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Merge pull request #210 from atillack/overflow_fix
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Fix for potential buffer overflow in results processing
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@diogomart
diogomart committed Oct 20, 2022
2 parents 2ecd342 + 26172d3 commit fea5d22
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Showing 3 changed files with 21 additions and 23 deletions.
2 changes: 1 addition & 1 deletion host/src/main.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -502,7 +502,7 @@ int main(int argc, char* argv[])
if(n_files>1){
printf("Savings from multithreading: %.3f sec\n",(total_setup_time+total_processing_time+total_exec_time) - seconds_since(time_start));
if(!initial_pars.xml2dlg) // in xml2dlg mode, there's only "idle time" (aka overlapped processing)
printf("Idle time of execution thread: %.3f sec\n",seconds_since(time_start) - total_exec_time);
printf("Idle time of execution thread: %.3f sec\n",total_setup_time+total_processing_time);
if (get_profiles && filelist.used && !initial_pars.xml2dlg) // output profile with filelist name or dpf file name (depending on what is available)
profiler.write_profiles_to_file((filelist.filename!=NULL) ? filelist.filename : initial_pars.dpffile);
} else printf("Processing time: %.3f sec\n",total_processing_time);
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8 changes: 4 additions & 4 deletions host/src/processligand.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -1330,7 +1330,6 @@ int gen_new_pdbfile(
// If the operation was successful, the function returns 0, if not, it returns 1.
{
FILE* fp;
char tempstr [256];

fp = fopen(filename, "w");
if (fp == NULL)
Expand All @@ -1341,10 +1340,10 @@ int gen_new_pdbfile(

unsigned int line_count = 0;
unsigned int atom_cnt = 0;
char tempstr [32];
while (line_count < myligand->file_content.size())
{
strcpy(tempstr,myligand->file_content[line_count].c_str());
line_count++;
strncpy(tempstr,myligand->file_content[line_count].c_str(),32);
if ((strncmp("ATOM", tempstr, 4) == 0) || (strncmp("HETATM", tempstr, 6) == 0))
{
tempstr[30] = '\0';
Expand All @@ -1355,7 +1354,8 @@ int gen_new_pdbfile(
myligand->atom_idxyzq[atom_cnt][4], // q
myligand->atom_types[((int)myligand->atom_idxyzq[atom_cnt][0])]); // type
atom_cnt++;
} else fputs(tempstr, fp);
} else fputs(myligand->file_content[line_count].c_str(), fp);
line_count++;
}

fclose(fp);
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34 changes: 16 additions & 18 deletions host/src/processresult.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -683,7 +683,6 @@ void generate_output(
double sum_energy [1000];
double best_energy [1000];
int best_energy_runid [1000];
char tempstr [256];

double cluster_tolerance = mypars->rmsd_tolerance;

Expand Down Expand Up @@ -719,7 +718,6 @@ void generate_output(

std::string pdbqt_template;
std::vector<unsigned int> atom_data;
char lineout [264];
bool output_ref_calcs = mypars->reflig_en_required;
if(mypars->given_xrayligandfile){
// writing xray ligand pdbqt file
Expand All @@ -730,9 +728,8 @@ void generate_output(
unsigned int line_count = 0;
while (line_count < ligand_xray->ligand_line_count)
{
strcpy(tempstr,ligand_xray->file_content[line_count].c_str());
fprintf(fp, "XRAY-LIGAND-PDBQT: %s", ligand_xray->file_content[line_count].c_str());
line_count++;
fprintf(fp, "XRAY-LIGAND-PDBQT: %s", tempstr);
}
fprintf(fp, "\n\n");
}
Expand All @@ -741,53 +738,53 @@ void generate_output(
if(mypars->free_roaming_ligand){
fprintf(fp, " INPUT LIGAND PDBQT FILE:\n ________________________\n\n\n");
ligand_calc_output(fp, "INPUT-LIGAND-PDBQT: USER", tables, ligand_ref, mypars, mygrid, mypars->contact_analysis, output_ref_calcs);
char tempstr [32];
while (line_count < ligand_ref->ligand_line_count)
{
strcpy(tempstr,ligand_ref->file_content[line_count].c_str());
line_count++;
fprintf(fp, "INPUT-LIGAND-PDBQT: %s", tempstr);
strncpy(tempstr,ligand_ref->file_content[line_count].c_str(),32);
fprintf(fp, "INPUT-LIGAND-PDBQT: %s", ligand_ref->file_content[line_count].c_str());
if ((strncmp("ATOM", tempstr, 4) == 0) || (strncmp("HETATM", tempstr, 6) == 0))
{
tempstr[30] = '\0';
sprintf(lineout, "DOCKED: %s", tempstr);
pdbqt_template += lineout;
pdbqt_template += "DOCKED: ";
pdbqt_template += tempstr;
atom_data.push_back(pdbqt_template.length());
} else{
if (strncmp("ROOT", tempstr, 4) == 0)
{
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;
pdbqt_template += "DOCKED: " + ligand_ref->file_content[line_count];
}
line_count++;
}
fprintf(fp, "\n\n");
}
// writing input flexres pdbqt file if specified
if (mypars->flexresfile) {
if ( strlen(mypars->flexresfile)>0 ) {
fprintf(fp, " INPUT FLEXRES PDBQT FILE:\n ________________________\n\n\n");
char tempstr [32];
while (line_count < ligand_ref->file_content.size())
{
strcpy(tempstr,ligand_ref->file_content[line_count].c_str());
line_count++;
fprintf(fp, "INPUT-FLEXRES-PDBQT: %s", tempstr);
strncpy(tempstr,ligand_ref->file_content[line_count].c_str(),32);
fprintf(fp, "INPUT-FLEXRES-PDBQT: %s", ligand_ref->file_content[line_count].c_str());
if ((strncmp("ATOM", tempstr, 4) == 0) || (strncmp("HETATM", tempstr, 6) == 0))
{
tempstr[30] = '\0';
sprintf(lineout, "DOCKED: %s", tempstr);
pdbqt_template += lineout;
pdbqt_template += "DOCKED: ";
pdbqt_template += tempstr;
atom_data.push_back(pdbqt_template.length());
} else{
if (strncmp("ROOT", tempstr, 4) == 0)
{
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;
pdbqt_template += "DOCKED: " + ligand_ref->file_content[line_count];
}
line_count++;
}
fprintf(fp, "\n\n");
}
Expand Down Expand Up @@ -930,6 +927,7 @@ void generate_output(
curr_model = pdbqt_template;
// inserting text from the end means prior text positions won't shift
// so there's less to keep track off ;-)
char lineout[51];
for(atom_cnt = ligand_ref->num_of_atoms; atom_cnt-->0;)
{
char* line = lineout;
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