extern "C" char *
ob_mol_to_canonical_smiles (char *molfile, int omit_iso_and_chiral_markings)
{
OBMol mol;
OBConversion conv;
string tmpStr (molfile);
string outstring;
istringstream molstream (tmpStr);
ostringstream smilesstream;
char *tmpSmiles;
conv.SetInAndOutFormats ("MDL", "CAN");
conv.AddOption ("n", OBConversion::OUTOPTIONS);
//conv.AddOption ("c", OBConversion::OUTOPTIONS);
if (omit_iso_and_chiral_markings != 0)
{
conv.AddOption ("i", OBConversion::OUTOPTIONS);
}
conv.Read (&mol, &molstream);
if (mol.Empty ())
return NULL;
conv.Write (&mol, &smilesstream);
outstring = smilesstream.str ();
outstring = outstring.substr (0, outstring.length () - 1);
tmpSmiles = strdup (outstring.c_str ());
return (tmpSmiles);
}
extern "C" char *
ob_V3000_to_mol (char *V3000)
{
OBMol mol;
OBConversion conv;
string tmpStr (V3000);
string outstring;
istringstream V3000stream (tmpStr);
ostringstream molstream;
char *tmpMolfile;
conv.SetInAndOutFormats ("MDL", "MDL");
conv.AddOption ("3", OBConversion::INOPTIONS);
conv.AddOption ("2", OBConversion::OUTOPTIONS);
conv.Read (&mol, &V3000stream);
conv.Write (&mol, &molstream);
outstring = molstream.str ();
// remove the trailling $$$$\n from the SDFile
if (outstring.find ("$$$$\n", 0) != string::npos)
{
outstring = outstring.substr (0, outstring.length () - 5);
}
else if (outstring.find ("$$$$\r\n", 0) != string::npos)
{
outstring = outstring.substr (0, outstring.length () - 6);
}
tmpMolfile = strdup (outstring.c_str ());
return (tmpMolfile);
}
void DoOption(const char* p, OBConversion& Conv,
OBConversion::Option_type typ, int& arg, int argc, char *argv[])
{
while(p && *p) //can have multiple single char options
{
char ch[2]="?";
*ch = *p++;
const char* txt=NULL;
//Get the option text if needed
int nParams = Conv.GetOptionParams(ch, typ);
if(nParams)
{
if(*p)
{
txt = p; //use text immediately following the option letter
p=NULL; //no more single char options
}
else if(arg<argc-1)
{
txt = argv[++arg]; //use text from next arg
if(*txt=='-')
{
//...unless it is another option
cerr << "Option -" << ch << " takes a parameter" << endl;
exit(0);
}
}
}
Conv.AddOption(ch, typ, txt);
}
}
void testPdbOccupancies()
{
// See https://github.com/openbabel/openbabel/pull/1558
OBConversion conv;
OBMol mol;
conv.SetInFormat("cif");
conv.SetOutFormat("pdb");
conv.ReadFile(&mol, GetFilename("test08.cif"));
string pdb = conv.WriteString(&mol);
conv.AddOption("o", OBConversion::OUTOPTIONS);
pdb = conv.WriteString(&mol);
OB_ASSERT(pdb.find("HETATM 1 NA UNL 1 0.325 0.000 4.425 0.36") != string::npos);
OB_ASSERT(pdb.find("HETATM 17 O UNL 8 1.954 8.956 3.035 1.00") != string::npos);
OBMol mol_pdb;
conv.SetInFormat("pdb");
conv.ReadFile(&mol_pdb, GetFilename("test09.pdb"));
pdb = conv.WriteString(&mol_pdb);
OB_ASSERT(pdb.find("HETATM 1 NA UNL 1 0.325 0.000 4.425 0.36") != string::npos);
OB_ASSERT(pdb.find("HETATM 2 NA UNL 1 0.002 8.956 1.393 0.10") != string::npos);
OB_ASSERT(pdb.find("HETATM 17 O UNL 8 1.954 8.956 3.035 1.00") != string::npos);
}
Molecule * OpenbabelWrapper::openFile(const QString &fileName,
const QString &fileType,
const QString &fileOptions)
{
// Check that the file can be read from disk
if (!canOpen(fileName, QFile::ReadOnly | QFile::Text))
return 0;
// Construct the OpenBabel objects, set the file type
OBConversion conv;
OBFormat *inFormat;
if (!fileType.isEmpty() && !conv.SetInFormat(fileType.toAscii().data()))
// Input format not supported
return 0;
else {
inFormat = conv.FormatFromExt(fileName.toAscii().data());
if (!conv.SetInFormat(inFormat))
// Input format not supported
return 0;
}
// set any options
if (!fileOptions.isEmpty()) {
foreach(const QString &option,
fileOptions.split('\n', QString::SkipEmptyParts)) {
conv.AddOption(option.toAscii().data(), OBConversion::INOPTIONS);
}
