81 |
|
vector<int> tor; |
82 |
|
vector<int> atoms; |
83 |
|
|
84 |
< |
obErrorLog.ThrowError(__FUNCTION__, |
84 |
> |
obErrorLog.ThrowError(__func__, |
85 |
|
"Ran OpenBabel::SetTorsion", obAuditMsg); |
86 |
|
|
87 |
|
tor.push_back(a->GetCIdx()); |
632 |
|
{ |
633 |
|
if ((unsigned)idx < 1 || (unsigned)idx > NumAtoms()) |
634 |
|
{ |
635 |
< |
obErrorLog.ThrowError(__FUNCTION__, "Requested Atom Out of Range", obDebug); |
635 |
> |
obErrorLog.ThrowError(__func__, "Requested Atom Out of Range", obDebug); |
636 |
|
return((OBAtom*)NULL); |
637 |
|
} |
638 |
|
|
650 |
|
{ |
651 |
|
if (idx < 0 || (unsigned)idx >= NumBonds()) |
652 |
|
{ |
653 |
< |
obErrorLog.ThrowError(__FUNCTION__, "Requested Bond Out of Range", obDebug); |
653 |
> |
obErrorLog.ThrowError(__func__, "Requested Bond Out of Range", obDebug); |
654 |
|
return((OBBond*)NULL); |
655 |
|
} |
656 |
|
|
678 |
|
{ |
679 |
|
if (idx < 0 || (unsigned)idx >= NumResidues()) |
680 |
|
{ |
681 |
< |
obErrorLog.ThrowError(__FUNCTION__, "Requested Residue Out of Range", obDebug); |
681 |
> |
obErrorLog.ThrowError(__func__, "Requested Residue Out of Range", obDebug); |
682 |
|
return((OBResidue*)NULL); |
683 |
|
} |
684 |
|
|
748 |
|
if (dp != NULL) // we already set the formula |
749 |
|
return dp->GetValue(); |
750 |
|
|
751 |
< |
obErrorLog.ThrowError(__FUNCTION__, |
751 |
> |
obErrorLog.ThrowError(__func__, |
752 |
|
"Ran OpenBabel::SetFormula -- Hill order formula", |
753 |
|
obAuditMsg); |
754 |
|
|
848 |
|
return(_totalCharge); |
849 |
|
else // calculate from atomic formal charges (seems the best default) |
850 |
|
{ |
851 |
< |
obErrorLog.ThrowError(__FUNCTION__, |
851 |
> |
obErrorLog.ThrowError(__func__, |
852 |
|
"Ran OpenBabel::GetTotalCharge -- calculated from formal charges", |
853 |
|
obAuditMsg); |
854 |
|
|
881 |
|
return(_totalSpin); |
882 |
|
else // calculate from atomic spin information (assuming high-spin case) |
883 |
|
{ |
884 |
< |
obErrorLog.ThrowError(__FUNCTION__, |
884 |
> |
obErrorLog.ThrowError(__func__, |
885 |
|
"Ran OpenBabel::GetTotalSpinMultiplicity -- calculating from atomic spins and high spin", |
886 |
|
obAuditMsg); |
887 |
|
|
1052 |
|
|
1053 |
|
bool OBMol::Clear() |
1054 |
|
{ |
1055 |
< |
obErrorLog.ThrowError(__FUNCTION__, |
1055 |
> |
obErrorLog.ThrowError(__func__, |
1056 |
|
"Ran OpenBabel::Clear Molecule", obAuditMsg); |
1057 |
|
|
1058 |
|
vector<OBNodeBase*>::iterator i; |
1134 |
|
{ |
1135 |
|
if (_mod == 0) |
1136 |
|
{ |
1137 |
< |
obErrorLog.ThrowError(__FUNCTION__, "_mod is negative - EndModify() called too many times", obDebug); |
1137 |
> |
obErrorLog.ThrowError(__func__, "_mod is negative - EndModify() called too many times", obDebug); |
1138 |
|
return; |
1139 |
|
} |
1140 |
|
|
1413 |
|
if (cfl.empty() || cfl.size() == 1) |
1414 |
|
return(false); |
