//calculate simple TMscore
double ZoomIn_Align::T_Similar(double *rotmat_,int *ali1,int *ali2)
{
int i;
int ii,jj;
double dist2;
double ori_d;
double score;
double d_0=d0;
XYZ temp;
score=0.0;
temp=0.0;
ori_d=d_0*d_0;
for(i=0;i<moln2;i++)
{
if(ali2[i]==-1)continue;
if(ali2[i]<0)ii=ali2[i]+INT_MAX_NUM;
else ii=ali2[i];
jj=i;
rot_point(mol1[ii],temp,rotmat_);
dist2=mol2[jj].distance_square(temp);
score+=1.0/(1.0+dist2/ori_d);
}
return score;
}
double TM_align::TM_Vector_Score_CB(int ii,int jj,double *rotmat_,
XYZ *mol1,XYZ *mol2,int moln1,int moln2)
{
XYZ temp1,temp2;
double v1[3],v2[3];
double d1,d2;
double score;
int range=0;
if(ii<0||jj<0)return 0.5;
if(ii+range>=moln1||jj+range>=moln2)return 0.5;
if(rotmat_!=0)
{
TMs_Cache_Point(mol1,ii,temp1,rotmat_);
rot_point(TM_cb1[ii],temp2,rotmat_);
}
else
{
temp1=mol1[ii];
temp2=TM_cb1[ii];
}
(temp1-temp2).xyz2double(v1);
(mol2[jj]-TM_cb2[jj]).xyz2double(v2);
d1=sqrt(dot(v1,v1,3));
d2=sqrt(dot(v2,v2,3));
if(d1>2.0||d2>2.0||d1<1.0||d2<1.0)return 0.0;
score=dot(v1,v2,3)/d1/d2;
score=limit(score,-1.0,1.0);
return (score+1.0)/2;
}
void ZoomIn_Align::Kill_Bad(double thres,double cutoff,double *rotmat_)
{
int i;
int ii,jj;
double cut;
double dist;
XYZ temp;
double Dou_Thres=thres*thres;
double SQURE_DIST=MAX_DIST*MAX_DIST;
for(i=0;i<moln2;i++)
{
ii=ali2[i];
jj=i;
if(ii>=0)
{
rot_point(mol1[ii],temp,rotmat_);
dist=mol2[jj].distance_square(temp);
if(dist>SQURE_DIST)
{
ali2[jj]=-1;
ali1[ii]=-1;
}
else if(dist>Dou_Thres)
{
cut=Ali3_Vector_Score_Forward(ii,jj,rotmat_,mol1,mol2,moln1,moln2,SCALE);
if(cut<cutoff)
{
ali2[jj]=-1;
ali1[ii]=-1;
}
}
}
}
}
double TM_align::TM_Align_Get_Score_Part_TMsco(XYZ *mol1,XYZ *mol2,double *rotmat_,
int moln1,int moln2,int *ali2)
{
int i;
double dist2;
double ori_d=d0*d0;
double tms;
int pos;
XYZ xyz;
double ws_sco=0.0;
//calc_score
for(i=0;i<moln2;i++)
{
pos=ali2[i];
if(pos<0 || pos>=moln1)continue;
//single
if(rotmat_!=0)rot_point(mol1[pos],xyz,rotmat_);
else xyz=mol1[pos];
dist2=mol2[i].distance_square(xyz);
tms=1.0/(1.0+dist2/ori_d);
//total score
ws_sco+=tms;
}
return ws_sco;
}
t_color texture_plan(t_obj object, t_point inter)
{
float x;
float y;
int colo;
t_point rot;
t_plan *tmp;
normal = normal_sphere(*(t_sphere *)(obj.obj), inter, ray);
if (!object.texture)
return (object.color);
tmp = ((t_plan *)object.obj);
rot = vec_dir(new_point(0, 0, 0), new_point(tmp->a, tmp->b, tmp->c));
x = rot.x + rot.y + rot.z;
inter = rot_point(new_point(inter.x - rot.x * (tmp->d / (tmp->a + tmp->b +
tmp->c)), inter.y - rot.y * (tmp->d / (tmp->a + tmp->b + tmp->c)),
inter.z - rot.z * (tmp->d / (tmp->a + tmp->b + tmp->c))),
get_rot_mat(M_PI / 2 * rot.z / x, 0, -M_PI / 2 * rot.x / x));
colo = 0;