}
void testPdbRemSpacesHMName()
{
// See https://github.com/openbabel/openbabel/pull/1558
OBConversion conv;
OBMol mol;
conv.SetInFormat("cif");
conv.SetOutFormat("pdb");
conv.ReadFile(&mol, GetFilename("test07.cif"));
string pdb = conv.WriteString(&mol);
conv.AddOption("o", OBConversion::OUTOPTIONS);
pdb = conv.WriteString(&mol);
OB_ASSERT(pdb.find("I41/amd:2") != string::npos);
}
void testPdbOutHexagonalAlternativeOrigin2()
{
// See https://github.com/openbabel/openbabel/pull/1558
OBConversion conv;
OBMol mol;
conv.SetInFormat("cif");
conv.SetOutFormat("pdb");
conv.ReadFile(&mol, GetFilename("test06.cif"));
string pdb = conv.WriteString(&mol);
conv.AddOption("o", OBConversion::OUTOPTIONS);
pdb = conv.WriteString(&mol);
OB_ASSERT(pdb.find("H -3 m") != string::npos);
}
void testPdbOutAlternativeOrigin()
{
// See https://github.com/openbabel/openbabel/pull/1558
OBConversion conv;
OBMol mol;
conv.SetInFormat("cif");
conv.SetOutFormat("pdb");
conv.ReadFile(&mol, GetFilename("test04.cif"));
string pdb = conv.WriteString(&mol);
// ending space is needed to check that there is no origin set
OB_ASSERT(pdb.find("P 4/n b m ") != string::npos);
conv.AddOption("o", OBConversion::OUTOPTIONS);
pdb = conv.WriteString(&mol);
OB_ASSERT(pdb.find("P 4/n b m:1") != string::npos);
}
bool OpReadConformers::ProcessVec(std::vector<OBBase*>& vec)
{
// DeferredFormat collects all the molecules, they are processed here, and Deferred Format outputs them
OBConversion smconv;
smconv.AddOption("n");
if(!smconv.SetOutFormat("smi"))
{
obErrorLog.ThrowError(__FUNCTION__, "SmilesFormat is not loaded" , obError, onceOnly);
return false;
}
std::string smiles, stored_smiles;
OBMol* stored_pmol=NULL;
std::vector<OBBase*>::iterator iter;
for(iter= vec.begin();iter!=vec.end();++iter)
{
OBMol* pmol = dynamic_cast<OBMol*>(*iter);
if(!pmol)
continue;
smiles = smconv.WriteString(pmol);
Trim(smiles);
if(stored_smiles==smiles)
{
//add the coordinates of the current mol to the stored one as a conformer, and delete current mol
double *confCoord = new double [pmol->NumAtoms() * 3];
memcpy((char*)confCoord,(char*)pmol->GetCoordinates(),sizeof(double)*3*pmol->NumAtoms());
stored_pmol->AddConformer(confCoord);
delete pmol;
*iter = NULL;
}
else
{
stored_pmol = pmol;
stored_smiles = smiles;
}
}
//erase the NULLS
vec.erase(std::remove(vec.begin(),vec.end(), (void*)NULL), vec.end());
return true;
}
void DoOption(const char* p, OBConversion& Conv,
OBConversion::Option_type typ, int& arg, int argc, char *argv[])
{
//Unlike babel, cannot have multiple concatenated single char options
//accepts: -sCCC -s CCC -s"CCC" -s CCC red -sCCC red
char ch[2]="?";
*ch = *p++;
std::string txt;
//Get the option text
if(*p)
txt = p; //use text immediately following the option letter, and keep looking
while(arg<argc-1 && *argv[arg+1]!='-')
{
//use text from subsequent args
if(!txt.empty())txt += ' '; //..space separated if more than one
txt += argv[++arg];
}
Conv.AddOption(ch, typ, txt.c_str());
}
int main(int argc,char *argv[])
{
OBConversion Conv(&cin, &cout); //default input and output are console
OBFormat* pInFormat = NULL;
OBFormat* pOutFormat = NULL;
vector<string> FileList, OutputFileList;
string OutputFileName;
// Parse commandline
bool gotInType = false, gotOutType = false;
bool SplitOrBatch=false;
char *oext = NULL;
char *iext = NULL;
//Save name of program without its path (and .exe)
string pn(argv[0]);
string::size_type pos;
#ifdef _WIN32
pos = pn.find(".exe");
if(pos!=string::npos)
argv[0][pos]='\0';
#endif
pos = pn.find_last_of("/\\");
if(pos==string::npos)
program_name=argv[0];
else
program_name=argv[0]+pos+1;
const char* p;
int arg;
for (arg = 1; arg < argc; ++arg)
{
if (argv[arg])
{
if (argv[arg][0] == '-')
{
char opchar[2]="?";
opchar[0]=argv[arg][1];
switch (opchar[0])
