Dear All,
I've noticed a problem with OB's internal representation of Proline. It's
essentially missing a bond. Here's a bonds list of a PDB containing a single,
standard Proline:
vector<OBBond*> resbonds = res->GetBonds(false);
cout << "---BONDS---" << endl;
for (int b = 0; b < resbonds.size(); b++)
{
OBAtom* beginAtom = resbonds[b]->GetBeginAtom();
OBAtom* endAtom = resbonds[b]->GetEndAtom();
cout << res->GetAtomID(beginAtom) << "---" << res->GetAtomID(endAtom) <<
endl;
}
---BONDS---
CA --- N
N --- CD
CD --- HD2
CD --- HD3
CB --- CG
HG3--- CG
CG --- HG2
HB3--- CB
CA --- CB
CB --- HB2
HA --- CA
CA --- C
C --- O
As you can see, CD - CG is missing. This is important to fix, as anycode trying
to modify Psi/Phi angles through SetTorsion(...) will inherently break for
Prolines.
Cheers,
Nick
PS: Below is the Proline PDB entry. Excuse the formatting, outlook does not
like copypasta.
ATOM 13 N PRO 2 18.343 22.469 0.670 N
ATOM 14 CD PRO 2 18.562 21.226 1.430 C
ATOM 15 HD2 PRO 2 18.753 22.245 1.765 H
ATOM 16 HD3 PRO 2 19.309 20.557 1.858 H
ATOM 17 CG PRO 2 17.148 20.774 1.723 C
ATOM 18 HG2 PRO 2 16.438 20.207 2.325 H
ATOM 19 HG3 PRO 2 18.078 20.213 1.634 H
ATOM 20 CB PRO 2 16.526 21.128 0.228 C
ATOM 21 HB2 PRO 2 15.701 21.008 0.929 H
ATOM 22 HB3 PRO 2 16.205 20.816 -0.766 H
ATOM 23 CA PRO 2 16.959 22.548 0.197 C
ATOM 24 HA PRO 2 16.973 22.781 -0.868 H
ATOM 25 C PRO 2 16.177 23.607 0.933 C
ATOM 26 O PRO 2 16.455 23.874 2.099 O
------------------------------------------------------------------------------
Developer Access Program for Intel Xeon Phi Processors
Access to Intel Xeon Phi processor-based developer platforms.
With one year of Intel Parallel Studio XE.
Training and support from Colfax.
Order your platform today. http://sdm.link/xeonphi
_______________________________________________
OpenBabel-Devel mailing list
OpenBabel-Devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-devel
