/*! \brief
* Function that does the analysis for a single frame.
*
* It is called once for each frame.
*/
static int analyze_frame(t_topology *top, t_trxframe *fr, t_pbc *pbc,
int nr, gmx_ana_selection_t *sel[], void *data)
{
t_analysisdata *d = (t_analysisdata *)data;
t_electrostatics dat;
/* Print the current frame number to the xvg file */
if (d->fp) {
fprintf(d->fp, "%10i ", d->framen);
}
/* Index the pqr file to the frame number */
std::string pqrname(d->pqr);
pqrname = pqrname.substr(0,pqrname.size()-4);
std::stringstream pqr;
pqr << pqrname << d->framen << ".pqr";
FILE *pqrout;
if ( d->dopqr ) {
pqrout = ffopen(pqr.str().c_str(), "w");
if ( pqrout == NULL ) {
gmx_fatal(FARGS, "\nFailed to open output file, '%s'\n",pqrout);
}
}
/* Get the bond vector and bond midpoint */
rvec bondvector, midpoint;
rvec_sub(fr->x[d->a2],fr->x[d->a1],bondvector);
double bondlength = pow( iprod(bondvector,bondvector), 0.5);
for (int i=0; i<3; i++){
midpoint[i] = fr->x[d->a1][i] + 0.5 * bondvector[i];
}
/*
* Defined axes based on the nitrile bond vector
* The z-axis is the bond axis
* The y-axis is from solving y0 = -(z1*y1+z2*y2)/z0, where (y1,y2)=(z2,-z0), then normalizing
* The x-axis is the cross product of the y-axis with the z-axis
*/
double zvec[3] = { bondvector[0] / bondlength, bondvector[1] / bondlength, bondvector[2] / bondlength };
double yvec[3] = { 1, 1, 1 };
if (zvec[0] != 0 ) {
yvec[0] = -(zvec[1]*yvec[1]+zvec[2]*yvec[2]) / zvec[0] ; }
else if (zvec[1] != 0 ) {
yvec[1] = -(zvec[0]*yvec[0]+zvec[2]*yvec[2]) / zvec[1] ; }
else if (zvec[2] != 0 ) {
yvec[2] = -(zvec[0]*yvec[0]+zvec[1]*yvec[1]) / zvec[2] ; }
else {
std::cerr << "\nERROR! Bond length is 0! This cannoy be correct!\n";
std::cerr << "BondVEC: " << bondvector[0] << " " << bondvector[1] << " " << bondvector[2] << std::endl;
std::cerr << "ZVEC: " << zvec[0] << " " << zvec[1] << " " << zvec[2] << std::endl;
}
/* Normalize */
double ylen = pow(dot(yvec,yvec),0.5);
for (int i=0; i<3;i++) {
yvec[i] = yvec[i]/ylen;
}
double xvec[3];
cross(yvec,zvec,xvec);
double xlen = pow(dot(xvec,xvec),0.5);
for (int i=0; i<3;i++) {
xvec[i] = xvec[i]/xlen;
}
/* Find the points that are Cho group-sites for calculating the potential */
std::vector<std::vector<double> > each_point;
int nsites = 0;
if (d->site_ndx.size() > 0) {
/*
* There are 8 sites from -a1, 8 sites from -a2, 1 site along the bond vector
* and 1 site for each atom in site_ndx
*/
nsites = d->site_ndx.size() + 17;
int n = 0;
each_point = std::vector<std::vector<double> > (nsites, std::vector<double> (3,0));
//std::vector<std::vector<double> > each_point(nsites,std::vector<double> (3,0));
/* Assign coordinates for the atoms in site_ndx */
for (int i=0; i<(int)d->site_ndx.size(); i++) {
for (int j=0; j<3; j++) {
