = sim_params->protein_model.external_k[0];
//if (sim_params->protein_model.external_potential_type == 5 && externalloss < -0.0 && !sim_params->NS && externalloss * RAND_MAX * external_k < -rand()) {
// return 0;
//}
//if (sim_params->protein_model.external_potential_type == 5 && !sim_params->NS && externalloss < -0.0 && exp(sim_params->thermobeta * externalloss *external_k) * RAND_MAX < rand()) {
// return 0; /* disregard rejected changes */
//}
//fprintf(stderr," accepted\n");
/*Nested Sampling criteria -- important second possibility is for FLEX and is otherwise ignored */
if(sim_params->NS && ((-logLstar > *currE && -logLstar < *currE - loss) || (-logLstar < *currE && loss < 0 ) )) {
//free(ADEnergy_Chaint);
//if (sim_params->protein_model.external_potential_type == 5)
//free(ADEnergy_Chaint);
return 0;
}
/* commit accepted changes */
for (i = start; i <= end; i++)
for (j = 1; j < chain->NAA; j++)
chain->Erg(reModNum(i, chain->NAA-1), j) = chain->Erg(j, reModNum(i, chain->NAA-1)) = chaint->Ergt(i, j);
if (sim_params->protein_model.external_potential_type == 5) {
for (j = start; j <= end; j++)
chain->Erg(0, reModNum(j, chain->NAA-1)) = ADEnergy_Chaint[j-start];
//free(ADEnergy_Chaint);
}
chain->Erg(0, 0) = 0.0;
for (j = 1; j < chain->NAA; j++) {
chain->Erg(0, 0) += chain->Erg(0, j);
}
if (sim_params->protein_model.external_potential_type2 == 4) {
chain->Erg(1, 0) = cyclicBondEnergy;
}
chain->Erg(chain->NAA - 1, 0) = SSEnergy;
*currE -= internalloss + externalloss;
//free(ADEnergy_Chaint);
return 1;
}
/* Make a transmutate move. A translational move to a featured point*/
void transmutate(Chain * chain, Chaint *chaint, Biasmap *biasmap, double ampl, double logLstar, double * currE, simulation_params *sim_params)
{
for (int i = 1; i < sim_params->NAA; i++) {
if (chain->aa[i].etc & FIXED) return;
}
if (sim_params->protein_model.external_potential_type != 5) {
return 0;
}
//no transPts identified. transPtsCount == 1 means only the center of box is found.
if (transPtsCount == 1) return;
double transvec[3];
//copy chain to chaint
for (int j = 1; j < chain->NAA; j++){
chaint->aat[j].etc = chain->aa[j].etc;
chaint->aat[j].num = chain->aa[j].num;
chaint->aat[j].id = chain->aa[j].id;
chaint->aat[j].chainid = chain->aa[j].chainid;
chaint->aat[j].SCRot = chain->aa[j].SCRot;
for(int i = 0; i < 3; i++){
chaint->aat[j].h[i] = chain->aa[j].h[i];
chaint->aat[j].n[i] = chain->aa[j].n[i];
chaint->aat[j].ca[i] = chain->aa[j].ca[i];
chaint->aat[j].c[i] = chain->aa[j].c[i];
chaint->aat[j].o[i] = chain->aa[j].o[i];
chaint->aat[j].cb[i] = chain->aa[j].cb[i];
chaint->aat[j].g[i] = chain->aa[j].g[i];
chaint->aat[j].g2[i] = chain->aa[j].g2[i];
chaint->xaat[j][i][0] = chain->xaa[j][i][0];
chaint->xaat[j][i][1] = chain->xaa[j][i][1];
chaint->xaat[j][i][2] = chain->xaa[j][i][2];
}
//chaint->aat[j] = chain->aa[j];
}
casttriplet(chaint->xaat[0], chain->xaa[0]);
for (int i = 1; i <= chain->NAA - 1; i++) {
casttriplet(chaint->xaat[i], chain->xaa[i]);
}
casttriplet(chaint->xaat_prev[chain->aa[1].chainid], chain->xaa_prev[chain->aa[1].chainid]);
//get a random transpoints
int transPtsID = rand() % transPtsCount;
//get the transvec
int centerAAID = (chain->NAA + 1) / 2;
transvec[0] = - chain->aa[centerAAID].c[0] + Xpts[transPtsID];
transvec[1] = - chain->aa[centerAAID].c[1] + Ypts[transPtsID];
