{

double A_DOT_B=A.DotProduct(B);

double A_length=A.CalculateLength();

double B_length=B.CalculateLength();

double AB=A_length*B_length;

double angle=180*acos(A_DOT_B/AB)/3.14;

return angle;

{

atom_pair x1;

x1=array[top];

int i = top - 1;

int j = bottom + 1;

atom_pair temp;

do

{

do

{

j--;

}while (x1.d>array[j].d);

do

{

i++;

} while (x1.d <array[i].d);

if (i < j)

{

temp = array[i]; // switch elements at positions i and j

//assign_atom_pair(temp,array[i]);

array[i] = array[j];

//assign_atom_pair(array[i],array[j]);

array[j] = temp;

//assign_atom_pair(array[j],temp);

}

}while (i < j);

return j; // returns middle index

{

// top = subscript of beginning of vector being considered

// bottom = subscript of end of vector being considered

// this process uses recursion - the process of calling itself

int middle;

if (top < bottom)

{

middle = partition(array, top, bottom);

quicksort(array, top, middle); // sort top partition

quicksort(array, middle+1, bottom); // sort bottom partition

}

return;

{

int i,j,rows,cols,num_total_aa,num_of_calpha,rows1,cols1,num_total_atom;

num_total_aa=0;

num_total_atom=0;

node<Residue> *cursor_ptr_aa;

node<Atom> *cursor_ptr_atom;

cursor_ptr_aa=head_aa;

while(cursor_ptr_aa!=NULL)

{

//cout<<cursor_ptr_aa->data;

cursor_ptr_atom=cursor_ptr_aa->data.GetAaHeadAtom();

while(cursor_ptr_atom!=NULL)

{

cout<<cursor_ptr_atom->data<<endl;

num_total_atom=num_total_atom+1;

cursor_ptr_atom=cursor_ptr_atom->next;

}

num_total_aa=num_total_aa+1;

cursor_ptr_aa=cursor_ptr_aa->next;

}

//rows=cols=num_total_aa;

cout<<"num_total_aa"<<num_total_aa<<endl;

cout<<"num_total_atom"<<num_total_atom<<endl;

/*

vector <atom> chain_all_atom;

for(i=0;i<w_c.size();i++)

{

for(j=0;j<w_c[i].atom_str.size();j++)

{

w_c[i].atom_str[j].res_num=w_c[i].res_num;

w_c[i].atom_str[j].chain_type=w_c[i].chain_type;

w_c[i].atom_str[j].res_id=new char[5];

w_c[i].atom_str[j].res_id=w_c[i].res_id;

chain_all_atom.push_back(w_c[i].atom_str[j]);

}

}

//center of structure

double ws_x,ws_y,ws_z;

double how_many_atom;

ws_x=0;

ws_y=0;

ws_z=0;

how_many_atom=0;

for(i=0;i<w_c.size();i++)

{

w_c[i].global_angle=0;

for(j=0;j<w_c[i].atom_str.size();j++)

{

ws_x=ws_x+w_c[i].atom_str[j].x;

ws_y=ws_y+w_c[i].atom_str[j].y;

ws_z=ws_z+w_c[i].atom_str[j].z;

how_many_atom=how_many_atom+1;

}

}

ws_x=ws_x/how_many_atom;

ws_y=ws_y/how_many_atom;

ws_z=ws_z/how_many_atom;

//cout<<ws_x<<" "<<ws_y<<" "<<ws_z<<" "<<endl;

vector<atom> surface_calpha_atom;

// int k=1;

for(i=0;i<chain_all_atom.size();i++)

{

if((strcmp(chain_all_atom[i].atom_id,"CA ")==0)&&chain_all_atom[i].asa>5&&

strncmp(chain_all_atom[i].res_id,"GLY",3)!=0)

{

//chain_all_atom[i].atomID=k;

surface_calpha_atom.push_back(chain_all_atom[i]);

//k++;

}//end if

}//end for

//consider all surface atom

vector<atom> surface_atom;

int k1=1;

for(i=0;i<chain_all_atom.size();i++)

