/* @funcstatic domainalign_stamp **********************************************
**
** Call STAMP and process files.
**
** @param [r] prevdomain [AjPDomain] Previous domain.
** @param [r] domain [AjPDomain] This domain.
** @param [r] daf [AjPDirout] Domain alignment files.
** @param [r] super [AjPDirout] Superimposition files.
** @param [r] singlets [AjPDirout] Singlet files.
** @param [r] align [AjPStr] Align.
** @param [r] alignc [AjPStr] Alignc.
** @param [r] dom [AjPStr] Dom.
** @param [r] name [AjPStr] Name.
** @param [r] set [AjPStr] Name of set file.
** @param [r] scan [AjPStr] Name of scan file.
** @param [r] sort [AjPStr] Name of sort file.
** @param [r] log [AjPStr] Lof file name.
** @param [r] out [AjPStr] Out file name.
** @param [r] keepsinglets [AjBool] Keep singlet sequences or not.
** @param [r] moden [ajint] Mode number.
** @param [r] noden [ajint] Node number.
** @param [r] nset [ajint] Number in set.
** @param [r] logf [AjPFile] Lof file.
**
**
** @return [void] True on success
** @@
****************************************************************************/
static void domainalign_stamp(AjPDomain prevdomain,
AjPDomain domain,
AjPDirout daf,
AjPDirout super,
AjPDirout singlets,
AjPStr align,
AjPStr alignc,
AjPStr dom,
AjPStr name,
AjPStr set,
AjPStr scan,
AjPStr sort,
AjPStr log,
AjPStr out,
AjBool keepsinglets,
ajint moden,
ajint noden,
ajint nset,
AjPFile logf)
{
AjPStr exec = NULL; /* The UNIX command line to be executed. */
AjPFile clusterf = NULL; /* File pointer for log file. */
ajint ncluster = 0; /* Counter for the number of clusters. */
AjPStr line = NULL; /* Holds a line from the log file. */
AjPRegexp rexp = NULL; /* For parsing no. of clusters in log file */
AjPStr temp = NULL; /* A temporary string. */
ajint x = 0; /* Loop counter. */
exec = ajStrNew();
line = ajStrNew();
temp = ajStrNew();
rexp = ajRegCompC("^(Cluster:)");
ajDebug("domainalign_stamp name: '%S'\n", name);
/* Call STAMP. */
ajFmtPrintS(&exec, "stamp -l %S -s -n 2 -slide 5 -prefix %S -d %S",
dom, name, set);
ajFmtPrint("\n%S\n\n", exec);
ajSysSystem(exec);
ajFmtPrintS(&exec, "sorttrans -f %S -s Sc 2.5",
scan);
ajFmtPrint("\n%S > %S\n\n", exec, sort);
ajSysSystemOut(exec, sort);
ajFmtPrintS(&exec, "stamp -l %S -prefix %S",
sort, name);
ajFmtPrint("\n%S > %S\n\n", exec, log);
ajSysSystemOut(exec, log);
ajFmtPrintS(&exec, "transform -f %S -g -o %S",
sort, alignc);
ajFmtPrint("\n%S\n\n", exec);
ajSysSystem(exec);
/* Count the number of clusters in the log file. */
if(!(clusterf=ajFileNewInNameS(log)))
ajFatal("Could not open log file '%S'\n", log);
ncluster=0;
while(ajReadlineTrim(clusterf,&line))
if(ajRegExec(rexp,line))
ncluster++;
ajFileClose(&clusterf);
ajDebug("ncluster: %d\n", ncluster);
/* Call STAMP ... calculate two fields for structural equivalence using
threshold Pij value of 0.5, see stamp manual v4.1 pg 27. */
ajFmtPrintS(&exec,"poststamp -f %S.%d -min 0.5",
name, ncluster);
ajFmtPrint("%S\n\n", exec);
ajSysSystem(exec);
/* Call STAMP ... convert block format alignment into clustal format. */
ajFmtPrintS(&exec,"ver2hor -f %S.%d.post",
name, ncluster);
ajFmtPrint("%S > %S\n\n", exec, out);
ajSysSystemOut(exec, out);
