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MMalign.h
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#include <cfloat>
#include "se.h"
void print_assign_list(int *assign1_list, const int chain1_num,
const vector<string> &chainID_list1,
const vector<string> &chainID_list2)
{
int i,j;
for (i=0;i<chain1_num;i++)
{
j=assign1_list[i];
if (j>=0)
cout<<chainID_list1[i]<<'\t'<<chainID_list2[j]<<endl;
}
}
/* count the number of nucleic acid chains (na_chain_num) and
* protein chains (aa_chain_num) in a complex */
int count_na_aa_chain_num(int &na_chain_num,int &aa_chain_num,
const vector<int>&mol_vec)
{
na_chain_num=0;
aa_chain_num=0;
for (size_t i=0;i<mol_vec.size();i++)
{
if (mol_vec[i]>0) na_chain_num++;
else aa_chain_num++;
}
return na_chain_num+aa_chain_num;
}
/* adjust chain assignment for dimer-dimer alignment
* return true if assignment is adjusted */
bool adjust_dimer_assignment(
const vector<vector<vector<double> > >&xa_vec,
const vector<vector<vector<double> > >&ya_vec,
const vector<int>&xlen_vec, const vector<int>&ylen_vec,
const vector<int>&mol_vec1, const vector<int>&mol_vec2,
int *assign1_list, int *assign2_list,
const vector<vector<string> >&seqxA_mat,
const vector<vector<string> >&seqyA_mat)
{
/* check currently assigned chains */
int i1,i2,j1,j2;
i1=i2=j1=j2=-1;
int chain1_num=xa_vec.size();
int i,j;
for (i=0;i<chain1_num;i++)
{
if (assign1_list[i]>=0)
{
if (i1<0)
{
i1=i;
j1=assign1_list[i1];
}
else
{
i2=i;
j2=assign1_list[i2];
}
}
}
/* normalize d0 by L */
int xlen=xlen_vec[i1]+xlen_vec[i2];
int ylen=ylen_vec[j1]+ylen_vec[j2];
int mol_type=mol_vec1[i1]+mol_vec1[i2]+
mol_vec2[j1]+mol_vec2[j2];
double D0_MIN, d0, d0_search;
double Lnorm=getmin(xlen,ylen);
parameter_set4final(getmin(xlen,ylen), D0_MIN, Lnorm, d0,
d0_search, mol_type);
double **xa,**ya, **xt;
NewArray(&xa, xlen, 3);
NewArray(&ya, ylen, 3);
NewArray(&xt, xlen, 3);
double RMSD = 0;
double dd = 0;
double t[3];
double u[3][3];
size_t L_ali=0; // index of residue in aligned region
size_t r=0; // index of residue in full alignment
/* total score using current assignment */
L_ali=0;
i=j=-1;
for (r=0;r<seqxA_mat[i1][j1].size();r++)
{
i+=(seqxA_mat[i1][j1][r]!='-');
j+=(seqyA_mat[i1][j1][r]!='-');
if (seqxA_mat[i1][j1][r]=='-' || seqyA_mat[i1][j1][r]=='-') continue;
xa[L_ali][0]=xa_vec[i1][i][0];
xa[L_ali][1]=xa_vec[i1][i][1];
xa[L_ali][2]=xa_vec[i1][i][2];
ya[L_ali][0]=ya_vec[j1][j][0];
ya[L_ali][1]=ya_vec[j1][j][1];
ya[L_ali][2]=ya_vec[j1][j][2];
L_ali++;
}
i=j=-1;
for (r=0;r<seqxA_mat[i2][j2].size();r++)
{
i+=(seqxA_mat[i2][j2][r]!='-');
j+=(seqyA_mat[i2][j2][r]!='-');
if (seqxA_mat[i2][j2][r]=='-' || seqyA_mat[i2][j2][r]=='-') continue;
xa[L_ali][0]=xa_vec[i2][i][0];
xa[L_ali][1]=xa_vec[i2][i][1];
xa[L_ali][2]=xa_vec[i2][i][2];
ya[L_ali][0]=ya_vec[j2][j][0];
ya[L_ali][1]=ya_vec[j2][j][1];
ya[L_ali][2]=ya_vec[j2][j][2];
L_ali++;
}
Kabsch(xa, ya, L_ali, 1, &RMSD, t, u);
do_rotation(xa, xt, L_ali, t, u);
double total_score1=0;
for (r=0;r<L_ali;r++)
{
dd=dist(xt[r],ya[r]);
total_score1+=1/(1+dd/d0*d0);
}
total_score1/=Lnorm;
/* total score using reversed assignment */
L_ali=0;