{

//if(chain_all_atom[i].asa>5

if(strcmp(chain_all_atom[i].atom_id,"CA ")==0)

//&&strncmp(chain_all_atom[i].res_id,"GLY",3)!=0)

{

chain_all_atom[i].atomID=k1;

surface_atom.push_back(chain_all_atom[i]);

k1++;

}//end if

}//end for

rows1=cols1=surface_atom.size();

tmatrix<atom_pair> distance_matrix1(rows1,cols1);

double t_all_surface_atom;

t_all_surface_atom=0;

for(i=0;i<surface_atom.size();i++)

{

for(j=0;j<surface_atom.size();j++)

{

distance_matrix1[i][j].ID1=surface_atom[i].atomID;

distance_matrix1[i][j].ID2=surface_atom[j].atomID;

distance_matrix1[i][j].d=sqrt(pow((surface_atom[i].x-surface_atom[j].x),2)+

pow((surface_atom[i].y-surface_atom[j].y),2)+

pow((surface_atom[i].z-surface_atom[j].z),2));

}

}

vector<atom_pair> min1;

for(i=0;i<rows1;i++)

{

for(j=0;j<cols1;j++)

{

if(distance_matrix1[i][j].d!=0)

{

min1.push_back(distance_matrix1[i][j]);

}

}

}

quicksort(min1, 0, min1.size());

int n_all_surface_atom,s_all_surface_atom;

vector<atom_pair> t1_all_surface_atom;

for(n_all_surface_atom=1;n_all_surface_atom<=rows1;n_all_surface_atom++)

{

for(i=min1.size();i>=0;i--)

{

if(min1[i].ID1==n_all_surface_atom)

{t1_all_surface_atom.push_back(min1[i]);}

}

}

cout<<"After sorting"<<endl;

for(i=0;i<t1_all_surface_atom.size();i++)

{

//if(t1_all_surface_atom[i].d<7.0)

{cout<<"("<<t1_all_surface_atom[i].ID1<<","<<t1_all_surface_atom[i].ID2<<","<<t1_all_surface_atom[i].d<<")"<<endl;

}

}

rows=cols=surface_calpha_atom.size();

tmatrix<atom_pair> distance_matrix(rows,cols);

double t;

t=0;

for(i=0;i<surface_calpha_atom.size();i++)

{

for(j=0;j<surface_calpha_atom.size();j++)

{

distance_matrix[i][j].ID1=surface_calpha_atom[i].atomID;

distance_matrix[i][j].ID2=surface_calpha_atom[j].atomID;

//cout<<distance_matrix[i][j].ID1<<" "<<distance_matrix[i][j].ID2<<endl;

distance_matrix[i][j].d=sqrt(pow((surface_calpha_atom[i].x-surface_calpha_atom[j].x),2)+

pow((surface_calpha_atom[i].y-surface_calpha_atom[j].y),2)+

pow((surface_calpha_atom[i].z-surface_calpha_atom[j].z),2));

}

}

vector<atom_pair> min;

for(i=0;i<rows;i++)

{

for(j=0;j<cols;j++)

{

if(distance_matrix[i][j].d!=0)

{

min.push_back(distance_matrix[i][j]);

}

}

}

quicksort(min, 0, min.size());

for(i=min.size();i>=0;i--)

{

//if(min[i].ID1==n)

//{t1.push_back(min[i]);}

cout<<" ID1 "<<min[i].ID1<<" ID2 "<<min[i].ID2<<" d "<<min[i].d<<endl;

}

int n,s;

vector<atom_pair> t1;

Vector3D Ca; //calpha atom (DV1)

Vector3D GcSc; //geometrical center of side chain (DV2)

Vector3D FnAtom; //First nearest atom to calpha (DV3)

Vector3D SnAtom; //Second nearest atom to calpha (DV4)

Vector3D Atom_3rd,Atom_3rd_Ca;

Vector3D Atom_4th,Atom_4th_Ca;

Vector3D Atom_5th,Atom_5th_Ca;

Vector3D Atom_6th,Atom_6th_Ca;

