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Merged
atillack merged 1 commit into from
Jun 27, 2022
Merged

Flexres output for --gbest and --npdb #198

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2 changes: 1 addition & 1 deletion host/inc/processligand.h
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Original file line number Diff line number Diff line change
Expand Up @@ -228,7 +228,7 @@ int parse_liganddata(
pair_mod* mod_atype_pairs
);

int gen_new_pdbfile(const char*, const char*, const Liganddata*);
int gen_new_pdbfile(const char*, const Liganddata*);

void get_movvec_to_origo(const Liganddata*, double []);

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75 changes: 22 additions & 53 deletions host/src/processligand.cpp
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Expand Up @@ -1323,73 +1323,42 @@ int parse_liganddata(
}

int gen_new_pdbfile(
const char* oldpdb,
const char* newpdb,
const char* filename,
const Liganddata* myligand
)
// The function opens old pdb file, which is supposed to be an AutoDock4 pdbqt file, and
// copies it to newpdb file, but switches the coordinate values to the atomic coordinates
// of myligand, so newpdb file will be identical to oldpdb except the coordinate values.
// Myligand has to be the ligand which was originally read from oldpdb.
// The function write the pdbqt file specified by filename with the current ligand's atomic coordinates
// If the operation was successful, the function returns 0, if not, it returns 1.
{
FILE* fp_old;
FILE* fp_new;
FILE* fp;
char tempstr [256];
char tempstr_short [32];
int acnt_oldlig;
int i,j;

acnt_oldlig = 0;

fp_old = fopen(oldpdb, "rb"); // fp_old = fopen(oldpdb, "r");
if (fp_old == NULL)
fp = fopen(filename, "w");
if (fp == NULL)
{
printf("Error: Can't open file %s.\n", oldpdb);
printf("Error: Can't create pdbqt output file %s.\n", filename);
return 1;
}

fp_new = fopen(newpdb, "w");
if (fp_new == NULL)
{
printf("Error: Can't create file %s.\n", newpdb);
fclose(fp_old);
return 1;
}

while (fgets(tempstr, 255, fp_old) != NULL) // reading a whole row from oldpdb
unsigned int line_count = 0;
unsigned int atom_cnt = 0;
while (line_count < myligand->file_content.size())
{
sscanf(tempstr, "%s", tempstr_short);
if ((strcmp(tempstr_short, "HETATM") == 0) || (strcmp(tempstr_short, "ATOM") == 0)) // if the row begins with HETATM/ATOM, coordinates must be switched
strcpy(tempstr,myligand->file_content[line_count].c_str());
line_count++;
if ((strncmp("ATOM", tempstr, 4) == 0) || (strncmp("HETATM", tempstr, 6) == 0))
{
if (acnt_oldlig >= myligand->num_of_atoms)
{
printf("Error: Ligand in file %s includes more atoms than current ligand.\n",oldpdb);
fclose(fp_old);
fclose(fp_new);
return 1;
}
for (i=0; i<3; i++)
{
sprintf(tempstr_short, "%7.3lf", myligand->atom_idxyzq [acnt_oldlig][1+i]);
for (j=0; j<7; j++)
tempstr [31+8*i+j] = tempstr_short [j];
}
acnt_oldlig++;
}
fprintf(fp_new, "%s", tempstr); // writing the row to newpdb
tempstr[30] = '\0';
fprintf(fp, "%s%8.3lf%8.3lf%8.3lf 0.00 0.00 %+6.3lf %-2s\n", tempstr,
myligand->atom_idxyzq[atom_cnt][1], // x
myligand->atom_idxyzq[atom_cnt][2], // y
myligand->atom_idxyzq[atom_cnt][3], // z
myligand->atom_idxyzq[atom_cnt][4], // q
myligand->atom_types[((int)myligand->atom_idxyzq[atom_cnt][0])]); // type
atom_cnt++;
} else fputs(tempstr, fp);
}

if (acnt_oldlig != myligand->num_of_atoms)
{
printf("%d %d \n", acnt_oldlig, myligand->num_of_atoms);
printf("Warning: New ligand consists of more atoms than original one (i.e. w/ flexres).\n");
printf(" Not all the atoms have been written to file!\n");
}

fclose(fp_old);
fclose(fp_new);

fclose(fp);
return 0;
}

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10 changes: 4 additions & 6 deletions host/src/processresult.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -500,15 +500,13 @@ void make_resfiles(
if (best_energy_of_all > accurate_interE + accurate_interflexE + accurate_intraE + accurate_intraflexE)
{
best_energy_of_all = accurate_interE + accurate_interflexE + accurate_intraE + accurate_intraflexE;

if (mypars->gen_best)
gen_new_pdbfile(basefile, "best.pdbqt", ligand_ref);
if (mypars->gen_best) gen_new_pdbfile("best.pdbqt", ligand_ref);
}

if (i < mypars->gen_pdbs) //if it is necessary, making new pdbqts for best entities
{
sprintf(name_ext_start, "_docked_run%d_entity%d.pdbqt", run_cnt+1, i+1); //name will be <original pdb filename>_docked_<number starting from 1>.pdb
gen_new_pdbfile(basefile, temp_filename, ligand_ref);
gen_new_pdbfile(temp_filename, ligand_ref);
}
if (mypars->gen_finalpop)
{
Expand Down Expand Up @@ -786,7 +784,7 @@ void generate_output(
{
pdbqt_template += "DOCKED: USER x y z vdW Elec q Type\n";
pdbqt_template += "DOCKED: USER _______ _______ _______ _____ _____ ______ ____\n";
}
}
sprintf(lineout, "DOCKED: %s", tempstr);
pdbqt_template += lineout;
}
Expand Down Expand Up @@ -1119,7 +1117,7 @@ void generate_output(
strcpy(xml_file_name, mypars->resname);
strcat(xml_file_name, ".xml");
fp_xml = fopen(xml_file_name, "w");
if(fp==NULL){
if(fp_xml==NULL){
printf("Error: Cannot create xml output file %s: %s\n",xml_file_name,strerror(errno));
exit(9);
}
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