i=j=-1;
for (r=0;r<seqxA_mat[i1][j2].size();r++)
{
i+=(seqxA_mat[i1][j2][r]!='-');
j+=(seqyA_mat[i1][j2][r]!='-');
if (seqxA_mat[i1][j2][r]=='-' || seqyA_mat[i1][j2][r]=='-') continue;
xa[L_ali][0]=xa_vec[i1][i][0];
xa[L_ali][1]=xa_vec[i1][i][1];
xa[L_ali][2]=xa_vec[i1][i][2];
ya[L_ali][0]=ya_vec[j2][j][0];
ya[L_ali][1]=ya_vec[j2][j][1];
ya[L_ali][2]=ya_vec[j2][j][2];
L_ali++;
}
i=j=-1;
for (r=0;r<seqxA_mat[i2][j1].size();r++)
{
i+=(seqxA_mat[i2][j1][r]!='-');
j+=(seqyA_mat[i2][j1][r]!='-');
if (seqxA_mat[i2][j1][r]=='-' || seqyA_mat[i2][j1][r]=='-') continue;
xa[L_ali][0]=xa_vec[i2][i][0];
xa[L_ali][1]=xa_vec[i2][i][1];
xa[L_ali][2]=xa_vec[i2][i][2];
ya[L_ali][0]=ya_vec[j1][j][0];
ya[L_ali][1]=ya_vec[j1][j][1];
ya[L_ali][2]=ya_vec[j1][j][2];
L_ali++;
}
Kabsch(xa, ya, L_ali, 1, &RMSD, t, u);
do_rotation(xa, xt, L_ali, t, u);
double total_score2=0;
for (r=0;r<L_ali;r++)
{
dd=dist(xt[r],ya[r]);
total_score2+=1/(1+dd/d0*d0);
}
total_score2/=Lnorm;
/* swap chain assignment */
if (total_score1<total_score2)
{
assign1_list[i1]=j2;
assign1_list[i2]=j1;
assign2_list[j1]=i2;
assign2_list[j2]=i1;
}
/* clean up */
DeleteArray(&xa, xlen);
DeleteArray(&ya, ylen);
DeleteArray(&xt, xlen);
return total_score1<total_score2;
}
/* count how many chains are paired */
int count_assign_pair(int *assign1_list,const int chain1_num)
{
int pair_num=0;
int i;
for (i=0;i<chain1_num;i++) pair_num+=(assign1_list[i]>=0);
return pair_num;
}
/* assign chain-chain correspondence */
double enhanced_greedy_search(double **TMave_mat,int *assign1_list,
int *assign2_list, const int chain1_num, const int chain2_num)
{
double total_score=0;
double tmp_score=0;
int i,j;
int maxi=0;
int maxj=0;
/* initialize parameters */
for (i=0;i<chain1_num;i++) assign1_list[i]=-1;
for (j=0;j<chain2_num;j++) assign2_list[j]=-1;
/* greedy assignment: in each iteration, the highest chain pair is
* assigned, until no assignable chain is left */
while(1)
{
tmp_score=-1;
for (i=0;i<chain1_num;i++)
{
if (assign1_list[i]>=0) continue;
for (j=0;j<chain2_num;j++)
{
if (assign2_list[j]>=0 || TMave_mat[i][j]<=0) continue;
if (TMave_mat[i][j]>tmp_score)
{
maxi=i;
maxj=j;
tmp_score=TMave_mat[i][j];
}
}
}
if (tmp_score<=0) break; // error: no assignable chain
assign1_list[maxi]=maxj;
assign2_list[maxj]=maxi;
total_score+=tmp_score;
}
if (total_score<=0) return total_score; // error: no assignable chain
//cout<<"assign1_list={";
//for (i=0;i<chain1_num;i++) cout<<assign1_list[i]<<","; cout<<"}"<<endl;
//cout<<"assign2_list={";
//for (j=0;j<chain2_num;j++) cout<<assign2_list[j]<<","; cout<<"}"<<endl;
/* iterative refinemnt */
double delta_score;
int *assign1_tmp=new int [chain1_num];
int *assign2_tmp=new int [chain2_num];
for (i=0;i<chain1_num;i++) assign1_tmp[i]=assign1_list[i];
for (j=0;j<chain2_num;j++) assign2_tmp[j]=assign2_list[j];
int old_i=-1;
int old_j=-1;
for (int iter=0;iter<getmin(chain1_num,chain2_num)*5;iter++)
{
delta_score=-1;
for (i=0;i<chain1_num;i++)
{
old_j=assign1_list[i];
for (j=0;j<chain2_num;j++)
{
// attempt to swap (i,old_j=assign1_list[i]) with (i,j)
if (j==assign1_list[i] || TMave_mat[i][j]<=0) continue;