{
case 'V':
{
cout << "Open Babel " << BABEL_VERSION << " -- "
<< __DATE__ << " -- " << __TIME__ << endl;
exit(0);
}
case 'i':
//Parameter is the input format which overrides any file extensions
gotInType = true;
iext = argv[arg] + 2;
if(!*iext)
iext = argv[++arg]; //space left after -i: use next argument
if (strncasecmp(iext, "MIME", 4) == 0)
{
// get the MIME type from the next argument
iext = argv[++arg];
pInFormat = Conv.FormatFromMIME(iext);
}
else
pInFormat = Conv.FindFormat(iext);
if(pInFormat==NULL)
{
cerr << program_name << ": cannot read input format!" << endl;
usage();
}
break;
case 'o':
//Parameter is the output format which overrides any file extension
gotOutType = true;
oext = argv[arg] + 2;
if(!*oext)
oext = argv[++arg]; //space left after -i: use next argument
if (strncasecmp(oext, "MIME", 4) == 0)
{
// get the MIME type from the next argument
oext = argv[++arg];
pOutFormat = Conv.FormatFromMIME(oext);
}
else
pOutFormat = Conv.FindFormat(oext);
if(pOutFormat==NULL)
{
cerr << program_name << ": cannot write output format!" << endl;
usage();
}
break;
case 'O':
OutputFileName = argv[arg] + 2;
if(OutputFileName.size()<3)
OutputFileName = argv[++arg]; //space left after -O: use next argument
break;
case 'L': //display a list of plugin type or classes
{
const char* param=NULL;
if(argc>arg+1)
param = argv[arg+2];
// First assume first arg is a plugin type and
// param is a subtype, like babel -L ops gen3D
// or first arg is a plugin ID, like babel -L cml
OBPlugin* plugin;
if(OBPlugin::GetPlugin("plugins", argv[arg+1])
&& (plugin = OBPlugin::GetPlugin(argv[arg+1], param))
|| (plugin = OBPlugin::GetPlugin(NULL, argv[arg+1])))
{
//Output details of subtype
string txt;
plugin->Display(txt, "verbose", argv[arg+1]);
cout << "One of the " << plugin->TypeID() << '\n' << txt << endl;
return 0;
}
//...otherwise assume it is a plugin type, like babel -L forcefields
//Output list of subtypes
OBPlugin::List(argv[arg+1], param);
return 0;
}
case '?':
case 'H':
if(isalnum(argv[arg][2]) || arg==argc-2)
{
if(strncasecmp(argv[arg]+2,"all",3))
{
OBFormat* pFormat
= (arg==argc-2) ? Conv.FindFormat(argv[arg+1]) : Conv.FindFormat(argv[arg]+2);
if(pFormat)
{
cout << argv[arg]+2 << " " << pFormat->Description() << endl;
if(pFormat->Flags() & NOTWRITABLE)
cout << " This format is Read-only" << endl;
if(pFormat->Flags() & NOTREADABLE)
cout << " This format is Write-only" << endl;
if(strlen(pFormat->SpecificationURL()))
cout << "Specification at: " << pFormat->SpecificationURL() << endl;
}
else
cout << "Format type: " << argv[arg]+2 << " was not recognized" <<endl;
}
else
{
OBPlugin::List("formats","verbose");
}
}
else
help();
return 0;
case '-': //long option --name text
{
//Option's text is in the next and subsequent args, until one starts with -
char* nam = argv[arg]+2;
if(!strcasecmp(nam, "help")) //special case handled here
{
help();
return 0;
}
if(*nam != '\0') //Do nothing if name is empty
{
string txt;
while(arg<argc-1 && *argv[arg+1]!='-')
{
//use text from subsequent args
if(!txt.empty())txt += ' '; //..space separated if more than one
txt += argv[++arg];
}
// If a API directive, e.g.---errorlevel
// send to the pseudoformat "obapi" (without any leading -)
if(*nam=='-')
{
OBConversion apiConv;
OBFormat* pAPI= OBConversion::FindFormat("obapi");
if(pAPI)
{
apiConv.SetOutFormat(pAPI);
apiConv.AddOption(nam+1, OBConversion::GENOPTIONS, txt.c_str());
apiConv.Write(NULL, &std::cout);
}
}
else
// Is a normal long option name, e.g --addtotitle
Conv.AddOption(nam,OBConversion::GENOPTIONS,txt.c_str());
}
}
break;
case 'm': //multiple output files
SplitOrBatch=true;
break;
case 'a': //single character input option
p = argv[arg]+2;
DoOption(p,Conv,OBConversion::INOPTIONS,arg,argc,argv);
break;
case 'x': //single character output option
