| 1 |
/********************************************************************** |
| 2 |
Copyright (C) 2000 by OpenEye Scientific Software, Inc. |
| 3 |
Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison |
| 4 |
Some portions Copyright (C) 2004 by Chris Morley |
| 5 |
|
| 6 |
This program is free software; you can redistribute it and/or modify |
| 7 |
it under the terms of the GNU General Public License as published by |
| 8 |
the Free Software Foundation version 2 of the License. |
| 9 |
|
| 10 |
This program is distributed in the hope that it will be useful, |
| 11 |
but WITHOUT ANY WARRANTY; without even the implied warranty of |
| 12 |
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
| 13 |
GNU General Public License for more details. |
| 14 |
***********************************************************************/ |
| 15 |
|
| 16 |
#include "mol.hpp" |
| 17 |
#include "obconversion.hpp" |
| 18 |
|
| 19 |
using namespace std; |
| 20 |
namespace OpenBabel |
| 21 |
{ |
| 22 |
|
| 23 |
class TinkerFormat : public OBFormat |
| 24 |
{ |
| 25 |
public: |
| 26 |
//Register this format type ID |
| 27 |
TinkerFormat() |
| 28 |
{ |
| 29 |
OBConversion::RegisterFormat("txyz",this); |
| 30 |
} |
| 31 |
|
| 32 |
virtual const char* Description() //required |
| 33 |
{ |
| 34 |
return |
| 35 |
"Tinker MM2 format\n \ |
| 36 |
No comments yet\n"; |
| 37 |
}; |
| 38 |
|
| 39 |
virtual const char* SpecificationURL() |
| 40 |
{return "http://dasher.wustl.edu/tinker/";}; //optional |
| 41 |
|
| 42 |
//Flags() can return be any the following combined by | or be omitted if none apply |
| 43 |
// NOTREADABLE READONEONLY NOTWRITABLE WRITEONEONLY |
| 44 |
virtual unsigned int Flags() |
| 45 |
{ |
| 46 |
return NOTREADABLE | WRITEONEONLY; |
| 47 |
}; |
| 48 |
|
| 49 |
//*** This section identical for most OBMol conversions *** |
| 50 |
//////////////////////////////////////////////////// |
| 51 |
/// The "API" interface functions |
| 52 |
virtual bool WriteMolecule(OBBase* pOb, OBConversion* pConv); |
| 53 |
|
| 54 |
//////////////////////////////////////////////////// |
| 55 |
/// The "Convert" interface functions |
| 56 |
virtual bool WriteChemObject(OBConversion* pConv) |
| 57 |
{ |
| 58 |
//Retrieve the target OBMol |
| 59 |
OBBase* pOb = pConv->GetChemObject(); |
| 60 |
OBMol* pmol = dynamic_cast<OBMol*> (pOb); |
| 61 |
bool ret=false; |
| 62 |
if(pmol) |
| 63 |
ret=WriteMolecule(pmol,pConv); |
| 64 |
|
| 65 |
std::string auditMsg = "OpenBabel::Write molecule "; |
| 66 |
std::string description(Description()); |
| 67 |
auditMsg += description.substr( 0, description.find('\n') ); |
| 68 |
obErrorLog.ThrowError(__FUNCTION__, |
| 69 |
auditMsg, |
| 70 |
obAuditMsg); |
| 71 |
|
| 72 |
delete pOb; |
| 73 |
return ret; |
| 74 |
}; |
| 75 |
}; |
| 76 |
//*** |
| 77 |
|
| 78 |
//Make an instance of the format class |
| 79 |
TinkerFormat theTinkerFormat; |
| 80 |
|
| 81 |
///////////////////////////////////////////////////////////////// |
| 82 |
|
| 83 |
bool TinkerFormat::WriteMolecule(OBBase* pOb, OBConversion* pConv) |
| 84 |
{ |
| 85 |
OBMol* pmol = dynamic_cast<OBMol*>(pOb); |
| 86 |
if(pmol==NULL) |
| 87 |
return false; |
| 88 |
|
| 89 |
//Define some references so we can use the old parameter names |
| 90 |
ostream &ofs = *pConv->GetOutStream(); |
| 91 |
OBMol &mol = *pmol; |
| 92 |
|
| 93 |
unsigned int i; |
| 94 |
char buffer[BUFF_SIZE]; |
| 95 |
OBBond *bond; |
| 96 |
vector<OBEdgeBase*>::iterator j; |
| 97 |
|
| 98 |
sprintf(buffer,"%6d %-20s MM2 parameters",mol.NumAtoms(),mol.GetTitle()); |
| 99 |
ofs << buffer << endl; |
| 100 |
|
| 101 |
ttab.SetFromType("INT"); |
| 102 |
|
| 103 |
OBAtom *atom; |
| 104 |
string str,str1; |
| 105 |
for(i = 1;i <= mol.NumAtoms(); i++) |
| 106 |
{ |
| 107 |
atom = mol.GetAtom(i); |
| 108 |
str = atom->GetType(); |
| 109 |
ttab.SetToType("MM2"); |
| 110 |
ttab.Translate(str1,str); |
| 111 |
sprintf(buffer,"%6d %2s %12.6f%12.6f%12.6f %5d", |
| 112 |
i, |
| 113 |
etab.GetSymbol(atom->GetAtomicNum()), |
| 114 |
atom->GetX(), |
| 115 |
atom->GetY(), |
| 116 |
atom->GetZ(), |
| 117 |
atoi((char*)str1.c_str())); |
| 118 |
ofs << buffer; |
| 119 |
|
| 120 |
for (bond = atom->BeginBond(j); bond; bond = atom->NextBond(j)) |
| 121 |
{ |
| 122 |
sprintf(buffer,"%6d", (bond->GetNbrAtom(atom))->GetIdx()); |
| 123 |
ofs << buffer; |
| 124 |
} |
| 125 |
|
| 126 |
ofs << endl; |
| 127 |
} |
| 128 |
|
| 129 |
return(true); |
| 130 |
} |
| 131 |
|
| 132 |
} //namespace OpenBabel |