/* Process STAMP alignment file and generate alignment file for output. */
domainalign_ProcessStampFile(out, align, prevdomain, noden, logf);
/* Remove all temporary files. */
for(x=1;x<ncluster+1;x++)
{
ajFmtPrintS(&temp, "%S.%d", name, x);
ajSysFileUnlink(temp);
}
ajFmtPrintS(&temp, "%S.%d.post", name, ncluster);
ajSysFileUnlink(temp);
ajStrDel(&exec);
ajStrDel(&line);
ajStrDel(&temp);
ajRegFree(&rexp);
return;
}
int main(ajint argc, char **argv)
{
AjPList pdb_path =NULL; /* Path of pdb files */
AjPStr pdb_name =NULL; /* Name of pdb file */
AjPDirout ccf_path =NULL; /* Path of ccf files */
AjPStr ccf_name =NULL; /* Name of ccf file */
AjPStr pdbid =NULL; /* PDB code */
AjPStr pdbid_temp =NULL; /* PDB code */
AjBool ccfnaming =ajFalse;
/* True == use the pdbid code to name the output file,
False== use the name of the original pdb file*/
/* Mask non-amino acid groups in protein chains that do not
contain a C-alpha atom. The group will not appear in either
the CO or SQ records of the clean coordinate file */
AjBool camask =ajFalse;
/* Mask amino acids in protein chains that do not contain a
C-alpha atom. The amino acid will appear not appear in the
CO record but will still be present in the SQ record of the
clean coordinate file */
AjBool camask1 =ajFalse;
/* Mask residues or groups in protein chains with a single atom only */
AjBool atommask =ajFalse;
AjPStr temp =NULL; /* Temp string */
AjPStr msg =NULL; /* Error message */
AjPStr base_name =NULL; /* Name of pdb file w/o path or
extension */
AjPFile pdb_inf =NULL; /* pdb input file pointer */
AjPFile ccf_outf =NULL; /* ccf output file pointer */
AjPFile logf =NULL; /* log file pointer*/
AjPPdb pdb =NULL; /* Pdb structure (for parsed data) */
ajint min_chain_size=0; /* Minimum length of a SEQRES chain
for it to be parsed */
ajint max_mismatch=0; /* Max. no. residues to trim when checking
for missing C-terminal SEQRES residues. */
ajint max_trim=0; /* Maximum number of permissible
mismatches between the ATOM and
SEQRES sequences */
ajint pos =0; /* Location of the file extension in
the pdb file name */
/* THIS_DIAGNOSTIC
tempstr=ajStrNew();
ajStrAssignC(&tempstr, "diagnostics");
tempfile=ajFileNewOutNameS(tempstr);
ajStrDel(&tempstr);*/
/* Initialise strings */
ccf_name = ajStrNew();
pdb_name = ajStrNew();
temp = ajStrNew();
msg = ajStrNew();
base_name = ajStrNew();
pdbid = ajStrNew();
pdbid_temp = ajStrNew();
/* Read data from acd */
embInitPV("pdbparse",argc,argv,"STRUCTURE",VERSION);
pdb_path = ajAcdGetDirlist("pdbpath");
ccf_path = ajAcdGetOutdir("ccfoutdir");
logf = ajAcdGetOutfile("logfile");
min_chain_size=ajAcdGetInt("chnsiz");
max_mismatch =ajAcdGetInt("maxmis");
max_trim =ajAcdGetInt("maxtrim");
ccfnaming = ajAcdGetBoolean("ccfnaming");
camask = ajAcdGetBoolean("camask");
camask1 = ajAcdGetBoolean("camaska");
atommask = ajAcdGetBoolean("atommask");
/* Check directories*/
/*Start of main application loop*/
while(ajListPop(pdb_path,(void **)&temp))
{
ajFmtPrint("Processing %S\n", temp);
ajFmtPrintF(logf, "%S\n", temp);
/* Read pdb file*/
if((pdb_inf=ajFileNewInNameS(temp))==NULL)
{
ajFmtPrintS(&msg, "Could not open for reading %S ",
temp);