p = argv[arg]+2;
DoOption(p,Conv,OBConversion::OUTOPTIONS,arg,argc,argv);
break;
//Not essential, but allows these options to be before input filenames
//since we know they take one parameter, and are the most likely options to be misplaced
case 'f':
case 'l':
p = argv[arg] + 2;
if(!*p)
p = argv[++arg]; //space left after -f: use next argument
Conv.AddOption(opchar, OBConversion::GENOPTIONS, p);
break;
case ':':
//e.g. -:c1ccccc1. SMILES passed as a file name and handled in OBConversion
FileList.push_back(argv[arg]);
break;
default: //single character general option
p = argv[arg]+1;
DoOption(p,Conv,OBConversion::GENOPTIONS,arg,argc,argv);
break;
}
}
else //filenames
FileList.push_back(argv[arg]);
}
}
#ifdef _WIN32
//Expand wildcards in input filenames and add to FileList
vector<string> tempFileList(FileList);
FileList.clear();
vector<string>::iterator itr;
for(itr=tempFileList.begin();itr!=tempFileList.end();++itr)
{
if((*itr)[0]=='-')
FileList.push_back(*itr);
else
DLHandler::findFiles (FileList, *itr);
}
#endif
if (!gotInType)
{
if(FileList.empty())
{
cerr << "No input file or format spec or possibly a misplaced option.\n"
"Options, other than -i -o -O -m, must come after the input files.\n" <<endl;
usage();
}
}
if (!gotOutType)
{
//check there is a valid output format, but the extension will be re-interpreted in OBConversion
pOutFormat = Conv.FormatFromExt(OutputFileName.c_str());
if(OutputFileName.empty() || pOutFormat==NULL)
{
cerr << "Missing or unknown output file or format spec or possibly a misplaced option.\n"
"Options, other than -i -o -O -m, must come after the input files.\n" <<endl;
usage();
}
}
if(!Conv.SetInFormat(pInFormat))
{
cerr << "Invalid input format" << endl;
usage();
}
if(!Conv.SetOutFormat(pOutFormat))
{
cerr << "Invalid output format" << endl;
usage();
}
if(SplitOrBatch)
{
//Put * into output file name before extension (or ext.gz)
if(OutputFileName.empty())
{
OutputFileName = "*.";
OutputFileName += oext;
}
else
{
string::size_type pos = OutputFileName.rfind(".gz");
if(pos==string::npos)
pos = OutputFileName.rfind('.');
else
pos = OutputFileName.rfind('.',pos-1);
if(pos==string::npos)
OutputFileName += '*';
else
OutputFileName.insert(pos,"*");
}
}
int count = Conv.FullConvert(FileList, OutputFileName, OutputFileList);
Conv.ReportNumberConverted(count);
if(OutputFileList.size()>1)
{
clog << OutputFileList.size() << " files output. The first is " << OutputFileList[0] <<endl;
}
//std::string messageSummary = obErrorLog.GetMessageSummary();
//if (messageSummary.size())
// {
// clog << messageSummary << endl;
// }
#ifdef _DEBUG
//CM keep window open
cout << "Press any key to finish" <<endl;
getch();
#endif
return 0;
}
bool OpNewS::Do(OBBase* pOb, const char* OptionText, OpMap* pmap, OBConversion* pConv)
{
OBMol* pmol = dynamic_cast<OBMol*>(pOb);
if(!pmol)
return false;
// The SMARTS and any other parameters are extracted on the first molecule
// and stored in the member variables. The parameter is cleared so that
// the original -s option in transform.cpp is inactive
//string txt(pmap->find(GetID())->second); // ID can be "s" or "v"
vector<OBQuery*>::iterator qiter;
if(OptionText && *OptionText)//(!pConv || pConv->IsFirstInput())
{
//Set up on first call
queries.clear();
query=NULL;
nPatternAtoms=0;
inv=false;
tokenize(vec, OptionText);
inv = GetID()[0]=='v';
if(vec[0][0]=='~')
{
inv = true;
vec[0].erase(0,1);
}
//Do not filter out any molecules if there is a parameter "showall";
//allows -s option to be used for highlighting substructures (--highlight also does this)
vector<string>::iterator it = std::remove(vec.begin(), vec.end(),"showall");
showAll = it != vec.end();
if(showAll)
vec.erase(it);
//Store the number of matches required, if as a number in the second parameter, else 0.
