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Modify info text output to write a json record. #114

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Modify info text output to write a json record. #114

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170 changes: 65 additions & 105 deletions src/fpout.c
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Original file line number Diff line number Diff line change
Expand Up @@ -50,7 +50,7 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI

## RETURN:
void

*/
extern char write_mode[10];
void write_out_fpocket(c_lst_pockets *pockets, s_pdb *pdb, char *pdbname)
Expand All @@ -65,47 +65,43 @@ void write_out_fpocket(c_lst_pockets *pockets, s_pdb *pdb, char *pdbname)
char command[370] = "";
int status;

if (pockets)
{
if (pockets) {
/* Extract path, pdb code... */
strcpy(pdb_code, pdbname);
extract_path(pdbname, pdb_path);
remove_ext(pdb_code);
remove_path(pdb_code);

if (strlen(pdb_path) > 0)
if (strlen(pdb_path) > 0) {
sprintf(out_path, "%s/%s_out", pdb_path, pdb_code);
else
} else {
sprintf(out_path, "%s_out", pdb_code);
}

sprintf(command, "mkdir -p %s", out_path);
status = system(command);
if (status != 0)
{
if (status != 0) {
return;
}

sprintf(out_path, "%s/%s", out_path, pdb_code);
sprintf(pdb_out_path, "%s_out.pdb", out_path);

sprintf(mmcif_out_path, "%s_out.cif", out_path);

/* Write vmd and pymol scripts */
sprintf(fout, "%s_out.pdb", pdb_code);
write_visualization(out_path, fout);

/* Writing full pdb */
//printf("%s\n",write_mode);
if(write_mode[0] == 'p' || write_mode[0] == 'b'){
sprintf(pdb_out_path, "%s_out.pdb", out_path);

write_pockets_single_pdb(pdb_out_path, pdb, pockets);
/* Writing full pdb */
if (write_mode[0] == 'p' || write_mode[0] == 'b') {
sprintf(pdb_out_path, "%s_out.pdb", out_path);
write_pockets_single_pdb(pdb_out_path, pdb, pockets);
}

/*Writing full mmcif*/
if(write_mode[0] == 'm' || write_mode[0] == 'b'){
sprintf(mmcif_out_path, "%s_out.cif", out_path);
write_pockets_single_mmcif(mmcif_out_path, pdb, pockets);
/* Writing full mmcif */
if (write_mode[0] == 'm' || write_mode[0] == 'b') {
sprintf(mmcif_out_path, "%s_out.cif", out_path);
write_pockets_single_mmcif(mmcif_out_path, pdb, pockets);
}

sprintf(info_out_path, "%s_info.txt", out_path);
Expand All @@ -116,17 +112,16 @@ void write_out_fpocket(c_lst_pockets *pockets, s_pdb *pdb, char *pdbname)
write_pockets_single_pqr(fout, pockets);

/* Writing individual pockets pqr */
if (strlen(pdb_path) > 0)
if (strlen(pdb_path) > 0) {
sprintf(out_path, "%s/%s_out", pdb_path, pdb_code);
else
} else {
sprintf(out_path, "%s_out", pdb_code);
}

sprintf(out_path, "%s/pockets", out_path);
sprintf(command, "mkdir %s", out_path);
status = system(command);
/*if(status != 0) {
return ;
}*/


write_each_pocket(out_path, pockets);
}
Expand All @@ -136,7 +131,7 @@ void write_out_fpocket(c_lst_pockets *pockets, s_pdb *pdb, char *pdbname)
write_out_fpocket_info_file

## SPECIFICATION:
Writing the pocket information file to the output directory
Writing the pocket information file to the output directory, as a json record

## PARAMETRES:
* @ c_lst_pockets *pockets : All pockets found and kept.
Expand All @@ -146,69 +141,52 @@ void write_out_fpocket(c_lst_pockets *pockets, s_pdb *pdb, char *pdbname)
void