transvec[2] = -chain->aa[centerAAID].c[2] + Zpts[transPtsID];
//apply the transvec to all atoms
double movement = 0;
//fprintf(stderr, "translational move %g %g %g %d \n", transvec[0][vecind], transvec[1][vecind], transvec[2][vecind],chain->NAA);
for (int i = 0; i < 3; i++) {
movement = transvec[i];
for (int j = 1; j < chain->NAA; j++) {
if (chaint->aat[j].etc & G__){
chaint->aat[j].g[i] += movement;
}
if (chaint->aat[j].etc & G2_){
chaint->aat[j].g2[i] += movement;
}
if (chaint->aat[j].id != 'P') {
chaint->aat[j].h[i] += movement;
}
chaint->aat[j].n[i] += movement;
chaint->aat[j].ca[i] += movement;
chaint->aat[j].c[i] += movement;
chaint->aat[j].o[i] += movement;
if (chaint->aat[j].id != 'G') {
chaint->aat[j].cb[i] += movement;
}
}
}
//score the external energy, the internal energy stays the same
double ADEnergy_Chaint[chain->NAA-1];
//double* ADEnergy_Chaint;
ADenergyNoClash(ADEnergy_Chaint, 1, chain->NAA-1,chain,chaint,&(sim_params->protein_model), 0);
//default is to accept all transmutate move and commit the move
casttriplet(chain->xaa[0], chaint->xaat[0]);
for (int i = 1; i <= chain->NAA - 1; i++) {
casttriplet(chain->xaa[i], chaint->xaat[i]);
}
chain->Erg(0, 0) = 0.0;
//if (transExtEne < -30) fprintf(stderr, "committing moved !!\n");
for (int j = 1; j < chain->NAA; j++) {
chain->Erg(0, j) = ADEnergy_Chaint[j - 1];
chain->Erg(0, 0) += chain->Erg(0, j);
}
for (int i = 1; i <= chain->NAA - 1; i++) {
chain->aa[i] = chaint->aat[i];
}
fprintf(stderr, "transmutate!!! %g %g %g\n", chain->aa[centerAAID].c[0], chain->aa[centerAAID].c[1], chain->aa[centerAAID].c[2]);
fprintf(stderr, "transmutate!!! %g %g %g\n", Xpts[transPtsID], Ypts[transPtsID], Zpts[transPtsID]);
//copybetween(chain, chaint);
//free(ADEnergy_Chaint);
}
/* Make a translation move. */
static int transmove(Chain * chain, Chaint *chaint, Biasmap *biasmap, double ampl, double logLstar, double * currE, simulation_params *sim_params)
{
/*translational move*/
//
//double transvec[3][chain->NAA - 1];
for (int i = 1; i < sim_params->NAA; i++) {
if (chain->aa[i].etc & FIXED) return 0;
}
if (sim_params->protein_model.external_potential_type != 5) {
return 0;
}
double transvec[3];
int i, j;
for (j = 1; j < chain->NAA; j++){
chaint->aat[j].etc = chain->aa[j].etc;
chaint->aat[j].num = chain->aa[j].num;
chaint->aat[j].id = chain->aa[j].id;
chaint->aat[j].chainid = chain->aa[j].chainid;
chaint->aat[j].SCRot = chain->aa[j].SCRot;
for(i = 0; i < 3; i++){
if (chaint->aat[j].id != 'P') {
chaint->aat[j].h[i] = chain->aa[j].h[i];
}
chaint->aat[j].n[i] = chain->aa[j].n[i];
chaint->aat[j].ca[i] = chain->aa[j].ca[i];
chaint->aat[j].c[i] = chain->aa[j].c[i];
chaint->aat[j].o[i] = chain->aa[j].o[i];
if (chaint->aat[j].id != 'G') {
chaint->aat[j].cb[i] = chain->aa[j].cb[i];
}
if (chaint->aat[j].etc & G__){
chaint->aat[j].g[i] = chain->aa[j].g[i];
}
if (chaint->aat[j].etc & G2_){
chaint->aat[j].g2[i] = chain->aa[j].g2[i];
}
chaint->xaat[j][i][0] = chain->xaa[j][i][0];
chaint->xaat[j][i][1] = chain->xaa[j][i][1];
chaint->xaat[j][i][2] = chain->xaa[j][i][2];
}
//chaint->aat[j] = chain->aa[j];
}
for(i = 0; i < 3; i++){
chaint->xaat_prev[0][i][0] = chain->xaa_prev[0][i][0];
chaint->xaat_prev[0][i][1] = chain->xaa_prev[0][i][1];
chaint->xaat_prev[0][i][2] = chain->xaa_prev[0][i][2];
}
//casttriplet(chaint->xaat[0], chain->xaa[0]);
