int main(int argc, char *argv[]) {
int all; /*Nombre d'atomes dans pdb*/
int atom; /*Nombre de carbone CA*/
int help_flag = 1;
char file_name[500];
char eigen_name[500] = "eigen.dat";
char out_name[500] = "b_factor.pdb";
int verbose = 0;
int mode = 6;
int i;
int toprint = 0;
int nconn;
int lig = 0;
for (i = 1;i < argc;i++) {
if (strcmp("-i",argv[i]) == 0) {strcpy(file_name,argv[i+1]);--help_flag;}
if (strcmp("-o",argv[i]) == 0) {strcpy(out_name,argv[i+1]);}
if (strcmp("-ieig",argv[i]) == 0) {strcpy(eigen_name,argv[i+1]);}
if (strcmp("-h",argv[i]) == 0) {help_flag = 1;}
if (strcmp("-v",argv[i]) == 0) {verbose = 1;}
if (strcmp("-lig",argv[i]) == 0) {lig= 1;}
if (strcmp("-print",argv[i]) == 0) {toprint= 1;}
if (strcmp("-m",argv[i]) == 0) {int temp;sscanf(argv[i+1],"%d",&temp);mode = temp;}
}
if (help_flag == 0) { } else {
printf("****************************\nHelp Section\n-i\tFile Input (PDB)\n-o\tOutput Name Motion\n-ieig\tFile Name Eigen\n-v\tVerbose\n-sp\tSuper Node Mode (CA, N, C)\n-m\tMode\n-nm\tNombre de mode\n-lig\tTient compte duligand (sauf HOH)\n****************************\n");
return(0);
}
//***************************************************
//* *
//*Build a structure contaning information on the pdb
//* *
//***************************************************
all = count_atom(file_name);
nconn = count_connect(file_name);
if (verbose == 1) {printf("Connect:%d\n",nconn);}
if (verbose == 1) {printf("Assigning Structure\n\tAll Atom\n");}
// Array qui comprend tous les connects
int **connect_h=(int **)malloc(nconn*sizeof(int *));
for(i=0;i<nconn;i++) { connect_h[i]=(int *)malloc(7*sizeof(int));}
assign_connect(file_name,connect_h);
// Assign tous les atoms
struct pdb_atom strc_all[all];
atom = build_all_strc(file_name,strc_all); // Retourne le nombre de Node
if (verbose == 1) {printf(" Node:%d\n Atom:%d\n",atom,all);}
check_lig(strc_all,connect_h,nconn,all);
// Assign les Nodes
if (verbose == 1) {printf(" CA Structure\n");}
//atom = count_atom_CA_n(strc_all,all,super_node,lig);
if (verbose == 1) {printf(" Node:%d\n",atom);}
struct pdb_atom strc_node[atom];
atom = build_cord_CA(strc_all, strc_node,all,lig,connect_h,nconn);
if (verbose == 1) {printf(" Assign Node:%d\n",atom);}
//***************************************************
//* *
//* Load eigenvector et eigenvalue *
//* *
//***************************************************
if (verbose == 1) {printf("Loading Eigenvector\n");}
gsl_vector *eval = gsl_vector_alloc(3*atom);
gsl_matrix *evec= gsl_matrix_alloc (3*atom,3*atom);
load_eigen(eval,evec,eigen_name,3*atom);
if (verbose == 1) {printf("Inversing Matrix\n");}
gsl_matrix *k_inverse = gsl_matrix_alloc(atom, atom); /*Déclare et crée une matrice qui va être le pseudo inverse*/
if (mode < 0) {
mode = atom*3+mode;
}
printf("Mode:%d\n",mode);
k_inverse_matrix_stem(k_inverse,atom,eval,evec,mode,atom*3);
assign_bfactor(strc_all,k_inverse,all,lig);
write_strc(out_name, strc_all,all,1.0);
gsl_matrix_free(k_inverse);
}
int main(int argc, char *argv[]) {
int all; /*Nombre d'atomes dans pdb*/
int atom; /*Nombre de carbone CA*/
int help_flag = 1;
char file_name[500];
char eigen_name[100] = "eigen.dat";
int verbose = 0;
int i,j,k;
int nb_mode = 2;
int mode = 6;
int lig = 1;
int nconn;
float ligalign = 5; // Flag/valeur pour aligner seulement les résidus dans un cutoff du ligand, 0, one le fait pas... > 0... le cutoff
for (i = 1;i < argc;i++) {
if (strcmp("-i",argv[i]) == 0) {strcpy(file_name,argv[i+1]);--help_flag;}
if (strcmp("-h",argv[i]) == 0) {help_flag = 1;}
if (strcmp("-v",argv[i]) == 0) {verbose = 1;}
if (strcmp("-lig",argv[i]) == 0) {lig= 1;}
if (strcmp("-m",argv[i]) == 0) {int temp;sscanf(argv[i+1],"%d",&temp);mode = temp;}
if (strcmp("-nm",argv[i]) == 0) {int temp;sscanf(argv[i+1],"%d",&temp);nb_mode = temp;}
if (strcmp("-ieig",argv[i]) == 0) {strcpy(eigen_name,argv[i+1]);}
if (strcmp("-ligc",argv[i]) == 0) {float temp;sscanf(argv[i+1],"%f",&temp);ligalign = temp;}
}
if (help_flag == 1) {
printf("****************************\nHelp Section\n-i\tFile Input (PDB)\n-v\tVerbose\n-w\tWeight Vector\n-t\tInitial Value of template (negative value for random)\n\tIf Load Template, multiply the template\n-lt\tLoad input template\n-sp\tSuper Node Mode (CA, N, C)\n-kt\tPoid de l'angle entre les nodes (1)\n-kr\tPoid de la distance entre les nodes (1)\n-f\tFile to fit\n****************************\n");
return(0);
}
//***************************************************
//* *
//*Build a structure contaning information on the pdb
//* *
//***************************************************
// Première strucutre
all = count_atom(file_name);
nconn = count_connect(file_name);
if (verbose == 1) {printf("First file:%s\n",file_name);}
if (verbose == 1) {printf("Connect:%d\n",nconn);}
if (verbose == 1) {printf("Assigning Structure\n\tAll Atom\n");}
// Array qui comprend tous les connects
int **connect_h=(int **)malloc(nconn*sizeof(int *));
for(i=0;i<nconn;i++) { connect_h[i]=(int *)malloc(7*sizeof(int));}
assign_connect(file_name,connect_h);
printf("HERE\n");
// Assign tous les atoms
struct pdb_atom strc_all[all];
atom = build_all_strc(file_name,strc_all); // Retourne le nombre de Node
if (verbose == 1) {printf(" Atom:%d\n",all);}
check_lig(strc_all,connect_h,nconn,all);
// Assign les Nodes
if (verbose == 1) {printf(" CA Structure\n");}
if (verbose == 1) {printf(" Node:%d\n",atom);}
struct pdb_atom strc_node[atom];
atom = build_cord_CA(strc_all, strc_node,all,lig,connect_h,nconn);
if (verbose == 1) {printf(" Assign Node:%d\n",atom);}
struct pdb_atom strc_node_t[atom];
copy_strc(strc_node_t, strc_node, atom);
int align[atom];
int score = node_align(strc_node,atom,strc_node_t,atom,align);
if (verbose == 1) {printf("Score: %d/%d\n",score,atom);}
if (score/atom < 0.8) {
printf("Low Score... Will try an homemade alignement !!!\n");
score = node_align_low(strc_node,atom,strc_node_t,atom,align);
}
printf("RMSD:%8.5f Score: %d/%d\n",sqrt(rmsd_no(strc_node,strc_node_t,atom, align)),score,atom);
if (ligalign > 0) {
score = node_align_lig(strc_node,atom,strc_node_t,atom,align,strc_all,all,strc_all,all,ligalign);
printf("RMSD:%8.5f Score: %d/%d\n",sqrt(rmsd_no(strc_node,strc_node_t,atom, align)),score,atom);
}
//***************************************************
