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flexalign.h
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flexalign.h
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/* Functions for the core TMalign algorithm, including the entry function
* flexalign_main */
#ifndef flexalign_h
#define flexalign_h 1
#include "TMalign.h"
void t_u2tu(double t0[3],double u0[3][3], vector<double> &tu_tmp)
{
int i,j,k;
for (i=0;i<3;i++) tu_tmp[i]=t0[i];
k=3;
for (i=0;i<3;i++) for (j=0;j<3;j++)
{
tu_tmp[k]=u0[i][j];
k++;
}
}
void tu2t_u(vector<double> tu_tmp, double t0[3],double u0[3][3])
{
int i,j,k;
for (i=0;i<3;i++) t0[i]=tu_tmp[i];
k=3;
for (i=0;i<3;i++) for (j=0;j<3;j++)
{
u0[i][j]=tu_tmp[k];
k++;
}
}
void aln2invmap(const string &seqxA, const string &seqyA, int *invmap)
{
int i,j,r;
int ylen=0;
for (r=0;r<seqyA.size();r++) ylen+=seqyA[r]!='-';
for(j=0; j<ylen; j++) invmap[j]=-1;
i=j=-1;
for (r=0;r<seqxA.size();r++)
{
i+=seqxA[r]!='-';
j+=seqyA[r]!='-';
if (seqxA[r]!='-' && seqyA[r]!='-') invmap[j]=i;
}
}
int flexalign_main(double **xa, double **ya,
const char *seqx, const char *seqy, const char *secx, const char *secy,
double t0[3], double u0[3][3], vector<vector<double> >&tu_vec,
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 int i_opt, const int a_opt,
const bool u_opt, const bool d_opt, const bool fast_opt,
const int mol_type, const int hinge_opt)
{
vector<double> tu_tmp(12,0);
int round2=tu_vec.size();
if (round2==0)
{
TMalign_main(xa, ya, seqx, seqy, secx, secy, t0, u0,
TM1, TM2, TM3, TM4, TM5, d0_0, TM_0,
d0A, d0B, d0u, d0a, d0_out, seqM, seqxA, seqyA,
rmsd0, L_ali, Liden, TM_ali, rmsd_ali, n_ali, n_ali8,
xlen, ylen, sequence, Lnorm_ass,
d0_scale, i_opt, a_opt, u_opt, d_opt, fast_opt, mol_type);
t_u2tu(t0,u0,tu_tmp);
tu_vec.push_back(tu_tmp);
}
int i,j,r;
int* invmap=new int[ylen+1];
for (j=0;j<ylen+1;j++) invmap[j]=-1;
double **xt;
NewArray(&xt, xlen, 3);
do_rotation(xa, xt, xlen, t0, u0);
TM1= TM2= TM3= TM4= TM5=rmsd0=0;
seqM="";
seqxA="";
seqyA="";
n_ali=n_ali8=0;
se_main(xt, ya, seqx, seqy, TM1, TM2, TM3, TM4, TM5, d0_0, TM_0,
d0A, d0B, d0u, d0a, d0_out, seqM, seqxA, seqyA,
rmsd0, L_ali, Liden, TM_ali, rmsd_ali, n_ali, n_ali8,
xlen, ylen, sequence, Lnorm_ass, d0_scale, i_opt,
a_opt, u_opt, d_opt, mol_type, 0, invmap, 1);
if (round2)
{
/* aligned structure A vs unaligned structure B */
int xlen_h=n_ali8;
int ylen_h=ylen - n_ali8;
char *seqx_h = new char[xlen + 1];
char *seqy_h = new char[ylen + 1];
char *secx_h = new char[xlen + 1];
char *secy_h = new char[ylen + 1];
seqx_h[xlen]=seqy_h[ylen]=0;
secx_h[xlen]=secy_h[ylen]=0;
double **xa_h, **ya_h;
NewArray(&xa_h, xlen, 3);
NewArray(&ya_h, ylen, 3);
int r1,r2;
i=j=-1;
r1=r2=0;
for (r=0;r<seqxA.size();r++)
{
i+=(seqxA[r]!='-');
j+=(seqyA[r]!='-');
if (seqxA[r]!='-' && seqyA[r]!='-')
{
seqx_h[r1]=seqx[i];
secx_h[r1]=secx[i];
xa_h[r1][0]=xa[i][0];
xa_h[r1][1]=xa[i][1];
xa_h[r1][2]=xa[i][2];
r1++;
}
if (seqxA[r]=='-')
{
seqy_h[r2]=seqx[j];
secy_h[r2]=secx[j];
ya_h[r2][0]=ya[j][0];
ya_h[r2][1]=ya[j][1];
ya_h[r2][2]=ya[j][2];
r2++;
}
}
double TM1_h, TM2_h;
double TM3_h, TM4_h, TM5_h; // for a_opt, u_opt, d_opt
double d0_0_h, TM_0_h;
double d0A_h, d0B_h, d0u_h, d0a_h;
double d0_out_h=5.0;
