read_amber_prmtop.c

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/* File read_amber_prmtop.c begun on 20080425 by BLFoley
        Purpose: read amber prmtop file info into an assembly 
        See also: amber_prmtop_structs.h */
//#include "molecules.h"
//#include "general.h"
#include "AMBER/amber_prmtop.h"
//#include "amber_prmtop_structs.h"
//#include "declarations.h"
//void read_amber_prmtop_asis(fileset F,amber_prmtop *P);
// the amber_prmtop *P should be -already- allocated and initialized


/********** assembly *read_amber_prmtop(fileset F) **********/
/* Main function for reading the prmtop file 
 * the amber_prmtop *P should be -already- allocated and initialized 
 * BUT, it should be otherwise empty  */
void read_amber_prmtop_asis(fileset F,amber_prmtop *P){
int aa=0,anl=0,sec=0,ent=0,fld=0; // generic, line, section, entry & field counters
int newflag=0,newline=0,iseof=1; // utility flags
char line[501],over[501],tmp[81],*s1,*s2,*fgets_check; 
fpos_t line_current;


// Open files and initialize some variables
//F.F=myfreopen(F.N,"r",F.F); // don't depend on calling function to have opened
F.F=myfopen(F.N,"r"); // 
P[0].FN=strdup(F.N); // the name of the file from which these data were taken
P[0].nS=0; // the prmtop structure should be empty
P[0].S=(amber_prmtop_section*)calloc(1,sizeof(amber_prmtop_section));
P[0].SN=(char**)calloc(1,sizeof(char*));

//
// Get the first line, which should be the "VERSION"
//
if(fgets(line,500,F.F)==NULL){read_fneek("Problem in read_amber_prmtop",1,0,F.N);}
// See if the first 500 chars includes a newline...
if(strchr(line,'\n')==NULL){ // if we didn't get the whole line
        fld=500;
        fprintf(stderr,"Unusually long VERSION line.\n");
        fprintf(stderr,"-- Ignoring characters beyond 500.\n");
        if(fgets(over,500,F.F)==NULL){// try to get rest of line
                read_fneek("Problem reading VERSION line in read_amber_prmtop.",1,fld,F.N);}
        while(strchr(over,'\n')==NULL){// try to get rest of line
                fld+=500;
                if(fgets(over,500,F.F)==NULL){
                        read_fneek("Problem readin VERSION line in read_amber_prmtop.",1,fld,F.N);}
                }
        } // close lengthy line check...
if(strncmp("\%VERSION",line,8)!=0){
        read_eek("First line not \%VERSION.",F.N);}
P[0].VERSION=strdup(line); 
anl=2;
fld=0;
//
// grab next line, which should be a flag line
//
if(fgets(line,500,F.F)==NULL){ 
        read_fneek("Problem in read_amber_prmtop",anl,fld,F.N);} 
// Check the line -- it should be a short-ish FLAG line

//printf("FLAG line read from top is >>>%s<<<\n",line);

