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reconstruction.c
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reconstruction.c
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/**********
This program is used to convert CG conf. to All-Atom structure
-developed by Ya-Zhou Shi,Xun-Xun Wang, Li-Zhou, Ya-Lan Tan based on the rmsd1.0.c from Xi Zhang:
***********/
#include<stdio.h>
#include<math.h>
#include<dirent.h>
#include<sys/types.h>
#include<sys/stat.h>
#include<time.h>
#include<string.h>
#include<stdlib.h>
#define w 0.02 //生成R矩阵时乘上这个系数是为了防止因矩阵元过大而导致特征值难以计算
#define RMSD_limit 3.0 //RMSD上限，如果片段与CG核苷酸RMSD大于该值，则无法匹配；
#define cut 1.60
#define nm_frag 8
FILE *fragA[20],*fragG[20],*fragC[20],*fragU[20],*CG,*out_AA;
FILE *inpdb, *outpdb;
char atom[20][5000],typen_A[20][50][4],typen_G[20][50][4],typen_C[20][50][4],typen_U[20][50][4],type[5000][4],typen_AA[20][5000][4];
char type_A[20][50][5],type_G[20][50][5],type_C[20][50][5],type_U[20][50][5],type_AA[20][5000][5];
float x_A[20][5][50],x_G[20][5][50],x_C[20][5][50],x_U[20][5][50],x[5][5000];
int id[20],idnu[20],duo1,duo2,NA[20],NG[20],NC[20],NU[20],N,N_AA[20],nucl_AA,atom_AA[20][5000];
char mark1,mark2,mark3,chain[20];
float r,Q,f;
float x_CG[20][5][5],y_CG[5][5],R[5][5],R_T[5][5], xmiddle[20][5],ymiddle[5];
double eigenvalue[5], lambda, Tao[5][5], A[5][5], U[20][5][5], B[5][5], dis, dis_r;
float x_AA[20][5][50],xy[5];
char atomCG[5000][5],typeACG[5000][5],chainCG[5000][5];
int idCG[5000],idnuCG[5000];
char QatomCG[5000][5],QtypeACG[5000][5],QchainCG[5000][5],Qtype[5000][5];
int QidCG[5000],QidnuCG[5000];
float Qx[5][5000];
int atom_number;
int condition;
/******************************************************************/
FILE *op;
char Oatom[10000],Otype_A[10000][5],Otypen_A[10000][5],Ochain[10000];
int Oid[10000],Oidnu[10000];
float Ox[10000],Oy[10000],Oz[10000],Omark1,Omark2;
int N_S;
int Npdb,Nii;
char infileN[1000][20],temp[4],fileN[500][4];
long double RMSD[20];
/*******************************************************************/
int main(int argc, char *argv[])
{
void Input(void),optimize(),reconstruction();
int readN(char file_name[1000][20]),readpdb();
int i;
Input();
inpdb=fopen(argv[1],"r+");
outpdb=fopen("AA_Result.pdb","w+");
N=readpdb();
fclose(inpdb);
if(QtypeACG[1][0]!='P')
{
condition=1;
for(i=1;i<=N;i++)
{
strcpy(atomCG[i+1],QatomCG[i]);
idCG[i+1]=QidCG[i];
strcpy(typeACG[i+1],QtypeACG[i]);
strcpy(type[i+1],Qtype[i]);
strcpy(chainCG[i+1],QchainCG[i]);
idnuCG[i+1]=QidnuCG[i];
x[1][i+1]=Qx[1][i];
x[2][i+1]=Qx[2][i];
x[3][i+1]=Qx[3][i];
}
strcpy(atomCG[1],QatomCG[1]);
idCG[1]=QidCG[1];
