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

		};
		if(!on_list(node->prev[i]->id,rootlist,rootnum)){
			if(s=num_cycle(node->prev[i])){
				for(r=0;r<cycle_size[s];r++){
				if(!on_list(cycles[s][r],rootlist,rootnum)){
					rootlist[rootnum++]=cycles[s][r];
					tempr=find_key(cycles[s][r],natom,head);
					tempr->root=1;
				};
				};/*for all the cycle members*/
			}else{
				node->prev[i]->root=1;
				rootlist[rootnum++]=node->prev[i]->id;
			};
		};
	};
	if(traverse_num==4&&check_tors(node->id,node->prev[i]->id))
	fprintf(outfile,"BRANCH %d %d\n",node->new_id,(node->prev[i])->new_id);
	if(k=num_cycle(node->prev[i])){
		newlist=is_cycle(node->prev[i]);
		traverse_cycle(newlist,k,0,list,index);
		if(traverse_num==2&&check_tors(node->id,node->prev[i]->id))
		nbranch--;
		if(traverse_num==4&&check_tors(node->id,node->prev[i]->id))
		fprintf(outfile,"ENDBRANCH %d %d\n",node->new_id,(node->prev[i])->new_id);
	}else{  	/*if not a cycle*/
	visit_prev(node->prev[i],list,index,nlist,nindex);
	if(traverse_num==2&&check_tors(node->id,node->prev[i]->id))
	nbranch--;
	if(traverse_num==4&&check_tors(node->id,node->prev[i]->id))
	fprintf(outfile,"ENDBRANCH %d %d\n",node->new_id,(node->prev[i])->new_id);
	};/*if a cycle or not if-else*/
	};
   }; /*for i to prev_num*/
	if(traverse_num==2){
/*NEED TO LOOK FOR 3H leaves in the case of C, 2 for N if valid tors*/
	switch (atmtype(atmptr,node->id)) {
		case 'C':
		case 'a':
		case 'b': if ((node->prev_num==3)&&atmtype(atmptr,node->prev[0]->id)=='H'&&atmtype(atmptr,node->prev[1]->id)=='H'&&atmtype(atmptr,node->prev[2]->id)=='H')torsdof--;break;
		case 'N': if ((node->prev_num==2)&&atmtype(atmptr,node->prev[0]->id)=='H'&&atmtype(atmptr,node->prev[1]->id)=='H')torsdof--;break;
	};/*switch*/
	};/*end of tordof correction on tn=3*/
	break;
};/*switch*/
}

void     visit_next(node,list,index,plist,pindex)
ATOM_NODE * node;
int *list,*index;
int *plist,*pindex;
{
	int i,j,k,r,s,*newlist;
        int connects;
	double mk;
	ATOM_NODE * tempr;

	if((node->next_num+node->prev_num)==1) return;
	if(on_list(node->id,list,*index)) return;
	if(num_cycle(node)){
		newlist=is_cycle(node);
       	        traverse_cycle(newlist,num_cycle(node),1,list,index);
		return;
     	};
	*(list + * index)=node->id;
	*index=*(index) + 1;
	check_h(node);
	if(traverse_num==1&&!((node->prev_num==1)&&on_list(node->prev[0],list,*index))){
		prev_next(node,list,index,plist,pindex);
		for(k=0;k<*pindex;k++){
			*(plist+k)=0;
		};
		*pindex=0;
	};