each_point[n][j] = fr->x[d->site_ndx[i]][j];
}
n++;
}
/* Assign coordinate for the site along the bond vector */
for (int i=0; i<3; i++) {
each_point[n][i] = fr->x[d->a2][i] + bondvector[i] / bondlength * d->ring_dist;
}
n++;
/* 8 points around -a1 */
ring_points( fr->x[d->a1], &xvec[0], &yvec[0], &zvec[0], d->ring_dist, each_point,n);
/* 8 points around -a2 */
ring_points( fr->x[d->a2], &xvec[0], &yvec[0], &zvec[0], d->ring_dist, each_point,n);
std::vector<double> minv(3,10);
std::vector<double> maxv(3,-10);
}
/* Find the dummy atom points */
/* midpoint xyz vectors */
double pzcomp[3], nzcomp[3], pycomp[3], nycomp[3], pxcomp[3], nxcomp[3];
/* -a1 xyz vectors */
double pzcomp1[3], nzcomp1[3], pycomp1[3], nycomp1[3], pxcomp1[3], nxcomp1[3];
/* -a2 xyz vectors */
double pzcomp2[3], nzcomp2[3], pycomp2[3], nycomp2[3], pxcomp2[3], nxcomp2[3];
for (int i=0; i<3; i++) {
/* midpoint xyz vectors */
pzcomp[i] = midpoint[i] + zvec[i] * d->delta;
nzcomp[i] = midpoint[i] - zvec[i] * d->delta;
pycomp[i] = midpoint[i] + yvec[i] * d->delta;
nycomp[i] = midpoint[i] - yvec[i] * d->delta;
pxcomp[i] = midpoint[i] + xvec[i] * d->delta;
nxcomp[i] = midpoint[i] - xvec[i] * d->delta;
/* -a1 xyz vectors */
pzcomp1[i] = fr->x[d->a1][i] + zvec[i] * d->delta;
nzcomp1[i] = fr->x[d->a1][i] - zvec[i] * d->delta;
pycomp1[i] = fr->x[d->a1][i] + yvec[i] * d->delta;
nycomp1[i] = fr->x[d->a1][i] - yvec[i] * d->delta;
pxcomp1[i] = fr->x[d->a1][i] + xvec[i] * d->delta;
nxcomp1[i] = fr->x[d->a1][i] - xvec[i] * d->delta;
/* -a2 xyz vectors */
pzcomp2[i] = fr->x[d->a2][i] + zvec[i] * d->delta;
nzcomp2[i] = fr->x[d->a2][i] - zvec[i] * d->delta;
pycomp2[i] = fr->x[d->a2][i] + yvec[i] * d->delta;
nycomp2[i] = fr->x[d->a2][i] - yvec[i] * d->delta;
pxcomp2[i] = fr->x[d->a2][i] + xvec[i] * d->delta;
nxcomp2[i] = fr->x[d->a2][i] - xvec[i] * d->delta;
}
/* Write all the dummy atoms to the pqr file */
if ( d->dopqr ) {
write_dummy_atom( pqrout, nzcomp, "MIDz" );
write_dummy_atom( pqrout, pzcomp, "MIDz" );
write_dummy_atom( pqrout, nycomp, "MIDy" );
write_dummy_atom( pqrout, pycomp, "MIDy" );
write_dummy_atom( pqrout, nxcomp, "MIDx" );
write_dummy_atom( pqrout, pxcomp, "MIDx" );
write_dummy_atom( pqrout, nzcomp1, (std::string)*top->atoms.atomname[d->a1]+"z" );
write_dummy_atom( pqrout, pzcomp1, (std::string)*top->atoms.atomname[d->a1]+"z" );
write_dummy_atom( pqrout, nycomp1, (std::string)*top->atoms.atomname[d->a1]+"y" );
write_dummy_atom( pqrout, pycomp1, (std::string)*top->atoms.atomname[d->a1]+"y" );
write_dummy_atom( pqrout, nxcomp1, (std::string)*top->atoms.atomname[d->a1]+"x" );
write_dummy_atom( pqrout, pxcomp1, (std::string)*top->atoms.atomname[d->a1]+"x" );
write_dummy_atom( pqrout, nzcomp2, (std::string)*top->atoms.atomname[d->a2]+"z" );
write_dummy_atom( pqrout, pzcomp2, (std::string)*top->atoms.atomname[d->a2]+"z" );