//* *
//* Load eigenvector et eigenvalue *
//* *
//***************************************************
if (verbose == 1) {printf("Loading Eigenvector\n");}
gsl_vector *eval = gsl_vector_alloc(3*atom+10);
gsl_matrix *evec = gsl_matrix_alloc (3*atom+10,3*atom+10);
load_eigen(eval,evec,eigen_name,3*atom);
for (k=0;k<nb_mode;++k) {
copy_strc(strc_node_t, strc_node, atom);
apply_eigen(strc_node_t,atom,evec,mode+k-1,1.0);
printf("Mode:%d RMSD:%.4f\n",mode+k,sqrt(rmsd_no(strc_node,strc_node_t,atom, align)));
}
free(connect_h);
return(0);
}
lexeme read_token(buffer_reader *reader) {
lexeme lex;
rune c;
lex.lexeme_type = LEXEME_UNKNOWN;
do {
lex.location = buffer_reader_get_current_pointer(reader);
buffer_reader_skip(reader);
c = *lex.location;
// c = buffer_reader_read_rune(reader);
} while(is_whitespace(c));
if(is_special_symbol(c)) {
lex.lexeme_type = LEXEME_ATOM;
lex.size = 1;
} else if(is_alpha(c)) {
lex.lexeme_type = LEXEME_ATOM;
lex.size = count_atom(reader);
} else if(is_numeric(c)) {
lex.lexeme_type = LEXEME_NUMBER;
lex.size = count_number(reader);
} else {
switch(c) {
case '\'':
lex.lexeme_type = LEXEME_CHAR;
lex.location++;
lex.size = 1;
check_char(reader);
break;
case '"':
lex.lexeme_type = LEXEME_STRING;
lex.location++;
lex.size = count_string(reader);
break;
case '{':
lex.lexeme_type = LEXEME_LEFT_BRACKET;
lex.size = 1;
break;
case '}':
lex.lexeme_type = LEXEME_RIGHT_BRACKET;
lex.size = 1;
break;
case 0x2190: // left arrow
lex.lexeme_type = LEXEME_LEFT_ARROW;
lex.size = 1;
break;
case 0x235D: // up shoe jot
lex.lexeme_type = LEXEME_COMMENT;
lex.size = count_until(reader, '\n') + 1;
break;
default:
printf("Unhandled character in lexer: %4x\n", c);
lex.size = 1;
}
}
return lex;
}
int main(int argc, char *argv[])
{
int all; /*Nombre d'atomes dans pdb*/
int atom; /*Nombre de carbone CA*/
int help_flag = 0;
char file_name[500];
char file_eigen[500] = "eigen.dat";
char check_name[500];
char check_eigen[500] = "eigen_t.dat";
int verbose = 0;
int mode = 6;
float vinit = 1; // Valeur de base
float bond_factor = 1; // Facteur pour poid des bond strechcing
float angle_factor = 1; // Facteur pour poid des angles
double K_phi1 = 1; // Facteurs pour angles dièdres
double K_phi3 = 0.5;
float init_templaate = 1;
float kp_factor = 1; // Facteur pour poid des angles dièdres
char inputname[500] ="none";
char matrix_name[500];
int i, j, k, l;
int nconn;
int lig = 0;
int lig_t = 0;
float factor = 1.0;
for (i = 1;i < argc;i++)
{
if (strcmp("-i",argv[i]) == 0) {strcpy(file_name,argv[i+1]);--help_flag;}
if (strcmp("-t",argv[i]) == 0) {strcpy(check_name,argv[i+1]);--help_flag;}
if (strcmp("-init",argv[i]) == 0) {float temp;sscanf(argv[i+1],"%f",&temp);vinit = temp;}
if (strcmp("-kr",argv[i]) == 0) {float temp;sscanf(argv[i+1],"%f",&temp);bond_factor = temp;}
if (strcmp("-kt",argv[i]) == 0) {float temp;sscanf(argv[i+1],"%f",&temp);angle_factor = temp;}
if (strcmp("-kpf",argv[i]) == 0) {float temp;sscanf(argv[i+1],"%f",&temp); kp_factor = temp;}
if (strcmp("-m",argv[i]) == 0) {strcpy(matrix_name,argv[i+1]);help_flag = 0;}
if (strcmp("-lig",argv[i]) == 0) {lig = 1;}
if (strcmp("-ligt",argv[i]) == 0) {lig_t = 1;}
if (strcmp("-h",argv[i]) == 0) {help_flag = 1;}
if (strcmp("-v",argv[i]) == 0) {verbose = 1;}
}
if (help_flag == 1)
{
printf("****************************\nHelp Section\n-i\tFile Input (PDB)\n-o\tOutput Name Motion\n-ieig\tFile Name Eigen\n-v\tVerbose\n-sp\tSuper Node Mode (CA, N, C)\n-m\tMode\n-nm\tNombre de mode\n-lig\tTient compte duligand (sauf HOH)\n-prox\tAffiche la probabilite que deux CA puissent interagir\n-prev\tAffiche les directions principales du mouvement de chaque CA ponderees par leur ecart-type\n****************************\n");
return(0);
}
//***************************************************
//* *
//*Builds a structure contaning information on the initial pdb structure
//* *
//***************************************************
all = count_atom(file_name);
nconn = count_connect(file_name);
if (verbose == 1) {printf("Connect:%d\n",nconn);}
if (verbose == 1) {printf("Assigning Structure\n\tAll Atom\n");}
// Array with all connects
int **connect_h=(int **)malloc(nconn*sizeof(int *));
for(i=0;i<nconn;i++) { connect_h[i]=(int *)malloc(6*sizeof(int));}
assign_connect(file_name,connect_h);
// Assigns all the atoms
struct pdb_atom strc_all[all];
atom = build_all_strc(file_name,strc_all); // Retourne le nombre de Node
if (atom > 800) {printf("Too much nodes .... To fix, ask [email protected]\n");return(1);}
if (verbose == 1) {printf(" Atom:%d\n",all);}
check_lig(strc_all,connect_h,nconn,all);
// Assigns all Nodes
if (verbose == 1) {printf(" CA Structure\n");}
if (verbose == 1) {printf(" Node:%d\n",atom);}
struct pdb_atom strc_node[atom];
atom = build_cord_CA(strc_all, strc_node,all,lig,connect_h,nconn);
if (verbose == 1) {printf(" Assign Node:%d\n",atom);}
// Free Connect
//for(i=0;i<nconn;i++) {printf("I:%d\n",i);free(connect_h[i]);}
//free(connect_h);
printf("Check 1\n");
//***************************************************
//* *
//*Builds a structure contaning information on the target pdb structure
//* *
//***************************************************
nconn = 0;
int all_t = count_atom(check_name);
nconn = count_connect(check_name);
if (verbose == 1) {printf("Connect:%d\n",nconn);}
if (verbose == 1) {printf("Assigning Structure\n\tAll Atom\n");}
// Array with all connects
int **connect_t=(int **)malloc(nconn*sizeof(int *));
for(i=0;i<nconn;i++) { connect_t[i]=(int *)malloc(6*sizeof(int));}
assign_connect(check_name,connect_t);
// Assigns all the atoms
struct pdb_atom strc_all_t[all_t];
int atom_t = build_all_strc(check_name,strc_all_t); // Retourne le nombre de Node
if (atom_t > 800) {printf("Too much node.... To fix, ask [email protected]\n");return(1);}
if (verbose == 1) {printf(" Atom:%d\n",all_t);}
check_lig(strc_all_t,connect_t,nconn,all_t);
// Assigns all Nodes
if (verbose == 1) {printf(" CA Structure\n");}
if (verbose == 1) {printf(" Node:%d\n",atom_t);}
struct pdb_atom strc_node_t[atom_t];
atom_t = build_cord_CA(strc_all_t, strc_node_t,all_t,lig_t,connect_t,nconn);
if (verbose == 1) {printf(" Assign Node:%d\n",atom_t);}
printf("Check 2\n");
//***************************************************