*/
void write_out_fpocket_info_file(c_lst_pockets *pockets, char *output_file_name)
{
void write_out_fpocket_info_file(c_lst_pockets *pockets, char *output_file_name) {
FILE *f = NULL;
f = fopen(output_file_name, "w");
node_pocket *pcur = NULL;
s_desc *pdesc = NULL;
int i = 0;
if (pockets)
{
fprintf(f, "[");
if (pockets) {
pcur = pockets->first;

while (pcur)
{
while (pcur) {
if (i > 0) {
fprintf(f, ",");
}
pdesc = pcur->pocket->pdesc;
fprintf(f, "Pocket %d :\n", i + 1);
// fprintf(f,"\tScore : \t\t\t%.3f\n",pcur->pocket->score);
// fprintf(f,"\tDruggability Score : \t\t%.3f\n",pdesc->drug_score);
// fprintf(f,"\tNumber of Alpha Spheres : \t%d\n",pcur->pocket->size);
// fprintf(f,"\tTotal SASA : \t\t\t%.3f\n",pdesc->surf_vdw14);
// fprintf(f,"\tPolar SASA : \t\t\t%.3f\n",pdesc->surf_pol_vdw14);
// fprintf(f,"\tApolar SASA : \t\t\t%.3f\n",pdesc->surf_apol_vdw14);
// fprintf(f,"\tVolume : \t\t\t%.3f\n",pdesc->volume);
// fprintf(f,"\tMean local hydrophobic density : %.3f\n",pdesc->mean_loc_hyd_dens);
// fprintf(f,"\tMean alpha sphere radius :\t%.3f\n",pdesc->mean_asph_ray);
// fprintf(f,"\tMean alp. sph. solvent access : %.3f\n",pdesc->masph_sacc);
// fprintf(f,"\tApolar alpha sphere proportion : %.3f\n",pdesc->apolar_asphere_prop);
// fprintf(f,"\tHydrophobicity score:\t\t%.3f\n",pdesc->hydrophobicity_score);
// fprintf(f,"\tVolume score: \t\t\t %.3f\n",pdesc->volume_score);
// fprintf(f,"\tPolarity score:\t\t\t %d\n",pdesc->polarity_score);
// fprintf(f,"\tCharge score :\t\t\t %d\n",pdesc->charge_score);
// fprintf(f,"\tProportion of polar atoms: \t%.3f\n",pdesc->prop_polar_atm);
// fprintf(f,"\tAlpha sphere density : \t\t%.3f\n",pdesc->as_density);
// fprintf(f,"\tCent. of mass - Alpha Sphere max dist: %.3f\n",pdesc->as_max_dst);
// fprintf(f,"\tFlexibility : \t\t\t %.3f\n",pdesc->flex);
fprintf(f, "\tScore : \t%.3f\n", pcur->pocket->score);
fprintf(f, "\tDruggability Score : \t%.3f\n", pdesc->drug_score);
fprintf(f, "\tNumber of Alpha Spheres : \t%d\n", pcur->pocket->size);
fprintf(f, "\tTotal SASA : \t%.3f\n", pdesc->surf_vdw14);
fprintf(f, "\tPolar SASA : \t%.3f\n", pdesc->surf_pol_vdw14);
fprintf(f, "\tApolar SASA : \t%.3f\n", pdesc->surf_apol_vdw14);
fprintf(f, "\tVolume : \t%.3f\n", pdesc->volume);
fprintf(f, "\tMean local hydrophobic density : \t%.3f\n", pdesc->mean_loc_hyd_dens);
fprintf(f, "\tMean alpha sphere radius :\t%.3f\n", pdesc->mean_asph_ray);
fprintf(f, "\tMean alp. sph. solvent access : \t%.3f\n", pdesc->masph_sacc);
fprintf(f, "\tApolar alpha sphere proportion : \t%.3f\n", pdesc->apolar_asphere_prop);
fprintf(f, "\tHydrophobicity score:\t%.3f\n", pdesc->hydrophobicity_score);
fprintf(f, "\tVolume score: \t %.3f\n", pdesc->volume_score);
fprintf(f, "\tPolarity score:\t %d\n", pdesc->polarity_score);
fprintf(f, "\tCharge score :\t %d\n", pdesc->charge_score);
fprintf(f, "\tProportion of polar atoms: \t%.3f\n", pdesc->prop_polar_atm);
fprintf(f, "\tAlpha sphere density : \t%.3f\n", pdesc->as_density);
fprintf(f, "\tCent. of mass - Alpha Sphere max dist: \t%.3f\n", pdesc->as_max_dst);
fprintf(f, "\tFlexibility : \t%.3f\n", pdesc->flex);
fprintf(f, "\n");
fprintf(f, "{");
fprintf(f, "\"Pocket\":%d", i + 1);
fprintf(f, ",\"Score\":%.5f", pcur->pocket->score);
fprintf(f, ",\"Druggability Score\":%.5f", pdesc->drug_score);
fprintf(f, ",\"Number of Alpha Spheres\":%d", pcur->pocket->size);
fprintf(f, ",\"Total SASA\":%.5f", pdesc->surf_vdw14);
fprintf(f, ",\"Polar SASA\":%.5f", pdesc->surf_pol_vdw14);
fprintf(f, ",\"Apolar SASA\":%.5f", pdesc->surf_apol_vdw14);
fprintf(f, ",\"Volume\":%.5f", pdesc->volume);
fprintf(f, ",\"Mean local hydrophobic density\":%.5f", pdesc->mean_loc_hyd_dens);
fprintf(f, ",\"Mean alpha sphere radius\":%.5f", pdesc->mean_asph_ray);
fprintf(f, ",\"Mean alp. sph. solvent access\":%.5f", pdesc->masph_sacc);
fprintf(f, ",\"Apolar alpha sphere proportion\":%.5f", pdesc->apolar_asphere_prop);
fprintf(f, ",\"Hydrophobicity score\":%.5f", pdesc->hydrophobicity_score);
fprintf(f, ",\"Volume score\": %.5f", pdesc->volume_score);
fprintf(f, ",\"Polarity score\":%d", pdesc->polarity_score);
fprintf(f, ",\"Charge score\":%d", pdesc->charge_score);
fprintf(f, ",\"Proportion of polar atoms\":%.5f", pdesc->prop_polar_atm);
fprintf(f, ",\"Alpha sphere density\":%.5f", pdesc->as_density);
fprintf(f, ",\"Cent. of mass - Alpha Sphere max dist\":%.5f", pdesc->as_max_dst);
fprintf(f, ",\"Flexibility\":%.5f", pdesc->flex);
fprintf(f, "}");