write_dummy_atom( pqrout, nycomp2, (std::string)*top->atoms.atomname[d->a2]+"y" );
write_dummy_atom( pqrout, pycomp2, (std::string)*top->atoms.atomname[d->a2]+"y" );
write_dummy_atom( pqrout, nxcomp2, (std::string)*top->atoms.atomname[d->a2]+"x" );
write_dummy_atom( pqrout, pxcomp2, (std::string)*top->atoms.atomname[d->a2]+"x" );
if (d->site_ndx.size() > 0) {
for (int i=0; i<nsites; i++) {
std::stringstream key;
key << "p" << i;
write_dummy_atom( pqrout, &each_point[i][0], key.str());
}
}
}
/* Initialize all the electrostatics, since they are the result of summing parts */
int nexclude = d->exclude_ndx.size();
dat.field_proj_total = 0.0f;
dat.field_proj_each_exclude = std::vector<double> (nexclude,0.0f);
dat.field_each_exclude = std::vector<std::vector<double> > (nexclude, std::vector<double> (3,0));
dat.field_proj_exclude = 0.0f;
for (int i=0; i<3; i++){
dat.field_exclude[i] = 0.0f;
dat.field_mid[i] = 0.0f;
dat.field_a1[i] = 0.0f;
dat.field_a2[i] = 0.0f;
}
dat.protein_site = std::vector<double> (nsites, 0.0f);
dat.water_site = std::vector<double> (nsites, 0.0f);
int g = 0;
int nresidues = top->atoms.atom[sel[g]->g->index[sel[g]->p.nr]].resind;
std::vector<float> field_per_residue (nresidues,0.0f);
int nwater=0;
/* Loop through everything */
for (int g = 0; g < nr; ++g) { // for each group
if (g > 1) {
fprintf(stderr,"\nWarning: More than 1 group was specified. Cowardly ignoring all additional groups\n");
break;
}
for (int i = 0; i < sel[g]->p.nr; ++i) { // for each atom in the group
int atom_ndx = sel[g]->g->index[i]; // how we get to the atom index
/* Get .dat parameters and write the atom to the .pqr file */
int resid = top->atoms.atom[atom_ndx].resind;
double charge = top->atoms.atom[atom_ndx].q;
char *atomname = *top->atoms.atomname[atom_ndx];
char *resname = *top->atoms.resinfo[resid].name;
double radius = -1;
int namber = d->amber.size();
for (int j=0; j<namber; j++) {
if (d->bVerbose) {
fprintf(stderr, "\nTrying to match: %s %s to %s (%d/%d)", resname, *top->atoms.atomtype[atom_ndx], d->amber[j].ambername, j, namber);
}
if ( strncmp(*top->atoms.atomtype[atom_ndx], d->amber[j].ambername, strlen(*top->atoms.atomtype[atom_ndx])+1) == 0 ) {
radius = d->amber[j].radius;
if (d->bVerbose) {
fprintf(stderr,"\nMatched %s on %s to %s! (%d/%d)",resname, *top->atoms.atomtype[atom_ndx], d->amber[j].ambername, j, namber);
}
break;
}
}
if (radius < 0) {
fprintf(stderr,"\nError: Frame %d, could not match %s %s %s %i\n",d->framen, atomname, resname, *top->atoms.atomtype[atom_ndx],i+1);
std::exit(1);
}
if ( d->dopqr ) {
fprintf(pqrout,"ATOM %6i %4s %4s %5i %11.3f %7.3f %7.3f %7.4f %7.3f\n",atom_ndx+1,atomname,resname,resid+1,fr->x[atom_ndx][XX]*10,fr->x[atom_ndx][YY]*10,fr->x[atom_ndx][ZZ]*10,charge,radius);
}