x = (inter.x - floor(inter.x / 30) * 30) / 30 * object.texture->width;
y = (10 - (inter.z - floor(inter.z / 10) * 10))
/ 10 * object.texture->height;
ft_memcpy(&colo, object.texture->data + ((int)x * (object.texture->bpp /
8)) + ((int)y * object.texture->sl), 3);
return (normalize(new_point((def.red * 2 - 255) / 255 + normal.x,
-(def.green * 2 - 255) / 255 + normal.y, (def.blue * 2 - 255)
/ 255 + normal.z)));
}
//==================== virtual function ====================//-> part[1]: score
//given alignment and rotmat, return scores (maybe TMscore,RMSD and LALI, etc)
double CLEFAPS::CLEPAPS_Make_Score(Align_Record & align_record)
{
int i;
int ii,jj;
double dist2;
double ori_d;
double sco;
double rms;
double tms;
int count;
int lali;
double rmsd;
//init equal
align_record.alignment.resize(moln2);
for(i=0;i<moln2;i++)align_record.alignment[i]=ali2[i];
align_record.rotmat.resize(12);
for(i=0;i<12;i++)align_record.rotmat[i]=CLEP_rotmat[i];
//calculate
double d_0=TM_d0;
XYZ temp=0.0;
ori_d=d_0*d_0;
sco=0.0;
rms=0.0;
count=0;
for(i=0;i<moln2;i++)
{
ii=ali2[i];
jj=i;
if(ii==-1)continue;
#ifdef DEBUG
overrange_debug_test(ii,moln1);
overrange_debug_test(jj,moln2);
lessrange_debug_test(ii,0);
lessrange_debug_test(jj,0);
#endif
rot_point(mol1[ii],temp,CLEP_rotmat);
dist2=mol2[jj].distance_square(temp);
sco+=1.0/(1.0+dist2/ori_d);
rms+=dist2;
count++;
}
//evaluate
rmsd=sqrt(1.0*rms/count);
lali=count;
tms=1.0*sco/TM_smaller;
//final
align_record.RMSD=rmsd;
align_record.lali=lali;
align_record.TMsco=tms;
align_record.main_sco=tms;
return tms;
}
double TM_align::TM_Align_Get_Score_Part_Rmsd(XYZ *mol1,XYZ *mol2,double *rotmat_,
int moln1,int moln2,int *ali2)
{
int i;
double dist2;
int pos;
XYZ xyz;
int lali=0;
double ws_sco=0.0;
//calc_score
for(i=0;i<moln2;i++)
{
pos=ali2[i];
if(pos<0 || pos>=moln1)continue;
//single
if(rotmat_!=0)rot_point(mol1[pos],xyz,rotmat_);
else xyz=mol1[pos];
dist2=mol2[i].distance_square(xyz);
//total score
ws_sco+=dist2;
lali++;
}
return 1.0*sqrt(1.0*ws_sco/lali);
}
void ZoomIn_Align::Elongation(double *rotmat_,double thres,int cutoff,int *ali1,int *ali2)
{
int i;
int ii,jj;
int index1,index2;
double Dou_Thres=thres*thres;
int success;
XYZ temp1,temp2,temp;
int cut1,cut2,cut;
//forward_elongation
for(i=0;i<moln2;i++)
{
if(ali2[i]<0)continue;
//forward
index1 = ali2[i];
index2 = i;
#ifdef DEBUG
overrange_debug_test(index1,moln1);
overrange_debug_test(index2,moln2);
lessrange_debug_test(index1,0);
lessrange_debug_test(index2,0);
#endif
for(;;)
{
success=0; //default:fail
index1++;
index2++;
if(index1>moln1-1 || index2>moln2-1) break;
jj=ali1[index1];
ii=ali2[index2];
if(jj!=-1 && ii!=-1) break;
else if(jj!=-1 && ii==-1)
{
rot_point(mol1[index1],temp,rotmat_);