strcpy(typeACG[1],"P");
strcpy(type[1],Qtype[1]);
strcpy(chainCG[1],QchainCG[1]);
idnuCG[1]=QidnuCG[1];
x[1][1]=Qx[1][1]+2.00;
x[2][1]=Qx[2][1]+2.00;
x[3][1]=Qx[3][1]+2.00;
strcpy(atomCG[N+1],QatomCG[N]);
idCG[N+1]=QidCG[N];
strcpy(typeACG[N+1],"P");
strcpy(type[N+1],Qtype[N]);
strcpy(chainCG[N+1],QchainCG[N]);
idnuCG[N+1]=QidnuCG[N];
x[1][N+2]=Qx[1][N]+2.00;
x[2][N+2]=Qx[2][N]+2.00;
x[3][N+2]=Qx[3][N]+2.00;
N=N+2;
}
else
{
condition=0;
for(i=1;i<=N;i++)
{
strcpy(atomCG[i],QatomCG[i]);
idCG[i]=QidCG[i];
strcpy(typeACG[i],QtypeACG[i]);
strcpy(type[i],Qtype[i]);
strcpy(chainCG[i],QchainCG[i]);
idnuCG[i]=QidnuCG[i];
x[1][i]=Qx[1][i];
x[2][i]=Qx[2][i];
x[3][i]=Qx[3][i];
}
strcpy(atomCG[N+1],QatomCG[N]);
idCG[N+1]=QidCG[N];
strcpy(typeACG[N+1],"P");
strcpy(type[N+1],Qtype[N]);
strcpy(chainCG[N+1],QchainCG[N]);
idnuCG[N+1]=QidnuCG[N];
x[1][N+1]=Qx[1][N]+2.00;
x[2][N+1]=Qx[2][N]+2.00;
x[3][N+1]=Qx[3][N]+2.00;
N=N+1;
}
reconstruction();
optimize();
fclose(outpdb);
return 0;
}
void reconstruction()
{
void Assemble();
atom_number=1;
Assemble();
}
void Input(void)
{
int i,ii;
char filename[40];
for(ii=1;ii<=nm_frag;ii++)
{
sprintf(filename,"fragment/A/fragA%d.pdb",ii); fragA[ii]=fopen(filename,"r+");
sprintf(filename,"fragment/G/fragG%d.pdb",ii); fragG[ii]=fopen(filename,"r+");
sprintf(filename,"fragment/C/fragC%d.pdb",ii); fragC[ii]=fopen(filename,"r+");
sprintf(filename,"fragment/U/fragU%d.pdb",ii); fragU[ii]=fopen(filename,"r+");
i = 0;
while(!feof(fragA[ii]))
{
i++;
fscanf(fragA[ii],"%s %d %s %s %s %d %f %f %f %s %s %s\n",&atom[ii][i],&id[ii],type_A[ii][i],typen_A[ii][i],&chain[ii],&idnu[ii],&x_A[ii][1][i],&x_A[ii][2][i],&x_A[ii][3][i],&mark1,&mark2,&mark3);
}
NA[ii]=i;
i = 0;
while(!feof(fragG[ii]))
{
i++;
fscanf(fragG[ii],"%s %d %s %s %s %d %f %f %f %s %s %s\n",&atom[ii][i],&id[ii],type_G[ii][i],typen_G[ii][i],&chain[ii],&idnu[ii],&x_G[ii][1][i],&x_G[ii][2][i],&x_G[ii][3][i],&mark1,&mark2,&mark3);
}
NG[ii]=i;
i = 0;
while(!feof(fragC[ii]))
{
i++;
fscanf(fragC[ii],"%s %d %s %s %s %d %f %f %f %s %s %s\n",&atom[ii][i],&id[ii],type_C[ii][i],typen_C[ii][i],&chain[ii],&idnu[ii],&x_C[ii][1][i],&x_C[ii][2][i],&x_C[ii][3][i],&mark1,&mark2,&mark3);
}
NC[ii]=i;
i = 0;
while(!feof(fragU[ii]))
{
i++;
fscanf(fragU[ii],"%s %d %s %s %s %d %f %f %f %s %s %s\n",&atom[ii][i],&id[ii],type_U[ii][i],typen_U[ii][i],&chain[ii],&idnu[ii],&x_U[ii][1][i],&x_U[ii][2][i],&x_U[ii][3][i],&mark1,&mark2,&mark3);
}
NU[ii]=i;
fclose(fragA[ii]);
fclose(fragG[ii]);
fclose(fragC[ii]);
fclose(fragU[ii]);
}
}
void Assemble()
{
int i,j,k,kk,ii;
void Rotate();
void Replace(int kk);
long double min;