nmatches = 0;
comparechar = '\0';
if(vec.size()>1)
{
comparechar = vec[1][0];
if(comparechar=='>' || comparechar=='<')
vec[1].erase(0,1);
else
comparechar = '\0';
nmatches = atoi(vec[1].c_str());
if(nmatches) //remove this parameter to still allow coloring
vec.erase(vec.begin()+1);
}
//Interpret as a filename if possible
MakeQueriesFromMolInFile(queries, vec[0], &nPatternAtoms, strstr(OptionText,"noH"));
vec.erase(remove(vec.begin(),vec.end(),"noH"),vec.end());//to prevent "noH2" being seen as a color
if(queries.empty())
{
//SMARTS supplied
// Explicit H in SMARTS requires explicit H in the molecule.
// Calling AddHydrogens() on a copy of the molecule is done in parsmart.cpp
// only when SMARTS contains [H]. Doing more has complications with atom typing,
// so AddHydrogens here on the molecule (not a copy) when #1 detected.
addHydrogens = (vec[0].find("#1]")!=string::npos);
// If extra target mols have been supplied, make a composite SMARTS
// to test for any of the targets.
if(ExtraMols.size()>0)
{
for(unsigned i=0;i<ExtraMols.size();++i)
{
OBConversion extraConv;
extraConv.AddOption("h");
if(!extraConv.SetOutFormat("smi"))
return false;
// Add option which avoids implicit H being added to the SMARTS.
// The parameter must be present but can be anything.
extraConv.AddOption("h",OBConversion::OUTOPTIONS, "X");
xsmarts += ",$(" + extraConv.WriteString(ExtraMols[i], true) + ")";
}
}
string ysmarts = xsmarts.empty() ? vec[0] : "[$(" + vec[0] + ")" + xsmarts +"]";
xsmarts.clear();
if(!sp.Init(ysmarts))
{
string msg = ysmarts + " cannot be interpreted as either valid SMARTS "
"or the name of a file with an extension known to OpenBabel "
"that contains one or more pattern molecules.";
obErrorLog.ThrowError(__FUNCTION__, msg, obError, onceOnly);
delete pmol;
pmol = NULL;
pConv->SetOneObjectOnly(); //stop conversion
return false;
}
}
else
{
// Target is in a file. Add extra targets if any supplied
for(unsigned i=0;i<ExtraMols.size();++i)
queries.push_back(CompileMoleculeQuery(static_cast<OBMol*>(ExtraMols[i])));
ExtraMols.clear();
}
if(vec.size()>1 && vec[1]=="exact")
{
if(queries.empty())
{
//Convert SMARTS to SMILES to count number of atoms
OBConversion conv;
OBMol patmol;
if(!conv.SetInFormat("smi") || !conv.ReadString(&patmol, vec[0]))
{
obErrorLog.ThrowError(__FUNCTION__, "Cannot read the parameter of -s option, "
"which has to be valid SMILES when the exact option is used.", obError, onceOnly);
delete pmol;
if(pConv)
pConv->SetOneObjectOnly(); //stop conversion
return false;
}
nPatternAtoms = patmol.NumHvyAtoms();
}
}
else
nPatternAtoms = 0;
//disable old versions
if(pConv)
pConv->AddOption(GetID(), OBConversion::GENOPTIONS, "");
}
bool match = false;
//These are a vector of each mapping, each containing atom indxs.
