autotors.c

c++编写的并行拉马克遗传算法的程序。实现分析对接程序

int key1,key2;
{
	TORS_ANGLE *temp1;
	int result;

	result=0;
	temp1=head_tors;
	while(temp1&&temp1->id1&&temp1->id2){
		if(((key1==temp1->id1&&key2==temp1->id2)||
		    (key1==temp1->id2&&key2==temp1->id1))&&temp1->status=='A') {
			result=1;
		};
		if(temp1->next){
			temp1=temp1->next;
		}else temp1=NULL;
	};
	return(result);
}

TORS_ANGLE *   add_tors(key1,key2,head)
int key1,key2;
TORS_ANGLE * head;

{    
	TORS_ANGLE * temp;

	if(!key1||!key2){
		printf("in add_tors with key error\n");
		exit(1);
	};
	ntors++;
	if(!head){
		head=get_new_tors(key1,key2);
		next_tors=head;
	} else {
		if(!check_tors(key1,key2)||(head!=head_tors)){
			temp=get_new_tors(key1,key2);
			next_tors->next=temp;
			next_tors=temp;
		};
	};
	return(head);
}




int  delete_tors(num)
int num;

{    
	TORS_ANGLE * temp1, *temp2;
	int result;

	result=0;
	temp1=head_tors;

	while(temp1){
		if(num==temp1->num) {
			temp1->status='I';
			result=1;
			return(result);
		};
		temp2=temp1;
		temp1=temp1->next;
	};/*while*/
	printf("didn't find tors %d to delete\n",num);
	return(result);
}



int check_aromatic(con_num)

{
int i,j,k;
char line[LINE_LEN];
ATOM_NODE *temp;
int m,n,o;		/*counters for neighbor search*/
int cnum;
int csize;

int counter;
int member[MAX_RECORD];		/*which cycle different atoms belong to*/
float norms[MAX_RECORD][3];		/*these will be the normals*/
float neighbornorms[MAX_RECORD][3];		/*these will be the normals*/
float sizes[MAX_RECORD];
float nsizes[MAX_RECORD]; 	/*sizes of the neighboring atoms normals*/
float x1,y1,z1,x2,y2,z2;	/*these will be for the length of the sides*/
float ax,ay,az;		/*temporary variables for calculations*/
float x3,y3,z3,x4,y4,z4;	/*these will be for the length of the sides*/
float bx,by,bz;		/*temporary variables for calculations*/
float cx,cy,cz;		/*temporary variables for calculations*/
float px,py,pz,qx,qy,qz;/*various vector coeffs*/
float p[3];
float psize,qsize,theta;


/*for each cycle check for aromaticity*/
for(i=1;i<cycle_count+1;i++){
fprintf(stderr, "checking cycle %d\n",i);
	counter=1;
	csize=cycle_size[i];
	for(j=0;j<csize;j++)member[j]=-1;

for(j=0;j<csize;j++){
	m=j+csize-1;
	n=m%csize;
	strncpy(line,atmptr+cycles[i][n]*LINE_LEN,LINE_LEN);
	sscanf(line+31,"%f",&x1);
	sscanf(line+39,"%f",&y1);
	sscanf(line+47,"%f",&z1);
	strncpy(line,atmptr+cycles[i][j]*LINE_LEN,LINE_LEN);
	sscanf(line+31,"%f",&x2);
	sscanf(line+39,"%f",&y2);
	sscanf(line+47,"%f",&z2);
	ax=x2-x1;
	ay=y2-y1;
	az=z2-z1;
	strncpy(line,atmptr+cycles[i][(j+1)%csize]*LINE_LEN,LINE_LEN);
	sscanf(line+31,"%f",&x3);
	sscanf(line+39,"%f",&y3);
	sscanf(line+47,"%f",&z3);
	bx=x3-x2;
	by=y3-y2;
	bz=z3-z2;
	px=ay*bz-az*by;
	py=az*bx-ax*bz;
	pz=ax*by-ay*bx;
	p[0]=px;
	p[1]=py;
	p[2]=pz;
	for(k=0;k<3;k++){
		norms[j][k]=p[k];
	};
	psize=sqrt(px*px+py*py+pz*pz);
	sizes[j]=psize;
};
/*after computing the normals, test for planarity by computing cos(theta)*/
for(j=0;j<csize;j++){
	for(k=j+1;k<csize;k++){
		px=norms[j][0];	
		py=norms[j][1];	
		pz=norms[j][2];	
		qx=norms[k][0];	
		qy=norms[k][1];	
		qz=norms[k][2];	
		psize=sizes[j];
		qsize=sizes[k];

