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/********************************************************************** |
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Copyright (C) 2000 by OpenEye Scientific Software, Inc. |
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Some portions Copyright (C) 2001-2006 by Geoffrey R. Hutchison |
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Some portions Copyright (C) 2004 by Chris Morley |
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|
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This program is free software; you can redistribute it and/or modify |
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it under the terms of the GNU General Public License as published by |
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the Free Software Foundation version 2 of the License. |
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|
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This program is distributed in the hope that it will be useful, |
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but WITHOUT ANY WARRANTY; without even the implied warranty of |
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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GNU General Public License for more details. |
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***********************************************************************/ |
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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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|
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#include <sstream> |
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|
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using namespace std; |
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namespace OpenBabel |
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{ |
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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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|
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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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|
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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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|
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virtual const char* GetMIMEType() |
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{ return "chemical/x-xyz"; }; |
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|
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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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|
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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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///////////////////////////////////////////////////////////////// |
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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(pmol==NULL) |
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return false; |
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|
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//Define some references so we can use the old parameter names |
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istream &ifs = *pConv->GetInStream(); |
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OBMol &mol = *pmol; |
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const char* title = pConv->GetTitle(); |
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|
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char buffer[BUFF_SIZE]; |
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|
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stringstream errorMsg; |
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|
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unsigned int natoms; // [ejk] assumed natoms could not be -ve |
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|
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if (!ifs.getline(buffer,BUFF_SIZE)) |
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{ |
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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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|
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if (sscanf(buffer, "%d", &natoms) == 0 || !natoms) |
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{ |
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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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|
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mol.ReserveAtoms(natoms); |
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|
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// The next line contains a title string for the molecule. Use this |
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// as the title for the molecule if the line is not |
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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(__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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string readTitle(buffer); |
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string::size_type location = readTitle.find("Energy"); |
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if (location != string::npos) |
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readTitle.erase(location); |
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Trim(readTitle); |
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|
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location = readTitle.find_first_not_of(" \t\n\r"); |
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if (location != string::npos) |
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mol.SetTitle(readTitle); |
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else |
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mol.SetTitle(title); |
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|
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mol.BeginModify(); |
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|
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// The next lines contain four items each, separated by white |
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// spaces: the atom type, and the coordinates of the atom |
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vector<string> vs; |
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for (unsigned int i = 1; i <= natoms; i ++) |
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{ |
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if (!ifs.getline(buffer,BUFF_SIZE)) |
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{ |
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errorMsg << "Problems reading an XYZ file: " |
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<< "Could not read line #" << i+2 << ", file error." << endl |
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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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|
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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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{ |
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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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<< "OpenBabel found the line '" << buffer << "'" << 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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|
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obErrorLog.ThrowError(__func__, errorMsg.str() , obWarning); |
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return(false); |
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} |
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|
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// Atom Type: get the atomic number from the element table, using |
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// the first entry in the currently read line. If the entry makes |
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// sense, set the atomic number and leave the atomic type open |
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// (the type is then later faulted in when atom->GetType() is |
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// called). If the entry does not make sense to use, set the atom |
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// type manually, assuming that the author of the xyz-file had |
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// something "special" in mind. |
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OBAtom *atom = mol.NewAtom(); |
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int atomicNum = etab.GetAtomicNum(vs[0].c_str()); |
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atom->SetAtomicNum(atomicNum); //set atomic number, or '0' if the atom type is not recognized |
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if (atomicNum == 0) |
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atom->SetType(vs[0]); |
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|
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// Read the atom coordinates |
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char *endptr; |
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double x = strtod((char*)vs[1].c_str(),&endptr); |
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if (endptr == (char*)vs[1].c_str()) |
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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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<< "OpenBabel found the line '" << buffer << "'" << 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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<< "OpenBabel could not interpret item #1 as a number."; |
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|
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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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if (endptr == (char*)vs[2].c_str()) |
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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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<< "OpenBabel found the line '" << buffer << "'" << 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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<< "OpenBabel could not interpret item #2 as a number."; |
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|
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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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if (endptr == (char*)vs[3].c_str()) |
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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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<< "OpenBabel found the line '" << buffer << "'" << 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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<< "OpenBabel could not interpret item #3 as a number."; |
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|
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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 |
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} |
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|
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// clean out any remaining blank lines |
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while(ifs.peek() != EOF && ifs.good() && |
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(ifs.peek() == '\n' || ifs.peek() == '\r')) |
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ifs.getline(buffer,BUFF_SIZE); |
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|
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if (!pConv->IsOption("b",OBConversion::INOPTIONS)) |
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mol.ConnectTheDots(); |
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if (!pConv->IsOption("s",OBConversion::INOPTIONS) && !pConv->IsOption("b",OBConversion::INOPTIONS)) |
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mol.PerceiveBondOrders(); |
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|
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mol.EndModify(); |
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|
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return(true); |
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} |
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|
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//////////////////////////////////////////////////////////////// |
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|
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bool XYZFormat::WriteMolecule(OBBase* pOb, OBConversion* pConv) |
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{ |
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OBMol* pmol = dynamic_cast<OBMol*>(pOb); |
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if(pmol==NULL) |
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return false; |
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|
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//Define some references so we can use the old parameter names |
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ostream &ofs = *pConv->GetOutStream(); |
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OBMol &mol = *pmol; |
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|
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unsigned int i; |
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char buffer[BUFF_SIZE]; |
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|
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snprintf(buffer, BUFF_SIZE, "%d", mol.NumAtoms()); |
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ofs << buffer << endl; |
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if (fabs(mol.GetEnergy()) > 1.0e-3) // nonzero energy field |
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snprintf(buffer, BUFF_SIZE, "%s\tEnergy: %15.7f", |
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mol.GetTitle(), mol.GetEnergy()); |
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else |
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snprintf(buffer, BUFF_SIZE, "%s", mol.GetTitle()); |
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ofs << buffer << endl; |
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|
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OBAtom *atom; |
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string str,str1; |
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for(i = 1;i <= mol.NumAtoms(); i++) |
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{ |
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atom = mol.GetAtom(i); |
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snprintf(buffer, BUFF_SIZE, "%3s%15.5f%15.5f%15.5f", |
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etab.GetSymbol(atom->GetAtomicNum()), |
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atom->GetX(), |
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atom->GetY(), |
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atom->GetZ()); |
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ofs << buffer << endl; |
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} |
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|
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return(true); |
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} |
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|
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} //namespace OpenBabel |