ajWarn(ajStrGetPtr(msg));
ajFmtPrintF(logf, "%-15s%S\n//\n", "FILE_OPEN", temp);
ajStrDel(&temp);
continue;
}
/* Assign pdb id code from file name */
ajStrAssignS(&pdbid, temp);
ajFilenameTrimPathExt(&pdbid);
if(MAJSTRGETLEN(pdbid)>4)
{
/* The file name is longer than expected (and probably contains a
prefix). Take the last four characters to be the pdbid code */
ajStrAssignSubS(&pdbid_temp, pdbid, pos-4, pos-1);
ajStrAssignS(&pdbid, pdbid_temp);
}
else if(MAJSTRGETLEN(pdbid)<4)
ajFatal("Could not determine pdbid code from file name (%S)", pdbid);
/* Parse pdb file and write pdb structure */
if(!(pdb=ajPdbReadRawNew(pdb_inf, pdbid, min_chain_size, max_mismatch,
max_trim, camask, camask1, atommask, logf)))
{
ajFmtPrintS(&msg, "Clean coordinate file not generated for %S", temp);
ajWarn(ajStrGetPtr(msg));
ajFmtPrintF(logf, "%-15s%S\n//\n", "NO_OUTPUT", temp);
ajFileClose(&pdb_inf);
ajStrDel(&temp);
continue;
}
/* Open clean coordinate file for writing*/
if(ccfnaming)
ajStrAssignS(&ccf_name, pdb->Pdb);
else
ajStrAssignS(&ccf_name, temp);
ajStrFmtLower(&ccf_name);
if(!(ccf_outf=ajFileNewOutNameDirS(ccf_name, ccf_path)))
{
ajFmtPrintS(&msg, "Could not open %S for writing",
ccf_name);
ajWarn(ajStrGetPtr(msg));
ajFmtPrintF(logf, "%-15s%S\n//\n", "FILE_OPEN", ccf_name);
ajFileClose(&pdb_inf);
ajPdbDel(&pdb);
ajStrDel(&temp);
continue;
}
/* Write pdb file */
if(!ajPdbWriteAll(ccf_outf, pdb))
{
ajFmtPrintS(&msg, "Could not write file %S", ccf_name);
ajWarn(ajStrGetPtr(msg));
ajFmtPrintF(logf, "%-15s%S\n//\n", "FILE_WRITE", ccf_name);
ajFmtPrintS(&temp, "rm %S", ccf_name);
ajFmtPrint("%S", temp);
ajSysSystem(temp);
ajFileClose(&pdb_inf);
ajFileClose(&ccf_outf);
ajPdbDel(&pdb);
ajStrDel(&temp);
continue;
}
/* Tidy up*/
ajFileClose(&pdb_inf);
ajFileClose(&ccf_outf);
ajPdbDel(&pdb);
ajStrDel(&temp);
ajFmtPrintF(logf, "//\n");
}
/*End of main application loop*/
/*Tidy up */
ajListFree(&pdb_path);
ajStrDel(&pdb_name);
ajDiroutDel(&ccf_path);
ajStrDel(&ccf_name);
ajStrDel(&base_name);
ajStrDel(&pdbid);
ajStrDel(&pdbid_temp);
ajStrDel(&msg);
ajFileClose(&logf);
/* DIAGNOSTIC
ajFileClose(&tempfile);
*/
/* Return */
ajExit();
return 0;
}
int main(ajint argc, char **argv)
{
AjPList ccfin = NULL; /* List of CCF (input) files. */
AjPDir pdbin = NULL; /* Path of pdb input files. */
AjPStr pdbprefix = NULL; /* Prefix of pdb input files. */
AjPStr pdb_name = NULL; /* Full name (path/name/extension) of
pdb format input file. */
AjPDirout ccfout = NULL; /* Path of coordinate output file. */
AjPStr randomname = NULL; /* Name for temp file tempf. */
AjPStr ccf_this = NULL;
AjPStr exec = NULL;
AjPStr naccess_str = NULL;
AjPStr line = NULL;
AjPStr syscmd = NULL; /* Command line arguments. */
AjPStr *mode = NULL; /* Mode of operation from acd. */
AjPFile errf = NULL; /* pdbplus error file pointer. */
AjPFile serrf = NULL; /* stride error file pointer. */
AjPFile nerrf = NULL; /* stride error file pointer. */
AjPFile tempf = NULL; /* Temp file for holding STRIDE output. */
AjPFile ccf_inf = NULL; /* Protein coordinate input file. */
AjPFile ccf_outf = NULL; /* Protein coordinate output file. */
AjIList iter = NULL;
AjBool done_naccess= ajFalse;
