Bump Bump!
Sorry, small error in the loop variable labels. Here is the correct version:
void createSingleBond(OBMol& mol, OBAtom * start, OBAtom * end) {
OBBond *bond = mol.NewBond();
bond->SetBegin(start);
bond->SetEnd(end);
bond->SetBondOrder(1);
start->AddBond(bond);
end->AddBond(bond);
double dist = start->GetDistance(end);
bond->SetLength(dist);
cout << "New bond length: " << dist << endl;
}
OBAtom * MoleculeBuilder::getAtomByAtomID(OBResidue *res, string type) {
for (OBAtom * atom : res->GetAtoms()) {
string atomID = res->GetAtomID(atom);
boost::trim(atomID);
if (atomID == type) {
return atom;
}
}
return NULL;
}
void MoleculeBuilder::fixProlines(OBMol & mol) {
for (int a = 0; a < mol.NumResidues(); a++) {
OBResidue* res = mol.GetResidue(a);
if (res->GetName() == "PRO") {
std::vector<OBBond *> bonds = res->GetBonds(false);
OBAtom * CA = getAtomByAtomID(res, "CA");
OBAtom * CB = getAtomByAtomID(res, "CB");
OBAtom * CG = getAtomByAtomID(res, "CG");
OBAtom * CD = getAtomByAtomID(res, "CD");
if (CA == NULL || CB == NULL || CG == NULL || CD ==
NULL) {
cout
<< "Cannot find proline ring
carbons! Torsion updates will not work."
<< endl;
cout << CA << " " << CB << " " << CG << " " <<
CD << endl;
return;
}
string names[4] = { "CA", "CB", "CG", "CD" };
OBAtom connect[4] = { CA, CB, CG, CD };
for (int b = 0; b < 3; b++) {
if (!connect[b]->IsConnected(connect[b + 1])) {
cout << names[b] << " and " << names[b
+ 1]
<< " are not connected
in OBMol, connecting."
<< endl;
createSingleBond(mol, connect[b],
connect[b + 1]);
}
}
}
}
}
________________________________________
From: Browning Nicholas John
Sent: Thursday, January 19, 2017 6:29 PM
To: OpenBabel-Devel@lists.sourceforge.net
Subject: Re: Proline Bond Lists
Bump!
Here is a very dirty fix. Torsion changes across any bond in proline will
rotate the corresponding atoms properly.
Nick
void createSingleBond(OBMol& mol, OBAtom * start, OBAtom * end) {
OBBond *bond = mol.NewBond();
bond->SetBegin(start);
bond->SetEnd(end);
bond->SetBondOrder(1);
start->AddBond(bond);
end->AddBond(bond);
double dist = start->GetDistance(end);
bond->SetLength(dist);
cout << "New bond length: " << dist << endl;
}
OBAtom * getAtomByAtomID(OBResidue *res, string type) {
for (OBAtom * atom : res->GetAtoms()) {
string atomID = res->GetAtomID(atom);
boost::trim(atomID);
if (atomID == type) {
return atom;
}
}
return NULL;
}
void fixProlines(OBMol & mol) {
for (int a = 0; a < mol.NumResidues(); a++) {
OBResidue* res = mol.GetResidue(a);
if (res->GetName() == "PRO") {
std::vector<OBBond *> bonds = res->GetBonds(false);
OBAtom * CA = getAtomByAtomID(res, "CA");
OBAtom * CB = getAtomByAtomID(res, "CB");
OBAtom * CG = getAtomByAtomID(res, "CG");
OBAtom * CD = getAtomByAtomID(res, "CD");
if (CA == NULL || CB == NULL || CG == NULL || CD ==
NULL) {
cout
<< "Cannot find proline ring
carbons! Torsion updates will not work."
<< endl;
cout << CA << " " << CB << " " << CG << " " <<
CD << endl;
return;
}
string names[4] = { "CA", "CB", "CG", "CD" };
OBAtom connect[4] = { CA, CB, CG, CD };
for (int a = 0; a < 3; a++) {
if (!connect[a]->IsConnected(connect[a + 1])) {
cout << names[a] << " and " << names[a
+ 1]
<< " are not connected
in OBMol, connecting."
<< endl;
createSingleBond(mol, connect[a],
connect[a + 1]);
}
}
}
}
}
________________________________________
From: Browning Nicholas John
Sent: Thursday, January 12, 2017 6:53 PM
To: OpenBabel-Devel@lists.sourceforge.net
Subject: Proline Bond Lists
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
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