vector<vector<int> > vecatomvec;
vector<vector<int> >* pMappedAtoms = NULL;
if(nPatternAtoms)
if(pmol->NumHvyAtoms() != nPatternAtoms)
return false;
unsigned int imol=0; //index of mol in pattern file
if(!queries.empty()) //filename supplied
{
//match is set true if any of the structures match - OR behaviour
for(qiter=queries.begin();qiter!=queries.end();++qiter, ++imol)
{
OBIsomorphismMapper* mapper = OBIsomorphismMapper::GetInstance(*qiter);
OBIsomorphismMapper::Mappings mappings;
mapper->MapUnique(pmol, mappings);
if( (match = !mappings.empty()) ) // extra parens to indicate truth value
{
OBIsomorphismMapper::Mappings::iterator ita;
OBIsomorphismMapper::Mapping::iterator itb;
for(ita=mappings.begin(); ita!=mappings.end();++ita)//each mapping
{
vector<int> atomvec;
for(itb=ita->begin(); itb!=ita->end();++itb)//each atom index
atomvec.push_back(itb->second+1);
vecatomvec.push_back(atomvec);
atomvec.clear();
}
pMappedAtoms = &vecatomvec;
break;
}
}
}
else //SMARTS supplied
{
if(addHydrogens)
pmol->AddHydrogens(false,false);
if( (match = sp.Match(*pmol)) ) // extra parens to indicate truth value
{
pMappedAtoms = &sp.GetMapList();
if(nmatches!=0)
{
int n = sp.GetUMapList().size();
if(comparechar=='>') match = (n > nmatches);
else if(comparechar=='<') match = (n < nmatches);
else match = (n == nmatches);
}
}
}
if((!showAll && (!match && !inv)) || (match && inv))
{
//delete a non-matching mol
delete pmol;
pmol = NULL;
return false;
}
if(match)
//Copy the idxes of the first match to a member variable so that it can be retrieved from outside
firstmatch.assign(pMappedAtoms->begin()->begin(), pMappedAtoms->begin()->end());
else
firstmatch.clear();
if(match && !inv && vec.size()>=2 && !vec[1].empty() && !nPatternAtoms)
{
vector<vector<int> >::iterator iter;
if (vec[1]=="extract" || (vec.size()>3 && vec[2]=="extract"))
{
//Delete all unmatched atoms. Use only the first match
ExtractSubstruct(pmol, *pMappedAtoms->begin());
return true;
}
// color the substructure if there is a second parameter which is not "exact" or "extract" or "noH"
// with multiple color parameters use the one corresponding to the query molecule, or the last
if(imol>vec.size()-2)
imol = vec.size()-2;
for(iter=pMappedAtoms->begin();iter!=pMappedAtoms->end();++iter)//each match
AddDataToSubstruct(pmol, *iter, "color", vec[imol+1]);
return true;
}
if(pConv && pConv->IsLast())
{
for(qiter=queries.begin();qiter!=queries.end();++qiter)
delete *qiter;
queries.clear();
}
return true;
}
// This function will call the Babel library to add
// hydrogens to the residues
void PDB::addHydrogensToPair(AminoAcid& a, AminoAcid& b, int cd1, int cd2)
{
OBMol mol;
string addedH;
istringstream tempss;
bool ligand;
if(b.atom[0]->line.find("HETATM") != string::npos)
{
ligand = true;
}
else
{
ligand = false;
}
// This section is just to suppress all of the
// warning message that aren't important to us
{
OBConversion apiConv;
OBFormat* pAPI = OBConversion::FindFormat("obapi");
if(pAPI)
{
apiConv.SetOutFormat(pAPI);
apiConv.AddOption("errorlevel", OBConversion::GENOPTIONS, "0");
apiConv.Write(NULL, &std::cout);
}
}
// Now, let's pack up the information into a string
string packedFile="";
for(unsigned int i=0; i < a.altlocs[cd1].size(); i++)
{
if( !a.altlocs[cd1][i]->skip )
{
packedFile += a.altlocs[cd1][i]->line + "\n";
}
}
int cd2_al = cd2;
if(b.residue == "ASP" || b.residue == "GLU")
{
cd2_al = cd2%(b.altlocs.size());
}
for(unsigned int i=0; i < b.altlocs[cd2_al].size(); i++)
{
if( !b.altlocs[cd2_al][i]->skip )
{
packedFile += b.altlocs[cd2_al][i]->line + "\n";
}
}
packedFile += a.makeConect(cd1);
packedFile += b.makeConect(cd2_al);
// Now, let's set up some Babel information
// First, we get the PDB format to tell
// Babel how to read the information and
// how to output it
OBFormat* pdbformat = this->conv.FindFormat("pdb");
this->conv.SetInFormat(pdbformat);
this->conv.SetOutFormat(pdbformat);
// Here is where Babel reads everything
// and adds hydrogens to the pair
// TO ADD: option to set pH
this->conv.ReadString(&mol,packedFile);
mol.AddHydrogens(false,true,PH_LEVEL);
// Let's write the newly written hydrogens to
// a string and parse it
addedH = this->conv.WriteString(&mol);
tempss.str(addedH);
// This ensures that the ligand hydrogens are labeled as
// HETATM instead of ATOM just for the sake of STAAR.
