Processor::Result ResidueChecker::operator () (Residue& residue)
{
String res_name;
if ((residue.getChain() != 0) && (residue.getChain()->getName() != BALL_CHAIN_DEFAULT_NAME))
{
res_name = residue.getChain()->getName() + ":";
}
res_name += residue.getName() + ":" + residue.getID();
// Check charges.
status_ &= checkCharge(residue, res_name);
// Check atom positions.
status_ &= checkAtomPositions(residue, res_name);
// if a fragment data base is defined, check for completeness
// of the residue
if (fragment_db_ != 0)
{
const Residue* reference = dynamic_cast<const Residue*>(fragment_db_->getReferenceFragment(residue));
if (reference == 0)
{
if (isEnabled(UNKNOWN_RESIDUES))
{
Log.warn() << "ResidueChecker: didn't find a reference fragment for " << res_name << endl;
status_ = false;
// If selection is enabled, mark the whol residue
if (selection_)
{
residue.select();
}
}
}
else
{
status_ &= checkCompleteness(residue, *reference, res_name);
status_ &= checkTemplate(residue, *reference, res_name);
}
}
return Processor::CONTINUE;
}
void MolecularInformation::getName_(Composite& composite)
{
String temp = "UNKNOWN";
switch(type_)
{
case TYPE__BOND:
{
temp.clear();
Bond* bond = RTTI::castTo<Bond>(composite);
Atom* a1 = (Atom*) bond->getFirstAtom();
Atom* a2 = (Atom*) bond->getSecondAtom();
temp = getBondAtomName_(a1) + " -> " + getBondAtomName_(a2);
}
break;
case TYPE__SYSTEM:
{
System* system = RTTI::castTo<System>(composite);
temp = system->getName();
}
break;
case TYPE__RESIDUE:
{
Residue* residue = RTTI::castTo<Residue>(composite);
temp = residue->getName();
temp += " ";
temp += residue->getID();
}
break;
case TYPE__MOLECULE:
case TYPE__PROTEIN:
case TYPE__CHAIN:
case TYPE__FRAGMENT:
case TYPE__SECONDARY_STRUCTURE:
{
AtomContainer* atom_container = RTTI::castTo<AtomContainer>(composite);
temp = atom_container->getName();
}
break;
case TYPE__ATOM:
{
Atom* atom = RTTI::castTo<Atom>(composite);
temp = atom->getName();
}
break;
default:
break;
}
if (type_ == TYPE__SECONDARY_STRUCTURE)
{
const SecondaryStructure* ss = dynamic_cast<SecondaryStructure*>(&composite);
if (ss != 0)
{
switch (ss->getType())
{
case SecondaryStructure::HELIX:
temp += " Helix";
break;
case SecondaryStructure::TURN:
temp += " Turn";
break;
case SecondaryStructure::STRAND:
temp += " Strand";
break;
case SecondaryStructure::COIL:
temp += " Coil";
break;
default:
temp += " Unknown";
}
}
else
{
temp += " Unknown";
}
}
else
{
if (temp == "")
{
temp = "<";
temp += type_name_;
temp += ">";
}
}
name_ = temp;
}
//TODO switch to real Angle
float calculateResidueChiAngles(const Residue& residue)
{
// some variables
Atom const* N = 0;
Atom const* CA = 0;
Atom const* CB = 0;
Atom const* X = 0;
int num_of_atoms = 0;
float angle = 0;//FLOAT_VALUE_NA;
String residue_name = residue.getName();
// we assume that GLY has no typical CHI_1 - angle
if (residue_name == "GLY" )
{
return angle;
}
AtomConstIterator r_it = residue.beginAtom();
for (; r_it != residue.endAtom(); ++r_it)
{
String name = r_it->getName();
if (name == "N")
{
N = &(*r_it);
num_of_atoms += 1;
}
else if (name == "CA")
{
CA = &(*r_it);
num_of_atoms += 1;
}
else if (name == "CB")
{
CB = &(*r_it);
num_of_atoms += 1;
}
}
if (num_of_atoms != 3)
{
Log.info() << "calculateResidueChiAngles: Torsion angle of " << residue_name<< std::endl;
return angle;
}
// determine the missing atom X
/* Sidechain dihedral angle chi1 is defined
(for non-Gly residues) as follows:
Chi1: N(i)-CA(i)-CB(i)-X(i)
where X is the following atom for the following
residue types:
X Residue type
---- ----------------------------
HB1 Ala (for models with protons,labelled 1HB in PDB files).