		theta=(px*qx+py*qy+pz*qz)/(psize*qsize);
		if((theta>=0.996||theta<=-0.996) && member[k]==-1){
			if(member[j]==-1){
				member[j]=j;
			};
			member[k]=member[j];
			counter++;
/*this keeps track of which cycle pt at k belongs to*/			
		};
	};
};
	if(counter==csize){
		for(j=0;j<csize;j++){
			if(*(atmptr+cycles[i][j]*LINE_LEN+13)=='C'){
				strncpy(atmptr+cycles[i][j]*LINE_LEN+13,"A",1);
				fprintf(stderr,"1->changed C to A for atom #%d \n",cycles[i][j]);
			};
			if(*(atmptr+cycles[i][j]*LINE_LEN+12)=='C'){
				strncpy(atmptr+cycles[i][j]*LINE_LEN+12,"A",1);
				fprintf(stderr,"2->changed C to A for atom #%d \n",cycles[i][j]);
			};
		};
	};
}
}

void print_out(key1,key2,neighbors)
int key1,key2,neighbors;

{    
	int i,j;
	char rec[7],*chptr;

	for(j=0;j<7;j++){
		rec[j]=0;
	};
	for(j=0;j<7;j++){
		rec[j]=*(atmptr+LINE_LEN*key1+j);
	};
	rec[7]='\0';
	chptr=rec;
	if(!key1||!key2){
		printf("in print_out with null key\n");
if(key1)printf("key1=%d\n",key1);
if(key2)printf("key2=%d\n",key2);
		exit(1);
	};
	if(cflag) sprintf(atmptr+LINE_LEN*key1+offset+6," %3d\n",neighbors);
	/*printf("%6s%4d %-4s",chptr,key2,atmptr+LINE_LEN*key1+12);*/
	fprintf(outfile,"%6s%4d %-4s",chptr,key2,atmptr+LINE_LEN*key1+12);

}

int check_h(node)
ATOM_NODE *node;

{
	int i,j,k;
	int nnum;
	int prevH,prevprevH;
	int nextH,nextnextH;
	char rec[7],*chptr;
	double mk;
	double mmk;
	TORS_ANGLE *tmp,*tmp2;

	prevH=0;
	nextH=0;