//* *
//*Aligns both structures *
//* *
//***************************************************
int align[atom];
int score = node_align(strc_node,atom,strc_node_t,atom_t,align);
printf("RMSD:%8.5f Score: %d/%d\n",sqrt(rmsd_no(strc_node,strc_node_t,atom, align)),score,atom);
if ((float)score/(float)atom < 0.8)
{
printf("Low Score... Will try an homemade alignement !!!\n");
score = node_align_onechain(strc_node,atom,strc_node_t,atom_t,align);
printf("RMSD:%8.5f Score: %d/%d\n",sqrt(rmsd_no(strc_node,strc_node_t,atom, align)),score,atom);
}
if ((float)score/(float)atom < 0.8)
{
printf("Low Score... Will try an homemade alignement !!!\n");
score = node_align_low(strc_node,atom,strc_node_t,atom_t,align);
printf("RMSD:%8.5f Score: %d/%d\n",sqrt(rmsd_no(strc_node,strc_node_t,atom, align)),score,atom);
}
printf("RMSD:%8.5f Score: %d/%d\n",sqrt(rmsd_yes(strc_node,strc_node_t,atom, align,strc_all,all)),score,atom);
printf("Check 4\n");
//***************************************************
//* *
//*Build hessian matrices *
//* *
//***************************************************
double **hessian=(double **)malloc(3*atom*sizeof(double *)); // Matrix of the Hessian 1 2 3 (bond, angle, dihedral)
for(i=0;i<3*atom;i++) { hessian[i]=(double *)malloc(3*atom*sizeof(double));}
for(i=0;i<3*atom;i++)for(j=0;j<(3*atom);j++){hessian[i][j]=0;}
gsl_matrix *hess = gsl_matrix_alloc(3*atom,3*atom);
gsl_matrix_set_all(hess, 0);
gsl_matrix *hess_t = gsl_matrix_alloc(3*atom_t,3*atom_t);
gsl_matrix_set_all(hess_t, 0);
assign_atom_type(strc_all, all);
if (strcmp(inputname,"none") == 0) {} else {assign_lig_type(strc_all, all, inputname);}
gsl_matrix *vcon = gsl_matrix_alloc(all,all);
gsl_matrix *inter_m = gsl_matrix_alloc(8,8);
gsl_matrix *templaate = gsl_matrix_alloc(atom*3, atom*3);
gsl_matrix_set_all(templaate,vinit);
gsl_matrix_set_all(vcon,0);
if (verbose == 1) {printf("Do Vcon !!!\n");}
vcon_file_dom(strc_all,vcon,all);
if (verbose == 1) {printf("Reading Interaction Matrix %s\n",matrix_name);}
load_matrix(inter_m,matrix_name);
//write_matrix("vcon_vince.dat", vcon,all,all);
if (verbose == 1) {printf("Building templaate\n");}
all_interaction(strc_all,all, atom, templaate,lig,vcon,inter_m,strc_node);
gsl_matrix_scale (templaate, init_templaate);
if (verbose == 1) {printf("Building Hessian\n");}
if (verbose == 1) {printf("\tCovalent Bond Potential\n");}
build_1st_matrix(strc_node,hessian,atom,bond_factor);
if (verbose == 1) {printf("\tAngle Potential\n");}
build_2_matrix(strc_node,hessian,atom,angle_factor);
if (verbose == 1) {printf("\tDihedral Potential\n");}
build_3_matrix(strc_node, hessian,atom,K_phi1/2+K_phi3*9/2,kp_factor);
if (verbose == 1) {printf("\tNon Local Interaction Potential\n");}
build_4h_matrix(strc_node,hessian,atom,1.0,templaate);
if (verbose == 1) {printf("\tAssigning Array\n");}
assignArray(hess,hessian,3*atom,3*atom);
gsl_matrix_free(vcon);
gsl_matrix_free(templaate);
double **hessian_t=(double **)malloc(3*atom_t*sizeof(double *)); // Matrix of the Hessian 1 2 3 (bond, angle, dihedral)
for(i=0;i<3*atom_t;i++) { hessian_t[i]=(double *)malloc(3*atom_t*sizeof(double));}
for(i=0;i<3*atom_t;i++)for(j=0;j<(3*atom_t);j++){hessian_t[i][j]=0;}
assign_atom_type(strc_all_t, all_t);
if (strcmp(inputname,"none") == 0) {} else {assign_lig_type(strc_all_t, all_t, inputname);}
gsl_matrix *vcon_t = gsl_matrix_alloc(all_t,all_t);
gsl_matrix *templaate_t = gsl_matrix_alloc(atom_t*3, atom_t*3);
gsl_matrix_set_all(templaate_t,vinit);
gsl_matrix_set_all(vcon_t,0);
if (verbose == 1) {printf("Do Vcon !!!\n");}
vcon_file_dom(strc_all_t,vcon_t,all_t);
//write_matrix("vcon_vince.dat", vcon,all,all);
if (verbose == 1) {printf("Building templaate\n");}
all_interaction(strc_all_t,all_t, atom_t, templaate_t,lig,vcon_t,inter_m,strc_node_t);
gsl_matrix_scale (templaate_t, init_templaate);
if (verbose == 1) {printf("Building Hessian\n");}
if (verbose == 1) {printf("\tCovalent Bond Potential\n");}
build_1st_matrix(strc_node_t,hessian_t,atom_t,bond_factor);
if (verbose == 1) {printf("\tAngle Potential\n");}
build_2_matrix(strc_node_t,hessian_t,atom_t,angle_factor);
if (verbose == 1) {printf("\tDihedral Potential\n");}
build_3_matrix(strc_node_t, hessian_t,atom_t,K_phi1/2+K_phi3*9/2,kp_factor);
if (verbose == 1) {printf("\tNon Local Interaction Potential\n");}
build_4h_matrix(strc_node_t,hessian_t,atom_t,1.0,templaate_t);
if (verbose == 1) {printf("\tAssigning Array\n");}
assignArray(hess_t,hessian_t,3*atom_t,3*atom_t);
gsl_matrix_free(vcon_t);
gsl_matrix_free(templaate_t);
printf("Check 5\n");
//***************************************************
//* *
//*Build mini hessian matrices *
//* *
//***************************************************
gsl_matrix *mini_hess = gsl_matrix_alloc(3*score, 3*score);
gsl_matrix_set_all(mini_hess, 0);
gsl_matrix *mini_hess_t = gsl_matrix_alloc(3*score, 3*score);
gsl_matrix_set_all(mini_hess_t, 0);
int sup_line = 0;
int sup_to_node[score];
for(i = 0; i < atom; i++)
{
if(align[i] == -1) {continue;}
sup_to_node[sup_line] = i;
int sup_col = 0;
for(j = 0; j < atom; j++)
{
if(align[j] == -1) {continue;}
for(k = 0; k < 3; k++)
{
for(l = 0; l < 3; l++)
{
gsl_matrix_set(mini_hess, 3*sup_line + k, 3*sup_col + l, gsl_matrix_get(hess, 3*i + k, 3*j + l));
gsl_matrix_set(mini_hess_t, 3*sup_line + k, 3*sup_col + l, gsl_matrix_get(hess_t, 3*align[i] + k, 3*align[j] + l));
}
}
sup_col ++;
}
sup_line++;
}
gsl_matrix_free(hess);
gsl_matrix_free(hess_t);
printf("Check 6\n");
gsl_vector *mini_eval = gsl_vector_alloc(3*score);
gsl_matrix *mini_evec = gsl_matrix_alloc (3*score,3*score);
gsl_vector *mini_eval_t = gsl_vector_alloc(3*score);
gsl_matrix *mini_evec_t = gsl_matrix_alloc (3*score,3*score);
diagonalyse_matrix(mini_hess,3*score,mini_eval,mini_evec);
diagonalyse_matrix(mini_hess_t,3*score,mini_eval_t,mini_evec_t);
gsl_matrix_set_all(mini_hess, 0);
gsl_matrix_set_all(mini_hess_t, 0);
for(i = 0; i < 3*score; i++)
{
if(gsl_vector_get(mini_eval, i) > 0.0000001)
{
gsl_vector_set(mini_eval, i, 1.0 / gsl_vector_get(mini_eval, i));
for(j = 0; j < 3*score; j++)
{
for(k = 0; k < 3*score; k++)
{
gsl_matrix_set(mini_hess, j, k, gsl_matrix_get(mini_hess, j, k) + gsl_matrix_get(mini_evec, j, i)*gsl_matrix_get(mini_evec, k, i)*gsl_vector_get(mini_eval, i));