SG Cys
CG Asp, Glu, Phe, His, Lys, Leu, Met,
Asn, Pro, Gln, Arg, Trp, Tyr
CG1 Ile, Val
OG Ser
OG1 Thr
In order to be conform with ShiftX we leave out GLY and ALA
*/
if (residue_name == "GLY")
{
Log.info() << "calculateResidueChiAngles: Torsion angle of a Glycine could not be computed!" << std::endl;
return angle;
}
else if (residue_name == "ALA")
{
r_it = residue.beginAtom();
for (;r_it != residue.endAtom(); ++r_it)
{
if (r_it->getName() == "HB1" || r_it->getName() == "1HB")
{
X = &(*r_it);
num_of_atoms += 1;
break;
}
}
}
else if (residue_name == "CYS")
{
r_it = residue.beginAtom();
for (;r_it != residue.endAtom(); ++r_it)
{
if (r_it->getName() == "SG")
{
X = &(*r_it);
num_of_atoms += 1;
break;
}
}
}
else if (residue_name == "ASP" || residue_name == "GLU" ||
residue_name == "PHE" || residue_name == "HIS" ||
residue_name == "LYS" || residue_name == "LEU" ||
residue_name == "MET" || residue_name == "ASN" ||
residue_name == "PRO" || residue_name == "GLN" ||
residue_name == "ARG" || residue_name == "TRP" || residue_name == "TYR")
{
r_it = residue.beginAtom();
for (;r_it != residue.endAtom(); ++r_it)
{
if (r_it->getName() == "CG")
{
X = &(*r_it);
num_of_atoms += 1;
break;
}
}
}
else if (residue_name == "VAL" || residue_name == "ILE")
{
r_it = residue.beginAtom();
for (;r_it != residue.endAtom(); ++r_it)
{
if (r_it->getName() == "CG1")
{
X = &(*r_it);
num_of_atoms += 1;
break;
}
}
}
else if (residue_name == "SER")
{
r_it = residue.beginAtom();
for (;r_it != residue.endAtom(); ++r_it)
{
if (r_it->getName() == "OG")
{
X = &(*r_it);
num_of_atoms += 1;
break;
}
}
}
else if (residue_name == "THR")
{
r_it = residue.beginAtom();
for (;r_it != residue.endAtom(); ++r_it)
{
if (r_it->getName() == "OG1")
{
X = &(*r_it);
num_of_atoms += 1;
break;
}
}
}
if (num_of_atoms != 4)
{
Log.info() << "calculateResidueChiAngles: Chi torsion angle of " << residue.getID() << "-"<< residue.getName() << " could not be computed!" << std::endl;
return angle;
}
Vector3 a = N->getPosition();
Vector3 b = CA->getPosition();
Vector3 c = CB->getPosition();
Vector3 d = X->getPosition();
//angle = getTorsionAngle(a.x, a.y, a.z, b.x, b.y, b.z,
// c.x, c.y, c.z, d.x, d.y, d.z)*180./M_PI;
angle = calculateTorsionAngle(*N,*CA,*CB,*X).toRadian();
while (angle < 0.)
{
angle = angle + 2*BALL::Constants::PI;
}
return angle; // TODO return real angle
}
//TODO switch to real Angle
float calculateResidueChi2Angles(const Residue& residue)
{
// some variables
Atom const* CA = 0;
Atom const* CB = 0;
Atom const* CG = 0;
Atom const* XG = 0;
int num_of_atoms = 0;
float angle = 0; // FLOAT_VALUE_NA;
String residue_name = residue.getName();
// GLY, ALA, SER and CYS have no typical CHI2 - angle
if ( (residue_name == "ALA")
|| (residue_name == "GLY")
|| (residue_name == "SER")
|| (residue_name == "CYS"))
{
Log.info() << "calculateResidueChi2Angles: Chi torsion angle of " << residue.getID() << "-"<< residue.getName() << " could not be computed!" << std::endl;
return angle;
}
// Sidechain dihedral angle chi2 is defined as follows:
//
// Chi2: CA(i)-CB(i)-CG(i)-XG(i)
// where XG is the following atom for the following
// residue types:
//
// CG XG residue
// -------------------------------------
// CG CD PRO, GLN, GLU, LYS, ARG
// CD1 LEU,TRP,PHE,TYR,
// OD1 ASN, ASP
// ND1 HIS
// SD MET
// CG1 CD1 ILE
// 1HG1 VAL
// CG2 (1HG2 VAL)
// 1HG2 THR
//
// Note: in some amino acids the atom names can be switched, i.e.
