| 1 |
/********************************************************************** |
| 2 |
obmolecformat.h - Subclass of OBFormat for conversion of OBMol. |
| 3 |
|
| 4 |
Copyright (C) 2005 Chris Morley |
| 5 |
|
| 6 |
This file is part of the Open Babel project. |
| 7 |
For more information, see <http://openbabel.sourceforge.net/> |
| 8 |
|
| 9 |
This program is free software; you can redistribute it and/or modify |
| 10 |
it under the terms of the GNU General Public License as published by |
| 11 |
the Free Software Foundation version 2 of the License. |
| 12 |
|
| 13 |
This program is distributed in the hope that it will be useful, |
| 14 |
but WITHOUT ANY WARRANTY; without even the implied warranty of |
| 15 |
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
| 16 |
GNU General Public License for more details. |
| 17 |
***********************************************************************/ |
| 18 |
|
| 19 |
#ifndef OB_MOLECULEFORMAT_H |
| 20 |
#define OB_MOLECULEFORMAT_H |
| 21 |
|
| 22 |
#include "mol.hpp" |
| 23 |
#include "obconversion.hpp" |
| 24 |
|
| 25 |
namespace OpenBabel { |
| 26 |
|
| 27 |
//! \brief An OBFormat convenience subclass for conversion to/from OBMol data |
| 28 |
//! |
| 29 |
//! An OBFormat which converts to and/or from OBMol can derive from this class |
| 30 |
//! to save duplicating the ReadChemObject() and/or WriteChemObject() methods. |
| 31 |
//! Derive directly from OBFormat if the object converted is not OBMol or |
| 32 |
//! if interaction with the framework is required during the execution |
| 33 |
//! of ReadMolecule() or WriteMolecule(), as for example in CMLFormat |
| 34 |
class OBMoleculeFormat : public OBFormat |
| 35 |
{ |
| 36 |
public: |
| 37 |
|
| 38 |
OBMoleculeFormat() |
| 39 |
{ |
| 40 |
OBConversion::RegisterOptionParam("b", this, 0, OBConversion::INOPTIONS); |
| 41 |
OBConversion::RegisterOptionParam("s", this, 0, OBConversion::INOPTIONS); |
| 42 |
//The follow are OBMol options, which should not be in OBConversion. |
| 43 |
//But here isn't entirely appropriate either, since could have |
| 44 |
//OBMol formats loaded but none of them derived from this class. |
| 45 |
//However, this possibility is remote. |
| 46 |
OBConversion::RegisterOptionParam("s", NULL, 1,OBConversion::GENOPTIONS); |
| 47 |
OBConversion::RegisterOptionParam("v", NULL, 1,OBConversion::GENOPTIONS); |
| 48 |
OBConversion::RegisterOptionParam("h", NULL, 0,OBConversion::GENOPTIONS); |
| 49 |
OBConversion::RegisterOptionParam("d", NULL, 0,OBConversion::GENOPTIONS); |
| 50 |
OBConversion::RegisterOptionParam("b", NULL, 0,OBConversion::GENOPTIONS); |
| 51 |
OBConversion::RegisterOptionParam("c", NULL, 0,OBConversion::GENOPTIONS); |
| 52 |
OBConversion::RegisterOptionParam("p", NULL, 0,OBConversion::GENOPTIONS); |
| 53 |
OBConversion::RegisterOptionParam("t", NULL, 0,OBConversion::GENOPTIONS); |
| 54 |
OBConversion::RegisterOptionParam("j", NULL, 0,OBConversion::GENOPTIONS); |
| 55 |
}; |
| 56 |
|
| 57 |
/// The "Convert" interface functions |
| 58 |
virtual bool ReadChemObject(OBConversion* pConv) |
| 59 |
{ |
| 60 |
std::istream &ifs = *pConv->GetInStream(); |
| 61 |
if (ifs.peek() == EOF || !ifs.good()) |
| 62 |
return false; |
| 63 |
|
| 64 |
static OBMol* pmol; |
| 65 |
|
| 66 |
std::string auditMsg = "OpenBabel::Read molecule "; |
| 67 |
std::string description(Description()); |
| 68 |
auditMsg += description.substr(0,description.find('\n')); |
| 69 |
obErrorLog.ThrowError(__func__, |
| 70 |
auditMsg, |
| 71 |
obAuditMsg); |
| 72 |
|
| 73 |
//With j option, reuse pmol except for the first mol |
| 74 |
if(!pConv->IsOption("j",OBConversion::GENOPTIONS) || pConv->IsFirstInput()) |
| 75 |
pmol = new OBMol; |
| 76 |
|
| 77 |
bool ret=ReadMolecule(pmol,pConv); |
| 78 |
if(ret && pmol->NumAtoms() > 0) //Do transformation and return molecule |
| 79 |
pConv->AddChemObject(pmol->DoTransformations(pConv->GetOptions(OBConversion::GENOPTIONS))); |
| 80 |
else |
| 81 |
pConv->AddChemObject(NULL); |
| 82 |
|
| 83 |
return ret; |
| 84 |
}; |
| 85 |
|
| 86 |
virtual bool WriteChemObject(OBConversion* pConv) |
| 87 |
{ |
| 88 |
//Retrieve the target OBMol |
| 89 |
OBBase* pOb = pConv->GetChemObject(); |
| 90 |
OBMol* pmol = dynamic_cast<OBMol*> (pOb); |
| 91 |
bool ret=false; |
| 92 |
if(pmol) |
| 93 |
{ |
| 94 |
if(pmol->NumAtoms()==0) |
| 95 |
{ |
| 96 |
std::string auditMsg = "OpenBabel::Molecule "; |
| 97 |
auditMsg += pmol->GetTitle(); |
| 98 |
auditMsg += " has 0 atoms"; |
| 99 |
obErrorLog.ThrowError(__func__, |
| 100 |
auditMsg, |
| 101 |
obInfo); |
| 102 |
} |
| 103 |
ret=true; |
| 104 |
|
| 105 |
std::string auditMsg = "OpenBabel::Write molecule "; |
| 106 |
std::string description(Description()); |
| 107 |
auditMsg += description.substr(0,description.find('\n')); |
| 108 |
obErrorLog.ThrowError(__func__, |
| 109 |
auditMsg, |
| 110 |
obAuditMsg); |
| 111 |
|
| 112 |
if(!pConv->IsOption("j",OBConversion::GENOPTIONS) || pConv->IsLast()) //With j option, output only at end |
| 113 |
{ |
| 114 |
ret=WriteMolecule(pmol,pConv); |
| 115 |
delete pOb; |
| 116 |
} |
| 117 |
} |
| 118 |
return ret; |
| 119 |
}; |
| 120 |
|
| 121 |
const std::type_info& GetType() |
| 122 |
{ |
| 123 |
return typeid(OBMol*); |
| 124 |
}; |
| 125 |
|
| 126 |
}; |
| 127 |
|
| 128 |
} |
| 129 |
#endif //OB_MOLECULEFORMAT_H |
| 130 |
|
| 131 |
//! \file obmolecformat.h |
| 132 |
//! \brief Subclass of OBFormat for conversion of OBMol. |
