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GNU General Public License for more details. |
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***********************************************************************/ |
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#include "mol.hpp" |
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#include "obconversion.hpp" |
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#include "obmolecformat.hpp" |
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#include "xyzformat.hpp" |
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#ifdef HAVE_SSTREAM |
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#include <sstream> |
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#else |
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#include <strstream> |
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#endif |
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using namespace std; |
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namespace OpenBabel |
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{ |
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class XYZFormat : public OBMoleculeFormat |
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{ |
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public: |
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//Register this format type ID |
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XYZFormat() |
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{ |
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OBConversion::RegisterFormat("xyz", this, "chemical/x-xyz"); |
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} |
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virtual const char* Description() //required |
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{ |
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return |
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"XYZ cartesian coordinates format\n \ |
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Read Options e.g. -as\n\ |
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s Output single bonds only\n\ |
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b Disable bonding entirely\n\n"; |
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}; |
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virtual const char* SpecificationURL() |
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{return "http://openbabel.sourceforge.net/formats/xyz.shtml";}; //optional |
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virtual const char* GetMIMEType() |
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{ return "chemical/x-xyz"; }; |
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//*** This section identical for most OBMol conversions *** |
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//////////////////////////////////////////////////// |
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/// The "API" interface functions |
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virtual bool ReadMolecule(OBBase* pOb, OBConversion* pConv); |
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virtual bool WriteMolecule(OBBase* pOb, OBConversion* pConv); |
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}; |
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//*** |
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//Make an instance of the format class |
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XYZFormat theXYZFormat; |
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///////////////////////////////////////////////////////////////// |
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bool XYZFormat::ReadMolecule(OBBase* pOb, OBConversion* pConv) |
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{ |
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OBMol* pmol = dynamic_cast<OBMol*>(pOb); |
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if (!ifs.getline(buffer,BUFF_SIZE)) |
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{ |
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obErrorLog.ThrowError(__FUNCTION__, |
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obErrorLog.ThrowError(__func__, |
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"Problems reading an XYZ file: Cannot read the first line.", obWarning); |
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return(false); |
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} |
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if (sscanf(buffer, "%d", &natoms) == 0 || !natoms) |
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{ |
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obErrorLog.ThrowError(__FUNCTION__, |
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obErrorLog.ThrowError(__func__, |
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"Problems reading an XYZ file: The first line must contain the number of atoms.", obWarning); |
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return(false); |
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} |
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// empty. Otherwise, use the title given by the calling function. |
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if (!ifs.getline(buffer,BUFF_SIZE)) |
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{ |
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obErrorLog.ThrowError(__FUNCTION__, |
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obErrorLog.ThrowError(__func__, |
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"Problems reading an XYZ file: Could not read the second line (title/comments).", obWarning); |
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return(false); |
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} |
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<< " According to line one, there should be " << natoms |
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<< " atoms, and therefore " << natoms+2 << " lines in the file."; |
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obErrorLog.ThrowError(__FUNCTION__, errorMsg.str() , obWarning); |
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obErrorLog.ThrowError(__func__, errorMsg.str() , obWarning); |
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return(false); |
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} |
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tokenize(vs,buffer); |
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if (vs.size() != 4) |
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if (vs.size() < 4) |
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{ |
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errorMsg << "Problems reading an XYZ file: " |
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<< "Could not read line #" << i+2 << "." << endl |
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<< "According to the specifications, this line should contain exactly 4 entries, separated by white space." << endl |
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<< "However, OpenBabel found " << vs.size() << " items."; |
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obErrorLog.ThrowError(__FUNCTION__, errorMsg.str() , obWarning); |
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obErrorLog.ThrowError(__func__, errorMsg.str() , obWarning); |
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return(false); |
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} |
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<< "According to the specifications, this line should contain exactly 4 entries, separated by white space." << endl |
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<< "OpenBabel could not interpret item #1 as a number."; |
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obErrorLog.ThrowError(__FUNCTION__, errorMsg.str() , obWarning); |
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obErrorLog.ThrowError(__func__, errorMsg.str() , obWarning); |
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return(false); |
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} |
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double y = strtod((char*)vs[2].c_str(),&endptr); |
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<< "According to the specifications, this line should contain exactly 4 entries, separated by white space." << endl |
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<< "OpenBabel could not interpret item #2 as a number."; |
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obErrorLog.ThrowError(__FUNCTION__, errorMsg.str() , obWarning); |
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obErrorLog.ThrowError(__func__, errorMsg.str() , obWarning); |
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return(false); |
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} |
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double z = strtod((char*)vs[3].c_str(),&endptr); |
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<< "According to the specifications, this line should contain exactly 4 entries, separated by white space." << endl |
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<< "OpenBabel could not interpret item #3 as a number."; |
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obErrorLog.ThrowError(__FUNCTION__, errorMsg.str() , obWarning); |
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obErrorLog.ThrowError(__func__, errorMsg.str() , obWarning); |
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return(false); |
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} |
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atom->SetVector(x,y,z); //set coordinates |
