void Confo_Back::Construct_Mol_II(XYZ pre,XYZ cur,XYZ nxt,double bend,double tort,double dist,XYZ &out)
{
XYZ xyz;
double x[3],y[3];
double z[3];
double cb1[3],cb2[3];
xyz=nxt-cur;
xyz.xyz2double(x);
xyz=cur-pre;
xyz.xyz2double(y);
//check
double angle=Vector_Angle(x,y,3);
if(fabs(angle)<1.e-3||fabs(angle-M_PI)<1.e-3)
{
x[0]+=0.05;
x[2]-=0.05;
y[0]-=0.05;
y[2]+=0.05;
}
//calc
cross(z,x,y);
Universal_Rotation(z,bend,Confo_Back_ROT_TOT);
Vector_Multiply(cb1,Confo_Back_ROT_TOT,x);
Universal_Rotation(x,tort,Confo_Back_ROT_TOT);
Vector_Multiply(cb2,Confo_Back_ROT_TOT,cb1);
Vector_Normalize(cb2,3);
Vector_Dot(cb2,dist,cb2,3);
out.double2xyz(cb2);
out+=nxt;
}
//--------------function------------//
//given CA+CB -> return dist,bend,tort
void Confo_Beta::Confo_Beta_CACB_To_Angle(XYZ *CA,XYZ *CB,int moln,double *bend,double *tort,double *dist)
{
int i;
double r,b,t;
XYZ xyz;
//process
for(i=1;i<moln-1;i++)
{
//get_point
xyz=(CA[i]-CA[i-1]);
xyz.xyz2double(beta_v1);
xyz=(CA[i+1]-CA[i]);
xyz.xyz2double(beta_v2);
xyz=(CB[i]-CA[i]);
xyz.xyz2double(beta_y);
//calc
r=dot(beta_y,beta_y);
if(r<1.e-3)
{
r=0.0;
b=0.0;
t=0.0;
}
else
{
//calc_bend
b=Vector_Angle(beta_v1,beta_y,3);
//calc_tort
cross(beta_x1,beta_v1,beta_v2);
cross(beta_x2,beta_v1,beta_y);
t=Vector_Angle(beta_x1,beta_x2,3);
if(dot(beta_x1,beta_y)<0.0)t*=-1.0;
}
//evaluate
if(dist!=NULL)dist[i]=r;
if(bend!=NULL)bend[i]=b;
if(tort!=NULL)tort[i]=t;
}
//assign head_tail
if(dist!=NULL)dist[0]=-1.0;
if(bend!=NULL)bend[0]=0.0;
if(tort!=NULL)tort[0]=0.0;
if(dist!=NULL)dist[moln-1]=-1.0;
if(bend!=NULL)bend[moln-1]=0.0;
if(tort!=NULL)tort[moln-1]=0.0;
}
//given CA -> return CB (Levitt's method)
void Confo_Beta::Confo_Beta_Levit_To_CACB(XYZ *CA,XYZ *CB,int moln,double *dist)
{
int i,j;
XYZ xyz;
double beta,theta;
//process
theta=Confo_Beta_Levit_Angle;
for(i=1;i<moln-1;i++) //omit head and tail
{
//init
if(dist==NULL)beta=Confo_Beta_Levit_Radii;
else beta=dist[i];
if(beta<0.0)
{
CB[i]=CA[i];
continue;
}
//calc
xyz=(CA[i]-CA[i-1]);
xyz.xyz2double(beta_v1);
xyz=(CA[i]-CA[i+1]);
xyz.xyz2double(beta_v2);
Vector_Addition(beta_x1,beta_v1,beta_v2,3);
Vector_Normalize(beta_x1,3);
cross(beta_x2,beta_v1,beta_v2);
Vector_Normalize(beta_x2,3);
//evaluate
CA[i].xyz2double(beta_ca);
for(j=0;j<3;j++)beta_cb[j]=beta_ca[j]+beta*(cos(theta)*beta_x1[j]+sin(theta)*beta_x2[j]);
CB[i].double2xyz(beta_cb);
}
//assign head_tail //this might be modified in the future...