old_i=assign2_list[j];
assign1_tmp[i]=j;
if (old_i>=0) assign1_tmp[old_i]=old_j;
assign2_tmp[j]=i;
if (old_j>=0) assign2_tmp[old_j]=old_i;
delta_score=TMave_mat[i][j];
if (old_j>=0) delta_score-=TMave_mat[i][old_j];
if (old_i>=0) delta_score-=TMave_mat[old_i][j];
if (old_i>=0 && old_j>=0) delta_score+=TMave_mat[old_i][old_j];
if (delta_score>0) // successful swap
{
assign1_list[i]=j;
if (old_i>=0) assign1_list[old_i]=old_j;
assign2_list[j]=i;
if (old_j>=0) assign2_list[old_j]=old_i;
total_score+=delta_score;
break;
}
else
{
assign1_tmp[i]=assign1_list[i];
if (old_i>=0) assign1_tmp[old_i]=assign1_list[old_i];
assign2_tmp[j]=assign2_list[j];
if (old_j>=0) assign2_tmp[old_j]=assign2_list[old_j];
}
}
if (delta_score>0) break;
}
if (delta_score<=0) break; // cannot swap any chain pair
}
/* clean up */
delete[]assign1_tmp;
delete[]assign2_tmp;
return total_score;
}
double calculate_centroids(const vector<vector<vector<double> > >&a_vec,
const int chain_num, double ** centroids)
{
int L=0;
int c,r; // index of chain and residue
for (c=0; c<chain_num; c++)
{
centroids[c][0]=0;
centroids[c][1]=0;
centroids[c][2]=0;
L=a_vec[c].size();
for (r=0; r<L; r++)
{
centroids[c][0]+=a_vec[c][r][0];
centroids[c][1]+=a_vec[c][r][1];
centroids[c][2]+=a_vec[c][r][2];
}
centroids[c][0]/=L;
centroids[c][1]/=L;
centroids[c][2]/=L;
//cout<<centroids[c][0]<<'\t'
//<<centroids[c][1]<<'\t'
//<<centroids[c][2]<<endl;
}
vector<double> d0_vec(chain_num,-1);
int c2=0;
double d0MM=0;
for (c=0; c<chain_num; c++)
{
for (c2=0; c2<chain_num; c2++)
{
if (c2==c) continue;
d0MM=sqrt(dist(centroids[c],centroids[c2]));
if (d0_vec[c]<=0) d0_vec[c]=d0MM;
else d0_vec[c]=getmin(d0_vec[c], d0MM);
}
}
d0MM=0;
for (c=0; c<chain_num; c++) d0MM+=d0_vec[c];
d0MM/=chain_num;
d0_vec.clear();
//cout<<d0MM<<endl;
return d0MM;
}
/* calculate MMscore of aligned chains
* MMscore = sum(TMave_mat[i][j]) * sum(1/(1+dij^2/d0MM^2))
* / (L* getmin(chain1_num,chain2_num))
* dij is the centroid distance between chain pair i and j
* d0MM is scaling factor. TMave_mat[i][j] is the TM-score between
* chain pair i and j multiple by getmin(Li*Lj) */
double calMMscore(double **TMave_mat,int *assign1_list,
const int chain1_num, const int chain2_num, double **xcentroids,
double **ycentroids, const double d0MM, double **r1, double **r2,
double **xt, double t[3], double u[3][3], const int L)
{
int Nali=0; // number of aligned chain
int i,j;
double MMscore=0;
for (i=0;i<chain1_num;i++)
{
j=assign1_list[i];
if (j<0) continue;
r1[Nali][0]=xcentroids[i][0];
r1[Nali][1]=xcentroids[i][1];
r1[Nali][2]=xcentroids[i][2];
r2[Nali][0]=ycentroids[j][0];
r2[Nali][1]=ycentroids[j][1];
r2[Nali][2]=ycentroids[j][2];
Nali++;
MMscore+=TMave_mat[i][j];
}
MMscore/=L;
double RMSD = 0;
double TMscore=0;
if (Nali>=3)
{
/* Kabsch superposition */
Kabsch(r1, r2, Nali, 1, &RMSD, t, u);
do_rotation(r1, xt, Nali, t, u);
/* calculate pseudo-TMscore */
double dd=0;
for (i=0;i<Nali;i++)
{
dd=dist(xt[i], r2[i]);
TMscore+=1/(1+dd/(d0MM*d0MM));
}
}
else if (Nali==2)
{
double dd=dist(r1[0],r2[0]);
TMscore=1/(1+dd/(d0MM*d0MM));
}
else TMscore=1; // only one aligned chain.