}
}
}
}
for(i = 0; i < 3*score; i++)
{
if(gsl_vector_get(mini_eval_t, i) > 0.0000001)
{
gsl_vector_set(mini_eval_t, i, 1.0 / gsl_vector_get(mini_eval_t, i));
for(j = 0; j < 3*score; j++)
{
for(k = 0; k < 3*score; k++)
{
gsl_matrix_set(mini_hess_t, j, k, gsl_matrix_get(mini_hess_t, j, k) + gsl_matrix_get(mini_evec_t, j, i)*gsl_matrix_get(mini_evec_t, k, i)*gsl_vector_get(mini_eval_t, i));
}
}
}
}
printf("Check 7\n");
printf("Dynamic distance : %1.10f\n", cmp_gauss(mini_hess, mini_eval, mini_hess_t, mini_eval_t, 3*score));
gsl_matrix_free(mini_hess);
gsl_matrix_free(mini_evec);
gsl_vector_free(mini_eval);
gsl_matrix_free(mini_hess_t);
gsl_matrix_free(mini_evec_t);
gsl_vector_free(mini_eval_t);
free(connect_h);
return(1);
}
int main(int argc, char *argv[])
{
int all; /*Number of atoms in the initial PDB*/
int atom; /*Number of initial CAs*/
int all_t; /*Number of atoms in the target PDB*/
int atom_t; /*Number of target CAs*/
int help_flag = 1;
char file_name[500];
char matrix_name[500];
char check_name[500];
int print_inter = 0;
int print_inter_t = 0;
char out_name[500];
char out_name_t[500];
char out_movie[500];
int print_movie = 0;
int verbose = 0;
float vinit = 1; // Valeur de base
float bond_factor = 1; // Facteur pour poid des bond strechcing
float angle_factor = 1; // Facteur pour poid des angles
double K_phi1 = 1; // Facteurs pour angles dièdres
double K_phi3 = 0.5;
float init_templaate = 1;
float kp_factor = 1; // Facteur pour poid des angles dièdres
char inputname[500] ="none";
double beta = 0.000005;
int morph = 0;
char morph_name[500];
int change_density = 0;
int i,j,k,l;
int lig = 0;
int ligt = 0;
int nconn;
int print_flag = 0;
float ligalign = 0; // Flag/valeur pour aligner seulement les résidus dans un cutoff du ligand, 0, one le fait pas... > 0... le cutoff
for (i = 1;i < argc;i++) {
if (strcmp("-i",argv[i]) == 0) {strcpy(file_name,argv[i+1]);--help_flag;}
if (strcmp("-h",argv[i]) == 0) {help_flag = 1;}
if (strcmp("-v",argv[i]) == 0) {verbose = 1;}
if (strcmp("-lig",argv[i]) == 0) {lig= 1;}
if (strcmp("-ligt",argv[i]) == 0) {ligt= 1;}
if (strcmp("-init",argv[i]) == 0) {float temp;sscanf(argv[i+1],"%f",&temp);vinit = temp;}
if (strcmp("-kr",argv[i]) == 0) {float temp;sscanf(argv[i+1],"%f",&temp);bond_factor = temp;}
if (strcmp("-kt",argv[i]) == 0) {float temp;sscanf(argv[i+1],"%f",&temp);angle_factor = temp;}
if (strcmp("-kpf",argv[i]) == 0) {float temp;sscanf(argv[i+1],"%f",&temp); kp_factor = temp;}
if (strcmp("-b",argv[i]) == 0) {float temp;sscanf(argv[i+1],"%f",&temp);beta = temp;}
if (strcmp("-t",argv[i]) == 0) {strcpy(check_name,argv[i+1]);help_flag = 0;}
if (strcmp("-m",argv[i]) == 0) {strcpy(matrix_name,argv[i+1]);help_flag = 0;}
if (strcmp("-o",argv[i]) == 0) {strcpy(out_name,argv[i+1]); print_inter = 1;}
if (strcmp("-ot",argv[i]) == 0) {strcpy(out_name_t,argv[i+1]); print_inter_t = 1;}
if (strcmp("-om",argv[i]) == 0) {strcpy(out_movie,argv[i+1]); print_movie = 1;}
if (strcmp("-ligc",argv[i]) == 0) {float temp;sscanf(argv[i+1],"%f",&temp);ligalign = temp;}
if (strcmp("-conf",argv[i]) == 0) {change_density = 1;}
if (strcmp("-morph",argv[i]) == 0) {strcpy(morph_name,argv[i+1]); morph = 1;}
}
if (help_flag == 1)
{
printf("****************************\nHelp Section\n-i\tFile Input (PDB)\n-v\tVerbose\n-w\tWeight Vector\n-t\tInitial Value of template (negative value for random)\n\tIf Load Template, multiply the template\n-lt\tLoad input template\n-sp\tSuper Node Mode (CA, N, C)\n-kt\tPoid de l'angle entre les nodes (1)\n-kr\tPoid de la distance entre les nodes (1)\n-f\tFile to fit\n****************************\n");
return(0);
}
//***************************************************
//* *
//*Builds a structure contaning information on the initial pdb structure
//* *
//***************************************************
all = count_atom(file_name);
nconn = count_connect(file_name);
if (verbose == 1) {printf("Connect:%d\n",nconn);}
if (verbose == 1) {printf("Assigning Structure\n\tAll Atom\n");}
// Array with all connects
int **connect_h=(int **)malloc(nconn*sizeof(int *));
for(i=0;i<nconn;i++) { connect_h[i]=(int *)malloc(6*sizeof(int));}
assign_connect(file_name,connect_h);
// Assigns all the atoms
struct pdb_atom strc_all[all];
atom = build_all_strc(file_name,strc_all); // Retourne le nombre de Node
if (atom > 800) {printf("Too much nodes .... To fix, ask [email protected]\n");return(1);}
if (verbose == 1) {printf(" Atom:%d\n",all);}
check_lig(strc_all,connect_h,nconn,all);
// Assigns all Nodes
if (verbose == 1) {printf(" CA Structure\n");}
if (verbose == 1) {printf(" Node:%d\n",atom);}
struct pdb_atom strc_node[atom];
atom = build_cord_CA(strc_all, strc_node,all,lig,connect_h,nconn);
if (verbose == 1) {printf(" Assign Node:%d\n",atom);}
// Free Connect
//for(i=0;i<nconn;i++) {printf("I:%d\n",i);free(connect_h[i]);}
//free(connect_h);
//***************************************************
//* *
//*Builds a structure contaning information on the target pdb structure
//* *
//***************************************************
nconn = 0;
all_t = count_atom(check_name);
nconn = count_connect(check_name);
if (verbose == 1) {printf("Connect:%d\n",nconn);}
if (verbose == 1) {printf("Assigning Structure\n\tAll Atom\n");}
// Array with all connects
int **connect_t=(int **)malloc(nconn*sizeof(int *));
for(i=0;i<nconn;i++) { connect_t[i]=(int *)malloc(6*sizeof(int));}
assign_connect(check_name,connect_t);
// Assigns all the atoms
struct pdb_atom strc_all_t[all_t];
atom_t = build_all_strc(check_name,strc_all_t); // Retourne le nombre de Node
if (atom_t > 800) {printf("Too much node.... To fix, ask [email protected]\n");return(1);}
if (verbose == 1) {printf(" Atom:%d\n",all_t);}
check_lig(strc_all_t,connect_t,nconn,all_t);
// Assigns all Nodes
if (verbose == 1) {printf(" CA Structure\n");}
if (verbose == 1) {printf(" Node:%d\n",atom_t);}
struct pdb_atom strc_node_t[atom_t];
atom_t = build_cord_CA(strc_all_t, strc_node_t,all_t,ligt,connect_t,nconn);
if (verbose == 1) {printf(" Assign Node:%d\n",atom_t);}
//***************************************************
//* *
//*Aligns both structures
//* *
//***************************************************
int align[atom];
int score = node_align(strc_node,atom,strc_node_t,atom_t,align);