string seqM_h, seqxA_h, seqyA_h;// for output alignment
double rmsd0_h = 0.0;
int L_ali_h=0; // Aligned length in standard_TMscore
double Liden_h=0;
double TM_ali_h, rmsd_ali_h; // TMscore and rmsd in standard_TMscore
int n_ali_h=0;
int n_ali8_h=0;
TMalign_main(xa_h, ya_h, seqx_h, seqy_h, secx_h, secy_h, t0, u0,
TM1_h, TM2_h, TM3_h, TM4_h, TM5_h, d0_0_h, TM_0_h,
d0A_h, d0B_h, d0u_h, d0a_h, d0_out_h, seqM_h, seqxA_h, seqyA_h,
rmsd0_h, L_ali_h, Liden_h, TM_ali_h, rmsd_ali_h, n_ali_h, n_ali8_h,
xlen_h, ylen_h, sequence, Lnorm_ass,
d0_scale, i_opt, a_opt, u_opt, d_opt, fast_opt, mol_type);
do_rotation(xa, xt, xlen, t0, u0);
t_u2tu(t0,u0,tu_vec[0]);
int* invmap_h=new int[ylen+1];
for (j=0;j<ylen+1;j++) invmap_h[j]=-1;
TM1_h= TM2_h= TM3_h= TM4_h= TM5_h=rmsd0_h=0;
seqM_h="";
seqxA_h="";
seqyA_h="";
n_ali_h=n_ali8_h=0;
se_main(xt, ya, seqx, seqy, TM1_h, TM2_h, TM3_h, TM4_h, TM5_h, d0_0,
TM_0, d0A, d0B, d0u, d0a, d0_out, seqM_h, seqxA_h, seqyA_h,
rmsd0_h, L_ali, Liden, TM_ali, rmsd_ali, n_ali_h, n_ali8_h,
xlen, ylen, sequence, Lnorm_ass, d0_scale, i_opt,
a_opt, u_opt, d_opt, mol_type, 0, invmap_h, 1);
/* unaligned structure A vs aligned structure B */
xlen_h=xlen - n_ali8;
ylen_h=n_ali8;
i=j=-1;
r1=r2=0;
for (r=0;r<seqxA.size();r++)
{
i+=(seqxA[r]!='-');
j+=(seqyA[r]!='-');
if (seqyA[r]=='-')
{
seqx_h[r1]=seqx[i];
secx_h[r1]=secx[i];
xa_h[r1][0]=xa[i][0];
xa_h[r1][1]=xa[i][1];
xa_h[r1][2]=xa[i][2];
r1++;
}
if (seqxA[r]!='-' && seqyA[r]!='-')
{
seqy_h[r2]=seqx[j];
secy_h[r2]=secx[j];
ya_h[r2][0]=ya[j][0];
ya_h[r2][1]=ya[j][1];
ya_h[r2][2]=ya[j][2];
r2++;
}
}
d0_out_h=5.0;
L_ali_h=Liden_h=0;
TM1= TM2= TM3= TM4= TM5=rmsd0=0;
seqM="";
seqxA="";
seqyA="";
n_ali=n_ali8=0;
TMalign_main(xa_h, ya_h, seqx_h, seqy_h, secx_h, secy_h, t0, u0,
TM1, TM2, TM3, TM4, TM5, d0_0_h, TM_0_h,
d0A_h, d0B_h, d0u_h, d0a_h, d0_out_h, seqM, seqxA, seqyA,
rmsd0, L_ali_h, Liden_h, TM_ali_h, rmsd_ali_h, n_ali, n_ali8,
xlen_h, ylen_h, sequence, Lnorm_ass,
d0_scale, i_opt, a_opt, u_opt, d_opt, fast_opt, mol_type);
do_rotation(xa, xt, xlen, t0, u0);
for (j=0;j<ylen+1;j++) invmap[j]=-1;
TM1= TM2= TM3= TM4= TM5=rmsd0=0;
seqM="";
seqxA="";
seqyA="";
n_ali=n_ali8=0;
se_main(xt, ya, seqx, seqy, TM1, TM2, TM3, TM4, TM5, d0_0,
TM_0, d0A, d0B, d0u, d0a, d0_out, seqM, seqxA, seqyA,
rmsd0, L_ali, Liden, TM_ali, rmsd_ali, n_ali, n_ali8,
xlen, ylen, sequence, Lnorm_ass, d0_scale, i_opt,
a_opt, u_opt, d_opt, mol_type, 0, invmap, 1);
double TM_h=(TM1_h>TM2_h)?TM1_h:TM2_h;
double TM =(TM1 >TM2 )?TM1 :TM2 ;
if (TM_h>TM)
{
TM1=TM1_h;
TM2=TM2_h;
TM3=TM3_h;
TM4=TM4_h;
TM5=TM5_h;
seqM=seqM_h;
seqxA=seqxA_h;
seqyA=seqyA_h;
rmsd0=rmsd0_h;
n_ali=n_ali_h;
n_ali8=n_ali8_h;
for (j=0;j<ylen+1;j++) invmap[j]=invmap_h[j];
}
else t_u2tu(t0,u0,tu_vec[0]);
/* clean up */
delete [] invmap_h;
DeleteArray(&xa_h, xlen);
DeleteArray(&ya_h, ylen);
seqM_h.clear();
seqxA_h.clear();
seqyA_h.clear();
delete [] seqx_h;
delete [] secx_h;
delete [] seqy_h;
delete [] secy_h;
}
for (r=0;r<seqM.size();r++) if (seqM[r]=='1') seqM[r]='0';
int minlen = min(xlen, ylen);
int hinge;
for (hinge=0;hinge<hinge_opt;hinge++)
{
if (minlen-n_ali8<5) break;
int xlen_h=xlen - n_ali8;
int ylen_h=ylen - n_ali8;
char *seqx_h = new char[xlen_h + 1];