for(i=1;i<=N;i++)
{
if(fmod(i,3)==0)
{
for(j=1;j<=3;j++)
{
y_CG[j][1]=x[j][i-2]; y_CG[j][2]=x[j][i-1]; y_CG[j][3]=x[j][i]; y_CG[j][4]=x[j][i+1]; //粗粒化单个核苷酸片段的坐标y_CG；
}
//////////////G////////////
for(ii=1;ii<=nm_frag;ii++)
{
if(strcmp(type[i],"G")==0)
{
N_AA[ii]=NG[ii];
for(j=1; j<=3; j++)
{
x_CG[ii][j][1]=x_G[ii][j][1];
x_CG[ii][j][2]=x_G[ii][j][6];
x_CG[ii][j][3]=x_G[ii][j][13];
x_CG[ii][j][4]=x_G[ii][j][24];
}
for(k=1;k<=N_AA[ii];k++)
{
atom_AA[ii][k]=i/3+k-1; strcpy(type_AA[ii][k],type_G[ii][k]); strcpy(typen_AA[ii][k],typen_G[ii][k]); nucl_AA=i/3;
for(j=1;j<=3;j++)
{
x_AA[ii][j][k]=x_G[ii][j][k];
}
}
}
//////////////A////////////
else if(strcmp(type[i],"A")==0)
{
N_AA[ii]=NA[ii];
for(j=1; j<=3; j++)
{
x_CG[ii][j][1]=x_A[ii][j][1];
x_CG[ii][j][2]=x_A[ii][j][6];
x_CG[ii][j][3]=x_A[ii][j][13];
x_CG[ii][j][4]=x_A[ii][j][23];
}
for(k=1;k<=N_AA[ii];k++)
{
atom_AA[ii][k]=i/3+k-1; strcpy(type_AA[ii][k],type_A[ii][k]); strcpy(typen_AA[ii][k],typen_A[ii][k]); nucl_AA=i/3;
for(j=1;j<=3;j++)
{
x_AA[ii][j][k]=x_A[ii][j][k];
}
}
}
//////////////C////////////
else if(strcmp(type[i],"C")==0)
{
N_AA[ii]=NC[ii];
for(j=1; j<=3; j++)
{
x_CG[ii][j][1]=x_C[ii][j][1];
x_CG[ii][j][2]=x_C[ii][j][6];
x_CG[ii][j][3]=x_C[ii][j][13];
x_CG[ii][j][4]=x_C[ii][j][21];
}
for(k=1;k<=N_AA[ii];k++)
{
atom_AA[ii][k]=i/3+k-1; strcpy(type_AA[ii][k],type_C[ii][k]); strcpy(typen_AA[ii][k],typen_C[ii][k]); nucl_AA=i/3;
for(j=1;j<=3;j++)
{
x_AA[ii][j][k]=x_C[ii][j][k];
}
}
}
//////////////U////////////
else
{
N_AA[ii]=NU[ii];
for(j=1; j<=3; j++)
{
x_CG[ii][j][1]=x_U[ii][j][1];
x_CG[ii][j][2]=x_U[ii][j][6];
x_CG[ii][j][3]=x_U[ii][j][13];
x_CG[ii][j][4]=x_U[ii][j][21];
}
for(k=1;k<=N_AA[ii];k++)
{
atom_AA[ii][k]=i/3+k-1; strcpy(type_AA[ii][k],type_U[ii][k]); strcpy(typen_AA[ii][k],typen_U[ii][k]); nucl_AA=i/3;
for(j=1;j<=3;j++)
{
x_AA[ii][j][k]=x_U[ii][j][k];
}
}
}
Rotate(x_CG,y_CG,ii); //用已有全原子片段重合替换粗粒化核苷酸；
}
min=RMSD[1];
for(ii=1;ii<=nm_frag;ii++)
{
if(RMSD[ii]<=min)
{
min=RMSD[ii];
kk=ii;
}
}
Replace(kk);
}
}
}
void Rotate(float xx_CG[10][5][5],float yy_CG[5][5],int ii)
{
int i,j,k,n;
float max, min, unit, xnew_CG[5][5];
double sigma, sigma0,xnew_CG_i;
//////////////////初始化////////////
for(i=0;i<=4;i++) //ininalization of matrix;
{
xmiddle[ii][i]=0.0; ymiddle[i]=0.0;
for(j=0;j<=4;j++)
{
R[i][j]=0.0; R_T[i][j]=0.0; Tao[i][j]=0.0; //U[i][j]=0.0; B[i][j]=0.0;
}
}
RMSD[ii]=0.0;
/////////////////////中心化///////////////
for(i=1;i<=4;i++)
{
xmiddle[ii][1] += xx_CG[ii][1][i]; xmiddle[ii][2] += xx_CG[ii][2][i]; xmiddle[ii][3] += xx_CG[ii][3][i];
ymiddle[1] += yy_CG[1][i]; ymiddle[2] += yy_CG[2][i]; ymiddle[3] += yy_CG[3][i];
