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se.h
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se.h
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#include "TMalign.h"
/* entry function for se
* outfmt_opt>=2 should not parse sequence alignment
* u_opt corresponds to option -L
* if u_opt==2, use d0 from Lnorm_ass for alignment
* if hinge>0, append to original invmap */
int se_main(
double **xa, double **ya, const char *seqx, const char *seqy,
double &TM1, double &TM2, double &TM3, double &TM4, double &TM5,
double &d0_0, double &TM_0,
double &d0A, double &d0B, double &d0u, double &d0a, double &d0_out,
string &seqM, string &seqxA, string &seqyA,
double &rmsd0, int &L_ali, double &Liden,
double &TM_ali, double &rmsd_ali, int &n_ali, int &n_ali8,
const int xlen, const int ylen, const vector<string> &sequence,
const double Lnorm_ass, const double d0_scale, const bool i_opt,
const bool a_opt, const int u_opt, const bool d_opt, const int mol_type,
const int outfmt_opt, int *invmap, const int hinge=0)
{
double D0_MIN; //for d0
double Lnorm; //normalization length
double score_d8,d0,d0_search,dcu0;//for TMscore search
double **score; // Input score table for dynamic programming
bool **path; // for dynamic programming
double **val; // for dynamic programming
int *m1=NULL;
int *m2=NULL;
double d;
if (outfmt_opt<2)
{
m1=new int[xlen]; //alignd index in x
m2=new int[ylen]; //alignd index in y
}
/***********************/
/* allocate memory */
/***********************/
NewArray(&score, xlen+1, ylen+1);
NewArray(&path, xlen+1, ylen+1);
NewArray(&val, xlen+1, ylen+1);
int *invmap0 = new int[ylen+1];
int i,j;
if (hinge==0) for (j=0;j<=ylen;j++) invmap0[j]=-1;
else for (j=0;j<ylen;j++) invmap0[j]=invmap[j];
vector<char> seqM_char;
if (hinge)
{
seqM_char.assign(ylen,hinge+'0');
j=-1;
for (int r=0;r<seqM.size();r++)
{
j+=seqyA[r]!='-';
if (seqM[r]!=' ') seqM_char[j]=seqM[r];
}
}
/* set d0 */
parameter_set4search(xlen, ylen, D0_MIN, Lnorm,
score_d8, d0, d0_search, dcu0); // set score_d8
parameter_set4final(xlen, D0_MIN, Lnorm,
d0B, d0_search, mol_type); // set d0B
parameter_set4final(ylen, D0_MIN, Lnorm,
d0A, d0_search, mol_type); // set d0A
if (a_opt)
parameter_set4final((xlen+ylen)*0.5, D0_MIN, Lnorm,
d0a, d0_search, mol_type); // set d0a
if (u_opt)
{
parameter_set4final(Lnorm_ass, D0_MIN, Lnorm,
d0u, d0_search, mol_type); // set d0u
if (u_opt==2)
{
parameter_set4search(Lnorm_ass, Lnorm_ass, D0_MIN, Lnorm,
score_d8, d0, d0_search, dcu0); // set score_d8
}
}
/* perform alignment */
if (hinge==0) for(j=0; j<ylen; j++) invmap[j]=-1;
if (!i_opt) NWDP_SE(path, val, xa, ya, xlen, ylen, d0*d0, 0, invmap, hinge);