//for (int i = 1; i <= chain->NAA - 1; i++) {
// casttriplet(chaint->xaat[i], chain->xaa[i]);
//}
//casttriplet(chaint->xaat_prev[chain->aa[1].chainid], chain->xaa_prev[chain->aa[1].chainid]);
double movement[3];
int vecind1 = 0;
vecind1 = rand()%(chain->NAA - 1) + 1;
int vecind2 = vecind1;
while (vecind2 == vecind1) {
vecind2 = rand()%(chain->NAA - 1) + 1;
}
transvec[0] = chain->aa[vecind1].c[0] - chain->aa[vecind2].c[0];
transvec[1] = chain->aa[vecind1].c[1] - chain->aa[vecind2].c[1];
transvec[2] = chain->aa[vecind1].c[2] - chain->aa[vecind2].c[2];
double length = (double)rand() / RAND_MAX;
//fprintf(stderr, "translational move %g %g %g %d \n", transvec[0][vecind], transvec[1][vecind], transvec[2][vecind],chain->NAA);
for (i = 0; i < 3; i++) {
movement[i] = 0.0;
if (chain->Erg(0, 0) > 0) {
if (length > 0.4) {
movement[i] = 2. * rand() / RAND_MAX - 1;
}
else {
movement[i] = transvec[i] * length / abs(vecind2 - vecind1);
}
}
else {
if (length > 0.4) {
movement[i] = 2. * rand() / RAND_MAX - 1;
}
else {
movement[i] = transvec[i] * length / abs(vecind2 - vecind1);
}
}
for (int j = 1; j < chain->NAA; j++) {
if (chaint->aat[j].etc & G__){
chaint->aat[j].g[i] += movement[i];
}
if (chaint->aat[j].etc & G2_){
chaint->aat[j].g2[i] += movement[i];
}
if (chaint->aat[j].id != 'P') {
chaint->aat[j].h[i] += movement[i];
}
chaint->aat[j].n[i] += movement[i];
chaint->aat[j].ca[i] += movement[i];
chaint->aat[j].c[i] += movement[i];
chaint->aat[j].o[i] += movement[i];
if (chaint->aat[j].id != 'G') {
chaint->aat[j].cb[i] += movement[i];
}
}
}
double ADEnergy_Chaint[chain->NAA-1];
//double* ADEnergy_Chaint;
double externalloss = 0.0;
//double* ADEnergy_Chaint;
if (sim_params->protein_model.external_potential_type == 5){
ADenergyNoClash(ADEnergy_Chaint, 1, chain->NAA-1,chain,chaint,&(sim_params->protein_model), 1);
//ADEnergy_Chaint = ADenergyNoClash(1, chain->NAA-1,chain,chaint,&(sim_params->protein_model), 0);
for (i = 1; i <= chain->NAA-1; i++){
externalloss += chain->Erg(0, i) - ADEnergy_Chaint[i-1];
}
}
//if loss is negative, it's worse, bad
//currTargetEnergy = (sim_params->protein_model.opt_extE_weight+sim_params->protein_model.opt_totE_weight)*(extenergy(chain)-externalloss);
double external_k = 1.0;
if (sim_params->protein_model.external_potential_type == 5 || sim_params->protein_model.external_potential_type2 == 4) external_k = sim_params->protein_model.external_k[0];
//if (externalloss < -10) external_k = 0.09 * external_k;
if (externalloss < -10) external_k = 0.05 * external_k;
//if ((targetBest > 0 || currTargetEnergy - targetBest < 25) && externalloss < -10) external_k = 0.05 * external_k;
//if (chain->Erg(0, 0) > 50) external_k = 0.2 * external_k;
//if (moved && allowed(chain, chaint, biasmap, 1, chain->NAA - 1, logLstar, currE, sim_params)) {
if (externalloss < 0.0 && externalloss * RAND_MAX * external_k < -rand()) {
//free(ADEnergy_Chaint);
return 0;
}
else {
//casttriplet(chain->xaa_prev[chain->aa[1].chainid], chaint->xaat_prev[chain->aa[1].chainid]);
//
//for (int i = 0; i <= chain->NAA - 1; i++) {
// casttriplet(chain->xaa[i], chaint->xaat[i]);
//}
chain->Erg(0, 0) = 0.0;
for (int j = 1; j < chain->NAA; j++) {
chain->Erg(0, j) = ADEnergy_Chaint[j - 1];
chain->Erg(0, 0) += chain->Erg(0, j);
}
for (int i = 1; i <= chain->NAA - 1; i++) {
chain->aa[i] = chaint->aat[i];