char *seqy_h = new char[ylen_h + 1];
char *secx_h = new char[xlen_h + 1];
char *secy_h = new char[ylen_h + 1];
seqx_h[xlen_h]=seqy_h[ylen_h]=0;
secx_h[xlen_h]=secy_h[ylen_h]=0;
double **xa_h, **ya_h;
NewArray(&xa_h, xlen_h, 3);
NewArray(&ya_h, ylen_h, 3);
vector<int> r1toi(xlen_h,0);
vector<int> r2toj(ylen_h,0);
int r1,r2;
i=j=-1;
r1=r2=0;
for (r=0;r<seqxA.size();r++)
{
i+=(seqxA[r]!='-');
j+=(seqyA[r]!='-');
if (seqyA[r]=='-')
{
seqx_h[r1]=seqx[i];
secx_h[r1]=secx[i];
xa_h[r1][0]=xa[i][0];
xa_h[r1][1]=xa[i][1];
xa_h[r1][2]=xa[i][2];
r1toi[r1]=i;
r1++;
}
if (seqxA[r]=='-')
{
seqy_h[r2]=seqx[j];
secy_h[r2]=secx[j];
ya_h[r2][0]=ya[j][0];
ya_h[r2][1]=ya[j][1];
ya_h[r2][2]=ya[j][2];
r2toj[r2]=j;
r2++;
}
}
double TM1_h, TM2_h;
double TM3_h, TM4_h, TM5_h; // for a_opt, u_opt, d_opt
double d0_0_h, TM_0_h;
double d0A_h, d0B_h, d0u_h, d0a_h;
double d0_out_h=5.0;
string seqM_h, seqxA_h, seqyA_h;// for output alignment
double rmsd0_h = 0.0;
int L_ali_h=0; // Aligned length in standard_TMscore
double Liden_h=0;
double TM_ali_h, rmsd_ali_h; // TMscore and rmsd in standard_TMscore
int n_ali_h=0;
int n_ali8_h=0;
TMalign_main(xa_h, ya_h, seqx_h, seqy_h, secx_h, secy_h, t0, u0,
TM1_h, TM2_h, TM3_h, TM4_h, TM5_h, d0_0_h, TM_0_h,
d0A_h, d0B_h, d0u_h, d0a_h, d0_out_h, seqM_h, seqxA_h, seqyA_h,
rmsd0_h, L_ali_h, Liden_h, TM_ali_h, rmsd_ali_h, n_ali_h, n_ali8_h,
xlen_h, ylen_h, sequence, Lnorm_ass,
d0_scale, i_opt, a_opt, u_opt, d_opt, fast_opt, mol_type);
do_rotation(xa, xt, xlen, t0, u0);
TM1_h=TM1;
TM2_h=TM2;
TM3_h=TM3;
TM4_h=TM4;
TM5_h=TM5;
seqM_h=seqM;
seqxA_h=seqxA;
seqyA_h=seqyA;
rmsd0_h=rmsd0;
n_ali_h=n_ali;
n_ali8_h=n_ali8;
int* invmap_h=new int[ylen+1];
for (j=0;j<ylen+1;j++) invmap_h[j]=invmap[j];
se_main(xt, ya, seqx, seqy, TM1_h, TM2_h, TM3_h, TM4_h, TM5_h, d0_0, TM_0,
d0A, d0B, d0u, d0a, d0_out, seqM_h, seqxA_h, seqyA_h,
rmsd0_h, L_ali, Liden, TM_ali, rmsd_ali, n_ali_h, n_ali8_h,
xlen, ylen, sequence, Lnorm_ass, d0_scale, i_opt,
a_opt, u_opt, d_opt, mol_type, 0, invmap_h, hinge+1);
int new_ali=0;
for (r=0;r<seqM_h.size();r++) new_ali+=(seqM_h[r]==hinge+'1');
if (n_ali8_h - n_ali8<5) new_ali=0;
if (new_ali>=5)
{
TM1=TM1_h;
TM2=TM2_h;
TM3=TM3_h;
TM4=TM4_h;
TM5=TM5_h;
seqM=seqM_h;
seqxA=seqxA_h;
seqyA=seqyA_h;
rmsd0=rmsd0_h;
n_ali=n_ali_h;
n_ali8=n_ali8_h;
t_u2tu(t0,u0,tu_tmp);
tu_vec.push_back(tu_tmp);
for (j=0;j<ylen+1;j++) invmap[j]=invmap_h[j];
//cout<<">hinge="<<hinge<<'\n'
//<<seqxA<<'\n'<<seqM<<'\n'<<seqyA<<endl;
//for (j=0;j<ylen;j++) if ((i=invmap[j])>=0) cout<<"("<<i<<","<<j<<")";
//cout<<endl;
}
/* clean up */
delete [] invmap_h;
DeleteArray(&xa_h, xlen_h);
DeleteArray(&ya_h, ylen_h);
r1toi.clear();
r2toj.clear();
seqM_h.clear();
seqxA_h.clear();
seqyA_h.clear();
delete [] seqx_h;
delete [] secx_h;
delete [] seqy_h;
delete [] secy_h;
if (new_ali<5) break;
}
if (tu_vec.size()<=1)
{
DeleteArray(&xt, xlen);
delete[] invmap;
return tu_vec.size();
}
/* re-derive alignment based on tu_vec */
vector<char> seqM_char(ylen,' ');
vector<double> di_vec(ylen,-1);
double d;
for (hinge=tu_vec.size()-1;hinge>=0;hinge--)
{
tu2t_u(tu_vec[hinge],t0,u0);
do_rotation(xa, xt, xlen, t0, u0);
for (j=0;j<ylen;j++)
{
i=invmap[j];
if (i<0) continue;
d=sqrt(dist(xt[i], ya[j]));