1415 |
|
|
1416 |
< |
obErrorLog.ThrowError(__FUNCTION__, |
1416 |
> |
obErrorLog.ThrowError(__func__, |
1417 |
|
"Ran OpenBabel::StripSalts", obAuditMsg); |
1418 |
|
|
1419 |
|
max = cfl.begin(); |
1448 |
|
vector<OBNodeBase*>::iterator i; |
1449 |
|
vector<OBNodeBase*> delatoms; |
1450 |
|
|
1451 |
< |
obErrorLog.ThrowError(__FUNCTION__, |
1451 |
> |
obErrorLog.ThrowError(__func__, |
1452 |
|
"Ran OpenBabel::DeleteHydrogens -- nonpolar", |
1453 |
|
obAuditMsg); |
1454 |
|
|
1489 |
|
vector<OBNodeBase*>::iterator i; |
1490 |
|
vector<OBNodeBase*> delatoms,va; |
1491 |
|
|
1492 |
< |
obErrorLog.ThrowError(__FUNCTION__, |
1492 |
> |
obErrorLog.ThrowError(__func__, |
1493 |
|
"Ran OpenBabel::DeleteHydrogens", obAuditMsg); |
1494 |
|
|
1495 |
|
for (atom = BeginAtom(i);atom;atom = NextAtom(i)) |
1627 |
|
SetHydrogensAdded(); |
1628 |
|
|
1629 |
|
if (!polaronly) |
1630 |
< |
obErrorLog.ThrowError(__FUNCTION__, |
1630 |
> |
obErrorLog.ThrowError(__func__, |
1631 |
|
"Ran OpenBabel::AddHydrogens", obAuditMsg); |
1632 |
|
else |
1633 |
< |
obErrorLog.ThrowError(__FUNCTION__, |
1633 |
> |
obErrorLog.ThrowError(__func__, |
1634 |
|
"Ran OpenBabel::AddHydrogens -- polar only", obAuditMsg); |
1635 |
|
|
1636 |
|
//count up number of hydrogens to add |
1831 |
|
return(true); |
1832 |
|
phmodel.CorrectForPH(*this); |
1833 |
|
|
1834 |
< |
obErrorLog.ThrowError(__FUNCTION__, |
1834 |
> |
obErrorLog.ThrowError(__func__, |
1835 |
|
"Ran OpenBabel::CorrectForPH", obAuditMsg); |
1836 |
|
|
1837 |
|
return(true); |
1845 |
|
|
1846 |
|
SetSpinMultiplicityAssigned(); |
1847 |
|
|
1848 |
< |
obErrorLog.ThrowError(__FUNCTION__, |
1848 |
> |
obErrorLog.ThrowError(__func__, |
1849 |
|
"Ran OpenBabel::AssignSpinMultiplicity", |
1850 |
|
obAuditMsg); |
1851 |
|
|
2114 |
|
vector<vector<int> > mlist; |
2115 |
|
vector<vector<int> >::iterator i; |
2116 |
|
|
2117 |
< |
obErrorLog.ThrowError(__FUNCTION__, |
2117 |
> |
obErrorLog.ThrowError(__func__, |
2118 |
|
"Ran OpenBabel::CorrectBadResonanceForm", obAuditMsg); |
2119 |
|
|
2120 |
|
OBSmartsPattern acid; |
2321 |
|
// Not quite sure why this is here -GRH 2003 |
2322 |
|
// if (NumAtoms() > 255) return(false); |
2323 |
|
|
2324 |
< |
obErrorLog.ThrowError(__FUNCTION__, |
2324 |
> |
obErrorLog.ThrowError(__func__, |
2325 |
|
"Ran OpenBabel::Kekulize", obAuditMsg); |
2326 |
|
|
2327 |
|
for (bond = BeginBond(i);bond;bond = NextBond(i)) |
2406 |
|
end = GetAtom(second); |
2407 |
|
if (!bgn || !end) |
2408 |
|
{ |
2409 |
< |
obErrorLog.ThrowError(__FUNCTION__, "Unable to add bond - invalid atom index", obDebug); |
2409 |
> |
obErrorLog.ThrowError(__func__, "Unable to add bond - invalid atom index", obDebug); |
2410 |
|
return(false); |
2411 |
|
} |
2412 |
|
bond->Set(_nbonds,bgn,end,order,stereo); |
2491 |
|
{ |
2492 |
|
vector<int> children; |