}
//copybetween(chain, chaint);
//free(ADEnergy_Chaint);
return 1;
}
}
/* Do a translational optimization in a Solis-Wets fashion. */
int transopt(Chain * chain, Chaint *chaint, Biasmap *biasmap, double ampl, double logLstar, double * currE, simulation_params *sim_params, int mod)
{
for (int i = 1; i < sim_params->NAA; i++) {
if (chain->aa[i].etc & FIXED) return 0;
}
if (sim_params->protein_model.external_potential_type != 5) {
return 0;
}
/*translational optimization*/
//
//double transvec[3][chain->NAA - 1];
double transvec[3];
//copy chain to chiant
int i, j;
for (j = 1; j < chain->NAA; j++){
chaint->aat[j].etc = chain->aa[j].etc;
chaint->aat[j].num = chain->aa[j].num;
chaint->aat[j].id = chain->aa[j].id;
chaint->aat[j].chainid = chain->aa[j].chainid;
chaint->aat[j].SCRot = chain->aa[j].SCRot;
for(i = 0; i < 3; i++){
chaint->aat[j].h[i] = chain->aa[j].h[i];
chaint->aat[j].n[i] = chain->aa[j].n[i];
chaint->aat[j].ca[i] = chain->aa[j].ca[i];
chaint->aat[j].c[i] = chain->aa[j].c[i];
chaint->aat[j].o[i] = chain->aa[j].o[i];
chaint->aat[j].cb[i] = chain->aa[j].cb[i];
chaint->aat[j].g[i] = chain->aa[j].g[i];
chaint->aat[j].g2[i] = chain->aa[j].g2[i];
chaint->xaat[j][i][0] = chain->xaa[j][i][0];
chaint->xaat[j][i][1] = chain->xaa[j][i][1];
chaint->xaat[j][i][2] = chain->xaa[j][i][2];
}
//chaint->aat[j] = chain->aa[j];
}
for(i = 0; i < 3; i++){
chaint->xaat_prev[0][i][0] = chain->xaa_prev[0][i][0];
chaint->xaat_prev[0][i][1] = chain->xaa_prev[0][i][1];
chaint->xaat_prev[0][i][2] = chain->xaa_prev[0][i][2];
}
double movement[3];
int noImprovStep = 0;
double currExtE = 0.0;
double currADEnergy[chain->NAA-1], ADEnergy_Chaint[chain->NAA-1];
double extE = chain->Erg(0,0); //This is the current best E and will be updated
int step = 0;
int maxStep = 10;
int maxNoImprovStep = 3;
if (mod == 1){
int maxStep = 30;
int maxNoImprovStep = 5;
}
for (step = 0; step < maxStep; step++) {
if (noImprovStep >= maxNoImprovStep) break;
for (i = 0; i < 3; i++) {
if (step == 0) movement[i] = 0.0;
if (step == 1) movement[i] = 0.2 * rand()/RAND_MAX - 0.1;
for (int j = 1; j < chain->NAA; j++) {
if (chaint->aat[j].etc & G__){
chaint->aat[j].g[i] += movement[i];
}
if (chaint->aat[j].etc & G2_){
chaint->aat[j].g2[i] += movement[i];
}
if (chaint->aat[j].id != 'P') {
chaint->aat[j].h[i] += movement[i];
}
chaint->aat[j].n[i] += movement[i];
chaint->aat[j].ca[i] += movement[i];
chaint->aat[j].c[i] += movement[i];
chaint->aat[j].o[i] += movement[i];
if (chaint->aat[j].id != 'G') {
chaint->aat[j].cb[i] += movement[i];
}
}
}
ADenergyNoClash(currADEnergy, 1, chain->NAA-1,chain,chaint,&(sim_params->protein_model), 1);
currExtE = 0.0;
for (i = 1; i <= chain->NAA-1; i++){
currExtE += currADEnergy[i-1];
//fprintf(stderr,"%g !!!", currADEnergy[i-1]);
}
//fprintf(stderr,"transopt %g \n!!!", currExtE);
if (currExtE < extE) {
//find better energy
extE = currExtE;
//free(ADEnergy_Chaint);
for (i = 1; i <= chain->NAA-1; i++){
ADEnergy_Chaint[i-1] = currADEnergy[i-1];
}
noImprovStep = 0;
for (i = 0; i < 3; i++) movement[i] = 0.2 * rand()/RAND_MAX - 0.1;
} else {
//redo the change and make the step smaller
for (i = 0; i < 3; i++) {
for (int j = 1; j < chain->NAA; j++) {
if (chaint->aat[j].etc & G__){
chaint->aat[j].g[i] -= movement[i];
}
if (chaint->aat[j].etc & G2_){
chaint->aat[j].g2[i] -= movement[i];
}