printf("RMSD:%8.5f Score: %d/%d\n",sqrt(rmsd_no(strc_node,strc_node_t,atom, align)),score,atom);
if ((float)score/(float)atom < 0.8)
{
printf("Low Score... Will try an homemade alignement !!!\n");
score = node_align_onechain(strc_node,atom,strc_node_t,atom_t,align);
printf("RMSD:%8.5f Score: %d/%d\n",sqrt(rmsd_no(strc_node,strc_node_t,atom, align)),score,atom);
}
if ((float)score/(float)atom < 0.8)
{
printf("Low Score... Will try an homemade alignement !!!\n");
score = node_align_low(strc_node,atom,strc_node_t,atom_t,align);
printf("RMSD:%8.5f Score: %d/%d\n",sqrt(rmsd_no(strc_node,strc_node_t,atom, align)),score,atom);
}
if (ligalign > 0)
{
score = node_align_lig(strc_node,atom,strc_node_t,atom_t,align,strc_all,all,strc_all_t,all_t,ligalign);
printf("RMSD:%8.5f Score: %d/%d\n",sqrt(rmsd_no(strc_node,strc_node_t,atom, align)),score,atom);
}
printf("RMSD:%8.5f Score: %d/%d\n",sqrt(rmsd_yes(strc_node,strc_node_t,atom, align,strc_all,all)),score,atom);
// Build hessians
double **hessian=(double **)malloc(3*atom*sizeof(double *)); // Matrix of the Hessian 1 2 3 (bond, angle, dihedral)
for(i=0;i<3*atom;i++) { hessian[i]=(double *)malloc(3*atom*sizeof(double));}
for(i=0;i<3*atom;i++)for(j=0;j<(3*atom);j++){hessian[i][j]=0;}
gsl_matrix *hess = gsl_matrix_alloc(3*atom,3*atom);
gsl_matrix_set_all(hess, 0);
gsl_matrix *hess_t = gsl_matrix_alloc(3*atom_t,3*atom_t);
gsl_matrix_set_all(hess_t, 0);
assign_atom_type(strc_all, all);
if (strcmp(inputname,"none") == 0) {} else {assign_lig_type(strc_all, all, inputname);}
gsl_matrix *vcon = gsl_matrix_alloc(all,all);
gsl_matrix *inter_m = gsl_matrix_alloc(8,8);
gsl_matrix *templaate = gsl_matrix_alloc(atom*3, atom*3);
gsl_matrix_set_all(templaate,vinit);
gsl_matrix_set_all(vcon,0);
if (verbose == 1) {printf("Do Vcon !!!\n");}
vcon_file_dom(strc_all,vcon,all);
if (verbose == 1) {printf("Reading Interaction Matrix %s\n",matrix_name);}
load_matrix(inter_m,matrix_name);
//write_matrix("vcon_vince.dat", vcon,all,all);
if (verbose == 1) {printf("Building templaate\n");}
all_interaction(strc_all,all, atom, templaate,lig,vcon,inter_m,strc_node);
gsl_matrix_scale (templaate, init_templaate);
if (verbose == 1) {printf("Building Hessian\n");}
if (verbose == 1) {printf("\tCovalent Bond Potential\n");}
build_1st_matrix(strc_node,hessian,atom,bond_factor);
if (verbose == 1) {printf("\tAngle Potential\n");}
build_2_matrix(strc_node,hessian,atom,angle_factor);
if (verbose == 1) {printf("\tDihedral Potential\n");}
build_3_matrix(strc_node, hessian,atom,K_phi1/2+K_phi3*9/2,kp_factor);
if (verbose == 1) {printf("\tNon Local Interaction Potential\n");}
build_4h_matrix(strc_node,hessian,atom,1.0,templaate);
if (verbose == 1) {printf("\tAssigning Array\n");}
assignArray(hess,hessian,3*atom,3*atom);
gsl_matrix_free(vcon);
gsl_matrix_free(templaate);
double **hessian_t=(double **)malloc(3*atom_t*sizeof(double *)); // Matrix of the Hessian 1 2 3 (bond, angle, dihedral)
for(i=0;i<3*atom_t;i++) { hessian_t[i]=(double *)malloc(3*atom_t*sizeof(double));}
for(i=0;i<3*atom_t;i++)for(j=0;j<(3*atom_t);j++){hessian_t[i][j]=0;}
assign_atom_type(strc_all_t, all_t);
if (strcmp(inputname,"none") == 0) {} else {assign_lig_type(strc_all_t, all_t, inputname);}
gsl_matrix *vcon_t = gsl_matrix_alloc(all_t,all_t);
gsl_matrix *templaate_t = gsl_matrix_alloc(atom_t*3, atom_t*3);
gsl_matrix_set_all(templaate_t,vinit);
gsl_matrix_set_all(vcon_t,0);
if (verbose == 1) {printf("Do Vcon !!!\n");}
vcon_file_dom(strc_all_t,vcon_t,all_t);
//write_matrix("vcon_vince.dat", vcon,all,all);
if (verbose == 1) {printf("Building templaate\n");}
all_interaction(strc_all_t,all_t, atom_t, templaate_t,lig,vcon_t,inter_m,strc_node_t);
gsl_matrix_scale (templaate_t, init_templaate);
if (verbose == 1) {printf("Building Hessian\n");}
if (verbose == 1) {printf("\tCovalent Bond Potential\n");}
build_1st_matrix(strc_node_t,hessian_t,atom_t,bond_factor);
if (verbose == 1) {printf("\tAngle Potential\n");}
build_2_matrix(strc_node_t,hessian_t,atom_t,angle_factor);
if (verbose == 1) {printf("\tDihedral Potential\n");}
build_3_matrix(strc_node_t, hessian_t,atom_t,K_phi1/2+K_phi3*9/2,kp_factor);
if (verbose == 1) {printf("\tNon Local Interaction Potential\n");}
build_4h_matrix(strc_node_t,hessian_t,atom_t,1.0,templaate_t);
if (verbose == 1) {printf("\tAssigning Array\n");}
assignArray(hess_t,hessian_t,3*atom_t,3*atom_t);
gsl_matrix_free(vcon_t);
gsl_matrix_free(templaate_t);
printf("Check 1\n");
// Build mini-hessians (calculated mini_hess object is equal to mini_hess + mini_hess_t
gsl_matrix *mini_hess = gsl_matrix_alloc(3*score, 3*score);
gsl_matrix_set_all(mini_hess, 0);
gsl_matrix *mini_hess_i = gsl_matrix_alloc(3*score, 3*score);
gsl_matrix_set_all(mini_hess_i, 0);
gsl_matrix *mini_hess_t = gsl_matrix_alloc(3*score, 3*score);
gsl_matrix_set_all(mini_hess_t, 0);
int sup_line = 0;
int sup_to_node[score];
for(i = 0; i < atom; i++)
{
if(align[i] == -1) {continue;}
sup_to_node[sup_line] = i;
int sup_col = 0;
for(j = 0; j < atom; j++)
{
if(align[j] == -1) {continue;}
for(k = 0; k < 3; k++)
{
for(l = 0; l < 3; l++)
{
gsl_matrix_set(mini_hess_i, 3*sup_line + k, 3*sup_col + l, gsl_matrix_get(hess, 3*i + k, 3*j + l));
gsl_matrix_set(mini_hess, 3*sup_line + k, 3*sup_col + l, gsl_matrix_get(hess, 3*i + k, 3*j + l) + gsl_matrix_get(hess_t, 3*align[i] + k, 3*align[j] + l));
gsl_matrix_set(mini_hess_t, 3*sup_line + k, 3*sup_col + l, gsl_matrix_get(hess_t, 3*align[i] + k, 3*align[j] + l));
}
}
sup_col ++;
}
sup_line++;
}
gsl_matrix_free(hess);
gsl_matrix_free(hess_t);
printf("Check 2\n");
// Invert mini_hess
gsl_vector *eval2 = gsl_vector_alloc(3*score);
gsl_matrix *evec2 = gsl_matrix_alloc (3*score,3*score);
diagonalyse_matrix(mini_hess, 3*score, eval2, evec2);
gsl_matrix_set_all(mini_hess, 0);
for(i = 0; i < 3*score; i++)
{
if(gsl_vector_get(eval2, i) > 0.00001)
{
for(j = 0; j < 3*score; j++)
{
for(k = 0; k < 3*score; k++)
{
gsl_matrix_set(mini_hess, j, k, gsl_matrix_get(mini_hess, j, k) + gsl_matrix_get(evec2, j, i)*gsl_matrix_get(evec2, k, i)/gsl_vector_get(eval2, i));
}
}
}
}
gsl_matrix_free(evec2);
gsl_vector_free(eval2);
printf("Check 3\n");
// Evaluate delta-conf of init to most stable transitionnal conformer and store delta-conf of init to target.