AjBool done_stride = ajFalse;
AjBool found = ajFalse;
AjPResidue temp_res = NULL; /* Pointer to Residue object. */
AjPPdb pdb_old = NULL; /* Pointer to PDB object - without new
stride elements. */
AjPPdb pdb = NULL; /* Pointer to PDB object. */
ajint idn = 0; /* Chain identifier as a number (1,2,...) */
ajint chain_num = 0; /* Chain identifier index (0,1,...). */
ajint tS = 0; /* User-defined threshold size for SSEs. */
ajint nostride = 0; /* No. times stride failed */
ajint nonaccess = 0; /* No. times naccess failed */
ajint nofile = 0; /* No. times of file error */
/* Variables for each item that will be parsed from the ASG line. */
AjPStr res = NULL; /* Residue id from STRIDE ASG line (ALA etc). */
AjPStr res_num = NULL; /* PDB residue number from STRIDE ASG line. */
char pcid = ' '; /* Protein chain identifier from STRIDE or
NACESS output (A,B, etc). */
char ss = ' '; /* One-letter secondary structure code from
STRIDE ASG line. */
float ph = 0.0; /* Phi angle from STRIDE ASG line. */
float ps = 0.0; /* Psi angle from STRIDE ASG line. */
float sa = 0.0; /* Residue solvent accessible area from STRIDE
ASG line. */
float f1 = 0;
float f2 = 0;
float f3 = 0;
float f4 = 0;
float f5 = 0;
float f6 = 0;
float f7 = 0;
float f8 = 0;
float f9 = 0;
float f10 = 0;
/* Allocate strings; this section is used for variables that are
allocated once only. */
pdb_name = ajStrNew();
res = ajStrNew();
res_num = ajStrNew();
randomname = ajStrNew();
syscmd = ajStrNew();
line = ajStrNew();
naccess_str = ajStrNew();
exec = ajStrNew();
/* Read data from acd. */
embInitPV("pdbplus",argc,argv,"STRUCTURE",VERSION);
ccfin = ajAcdGetDirlist("ccfinpath");
pdbin = ajAcdGetDirectory("pdbindir");
pdbprefix = ajAcdGetString("pdbprefix");
ccfout = ajAcdGetOutdir("ccfoutdir");
mode = ajAcdGetList("mode");
errf = ajAcdGetOutfile("logfile");
if(ajStrGetCharFirst(*mode) != '2')
serrf = ajAcdGetOutfile("slogfile");
if(ajStrGetCharFirst(*mode) != '1')
nerrf = ajAcdGetOutfile("nlogfile");
tS = ajAcdGetInt("thresholdsize");
ajRandomSeed();
ajFilenameSetTempname(&randomname);
/*
** Start of main application loop.
** Process each PDB/ protein coordinate file (EMBL format) in turn.
*/
while(ajListPop(ccfin,(void **)&ccf_this))
{
/* Open protein coordinate file. If it cannot be opened, write a
message to the error file, delete ccf_this and continue. */
if((ccf_inf = ajFileNewInNameS(ccf_this)) == NULL)
{
ajWarn("%s%S\n//\n",
"clean coordinate file not found: ", ccf_this);
ajFmtPrintF(errf, "%s%S\n//\n",
"clean coordinate file not found: ", ccf_this);
ajStrDel(&ccf_this);
nofile++;
continue;
}
ajFmtPrint("Processing %S\n", ccf_this);
fflush(stdout);
/* Parse protein coordinate data (from clean format file) into
AjPPdb object. ajPdbReadAllModelsNew will create the AjPPdb object. */
if(!(pdb_old=ajPdbReadAllModelsNew(ccf_inf)))
{
ajWarn("ERROR Clean coordinate file read"
"error: %S\n//\n", ccf_this);
ajFmtPrintF(errf, "ERROR Clean coordinate file read"
"error: %S\n//\n", ccf_this);
ajFileClose(&ccf_inf);
ajStrDel(&ccf_this);
nofile++;
continue;
}
ajFileClose(&ccf_inf);
ajPdbCopy(&pdb, pdb_old);
ajPdbDel(&pdb_old);
/* Construct name of corresponding PDB file.