if (di_vec[j]<0 || d<=di_vec[j])
{
di_vec[j]=d;
seqM_char[j]=hinge+'0';
}
}
}
j=-1;
for (r=0;r<seqM.size();r++)
{
if (seqyA[r]=='-') continue;
j++;
seqM[r]=seqM_char[j];
}
/* smooth out AFP assignment: remove singleton insert */
for (hinge=tu_vec.size()-1;hinge>=0;hinge--)
{
j=-1;
for (r=0;r<seqM.size();r++)
{
if (seqyA[r]=='-') continue;
j++;
if (seqM_char[j]!=hinge+'0') continue;
if (r<seqM.size()-1 && (seqM[r+1]==hinge+'0' || seqM[r+1]==' '))
continue;
if (r>0 && (seqM[r-1]==hinge+'0' || seqM[r-1]==' ')) continue;
if (r<seqM.size()-1 && r>0 && seqM[r-1]!=seqM[r+1]) continue;
if (r>0) seqM[r]=seqM_char[j]=seqM[r-1];
else seqM[r]=seqM_char[j]=seqM[r+1];
}
}
/* smooth out AFP assignment: remove singleton at the end of fragment */
char left_hinge=' ';
char right_hinge=' ';
for (hinge=tu_vec.size()-1;hinge>=0;hinge--)
{
j=-1;
for (r=0;r<seqM.size();r++)
{
if (seqyA[r]=='-') continue;
j++;
if (seqM[r]!=hinge+'0') continue;
if (r>0 && seqM[r-1]==' ' && r<seqM.size()-1 && seqM[r+1]==' ')
continue;
left_hinge=' ';
for (i=r-1;i>=0;i--)
{
if (seqM[i]==' ') continue;
left_hinge=seqM[i];
break;
}
if (left_hinge==hinge+'0') continue;
right_hinge=' ';
for (i=r+1;i<seqM.size();i++)
{
if (seqM[i]==' ') continue;
right_hinge=seqM[i];
break;
}
if (right_hinge==hinge+'0') continue;
if (left_hinge!=right_hinge && left_hinge!=' ' && right_hinge!=' ')
continue;
if (right_hinge!=' ') seqM[r]=seqM_char[j]=right_hinge;
else if (left_hinge!=' ') seqM[r]=seqM_char[j]=left_hinge;
}
}
/* smooth out AFP assignment: remove dimer insert */
for (hinge=tu_vec.size()-1;hinge>=0;hinge--)
{
j=-1;
for (r=0;r<seqM.size()-1;r++)
{
if (seqyA[r]=='-') continue;
j++;
if (seqM[r] !=hinge+'0'|| seqM[r+1]!=hinge+'0') continue;
if (r<seqM.size()-2 && (seqM[r+2]==' ' || seqM[r+2]==hinge+'0'))
continue;
if (r>0 && (seqM[r-1]==' ' || seqM[r-1]==hinge+'0')) continue;
if (r<seqM.size()-2 && r>0 && seqM[r-1]!=seqM[r+2]) continue;
if (r>0) seqM[r]=seqM_char[j]=seqM[r+1]=seqM_char[j+1]=seqM[r-1];
else seqM[r]=seqM_char[j]=seqM[r+1]=seqM_char[j+1]=seqM[r+2];
}
}
/* smooth out AFP assignment: remove disconnected singleton */
int i1,i2;
for (hinge=tu_vec.size()-1;hinge>=0;hinge--)
{
j=-1;
for (r=0;r<seqM.size();r++)
{
if (seqyA[r]=='-') continue;
j++;
if (seqM[r]!=hinge+'0') continue;
left_hinge=' ';
for (i=r-1;i>=0;i--)
{
if (seqM[i]==' ') continue;
left_hinge=seqM[i];
i1=(r-i);
break;
}
if (left_hinge==hinge+'0') continue;
right_hinge=' ';
for (i=r+1;i<seqM.size();i++)
{
if (seqM[i]==' ') continue;
right_hinge=seqM[i];
i2=(i-r);
break;
}
if (right_hinge==hinge+'0') continue;
if (right_hinge==' ') seqM[r]=seqM_char[j]=left_hinge;
else if (left_hinge==' ') seqM[r]=seqM_char[j]=right_hinge;
else
{
if (i1<i2) seqM[r]=seqM_char[j]=left_hinge;
else seqM[r]=seqM_char[j]=right_hinge;
}
}
}
/* recalculate all scores */
for (hinge=tu_vec.size()-1;hinge>=0;hinge--)
{
tu2t_u(tu_vec[hinge],t0,u0);
do_rotation(xa, xt, xlen, t0, u0);
for (j=0;j<ylen;j++)
{
i=invmap[j];
if (i<0) continue;
if (seqM_char[j]!=hinge+'0') continue;
d=sqrt(dist(xt[i], ya[j]));
if (di_vec[j]<0 || d<=di_vec[j])
{
di_vec[j]=d;
seqM_char[j]=hinge+'0';
}
}
}
rmsd0=TM1=TM2=TM3=TM4=TM5=0;
Liden=0;
for (r=0;r<seqM.size();r++) if (seqM[r]!=' ') Liden+=seqxA[r]==seqyA[r];