else
{
int i1 = -1;// in C version, index starts from zero, not from one
int i2 = -1;
int L1 = sequence[0].size();
int L2 = sequence[1].size();
int L = min(L1, L2);// Get positions for aligned residues
for (int kk1 = 0; kk1 < L; kk1++)
{
if (sequence[0][kk1] != '-') i1++;
if (sequence[1][kk1] != '-')
{
i2++;
if (i2 >= ylen || i1 >= xlen) kk1 = L;
else if (sequence[0][kk1] != '-') invmap[i2] = i1;
}
}
}
if (hinge==0) rmsd0=TM1=TM2=TM3=TM4=TM5=0;
else
{
TM2*=xlen;
TM1*=ylen;
TM3*=(xlen+ylen)*0.5;
TM4*=Lnorm_ass;
TM5*=ylen;
rmsd0=rmsd0*rmsd0*n_ali8;
}
int k=0;
n_ali=0;
n_ali8=0;
for(int i=0,j=0; j<ylen; j++)
{
i=invmap[j];
if(i>=0)//aligned
{
n_ali++;
d=sqrt(dist(&xa[i][0], &ya[j][0]));
if (d <= score_d8 || i_opt || invmap0[j]==i)
{
if (outfmt_opt<2)
{
m1[k]=i;
m2[k]=j;
}
k++;
if (invmap0[j]==i) continue;
TM2+=1/(1+(d/d0B)*(d/d0B)); // chain_1
TM1+=1/(1+(d/d0A)*(d/d0A)); // chain_2
if (a_opt) TM3+=1/(1+(d/d0a)*(d/d0a)); // -a
if (u_opt) TM4+=1/(1+(d/d0u)*(d/d0u)); // -u
if (d_opt) TM5+=1/(1+(d/d0_scale)*(d/d0_scale)); // -d
rmsd0+=d*d;
}
else if (hinge) invmap[j]=-1;
}
}
n_ali8=k;
TM2/=xlen;
TM1/=ylen;
TM3/=(xlen+ylen)*0.5;
TM4/=Lnorm_ass;
TM5/=ylen;
if (n_ali8) rmsd0=sqrt(rmsd0/n_ali8);
if (outfmt_opt>=2)
{
if (hinge) seqM_char.clear();
delete []invmap0;
DeleteArray(&score, xlen+1);
DeleteArray(&path, xlen+1);
DeleteArray(&val, xlen+1);
return 0;
}
/* extract aligned sequence */
int ali_len=xlen+ylen; //maximum length of alignment
seqxA.assign(ali_len,'-');
seqM.assign( ali_len,' ');
seqyA.assign(ali_len,'-');
int kk=0, i_old=0, j_old=0;
d=0;
Liden=0;
for(int k=0; k<n_ali8; k++)
{
for(int i=i_old; i<m1[k]; i++)
{
//align x to gap
seqxA[kk]=seqx[i];
seqyA[kk]='-';
seqM[kk]=' ';
kk++;
}
for(int j=j_old; j<m2[k]; j++)
{
//align y to gap
seqxA[kk]='-';
seqyA[kk]=seqy[j];
seqM[kk]=' ';
kk++;
}
seqxA[kk]=seqx[m1[k]];
seqyA[kk]=seqy[m2[k]];
Liden+=(seqxA[kk]==seqyA[kk]);
d=sqrt(dist(&xa[m1[k]][0], &ya[m2[k]][0]));
if(d<d0_out) seqM[kk]=':';
else seqM[kk]='.';
kk++;
i_old=m1[k]+1;
j_old=m2[k]+1;
}
//tail
for(int i=i_old; i<xlen; i++)
{
//align x to gap
seqxA[kk]=seqx[i];
seqyA[kk]='-';
seqM[kk]=' ';
kk++;
}
for(int j=j_old; j<ylen; j++)
{
//align y to gap
seqxA[kk]='-';
seqyA[kk]=seqy[j];
seqM[kk]=' ';
kk++;
}
seqxA=seqxA.substr(0,kk);
seqyA=seqyA.substr(0,kk);
seqM =seqM.substr(0,kk);
if (hinge)
{
j=-1;
for (int r=0;r<seqM.size();r++)
{
j+=seqyA[r]!='-';
if (seqM[r]!=' ') seqM[r]=seqM_char[j];
}
}
/* free memory */
delete [] invmap0;
delete [] m1;
delete [] m2;
DeleteArray(&score, xlen+1);
DeleteArray(&path, xlen+1);
DeleteArray(&val, xlen+1);
return 0; // zero for no exception
}