NACCESS does *not* generate an output file if the path is './' e.g.
naccess ./1rbp.ent , therefore replace './' with null. */
ajStrAssignS(&pdb_name, ajDirGetPath(pdbin));
if(ajStrMatchC(pdb_name, "./") || ajStrMatchC(pdb_name, "."))
ajStrAssignC(&pdb_name, "");
ajStrAppendS(&pdb_name, pdbprefix);
ajStrFmtLower(&pdb->Pdb);
ajStrAppendS(&pdb_name, pdb->Pdb);
ajStrAppendC(&pdb_name, ".");
ajStrAppendS(&pdb_name, ajDirGetExt(pdbin));
/* Check corresponding PDB file exists for reading using ajFileStat. */
if(!(ajFilenameExistsRead(pdb_name)))
{
ajFmtPrintF(errf, "%s%S\n//\n", "PDB file not found: ", pdb_name);
ajWarn("%s%S\n//\n", "PDB file not found: ", pdb_name);
ajStrDel(&ccf_this);
ajPdbDel(&pdb);
nofile++;
continue;
}
if(ajStrGetCharFirst(*mode) != '2')
{
/*
** Create a string containing the STRIDE command line (it needs
** PDB file name & name of temp output file).
** Call STRIDE by using ajSystem.
*/
ajFmtPrintS(&syscmd, "%S %S -f%S >> %s 2>&1",
ajAcdGetpathC("stride"),
pdb_name, randomname, ajFileGetNameC(serrf));
ajFmtPrint("%S %S -f%S >> %s 2>&1\n",
ajAcdGetpathC("stride"),
pdb_name, randomname,ajFileGetNameC(serrf));
system(ajStrGetPtr(syscmd));
/* Open the stride output file */
if (((tempf = ajFileNewInNameS(randomname)) == NULL))
{
ajWarn("%s%S\n//\n",
"no stride output for: ", pdb_name);
ajFmtPrintF(errf, "%s%S\n//\n",
"no stride output for: ", pdb_name);
nostride++;
ajStrDel(&ccf_this);
ajPdbDel(&pdb);
continue;
}
else
ajFmtPrintF(errf, "%s%S\n//\n",
"stride output for: ", pdb_name);
done_stride = ajFalse;
/* Parse STRIDE output from temp output file a line at a time. */
while(ajReadlineTrim(tempf,&line))
{
if(ajStrPrefixC(line,"ASG"))
{
ajFmtScanS(line, "%*S %S %c %S %*d %c %*S %f %f %f %*S",
&res, &pcid, &res_num, &ss, &ph, &ps, &sa);
/*
** Populate pdbplus object with the data from this parsed
** line. This means first identifying the chain, then
** finding the residue.
*/
/* Determine the chain number. ajDmxPdbplusChain does not
recognise '-', so change '-' to '.' */
if (pcid == '-')
pcid = '.';
/* Get chain number from the chain identifier. */
if(!ajPdbChnidToNum(pcid, pdb, &idn))
{
ajWarn("Could not convert chain id %c to chain"
" number in pdb file %S\n//\n",
pcid, pdb_name);
ajFmtPrintF(errf, "Could not convert chain id %c "
"to chain number in pdb file %S\n//\n",
pcid, pdb_name);
continue;
}
/*
** The chain number that will get written starts at 1, but
** we want an index into an array which must start at 0,
** so subtract 1 from the chain number to get the index.
*/
chain_num = idn-1;