/* Do the field calculations now */
bool keepAtom = true;
std::vector<double> anatom (3,0.0f);
calculate_field(midpoint, atom_ndx, *top, *fr, &anatom[0], 1);
for (int j=0; j<nexclude; j++) {
if (atom_ndx == d->exclude_ndx[j]) {
keepAtom = false;
break;
}
}
if (keepAtom) {
field_per_residue[resid] += d->rpdie * project_field(bondvector,&anatom[0]);
}
for (int j=0; j<3; j++) {
dat.field_mid[j] += anatom[j];
}
/* Get the field due to each excluded atom */
keepAtom = true;
for (int j=0; j<nexclude ; j++) {
if (atom_ndx == d->exclude_ndx[j]) {
calculate_field(midpoint, d->exclude_ndx[j], *top, *fr, &dat.field_each_exclude[j][0], 1);
keepAtom = false;
break;
}
}
if (keepAtom) {
calculate_field(midpoint, atom_ndx, *top, *fr, dat.field_exclude, 1);
calculate_field(fr->x[d->a1], atom_ndx, *top, *fr, dat.field_a1, 1);
calculate_field(fr->x[d->a2], atom_ndx, *top, *fr, dat.field_a2, 1);
}
//d->field_per_residue[resid] += d->rpdie * project_field(
/* Do the potential calculations now */
/* We want to exclude atoms at the sites */
/* We are also going to exclude atoms in the exclude group */
if ((int)d->site_ndx.size() > 0) {
if (keepAtom) {
for (int j=0; j<(int)d->site_ndx.size(); j++) {
if (atom_ndx == d->site_ndx[j] ) {
keepAtom = false;
break;
}
}
}
if (keepAtom) {
if (strncmp("SOL", resname, sizeof(resname)+1) == 0 ||
strncmp("HOH", resname, sizeof(resname)+1) == 0 ) {
for (int j=0; j<nsites; j++) {
double r = calculate_r( &each_point[j][0], atom_ndx, *top, *fr);
dat.water_site[j] += calculate_potential( r, atom_ndx, *top, *fr);
}
nwater++;
}
else {
for (int j=0; j<nsites; j++) {
double r = calculate_r( &each_point[j][0], atom_ndx, *top, *fr);
dat.protein_site[j] += calculate_potential( r, atom_ndx, *top, *fr);
}
}
}
}
}
}
/* Write all output to xvg file */
if (d->fp) {
fprintf(d->fp, "%.6e ", d->rpdie * project_field(bondvector, dat.field_mid));
for (int i=0; i<nexclude; i++) {
fprintf(d->fp, "%.6e ", d->rpdie * project_field(bondvector, &dat.field_each_exclude[i][0]));
}
fprintf(d->fp, "%.6e ", d->rpdie * project_field(bondvector, dat.field_exclude));
fprintf(d->fp, "%.6e ", d->rpdie * project_field(xvec,dat.field_exclude));
fprintf(d->fp, "%.6e ", d->rpdie * project_field(yvec,dat.field_exclude));
fprintf(d->fp, "%.6e ", d->rpdie * project_field(zvec,dat.field_exclude));
fprintf(d->fp, "%.6e ", d->rpdie * project_field(xvec,dat.field_a1));
fprintf(d->fp, "%.6e ", d->rpdie * project_field(yvec,dat.field_a1));
fprintf(d->fp, "%.6e ", d->rpdie * project_field(zvec,dat.field_a1));
fprintf(d->fp, "%.6e ", d->rpdie * project_field(xvec,dat.field_a2));
fprintf(d->fp, "%.6e ", d->rpdie * project_field(yvec,dat.field_a2));
fprintf(d->fp, "%.6e ", d->rpdie * project_field(zvec,dat.field_a2));
if ((int)d->site_ndx.size() > 0) {
for (int i=0; i<nsites; i++) {