TMscore/=getmin(chain1_num,chain2_num);
MMscore*=TMscore;
return MMscore;
}
/* check if this is alignment of heterooligomer or homooligomer
* return het_deg, which ranges from 0 to 1.
* The larger the value, the more "hetero";
* Tthe smaller the value, the more "homo" */
double check_heterooligomer(double **TMave_mat, const int chain1_num,
const int chain2_num)
{
double het_deg=0;
double min_TM=-1;
double max_TM=-1;
int i,j;
for (i=0;i<chain1_num;i++)
{
for (j=0;j<chain2_num;j++)
{
if (min_TM<0 || TMave_mat[i][j] <min_TM) min_TM=TMave_mat[i][j];
if (max_TM<0 || TMave_mat[i][j]>=max_TM) max_TM=TMave_mat[i][j];
}
}
het_deg=(max_TM-min_TM)/max_TM;
//cout<<"min_TM="<<min_TM<<endl;
//cout<<"max_TM="<<max_TM<<endl;
return het_deg;
}
/* reassign chain-chain correspondence, specific for homooligomer */
double homo_refined_greedy_search(double **TMave_mat,int *assign1_list,
int *assign2_list, const int chain1_num, const int chain2_num,
double **xcentroids, double **ycentroids, const double d0MM,
const int L, double **ut_mat)
{
double MMscore_max=0;
double MMscore=0;
int i,j;
int c1,c2;
int max_i=-1; // the chain pair whose monomer u t yields highest MMscore
int max_j=-1;
int chain_num=getmin(chain1_num,chain2_num);
int *assign1_tmp=new int [chain1_num];
int *assign2_tmp=new int [chain2_num];
double **xt;
NewArray(&xt, chain1_num, 3);
double t[3];
double u[3][3];
int ui,uj,ut_idx;
double TMscore=0; // pseudo TM-score
double TMsum =0;
double TMnow =0;
double TMmax =0;
double dd=0;
size_t total_pair=chain1_num*chain2_num; // total pair
double *ut_tmc_mat=new double [total_pair]; // chain level TM-score
vector<pair<double,int> > ut_tm_vec(total_pair,make_pair(0.0,0)); // product of both
for (c1=0;c1<chain1_num;c1++)
{
for (c2=0;c2<chain2_num;c2++)
{
if (TMave_mat[c1][c2]<=0) continue;
ut_idx=c1*chain2_num+c2;
for (ui=0;ui<3;ui++)
for (uj=0;uj<3;uj++) u[ui][uj]=ut_mat[ut_idx][ui*3+uj];
for (uj=0;uj<3;uj++) t[uj]=ut_mat[ut_idx][9+uj];
do_rotation(xcentroids, xt, chain1_num, t, u);
for (i=0;i<chain1_num;i++) assign1_tmp[i]=-1;
for (j=0;j<chain2_num;j++) assign2_tmp[j]=-1;
for (i=0;i<chain1_num;i++)
{
for (j=0;j<chain2_num;j++)
{
ut_idx=i*chain2_num+j;
ut_tmc_mat[ut_idx]=0;
ut_tm_vec[ut_idx].first=-1;
ut_tm_vec[ut_idx].second=ut_idx;
if (TMave_mat[i][j]<=0) continue;
dd=dist(xt[i],ycentroids[j]);
ut_tmc_mat[ut_idx]=1/(1+dd/(d0MM*d0MM));
ut_tm_vec[ut_idx].first=
ut_tmc_mat[ut_idx]*TMave_mat[i][j];
//cout<<"TM["<<ut_idx<<"]="<<ut_tm_vec[ut_idx].first<<endl;
}
}
//cout<<"sorting "<<total_pair<<" chain pairs"<<endl;
/* initial assignment */
assign1_tmp[c1]=c2;
assign2_tmp[c2]=c1;
TMsum=TMave_mat[c1][c2];
TMscore=ut_tmc_mat[c1*chain2_num+c2];
/* further assignment */
sort(ut_tm_vec.begin(), ut_tm_vec.end()); // sort in ascending order
for (ut_idx=total_pair-1;ut_idx>=0;ut_idx--)
{
j=ut_tm_vec[ut_idx].second % chain2_num;
i=int(ut_tm_vec[ut_idx].second / chain2_num);
if (TMave_mat[i][j]<=0) break;
if (assign1_tmp[i]>=0 || assign2_tmp[j]>=0) continue;
assign1_tmp[i]=j;
assign2_tmp[j]=i;
TMsum+=TMave_mat[i][j];
TMscore+=ut_tmc_mat[i*chain2_num+j];