// This may be wrong, but it should be fine since we are
// stripping out that information later when we write
// the GAMESS inp files
if( ligand )
{
string line;
string f = "";
while( getline(tempss,line) )
{
if( line.find(b.residue) != string::npos )
{
line.replace(0,6,"HETATM");
}
f += line + "\n";
}
tempss.seekg(ios_base::beg);
tempss.clear();
tempss.str(f);
}
this->failure = false;
this->parsePDB(tempss,99999.99);
// This is just to ensure that all of the atoms
// are grouped together because Babel just
// appends the H to the end of the file
if( !ligand )
this->sortAtoms();
// Split the atoms up into amino acids and chains
this->populateChains(true);
}
int main(int argc,char *argv[])
{
OBConversion Conv(&cin, &cout); //default input and output are console
OBFormat* pInFormat = NULL;
OBFormat* pOutFormat = NULL;
bool inGzip = false;
bool outGzip = false;
vector<string> FileList, OutputFileList;
string OutputFileName;
// Parse commandline
bool gotInType = false, gotOutType = false;
bool SplitOrBatch=false;
char *oext = NULL;
char *iext = NULL;
//load plugs to fully initialize option parameters
OBPlugin::LoadAllPlugins();
//Save name of program without its path (and .exe)
string pn(argv[0]);
string::size_type pos;
#ifdef _WIN32
pos = pn.find(".exe");
if(pos!=string::npos)
argv[0][pos]='\0';
#endif
pos = pn.find_last_of("/\\");
if(pos==string::npos)
program_name=argv[0];
else
program_name=argv[0]+pos+1;
const char* p;
int arg;
for (arg = 1; arg < argc; ++arg)
{
if (argv[arg])
{
if (argv[arg][0] == '-')
{
switch (argv[arg][1])
{
case 'V':
{
cout << "Open Babel " << BABEL_VERSION << " -- "
<< __DATE__ << " -- " << __TIME__ << endl;
exit(0);
}
case 'i':
gotInType = true;
iext = argv[arg] + 2;
if(!*iext)
iext = argv[++arg]; //space left after -i: use next argument
if (strncasecmp(iext, "MIME", 4) == 0)
{
// get the MIME type from the next argument
iext = argv[++arg];
pInFormat = Conv.FormatFromMIME(iext);
}
else
{
//The ID provided by the OBFormat class is used as the identifying file extension
pInFormat = Conv.FindFormat(iext);
}
if(pInFormat==NULL)
{
cerr << program_name << ": cannot read input format!" << endl;
usage();
}
break;
case 'o':
gotOutType = true;
oext = argv[arg] + 2;
if(!*oext)
oext = argv[++arg]; //space left after -i: use next argument
if (arg >= argc)
usage(); // error in parsing command-line
if (strncasecmp(oext, "MIME", 4) == 0)
{
// get the MIME type from the next argument
oext = argv[++arg];
pOutFormat = Conv.FormatFromMIME(oext);
}
else
pOutFormat = Conv.FindFormat(oext);
if(pOutFormat==NULL)
{
cerr << program_name << ": cannot write output format!" << endl;
usage();
}
break;
case 'L': //display a list of plugin type or classes
{
const char* param=NULL;
if(argc>arg+1)
param = argv[arg+2];
// First assume first arg is a plugin type and
// param is a subtype, like babel -L ops gen3D
// or first arg is a plugin ID, like babel -L cml
OBPlugin* plugin;
if ((OBPlugin::GetPlugin("plugins", argv[arg+1]) &&
(plugin = OBPlugin::GetPlugin(argv[arg+1], param))) ||
(plugin = OBPlugin::GetPlugin(NULL, argv[arg+1])))
{
//Output details of subtype
string txt;
plugin->Display(txt, "verbose", argv[arg+1]);
cout << "One of the " << plugin->TypeID() << '\n' << txt << endl;
return 0;
}
//...otherwise assume it is a plugin type, like babel -L forcefields
//Output list of subtypes
OBPlugin::List(argv[arg+1], param);
return 0;
}
case '?':
case 'H':
if(isalnum(argv[arg][2]) || arg==argc-2)
{
if(strncasecmp(argv[arg]+2,"all",3))
{
const char* pID= (arg==argc-2) ? argv[arg+1] : argv[arg]+2;
OBFormat* pFormat = Conv.FindFormat(pID);
if(pFormat)
{
cout << pID << " " << pFormat->Description() << endl;
