| 13 |
|
GNU General Public License for more details. |
| 14 |
|
***********************************************************************/ |
| 15 |
|
|
| 16 |
< |
#include "babelconfig.hpp" |
| 17 |
< |
#include "mol.hpp" |
| 18 |
< |
#include "obconversion.hpp" |
| 19 |
< |
#include "obmolecformat.hpp" |
| 16 |
> |
#include "pdbformat.hpp" |
| 17 |
|
|
| 18 |
+ |
|
| 19 |
|
#if !HAVE_SNPRINTF |
| 20 |
|
extern "C" int snprintf( char *, size_t, const char *, /* args */ ...); |
| 21 |
|
#endif |
| 33 |
|
namespace OpenBabel |
| 34 |
|
{ |
| 35 |
|
|
| 38 |
– |
class PDBFormat : public OBMoleculeFormat |
| 39 |
– |
{ |
| 40 |
– |
public: |
| 41 |
– |
//Register this format type ID |
| 42 |
– |
PDBFormat() |
| 43 |
– |
{ |
| 44 |
– |
OBConversion::RegisterFormat("pdb",this, "chemical/x-pdb"); |
| 45 |
– |
OBConversion::RegisterFormat("ent",this, "chemical/x-pdb"); |
| 46 |
– |
} |
| 47 |
– |
|
| 48 |
– |
virtual const char* Description() //required |
| 49 |
– |
{ |
| 50 |
– |
return |
| 51 |
– |
"Protein Data Bank format\n \ |
| 52 |
– |
Read Options e.g. -as\n\ |
| 53 |
– |
s Output single bonds only\n\ |
| 54 |
– |
b Disable bonding entirely\n\n"; |
| 55 |
– |
}; |
| 56 |
– |
|
| 57 |
– |
virtual const char* SpecificationURL() |
| 58 |
– |
{ return "http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html";}; |
| 59 |
– |
|
| 60 |
– |
virtual const char* GetMIMEType() |
| 61 |
– |
{ return "chemical/x-pdb"; }; |
| 62 |
– |
|
| 63 |
– |
//Flags() can return be any the following combined by | or be omitted if none apply |
| 64 |
– |
// NOTREADABLE READONEONLY NOTWRITABLE WRITEONEONLY |
| 65 |
– |
virtual unsigned int Flags() |
| 66 |
– |
{ |
| 67 |
– |
return READONEONLY; |
| 68 |
– |
}; |
| 69 |
– |
|
| 70 |
– |
//*** This section identical for most OBMol conversions *** |
| 71 |
– |
//////////////////////////////////////////////////// |
| 72 |
– |
/// The "API" interface functions |
| 73 |
– |
virtual bool ReadMolecule(OBBase* pOb, OBConversion* pConv); |
| 74 |
– |
virtual bool WriteMolecule(OBBase* pOb, OBConversion* pConv); |
| 75 |
– |
|
| 76 |
– |
}; |
| 77 |
– |
//*** |
| 78 |
– |
|
| 79 |
– |
//Make an instance of the format class |
| 80 |
– |
PDBFormat thePDBFormat; |
| 81 |
– |
|
| 82 |
– |
///////////////////////////////////////////////////////////////// |
| 83 |
– |
|
| 84 |
– |
|
| 36 |
|
static bool ParseAtomRecord(char *, OBMol &,int); |
| 37 |
|
static bool ParseConectRecord(char *,OBMol &); |
| 38 |
|
|
| 364 |
|
<< " According to the PDB specification,\n" |
| 365 |
|
<< " the record should have 70 columns, but OpenBabel found " |
| 366 |
|
<< strlen(buffer) << " columns."; |
| 367 |
< |
obErrorLog.ThrowError(__FUNCTION__, errorMsg.str() , obInfo); |
| 367 |
> |
obErrorLog.ThrowError(__func__, errorMsg.str() , obInfo); |
| 368 |
|
} |
| 369 |
|
|
| 370 |
|
// Serial number of the first atom, read from column 7-11 of the |
| 377 |
|
<< " According to the PDB specification,\n" |
| 378 |
|
<< " columns 7-11 should contain the serial number of an atom.\n" |
| 379 |
|
<< " THIS CONECT RECORD WILL BE IGNORED."; |
| 380 |
< |
obErrorLog.ThrowError(__FUNCTION__, errorMsg.str() , obWarning); |
| 380 |
> |
obErrorLog.ThrowError(__func__, errorMsg.str() , obWarning); |
| 381 |
|
return(false); |
| 382 |
|
} |
| 383 |
|
|
| 399 |
|
<< " columns 7-11 should contain the serial number of an atom.\n" |
| 400 |
|
<< " No atom was found with this serial number.\n" |
| 401 |
|
<< " THIS CONECT RECORD WILL BE IGNORED."; |
| 402 |
< |
obErrorLog.ThrowError(__FUNCTION__, errorMsg.str() , obWarning); |
| 402 |
> |
obErrorLog.ThrowError(__func__, errorMsg.str() , obWarning); |
| 403 |
|
return(false); |
| 404 |
|
} |
| 405 |
|
|
| 448 |
|
<< " should be connected\n" |
| 449 |
|
<< " However, an atom with serial #" << boundedAtomsSerialNumbers[k] << " was not found.\n" |
| 450 |
|
<< " THIS CONECT RECORD WILL BE IGNORED."; |
| 451 |
< |
obErrorLog.ThrowError(__FUNCTION__, errorMsg.str() , obWarning); |
| 451 |
> |
obErrorLog.ThrowError(__func__, errorMsg.str() , obWarning); |
| 452 |
|
break; |
| 453 |
|
} |
| 454 |
|
|