//cout<<"ut_idx="<<ut_tm_vec[ut_idx].second
//<<"\ti="<<i<<"\tj="<<j<<"\ttm="<<ut_tm_vec[ut_idx].first<<endl;
}
/* final MMscore */
MMscore=(TMsum/L)*(TMscore/chain_num);
if (max_i<0 || max_j<0 || MMscore>MMscore_max)
{
max_i=c1;
max_j=c2;
MMscore_max=MMscore;
for (i=0;i<chain1_num;i++) assign1_list[i]=assign1_tmp[i];
for (j=0;j<chain2_num;j++) assign2_list[j]=assign2_tmp[j];
//cout<<"TMsum/L="<<TMsum/L<<endl;
//cout<<"TMscore/chain_num="<<TMscore/chain_num<<endl;
//cout<<"MMscore="<<MMscore<<endl;
//cout<<"assign1_list={";
//for (i=0;i<chain1_num;i++)
//cout<<assign1_list[i]<<","; cout<<"}"<<endl;
//cout<<"assign2_list={";
//for (j=0;j<chain2_num;j++)
//cout<<assign2_list[j]<<","; cout<<"}"<<endl;
}
}
}
/* clean up */
delete[]assign1_tmp;
delete[]assign2_tmp;
delete[]ut_tmc_mat;
ut_tm_vec.clear();
DeleteArray(&xt, chain1_num);
return MMscore;
}
/* reassign chain-chain correspondence, specific for heterooligomer */
double hetero_refined_greedy_search(double **TMave_mat,int *assign1_list,
int *assign2_list, const int chain1_num, const int chain2_num,
double **xcentroids, double **ycentroids, const double d0MM, const int L)
{
double MMscore_old=0;
double MMscore=0;
int i,j;
double **r1;
double **r2;
double **xt;
int chain_num=getmin(chain1_num,chain2_num);
NewArray(&r1, chain_num, 3);
NewArray(&r2, chain_num, 3);
NewArray(&xt, chain_num, 3);
double t[3];
double u[3][3];
/* calculate MMscore */
MMscore=MMscore_old=calMMscore(TMave_mat, assign1_list, chain1_num,
chain2_num, xcentroids, ycentroids, d0MM, r1, r2, xt, t, u, L);
//cout<<"MMscore="<<MMscore<<endl;
//cout<<"TMave_mat="<<endl;
//for (i=0;i<chain1_num;i++)
//{
//for (j=0; j<chain2_num; j++)
//{
//if (j<chain2_num-1) cout<<TMave_mat[i][j]<<'\t';
//else cout<<TMave_mat[i][j]<<endl;
//}
//}
/* iteratively refine chain assignment. in each iteration, attempt
* to swap (i,old_j=assign1_list[i]) with (i,j) */
double delta_score=-1;
int *assign1_tmp=new int [chain1_num];
int *assign2_tmp=new int [chain2_num];
for (i=0;i<chain1_num;i++) assign1_tmp[i]=assign1_list[i];
for (j=0;j<chain2_num;j++) assign2_tmp[j]=assign2_list[j];
int old_i=-1;
int old_j=-1;
//cout<<"assign1_list={";
//for (i=0;i<chain1_num;i++) cout<<assign1_list[i]<<","; cout<<"}"<<endl;
//cout<<"assign2_list={";
//for (j=0;j<chain2_num;j++) cout<<assign2_list[j]<<","; cout<<"}"<<endl;
for (int iter=0;iter<chain1_num*chain2_num;iter++)
{
delta_score=-1;
for (i=0;i<chain1_num;i++)
{
old_j=assign1_list[i];
for (j=0;j<chain2_num;j++)
{
if (j==assign1_list[i] || TMave_mat[i][j]<=0) continue;
old_i=assign2_list[j];
assign1_tmp[i]=j;
if (old_i>=0) assign1_tmp[old_i]=old_j;
assign2_tmp[j]=i;
if (old_j>=0) assign2_tmp[old_j]=old_i;
MMscore=calMMscore(TMave_mat, assign1_tmp, chain1_num,
chain2_num, xcentroids, ycentroids, d0MM,
r1, r2, xt, t, u, L);
//cout<<"(i,j,old_i,old_j,MMscore)=("<<i<<","<<j<<","
//<<old_i<<","<<old_j<<","<<MMscore<<")"<<endl;
if (MMscore>MMscore_old) // successful swap
{
assign1_list[i]=j;
if (old_i>=0) assign1_list[old_i]=old_j;
assign2_list[j]=i;
if (old_j>=0) assign2_list[old_j]=old_i;