Vector3D FnCa; //FnAtom-Ca

Vector3D SnCa; //SnAtom-Ca

Vector3D Pn; // FnCa X SnCa normal vector of plane FnCa X SnCa

Vector3D SnCa_3rd;

Vector3D Atom_3rd_4th;

Vector3D Atom_4th_5th;

Vector3D Atom_5th_6th;

Vector3D Atom_6th_Fn;

// triangle by FnAtom,SnAtom,Atom_3rd

Vector3D Sn_Fn; // SnAtom-FnAtom

Vector3D Atom_3rd_Fn; // Atom_3rd-FnAtom

Vector3D Pn_3; // normal vector of triangle by FnAtom,SnAtom,Atom_3rd

Vector3D Pn_3_re;

Vector3D Tc_3; // centroid of triangle by FnAtom,SnAtom,Atom_3rd

Vector3D Tc_3_Ca; // Ca-Tc_3

Vector3D Tc; //centroid of triangle from Ca,FnAtom,SnAtom

Vector3D TcCa; //Ca-Tc

Vector3D ScCa; //Ca-GCSc

Vector3D Ave_all_6;

Vector3D Plane_Normal;

Vector3D triangle_center;

Vector3D t_add_n;

Vector3D w_t_c;

Point v1,v2,v3;

Triangle triangle;

node<Triangle> *head_node,*previous_node;

previous_node=NULL;

double TcScp,TcCaPnp; //TcCa*ScCa

int p1,p2,m,aa_key;

double tx,ty,tz,ax,ay,az;

for(n=1;n<=rows;n++)

{

for(i=min.size();i>=0;i--)

{

if(min[i].ID1==n)

{t1.push_back(min[i]);}

}

for(p1=0;p1<surface_calpha_atom.size();p1++)

{

//take calpha atom, geometrical center of main residue

if(surface_calpha_atom[p1].atomID==n)

{

Ca.SetXComponent(surface_calpha_atom[p1].x);

Ca.SetYComponent(surface_calpha_atom[p1].y);

Ca.SetZComponent(surface_calpha_atom[p1].z);

for(p2=0;p2<w_c.size();p2++)

{

w_c[p2].angle=-100;

//w_c[p2].global_angle=0;

if(w_c[p2].res_num==surface_calpha_atom[p1].res_num&&

w_c[p2].chain_type==surface_calpha_atom[p1].chain_type&&

strcmp(w_c[p2].res_id,surface_calpha_atom[p1].res_id)==0)

{

tx=0;ty=0;tz=0;ax=0;ay=0;az=0;

m=0;

aa_key=p2;

//cout<<w_c[p2].res_id<<endl;

for(j=0;j<w_c[p2].atom_str.size();j++)

{

//cout<<w_c[p2].atom_str[j].atom_id<<endl;

if(strncmp(w_c[p2].atom_str[j].atom_id,"CA ",3)!=0&&strncmp(w_c[p2].atom_str[j].atom_id,"C ",3)!=0

&&strncmp(w_c[p2].atom_str[j].atom_id,"N ",3)!=0&&strncmp(w_c[p2].atom_str[j].atom_id,"O ",3)!=0)

{

tx=tx+w_c[p2].atom_str[j].x;

ty=ty+w_c[p2].atom_str[j].y;

tz=tz+w_c[p2].atom_str[j].z;

m=m+1;

} //end if(strncmp

}// end for(j=0

if(m!=0)

{ax=tx/m;

ay=ty/m;

az=tz/m;

}

} //end if(w_c[p2]

}//end for(p2=0..

GcSc.SetXComponent(ax);

GcSc.SetYComponent(ay);

GcSc.SetZComponent(az);

}//end if(surface_calpha..