switch(node->next_num) {
case 0  : return;
case 1  :connects=node->next[0]->prev_num+node->next[0]->next_num;
	if(((connects>0)||num_cycle(node->next[0]))&&!on_list(node->next[0]->id,list,*index)){
	   if(!on_list(node->next[0]->id,rootlist,rootnum)&&connects>1&& traverse_num==1){
		if(aflag && is_amide(node)>0)printf("3:found amide next %d\n",node->id);
		else
		if(!(bflag && check_back(node,0,'n')))
		head_tors=add_tors(node->id,(node->next[0])->id,head_tors);
           };
	if(traverse_num==2&&check_tors(node->id,node->next[0]->id))
	nbranch++;
	if(traverse_num==2&&!nbranch&&!check_tors(node->id,node->next[0]->id)){
		if(!on_list(node->id,rootlist,rootnum)){
		node->root=1;
		rootlist[rootnum++]=node->id;
		};
		if(!on_list(node->next[0]->id,rootlist,rootnum)){
			if(s=num_cycle(node->next[0])){
				for(r=0;r<cycle_size[s];r++){
				if(!on_list(cycles[s][r],rootlist,rootnum)){
					rootlist[rootnum++]=cycles[s][r];
					tempr=find_key(cycles[s][r],natom,head);
					tempr->root=1;
				};
				};/*for all the cycle members*/
			}else{
			node->next[0]->root=1;
			rootlist[rootnum++]=node->next[0]->id;
			};
		};
	};
	if(traverse_num==4&&check_tors(node->id,node->next[0]->id))
	fprintf(outfile,"TORS %d %d\n",node->new_id,node->next[0]->new_id);
	if(k=num_cycle(node->next[0])){
		newlist=is_cycle(node->next[0]);
		traverse_cycle(newlist,k,1,list,index);
	        if(traverse_num==2&&check_tors(node->id,node->next[0]->id))
		nbranch--;
	        if(traverse_num==4&&check_tors(node->id,node->next[0]->id))
	        fprintf(outfile,"ENDTORS %d %d\n",node->new_id,node->next[0]->new_id);
	}else{ /*else2*/
	visit_next(node->next[0],list,index,plist,pindex);
	if(traverse_num==2&&check_tors(node->id,node->next[0]->id))
	nbranch--;
	if(traverse_num==4&&check_tors(node->id,node->next[0]->id))
	fprintf(outfile,"ENDTORS %d %d\n",node->new_id,node->next[0]->new_id);
	};
	};/*if case1*/
	break;
default: for(i=0;i<node->next_num;i++){
               connects=node->next[i]->prev_num+node->next[i]->next_num;
	if(((connects>0)||num_cycle(node->next[i]))&&!on_list(node->next[i]->id,list,*index)){
	   if(!on_list(node->next[i]->id,rootlist,rootnum)&&connects>1&&traverse_num==1){
		if(aflag && is_amide(node)>0)printf("4:found amide next %d\n",node->id);
		else
		if(!(bflag && check_back(node,i,'n')))
		head_tors=add_tors(node->id,node->next[i]->id,head_tors);
	   };
	if(traverse_num==2&&check_tors(node->id,node->next[i]->id))
	nbranch++;
	if(traverse_num==2&&!nbranch&&!check_tors(node->id,node->next[i]->id)){
		if(!on_list(node->id,rootlist,rootnum)){
		node->root=1;
		rootlist[rootnum++]=node->id;
		};	
		if(!on_list(node->next[i]->id,rootlist,rootnum)){
			if(s=num_cycle(node->next[i])){
				for(r=0;r<cycle_size[s];r++){
				if(!on_list(cycles[s][r],rootlist,rootnum)){
					rootlist[rootnum++]=cycles[s][r];
					tempr=find_key(cycles[s][r],natom,head);
					tempr->root=1;
				};
				};/*for all the cycle members*/
			}else{
			node->next[i]->root=1;
			rootlist[rootnum++]=node->next[i]->id;
			};
		};	
	};
	if(traverse_num==4&&check_tors(node->id,node->next[i]->id)){
	fprintf(outfile,"BRANCH %d %d\n",node->new_id,node->next[i]->new_id);
	};
	if(k=num_cycle(node->next[i])){
		newlist=is_cycle(node->next[i]);
		traverse_cycle(newlist,k,1,list,index);
	        if(traverse_num==2&&check_tors(node->id,node->next[i]->id))
		nbranch--;
	        if(traverse_num==4&&check_tors(node->id,node->next[i]->id)){
	        fprintf(outfile,"ENDBRANCH %d %d\n",node->new_id,node->next[i]->new_id);
		};
	}else{ /*else2*/
	   visit_next(node->next[i],list,index,plist,pindex);
	if(traverse_num==2&&check_tors(node->id,node->next[i]->id))
	nbranch--;
	if(traverse_num==4&&check_tors(node->id,node->next[i]->id))
	fprintf(outfile,"ENDBRANCH %d %d\n",node->new_id,node->next[i]->new_id);
	};	
	};
	};/*forall nexts*/
	if(traverse_num==2){
/*NEED TO LOOK FOR 3 H leaves in the case of C, 2 for N if valid tors*/
	switch (atmtype(atmptr,node->id)){
		case 'a':
		case 'b': if ((node->next_num==3)&&atmtype(atmptr,node->next[0]->id)=='H'&&atmtype(atmptr,node->next[1]->id)=='H'&&atmtype(atmptr,node->next[2]->id)=='H')torsdof--;break;
/*need to decrement torsdof*/
		case 'N': if ((node->next_num==3)&&atmtype(atmptr,node->next[0]->id)=='H'&&atmtype(atmptr,node->next[1]->id)=='H')torsdof--;break;
	};/*switch*/
	};/*end of tordof correction on tn=3*/
	break; /*for the nexts*/
};/*switch on node->next_num*/
}