}
xmiddle[ii][1] /= 4.0; xmiddle[ii][2] /= 4.0; xmiddle[ii][3] /= 4.0;
ymiddle[1] /= 4.0; ymiddle[2] /= 4.0; ymiddle[3] /= 4.0; //几何中心
for(i=1; i<=4; i++)
{
for(j=1; j<=3; j++)
{
xx_CG[ii][j][i] -= xmiddle[ii][j]; //各自的几何中心移动到0点
yy_CG[j][i] -= ymiddle[j];
}
}
/////////////计算旋转矩阵//////////////
for(i=1; i<=3; i++)
{
for(j=1; j<=3; j++)
{
for(k=1; k<=4; k++)
{
R[i][j] += yy_CG[i][k]*xx_CG[ii][j][k]*w; //w取值如何定？
}
}
}
for(i=1; i<=3; i++)
{
for(j=1; j<=3; j++)
{
R_T[i][j] = R[j][i];
}
}
for(i=1; i<=3; i++)
{
for(j=1; j<=3; j++)
{
for(k=1; k<=3; k++)
{
Tao[i][j] += R_T[i][k]*R[k][j];
}
}
}
/////////////////////////本征值求解////////////////////////////
min = -100.; max = 10000.; unit = 0.0001; sigma0 = 0; n = 0; dis=0.0;
lambda = min;
do
{
//解特征值，这样看可能比较难理解。其实这里就是求特征值中的求行列式
sigma = (Tao[1][1]-lambda)*(Tao[2][2]-lambda)*(Tao[3][3]-lambda) + Tao[1][2]*Tao[2][3]*Tao[3][1] + Tao[1][3]*Tao[2][1]*Tao[3][2] - Tao[1][3]*Tao[3][1]*(Tao[2][2]-lambda) - Tao[1][2]*Tao[2][1]*(Tao[3][3]-lambda) - Tao[2][3]*Tao[3][2]*(Tao[1][1]-lambda);
if(sigma * sigma0 < 0) //前后两次计算的sigma相乘为0意味着两个sigma负号不同，所以解（过0点）一定在两个sigma之间
{
n++;
eigenvalue[n] = lambda - unit/2.; //求得特征值lambda后，记录下这个特征值eigenvalue[]
}
sigma0 = sigma;
lambda += unit;
}
while( !(n==3 || lambda > max) ); //求完三个特征值就跳出，后面那个跳出条件我忘了是啥意思了。。
for(i=0; i<=4; i++)
{
for(j=0; j<=4; j++)
{
A[i][j] = 0.; B[i][j]=0.;U[ii][i][j]=0.; xnew_CG[i][j]=0.; //xnew[i][k]=0.; //初始化
}
}
for(i=1; i<=3; i++) //计算旋转矩阵，就是把三个本征矢量塞进一个3×3矩阵里面。注意，这里三个本征矢量的顺序将决定后面把哪一根轴转成x，哪一根转成z
{
A[1][i] = 1.; //解本征矢本征不需要三个变量，因此将第一个值定为1,其实定为其他也可以，噢，不能为0
A[3][i] = ( Tao[2][1] + (Tao[2][2] - eigenvalue[i])*(eigenvalue[i]-Tao[1][1])/Tao[1][2] ) / ( Tao[1][3]*(Tao[2][2]-eigenvalue[i])/Tao[1][2] - Tao[2][3] ); //看着很复杂，找张纸推导一下就可以了
A[2][i] = ( eigenvalue[i]-Tao[1][1]-Tao[1][3] * A[3][i] ) / Tao[1][2];
}
for(i=1; i<=3; i++)
{
dis = sqrt( A[1][i]*A[1][i] + A[2][i]*A[2][i] + A[3][i]*A[3][i] );
A[1][i] /= dis; //注意，这个矩阵是由本征矢合并成的本征矩阵
A[2][i] /= dis;
A[3][i] /= dis;
// test = Tao[3][1] * A[1][i] + Tao[3][2] * A[2][i] + (Tao[3][3] - eigenvalue[i]) * A[3][i]; //解方程用前两条，检验用第三条，会有误差，主要来源于数值解法的本征矢
// printf("test if = 0 test = %f\n", test); //越接近0,误差越小
}
for(i=1; i<=3; i++)
{
for(j=1; j<=3; j++)
{
for(k=1; k<=3; k++)
{
B[j][i] += R[j][k]*A[k][i]/ sqrt(eigenvalue[i]); //求B矩阵
}
}
}
// printf("\nthe U matrix\n");
for(i=1; i<=3; i++)
{
for(j=1; j<=3; j++)
{
for(k=1; k<=3; k++)
{
U[ii][i][j] += B[i][k]*A[j][k]; //求旋转矩阵U
}
}
}
///////////////////旋转整个片段，以尽可能重合/////////
for(k=1; k<=4; k++)
{
dis_r = 0.;
for(i=1; i<=3; i++)
{
xnew_CG_i=0.;
for(j=1; j<=3; j++)
{
xnew_CG_i += U[ii][i][j]*xx_CG[ii][j][k];