/*
** Iiterate through the list of residues in the Pdb object,
** found switches to true when first residue corresponding
** to the line is found.
*/
/* iter = ajListIterNewread(pdb->Chains[chain_num]->Atoms); */
iter = ajListIterNewread(pdb->Chains[chain_num]->Residues);
found = ajFalse;
while((temp_res = (AjPResidue)ajListIterGet(iter)))
{
/* If we have found the residue we want */
if((ajStrMatchS(res_num, temp_res->Pdb) &&
ajStrMatchS(res, temp_res->Id3)))
{
done_stride = ajTrue;
found = ajTrue;
temp_res->eStrideType = ss;
temp_res->Phi = ph;
temp_res->Psi = ps;
temp_res->Area = sa;
}
/* If the matching residue has been processed
move on to next ASG line, next residue. */
else if(found == ajTrue)
break;
else
/* Matching residue not found yet. */
continue;
}
ajListIterDel(&iter);
} /* End of if ASG loop. */
} /* End of while line loop. */
if(done_stride)
ajFmtPrintF(errf, "%s%S\n//\n",
"stride data for: ", pdb_name);
else
{
ajFmtPrintF(errf, "%s%S\n//\n",
"no stride data for: ", pdb_name);
ajWarn("%s%S\n//\n", "no stride data for: ", pdb_name);
nostride++;
}
/* Close STRIDE temp file. & tidy up. */
ajFileClose(&tempf);
/* Remove temporary file (stride output file). */
ajFmtPrintS(&exec, "rm %S", randomname);
ajSysSystem(exec);
/*
** Calculate element serial numbers (eStrideNum)& ammend residue
** objects, count no's of elements and ammend chain object
** (numHelices, num Strands).
*/
pdbplus_sort(pdb, tS);
}
if(ajStrGetCharFirst(*mode) != '1')
{
/*
** Create a string containing the NACCESS command line (it needs
** PDB file name & name of temp output file) & call NACCESS.
** If e.g. /data/structure/pdbfred.ent was parsed and the program
** was run from /stuff, then /stuff/fred.asa and /stuff/fred.rsa
** would be written. These must be deleted once parsed (only
** use the .rsa file here).
*/
ajFmtPrintS(&syscmd, "%S %S >> %s 2>&1",
ajAcdGetpathC("naccess"), pdb_name,
ajFileGetNameC(nerrf));
ajFmtPrint("%S %S >> %s 2>&1\n",
ajAcdGetpathC("naccess"), pdb_name,
ajFileGetNameC(nerrf));
system(ajStrGetPtr(syscmd));
ajStrAssignS(&naccess_str, pdbprefix);
ajStrAppendS(&naccess_str, pdb->Pdb);
ajStrAppendC(&naccess_str, ".rsa");
/* Open the NACCESS output file. */
if (((tempf = ajFileNewInNameS(naccess_str)) == NULL))
{
ajFmtPrintF(errf, "%s%S\n//\n",
"no naccess output for: ", pdb_name);
ajWarn("%s%S\n//\n", "no naccess output for: ", pdb_name);
nonaccess++;
ajStrDel(&ccf_this);
ajPdbDel(&pdb);
continue;
}
else
ajFmtPrintF(errf, "%s%S\n//\n",
"naccess output for: ", pdb_name);
done_naccess = ajFalse;
/* Parse NACCESS output from temp output file a line at a time. */
while(ajReadlineTrim(tempf,&line))
{
if(ajStrPrefixC(line,"RES"))
{
/* Read data from lines. */
if((pcid = line->Ptr[8]) == ' ')
ajFmtScanS(line, "%*S %S %S %f %f %f "
"%f %f %f %f %f %f %f",
&res, &res_num, &f1, &f2, &f3, &f4, &f5,
&f6, &f7, &f8, &f9, &f10);
else
ajFmtScanS(line, "%*S %S %*c %S %f %f "
"%f %f %f %f %f %f %f %f",
&res, &res_num, &f1, &f2, &f3, &f4, &f5,
&f6, &f7, &f8, &f9, &f10);
/* Identify the chain, then finding all the residues
corresponding to the residue. */
/* Get the chain number from the chain identifier. */
if(!ajPdbChnidToNum(pcid, pdb, &idn))
{
ajWarn("Could not convert chain id %c to chain"
" number in pdb file %S\n//\n",
pcid, pdb_name);
ajFmtPrintF(errf, "Could not convert chain id"
" %c to chain number in pdb file %S\n//\n",
pcid, pdb_name);
continue;