// for chi2 in amino acids PHE: CD1 <-> CD2
// TYR: CD1 <-> CD2
// ASP: OD1 <-> OD2
AtomConstIterator r_it = residue.beginAtom();
for (; r_it != residue.endAtom(); ++r_it)
{
String name = r_it->getName();
if (name == "CA")
{
CA = &(*r_it);
num_of_atoms += 1;
}
else if (name == "CB")
{
CB = &(*r_it);
num_of_atoms += 1;
}
if (name == "CG")
{
CG = &(*r_it);
num_of_atoms += 1;
}
}
//look for XG
if ( (residue_name == "ARG") || (residue_name == "GLN")
|| (residue_name == "GLU") || (residue_name == "LYS")
|| (residue_name == "PRO"))
{
r_it = residue.beginAtom();
for (;r_it != residue.endAtom(); ++r_it)
{
if (r_it->getName() == "CD")
{
XG = &(*r_it);
num_of_atoms += 1;
break;
}
}
}
else if ( (residue_name == "ASN") || (residue_name == "ASP") )
{
r_it = residue.beginAtom();
for (;r_it != residue.endAtom(); ++r_it)
{
if (r_it->getName() == "OD1")
{
XG = &(*r_it);
num_of_atoms += 1;
break;
}
}
}
else if ( (residue_name == "LEU") || (residue_name == "TRP")
||(residue_name == "PHE") || (residue_name == "TYR") )
{
r_it = residue.beginAtom();
for (;r_it != residue.endAtom(); ++r_it)
{
if (r_it->getName() == "CD1")
{
XG = &(*r_it);
num_of_atoms += 1;
break;
}
}
}
else if (residue_name == "HIS")
{
r_it = residue.beginAtom();
for (;r_it != residue.endAtom(); ++r_it)
{
if (r_it->getName() == "ND1")
{
XG = &(*r_it);
num_of_atoms += 1;
break;
}
}
}
else if(residue_name == "MET")
{
r_it = residue.beginAtom();
for (;r_it != residue.endAtom(); ++r_it)
{
if (r_it->getName() == "SD")
{
XG = &(*r_it);
num_of_atoms += 1;
break;
}
}
}
// we have to take special care about ILE, VAL and THR
else if(residue_name == "ILE")
{
r_it = residue.beginAtom();
for (;r_it != residue.endAtom(); ++r_it)
{
if (r_it->getName() == "CG1")
{
CG = &(*r_it);
num_of_atoms += 1;
}
else if (r_it->getName() == "CD1")
{
XG = &(*r_it);
num_of_atoms += 1;
}
}
}
else if(residue_name == "VAL")
{
r_it = residue.beginAtom();
for (;r_it != residue.endAtom(); ++r_it)
{
if (r_it->getName() == "1HG1")
{
XG = &(*r_it);
num_of_atoms += 1;
}
else if (r_it->getName() == "CG1")
{
CG = &(*r_it);
num_of_atoms += 1;
}
}
}
else if(residue_name == "THR")
{
r_it = residue.beginAtom();
for (;r_it != residue.endAtom(); ++r_it)
{
if (r_it->getName() == "1HG2")
{
XG = &(*r_it);
num_of_atoms += 1;
}
else if (r_it->getName() == "CG2")
{
CG = &(*r_it);
num_of_atoms += 1;
}
}
}
if (num_of_atoms != 4)
{
Log.info() << "calculateResidueChi2Angles: Chi torsion angle of " << residue.getID() << "-"<< residue.getName() << " could not be computed!" << std::endl;
return angle;
}
Vector3 a = CA->getPosition();
Vector3 b = CB->getPosition();
Vector3 c = CG->getPosition();
Vector3 d = XG->getPosition();
angle = calculateTorsionAngle(*CA,*CB,*CG,*XG).toRadian();
while (angle < 0.)
{
angle = angle + 2*BALL::Constants::PI;
}
return angle; // TODO return real angle
}