	mk=atof(atmptr+LINE_LEN*node->id+offset);
	if(traverse_num==3)node->new_id=outatom++;
	if(hflag){
	for(i=0;i<node->prev_num;i++){
if(!num_cycle(node->prev[i])&&!on_list(node->prev[i]->id,rootlist,rootnum)){
		mmk=atof(atmptr+LINE_LEN*node->prev[i]->id+offset);
		prevprevH=0;
		nextnextH=0;
	for(j=0;j<node->prev[i]->prev_num;j++){
	if((*(atmptr+LINE_LEN*node->prev[i]->id+13)=='C')&&
	   ((*(atmptr+LINE_LEN*node->prev[i]->prev[j]->id+12)=='H')||
	   (*(atmptr+LINE_LEN*node->prev[i]->prev[j]->id+13)=='H'))){
		mmk=mmk+atof(atmptr+LINE_LEN*node->prev[i]->prev[j]->id+offset);
		nonpolarH++;
		prevprevH++;
		node->prev[i]->prev[j]=NULL;
	};/*if non-polar prev-H*/
	};/*for all the prev's prev's*/
	for(j=0;j<node->prev[i]->next_num;j++){
	if((*(atmptr+LINE_LEN*node->prev[i]->id+13)=='C')&&
	   ((*(atmptr+LINE_LEN*node->prev[i]->next[j]->id+12)=='H')||
	   (*(atmptr+LINE_LEN*node->prev[i]->next[j]->id+13)=='H'))){
		mmk=mmk+atof(atmptr+LINE_LEN*node->prev[i]->next[j]->id+offset);
		nonpolarH++;
		nextnextH++;
		node->prev[i]->next[j]=NULL;
	};/*if non-polar next-H*/
	};/*for all the prev's next's*/
	if(traverse_num==1){
		for(j=0;j<node->prev[i]->prev_num;j++){
			if(!node->prev[i]->prev[j]){
				for(k=j+1;k<node->prev[i]->prev_num;k++){
					if(node->prev[i]->prev[k]){
					node->prev[i]->prev[j]=node->prev[i]->prev[k];
					node->prev[i]->prev[k]=NULL;
					break;
					};/*if*/
				};/*for*/
			};/*if*/
		};/*for*/
		for(j=0;j<node->prev[i]->next_num;j++){
			if(!node->prev[i]->next[j]){
				for(k=j+1;k<node->prev[i]->next_num;k++){
					if(node->prev[i]->next[k]){
					node->prev[i]->next[j]=node->prev[i]->next[k];
					node->prev[i]->next[k]=NULL;
					break;
					};/*if*/
				};/*for*/
			};/*if*/
		};/*for*/
		node->prev[i]->prev_num=node->prev[i]->prev_num-prevprevH;
		node->prev[i]->next_num=node->prev[i]->next_num-nextnextH;
		if((node->prev[i]->next_num+node->prev[i]->prev_num)==1){
			tmp=head_tors;
			while(tmp){
				if((node->prev[i]->id==tmp->id1)||(node->prev[i]->id==tmp->id2)){
					if(tmp==head_tors){
						head_tors=tmp->next;
					}else{
						tmp2->next=tmp->next;
						if(tmp==next_tors)next_tors=tmp2;
						tmp->next=NULL;
					};
				};
				tmp2=tmp;
				tmp=tmp->next;
			};
		};
	if(prevprevH+nextnextH){
		sprintf(atmptr+LINE_LEN*node->prev[i]->id+offset,"% 4.3f\n",mmk);
		if(debug)printf("new charge on %d =% 4.3f\n",node->prev[i]->id,mmk);
	};/*if traverse_num==1*/
	};/*for all of current nodes's prev of i-j prevs*/
	