fprintf(d->fp, "%.6e %.6e ", d->rpdie * dat.protein_site[i], d->rpdie * dat.water_site[i]);
}
}
fprintf(d->fp, "\n");
}
/* close the pqr file */
if ( d->dopqr ) {
fclose(pqrout);
}
/* Print the current frame number to the xvg file */
if (d->fpr) {
fprintf(d->fpr, "%10i ", d->framen);
for (int i=0;i<nresidues;i++) {
fprintf(d->fpr,"%12.6e ",field_per_residue[i]);
}
fprintf(d->fpr,"\n");
}
/* increment the frame number */
d->framen++;
/* We need to return 0 to tell that everything went OK */
return 0;
}
int main() {
int k = 1, err = 10, iter = 0;
float ratio = 0;
int A[4][5] = {
{ 1, 1, 1, 1, 1},
{ 1, 0, 0, 0, 1},
{ 1, 1, 1, 1, 1},
{ 1, 0, 0, 0, 1} };
int C[4][5] = {
{ 1, 1, 1, 1, 1},
{ 1, 0, 0, 0, 0},
{ 1, 0, 0, 0, 0},
{ 1, 1, 1, 1, 1} };
int L[4][5];
int last_used_matrix[4][5] = {
{ -1, -1, -1, -1, -1},
{ -1, -1, -1, -1, -1},
{ -1, -1, -1, -1, -1},
{ -1, -1, -1, -1, -1} };
t_neuron d_neuron = { .potential = 0, .threshold = 0.5, .output = 0 };
t_synapse synapses[20];
// Création du réseau
for (int i = 0; i < 20; i++) {
synapses[i].source = create_sensor();
synapses[i].target = &d_neuron;
synapses[i].weight = 0;
}
// Phase d'apprentissage
do {
feed_neural_network(&synapses, A);
learning_phase(&synapses, EPSILON, 1, 0);
feed_neural_network(&synapses, C);
learning_phase(&synapses, EPSILON, 0, 1);
feed_neural_network(&synapses, A);
calculate_potential(&synapses, &d_neuron);
if (d_neuron.output != 1)
err++;
feed_neural_network(&synapses, C);
calculate_potential(&synapses, &d_neuron);
if (d_neuron.output != 0)
err++;
iter++;
ratio = (float) iter / (float) err;
//printf("iter: %d && err: %d\n", iter, err);
//printf("ratio:%f\n", ratio);
} while ( ratio < 0.8);
// Phase de test pour A
while (k < 20) {
int i = 0;
int success = 0;
while (i < 100000) {
while (true) {
// Generer copie d'une lettre
lcpy(&L, &A);
// Generer du bruit sur cette copie
generate_noise(&L, k);
//print_letter(L);
//printf("\n");
if (!matrices_are_equal(L, last_used_matrix)) {
lcpy(&last_used_matrix, &L);
break;
}
}
feed_neural_network(&synapses, L);
calculate_potential(&synapses, &d_neuron);
if (d_neuron.output == 1)
success++;
i++;
}
success /= 1000;
printf("%d%% de succes sur %d essais avec %d%% de bruit.\n", success, i, k*5);
k++;
}
// Phase de test pour C
k = 1;
while (k < 20) {
int i = 0;
int success = 0;
while (i < 100000) {
while (true) {
// Generer copie d'une lettre
lcpy(&L, &C);
// Generer du bruit sur cette copie
generate_noise(&L, k);
if (!matrices_are_equal(L, last_used_matrix)) {
lcpy(&last_used_matrix, &L);
break;
}
}
feed_neural_network(&synapses, L);
calculate_potential(&synapses, &d_neuron);
if (d_neuron.output == 0)
success++;
i++;
}
success /= 1000;
printf("%d%% de succes sur %d essais avec %d%% de bruit.\n", success, i, k*5);
k++;
}
}