}
xnew_CG[i][k]=xnew_CG_i;
dis_r += (xnew_CG[i][k]-yy_CG[i][k])*(xnew_CG[i][k]-yy_CG[i][k]);
}
RMSD[ii] += dis_r;
}
RMSD[ii] = sqrt(RMSD[ii]/4.0);
for(k=1;k<=4; k++)
{
for(j=1; j<=3; j++)
{
xnew_CG[j][k] += ymiddle[j]; //各自的几何中心移动到0点
yy_CG[j][k] += ymiddle[j];
}
}
}
void Replace(int ii)
{
int i,j,k;
float xnew[5][50];
for(k=1;k<=N_AA[ii];k++)
{
for(i=1;i<=3;i++)
{
x_AA[ii][i][k] -= xmiddle[ii][i]; xnew[i][k]=0.;
}
}
for(k=1;k<=N_AA[ii];k++)
{
for(i=1;i<=3;i++)
{
for(j=1;j<=3;j++)
{
xnew[i][k] += U[ii][i][j]*x_AA[ii][j][k];
}
xnew[i][k]=xnew[i][k]+ymiddle[i];
}
}
for(k=1;k<=N_AA[ii]-3;k++)
{
Oid[atom_number]=atom_number;
strcpy(Otype_A[atom_number],type_AA[ii][k]);
strcpy(Otypen_A[atom_number],typen_AA[ii][k]);
Oidnu[atom_number]=nucl_AA;
Ox[atom_number]=xnew[1][k];
Oy[atom_number]=xnew[2][k];
Oz[atom_number]=xnew[3][k];
atom_number++;
}
}
void optimize()
{
int i=1,number;
float centerx,centery,centerz;
float allx=0.0,ally=0.0,allz=0.0;
number=atom_number-1;
// printf("%d\n",number);
for(i=1;i<=number;i++)
{
allx=allx+Ox[i];
ally=ally+Oy[i];
allz=allz+Oz[i];
}
centerx=allx/number;
centery=ally/number;
centerz=allz/number;
for(i=1;i<=number;i++)
{
Ox[i]=Ox[i]-centerx;
Oy[i]=Oy[i]-centery;
Oz[i]=Oz[i]-centerz;
}
if(condition==1)
{
for(i=4;i<=number;i++)
{
fprintf(outpdb,"%-6s%5d %-4s %2s %s%4d %11.3f%8.3f%8.3f\n","ATOM",Oid[i],Otype_A[i],Otypen_A[i],"A",Oidnu[i],Ox[i],Oy[i],Oz[i]);
}
}
else
{
for(i=1;i<=number;i++)
{
fprintf(outpdb,"%-6s%5d %-4s %2s %s%4d %11.3f%8.3f%8.3f\n","ATOM",Oid[i],Otype_A[i],Otypen_A[i],"A",Oidnu[i],Ox[i],Oy[i],Oz[i]);
}
}
}
int readpdb()
{
char numl1[10000][10],numl2[10000][10];
char x1[10000][10], y1[10000][10], z1[10000][10];
char a[500];
int i,j;
i=1;
memset(x1, 0, sizeof(x1));
memset(y1, 0, sizeof(y1));
memset(z1, 0, sizeof(z1));
while(fgets(a,500,inpdb)!=NULL)
{
sprintf(QatomCG[i],"%c%c%c%c",a[0],a[1],a[2],a[3]);
sprintf(numl1[i],"%c%c%c%c",a[8],a[9],a[10],a[11]);
QidCG[i]=atof(numl1[i]);
sprintf(QtypeACG[i],"%c%c%c",a[13],a[14],a[15]);
sprintf(Qtype[i],"%c",a[19]);//residue_type
sprintf(QchainCG[i],"%c",a[21]);//chain_type
sprintf(numl2[i],"%c%c%c%c",a[22],a[23],a[24],a[25]);//residue_number
QidnuCG[i]=atof(numl2[i]);
sprintf(x1[i],"%c%c%c%c%c%c%c%c",a[30],a[31],a[32],a[33],a[34],a[35],a[36],a[37]);//x_coordinate
Qx[1][i]=atof(x1[i]);
sprintf(y1[i],"%c%c%c%c%c%c%c%c",a[38],a[39],a[40],a[41],a[42],a[43],a[44],a[45]);//y_coordinate
Qx[2][i]=atof(y1[i]);
sprintf(z1[i],"%c%c%c%c%c%c%c%c",a[46],a[47],a[48],a[49],a[50],a[51],a[52],a[53]);//z_coordinate
Qx[3][i]=atof(z1[i]);
i++;
}
memset(a,0,sizeof(a));
j=i-1;
return j;
}