//take 1st nearest calpha atom to main alpha atom

if(surface_calpha_atom[p1].atomID==t1[0].ID2)

{

FnAtom.SetXComponent(surface_calpha_atom[p1].x);

FnAtom.SetYComponent(surface_calpha_atom[p1].y);

FnAtom.SetZComponent(surface_calpha_atom[p1].z);

//cout<<t1[0].ID2<<endl;

v1.SetPointIndex(t1[0].ID2);

}

//take 2nd nearest calpha atom to main alpha atom

if(surface_calpha_atom[p1].atomID==t1[1].ID2)

{

SnAtom.SetXComponent(surface_calpha_atom[p1].x);

SnAtom.SetYComponent(surface_calpha_atom[p1].y);

SnAtom.SetZComponent(surface_calpha_atom[p1].z);

//cout<<t1[1].ID2<<endl;

v2.SetPointIndex(t1[1].ID2);

}

//take 3rd nearest calpha atom to main alpha atom

if(surface_calpha_atom[p1].atomID==t1[2].ID2)

{

Atom_3rd.SetXComponent(surface_calpha_atom[p1].x);

Atom_3rd.SetYComponent(surface_calpha_atom[p1].y);

Atom_3rd.SetZComponent(surface_calpha_atom[p1].z);

//cout<<t1[2].ID2<<endl;

v3.SetPointIndex(t1[2].ID2);

}

//take 4th nearest calpha atom to main alpha atom

if(surface_calpha_atom[p1].atomID==t1[3].ID2)

{

Atom_4th.SetXComponent(surface_calpha_atom[p1].x);

Atom_4th.SetYComponent(surface_calpha_atom[p1].y);

Atom_4th.SetZComponent(surface_calpha_atom[p1].z);

}

//take 5th nearest calpha atom to main alpha atom

if(surface_calpha_atom[p1].atomID==t1[4].ID2)

{

Atom_5th.SetXComponent(surface_calpha_atom[p1].x);

Atom_5th.SetYComponent(surface_calpha_atom[p1].y);

Atom_5th.SetZComponent(surface_calpha_atom[p1].z);

}

//take 6th nearest calpha atom to main alpha atom

if(surface_calpha_atom[p1].atomID==t1[5].ID2)

{

Atom_6th.SetXComponent(surface_calpha_atom[p1].x);

Atom_6th.SetYComponent(surface_calpha_atom[p1].y);

Atom_6th.SetZComponent(surface_calpha_atom[p1].z);

}

} //end for(p1=0

//vector point from gcsc to ca

ScCa=Ca-GcSc;

double x1,y1,z1,x2,y2,z2,x3,y3,z3,A,B,C,D;

x1=FnAtom.GetXComponent();

y1=FnAtom.GetYComponent();

z1=FnAtom.GetZComponent();

v1.SetPointCoordinate(x1,y1,z1);

//triangle.first.x=x1;

//triangle.first.y=y1;

//triangle.first.z=z1;

x2=SnAtom.GetXComponent();

y2=SnAtom.GetYComponent();

z2=SnAtom.GetZComponent();

v2.SetPointCoordinate(x2,y2,z2);

//triangle.Second.x=x2;

//triangle.second.y=y2;

//triangle.Second.z=z2;

x3=Atom_3rd.GetXComponent();

y3=Atom_3rd.GetYComponent();

z3=Atom_3rd.GetZComponent();

v3.SetPointCoordinate(x3,y3,z2);

//v3.SetPointIndex(12);

//cout<<v1;

//cout<<v2;

//cout<<v3;

//cout<<"here is triangle"<<endl;

triangle.SetTriangleThreePoint(v1,v2,v3);

//cout<<triangle<<endl;

insert_an_node(head_node,previous_node,triangle);

//cout<<"head"<<head_node->data<<endl;

//cout<<"previous"<<previous_node->data<<endl;

//triangle.third.x=x3;

//triangle.third.y=y3;

//triangle.third.z=z3;

//triangle center by FnAtom,SnAtom,Atom_3rd

double t_c_x,t_c_y,t_c_z;

t_c_x=(x1+x2+x3)/3;

t_c_y=(y1+y2+y3)/3;

t_c_z=(z1+z2+z3)/3;