if (chaint->aat[j].id != 'P') {
chaint->aat[j].h[i] -= movement[i];
}
chaint->aat[j].n[i] -= movement[i];
chaint->aat[j].ca[i] -= movement[i];
chaint->aat[j].c[i] -= movement[i];
chaint->aat[j].o[i] -= movement[i];
if (chaint->aat[j].id != 'G') {
chaint->aat[j].cb[i] -= movement[i];
}
}
if (rand()%100 > 20)
movement[i] = -movement[i]/2;
}
noImprovStep += 1;
}
//for (int i = 1; i <= chain->NAA -1; i++) {
// fprintf(stderr, " %d", (chaint->aat + i)->SCRot);
//}
//fprintf(stderr," transopt %g %g %g %g %g %d!!!\n", currExtE, extE ,movement[0] ,movement[1], movement[2], noImprovStep);
}
if (extE - chain->Erg(0,0) > -0.00001) return 0;
//casttriplet(chain->xaa_prev[chain->aa[1].chainid], chaint->xaat_prev[chain->aa[1].chainid]);
//
//for (int i = 0; i <= chain->NAA - 1; i++) {
// casttriplet(chain->xaa[i], chaint->xaat[i]);
//}
//fprintf(stderr," transopt %g %g %g %g %g %d!!!\n", chain->Erg(0, 0), extE ,chaint->aat[1].c[0] - chain->aa[1].c[0], chaint->aat[1].c[1] - chain->aa[1].c[1], chaint->aat[1].c[2] - chain->aa[1].c[2], step);
chain->Erg(0, 0) = 0.0;
for (int j = 1; j < chain->NAA; j++) {
chain->Erg(0, j) = ADEnergy_Chaint[j - 1];
chain->Erg(0, 0) += chain->Erg(0, j);
}
//free(ADEnergy_Chaint);
//free(currADEnergy);
for (int i = 1; i <= chain->NAA - 1; i++) {
chain->aa[i] = chaint->aat[i];
}
//copybetween(chain, chaint);
return step;
}
/* Make a crankshaft move. This is a local move that involves
the crankshaft rotation of up to 4 peptde bonds. Propose a
move, and apply the Metropolis criteria. */
static int crankshaft(Chain * chain, Chaint *chaint, Biasmap *biasmap, double ampl, double logLstar, double * currE, simulation_params *sim_params)
{
int start, end, len, toss;
double alpha;
vector a;
matrix t;
const double discrete = 2.0 / RAND_MAX;
//if(sim_params->NS){
for (int i = 1; i < chain->NAA; i++){
chaint->aat[i].etc = chain->aa[i].etc;
chaint->aat[i].num = chain->aa[i].num;
chaint->aat[i].id = chain->aa[i].id;
chaint->aat[i].chainid = chain->aa[i].chainid;
chaint->aat[i].SCRot = chain->aa[i].SCRot;
}
//}
/* setup sidechain dihedral angles */
/* They change with P = 1/4 (unless fixed) */
if ((sim_params->protein_model).use_gamma_atoms != NO_GAMMA) {
if (!(sim_params->protein_model).fix_chi_angles && rand()/(double)RAND_MAX < 0.25) { /* change chi angles */
for (int i = 1; i < chain->NAA; i++){
//fprintf(stderr,"chi angles of amino acid %d",i);
//fprintf(stderr," %c",chain->aa[i].id);
//fprintf(stderr," %g",chain->aa[i].chi1); //would fail for G,A
//fprintf(stderr," %g\n",chain->aa[i].chi2); //would fail for all but V,I,T
if(chain->aa[i].id != 'G' && chain->aa[i].id != 'A' && chain->aa[i].chi1 != DBL_MAX) {
chaint->aat[i].chi1 = sidechain_dihedral(chain->aa[i].id, sim_params->protein_model.sidechain_properties);//aa[i].chi1;
}
if((chain->aa[i].id == 'V' || chain->aa[i].id == 'I' || chain->aa[i].id == 'T') && chain->aa[i].chi2 != DBL_MAX) {
chaint->aat[i].chi2 = sidechain_dihedral2(chain->aa[i].id,chaint->aat[i].chi1, sim_params->protein_model.sidechain_properties);//aa[i].chi2;
}
}
} else {
for (int i = 1; i < chain->NAA; i++){
//TODO: we might need this here: if(chain->aa[i].id != 'G' && chain->aa[i].id != 'A') {
chaint->aat[i].chi1 = chain->aa[i].chi1;
chaint->aat[i].chi2 = chain->aa[i].chi2;
//}
}
}
}
// Calculate the look-up table of allowed MC moves on the 1st call.