for(j=0; j<ylen; j++)
{
i=invmap[j];
if(i<0) continue;
{
d=di_vec[j];
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;
}
}
TM2/=xlen;
TM1/=ylen;
TM3/=(xlen+ylen)*0.5;
TM4/=Lnorm_ass;
TM5/=ylen;
if (n_ali8) rmsd0=sqrt(rmsd0/n_ali8);
for (hinge=tu_vec.size()-1;hinge>0;hinge--)
{
int afp_len=0;
for (r=0;r<seqM.size();r++) afp_len+=seqM[r]==hinge+'0';
if (afp_len) break;
tu_vec.pop_back(); // remove unnecessary afp
}
/* clean up */
seqM_char.clear();
di_vec.clear();
DeleteArray(&xt, xlen);
delete[] invmap;
return tu_vec.size();
}
/* extract rotation matrix based on TMscore8 */
void output_flexalign_rotation_matrix(const char* fname_matrix,
const vector<vector<double> >&tu_vec, double t[3], double u[3][3])
{
stringstream ss;
char dest[1000];
for (int hinge=0;hinge<tu_vec.size();hinge++)
{
tu2t_u(tu_vec[hinge],t,u);
ss << "------ The rotation matrix to rotate Structure_1 to Structure_2 ------\n";
sprintf(dest, "m %18s %14s %14s %14s\n", "t[m]", "u[m][0]", "u[m][1]", "u[m][2]");
ss << string(dest);
for (int k = 0; k < 3; k++)
{
sprintf(dest, "%d %18.10f %14.10f %14.10f %14.10f\n", k, t[k], u[k][0], u[k][1], u[k][2]);
ss << string(dest);
}
}
ss << "\nCode for rotating Structure 1 from (x,y,z) to (X,Y,Z):\n"
"for(i=0; i<L; i++)\n"
"{\n"
" X[i] = t[0] + u[0][0]*x[i] + u[0][1]*y[i] + u[0][2]*z[i];\n"
" Y[i] = t[1] + u[1][0]*x[i] + u[1][1]*y[i] + u[1][2]*z[i];\n"
" Z[i] = t[2] + u[2][0]*x[i] + u[2][1]*y[i] + u[2][2]*z[i];\n"
"}\n";
if (strcmp(fname_matrix,(char *)("-"))==0)
cout<<ss.str();
else
{
fstream fout;
fout.open(fname_matrix, ios::out | ios::trunc);
if (fout)
{
fout<<ss.str();
fout.close();
}
else cout << "Open file to output rotation matrix fail.\n";
}
ss.str(string());
}
void output_flexalign_rasmol(const string xname, const string yname,
const string fname_super,const vector<vector<double> >&tu_vec,
double t[3], double u[3][3], const int ter_opt,
const int mm_opt, const int split_opt, const int mirror_opt,
const char *seqM, const char *seqxA, const char *seqyA,
const vector<string>&resi_vec1, const vector<string>&resi_vec2,
const string chainID1, const string chainID2,
const int xlen, const int ylen, const double d0A, const int n_ali8,
const double rmsd, const double TM1, const double Liden)
{
stringstream buf;
stringstream buf_all;
stringstream buf_atm;
stringstream buf_all_atm;
stringstream buf_all_atm_lig;
//stringstream buf_pdb;
stringstream buf_tm;
string line;
double x[3]; // before transform
double x1[3]; // after transform
bool after_ter; // true if passed the "TER" line in PDB
string asym_id; // chain ID
map<string,int> resi2hinge_dict;
int r,i,j;
j=-1;
char hinge_char=0;
int ali_len=strlen(seqM);
for (r=0;r<strlen(seqxA);r++)
{
if (seqxA[r]=='-') continue;
j++;
hinge_char=seqM[r];
if (hinge_char==' ')
{
for (i=1;i<ali_len;i++)
{
if (r-i>=0 && seqM[r-i]!=' ')
hinge_char=seqM[r-i];
else if (r+i<xlen && seqM[r+i]!=' ')
hinge_char=seqM[r+i];
if (hinge_char!=' ') break;
}
}
resi2hinge_dict[resi_vec1[j]]=hinge_char-'0';
}
string resi=resi_vec1[0];
int read_resi=resi.size()-4;
buf_tm<<"REMARK US-align"
<<"\nREMARK Structure 1:"<<setw(11)<<left<<xname+chainID1<<" Size= "<<xlen