delta_score=(MMscore-MMscore_old);
MMscore_old=MMscore;
//cout<<"MMscore="<<MMscore<<endl;
break;
}
else
{
assign1_tmp[i]=assign1_list[i];
if (old_i>=0) assign1_tmp[old_i]=assign1_list[old_i];
assign2_tmp[j]=assign2_list[j];
if (old_j>=0) assign2_tmp[old_j]=assign2_list[old_j];
}
}
}
//cout<<"iter="<<iter<<endl;
//cout<<"assign1_list={";
//for (i=0;i<chain1_num;i++) cout<<assign1_list[i]<<","; cout<<"}"<<endl;
//cout<<"assign2_list={";
//for (j=0;j<chain2_num;j++) cout<<assign2_list[j]<<","; cout<<"}"<<endl;
if (delta_score<=0) break; // cannot swap any chain pair
}
MMscore=MMscore_old;
//cout<<"MMscore="<<MMscore<<endl;
/* clean up */
delete[]assign1_tmp;
delete[]assign2_tmp;
DeleteArray(&r1, chain_num);
DeleteArray(&r2, chain_num);
DeleteArray(&xt, chain_num);
return MMscore;
}
void copy_chain_data(const vector<vector<double> >&a_vec_i,
const vector<char>&seq_vec_i,const vector<char>&sec_vec_i,
const int len,double **a,char *seq,char *sec)
{
int r;
for (r=0;r<len;r++)
{
a[r][0]=a_vec_i[r][0];
a[r][1]=a_vec_i[r][1];
a[r][2]=a_vec_i[r][2];
seq[r]=seq_vec_i[r];
sec[r]=sec_vec_i[r];
}
seq[len]=0;
sec[len]=0;
}
/* clear chains with L<3 */
void clear_full_PDB_lines(vector<vector<string> > PDB_lines,const string atom_opt)
{
int chain_i;
int Lch;
int a;
bool select_atom;
string line;
for (chain_i=0;chain_i<PDB_lines.size();chain_i++)
{
Lch=0;
for (a=0;a<PDB_lines[chain_i].size();a++)
{
line=PDB_lines[chain_i][a];
if (atom_opt=="auto")
{
if (line[17]==' ' && (line[18]=='D'||line[18]==' '))
select_atom=(line.compare(12,4," C3'")==0);
else select_atom=(line.compare(12,4," CA ")==0);
}
else select_atom=(line.compare(12,4,atom_opt)==0);
Lch+=select_atom;
}
if (Lch<3)
{
for (a=0;a<PDB_lines[chain_i].size();a++)
PDB_lines[chain_i][a].clear();
PDB_lines[chain_i].clear();
}
}
line.clear();
}
size_t get_full_PDB_lines(const string filename,
vector<vector<string> >&PDB_lines, const int ter_opt,
const int infmt_opt, const int split_opt, const int het_opt)
{
size_t i=0; // resi i.e. atom index
string line;
char chainID=0;
vector<string> tmp_str_vec;
int compress_type=0; // uncompressed file
ifstream fin;
#ifndef REDI_PSTREAM_H_SEEN
ifstream fin_gz;
#else
redi::ipstream fin_gz; // if file is compressed
if (filename.size()>=3 &&
filename.substr(filename.size()-3,3)==".gz")
{
fin_gz.open("gunzip -c '"+filename+"'");
compress_type=1;
}
else if (filename.size()>=4 &&
filename.substr(filename.size()-4,4)==".bz2")
{
fin_gz.open("bzcat '"+filename+"'");
compress_type=2;
}
else
#endif
fin.open(filename.c_str());
if (infmt_opt==0||infmt_opt==-1) // PDB format
{
while (compress_type?fin_gz.good():fin.good())
{
if (compress_type) getline(fin_gz, line);
else getline(fin, line);
if (infmt_opt==-1 && line.compare(0,5,"loop_")==0) // PDBx/mmCIF
return get_full_PDB_lines(filename,PDB_lines,
ter_opt, 3, split_opt,het_opt);
if (i > 0)
{
if (ter_opt>=1 && line.compare(0,3,"END")==0) break;
else if (ter_opt>=3 && line.compare(0,3,"TER")==0) break;
}
if (split_opt && line.compare(0,3,"END")==0) chainID=0;
if (line.size()>=54 && (line[16]==' ' || line[16]=='A') && (