// This will avoid moves involving residues on more than 1 chain
// TODO: and fixed atoms.
if (sim_params->MC_lookup_table == NULL) {
fprintf(stderr,"creating MC move lookup table.\n");
// Use the sequence for this, where chain breaks are marked.
if (sim_params->seq == NULL || sim_params->sequence == NULL) {
fprintf(stderr,"sim_params->seq: %s\n",sim_params->seq);
fprintf(stderr,"sim_params->sequence: %s\n",sim_params->sequence);
stop("sequence is not present in sim_params for MC lookup table calculation\n");
}
//allocate memory
//fprintf(stderr,"allocating memory: 4 * (%d-1+%d) integers.\n",sim_params->NAA,sim_params->Nchains);
int N = (sim_params->NAA - 1 + sim_params->Nchains);
sim_params->MC_lookup_table = (int *)malloc(sizeof(int) * 4 * N);
sim_params->MC_lookup_table_n = (int *)malloc(sizeof(int) * 4);
if (!sim_params->MC_lookup_table || !sim_params->MC_lookup_table_n) stop("Unable to allocate memory for sim_params->MC_lookup_table.");
fprintf(stderr,"Sequence: ");
for (int i=1; i<sim_params->NAA; i++) {
fprintf(stderr,"%c",chain->aa[i].id);
}
fprintf(stderr,"\n");
fprintf(stderr,"Fixed: ");
for (int i=1; i<sim_params->NAA; i++) {
if (chain->aa[i].etc & FIXED)
fprintf(stderr,"x");
else
fprintf(stderr," ");
}
fprintf(stderr,"\n");
fprintf(stderr,"Constrained: ");
for (int i=1; i<sim_params->NAA; i++) {
if (chain->aa[i].etc & CONSTRAINED)
fprintf(stderr,"x");
else
fprintf(stderr," ");
}
fprintf(stderr,"\n");
fprintf(stderr,"Chain: ");
for (int i=1; i<sim_params->NAA; i++) {
fprintf(stderr,"%d",chain->aa[i].chainid % 10);
}
fprintf(stderr,"\n");
//fprintf(stderr,"lookup table:\n");
//fill in lookup table
for (int i=0; i<4; i++) { // loop length can be 0-4
int next = 0;
fprintf(stderr,"len %d bonds, Nchains %d:", i+1, sim_params->Nchains);
int fixed_moves = 0; //counter for moves disallowed due to fixed atoms
for (int j=1; j<(sim_params->NAA - i); j++){ //start of loop
//Check if any of the atoms would be fixed
int any_fixed = 0;
for (int k=j; k<j+i+1; k++) {
if ((chain->aa[k].etc & FIXED) && (chain->aa[j].chainid == chain->aa[k].chainid)) any_fixed = 1;
}
if (any_fixed) {
if (chain->aa[j].chainid == chain->aa[j + i].chainid) {
fprintf(stderr, "fixed amino acid in %d-%d, skipping", j, j + i + 1);
fixed_moves++;
}
//also count the extra move at the beginning of the chain
if (j == 1) {
if (chain->aa[j].chainid == chain->aa[j+i].chainid) fixed_moves ++;
} else {
if (chain->aa[j].chainid != chain->aa[j-1].chainid && chain->aa[j].chainid == chain->aa[j+i].chainid) fixed_moves ++;
}
//also count the extra move at the end of the mid-chain
if (chain->aa[j].chainid != chain->aa[j + 1].chainid && !chain->aa[j + 1].etc & FIXED) fixed_moves++;
continue;
}
//no fixed atoms, add the move(s).