gsl_vector *del_conf = gsl_vector_alloc(3*score);
gsl_vector_set_all(del_conf, 0);
gsl_vector *copy_conf = gsl_vector_alloc(3*score);
for(i = 0; i < score; i++)
{
gsl_vector_set(copy_conf, 3*i, strc_node_t[align[i]].x_cord - strc_node[i].x_cord);
gsl_vector_set(copy_conf, 3*i + 1, strc_node_t[align[i]].y_cord - strc_node[i].y_cord);
gsl_vector_set(copy_conf, 3*i + 2, strc_node_t[align[i]].z_cord - strc_node[i].z_cord);
}
for(i = 0; i < 3*score; i++)
{
for(j = 0; j < 3*score; j++)
{
gsl_vector_set(del_conf, i, gsl_vector_get(del_conf, i) + gsl_matrix_get(mini_hess_t, i, j)*gsl_vector_get(copy_conf, j));
}
}
for(i = 0; i < 3*score; i++)
{
gsl_vector_set(copy_conf, i, gsl_vector_get(del_conf, i));
}
gsl_vector_set_all(del_conf, 0);
for(i = 0; i < 3*score; i++)
{
for(j = 0; j < 3*score; j++)
{
gsl_vector_set(del_conf, i, gsl_vector_get(del_conf, i) + gsl_matrix_get(mini_hess, i, j)*gsl_vector_get(copy_conf, j));
}
}
for(i = 0; i < score; i++)
{
gsl_vector_set(copy_conf, 3*i, strc_node_t[align[i]].x_cord - strc_node[i].x_cord);
gsl_vector_set(copy_conf, 3*i + 1, strc_node_t[align[i]].y_cord - strc_node[i].y_cord);
gsl_vector_set(copy_conf, 3*i + 2, strc_node_t[align[i]].z_cord - strc_node[i].z_cord);
}
printf("Check 4\n");
// Translate all the nodes (and all its atoms) of both structures to delta-conf of most stable conformer.
for(i = 0; i < score; i++)
{
for(j = 0; j < all; j++)
{
if(strc_all[j].node == sup_to_node[i])
{
strc_all[j].x_cord += gsl_vector_get(del_conf, 3*i);
strc_all[j].y_cord += gsl_vector_get(del_conf, 3*i + 1);
strc_all[j].z_cord += gsl_vector_get(del_conf, 3*i + 2);
}
}
for(j = 0; j < all_t; j++)
{
if(strc_all_t[j].node == align[sup_to_node[i]])
{
strc_all_t[j].x_cord += gsl_vector_get(del_conf, 3*i) - gsl_vector_get(copy_conf, 3*i);
strc_all_t[j].y_cord += gsl_vector_get(del_conf, 3*i + 1) - gsl_vector_get(copy_conf, 3*i + 1);
strc_all_t[j].z_cord += gsl_vector_get(del_conf, 3*i + 2) - gsl_vector_get(copy_conf, 3*i + 2);
}
}
}
gsl_matrix_free(mini_hess);
printf("Check 5\n");
int aligned[atom_t];
for(i = 0; i < atom_t; i++)
{
aligned[i] = -1;
}
for(i = 0; i < atom; i++)
{
if(align[i] != -1)
{
aligned[align[i]] = 1;
}
}
// Print transition from init
if(print_inter == 1)
{
FILE *out_file;
out_file = fopen(out_name, "w");
for (i = 0; i < all; i++)
{
if(align[strc_all[i].node] != -1)
{
if (strc_all[i].atom_type == 1) {fprintf(out_file,"ATOM ");}
if (strc_all[i].atom_type == 2) {fprintf(out_file,"HETATM");}
if (strc_all[i].atom_type == 3) {fprintf(out_file,"HETATM");}
fprintf(out_file,"%5.d %s%s %s%4.d%12.3f%8.3f%8.3f 1.00 %2.2f\n",
strc_all[i].atom_number,
strc_all[i].atom_prot_type,
strc_all[i].res_type,
strc_all[i].chain,
strc_all[i].res_number,
strc_all[i].x_cord,
strc_all[i].y_cord,
strc_all[i].z_cord,
strc_all[i].b_factor
);
}
}
fclose(out_file);
}
printf("Check 6\n");
// Print transition from target
if(print_inter_t == 1)
{
FILE *out_file_t;
out_file_t = fopen(out_name_t, "w");
for (i = 0; i < all_t; i++)
{
if(aligned[strc_all_t[i].node] != -1)
{
if (strc_all_t[i].atom_type == 1) {fprintf(out_file_t,"ATOM ");}
if (strc_all_t[i].atom_type == 2) {fprintf(out_file_t,"HETATM");}
if (strc_all_t[i].atom_type == 3) {fprintf(out_file_t,"HETATM");}
fprintf(out_file_t,"%5.d %s%s %s%4.d%12.3f%8.3f%8.3f 1.00 %2.2f\n",
strc_all_t[i].atom_number,
strc_all_t[i].atom_prot_type,
strc_all_t[i].res_type,
strc_all_t[i].chain,
strc_all_t[i].res_number,
strc_all_t[i].x_cord,
strc_all_t[i].y_cord,
strc_all_t[i].z_cord,
strc_all_t[i].b_factor
);
}
}
fclose(out_file_t);
}
printf("Check 7\n");
// Translate all the nodes (and all its atoms) of init structure back to its original conformation.
for(i = 0; i < score; i++)
{
for(j = 0; j < all; j++)
{
if(strc_all[j].node == sup_to_node[i])
{
strc_all[j].x_cord -= gsl_vector_get(del_conf, 3*i);
strc_all[j].y_cord -= gsl_vector_get(del_conf, 3*i + 1);
strc_all[j].z_cord -= gsl_vector_get(del_conf, 3*i + 2);
}
}
}
// Print transition from init to target passing by inter
if(print_movie == 1)
{
FILE *out_file_m;
out_file_m = fopen(out_movie, "w");
for(j = 0; j < 30; j++)
{
fprintf(out_file_m, "Model %1i\n", j + 1);
for (i = 0; i < all; i++)
{
if(align[strc_all[i].node] != -1)
{
if (strc_all[i].atom_type == 1) {fprintf(out_file_m,"ATOM ");}
if (strc_all[i].atom_type == 2) {fprintf(out_file_m,"HETATM");}
if (strc_all[i].atom_type == 3) {fprintf(out_file_m,"HETATM");}
fprintf(out_file_m,"%5.d %s%s %s%4.d%12.3f%8.3f%8.3f 1.00 %2.2f\n",
strc_all[i].atom_number,
strc_all[i].atom_prot_type,
strc_all[i].res_type,
strc_all[i].chain,
strc_all[i].res_number,
strc_all[i].x_cord,
strc_all[i].y_cord,
strc_all[i].z_cord,
strc_all[i].b_factor
);
}
}
fprintf(out_file_m, "TER\nENDMDL\n\n");
for(i = 0; i < score; i++)
{
for(k = 0; k < all; k++)
{
if(strc_all[k].node == sup_to_node[i])
{
strc_all[k].x_cord += gsl_vector_get(del_conf, 3*i)/30.0;
strc_all[k].y_cord += gsl_vector_get(del_conf, 3*i + 1)/30.0;
strc_all[k].z_cord += gsl_vector_get(del_conf, 3*i + 2)/30.0;
}
}
}
}
for(j = 0; j < 31; j++)
{
fprintf(out_file_m, "Model %1i\n", j + 31);
for (i = 0; i < all_t; i++)
{
if(aligned[strc_all_t[i].node] != -1)
{
if (strc_all_t[i].atom_type == 1) {fprintf(out_file_m,"ATOM ");}
if (strc_all_t[i].atom_type == 2) {fprintf(out_file_m,"HETATM");}
if (strc_all_t[i].atom_type == 3) {fprintf(out_file_m,"HETATM");}
fprintf(out_file_m,"%5.d %s%s %s%4.d%12.3f%8.3f%8.3f 1.00 %2.2f\n",
strc_all_t[i].atom_number,
strc_all_t[i].atom_prot_type,
strc_all_t[i].res_type,
strc_all_t[i].chain,
strc_all_t[i].res_number,
strc_all_t[i].x_cord,
strc_all_t[i].y_cord,
strc_all_t[i].z_cord,
strc_all_t[i].b_factor
);
}
}
fprintf(out_file_m, "TER\nENDMDL\n\n");
for(i = 0; i < score; i++)
{
for(k = 0; k < all_t; k++)
{
if(strc_all_t[k].node == align[sup_to_node[i]])
{
strc_all_t[k].x_cord -= (gsl_vector_get(del_conf, 3*i) - gsl_vector_get(copy_conf, 3*i))/30.0;
strc_all_t[k].y_cord -= (gsl_vector_get(del_conf, 3*i + 1) - gsl_vector_get(copy_conf, 3*i + 1))/30.0;