<<"\nREMARK Structure 2:"<<setw(11)<<yname+chainID2<<right<<" Size= "<<ylen
<<" (TM-score is normalized by "<<setw(4)<<ylen<<", d0="
<<setiosflags(ios::fixed)<<setprecision(2)<<setw(6)<<d0A<<")"
<<"\nREMARK Aligned length="<<setw(4)<<n_ali8<<", RMSD="
<<setw(6)<<setiosflags(ios::fixed)<<setprecision(2)<<rmsd
<<", TM-score="<<setw(7)<<setiosflags(ios::fixed)<<setprecision(5)<<TM1
<<", ID="<<setw(5)<<setiosflags(ios::fixed)<<setprecision(3)
<<((n_ali8>0)?Liden/n_ali8:0)<<endl;
string rasmol_CA_header="load inline\nselect *A\nwireframe .45\nselect *B\nwireframe .20\nselect all\ncolor white\n";
string rasmol_cartoon_header="load inline\nselect all\ncartoon\nselect *A\ncolor blue\nselect *B\ncolor red\nselect ligand\nwireframe 0.25\nselect solvent\nspacefill 0.25\nselect all\nexit\n"+buf_tm.str();
if (!mm_opt) buf<<rasmol_CA_header;
buf_all<<rasmol_CA_header;
if (!mm_opt) buf_atm<<rasmol_cartoon_header;
buf_all_atm<<rasmol_cartoon_header;
buf_all_atm_lig<<rasmol_cartoon_header;
/* selecting chains for -mol */
string chain1_sele;
string chain2_sele;
if (!mm_opt)
{
if (split_opt==2 && ter_opt>=1) // align one chain from model 1
{
chain1_sele=chainID1.substr(1);
chain2_sele=chainID2.substr(1);
}
else if (split_opt==2 && ter_opt==0) // align one chain from each model
{
for (i=1;i<chainID1.size();i++) if (chainID1[i]==',') break;
chain1_sele=chainID1.substr(i+1);
for (i=1;i<chainID2.size();i++) if (chainID2[i]==',') break;
chain2_sele=chainID2.substr(i+1);
}
}
/* for PDBx/mmCIF only */
map<string,int> _atom_site;
int atom_site_pos;
vector<string> line_vec;
string atom; // 4-character atom name
string AA; // 3-character residue name
string inscode; // 1-character insertion code
string model_index; // model index
bool is_mmcif=false;
/* used for CONECT record of chain1 */
int ca_idx1=0; // all CA atoms
int lig_idx1=0; // all atoms
vector <int> idx_vec;
/* used for CONECT record of chain2 */
int ca_idx2=0; // all CA atoms
int lig_idx2=0; // all atoms
/* extract aligned region */
vector<string> resi_aln1;
vector<string> resi_aln2;
int i1=-1;
int i2=-1;
if (!mm_opt)
{
for (i=0;i<strlen(seqM);i++)
{
i1+=(seqxA[i]!='-');
i2+=(seqyA[i]!='-');
if (seqM[i]==' ') continue;
resi_aln1.push_back(resi_vec1[i1].substr(0,4));
resi_aln2.push_back(resi_vec2[i2].substr(0,4));
if (seqM[i]!=':') continue;
buf <<"select "<<resi_aln1.back()<<":A,"
<<resi_aln2.back()<<":B\ncolor red\n";
buf_all<<"select "<<resi_aln1.back()<<":A,"
<<resi_aln2.back()<<":B\ncolor red\n";
}
buf<<"select all\nexit\n"<<buf_tm.str();
}
buf_all<<"select all\nexit\n"<<buf_tm.str();
ifstream fin;
/* read first file */
after_ter=false;
asym_id="";
fin.open(xname.c_str());
int hinge=0;
while (fin.good())
{
getline(fin, line);
if (ter_opt>=3 && line.compare(0,3,"TER")==0) after_ter=true;
if (is_mmcif==false && line.size()>=54 &&
(line.compare(0, 6, "ATOM ")==0 ||
line.compare(0, 6, "HETATM")==0)) // PDB format
{
if (line[16]!='A' && line[16]!=' ') continue;
x[0]=atof(line.substr(30,8).c_str());
x[1]=atof(line.substr(38,8).c_str());
x[2]=atof(line.substr(46,8).c_str());
if (mirror_opt) x[2]=-x[2];
if (read_resi==1) resi=line.substr(22,5);
else resi=line.substr(22,5)+line[21];
hinge=0;
if (resi2hinge_dict.count(resi)) hinge=resi2hinge_dict[resi];