(line.compare(0, 6, "ATOM ")==0) ||
(line.compare(0, 6, "HETATM")==0 && het_opt==1) ||
(line.compare(0, 6, "HETATM")==0 && het_opt==2 &&
line.compare(17,3, "MSE")==0)))
{
if (!chainID)
{
chainID=line[21];
PDB_lines.push_back(tmp_str_vec);
}
else if (ter_opt>=2 && chainID!=line[21]) break;
if (split_opt==2 && chainID!=line[21])
{
chainID=line[21];
PDB_lines.push_back(tmp_str_vec);
}
PDB_lines.back().push_back(line);
i++;
}
}
}
else if (infmt_opt==1) // SPICKER format
{
size_t L=0;
float x,y,z;
stringstream i8_stream;
while (compress_type?fin_gz.good():fin.good())
{
if (compress_type) fin_gz>>L>>x>>y>>z;
else fin >>L>>x>>y>>z;
if (compress_type) getline(fin_gz, line);
else getline(fin, line);
if (!(compress_type?fin_gz.good():fin.good())) break;
for (i=0;i<L;i++)
{
if (compress_type) fin_gz>>x>>y>>z;
else fin >>x>>y>>z;
i8_stream<<"ATOM "<<setw(4)<<i+1<<" CA UNK "<<setw(4)
<<i+1<<" "<<setiosflags(ios::fixed)<<setprecision(3)
<<setw(8)<<x<<setw(8)<<y<<setw(8)<<z;
line=i8_stream.str();
i8_stream.str(string());
PDB_lines.back().push_back(line);
}
if (compress_type) getline(fin_gz, line);
else getline(fin, line);
}
}
else if (infmt_opt==2) // xyz format
{
size_t L=0;
stringstream i8_stream;
while (compress_type?fin_gz.good():fin.good())
{
if (compress_type) getline(fin_gz, line);
else getline(fin, line);
L=atoi(line.c_str());
if (compress_type) getline(fin_gz, line);
else getline(fin, line);
for (i=0;i<line.size();i++)
if (line[i]==' '||line[i]=='\t') break;
if (!(compress_type?fin_gz.good():fin.good())) break;
PDB_lines.push_back(tmp_str_vec);
for (i=0;i<L;i++)
{
if (compress_type) getline(fin_gz, line);
else getline(fin, line);
i8_stream<<"ATOM "<<setw(4)<<i+1<<" CA "
<<AAmap(line[0])<<" "<<setw(4)<<i+1<<" "
<<line.substr(2,8)<<line.substr(11,8)<<line.substr(20,8);
line=i8_stream.str();
i8_stream.str(string());
PDB_lines.back().push_back(line);
}
}
}
else if (infmt_opt==3) // PDBx/mmCIF format
{
bool loop_ = false; // not reading following content
map<string,int> _atom_site;
int atom_site_pos;
vector<string> line_vec;
string alt_id="."; // alternative location indicator
string asym_id="."; // this is similar to chainID, except that
// chainID is char while asym_id is a string
// with possibly multiple char
string prev_asym_id="";
string AA=""; // residue name
string atom="";
string resi="";
string model_index=""; // the same as model_idx but type is string
stringstream i8_stream;
while (compress_type?fin_gz.good():fin.good())
{
if (compress_type) getline(fin_gz, line);
else getline(fin, line);
if (line.size()==0) continue;
if (loop_) loop_ = (line.size()>=2)?(line.compare(0,2,"# ")):(line.compare(0,1,"#"));
if (!loop_)
{
if (line.compare(0,5,"loop_")) continue;
while(1)
{
if (compress_type)
{
if (fin_gz.good()) getline(fin_gz, line);
else PrintErrorAndQuit("ERROR! Unexpected end of "+filename);
}
else
{
if (fin.good()) getline(fin, line);
else PrintErrorAndQuit("ERROR! Unexpected end of "+filename);
}
if (line.size()) break;
}
if (line.compare(0,11,"_atom_site.")) continue;
loop_=true;
_atom_site.clear();
atom_site_pos=0;