//if it's the beginning of the chain, and the chain is long enough, also add the previous amino acid
if (j == 1) { //first beginning
if (chain->aa[j].chainid == chain->aa[j+i].chainid) {
sim_params->MC_lookup_table[i*N+next] = j-1;
fprintf(stderr,"*%d ",j-1);
next ++;
}
} else { // j > 1, also check chainID differs from previous aa
if (chain->aa[j].chainid != chain->aa[j-1].chainid && chain->aa[j].chainid == chain->aa[j+i].chainid && !chain->aa[j - i].etc & FIXED) {
sim_params->MC_lookup_table[i*N+next] = j-1;
fprintf(stderr,"*%d ",j-1);
next ++;
}
}
//if it's inside the chain or at the end
if (chain->aa[j].chainid == chain->aa[j+i].chainid) {
sim_params->MC_lookup_table[i*N+next] = j;
fprintf(stderr,"x%d ",j);
next ++;
}
}
//fprintf(stderr,"(next=%d)",next);
fprintf(stderr, "%d+%d != (%d-1+(1-%d)*%d\n", next, fixed_moves, sim_params->NAA, i, sim_params->Nchains);
int N_len = (sim_params->NAA - 1) + (1 - i) * sim_params->Nchains; //number of possibilities for this len
if ((next + fixed_moves) != N_len) {
//fprintf(stderr,"%d+%d != (%d-1+(1-%d)*%d\n", next, fixed_moves, sim_params->NAA,i,sim_params->Nchains);
stop("Something has gone wrong. Maybe too short chains?\n");
//} else {
// fprintf(stderr,"%d == (%d-1+(1-%d)*%d\n", (next), sim_params->NAA,i,sim_params->Nchains);
}
sim_params->MC_lookup_table_n[i] = next; //the number of valid moves
for (int j = next; j<(sim_params->NAA - 1 + sim_params->Nchains); j++) {
sim_params->MC_lookup_table[i*N+next] = -1;
fprintf(stderr,"%d ",-1);
next ++;
}
fprintf(stderr,"\n");
}
}
//stop("Everything is OK.");
//TODO multi-chain protein
int pivot_around_end = 0;
int pivot_around_start = 0;
toss = rand();
/* segment length */
len = toss & 0x3; /* segment length minus one */
if (len > chain->NAA - 2)
len = chain->NAA - 2;
//fprintf(stderr,"MC move len = %d,",len);
/* amino acids are numbered from 1 to NAA-1 */
/* segment could start 1 before the first amino acid and end 1 after the last amino acid (pivot moves) or within the chain (crankshaft moves) */
int N = (sim_params->NAA - 1 + sim_params->Nchains);
//int N_len = (chain->NAA - 1) + (1 - len) * sim_params->Nchains; //number of possibilities for this len (this has been checked when building the lookup table)
int N_len = sim_params->MC_lookup_table_n[len]; //the number of valid moves (taking into account fixed amino acids)
//fprintf(stderr," random number in [ 0, %d ],",N_len-1);
/* segment start */
start = sim_params->MC_lookup_table[len*N + (toss >> 2) % N_len ];
/* segment end */
if ((sim_params->protein_model).fix_CA_atoms) {
end = start + 1;
} else {
end = start + len + 1;
}
if (start < 0 || end < 0) { //hit a -1 in the table!
stop("Something has gone wrong when selecting amino acids for the MC move.\n");
}
//fprintf(stderr,"move residues %d -- %d (len: %d bonds),",start,end,len+1);
for (int ai=start; ai<end; ai++) {
if (chain->aa[ai].etc & FIXED) {
fprintf(stderr,"residues %d -- %d (len: %d bonds),",start,end,len+1);
fprintf(stderr,"\n%d is fixed\n",ai);
stop("crankshaft: tried to move fixed amino acid.\n");
}
}
int swappp = 0;
//for cyclic peptide Gary Hack
while (sim_params->protein_model.external_potential_type2 == 4 && (start == 0 || end == chain->NAA) && ((toss%50) > chain->Erg(1, 0))) {
toss = rand();
len = toss & 0x3; /* segment length minus one */
if (len > chain->NAA - 2)
len = chain->NAA - 2;
N_len = sim_params->MC_lookup_table_n[len];
start = sim_params->MC_lookup_table[len*N + (toss >> 2) % N_len];
if ((sim_params->protein_model).fix_CA_atoms) {
end = start + 1;
}
else {
end = start + len + 1;
}
swappp = 1;
//fprintf(stderr, "s %d e %d \n", start,end);
}
//if (swappp == 1) fprintf(stderr, "s %d e %d \n", start, end);
//fprintf(stderr, "s2 %d e %d\n", start, end);
if (chain->Erg(0,0)>1000)
ampl = 2 * ampl;
/* pivot or crankshaft */
if (start == 0) {
pivot_around_end = 1;
//fprintf(stderr," pivot around end\n");
ampl = 1.5 * ampl;
} else if (end == sim_params->NAA) {
pivot_around_start = 1;
ampl = 1.5 * ampl;
//fprintf(stderr," pivot around start\n");
} else if (chain->aa[start].chainid != chain->aa[end].chainid) {
//fprintf(stderr," chainid[start] = %d, chainid[end] = %d\n",chain->aa[start].chainid,chain->aa[end].chainid);
if (len == 0) {
/* special case for multi-chain protein at chain break for len=0 (2 amino acids) */
if (rand() & 0x2) {
pivot_around_start = 1;
//fprintf(stderr," pivot around start\n");
} else {
pivot_around_end = 1;
//fprintf(stderr," pivot around end\n");
}
} else {
if (chain->aa[start].chainid == chain->aa[start+1].chainid) {
pivot_around_start = 1;
//fprintf(stderr," pivot around start\n");
} else if (chain->aa[end].chainid == chain->aa[end-1].chainid) {
pivot_around_end = 1;
//fprintf(stderr," pivot around end\n");
} else {
stop("something has gone wrong at the MC move selection\n");
}
}
//} else {// else crankshaft
//fprintf(stderr," chainid[start] = %d, chainid[end] = %d\n",chain->aa[start].chainid,chain->aa[end].chainid);
//fprintf(stderr," crankshaft\n");
}
/* setup fixed ends for crankshaft or pivot */
if (pivot_around_end != 1) { // there is a fixed start site
casttriplet(chaint->xaat[start], chain->xaa[start]); //TODO: use start - 1 ??