tu2t_u(tu_vec[hinge],t,u);
transform(t, u, x, x1);
//buf_pdb<<line.substr(0,30)<<setiosflags(ios::fixed)
//<<setprecision(3)
//<<setw(8)<<x1[0] <<setw(8)<<x1[1] <<setw(8)<<x1[2]
//<<line.substr(54)<<'\n';
if (after_ter && line.compare(0,6,"ATOM ")==0) continue;
lig_idx1++;
buf_all_atm_lig<<line.substr(0,6)<<setw(5)<<lig_idx1
<<line.substr(11,9)<<" A"<<line.substr(22,8)
<<setiosflags(ios::fixed)<<setprecision(3)
<<setw(8)<<x1[0]<<setw(8)<<x1[1] <<setw(8)<<x1[2]<<'\n';
if (chain1_sele.size() && line[21]!=chain1_sele[0]) continue;
if (after_ter || line.compare(0,6,"ATOM ")) continue;
if (ter_opt>=2)
{
if (ca_idx1 && asym_id.size() && asym_id!=line.substr(21,1))
{
after_ter=true;
continue;
}
asym_id=line[21];
}
buf_all_atm<<"ATOM "<<setw(5)<<lig_idx1
<<line.substr(11,9)<<" A"<<line.substr(22,8)
<<setiosflags(ios::fixed)<<setprecision(3)
<<setw(8)<<x1[0]<<setw(8)<<x1[1] <<setw(8)<<x1[2]<<'\n';
if (!mm_opt && find(resi_aln1.begin(),resi_aln1.end(),
line.substr(22,4))!=resi_aln1.end())
{
buf_atm<<"ATOM "<<setw(5)<<lig_idx1
<<line.substr(11,9)<<" A"<<line.substr(22,8)
<<setiosflags(ios::fixed)<<setprecision(3)
<<setw(8)<<x1[0]<<setw(8)<<x1[1] <<setw(8)<<x1[2]<<'\n';
}
if (line.substr(12,4)!=" CA " && line.substr(12,4)!=" C3'") continue;
ca_idx1++;
buf_all<<"ATOM "<<setw(5)<<ca_idx1<<' '
<<line.substr(12,4)<<' '<<line.substr(17,3)<<" A"<<line.substr(22,8)
<<setiosflags(ios::fixed)<<setprecision(3)
<<setw(8)<<x1[0]<<setw(8)<<x1[1]<<setw(8)<<x1[2]<<'\n';
if (find(resi_aln1.begin(),resi_aln1.end(),
line.substr(22,4))==resi_aln1.end()) continue;
if (!mm_opt) buf<<"ATOM "<<setw(5)<<ca_idx1<<' '
<<line.substr(12,4)<<' '<<line.substr(17,3)<<" A"<<line.substr(22,8)
<<setiosflags(ios::fixed)<<setprecision(3)
<<setw(8)<<x1[0]<<setw(8)<<x1[1]<<setw(8)<<x1[2]<<'\n';
idx_vec.push_back(ca_idx1);
}
else if (line.compare(0,5,"loop_")==0) // PDBx/mmCIF
{
while(1)
{
if (fin.good()) getline(fin, line);
else PrintErrorAndQuit("ERROR! Unexpected end of "+xname);
if (line.size()) break;
}
if (line.compare(0,11,"_atom_site.")) continue;
_atom_site.clear();
atom_site_pos=0;
_atom_site[line.substr(11,line.size()-12)]=atom_site_pos;
while(1)
{
if (fin.good()) getline(fin, line);
else PrintErrorAndQuit("ERROR! Unexpected end of "+xname);
if (line.size()==0) continue;
if (line.compare(0,11,"_atom_site.")) break;
_atom_site[line.substr(11,line.size()-12)]=++atom_site_pos;
}
if (is_mmcif==false)
{
//buf_pdb.str(string());
is_mmcif=true;
}
while(1)
{
line_vec.clear();
split(line,line_vec);
if (line_vec[_atom_site["group_PDB"]]!="ATOM" &&
line_vec[_atom_site["group_PDB"]]!="HETATM") break;
if (_atom_site.count("pdbx_PDB_model_num"))
{
if (model_index.size() && model_index!=
line_vec[_atom_site["pdbx_PDB_model_num"]])
break;
model_index=line_vec[_atom_site["pdbx_PDB_model_num"]];
}
x[0]=atof(line_vec[_atom_site["Cartn_x"]].c_str());
x[1]=atof(line_vec[_atom_site["Cartn_y"]].c_str());
x[2]=atof(line_vec[_atom_site["Cartn_z"]].c_str());
if (mirror_opt) x[2]=-x[2];
if (_atom_site.count("auth_seq_id"))
resi=line_vec[_atom_site["auth_seq_id"]];
else resi=line_vec[_atom_site["label_seq_id"]];
if (_atom_site.count("pdbx_PDB_ins_code") &&
line_vec[_atom_site["pdbx_PDB_ins_code"]]!="?")
