diff --git a/modules/bindings/src/tmalign/TMalign.h b/modules/bindings/src/tmalign/TMalign.h
index 79abc61af1f744ae16032b5a42f1d83bee2ee63c..08caeec3a2b97f6cdb49a1a7d22b660b2c60b2eb 100644
--- a/modules/bindings/src/tmalign/TMalign.h
+++ b/modules/bindings/src/tmalign/TMalign.h
@@ -794,7 +794,7 @@ bool overlap(const int a1,const int b1,const int c1,const int d1,
void sec_str(int len,char *seq, const vector<vector<bool> >&bp,
int a, int b,int &c, int &d)
{
- int i,j;
+ int i;
for (i=0;i<len;i++)
{
@@ -811,8 +811,8 @@ void sec_str(int len,char *seq, const vector<vector<bool> >&bp,
* 1->unpair, 2->paired with upstream, 3->paired with downstream */
void make_sec(char *seq, double **x, int len, int *sec,const string atom_opt)
{
- int ii,jj,i,j;
-
+ int ii,jj,j;
+ unsigned int i;
float lb=12.5; // lower bound for " C3'"
float ub=15.0; // upper bound for " C3'"
if (atom_opt==" C4'") {lb=14.0;ub=16.0;}
@@ -825,7 +825,7 @@ void make_sec(char *seq, double **x, int len, int *sec,const string atom_opt)
vector<bool> bp_tmp(len,false);
vector<vector<bool> > bp(len,bp_tmp);
bp_tmp.clear();
- for (i=0; i<len; i++)
+ for (i=0;(int) i<len; i++)
{
sec[i]=1;
for (j=i+1; j<len; j++)
@@ -843,7 +843,7 @@ void make_sec(char *seq, double **x, int len, int *sec,const string atom_opt)
// From 5' to 3': A0 C0 D0 B0: A0 paired to B0, C0 paired to D0
vector<int> A0,B0,C0,D0;
- for (i=0; i<len-2; i++)
+ for (i=0;(int) i<len-2; i++)
{
for (j=i+3; j<len; j++)
{
@@ -858,8 +858,8 @@ void make_sec(char *seq, double **x, int len, int *sec,const string atom_opt)
}
}
- int sign;
- for (i=0;i<A0.size();i++)
+ //int sign;
+ for (i=0; i<A0.size();i++)
{
/*
sign=0;
@@ -1483,8 +1483,8 @@ void output_superpose(const string filename, const char *fname_super,
double x1[3]; // after transform
/* for PDBx/mmCIF only */
- map<string,int> _atom_site;
- int atom_site_pos;
+ map<string,unsigned int> _atom_site;
+ unsigned int atom_site_pos;
vector<string> line_vec;
while (compress_type?fin_gz.good():fin.good())
@@ -1545,7 +1545,7 @@ void output_superpose(const string filename, const char *fname_super,
transform(t, u, x, x1);
for (atom_site_pos=0; atom_site_pos<_atom_site.size(); atom_site_pos++)
- {
+ {
if (atom_site_pos==_atom_site["Cartn_x"])
buf<<setiosflags(ios::fixed)<<setprecision(3)
<<setw(8)<<x1[0]<<' ';
@@ -2324,7 +2324,6 @@ int TMalign_main(double **xa, double **ya,
TM2 = TMscore8_search(r1, r2, xtm, ytm, xt, n_ali8, t, u, simplify_step,
score_sum_method, &rmsd, local_d0_search, Lnorm, score_d8, d0);
- double Lnorm_d0;
if (a_opt>0)
{
//normalized by average length of structures A, B
@@ -2360,7 +2359,6 @@ int TMalign_main(double **xa, double **ya,
d0_out=d0_scale;
d0_0=d0_scale;
//Lnorm_0=ylen;
- Lnorm_d0=Lnorm_0;
local_d0_search = d0_search;
TM5 = TMscore8_search(r1, r2, xtm, ytm, xt, n_ali8, t0, u0,
simplify_step, score_sum_method, &rmsd, local_d0_search, Lnorm,
diff --git a/modules/bindings/src/tmalign/basic_fun.h b/modules/bindings/src/tmalign/basic_fun.h
index 8274428ee8d56b061180855f6205df214ed32e49..3dadccc30faf0dde5403b9adc123d2cf376bb867 100644
--- a/modules/bindings/src/tmalign/basic_fun.h
+++ b/modules/bindings/src/tmalign/basic_fun.h
@@ -124,7 +124,7 @@ void split(const string &line, vector<string> &line_vec,
const char delimiter=' ')
{
bool within_word = false;
- for (int pos=0;pos<line.size();pos++)
+ for (unsigned int pos=0;pos<line.size();pos++)
{
if (line[pos]==delimiter)
{
@@ -276,7 +276,7 @@ size_t get_PDB_lines(const string filename,
chainID_list.push_back(i8_stream.str());
PDB_lines.push_back(tmp_str_vec);
mol_vec.push_back(0);
- for (i=0;i<L;i++)
+ for (i=0;(int) i<L;i++)
{
if (compress_type) fin_gz>>x>>y>>z;
else fin >>x>>y>>z;
@@ -294,7 +294,6 @@ size_t get_PDB_lines(const string filename,
else if (infmt_opt==2) // xyz format
{
int L=0;
- char A;
stringstream i8_stream;
while (compress_type?fin_gz.good():fin.good())
{
@@ -309,7 +308,7 @@ size_t get_PDB_lines(const string filename,
chainID_list.push_back(':'+line.substr(0,i));
PDB_lines.push_back(tmp_str_vec);
mol_vec.push_back(0);
- for (i=0;i<L;i++)
+ for (i=0;(int) i<L;i++)
{
if (compress_type) getline(fin_gz, line);
else getline(fin, line);
@@ -511,7 +510,7 @@ size_t get_FASTA_lines(const string filename,
{
string line;
vector<string> tmp_str_vec;
- int l;
+ unsigned int l;
int compress_type=0; // uncompressed file
ifstream fin;
@@ -640,7 +639,7 @@ int extract_aln_from_resi(vector<string> &sequence, char *seqx, char *seqy,
int read_PDB(const vector<string> &PDB_lines, double **a, char *seq,
vector<string> &resi_vec, const int byresi_opt)
{
- int i;
+ unsigned int i;
for (i=0;i<PDB_lines.size();i++)
{
a[i][0] = atof(PDB_lines[i].substr(30, 8).c_str());
@@ -733,7 +732,7 @@ void read_user_alignment(vector<string>&sequence, const string &fname_lign,
if (I_opt)
{
int aligned_resNum=0;
- for (int i=0;i<sequence[0].size();i++)
+ for (unsigned int i=0;i<sequence[0].size();i++)
aligned_resNum+=(sequence[0][i]!='-' && sequence[1][i]!='-');
if (aligned_resNum<3)
PrintErrorAndQuit("ERROR! Superposition is undefined for <3 aligned residues.");