void traverse_cycle(cyclelist,cyclenum,to_next,tlist,tnum)
int  *cyclelist,cyclenum,to_next;
int *tlist,*tnum;

{
	int i,j,k,m,n,r,p_num,n_num,connect_num,h_num;
	int prev_con, next_con;
	int connects;
        int np_num;
        int *nplist, *np_index;
	double mk;
	char rec[7],*chptr;/*for firstpart ofoutput*/
	ATOM_NODE * temp1,* temp2;
	TORS_ANGLE * tempt;

	nplist=(int*) calloc(natom,sizeof(n_num));
	np_index=(int*) calloc(1,sizeof(n_num));
	*np_index=0;
if(!cyclelist){
	printf("error in traverse_cycle\n");
	exit(1);
	};
	n=cycle_size[cyclenum];
	for(i=0;i<n;i++){
	temp1=find_key(cyclelist[i],n,head);
	if(!temp1){
		printf("error in finding %d\n",cyclelist[i]);
		exit(1);
	};
	if(!on_list(cyclelist[i],tlist,*tnum)){
		*(tlist + *tnum)=cyclelist[i];
		*tnum=(*tnum)+1;
	};
	if(traverse_num==2&&!nbranch&&!on_list(cyclelist[i],rootlist,rootnum)){
		rootlist[rootnum++]=cyclelist[i];
	};		
	check_h(temp1);
	connect_num=temp1->prev_num + temp1->next_num;
	p_num=temp1->prev_num;
	n_num=temp1->next_num;
/*printf("tc:switching on %d's p_num=%d,n_num=%d\n",temp1->id,p_num,n_num);*/
	switch(connect_num){
	case 0 : break;
	case 1 : printf("error in traverse_cycle:cycle with 1 connection\n");
		 exit(1);
	case 2 : for(j=0;j<p_num;j++){
 	if(!on_list(temp1->prev[j]->id,rootlist,rootnum)&&!on_list(temp1->prev[j]->id,tlist,*tnum)){
		 if(!eq_cycle(temp1->prev[j]->id,temp1->id)){
		connects=temp1->prev[j]->prev_num+temp1->prev[j]->next_num;
		if(traverse_num==1){
		       if(!to_next)
			next_prev(temp1->prev[j],tlist,tnum,nplist,np_index);
		       if(to_next)
			prev_next(temp1->prev[j],tlist,tnum,nplist,np_index);
			for(k=0;k<*np_index;k++){
				*(nplist+k)=0;
			};
			*np_index=0;
		if(aflag && is_amide(temp1)<0)printf("5:found amide prev %d\n",temp1->id);
		else
		if(connects>1&&!(bflag&&check_back(temp1,j,'p')))
		head_tors=add_tors(temp1->id,temp1->prev[j]->id,head_tors);
		};
	if(traverse_num==2&&check_tors(temp1->id,temp1->prev[j]->id))
	nbranch++;
	if(traverse_num==2&&!nbranch&&!check_tors(temp1->id,temp1->prev[j]->id)){
		if(!on_list(temp1->id,rootlist,rootnum)){
		temp1->root=1;
		rootlist[rootnum++]=temp1->id;
		};
		if(!on_list(temp1->prev[j]->id,rootlist,rootnum)){
		temp1->prev[j]->root=1;
		rootlist[rootnum++]=temp1->prev[j]->id;
		};
	};
      	if(traverse_num==4&&check_tors(temp1->id,temp1->prev[j]->id))
	fprintf(outfile,"TORS %d %d\n",temp1->new_id,temp1->prev[j]->new_id);
      	visit_prev(temp1->prev[j],tlist,tnum,nplist,np_index);
      	if(traverse_num==2&&check_tors(temp1->id,temp1->prev[j]->id))
		nbranch--;
      	if(traverse_num==4&&check_tors(temp1->id,temp1->prev[j]->id)){
	fprintf(outfile,"ENDTORS %d %d\n",temp1->new_id,temp1->prev[j]->new_id);
			};
   		};
  	};/*if not on rootlist and not on tlist*/
 	};/*case2:prevs*/
	for(j=0;j<n_num;j++){
 	if(!on_list(temp1->next[j]->id,rootlist,rootnum)&&!on_list(temp1->next[j]->id,tlist,*tnum)){
		 if(!eq_cycle(temp1->next[j]->id,temp1->id)){