if(strchr(line,'\n')==NULL){// die if line too long
read_eek("FLAG line over 500 chars... \n",F.N);}
//
// Read the FLAG entry
//
if(strncmp("\%FLAG",line,5)!=0){ // must start with %FLAG
read_fneek("Entry not FLAG in read_amber_prmtop",anl,fld,F.N);}
// Parse the FLAG line
if(sscanf(line,"%s %s",over,tmp)!=2){mywhine("Problem in read_amber_prmtop with 1st FLAG read.");}
newflag=0;
//
// Start main read of topology file
// 
while(newflag==0){// while we have found another flag entry
        // We have a FLAG entry, so increment the number of sections
//printf("line (FLAG) is >>%s<<\n",line);
        sec=P[0].nS;
        P[0].nS++; 
        // Allocate memory 
        P[0].S=(amber_prmtop_section*)realloc(P[0].S,P[0].nS*sizeof(amber_prmtop_section));
        P[0].SN=(char**)realloc(P[0].SN,P[0].nS*sizeof(char*));
        P[0].SN[sec]=strdup(tmp); // record FLAG entry in
        P[0].S[sec].N=strdup(tmp); // both locations 
        // clear the other entries in the new structure
        P[0].S[sec].FORMAT=NULL;
        P[0].S[sec].TYPE=NULL;
        P[0].S[sec].desc=NULL;
        P[0].S[sec].is_standard=0;
        P[0].S[sec].nc=0;
        P[0].S[sec].npl=0;
        P[0].S[sec].nt=0;
        P[0].S[sec].ns=0;
        P[0].S[sec].nu=0;
        P[0].S[sec].D=NULL; 
        //
        // Read the FORMAT entry
        // 
        anl++;
        if(fgets(line,500,F.F)==NULL){ // if we can't read the line, die
                read_fneek("Problem in read_amber_prmtop.",anl,fld,F.N);}
//printf("FORMAT line read from top is >>>%s<<<\n",line);
        if(strchr(line,'\n')==NULL){ // FORMAT lines should be short-ish
                read_fneek("FORMAT line over 500 chars... \n",anl,fld,F.N);}
        if(strncmp("\%FORMAT",line,7)!=0){// must start with %FORMAT
                read_fneek("Entry not FORMAT in read_amber_prmtop",anl,fld,F.N);} 
//printf("line (FORMAT) is >>%s<<\n",line); 
        // split line by parentheses as tokens
        s1=strdup(strtok(line,"()"));// toss out the "%FORMAT" part
        P[0].S[sec].FORMAT=strdup(strtok(NULL,"()")); // save next
        s1=strdup(P[0].S[sec].FORMAT); // save a char string to tear apart
        // parse the format string
        s2=strdup(strtok(s1,"aAiIfFeE")); // up to the format identifier
        sscanf(s2,"%d",&P[0].S[sec].npl); // max entries expected per line
        s2=strdup(strtok(NULL,".")); // up to any periods
        if((strchr(s2,'S')!=NULL)||(strchr(s2,'N')!=NULL)){over[0]='0';} // EN or ES
        sscanf(s2,"%d",&P[0].S[sec].nc); // number of chars in format 
//printf("parsed format:  npl is %d ; nc is %d \n",P[0].S[sec].npl,P[0].S[sec].nc);
        //
        // Read the section
        // 
        P[0].S[sec].D=(char**)calloc(1,sizeof(char*)); // initially allocate **D
        P[0].S[sec].nt=0; // total pieces of data found 
        ent=0;
        if(fgetpos(F.F,&line_current)!=0){mywhine("Problem getting line_start position in read_amber_prmtop.");}
        fgets_check=fgets(line,6,F.F);
        while(fgets_check!=NULL){
//printf("the new section fgets's line is >>%s<<\n",line);
                if(strcspn(line,"\0")==0){ //printf("found empty line\n");
                        if(fgetpos(F.F,&line_current)!=0){mywhine("Problem getting line_current position in read_amber_prmtop.");}
                        fgets_check=fgets(line,6,F.F);
                        continue;
                        }
                anl++; // we have a new line
                fld=0; // start field count over
                // check to see if first 5 chars match "%FLAG"
                if(strncmp(line,"\%FLAG",5)==0){ 
//printf("found a FLAG line, resetting line start\n"); 
                        if(fsetpos(F.F,&line_current)!=0){mywhine("Problem resetting line_start position in read_amber_prmtop.");}
                        break;} // if so, stop this
                if(strcspn(line,"\n")==0){
                        fprintf(stderr,"Unexpected blank line in read_amber_prmtop\n");
                        fprintf(stderr,"   at line number %d in file %s.  Ignoring.\n",anl,F.N);
                        fprintf(stderr,"The section (%d) FLAG is:  %s\n",sec,P[0].SN[sec]);
                        if(fgetpos(F.F,&line_current)!=0){mywhine("Problem getting line_current position in read_amber_prmtop.");}
                        fgets_check=fgets(line,6,F.F);
                        continue;
                        }
// 
// Now read the rest of the line...
// 
//printf("reading the rest of the line.\n");
if(fsetpos(F.F,&line_current)!=0){mywhine("Problem resetting line_start position in read_amber_prmtop.");}
newline=1;
while(newline!=0){
        if(fgets(line,(P[0].S[sec].nc+1),F.F)==NULL){
                read_fneek("problem reading data line in read_amber_prmtop",anl,ent,F.N);}
//printf("the line-bit for P[0].S[sec].nc=%d is >>>%s<<<\n",P[0].S[sec].nc,line);
//printf("in ascii decimal: ");
//for(ae=0;ae<P[0].S[sec].nc+1;ae++){printf(" %d ",line[ae]);}
//printf("\n");
        if(strcspn(line,"\0")==0){ //printf("found empty string\n");
                newline=0;
                break;}
        if(strcspn(line,"\n")==0){ // at end of line, no new data
                newline=0;
                break;}
        if(strchr(line,'\n')!=NULL){ // this is the end of a line, but with data 
                for(aa=0;aa<strlen(line);aa++){ //check for all whitespace
                        if(isspace(line[aa])==0) newline=-1; // something isn't white
                        }
                if(newline==-1){
                        line[strcspn(line,"\n")]='\0'; 
                        ent=P[0].S[sec].nt; // for convenience
                        // allocate space for the next entry
                        P[0].S[sec].nt++;
                        P[0].S[sec].D=(char**)realloc(P[0].S[sec].D,P[0].S[sec].nt*sizeof(char*));
                        P[0].S[sec].D[ent]=(char*)calloc(P[0].S[sec].nc+1,sizeof(char));
                        strncpy(P[0].S[sec].D[ent],line,P[0].S[sec].nc+1);
//printf("the entry for P[0].S[%d].D[%d] is -now- >>>%s<<< ; nt is %d\n",sec,ent,P[0].S[sec].D[ent],P[0].S[sec].nt);
                        }
                newline=0;
                break;
                }
        ent=P[0].S[sec].nt; // for convenience
        // allocate space for the next entry
        P[0].S[sec].nt++;
        P[0].S[sec].D=(char**)realloc(P[0].S[sec].D,P[0].S[sec].nt*sizeof(char*));
        P[0].S[sec].D[ent]=(char*)calloc(P[0].S[sec].nc+1,sizeof(char));
        strncpy(P[0].S[sec].D[ent],line,P[0].S[sec].nc+1); 
//printf("the entry for P[0].S[%d].D[%d] is -now- >>>%s<<< ; nt is %d\n",sec,ent,P[0].S[sec].D[ent],P[0].S[sec].nt);
//printf("the entry for P[0].S[%d].D[%d] is -now- >>>%s<<<\n",sec,ent,P[0].S[sec].D[ent]);
        } // close while not a new line
        if(fgetpos(F.F,&line_current)!=0){mywhine("Problem getting line_current position in read_amber_prmtop.");}
        fgets_check=fgets(line,6,F.F);
        }// close fgets within a section 