pcur = pcur->next;
i++;
}
} else {
fprintf(f, "{\"Error\":\"No pockets found\"}");
}
else
{
fprintf(f, "No pockets found\n");
}
fprintf(f, "]");
}

/**-----------------------------------------------------------------------------
## FUNCTION:
void write_out(c_lst_pockets *pockets)
Expand All @@ -217,26 +195,26 @@ void write_out_fpocket_info_file(c_lst_pockets *pockets, char *output_file_name)
Output routine.
-----------------------------------------------------------------------------
*/
void write_out_fpocket_DB(c_lst_pockets *pockets, s_pdb *pdb, char *input_name) //s_fparams *params)
{
void write_out_fpocket_DB(c_lst_pockets *pockets, s_pdb *pdb, char *input_name) {
char pdb_code[350] = "";
char pdb_path[350] = "";
char out_path[350] = "";
char pdb_out_path[350] = "";
char command[370] = "";

if (pockets)
{
if (pockets) {
// Extract path, pdb code...
strcpy(pdb_code, input_name);
extract_path(input_name, pdb_path);
remove_ext(pdb_code);
remove_path(pdb_code);
/*sprintf(out_path, "%s/%s_out", pdb_path, pdb_code) ;*/
if (strlen(pdb_path) > 0)
if (strlen(pdb_path) > 0) {
sprintf(out_path, "%s/%s_out", pdb_path, pdb_code);
else
} else {
sprintf(out_path, "%s_out", pdb_code);
}

sprintf(command, "mkdir -p %s", out_path);
int status = system(command);
// Writing full pdb
Expand All @@ -247,9 +225,7 @@ void write_out_fpocket_DB(c_lst_pockets *pockets, s_pdb *pdb, char *input_name)
}
}

void write_descriptors_DB(c_lst_pockets *pockets, FILE *f)
{

void write_descriptors_DB(c_lst_pockets *pockets, FILE *f) {
/*Todo adapt things here*/

