misc.c

药物开发中的基于结构的从头设计代码

# include "process.h"

float Distance(float a[3], float b[3])
{
	float d,tmpx,tmpy,tmpz;

	tmpx=(a[0]-b[0])*(a[0]-b[0]);
	tmpy=(a[1]-b[1])*(a[1]-b[1]);
	tmpz=(a[2]-b[2])*(a[2]-b[2]);

	d=sqrt((double)(tmpx+tmpy+tmpz));

	return d;
}

float Distance2(float a[3], float b[3])
{
	float d2,tmpx,tmpy,tmpz;

	tmpx=(a[0]-b[0])*(a[0]-b[0]);
	tmpy=(a[1]-b[1])*(a[1]-b[1]);
	tmpz=(a[2]-b[2])*(a[2]-b[2]);

	d2=tmpx+tmpy+tmpz;

	return d2;
}

void Translate_Point(float start[3], float move[3], float end[3])
{
	end[0]=start[0]+move[0];
	end[1]=start[1]+move[1];
	end[2]=start[2]+move[2];

	return;
}

void Rotate_Point(float theta, float axis[3], float origin[3], 
		  float start[3], float end[3])
{
        float mat[3][3],p[3];
        float a,b;
        int i,j;

	Unify_Vector(axis);

        a=sin((double)(theta*3.1416/180.0));
        b=cos((double)(theta*3.1416/180.0));

        for(i=0;i<=2;i++) end[i]=start[i]-origin[i];

        mat[0][0]=axis[0]*axis[0]+(1-axis[0]*axis[0])*b;
        mat[1][0]=axis[0]*axis[1]*(1-b)-axis[2]*a;
        mat[2][0]=axis[0]*axis[2]*(1-b)+axis[1]*a;
        mat[0][1]=axis[0]*axis[1]*(1-b)+axis[2]*a;
        mat[1][1]=axis[1]*axis[1]+(1-axis[1]*axis[1])*b;
        mat[2][1]=axis[1]*axis[2]*(1-b)-axis[0]*a;
        mat[0][2]=axis[0]*axis[2]*(1-b)-axis[1]*a;
        mat[1][2]=axis[1]*axis[2]*(1-b)+axis[0]*a;
        mat[2][2]=axis[2]*axis[2]+(1-axis[2]*axis[2])*b;

        for(i=0;i<=2;i++)
                {
                 p[i]=0.0;
                 for(j=0;j<=2;j++) p[i]+=(end[j]*mat[j][i]);
                }

        for(i=0;i<=2;i++) end[i]=p[i]+origin[i];

	return;
}

void Cross_Multiply(float v1[3], float v2[3], float result[3])
{
        result[0]=v1[1]*v2[2]-v2[1]*v1[2];
        result[1]=v1[2]*v2[0]-v2[2]*v1[0];
        result[2]=v1[0]*v2[1]-v2[0]*v1[1];

        return;
}

float Point_Multiply(float v1[3], float v2[3])
{
	float result;

	result=v1[0]*v2[0]+v1[1]*v2[1]+v1[2]*v2[2];

	return result;
}

float Angle_Of_Two_Vectors(float v1[3], float v2[3])
{
        float angle;
        float l1,l2,tmp;

        l1=sqrt((double)(v1[0]*v1[0]+v1[1]*v1[1]+v1[2]*v1[2]));
        l2=sqrt((double)(v2[0]*v2[0]+v2[1]*v2[1]+v2[2]*v2[2]));
        tmp=v1[0]*v2[0]+v1[1]*v2[1]+v1[2]*v2[2];

        angle=acos((double)(tmp/(l1*l2)));
        angle=angle/3.1416*180.0;

        return angle;
}

float Torsion_Angle(float p1[3], float p2[3], float p3[3], float p4[3])
{
        int i;
        float angle;
        float v12[3],v23[3],v34[3],v1[3],v2[3],v3[3];

        for(i=0;i<=2;i++)
                {
                 v12[i]=p2[i]-p1[i];
                 v23[i]=p3[i]-p2[i];
                 v34[i]=p4[i]-p3[i];
                }

        Cross_Multiply(v12,v23,v1);
        Cross_Multiply(v23,v34,v2);

        angle=Angle_Of_Two_Vectors(v1,v2);