        if(newflag==-1){break;}
        if(fgets(line,500,F.F)==NULL){ 
                if(fgetc(F.F)==EOF){
                        iseof=1;
                        newflag=-1;
                        break;}
                else{read_fneek("Problem in FLAG line read read_amber_prmtop",anl,0,F.N);}
                } 
        if(newflag==-1){break;}
        // If here, then we found a FLAG, read it in, exit loop and start new
        // Check the line -- it should be a short-ish FLAG line
        if(strchr(line,'\n')==NULL){// die if line too long
        read_eek("FLAG line over 500 chars... \n",F.N);}
        //
        // Read the FLAG entry
        //
        // Parse the FLAG line
//printf("Flag line is >>>%s<<<\n",line);
        if(sscanf(line,"%s %s",over,tmp)!=2){
                read_fneek("Problem FLAG entry scan, read_amber_prmtop.",anl,1,F.N);}
        } // close fgets for reading file

fclose(F.F);

/*
F.F=myfopen("test_rewrite_of_prmtop","w");
fprintf(F.F,"%s",P[0].VERSION);
for(sec=0;sec<P[0].nS;sec++){ // for each section found
        fprintf(F.F,"%%FLAG %s\n",P[0].S[sec].N);
        fprintf(F.F,"%%FORMAT(%s)\n",P[0].S[sec].FORMAT);
        for(aa=0;aa<P[0].S[sec].nt;aa++){
                fprintf(F.F,"%s",P[0].S[sec].D[aa]);
                //fprintf(F.F,"D[%d] is >>>%s<<<\n",aa,P[0].S[sec].D[aa]);
                fflush(F.F);
//printf("\naa is %d ; P[0].S[%d].npl is %d ; (aa+1)%%npl is %d\n",aa,sec,P[0].S[sec].npl,);
                if((((aa+1)%P[0].S[sec].npl))==0){fprintf(F.F,"\n");} 
                //if((((aa+1)*P[0].S[sec].nc))%80==0){printf("\n");} 
                }
        if(((aa)*P[0].S[sec].nc)%80!=0){fprintf(F.F,"\n");} 
        }
fclose(F.F);
*/

return;
}