static void jaspextract_readmatrixlist(AjPTable mtable, const AjPStr directory) { const AjPStr datadir = NULL; AjPStr matrixfile = NULL; AjPFile inf = NULL; AjPStr line = NULL; AjPStr key = NULL; AjPStr value = NULL; matrixfile = ajStrNew(); datadir = ajDatafileValuePath(); if(!datadir) ajFatal("jaspextract: Cannot determine the EMBOSS data directory"); ajFmtPrintS(&matrixfile,"%S%s",directory,MATRIXFILE); if(!ajFilenameExistsRead(matrixfile)) ajFatal("jaspextract: Directory (%S) doesn't appear to be a JASPAR " "one\nNo matrix_list.txt file found",directory); inf = ajFileNewInNameS(matrixfile); if(!inf) ajFatal("Cannot open input file: %S",matrixfile); while(ajReadline(inf,&line)) { key = ajStrNew(); if(ajFmtScanS(line,"%S",&key) != 1) { ajStrDel(&key); continue; } value = ajStrNew(); ajStrAssignS(&value,line); ajTablePut(mtable,(void *)key, (void *)value); } ajFileClose(&inf); ajStrDel(&matrixfile); ajStrDel(&line); return; }
static void jaspextract_copyfiles(AjPStr directory) { AjPStr matrixfile = NULL; AjPList flist = NULL; AjPStr wild = NULL; AjPStr entry = NULL; AjPStr bname = NULL; AjPStr line = NULL; AjPStr dest = NULL; const AjPStr datadir = NULL; ajuint preflen = 0; ajuint i = 0; const char *p = NULL; AjPFile inf = NULL; AjPFile outf = NULL; matrixfile = ajStrNew(); flist = ajListNew(); wild = ajStrNewC("*.pfm"); bname = ajStrNew(); line = ajStrNew(); dest = ajStrNew(); datadir = ajDatafileValuePath(); if(!datadir) ajFatal("jaspextract: Cannot determine the EMBOSS data directory"); ajFmtPrintS(&matrixfile,"%S%s",directory,MATRIXFILE); if(!ajFilenameExistsRead(matrixfile)) ajFatal("jaspextract: Directory (%S) doesn't appear to be a JASPAR " "one\nNo matrix_list.txt file found",directory); ajFilelistAddPathWild(flist, directory, wild); while(ajListPop(flist,(void **)&entry)) { ajStrAssignS(&bname,entry); ajFilenameTrimPath(&bname); i = 0; while(Jprefix[i].Prefix) { if(!ajStrPrefixC(bname,Jprefix[i].Prefix)) { ++i; continue; } preflen = strlen(Jprefix[i].Prefix); p = ajStrGetPtr(bname); if(p[preflen]>='0' && p[preflen]<='9') break; ++i; } if(!Jprefix[i].Prefix) { ajStrDel(&entry); continue; } ajFmtPrintS(&dest,"%S%s%c%S",datadir,Jprefix[i].Directory,SLASH_CHAR, bname); outf = ajFileNewOutNameS(dest); if(!outf) ajFatal("Cannot open output file %S",dest); /* Avoid UNIX copy for portability */ inf = ajFileNewInNameS(entry); if(!inf) ajFatal("Cannot open input file: %S",entry); while(ajReadlineTrim(inf,&line)) ajFmtPrintF(outf,"%S\n",line); ajFileClose(&inf); ajFileClose(&outf); ajStrDel(&entry); } ajListFree(&flist); ajStrDel(&wild); ajStrDel(&dest); ajStrDel(&line); ajStrDel(&bname); ajStrDel(&matrixfile); return; }
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; }