	if((*(atmptr+LINE_LEN*node->id+13)=='C')&&
	   ((*(atmptr+LINE_LEN*node->prev[i]->id+12)=='H')||
	   (*(atmptr+LINE_LEN*node->prev[i]->id+13)=='H'))){
		if(traverse_num==1){
			nonpolarH++;
			prevH++;
	   		mk=mk+atof(atmptr+LINE_LEN*node->prev[i]->id+offset);
			node->prev[i]=NULL;
		};
	};
	};/*if not cycle or on rootlist*/
	};/*for all i-prev's*/
	for(i=0;i<node->next_num;i++){
if(!(num_cycle(node->next[i]))&&!(on_list(node->next[i]->id,rootlist,rootnum))){
		mmk=atof(atmptr+LINE_LEN*node->next[i]->id+offset);
		prevprevH=0;
		nextnextH=0;
	for(j=0;j<node->next[i]->prev_num;j++){
	if((*(atmptr+LINE_LEN*node->next[i]->id+13)=='C')&&
	   ((*(atmptr+LINE_LEN*node->next[i]->prev[j]->id+12)=='H')||
	   (*(atmptr+LINE_LEN*node->next[i]->prev[j]->id+13)=='H'))){
		mmk=mmk+atof(atmptr+LINE_LEN*node->next[i]->prev[j]->id+offset);
		nonpolarH++;
		prevprevH++;
		node->next[i]->prev[j]=NULL;
	};/*if non-polar prev-H*/
	};/*for all the next's prev's*/
	for(j=0;j<node->next[i]->next_num;j++){
	if((*(atmptr+LINE_LEN*node->next[i]->id+13)=='C')&&
	   ((*(atmptr+LINE_LEN*node->next[i]->next[j]->id+12)=='H')||
	   (*(atmptr+LINE_LEN*node->next[i]->next[j]->id+13)=='H'))){
		mmk=mmk+atof(atmptr+LINE_LEN*node->next[i]->next[j]->id+offset);
		nonpolarH++;
		nextnextH++;
		node->next[i]->next[j]=NULL;
	};/*if non-polar next-H*/
	};/*for all the next's next's*/
	if(traverse_num==1){
		for(j=0;j<node->next[i]->prev_num;j++){
			if(!node->next[i]->prev[j]){
				for(k=j+1;k<node->next[i]->prev_num;k++){
					if(node->next[i]->prev[k]){
					node->next[i]->prev[j]=node->next[i]->prev[k];
					node->next[i]->prev[k]=NULL;
					break;
					};/*if*/
				};/*for*/
			};/*if*/
		};/*for*/
		for(j=0;j<node->next[i]->next_num;j++){
			if(!node->next[i]->next[j]){
				for(k=j+1;k<node->next[i]->next_num;k++){
					if(node->next[i]->next[k]){
					node->next[i]->next[j]=node->next[i]->next[k];
					node->next[i]->next[k]=NULL;
					break;
					};/*if*/
				};/*for*/
			};/*if*/
		};/*for*/
		node->next[i]->prev_num=node->next[i]->prev_num-prevprevH;
		node->next[i]->next_num=node->next[i]->next_num-nextnextH;
		if((node->next[i]->next_num+node->next[i]->prev_num)==1){
			tmp=head_tors;
			while(tmp){
				if((node->next[i]->id==tmp->id1)||(node->next[i]->id==tmp->id2)){
					if(tmp==head_tors){
						head_tors=tmp->next;
					}else{
						tmp2->next=tmp->next;
						if(tmp==next_tors)next_tors=tmp2;
						tmp->next=NULL;
					};
				};
				tmp2=tmp;
				tmp=tmp->next;
			};
		};
	if(prevprevH+nextnextH){
		sprintf(atmptr+LINE_LEN*node->next[i]->id+offset,"% 4.3f\n",mmk);
		if(debug)printf("new charge on %d =% 4.3f\n",node->next[i]->id,mmk);
	};/*if traverse_num==1*/
	};/*for all of current nodes's prev of i-j prevs*/
	nnum=node->next[i]->next_num+node->next[i]->prev_num;
	if((*(atmptr+LINE_LEN*node->id+13)=='C')&&
	   ((*(atmptr+LINE_LEN*node->next[i]->id+12)=='H')||
	   (*(atmptr+LINE_LEN*node->next[i]->id+13)=='H'))){
		if(traverse_num==1){
			nonpolarH++;
			nextH++;
	   		mk=mk+atof(atmptr+LINE_LEN*node->next[i]->id+offset);
			node->next[i]=NULL;
		};
	};/*if non-polar H*/
	};/*if not on rootlist or cycle*/
	};/*for all next's*/
	if(traverse_num==1){
		for(j=0;j<node->prev_num;j++){
			if(!node->prev[j]){
				for(k=j+1;k<node->prev_num;k++){
					if(node->prev[k]){
					node->prev[j]=node->prev[k];
					node->prev[k]=NULL;
					break;
					};/*if*/
				};/*for*/
			};/*if*/
		};/*for*/
		for(j=0;j<node->next_num;j++){
			if(!node->next[j]){
				for(k=j+1;k<node->next_num;k++){
					if(node->next[k]){
					node->next[j]=node->next[k];
					node->next[k]=NULL;
					break;
					};/*if*/
				};/*for*/
			};/*if*/
		};/*for*/
		node->prev_num=node->prev_num-prevH;
		node->next_num=node->next_num-nextH;
		if((node->next_num+node->prev_num)==1){
			tmp=head_tors;
			while(tmp){
				if((node->id==tmp->id1)||(node->id==tmp->id2)){
					if(tmp==head_tors){
						head_tors=tmp->next;
					}else{
						tmp2->next=tmp->next;
						if(tmp==next_tors)next_tors=tmp2;
						tmp->next=NULL;
					};
				};
				tmp2=tmp;
				tmp=tmp->next;
			};
		};
		if(prevH+nextH){
			sprintf(atmptr+LINE_LEN*node->id+offset,"% 4.3f\n",mk);
			if(debug)printf("new charge on %d =% 4.3f\n",node->id,mk);
		};
	};
	for(j=0;j<7;j++){
		rec[j]=0;
	};
	for(j=0;j<7;j++){
		rec[j]=*(atmptr+LINE_LEN*node->id+j);
	};
	rec[7]='\0';
	chptr=rec;
	if(traverse_num==4){
		if(cflag)sprintf(atmptr+LINE_LEN*node->id+offset+6," %3d\n",node->next_num+node->prev_num);
		printf("%6s%4d %-4s",chptr,node->new_id,atmptr+LINE_LEN*node->id+12);