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. |