2493 |
|
|
2494 |
< |
obErrorLog.ThrowError(__FUNCTION__, |
2494 |
> |
obErrorLog.ThrowError(__func__, |
2495 |
|
"Ran OpenBabel::Align", obAuditMsg); |
2496 |
|
|
2497 |
|
//find which atoms to rotate |
2541 |
|
double mass = 0.0; |
2542 |
|
double center[3],m[3][3]; |
2543 |
|
|
2544 |
< |
obErrorLog.ThrowError(__FUNCTION__, |
2544 |
> |
obErrorLog.ThrowError(__func__, |
2545 |
|
"Ran OpenBabel::ToInertialFrame", obAuditMsg); |
2546 |
|
|
2547 |
|
for (i = 0;i < 3;i++) |
2890 |
|
if (Empty()) |
2891 |
|
return; |
2892 |
|
|
2893 |
< |
obErrorLog.ThrowError(__FUNCTION__, |
2893 |
> |
obErrorLog.ThrowError(__func__, |
2894 |
|
"Ran OpenBabel::RenumberAtoms", obAuditMsg); |
2895 |
|
|
2896 |
|
OBAtom *atom; |
2962 |
|
return; |
2963 |
|
if (_dimension != 3) return; // not useful on non-3D structures |
2964 |
|
|
2965 |
< |
obErrorLog.ThrowError(__FUNCTION__, |
2965 |
> |
obErrorLog.ThrowError(__func__, |
2966 |
|
"Ran OpenBabel::ConnectTheDots", obAuditMsg); |
2967 |
|
|
2968 |
|
int j,k,max; |
3087 |
|
return; |
3088 |
|
if (_dimension != 3) return; // not useful on non-3D structures |
3089 |
|
|
3090 |
< |
obErrorLog.ThrowError(__FUNCTION__, |
3090 |
> |
obErrorLog.ThrowError(__func__, |
3091 |
|
"Ran OpenBabel::PerceiveBondOrders", obAuditMsg); |
3092 |
|
|
3093 |
|
OBAtom *atom, *b, *c; |
3363 |
|
size = NumAtoms(); |
3364 |
|
fsize = -1.0/(double)NumAtoms(); |
3365 |
|
|
3366 |
< |
obErrorLog.ThrowError(__FUNCTION__, |
3366 |
> |
obErrorLog.ThrowError(__func__, |
3367 |
|
"Ran OpenBabel::Center", obAuditMsg); |
3368 |
|
|
3369 |
|
vector<double*>::iterator i; |
3393 |
|
|
3394 |
|
vector3 OBMol::Center(int nconf) |
3395 |
|
{ |
3396 |
< |
obErrorLog.ThrowError(__FUNCTION__, |
3396 |
> |
obErrorLog.ThrowError(__func__, |
3397 |
|
"Ran OpenBabel::Center", obAuditMsg); |
3398 |
|
|
3399 |
|
SetConformer(nconf); |
3438 |
|
positions in the current conformer are translated. */ |
3439 |
|
void OBMol::Translate(const vector3 &v,int nconf) |
3440 |
|
{ |
3441 |
< |
obErrorLog.ThrowError(__FUNCTION__, |
3441 |
> |
obErrorLog.ThrowError(__func__, |
3442 |
|
"Ran OpenBabel::Translate", obAuditMsg); |
3443 |
|
|
3444 |
|
int i,size; |
3481 |
|
double x,y,z; |
3482 |
|
double *c = (nconf == OB_CURRENT_CONFORMER)? _c : GetConformer(nconf); |
3483 |
|
|
3484 |
< |
obErrorLog.ThrowError(__FUNCTION__, |
3484 |
> |
obErrorLog.ThrowError(__func__, |
3485 |
|
"Ran OpenBabel::Rotate", obAuditMsg); |
3486 |
|
|
3487 |
|
size = NumAtoms(); |
3539 |
|
///Converts for instance [N+]([O-])=O to N(=O)=O |
3540 |
|
bool OBMol::ConvertDativeBonds() |
3541 |
|
{ |
3542 |
< |
obErrorLog.ThrowError(__FUNCTION__, |
3542 |
> |
obErrorLog.ThrowError(__func__, |
3543 |
|
"Ran OpenBabel::ConvertDativeBonds", obAuditMsg); |
3544 |
|
|
3545 |
|
//Look for + and - charges on adjacent atoms |