if(pFormat->Flags() & NOTWRITABLE)
cout << " This format is Read-only" << endl;
if(pFormat->Flags() & NOTREADABLE)
cout << " This format is Write-only" << endl;
if(strlen(pFormat->SpecificationURL()))
cout << "Specification at: " << pFormat->SpecificationURL() << endl;
}
else
cout << "Format type: " << pID << " was not recognized" <<endl;
}
else
{
OBPlugin::List("formats","verbose");
}
}
else
help();
return 0;
case '-': //long option --name text
{
//Do nothing if name is empty
//Option's text is the next arg provided it doesn't start with -
char* nam = argv[arg]+2;
if(*nam != '\0')
{
string txt;
int i;
for(i=0; i<Conv.GetOptionParams(nam, OBConversion::GENOPTIONS)
&& arg<argc-1 && argv[arg+1];++i) //removed && *argv[arg+1]!='-'
{
if(!txt.empty()) txt+=' ';
txt += argv[++arg];
}
if(*nam=='-')
{
// Is a API directive, e.g.---errorlevel
//Send to the pseudoformat "obapi" (without any leading -)
OBConversion apiConv;
OBFormat* pAPI= OBConversion::FindFormat("obapi");
if(pAPI)
{
apiConv.SetOutFormat(pAPI);
apiConv.AddOption(nam+1, OBConversion::GENOPTIONS, txt.c_str());
apiConv.Write(NULL, &std::cout);
}
}
else
// Is a long option name, e.g --addtotitle
Conv.AddOption(nam,OBConversion::GENOPTIONS,txt.c_str());
}
}
break;
case 'm': //multiple output files
SplitOrBatch=true;
break;
case 'a': //single character input option
p = argv[arg]+2;
DoOption(p,Conv,OBConversion::INOPTIONS,arg,argc,argv);
break;
case 'x': //single character output option
p = argv[arg]+2;
DoOption(p,Conv,OBConversion::OUTOPTIONS,arg,argc,argv);
break;
default: //single character general option
p = argv[arg]+1;
DoOption(p,Conv,OBConversion::GENOPTIONS,arg,argc,argv);
break;
}
}
else
{
//filenames
if(!gotOutType)
FileList.push_back(argv[arg]);
else
OutputFileName = argv[arg];
}
}
}
if(!gotOutType) //the last file is the output
{
if(FileList.empty())
{
cerr << "No output file or format spec!" << endl;
usage();
}
OutputFileName = FileList.back();
FileList.pop_back();
}
#if defined(_WIN32) && defined(USING_DYNAMIC_LIBS)
//Expand wildcards in input filenames and add to FileList
vector<string> tempFileList(FileList);
FileList.clear();
vector<string>::iterator itr;
for(itr=tempFileList.begin();itr!=tempFileList.end();++itr)
DLHandler::findFiles (FileList, *itr);
#endif
if (!gotInType)
{
if(FileList.empty())
{
cerr << "No input file or format spec!" <<endl;
usage();
}
}
if (!gotOutType)
{
pOutFormat = Conv.FormatFromExt(OutputFileName.c_str(), outGzip);
if(pOutFormat==NULL)
{
cerr << program_name << ": cannot write output format!" << endl;
usage();
}
}
if(!Conv.SetInFormat(pInFormat))
{
cerr << "Invalid input format" << endl;
usage();
}
if(!Conv.SetOutFormat(pOutFormat, outGzip))
{
cerr << "Invalid output format" << endl;
usage();
}
if(SplitOrBatch)
{
//Put * into output file name before extension (or ext.gz)
if(OutputFileName.empty())
{
OutputFileName = "*.";
if (oext != NULL)
OutputFileName += oext;
}
else
{
string::size_type pos = OutputFileName.rfind(".gz");
if(pos==string::npos)
pos = OutputFileName.rfind('.');
else
pos = OutputFileName.rfind('.',pos-1);
if(pos==string::npos)
OutputFileName += '*';
else
OutputFileName.insert(pos,"*");
}
}
int count = Conv.FullConvert(FileList, OutputFileName, OutputFileList);
Conv.ReportNumberConverted(count);
if(OutputFileList.size()>1)
{
clog << OutputFileList.size() << " files output. The first is " << OutputFileList[0] <<endl;
}
std::string messageSummary = obErrorLog.GetMessageSummary();
if (messageSummary.size())
{
clog << messageSummary << endl;
}
#ifdef _DEBUG
//CM keep window open
cout << "Press any key to finish" <<endl;
getch();
#endif
return 0;
}