strc_all_t[k].z_cord -= (gsl_vector_get(del_conf, 3*i + 2) - gsl_vector_get(copy_conf, 3*i + 2))/30.0;
}
}
}
}
fclose(out_file_m);
}
printf("Check 8\n");
// Translate all the nodes (and all its atoms) of init structure back to its original conformation if print_movie == 1
if(print_movie == 1)
{
for(i = 0; i < score; i++)
{
for(j = 0; j < all; j++)
{
if(strc_all[j].node == sup_to_node[i])
{
strc_all[j].x_cord -= gsl_vector_get(del_conf, 3*i);
strc_all[j].y_cord -= gsl_vector_get(del_conf, 3*i + 1);
strc_all[j].z_cord -= gsl_vector_get(del_conf, 3*i + 2);
}
}
}
}
printf("Check 8.1\n");
// Print transition from init to target by morphing
if(morph == 1)
{
FILE *out_file_morph;
out_file_morph = fopen(morph_name, "w");
printf("Check 8.2\n");
for(j = 0; j < 60; j++)
{
fprintf(out_file_morph, "Model %1i\n", j + 1);
for (i = 0; i < all; i++)
{
if(align[strc_all[i].node] != -1)
{
if (strc_all[i].atom_type == 1) {fprintf(out_file_morph,"ATOM ");}
if (strc_all[i].atom_type == 2) {fprintf(out_file_morph,"HETATM");}
if (strc_all[i].atom_type == 3) {fprintf(out_file_morph,"HETATM");}
fprintf(out_file_morph,"%5.d %s%s %s%4.d%12.3f%8.3f%8.3f 1.00 %2.2f\n",
strc_all[i].atom_number,
strc_all[i].atom_prot_type,
strc_all[i].res_type,
strc_all[i].chain,
strc_all[i].res_number,
strc_all[i].x_cord,
strc_all[i].y_cord,
strc_all[i].z_cord,
strc_all[i].b_factor
);
}
}
fprintf(out_file_morph, "TER\nENDMDL\n\n");
printf("Check 8.3\n");
for(i = 0; i < score; i++)
{
for(k = 0; k < all; k++)
{
if(strc_all[k].node == sup_to_node[i])
{
strc_all[k].x_cord += gsl_vector_get(copy_conf, 3*i)/60.0;
strc_all[k].y_cord += gsl_vector_get(copy_conf, 3*i + 1)/60.0;
strc_all[k].z_cord += gsl_vector_get(copy_conf, 3*i + 2)/60.0;
}
}
}
printf("Check 8.4\n");
}
fclose(out_file_morph);
}
printf("Check 9\n");
// Evaluate theoretical delta-G
gsl_vector *dummy_conf = gsl_vector_alloc(3*score);
gsl_vector_set_all(dummy_conf, 0);
gsl_vector *dummy_conf_t = gsl_vector_alloc(3*score);
gsl_vector_set_all(dummy_conf_t, 0);
for(i = 0; i < 3*score; i++)
{
for(j = 0; j < 3*score; j++)
{
gsl_vector_set(dummy_conf, i, gsl_vector_get(dummy_conf, i) + gsl_vector_get(del_conf, j)*gsl_matrix_get(mini_hess_i, j, i));
gsl_vector_set(dummy_conf_t, i, gsl_vector_get(dummy_conf_t, i) + (gsl_vector_get(del_conf, j) - gsl_vector_get(copy_conf, j))*gsl_matrix_get(mini_hess_t, j, i));
}
}
double energy_ic = 0.0;
double energy_tc = 0.0;
for(i = 0; i < 3*score; i++)
{
energy_ic += gsl_vector_get(dummy_conf, i)*gsl_vector_get(del_conf, i);
energy_tc += gsl_vector_get(dummy_conf_t, i)*(gsl_vector_get(del_conf, i) - gsl_vector_get(copy_conf, i));
}
gsl_vector_free(dummy_conf_t);
gsl_vector_free(del_conf);
printf("Check 10\n");
if(change_density == 1)
{
gsl_vector_set_all(dummy_conf, 0);
gsl_vector *eval = gsl_vector_alloc(3*score);
gsl_vector_set_all(eval, 0);
gsl_vector *eval_t = gsl_vector_alloc(3*score);
gsl_vector_set_all(eval_t, 0);
gsl_matrix *evec = gsl_matrix_alloc (3*score,3*score);
gsl_matrix_set_all(evec, 0);
gsl_matrix *evec_t = gsl_matrix_alloc (3*score,3*score);
gsl_matrix_set_all(evec_t, 0);
diagonalyse_matrix(mini_hess_i, 3*score, eval, evec);
diagonalyse_matrix(mini_hess_t, 3*score, eval_t, evec_t);
gsl_matrix_free(mini_hess_i);
gsl_matrix_free(mini_hess_t);
gsl_matrix *comb_hess = gsl_matrix_alloc(3*score, 3*score);
gsl_matrix_set_all(comb_hess, 0);
double entro = 0.0;
double entro_t = 0.0;
for(i = 0; i < 3*score; i++)
{
if(gsl_vector_get(eval, i) > 0.00001)
{
for(j = 0; j < 3*score; j++)
{
for(k = 0; k < 3*score; k++)
{
gsl_matrix_set(comb_hess, j, k, gsl_matrix_get(comb_hess, j, k) + gsl_matrix_get(evec, j, i)*gsl_matrix_get(evec, k, i)/gsl_vector_get(eval, i));
}
}
entro += log(3.141592653589793238462643383279) - log(beta * gsl_vector_get(eval, i));
}
if(gsl_vector_get(eval_t, i) > 0.00001)
{
for(j = 0; j < 3*score; j++)
{
for(k = 0; k < 3*score; k++)
{
gsl_matrix_set(comb_hess, j, k, gsl_matrix_get(comb_hess, j, k) + gsl_matrix_get(evec_t, j, i)*gsl_matrix_get(evec_t, k, i)/gsl_vector_get(eval_t, i));
}
}
entro_t += log(3.141592653589793238462643383279) - log(beta * gsl_vector_get(eval_t, i));
}
}
gsl_vector_free(eval_t);
gsl_matrix_free(evec_t);
gsl_vector_set_all(eval, 0);
gsl_matrix_set_all(evec, 0);
diagonalyse_matrix(comb_hess, 3*score, eval, evec);
gsl_matrix_set_all(comb_hess, 0);
// double comb_det = 1.0;
for(i = 0; i < 3*score; i++)
{
if(gsl_vector_get(eval, i) > 0.00001)
{
for(j = 0; j < 3*score; j++)
{
for(k = 0; k < 3*score; k++)
{
gsl_matrix_set(comb_hess, j, k, gsl_matrix_get(comb_hess, j, k) + gsl_matrix_get(evec, j, i)*gsl_matrix_get(evec, k, i)/gsl_vector_get(eval, i));
}
}
// comb_det *= beta / (3.141592653589793238462643383279 * gsl_vector_get(eval, i));
}
}
for(i = 0; i < 3*score; i++)
{
for(j = 0; j < 3*score; j++)
{
gsl_vector_set(dummy_conf, i, gsl_vector_get(dummy_conf, i) + gsl_vector_get(copy_conf, j)*gsl_matrix_get(comb_hess, j, i));
}
}
double energy_conf = 0.0;
for(i = 0; i < 3*score; i++)
{
energy_conf += gsl_vector_get(dummy_conf, i)*gsl_vector_get(copy_conf, i);
}
double dummy_energy = 0.0;
double prob_conf = 0.0;
dummy_energy = -1.0 * beta * energy_conf;
prob_conf = exp(dummy_energy);
printf("Weighted probability density of exact conformational change at beta = %1.10f : %1.100f\n", beta, prob_conf);
printf("Delta-S (target - init) : %1.10f\n", entro_t - entro);
printf("Delta-H (target - init) : %1.10f\n", energy_ic - energy_tc);
dummy_energy = -310.25 * (entro_t - entro) + energy_ic - energy_tc;
printf("Delta-G (target - init) : %1.10f\n", dummy_energy);
double K_eq = exp(-1.0 * dummy_energy / (310.25 * 8.3145));
printf("Equilibrium constant (target / init) : %1.10f\n", K_eq);
}
else
{
printf("Energy from init to inter : %1.10f\nEnergy from target to inter : %1.10f\nDelta-H (target - init) : %1.10f\n", energy_ic, energy_tc, energy_ic - energy_tc);
}
gsl_vector_free(copy_conf);