if(moln>1)
{
CB[0]=CB[1]-CA[1]+CA[0];
CB[moln-1]=CB[moln-2]-CA[moln-2]+CA[moln-1];
}
else
{
CB[0]=CA[0];
CB[moln-1]=CA[moln-1];
}
}
//given CA and dist,bend,tort -> return CB (Zheng & Liu's method)
void Confo_Beta::Confo_Beta_Angle_To_CACB(XYZ *CA,XYZ *CB,int moln,double *bend,double *tort,double *dist)
{
int i,j;
XYZ xyz;
double beta,radii;
//process
for(i=1;i<moln-1;i++)
{
//init
if(dist==NULL)beta=Confo_Beta_Levit_Radii;
else beta=dist[i];
if(beta<0.0)
{
CB[i]=CA[i];
continue;
}
//calc
xyz=(CA[i]-CA[i-1]);
xyz.xyz2double(beta_v1);
xyz=(CA[i+1]-CA[i]);
xyz.xyz2double(beta_v2);
cross(beta_y,beta_v1,beta_v2);
Universal_Rotation(beta_y,bend[i],Confo_Beta_rotmat);
Vector_Multiply(beta_x1,Confo_Beta_rotmat,beta_v1);
Universal_Rotation(beta_v1,tort[i],Confo_Beta_rotmat);
Vector_Multiply(beta_x2,Confo_Beta_rotmat,beta_x1);
//evaluate
radii=sqrt(dot(beta_x2,beta_x2));
CA[i].xyz2double(beta_ca);
for(j=0;j<3;j++)beta_cb[j]=beta_ca[j]+beta*beta_x2[j]/radii;
CB[i].double2xyz(beta_cb);
}
//assign head_tail //this might be modified in the future...
if(moln>1)
{
CB[0]=CB[1]-CA[1]+CA[0];
CB[moln-1]=CB[moln-2]-CA[moln-2]+CA[moln-1];
}
else
{
CB[0]=CA[0];
CB[moln-1]=CA[moln-1];
}
}
void Confo_Back::Construct_CB(XYZ N,XYZ Ca,XYZ C,double bend,double tort,double dist,XYZ &Cb)
{
XYZ xyz;
double x[3],y[3];
double z[3];
double cb1[3],cb2[3];
xyz=C-Ca;
xyz.xyz2double(x);
xyz=Ca-N;
xyz.xyz2double(y);
cross(z,x,y);
Universal_Rotation(z,-1.0*bend,Confo_Back_ROT_TOT);
Vector_Multiply(cb1,Confo_Back_ROT_TOT,x);
Universal_Rotation(x,-1.0*tort,Confo_Back_ROT_TOT);
Vector_Multiply(cb2,Confo_Back_ROT_TOT,cb1);
Vector_Normalize(cb2,3);
Vector_Dot(cb2,dist,cb2,3);
Cb.double2xyz(cb2);
Cb+=Ca;
}
//===================== Recon_Beta ==================//
//given CA+CB, and AMI_Dist, update SC
void Confo_Beta::Recon_Beta_1(XYZ *CA,XYZ *CB,int moln,char *ami) //return SC
{
int i;
XYZ xyz;
double radii;
double multi;
double v[3];
for(i=0;i<moln;i++)
{
xyz=(CB[i]-CA[i]);
xyz.xyz2double(v);
radii=dot(v,v);
if(radii<1.e-3)continue;
Vector_Normalize(v,3);
multi=CB_AMI_Dist[ami[i]-'A'];
if(multi<0.0)continue;
Vector_Dot(v,multi,v,3);
xyz.double2xyz(v);
CB[i]=CA[i]+xyz;
}
}