cut1=Ali3_Vector_Score_Forward(index1,index2,rotmat_,mol1,mol2,moln1,moln2,SCALE);
cut2=Ali3_Vector_Score_Forward(index1,jj,rotmat_,mol1,mol2,moln1,moln2,SCALE);
if((mol2[index2].distance_square(temp) < mol2[jj].distance_square(temp)) || cut1>cut2)
{
ali2[jj]=-1;
ali1[index1]=index2;
ali2[index2]=index1;
success=1; //now success
}
}
else if(jj==-1 && ii!=-1)
{
rot_point(mol1[index1],temp1,rotmat_);
rot_point(mol1[ii],temp2,rotmat_);
cut1=Ali3_Vector_Score_Forward(index1,index2,rotmat_,mol1,mol2,moln1,moln2,SCALE);
cut2=Ali3_Vector_Score_Forward(ii,index2,rotmat_,mol1,mol2,moln1,moln2,SCALE);
if((mol2[index2].distance_square(temp1) < mol2[index2].distance_square(temp2)) || cut1>cut2)
{
ali1[ii]=-1;
ali1[index1]=index2;
ali2[index2]=index1;
success=1; //now success
}
}
else
{
rot_point(mol1[index1],temp,rotmat_);
cut=Ali3_Vector_Score_Forward(index1,index2,rotmat_,mol1,mol2,moln1,moln2,SCALE);
if(mol2[index2].distance_square(temp) < Dou_Thres || cut>cutoff)
{
ali1[index1]=index2;
ali2[index2]=index1;
success=1; //now success
}
}
if(success==0)break; //failed
i++;
}//end of FOR(;;)
}//end of FOR(i)
//backward_elongation
for(i=moln2-1;i>=0;i--)
{
if(ali2[i]<0)continue;
//forward
index1 = ali2[i];
index2 = i;
#ifdef DEBUG
overrange_debug_test(index1,moln1);
overrange_debug_test(index2,moln2);
lessrange_debug_test(index1,0);
lessrange_debug_test(index2,0);
#endif
for(;;)
{
success=0; //default:fail
index1--;
index2--;
if(index1<0 || index2<0) break;
jj=ali1[index1];
ii=ali2[index2];
if(jj!=-1 && ii!=-1) break;
else if(jj!=-1 && ii==-1)
{
rot_point(mol1[index1],temp,rotmat_);
cut1=Ali3_Vector_Score_Backward(index1,index2,rotmat_,mol1,mol2,moln1,moln2,SCALE);
cut2=Ali3_Vector_Score_Backward(index1,jj,rotmat_,mol1,mol2,moln1,moln2,SCALE);
if((mol2[index2].distance_square(temp) < mol2[jj].distance_square(temp)) || cut1>cut2)
{
ali2[jj]=-1;
ali1[index1]=index2;
ali2[index2]=index1;
success=1; //now success
}
}
else if(jj==-1 && ii!=-1)
{
rot_point(mol1[index1],temp1,rotmat_);
rot_point(mol1[ii],temp2,rotmat_);
cut1=Ali3_Vector_Score_Backward(index1,index2,rotmat_,mol1,mol2,moln1,moln2,SCALE);
cut2=Ali3_Vector_Score_Backward(ii,index2,rotmat_,mol1,mol2,moln1,moln2,SCALE);
if((mol2[index2].distance_square(temp1) < mol2[index2].distance_square(temp2)) || cut1>cut2)
{
ali1[ii]=-1;
ali1[index1]=index2;
ali2[index2]=index1;
success=1; //now success
}
}
else
{
rot_point(mol1[index1],temp,rotmat_);
cut=Ali3_Vector_Score_Backward(index1,index2,rotmat_,mol1,mol2,moln1,moln2,SCALE);
if(mol2[index2].distance_square(temp) < Dou_Thres || cut>cutoff)
{
ali1[index1]=index2;
ali2[index2]=index1;
success=1; //now success
}
}
if(success==0)break; //failed
i--;
}//end of FOR(;;)
}//end of FOR(i)
}