//create 3D Vector: whole structure center -> t_c_of_triangle

double w_t_c_x,w_t_c_y,w_t_c_z;

w_t_c_x=t_c_x-ws_x;

w_t_c_y=t_c_y-ws_y;

w_t_c_z=t_c_z-ws_z;

w_t_c.SetXComponent(w_t_c_x);

w_t_c.SetYComponent(w_t_c_y);

w_t_c.SetZComponent(w_t_c_z);

//create a artificial atom

atom t_c;

t_c.atom_id =new char[5];

t_c.atom_id="T_C";

t_c.x=t_c_x;

t_c.y=t_c_y;

t_c.z=t_c_z;

t_c.asa=0;

t_c.b=0;

w_c[aa_key].atom_str.push_back(t_c);

triangle_center.SetXComponent(t_c_x);

triangle_center.SetYComponent(t_c_x);

triangle_center.SetZComponent(t_c_x);

//triangle_center.Normalize();

A=y1*(z2-z3)+y2*(z3-z1)+y3*(z1-z2);

B=z1*(x2-x3)+z2*(x3-x1)+z3*(x1-x2);

C=x1*(y2-y3)+x2*(y3-y1)+x3*(y1-y2);

D=(-1)*(x1*(y2*z3-y3*z2)+x2*(y3*z1-y1*z3)+x3*(y1*z2-y2*z1));

Plane_Normal.SetXComponent(A);

Plane_Normal.SetYComponent(B);

Plane_Normal.SetZComponent(C);

//angle between w_t_c and Plane_Normal

double global_angle=angle_between_two_vectors(w_t_c,Plane_Normal);

//double length_plane_normal;

//length_plane_normal=Plane_Normal.CalculateLength();

//Plane_Normal.Normalize();

t_add_n=triangle_center+Plane_Normal;

// t_add_n.Normalize();

double t_add_n_x,t_add_n_y,t_add_n_z;

t_add_n_x=t_add_n.GetXComponent();

t_add_n_y=t_add_n.GetYComponent();

t_add_n_z=t_add_n.GetZComponent();

//create another artificial atom

atom n_t;

n_t.atom_id =new char[5];

n_t.atom_id="N_T";

n_t.x=t_add_n_x;

n_t.y=t_add_n_y;

n_t.z=t_add_n_z;

n_t.asa=0;

n_t.b=0;

w_c[aa_key].atom_str.push_back(n_t);

double x,y,z,sign_calpha,sign_gcsc,x_gcsc,y_gcsc,z_gcsc;

x=Ca.GetXComponent();

y=Ca.GetYComponent();

z=Ca.GetZComponent();

x_gcsc=GcSc.GetXComponent();

y_gcsc=GcSc.GetYComponent();

z_gcsc=GcSc.GetZComponent();

sign_calpha=A*x+B*y+C*z+D;

sign_gcsc=A*x_gcsc+B*y_gcsc+C*z_gcsc+D;

//cout<<"sign_calpha"<<sign_calpha<<"sign_gcsc"<<sign_gcsc<<endl;

Pn=Pn.CrossProduct(FnCa,SnCa);//1stx2nd

SnCa_3rd=SnCa_3rd.CrossProduct(SnCa,Atom_3rd_Ca);//2ndx3rd

Atom_3rd_4th=Atom_3rd_4th.CrossProduct(Atom_3rd_Ca,Atom_4th_Ca);//3rdx4th

Atom_4th_5th=Atom_4th_5th.CrossProduct(Atom_4th_Ca,Atom_5th_Ca);//4thx5th

Atom_5th_6th=Atom_5th_6th.CrossProduct(Atom_5th_Ca,Atom_6th_Ca);//5thx6th

Atom_6th_Fn=Atom_6th_Fn.CrossProduct(Atom_6th_Ca,FnCa);//6thx1st

Tc=Ca+FnAtom+SnAtom;

Tc=Tc*0.33333;

Ave_all_6=Pn+SnCa_3rd+Atom_3rd_4th+Atom_4th_5th+Atom_5th_6th+Atom_6th_Fn;

Ave_all_6=Ave_all_6*0.16667;

TcCa=Ca-Tc;