		connects=temp1->next[j]->prev_num+temp1->next[j]->next_num;
		if(traverse_num==1){
		       if(!to_next)
			next_prev(temp1->next[j],tlist,tnum,nplist,np_index);
		       if(to_next)
			prev_next(temp1->next[j],tlist,tnum,nplist,np_index);
			for(k=0;k<*np_index;k++){
				*(nplist+k)=0;
			};
			*np_index=0;
		if(aflag && is_amide(temp1)>0)printf("6:found amide next %d\n",temp1->id);
		else
		if(connects>1&&!(bflag&&check_back(temp1,j,'n')))
		head_tors=add_tors(temp1->id,temp1->next[j]->id,head_tors);
		};
	if(traverse_num==2&&check_tors(temp1->id,temp1->next[j]->id))
	nbranch++;
	if(traverse_num==2&&!nbranch&&!check_tors(temp1->id,temp1->next[j]->id)){
		if(!on_list(temp1->id,rootlist,rootnum)){
		temp1->root=1;
		rootlist[rootnum++]=temp1->id;
		};
		if(!on_list(temp1->next[j]->id,rootlist,rootnum)){
		temp1->next[j]->root=1;
		rootlist[rootnum++]=temp1->next[j]->id;
		};
	};
      	if(traverse_num==4&&check_tors(temp1->id,temp1->next[j]->id))
	fprintf(outfile,"TORS %d %d\n",temp1->new_id,temp1->next[j]->new_id);
	visit_next(temp1->next[j],tlist,tnum,nplist,np_index);
	if(traverse_num==2&&check_tors(temp1->id,temp1->next[j]->id))
		nbranch--;
	if(traverse_num==4&&check_tors(temp1->id,temp1->next[j]->id))
       	fprintf(outfile,"ENDTORS %d %d\n",temp1->new_id,temp1->next[j]->new_id);
    		};/*!num_cycle*/
  	};/*!on_list*/
	};/*for case 2 nexts*/
	break;