_atom_site[Trim(line.substr(11))]=atom_site_pos;
while(1)
{
if (compress_type) getline(fin_gz, line);
else getline(fin, line);
if (line.size()==0) continue;
if (line.compare(0,11,"_atom_site.")) break;
_atom_site[Trim(line.substr(11))]=++atom_site_pos;
}
if (_atom_site.count("group_PDB")*
_atom_site.count("label_atom_id")*
_atom_site.count("label_comp_id")*
(_atom_site.count("auth_asym_id")+
_atom_site.count("label_asym_id"))*
(_atom_site.count("auth_seq_id")+
_atom_site.count("label_seq_id"))*
_atom_site.count("Cartn_x")*
_atom_site.count("Cartn_y")*
_atom_site.count("Cartn_z")==0)
{
loop_ = false;
cerr<<"Warning! Missing one of the following _atom_site data items: group_PDB, label_atom_id, label_comp_id, auth_asym_id/label_asym_id, auth_seq_id/label_seq_id, Cartn_x, Cartn_y, Cartn_z"<<endl;
continue;
}
}
line_vec.clear();
split(line,line_vec);
if ((line_vec[_atom_site["group_PDB"]]!="ATOM" &&
line_vec[_atom_site["group_PDB"]]!="HETATM") ||
(line_vec[_atom_site["group_PDB"]]=="HETATM" &&
(het_opt==0 ||
(het_opt==2 && line_vec[_atom_site["label_comp_id"]]!="MSE")))
) continue;
alt_id=".";
if (_atom_site.count("label_alt_id")) // in 39.4 % of entries
alt_id=line_vec[_atom_site["label_alt_id"]];
if (alt_id!="." && alt_id!="A") continue;
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) continue;
if (atom.size()==1) atom=" "+atom+" ";
else if (atom.size()==2) atom=" "+atom+" "; // wrong for sidechain H
else if (atom.size()==3) atom=" "+atom;
else if (atom.size()>=5) continue;
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) continue;
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=" ";
if (_atom_site.count("pdbx_PDB_model_num") &&
model_index!=line_vec[_atom_site["pdbx_PDB_model_num"]])
{
model_index=line_vec[_atom_site["pdbx_PDB_model_num"]];
if (PDB_lines.size() && ter_opt>=1) break;
if (PDB_lines.size()==0 || split_opt>=1)
{
PDB_lines.push_back(tmp_str_vec);
prev_asym_id=asym_id;
}
}
if (prev_asym_id!=asym_id)
{
if (prev_asym_id!="" && ter_opt>=2) break;
if (split_opt>=2) PDB_lines.push_back(tmp_str_vec);
}
if (prev_asym_id!=asym_id) prev_asym_id=asym_id;
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+=" ";
i++;
i8_stream<<"ATOM "
<<setw(5)<<i<<" "<<atom<<" "<<AA<<setw(2)<<asym_id.substr(0,2)
<<setw(5)<<resi.substr(0,5)<<" "
<<setw(8)<<line_vec[_atom_site["Cartn_x"]].substr(0,8)
<<setw(8)<<line_vec[_atom_site["Cartn_y"]].substr(0,8)
<<setw(8)<<line_vec[_atom_site["Cartn_z"]].substr(0,8);
PDB_lines.back().push_back(i8_stream.str());
i8_stream.str(string());
}
_atom_site.clear();
line_vec.clear();
alt_id.clear();
asym_id.clear();
AA.clear();
}
if (compress_type) fin_gz.close();
else fin.close();
line.clear();
return PDB_lines.size();
}
void output_dock(const vector<string>&chain_list, const int ter_opt,
const int split_opt, const int infmt_opt, const string atom_opt,
const int mirror_opt, double **ut_mat, const string&fname_super)
{
size_t i;
int chain_i,a;
string name;
int chainnum;
double x[3]; // before transform
double x1[3]; // after transform
string line;
vector<vector<string> >PDB_lines;