bool OpAlign::Do(OBBase* pOb, const char* OptionText, OpMap* pmap, OBConversion* pConv)
{
OBMol* pmol = dynamic_cast<OBMol*>(pOb);
if(!pmol)
return false;
map<string,string>::const_iterator itr;
// Is there an -s option?
if(pConv->IsFirstInput())
{
_pOpIsoM = NULL; //assume no -s option
itr = pmap->find("s");
if(itr!=pmap->end())
{
//There is an -s option; check it is ok
_pOpIsoM = static_cast<OpNewS*>(OBOp::FindType("s"));
_stext = itr->second; //get its parameter(s)
if(!_pOpIsoM || _stext.empty())
{
obErrorLog.ThrowError(__FUNCTION__,
"No parameter on -s option, or its OBOp version is not loaded", obError);
pConv->SetOneObjectOnly(); //to finish
return false;
}
}
}
// If the output format is a 2D depiction format, then we should align
// on the 2D coordinates and not the 3D coordinates (if present). This
//means we need to generate the 2D coordinates at this point.
if(pmol->GetDimension()==3 && (pConv->GetOutFormat()->Flags() & DEPICTION2D))
{
OBOp* pgen = OBOp::FindType("gen2D");
if(pgen)
pgen->Do(pmol);
}
// All molecules must have coordinates, so add them if 0D
// They may be added again later when gen2D or gen3D is called, but they will be the same.
// It would be better if this op was called after them, which would happen
// if its name was alphabetically after "gen" (and before "s").
if(pmol->GetDimension()==0)
{
//Will the coordinates be 2D or 3D?
itr = pmap->find("gen3D");
OBOp* pgen = (itr==pmap->end()) ? OBOp::FindType("gen2D") : OBOp::FindType("gen3D");
if(pgen)
pgen->Do(pmol);
}
//Do the alignment in 2D if the output format is svg, png etc. and there is no -xn option
if(pmol->GetDimension()==3 && pConv && !pConv->IsOption("n"))
{
OBFormat* pOutFormat = pConv->GetOutFormat();
if(pOutFormat->Flags() & DEPICTION2D)
{
OBOp* pgen = OBOp::FindType("gen2D");
if(pgen)
pgen->Do(pmol);
}
}
if(pConv->IsFirstInput() || _refMol.NumAtoms()==0)
{
_refvec.clear();
// Reference molecule is basically the first molecule
_refMol = *pmol;
if(!_pOpIsoM)
//no -s option. Use a molecule reference.
_align.SetRefMol(_refMol);
else
{
//If there is a -s option, reference molecule has only those atoms that are matched
//Call the -s option from here
bool ret = _pOpIsoM->Do(pmol, _stext.c_str(), pmap, pConv);
// Get the atoms that were matched
vector<int> ats = _pOpIsoM->GetMatchAtoms();
if(!ats.empty())
{
// Make a vector of the matching atom coordinates...
for(vector<int>::iterator iter=ats.begin(); iter!=ats.end(); ++iter)
_refvec.push_back((pmol->GetAtom(*iter))->GetVector());
// ...and use a vector reference
_align.SetRef(_refvec);
}
// Stop -s option being called normally, although it will still be called once
// in the DoOps loop already started for the current (first) molecule.
pConv->RemoveOption("s",OBConversion::GENOPTIONS);
if(!ret)
{
// the first molecule did not match the -s option so a reference molecule
// could not be made. Keep trying.
_refMol.Clear();
//obErrorLog.ThrowError(__FUNCTION__, "The first molecule did not match the -s option\n"
// "so the reference structure was not derived from it", obWarning, onceOnly);
return false; //not matched
}
}
}
//All molecules
if(pmol->GetDimension()!= _refMol.GetDimension())
{
stringstream ss;
ss << "The molecule" << pmol->GetTitle()
<< " does not have the same dimensions as the reference molecule "
<< _refMol.GetTitle() << " and is ignored.";
obErrorLog.ThrowError(__FUNCTION__, ss.str().c_str(), obError);
return false;
}
if(_pOpIsoM) //Using -s option
{
//Ignore mol if it does not pass -s option
if(!_pOpIsoM->Do(pmol, "", pmap, pConv)) // "" means will use existing parameters
return false;
// Get the atoms equivalent to those in ref molecule
vector<int> ats = _pOpIsoM->GetMatchAtoms();
// Make a vector of their coordinates and get the centroid
vector<vector3> vec;
vector3 centroid;
for(vector<int>::iterator iter=ats.begin(); iter!=ats.end(); ++iter) {
vector3 v = pmol->GetAtom(*iter)->GetVector();
centroid += v;
vec.push_back(v);
}
centroid /= vec.size();
// Do the alignment
_align.SetTarget(vec);
if(!_align.Align())
return false;
// Get the centroid of the reference atoms
vector3 ref_centroid;
for(vector<vector3>::iterator iter=_refvec.begin(); iter!=_refvec.end(); ++iter)
ref_centroid += *iter;
ref_centroid /= _refvec.size();
//subtract the centroid, rotate the target molecule, then add the centroid
matrix3x3 rotmatrix = _align.GetRotMatrix();
for (unsigned int i = 1; i <= pmol->NumAtoms(); ++i)
{
vector3 tmpvec = pmol->GetAtom(i)->GetVector();
tmpvec -= centroid;
tmpvec *= rotmatrix; //apply the rotation
tmpvec += ref_centroid;
pmol->GetAtom(i)->SetVector(tmpvec);
}
}
else //Not using -s option)
{
_align.SetTargetMol(*pmol);
if(!_align.Align())
return false;
_align.UpdateCoords(pmol);
}
//Save rmsd as a property
OBPairData* dp = new OBPairData;
dp->SetAttribute("rmsd");
double val = _align.GetRMSD();
if(val<1e-12)
val = 0.0;
dp->SetValue(toString(val));
dp->SetOrigin(local);
pmol->SetData(dp);
return true;
}
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;
}
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;
}