castvec(chaint->aat[start].ca, chain->aa[start].ca);
//TODO we will also need xaa[start-1]
if (start == 1) {//if chain start, use x_prev
casttriplet(chaint->xaat_prev[chain->aa[end].chainid], chain->xaa_prev[chain->aa[end].chainid]);
//fprintf(stderr,"copying xaat_prev0 %d \n",chain->aa[end].chainid);
//fprintf(stderr," %g %g %g %g %g %g %g %g %g\n",chaint->xaat_prev[chain->aa[end].chainid][0][0],chaint->xaat_prev[chain->aa[end].chainid][0][1],chaint->xaat_prev[chain->aa[end].chainid][0][2],chaint->xaat_prev[chain->aa[end].chainid][1][0],chaint->xaat_prev[chain->aa[end].chainid][1][1],chaint->xaat_prev[chain->aa[end].chainid][1][2],chaint->xaat_prev[chain->aa[end].chainid][2][0],chaint->xaat_prev[chain->aa[end].chainid][2][1],chaint->xaat_prev[chain->aa[end].chainid][2][2]);
} else if (chain->aa[start].chainid != chain->aa[start - 1].chainid) {
casttriplet(chaint->xaat_prev[chain->aa[end].chainid], chain->xaa_prev[chain->aa[end].chainid]);
//fprintf(stderr,"copying xaat_prev1 %d\n",chain->aa[end].chainid);
//fprintf(stderr," %g %g %g %g %g %g %g %g %g\n",chaint->xaat_prev[chain->aa[end].chainid][0][0],chaint->xaat_prev[chain->aa[end].chainid][0][1],chaint->xaat_prev[chain->aa[end].chainid][0][2],chaint->xaat_prev[chain->aa[end].chainid][1][0],chaint->xaat_prev[chain->aa[end].chainid][1][1],chaint->xaat_prev[chain->aa[end].chainid][1][2],chaint->xaat_prev[chain->aa[end].chainid][2][0],chaint->xaat_prev[chain->aa[end].chainid][2][1],chaint->xaat_prev[chain->aa[end].chainid][2][2]);
} else {
casttriplet(chaint->xaat[start-1], chain->xaa[start-1]);
}
} else {
//we will also need the xaa[start-1], stored in xaa_prev for chain beginnings
casttriplet(chaint->xaat_prev[chain->aa[end].chainid], chain->xaa_prev[chain->aa[end].chainid]);
//fprintf(stderr,"copying xaat_prev2\n");
//fprintf(stderr," %g %g %g %g %g %g %g %g %g\n",chaint->xaat_prev[chain->aa[end].chainid][0][0],chaint->xaat_prev[chain->aa[end].chainid][0][1],chaint->xaat_prev[chain->aa[end].chainid][0][2],chaint->xaat_prev[chain->aa[end].chainid][1][0],chaint->xaat_prev[chain->aa[end].chainid][1][1],chaint->xaat_prev[chain->aa[end].chainid][1][2],chaint->xaat_prev[chain->aa[end].chainid][2][0],chaint->xaat_prev[chain->aa[end].chainid][2][1],chaint->xaat_prev[chain->aa[end].chainid][2][2]);
}
if (pivot_around_start != 1) { // there is a fixed end site
casttriplet(chaint->xaat[end], chain->xaa[end]);
castvec(chaint->aat[end].ca, chain->aa[end].ca);
}
/* magnitude of rotation */
/* rotate triplets, alpha in [-ampl; +ampl] */
alpha = ampl * (discrete * rand() - 1.0);