Dear Craig,
I have faced the identical problem with MMFF94, and I have previously
submitted a similar patch which has already been applied to SVN
OpenBabel. However, now I realize that my fix had only solved my own
problem, but not a more general problem connected with formal charges.
So I have attached a much better patch, which reverts my previous one,
and instead applies it on the OBMol copy constructor, so that it becomes
of general use.
To make a long story short, if you patch the current OpenBabel SVN
version with the attached patch your issue will be solved.
From the OpenBabel root folder:
patch -p0 < patch_17-05-2012.patch
Dear Geoff, would you please apply it also to the SVN trunk so that also
other OpenBabel users may benefit from that? It also includes a small
patch on "A T O M T Y P E S" logging that I had left behind previously.
Best regards,
Paolo
On 05/17/2012 01:44 AM, Craig James wrote:
Here's another problem in 2.3.x that's not in 2.2.x. I realize these
are bogus molecules, but it illustrates a serious problem.
$ echo "[Fe+2][Fe-2].[Fe+2].[Fe-2]" | babel -i smi -o can
[Fe-2][Fe+2].[Fe-2].[Fe+2]
Everything looks good -- charges are maintained. Now go through the
SDF format:
$ echo "[Fe+2][Fe-2].[Fe+2].[Fe-2]" | babel -i smi -o sdf | babel -i
sdf -o can
[Fe+2][Fe].[Fe].[Fe]
Not so good -- charges are dropped. Where is the problem? It turns
out the SDF is correct:
$ echo "[Fe+2][Fe-2].[Fe+2].[Fe-2]" | babel -i smi -o sdf
OpenBabel05161216052D
4 1 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 Fe 0 2 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 Fe 0 6 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 Fe 0 2 0 0 0 15 0 0 0 0 0 0
0.0000 0.0000 0.0000 Fe 0 6 0 0 0 15 0 0 0 0 0 0
1 2 1 0 0 0 0
M CHG 4 1 2 2 -2 3 2 4 -2
M END
$$$$
The charges are all properly marked in the atom block and in the M CHG
line. And the "15" in atoms 3 and 4 means "zero valence" which is
right. Yet the SMILES is wrong.
It turns out this same thing happens if you use
atom->SetFormalCharge(). It sometimes works and sometimes doesn't.
Note that it works correctly in OpenBabel 2.2.x:
$ echo "[Fe+2][Fe-2].[Fe+2].[Fe-2]" | babel -i smi -o sdf | babel -i
sdf -o can
[Fe-2].[Fe-2][Fe+2].[Fe+2]
Anyone have any idea what changed, either in the OpenBabel internals
or the SMILES generator, that would affect the way charges are
interpreted?
Craig
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--
==========================================================
Paolo Tosco, Ph.D. Phone: +39 011 6707680
Department of Drug Science Fax: +39 011 6707687
and Technology Mob: +39 348 5537206
Via Pietro Giuria, 9
10125 Torino, Italy
http://open3dalign.org
E-mail: paolo.to...@unito.it http://open3dqsar.org
==========================================================
*** src/forcefield.cpp.orig 2012-05-17 11:53:17.393007026 +0200
--- src/forcefield.cpp 2012-05-17 11:57:30.640008358 +0200
***************
*** 779,788 ****
{
IF_OBFF_LOGLVL_LOW {
OBFFLog("\nA T O M T Y P E S\n\n");
! OBFFLog("IDX\tTYPE\n");
FOR_ATOMS_OF_MOL (a, _mol) {
! snprintf(_logbuf, BUFF_SIZE, "%d\t%s\n", a->GetIdx(), a->GetType());
OBFFLog(_logbuf);
}
}
--- 779,789 ----
{
IF_OBFF_LOGLVL_LOW {
OBFFLog("\nA T O M T Y P E S\n\n");
! OBFFLog("IDX\tTYPE\tRING\n");
FOR_ATOMS_OF_MOL (a, _mol) {
! snprintf(_logbuf, BUFF_SIZE, "%d\t%s\t%s\n", a->GetIdx(), a->GetType(),
! (a->IsInRing() ? (a->IsAromatic() ? "AR" : "AL") : "NO"));
OBFFLog(_logbuf);
}
}
***************
*** 855,875 ****
}
if (IsSetupNeeded(mol)) {
- int *formal_charge = new int[mol.NumAtoms()];
- int i;
-
- i = 0;
- FOR_ATOMS_OF_MOL (atom, mol) {
- formal_charge[i] = atom->GetFormalCharge();
- ++i;
- }
_mol = mol;
- i = 0;
- FOR_ATOMS_OF_MOL (atom, _mol) {
- atom->SetFormalCharge(formal_charge[i]);
- ++i;
- }
- delete [] formal_charge;
_ncoords = _mol.NumAtoms() * 3;
if (_velocityPtr)
--- 856,862 ----
***************
*** 925,945 ****
}
if (IsSetupNeeded(mol)) {
- int *formal_charge = new int[mol.NumAtoms()];
- int i;
-
- i = 0;
- FOR_ATOMS_OF_MOL (atom, mol) {
- formal_charge[i] = atom->GetFormalCharge();
- ++i;
- }
_mol = mol;
- i = 0;
- FOR_ATOMS_OF_MOL (atom, _mol) {
- atom->SetFormalCharge(formal_charge[i]);
- ++i;
- }
- delete [] formal_charge;
_ncoords = _mol.NumAtoms() * 3;
if (_velocityPtr)
--- 912,918 ----
*** src/mol.cpp.orig 2012-05-17 11:53:45.445195944 +0200
--- src/mol.cpp 2012-05-17 11:53:55.225196004 +0200
***************
*** 1252,1257 ****
--- 1252,1263 ----
OBAtom *atom;
OBBond *bond;
+ int *formal_charge = new int[src.NumAtoms()];
+ int n = 0;
+ FOR_ATOMS_OF_MOL (atom, src) {
+ formal_charge[n] = atom->GetFormalCharge();
+ ++n;
+ }
Clear();
BeginModify();
***************
*** 1262,1267 ****
--- 1268,1278 ----
for (atom = src.BeginAtom(i);atom;atom = src.NextAtom(i))
AddAtom(*atom);
+ for (n = 0, atom = this->BeginAtom(i);atom;atom = this->NextAtom(i)) {
+ (*atom).SetFormalCharge(formal_charge[n]);
+ ++n;
+ }
+ delete [] formal_charge;
for (bond = src.BeginBond(j);bond;bond = src.NextBond(j))
AddBond(*bond);
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