resi+=line_vec[_atom_site["pdbx_PDB_ins_code"]][0];
else resi+=" ";
if (read_resi>=2)
{
if (_atom_site.count("auth_asym_id"))
asym_id=line_vec[_atom_site["auth_asym_id"]];
else asym_id=line_vec[_atom_site["label_asym_id"]];
if (asym_id==".") asym_id=" ";
resi+=asym_id[0];
}
hinge=0;
if (resi2hinge_dict.count(resi)) hinge=resi2hinge_dict[resi];
tu2t_u(tu_vec[hinge],t,u);
transform(t, u, x, x1);
if (_atom_site.count("label_alt_id")==0 ||
line_vec[_atom_site["label_alt_id"]]=="." ||
line_vec[_atom_site["label_alt_id"]]=="A")
{
atom=line_vec[_atom_site["label_atom_id"]];
if (atom[0]=='"') atom=atom.substr(1);
if (atom.size() && atom[atom.size()-1]=='"')
atom=atom.substr(0,atom.size()-1);
if (atom.size()==0) atom=" ";
else if (atom.size()==1) atom=" "+atom+" ";
else if (atom.size()==2) atom=" "+atom+" ";
else if (atom.size()==3) atom=" "+atom;
else if (atom.size()>=5) atom=atom.substr(0,4);
AA=line_vec[_atom_site["label_comp_id"]]; // residue name
if (AA.size()==1) AA=" "+AA;
else if (AA.size()==2) AA=" " +AA;
else if (AA.size()>=4) AA=AA.substr(0,3);
if (_atom_site.count("auth_seq_id"))
resi=line_vec[_atom_site["auth_seq_id"]];
else resi=line_vec[_atom_site["label_seq_id"]];
while (resi.size()<4) resi=' '+resi;
if (resi.size()>4) resi=resi.substr(0,4);
inscode=' ';
if (_atom_site.count("pdbx_PDB_ins_code") &&
line_vec[_atom_site["pdbx_PDB_ins_code"]]!="?")
inscode=line_vec[_atom_site["pdbx_PDB_ins_code"]][0];
if (_atom_site.count("auth_asym_id"))
{
if (chain1_sele.size()) after_ter
=line_vec[_atom_site["auth_asym_id"]]!=chain1_sele;
else if (ter_opt>=2 && ca_idx1 && asym_id.size() &&
asym_id!=line_vec[_atom_site["auth_asym_id"]])
after_ter=true;
asym_id=line_vec[_atom_site["auth_asym_id"]];
}
else if (_atom_site.count("label_asym_id"))
{
if (chain1_sele.size()) after_ter
=line_vec[_atom_site["label_asym_id"]]!=chain1_sele;
if (ter_opt>=2 && ca_idx1 && asym_id.size() &&
asym_id!=line_vec[_atom_site["label_asym_id"]])
after_ter=true;
asym_id=line_vec[_atom_site["label_asym_id"]];
}
//buf_pdb<<left<<setw(6)
//<<line_vec[_atom_site["group_PDB"]]<<right
//<<setw(5)<<lig_idx1%100000<<' '<<atom<<' '
//<<AA<<" "<<asym_id[asym_id.size()-1]
//<<resi<<inscode<<" "
//<<setiosflags(ios::fixed)<<setprecision(3)
//<<setw(8)<<x1[0]
//<<setw(8)<<x1[1]
//<<setw(8)<<x1[2]<<'\n';
if (after_ter==false ||
line_vec[_atom_site["group_pdb"]]=="HETATM")
{
lig_idx1++;
buf_all_atm_lig<<left<<setw(6)
<<line_vec[_atom_site["group_PDB"]]<<right
<<setw(5)<<lig_idx1%100000<<' '<<atom<<' '
<<AA<<" A"<<resi<<inscode<<" "
<<setiosflags(ios::fixed)<<setprecision(3)
<<setw(8)<<x1[0]
<<setw(8)<<x1[1]
<<setw(8)<<x1[2]<<'\n';
if (after_ter==false &&
line_vec[_atom_site["group_PDB"]]=="ATOM")
{
buf_all_atm<<"ATOM "<<setw(6)
<<setw(5)<<lig_idx1%100000<<' '<<atom<<' '
<<AA<<" A"<<resi<<inscode<<" "
<<setiosflags(ios::fixed)<<setprecision(3)
<<setw(8)<<x1[0]
<<setw(8)<<x1[1]
<<setw(8)<<x1[2]<<'\n';
if (!mm_opt && find(resi_aln1.begin(),
resi_aln1.end(),resi)!=resi_aln1.end())
{
buf_atm<<"ATOM "<<setw(6)
<<setw(5)<<lig_idx1%100000<<' '
<<atom<<' '<<AA<<" A"<<resi<<inscode<<" "
<<setiosflags(ios::fixed)<<setprecision(3)
<<setw(8)<<x1[0]
<<setw(8)<<x1[1]