}
/*
** Chain number will start at 1, but we want an index
** into an array which must start at 0, so subtract 1
** from the chain number to get the index.
*/
chain_num = idn-1;
/*
** Iiterate through the list of residues in the Pdb object,
** temp_res is an AjPResidue used to point to the current
** residue.
** ajBool found switches to true when first residue
** corresponding to the line is found.
*/
iter = ajListIterNewread(pdb->Chains[chain_num]->Residues);
found = ajFalse;
while((temp_res = (AjPResidue)ajListIterGet(iter)))
{
/* If we have found the residue we want, write the residue
object. */
if((ajStrMatchS(res_num, temp_res->Pdb) &&
ajStrMatchS(res, temp_res->Id3)))
{
found = ajTrue;
done_naccess = ajTrue;
temp_res->all_abs = f1;
temp_res->all_rel = f2;
temp_res->side_abs = f3;
temp_res->side_rel = f4;
temp_res->main_abs = f5;
temp_res->main_rel = f6;
temp_res->npol_abs = f7;
temp_res->npol_rel = f8;
temp_res->pol_abs = f9;
temp_res->pol_rel = f10;
}
/* If the matching residues have all been processed.
move on to next ASG line, next residue. */
else if(found == ajTrue)
break;
else
/* Matching residues not found yet, move on to next
residue. */
continue;
}
ajListIterDel(&iter);
}
}
if(done_naccess)
ajFmtPrintF(errf, "%s%S\n//\n",
"naccess data for: ", pdb_name);
else
{
ajFmtPrintF(errf, "%s%S\n//\n",
"no naccess data for: ", pdb_name);
ajWarn("%s%S\n//\n", "no naccess data for: ", pdb_name);
nonaccess++;
}
/* Remove temporary file (naccess output files). */
ajFileClose(&tempf);
ajFmtPrintS(&exec, "rm %S", naccess_str);
ajSysSystem(exec);
ajStrAssignS(&naccess_str, pdbprefix);
ajStrAppendS(&naccess_str, pdb->Pdb);
ajStrAppendC(&naccess_str, ".asa");
ajFmtPrintS(&exec, "rm %S", naccess_str);
ajSysSystem(exec);
ajStrAssignS(&naccess_str, pdbprefix);
ajStrAppendS(&naccess_str, pdb->Pdb);
ajStrAppendC(&naccess_str, ".log");
ajFmtPrintS(&exec, "rm %S", naccess_str);
ajSysSystem(exec);
}
/* Open CCF (output) file. */
ccf_outf = ajFileNewOutNameDirS(pdb->Pdb, ccfout);
/* Write AjPPdb object to the output file in clean format. */
if(!ajPdbWriteAll(ccf_outf, pdb))
{
ajWarn("%s%S\n//\n","Could not write results file for: ",
pdb->Pdb);
ajFmtPrintF(errf,"%s%S\n//\n","Could not write results file for ",
pdb->Pdb);
}
ajFileClose(&ccf_outf);
ajPdbDel(&pdb);
ajStrDel(&ccf_this);
} /* End of main application loop. */
ajFmtPrint("STRIDE failures: %d\n", nostride);
ajFmtPrint("NACCESS failures: %d\n", nonaccess);
ajFmtPrintF(errf, "\n\nSTRIDE failures: %d\nNACCESS failures: %d\n",
nostride, nonaccess);
ajListFree(&ccfin);
ajDirDel(&pdbin);
ajStrDel(&pdbprefix);
ajStrDel(&pdb_name);
ajDiroutDel(&ccfout);
ajStrDel(&res);
ajStrDel(&res_num);
ajStrDel(&randomname);
ajStrDel(&line);
ajStrDel(&naccess_str);
ajStrDel(&exec);
ajStrDel(&syscmd);
ajFileClose(&errf);
if(ajStrGetCharFirst(*mode) != '2')
ajFileClose(&serrf);
if(ajStrGetCharFirst(*mode) != '1')
ajFileClose(&nerrf);
ajStrDel(&mode[0]);
AJFREE(mode);
ajExit();
return 0;
}