gsl_vector_free(dummy_conf);
}
int main(int argc, char *argv[]) {
int all; /*Nombre d'atomes dans pdb*/
int all_t; /*Nombre d'atomes dans pdb*/
int help_flag = 1;
char file_name[500];
char check_name[500];
char out_name[500];
int verbose = 0;
int i;
for (i = 1;i < argc;i++) {
if (strcmp("-i",argv[i]) == 0) {strcpy(file_name,argv[i+1]);--help_flag;}
if (strcmp("-h",argv[i]) == 0) {help_flag = 1;}
if (strcmp("-dist",argv[i]) == 0) {dens_flag = 0;}
if (strcmp("-v",argv[i]) == 0) {verbose = 1;}
if (strcmp("-pi",argv[i]) == 0) {strcpy(wholeinit,argv[i+1]);}
if (strcmp("-pt",argv[i]) == 0) {strcpy(wholetarg,argv[i+1]);}
if (strcmp("-t",argv[i]) == 0) {strcpy(check_name,argv[i+1]);help_flag = 0;}
if (strcmp("-o",argv[i]) == 0) {strcpy(out_name,argv[i+1]);++print_flag;}
if (strcmp("-it",argv[i]) == 0) {int temp;sscanf(argv[i+1],"%d",&temp);it = temp;}
if (strcmp("-temp",argv[i]) == 0) {float temp;sscanf(argv[i+1],"%f",&temp);temperature = temp;}
if (strcmp("-li",argv[i]) == 0) {strcpy(liginit,argv[i+1]);}
if (strcmp("-lt",argv[i]) == 0) {strcpy(ligtarg,argv[i+1]);}
}
if (help_flag == 1) {
printf("****************************\nHelp Section\n-i\tFile Input (PDB)\n-v\tVerbose\n-w\tWeight Vector\n-t\tInitial Value of template (negative value for random)\n\tIf Load Template, multiply the template\n-lt\tLoad input template\n-sp\tSuper Node Mode (CA, N, C)\n-kt\tPoid de l'angle entre les nodes (1)\n-kr\tPoid de la distance entre les nodes (1)\n-f\tFile to fit\n****************************\n");
return(0);
}
//***************************************************
//* *
//*Build a structure contaning information on the pdb
//* *
//***************************************************
// Première strucutre
all = count_atom(file_name);
nconn = count_connect(file_name);
if (verbose == 1) {printf("File I:%s\n",file_name);}
if (verbose == 1) {printf("Connect:%d\n",nconn);}
if (verbose == 1) {printf("Assigning Structure\n\tAll Atom\n");}
// Array qui comprend tous les connects
int **connect_h=(int **)malloc(nconn*sizeof(int *));
for(i=0;i<nconn;i++) { connect_h[i]=(int *)malloc(6*sizeof(int));}
assign_connect(file_name,connect_h);
// Assign tous les atoms
struct pdb_atom strc_all[all];
build_all_strc(file_name,strc_all); // Retourne le nombre de Node
if (verbose == 1) {printf(" Atom:%d\n",all);}
check_lig(strc_all,connect_h,nconn,all);
//Construit la structure a comparer
nconn = 0;
all_t = count_atom(check_name);
nconn = count_connect(check_name);
if (verbose == 1) {printf("File T:%s\n",check_name);}
if (verbose == 1) {printf("Connect:%d\n",nconn);}
if (verbose == 1) {printf("Assigning Structure\n\tAll Atom\n");}
// Array qui comprend tous les connects
int **connect_t=(int **)malloc(nconn*sizeof(int *));
for(i=0;i<nconn;i++) { connect_t[i]=(int *)malloc(6*sizeof(int));}
assign_connect(check_name,connect_t);
// Assign tous les atoms
struct pdb_atom strc_all_t[all_t];
build_all_strc(check_name,strc_all_t); // Retourne le nombre de Node
// Va faire l'alignement de strc
assign_atom_type(strc_all,all);
assign_atom_type(strc_all_t,all_t);
printf("I found %d Anisou with %d atom !\n",load_anisou(strc_all_t,check_name,all_t),all_t);
}
int main(int argc, char *argv[]) {
int i,j;
char eigen_name[100] = "eigen.dat";
char pca_name[100] = "pca_eigen.dat";
int atom[2];
int mode = 6;
int nm = 10;
char filename[100] = "undefined";
int verbose =1 ;
int lig = 0;
for (i = 1;i < argc;i++) {
if (strcmp("-i",argv[i]) == 0) {strcpy(filename,argv[i+1]);}
if (strcmp("-lig",argv[i]) == 0) {++lig;}
if (strcmp("-ieig1",argv[i]) == 0) {strcpy(eigen_name,argv[i+1]);}
if (strcmp("-ieig2",argv[i]) == 0) {strcpy(pca_name,argv[i+1]);}
if (strcmp("-m",argv[i]) == 0) {sscanf(argv[i+1],"%d",&mode);}
if (strcmp("-nm",argv[i]) == 0) {sscanf(argv[i+1],"%d",&nm);}
}
printf("-ieig1 %s -ieig2 %s -i %s\n",eigen_name,pca_name,filename);
if (strcmp("undefined",filename) == 0) {
printf("You need to give the WT form pdb\n");
return(0);
}
int all = count_atom(filename);
int nconn = count_connect(filename);
if (verbose == 1) {printf("Connect:%d\n",nconn);}
if (verbose == 1) {printf("Assigning Structure\n\tAll Atom\n");}
// Array qui comprend tous les connects
int **connect_h=(int **)malloc(nconn*sizeof(int *));
for(i=0;i<nconn;i++) { connect_h[i]=(int *)malloc(7*sizeof(int));}
assign_connect(filename,connect_h);
// Assign tous les atoms
struct pdb_atom strc_all[all];
int atom_strc = build_all_strc(filename,strc_all); // Retourne le nombre de Node
if (verbose == 1) {printf(" Node:%d\n Atom:%d\n",atom_strc,all);}
check_lig(strc_all,connect_h,nconn,all);
// Assign les Nodes
if (verbose == 1) {printf(" CA Structure\n");}
//atom = count_atom_CA_n(strc_all,all,super_node,lig);
if (verbose == 1) {printf(" Node:%d\n",atom_strc);}
struct pdb_atom strc_node[atom_strc];
atom_strc = build_cord_CA(strc_all, strc_node,all,lig,connect_h,nconn);
if (verbose == 1) {printf(" Assign Node:%d\n",atom_strc);}
if (verbose == 1) {printf("Open eigen 1:%s\n",eigen_name);}
atom[0] = count_eigen(eigen_name);
gsl_vector *eval = gsl_vector_alloc(atom[0]);
gsl_matrix *evec = gsl_matrix_alloc (atom[0],atom[0]);
load_eigen(eval,evec,eigen_name,atom[0]);
if (verbose == 1) {printf("Open eigen 2:%s\n",pca_name);}
atom[1] = count_eigen(pca_name);
gsl_vector *evalpca = gsl_vector_alloc(atom[1]);
gsl_matrix *evecpca = gsl_matrix_alloc (atom[1],atom[1]);
load_eigen(evalpca,evecpca,pca_name,atom[1]);
printf("Atom: %d::%d\n",atom[0],atom[1]);
if (atom[0] != atom[1]) {printf("I exited, car pas même nombre de Ca entre les eigenvecoctors.... la première structure de build_pca, est la strc de référence pour comparer\n");return(1);}
float corr;
int k;
printf("J:NMA I:PCA\n");
//float overlap;
for(i=mode-1;i<nm+mode-1;++i) {
for(j=mode-1;j<nm+mode-1;++j) {
corr = over_eigen(evec,evecpca,atom[0],i,j, strc_node);
printf("I:%3d J:%3d %8.5f Val %8.5f :: %8.5f\n",i,j,corr*corr,gsl_vector_get(eval,i),gsl_vector_get(evalpca,j));
}
}
return(1);
}