//angle between TcCa and ScCa

double local_angle=angle_between_two_vectors(TcCa,ScCa);

//angle between TcCa and Pn

double PnTcCa_angle=angle_between_two_vectors(TcCa,Pn);

//angle between ScCa and Ave_all_6

double ScCa_all_angle=angle_between_two_vectors(ScCa,Ave_all_6);

FnCa=FnAtom-Ca;

SnCa=SnAtom-Ca;

Atom_3rd_Ca=Atom_3rd-Ca;

Atom_4th_Ca=Atom_4th-Ca;

Atom_5th_Ca=Atom_5th-Ca;

Atom_6th_Ca=Atom_6th-Ca;

//triangle from FnAtom,SnAtom,Atom_3rd;

Sn_Fn=SnAtom-FnAtom;

Atom_3rd_Fn=Atom_3rd-FnAtom;

Pn_3=Pn_3.CrossProduct(Sn_Fn,Atom_3rd_Fn);

Pn_3_re=Pn_3_re.CrossProduct(Atom_3rd_Fn,Sn_Fn);

double distance1=abs((A*x+B*y+C*z+D)/sqrt(A*A+B*B+C*C));

double distance2=abs((A*x_gcsc+B*y_gcsc+C*z_gcsc+D)/sqrt(A*A+B*B+C*C));

Tc_3=FnAtom+SnAtom+Atom_3rd;

Tc_3=Tc_3*0.33333;

Tc_3_Ca=Ca-Tc_3;

//angle between Tc_3_Ca and ScCa

double angle_3=angle_between_two_vectors(Tc_3_Ca,ScCa);

//angle between Tc_3_Ca and Pn_3

double angle_4=angle_between_two_vectors(Tc_3_Ca,Pn_3);

//angle between ScCa and Pn_3

double angle_5;

if(global_angle>=90)

{Pn_3=Pn_3*(-1);

angle_5=angle_between_two_vectors(ScCa,Pn_3);

}

else

{

angle_5=angle_between_two_vectors(ScCa,Pn_3);

}

//angle between ScCa and Pn_3_re

double angle_6=angle_between_two_vectors(ScCa,Pn_3_re);

double angle_7=180-angle_5;

//cout<<w_c[aa_key].res_id<<" "<<angle_3<<" "<<angle_4<<" "<<angle_5<<" "<<angle_6<<" "<<angle_7<<endl;

//double angle_8,angle_9,angle_10,angle_11;

if(sign_calpha>0&&sign_gcsc>0)

{

angle_8=angle_between_two_vectors(ScCa,Plane_Normal);

}

if(sign_calpha<0&&sign_gcsc<0)

{

angle_9=angle_between_two_vectors(ScCa,Plane_Normal);

}

if(sign_calpha>0&&sign_gcsc<0)

{

angle_10=angle_between_two_vectors(ScCa,Plane_Normal);

}

if(sign_calpha<0&&sign_gcsc>0)

{

angle_11=angle_between_two_vectors(ScCa,Plane_Normal);

}

w_c[aa_key].global_angle=global_angle;

w_c[aa_key].angle=local_angle;

w_c[aa_key].app_angle=ScCa_all_angle;

w_c[aa_key].angle_atom_3c=angle_3;

w_c[aa_key].angle_atom_3n=angle_5;

w_c[aa_key].distance_calpha_to_3atom_plane=distance1;

w_c[aa_key].distance_scgc_to_3atom_plane=distance2;

//w_c[aa_key].distance_scgc_to_3atom_plane=distance2;

//w_c[aa_key].angle_8=angle_8;

//w_c[aa_key].angle_9=angle_9;

//w_c[aa_key].angle_10=angle_10;

//w_c[aa_key].angle_11=angle_11;

w_c[aa_key].sign_calpha=sign_calpha;

w_c[aa_key].sign_gcsc=sign_gcsc;

//cout<<" distance1 is "<<distance1<<"distance2 is "<<distance2<<"angle_5 is"<<angle_5<<endl;

sp.push_back(w_c[aa_key]);

t1.clear();

}

//display_node_list(head_node);

*/