71 |
|
return typeid(this); //rubbish return if DefaultFormat not set |
72 |
|
} |
73 |
|
|
74 |
– |
//*************************************************** |
74 |
|
|
76 |
– |
/** @class OBConversion |
77 |
– |
OBConversion maintains a list of the available formats, |
78 |
– |
provides information on them, and controls the conversion process. |
79 |
– |
|
80 |
– |
A conversion is carried out by the calling routine, usually in a |
81 |
– |
user interface or an application program, making an instance of |
82 |
– |
OBConversion. It is loaded with the in and out formats, any options |
83 |
– |
and (usually) the default streams for input and output. Then either |
84 |
– |
the Convert() function is called, which allows a single input file |
85 |
– |
to be converted, or the extended functionality of FullConvert() |
86 |
– |
is used. This allows multiple input and output files, allowing: |
87 |
– |
- aggregation - the contents of many input files converted |
88 |
– |
and sent to one output file; |
89 |
– |
- splitting - the molecules from one input file sent to |
90 |
– |
separate output files; |
91 |
– |
- batch conversion - each input file converted to an output file. |
92 |
– |
|
93 |
– |
These procedures constitute the "Convert" interface. OBConversion |
94 |
– |
and the user interface or application program do not need to be |
95 |
– |
aware of any other part of OpenBabel - mol.h is not \#included. This |
96 |
– |
allows any chemical object derived from OBBase to be converted; |
97 |
– |
the type of object is decided by the input format class. |
98 |
– |
However,currently, almost all the conversions are for molecules of |
99 |
– |
class OBMol. |
100 |
– |
/// |
101 |
– |
OBConversion can also be used with an "API" interface |
102 |
– |
called from programs which manipulate chemical objects. Input/output is |
103 |
– |
done with the Read() and Write() functions which work with any |
104 |
– |
chemical object, but need to have its type specified. (The |
105 |
– |
ReadMolecule() and WriteMolecule() functions of the format classes |
106 |
– |
can also be used directly.) |
107 |
– |
|
108 |
– |
|
109 |
– |
Example code using OBConversion |
110 |
– |
|
111 |
– |
<b>To read in a molecule, manipulate it and write it out.</b> |
112 |
– |
|
113 |
– |
Set up an istream and an ostream, to and from files or elsewhere. |
114 |
– |
(cin and cout are used in the example). Specify the file formats. |
115 |
– |
|
116 |
– |
@code |
117 |
– |
OBConversion conv(&cin,&cout); |
118 |
– |
if(conv.SetInAndOutFormats("SMI","MOL")) |
119 |
– |
{ |
120 |
– |
OBMol mol; |
121 |
– |
if(conv.Read(&mol)) |
122 |
– |
...manipulate molecule |
123 |
– |
|
124 |
– |
conv->Write(&mol); |
125 |
– |
} |
126 |
– |
@endcode |
127 |
– |
|
128 |
– |
A two stage construction is used to allow error handling |
129 |
– |
if the format ID is not recognized. This is necessary now that the |
130 |
– |
formats are dynamic and errors are not caught at compile time. |
131 |
– |
OBConversion::Read() is a templated function so that objects derived |
132 |
– |
from OBBase can also be handled, in addition to OBMol, if the format |
133 |
– |
routines are written appropriately. |
134 |
– |
|
135 |
– |
<b>To make a molecule from a SMILES string.</b> |
136 |
– |
@code |
137 |
– |
std::string SmilesString; |
138 |
– |
OBMol mol; |
139 |
– |
stringstream ss(SmilesString) |
140 |
– |
OBConversion conv(&ss); |
141 |
– |
if(conv.SetInFormat("smi") && conv.Read(&mol)) |
142 |
– |
... |
143 |
– |
@endcode |
144 |
– |
|
145 |
– |
<b>To do a file conversion without manipulating the molecule.</b> |
146 |
– |
|
147 |
– |
@code |
148 |
– |
#include "obconversion.h" //mol.h is not needed |
149 |
– |
...set up an istream is and an ostream os |
150 |
– |
OBConversion conv(&is,&os); |
151 |
– |
if(conv.SetInAndOutFormats("SMI","MOL")) |
152 |
– |
{ |
153 |
– |
conv.SetOptions("h"); //Optional; (h adds expicit hydrogens) |
154 |
– |
conv.Convert(); |
155 |
– |
} |
156 |
– |
@endcode |
157 |
– |
|
158 |
– |
<b>To add automatic format conversion to an existing program.</b> |
159 |
– |
|
160 |
– |
The existing program inputs from the file identified by the |
161 |
– |
const char* filename into the istream is. The file is assumed to have |
162 |
– |
a format ORIG, but otherformats, identified by their file extensions, |
163 |
– |
can now be used. |
164 |
– |
|
165 |
– |
@code |
166 |
– |
ifstream ifs(filename); //Original code |
167 |
– |
|
168 |
– |
OBConversion conv; |
169 |
– |
OBFormat* inFormat = conv.FormatFromExt(filename); |
170 |
– |
OBFormat* outFormat = conv.GetFormat("ORIG"); |
171 |
– |
istream* pIn = &ifs; |
172 |
– |
stringstream newstream; |
173 |
– |
if(inFormat && outFormat) |
174 |
– |
{ |
175 |
– |
conv.SetInAndOutFormats(inFormat,outFormat); |
176 |
– |
conv.Convert(pIn,&newstream); |
177 |
– |
pIn=&newstream; |
178 |
– |
} |
179 |
– |
//else error; new features not available; fallback to original functionality |
180 |
– |
|
181 |
– |
...Carry on with original code using pIn |
182 |
– |
@endcode |
183 |
– |
|
184 |
– |
In Windows a degree of independence from OpenBabel can be achieved using DLLs. |
185 |
– |
This code would be linked with obconv.lib. |
186 |
– |
At runtime the following DLLs would be in the executable directory: |
187 |
– |
obconv.dll, obdll.dll, one or more *.obf format files. |
188 |
– |
*/ |
189 |
– |
|
75 |
|
int OBConversion::FormatFilesLoaded = 0; |
76 |
|
|
77 |
|
OBFormat* OBConversion::pDefaultFormat=NULL; |