        Cross_Multiply(v1,v2,v3);

        if((v23[0]/v3[0]>0)||(v23[1]/v3[1]>0)||(v23[2]/v3[2])>0) return angle;
        else return -angle;
}

void Unify_Vector(float vect[3])
{
	int i;
	float d;

	d=sqrt((double)(vect[0]*vect[0]+vect[1]*vect[1]+vect[2]*vect[2]));

	for(i=0;i<=2;i++) vect[i]/=d;

	return;
}

void Set_Random_Number()
{
	long seed;
	struct tm *ptr;
	time_t lt;

	lt=time(NULL);
	ptr=localtime(&lt);

	seed=10000*ptr->tm_hour+100*ptr->tm_min+ptr->tm_sec;

	srand48(seed);	// Initialize drand48()

	return;
}

char *Get_Time()
{
        struct tm *ptr;
        time_t lt;

        lt=time(NULL);
        ptr=localtime(&lt);

        return asctime(ptr);
}

void Get_Sp3_Coordinates(float v1[3], float v2[3], float v3[3], float v4[3])
// v1 and v2 are known vectors while v3 and v4 are desired vectors.
// v1, v2, v3, and v4 are all unified vectors.
{
	int i;
	float anchor[3], axis[3];

	for(i=0;i<3;i++) 
		{
		 axis[i]=-(v1[i]+v2[i]);
		 anchor[i]=0.000;
		 v3[i]=v4[i]=0.000;
		}

	Rotate_Point(90.0,axis,anchor,v1,v3);
	Rotate_Point(90.0,axis,anchor,v2,v4);

	for(i=0;i<3;i++)
		{
		 v3[i]=-v3[i];
		 v4[i]=-v4[i];
		}

	return;
}

void Get_Sp2_Coordinates(float v1[3], float v2[3], float v3[3])
// v1 and v2 are known vectors and v3 is the desired vector.
// v1, v2, and v3 are all unified vectors.
{
	int i;

	for(i=0;i<3;i++)
		{
		 v3[i]=-(v1[i]+v2[i]);
		}

	Unify_Vector(v3);

	return;
}

int Pow(int x, int y)
{
	int i,result;

	if(y<=0) return 1;
	
	result=1;

	for(i=1;i<=y;i++) result*=x;

	return result;
}

int Blank_Line_Check(char *line)
{
	int i,mark;
	int len=0;

	len=strlen(line);
	if(len<1) return TRUE;	// blank line!

	mark=0;

	for(i=0;i<len;i++)
		{
		 if(line[i]==' ') continue;
		 else if(line[i]=='\t') continue;
		 else if(line[i]=='\n') break;
		 else mark++;
		}

	if(mark==0) return TRUE;	// blank line
	else return FALSE;		// not a blank line
}	

void Memory_Allocation_Error()
{
	printf("\n");
	printf("Memory allocation error!\n");
	printf("Maybe there is not enough memory to run the program.\n");
	printf("So vote for another person as the President.\n");
	printf("Hope he would increase the budget for education & science.\n");
	exit(1);
}

void Openning_File_Error(char *filename)
{
	printf("\n");
	printf("Error: cannot open the file %s\n", filename);
	printf("Please make sure it exists.\n");
	exit(1);
}

void Reading_File_Error(char *filename)
{
	printf("\n");
	printf("Error: something wrong with %s\n", filename);
	printf("It may not have the correct format.\n");
	printf("Please check this file and try again.\n");
	exit(1);
}

void PDB_Format_Error(char *filename)
{
        printf("\n");
        printf("Error: %s lacks necessary information.\n", filename);
        printf("This file may not be in PDB format.\n");
        printf("Please check it and try again.\n");
        exit(1);
}

void Mol2_Format_Error(char *filename)
{
	printf("\n");
	printf("Error: %s lacks necessary information.\n", filename);
	printf("This file may not be in Mol2 format.\n");
	printf("Please check it and try again.\n");
	exit(1);
}

void Lig_Format_Error(char *filename)
{
	printf("\n");
	printf("Error: %s lacks necessary information.\n", filename);
	printf("This file may not be in Lig format.\n");
	printf("Please check it and try again.\n");
	exit(1);
}

void Missing_Parameter_Error(char *name)
{
        printf("\n");
        printf("Error: You have probably forgot telling me %s.\n", name);
        return;
}

void Invalid_Parameter_Error(char *name)
{
        printf("\n");
        printf("Error: %s has an invalid value.\n", name);
        return;
}

void Check_Directory(char *name)
// add the end of '/' to the directory name automatically
{
	int len;

	len=strlen(name);

	if(name[len-1]!='/') strcat(name,"/");

	return;
}