	default  :
	for(j=0;j<p_num;j++){
   		prev_con=temp1->prev[j]->prev_num+temp1->prev[j]->next_num;
   		if(!on_list(temp1->prev[j]->id,rootlist,rootnum)&&!on_list(temp1->prev[j]->id,tlist,*tnum)){
		if(!eq_cycle(temp1->prev[j]->id,temp1->id)){
		if(traverse_num==1){
                      if(!to_next){
			next_prev(temp1->prev[j],tlist,tnum,nplist,np_index);
			};
                      if(to_next)
			prev_next(temp1->prev[j],tlist,tnum,nplist,np_index);
				for(k=0;k<*np_index;k++){
					*(nplist+k)=0;
				};
				*np_index=0;
				if((traverse_num==1)&&(prev_con>1)){
					if(aflag && is_amide(temp1)<0)printf("7:found amide prev %d\n",temp1->id);
					else
					if(!(bflag&&check_back(temp1,j,'p')))
					head_tors=add_tors(temp1->id,(temp1->prev[j])->id,head_tors);
				};
		};/*first traversal*/
	if(traverse_num==2&&check_tors(temp1->id,temp1->prev[j]->id))
	nbranch++;
	if(traverse_num==2&&!nbranch&&!check_tors(temp1->id,temp1->prev[j]->id)){
		if(!on_list(temp1->id,rootlist,rootnum)){
		temp1->root=1;
		rootlist[rootnum++]=temp1->id;
		};
		if(!on_list(temp1->prev[j]->id,rootlist,rootnum)){
		temp1->prev[j]->root=1;
		rootlist[rootnum++]=temp1->prev[j]->id;
		};
	};
	if(traverse_num==4&&check_tors(temp1->id,temp1->prev[j]->id))
	fprintf(outfile,"BRANCH %d %d\n",temp1->new_id,temp1->prev[j]->new_id);
	/*in any case visit the node*/
	visit_prev(temp1->prev[j],tlist,tnum,nplist,np_index);
	if(traverse_num==2&&check_tors(temp1->id,temp1->prev[j]->id))
	nbranch--;
	if(traverse_num==4&&check_tors(temp1->id,temp1->prev[j]->id))
	fprintf(outfile,"ENDBRANCH %d %d\n",temp1->new_id,temp1->prev[j]->new_id);
   	};/*not a cycle atom*/
       	};/*not previously visited*/
	}; /*for-prev*/
	for(j=0;j<n_num;j++) {
   		next_con=temp1->next[j]->prev_num+temp1->next[j]->next_num;
   		if(!on_list(temp1->next[j]->id,rootlist,rootnum)&&!on_list(temp1->next[j]->id,tlist,*tnum)){
               if(!eq_cycle(temp1->next[j]->id,temp1->id)){
		if(traverse_num==1){
                      if(!to_next)
			next_prev(temp1->next[j],tlist,tnum,nplist,np_index);
                      if(to_next)
			prev_next(temp1->next[j],tlist,tnum,nplist,np_index);
			for(k=0;k<*np_index;k++){
				*(nplist+k)=0;
			};
			*np_index=0;
			if(traverse_num==1&&(next_con>1)){
					if(aflag && is_amide(temp1)>0)printf("8:found amide next %d\n",temp1->id);
					else
					if(!(bflag&&check_back(temp1,j,'n')))
					head_tors=add_tors(temp1->id,temp1->next[j]->id,head_tors);
			};
		};/*first traversal*/
	if(traverse_num==2&&check_tors(temp1->id,temp1->next[j]->id))
	nbranch++;
	if(traverse_num==2&&!nbranch&&!check_tors(temp1->id,temp1->next[j]->id)){
		if(!on_list(temp1->id,rootlist,rootnum)){
		temp1->root=1;
		rootlist[rootnum++]=temp1->id;
		};
		if(!on_list(temp1->next[j]->id,rootlist,rootnum)){
		temp1->next[j]->root=1;
		rootlist[rootnum++]=temp1->next[j]->id;
		};
	};
	if(traverse_num==4&&check_tors(temp1->id,temp1->next[j]->id))
	fprintf(outfile,"BRANCH %d %d\n",temp1->new_id,temp1->next[j]->new_id);
	/* any case visit the node*/
	visit_next(temp1->next[j],tlist,tnum,nplist,np_index);
	if(traverse_num==2&&check_tors(temp1->id,temp1->next[j]->id))
	nbranch--;
	if(traverse_num==4&&check_tors(temp1->id,temp1->next[j]->id))
	fprintf(outfile,"ENDBRANCH %d %d\n",temp1->new_id,temp1->next[j]->new_id);
   			};
		};
	}; /*for-next*/
	break;
}; /*end of switch  on to_next statement*/
};/*for each node*/
	/*free(nplist);*/
}

void traverse(rootlist,root_num,con_num)
int rootlist[],root_num,con_num;

{
	int i,j,k,n,p_num,n_num,connect_num,h_num;
        int *newlist;
	int prev_con, next_con;
	int *travlist,trav_index;
        int np_num;
        int *nplist,*np_index;
	double mk;
	char rec[7],*chptr;/*for firstpart ofoutput*/
	ATOM_NODE * temp_root,* temp;

	h_num=0;
	trav_index=0;
	np_num=0;
        np_index=&np_num;
        n=0;
	travlist = (int*) calloc (con_num,sizeof(next_con));
	nplist = (int*) calloc (con_num,sizeof(next_con));
	if(traverse_num==4)fprintf(outfile,"ROOT\n");
	for(i=0;i<root_num;i++){
		temp_root=find_key(rootlist[i],con_num,head);
		if(!temp_root){
			printf("error in finding %d\n",rootlist[i]);
			exit(1);
		};
		*(travlist + trav_index)=rootlist[i];
		trav_index++;
		check_h(temp_root);
	};/*end of first for loop on all the roots*/
	/*at this point update outatom*/
	outatom=outatom+h_num;
	if(traverse_num==4)fprintf(outfile,"ENDROOT\n");