int n = 1;
Expand All @@ -263,39 +239,23 @@ void write_descriptors_DB(c_lst_pockets *pockets, FILE *f)
"ala cys asp glu phe gly his ile lys leu met asn pro gln arg ser thr val trp tyr "
"chain_1_type chain_2_type num_res_chain_1 "
"num_res_chain_2 lig_het_tag name_chain_1 name_chain_2\n");
while (npcur)
{
while (npcur) {
p = npcur->pocket;
// python counter part entry={"pdb_id":pdbFile,"cav_id":int(r[0]),"drug_score":r[1],"nb_asph":int(r[2]),"inter_chain":int(r[3]),"apol_asph_proportion":
//float(r[4]),"mean_asph_radius":float(r[5]),"mean_asph_solv_acc":float(r[6]),"mean_loc_hyd_dens":float(r[7]),"flex":r[8],"hydrophobicity_score":float(r[9]),
//"volume_score":float(r[10]),"charge_score":int(r[11]),"polarity_score":int(r[12]),"a0_apol":float(r[13]),"a0_pol":float(r[14]),"af_apol":float(r[15]),
//"af_pol":float(r[16]),"n_abpa":int(r[17]),"ala":int(r[18]),"cys":int(r[19]),"asp":int(r[20]),"glu":int(r[21]),"phe":int(r[22]),"gly":int(r[23]),
//"his":int(r[24]),"ile":int(r[25]),"lys":int(r[26]),"leu":int(r[27]),"met":int(r[28]),"asn":int(r[29]),"pro":int(r[30]),"gln":int(r[31]),"arg":int(r[32]),
//"ser":int(r[33]),"thr":int(r[34]),"val":int(r[35]),"trp":int(r[36]),"tyr":int(r[37])}
//entry={"pdb_id":pdbFile,"cav_id":int(r[0]),"chain_1_type":int(r[38]), "chain_2_type":int(r[39]), "num_res_chain_1":int(r[40]),"num_res_chain_2":int(r[41])}
// entry={"pdb_id":pdbFile,"cav_id":int(r[0]),"lig_het_tag":str(r[42])}
fprintf(f, "%d %.4f %.4f %d %d %.4f %.4f", r, p->pdesc->drug_score, p->pdesc->volume,
p->pdesc->nb_asph, p->pdesc->interChain, (float)p->nAlphaApol / (float)p->pdesc->nb_asph, p->pdesc->mean_asph_ray);
fprintf(f, " %.4f %.4f %.4f %.4f %.4f %.4f %d", p->pdesc->as_density, p->pdesc->masph_sacc, p->pdesc->mean_loc_hyd_dens, p->pdesc->flex, p->pdesc->hydrophobicity_score,
p->pdesc->volume_score, p->pdesc->charge_score);
fprintf(f, " %d %.4f %.4f %.4f %.4f %d", p->pdesc->polarity_score, p->pdesc->surf_apol_vdw14, p->pdesc->surf_pol_vdw14,
p->pdesc->surf_apol_vdw22, p->pdesc->surf_pol_vdw22, p->pdesc->n_abpa);
for (i = 0; i < 20; i++)
for (i = 0; i < 20; i++) {
fprintf(f, " %d", p->pdesc->aa_compo[i]);
}

fprintf(f, " %d %d %d %d %s %s %s", p->pdesc->characterChain1, p->pdesc->characterChain2, p->pdesc->numResChain1, p->pdesc->numResChain2, p->pdesc->ligTag, p->pdesc->nameChain1, p->pdesc->nameChain2);
//fprintf(f,"%s %s %s",p->pdesc->nameChain1,p->pdesc->nameChain2);
fprintf(f, "\n");
fflush(f);

/* sprintf(filename,"pocket_%d.txt",n);
f=fopen(filename,"w");
fprintf(f,"probe apolar_surface polar_surface\n");

int i;
for(i=0;i<l;i++){
fprintf(f,"%.3f %.3f %.3f\n",p->probe_size[i], p->apol_asa_probe[i],p->pol_asa_probe[i]);
}
fclose(f);*/
npcur = npcur->next;
n++;
r++;
Expand Down