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;
}
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;
}
}
//input Confo_Angle (*dist,*bend,*tort), output XYZ_Type data_structure (*r)
//dist[0] : -1.0;
//dist[1]-[n]: normal
//bend[0]-[1]: -9.9
//bend[2]-[n]: normal
//tort[0]-[2]: -9.9
//tort[3]-[n]: normal
void Confo_Lett::ctc_ori(double *dist,double *bend,double *tort,int n,XYZ *r,XYZ *init)
{
int i;
double radi;
XYZ xyz;
xyz=0.0;
XYZ ori[3],pos[3];
//real_process//
Matrix_Unit(cle_T_Back,1.0);
for(i=0;i<n;i++)
{
if(dist==NULL)radi=3.8;
else radi=dist[i];
if(i==0)r[i]=0.0;
else if(i==1)
{
r[i]=0.0;
r[i].X=radi;
}
else if(i==2)
{
Universal_Rotation(cle_Z_Axis,bend[i],cle_R_Theta);
Vector_Dot(cle_D_Back,radi,cle_X_Axis,3);
Matrix_Multiply(cle_T_Pre,cle_T_Back,cle_R_Theta);
Vector_Multiply(cle_D_Pre,cle_T_Pre,cle_D_Back);
Matrix_Equal(cle_T_Back,cle_T_Pre);
xyz.double2xyz(cle_D_Pre);
r[i]=r[i-1]+xyz;
}
else
{
Universal_Rotation(cle_Z_Axis,bend[i],cle_R_Theta);
Universal_Rotation(cle_X_Axis,tort[i],cle_R_Thor);
Vector_Dot(cle_D_Back,radi,cle_X_Axis,3);
Matrix_Multiply(cle_temp,cle_R_Thor,cle_R_Theta);
Matrix_Multiply(cle_T_Pre,cle_T_Back,cle_temp);
Vector_Multiply(cle_D_Pre,cle_T_Pre,cle_D_Back);
Matrix_Equal(cle_T_Back,cle_T_Pre);
xyz.double2xyz(cle_D_Pre);
r[i]=r[i-1]+xyz;
}
}
//whether do ini_vector
if(init!=NULL && n>=3)
{
for(i=0;i<3;i++)
{
ori[i]=init[i];
pos[i]=r[i];
}
Get_Initial(ori,pos,cle_r1,cle_r2);
Matrix_Multiply(cle_T_Pre,cle_r2,cle_r1);
for(i=0;i<n;i++)
{
r[i].xyz2double(cle_D_Back);
Vector_Multiply(cle_D_Pre,cle_T_Pre,cle_D_Back);
xyz.double2xyz(cle_D_Pre);
r[i]=ori[0]+xyz;
}
}
}