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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
#include <BALL/STRUCTURE/atomBijection.h>
#include <BALL/STRUCTURE/geometricProperties.h>
#include <BALL/KERNEL/PTE.h>
#include <BALL/KERNEL/extractors.h>
#include <BALL/KERNEL/residue.h>
#include <BALL/DATATYPE/hashGrid.h>
using namespace std;
namespace BALL
{
AtomBijection::AtomBijection(AtomContainer& A, AtomContainer& B, bool limit_to_selection)
: std::vector<std::pair<Atom*, Atom*> >()
{
assignByName(A, B, limit_to_selection);
}
/* Calculate the root mean squared deviation */
double AtomBijection::calculateRMSD() const
{
double sum_of_squares = 0.0;
if (!empty())
{
for (Size i = 0; i < size(); ++i)
{
Vector3& r(operator [] (i).first->getPosition());
sum_of_squares += r.getSquareDistance(operator [] (i).second->getPosition());
}
// calculate mean square deviation
sum_of_squares = sqrt(sum_of_squares / (double)size());
}
// return RMSD
return sum_of_squares;
}
Size AtomBijection::assignByName(AtomContainer& A, AtomContainer& B, bool limit_to_selection)
{
// Clear old bijection.
clear();
// Remember the names of A and their atom pointers.
StringHashMap<Atom*> A_names;
for (AtomIterator ai = A.beginAtom(); +ai; ++ai)
{
A_names.insert(std::pair<String, Atom*>(ai->getFullName(Atom::ADD_VARIANT_EXTENSIONS_AND_ID), &*ai));
}
// Iterate over all atoms of B and try to find an
// atom in A identical names.
for (AtomIterator ai = B.beginAtom(); +ai; ++ai)
{
if (A_names.has(ai->getFullName(Atom::ADD_VARIANT_EXTENSIONS_AND_ID)))
{
if ( !limit_to_selection
|| (ai->isSelected() || A_names[ai->getFullName(Atom::ADD_VARIANT_EXTENSIONS_AND_ID)]->isSelected()))
{
// We found two matching atoms. Remember them.
push_back(AtomPair(A_names[ai->getFullName(Atom::ADD_VARIANT_EXTENSIONS_AND_ID)], &*ai));
}
// Throw away the hash map entry in order to avoid
// 1:n mappings.
A_names.erase(ai->getFullName(Atom::ADD_VARIANT_EXTENSIONS_AND_ID));
}
}
// Check whether we could map anything.
// If not, try to map by atom name alone.
if (size() == 0)
{
// Next stage: try to map by atom name only.
A_names.clear();
for (AtomIterator ai = A.beginAtom(); +ai; ++ai)
{
A_names.insert(std::pair<String, Atom*>(ai->getName(), &*ai));
}
clear();
for (AtomIterator ai = B.beginAtom(); +ai; ++ai)
{
if (A_names.has(ai->getName()))
{
if ( !limit_to_selection
|| (ai->isSelected() || A_names[ai->getName()]->isSelected()))
{
// We found two matching atoms. Remember them.
push_back(std::pair<Atom*, Atom*>(A_names[ai->getName()], &*ai));
}
// Throw away the hash map entry in order to avoid
// 1:n mappings.
A_names.erase(ai->getName());
}
}
}
return size();
}
Size AtomBijection::assignTrivial(AtomContainer& A, AtomContainer& B, bool limit_to_selection)
{
// Delete old bijection.
clear();
// Map in order -- first atom of A onto
// first atom of B and so on.
AtomIterator ai(A.beginAtom());
AtomIterator bi(B.beginAtom());
for (; +ai && +bi; ++ai, ++bi)
{
if ( !limit_to_selection
|| (ai->isSelected() || bi->isSelected()))
{
push_back(std::pair<Atom*, Atom*>(&*ai, &*bi));
}
}
return size();
}
Size AtomBijection::assignCAlphaAtoms(AtomContainer& A, AtomContainer& B, bool limit_to_selection)
{
// Delete old bijection.
clear();
// Extract all residues in A and B
ResidueList rla(residues(A));
ResidueList rlb(residues(B));
// Walk over the residues in parallel
ResidueList::iterator ita(rla.begin());
ResidueList::iterator itb(rlb.begin());
for (; ita != rla.end() && itb != rlb.end(); ++ita, ++itb)
{
// If the two residues do have an atom named CA, push back the pair.
Atom* caa = (*ita)->getAtom("CA");
Atom* cab = (*itb)->getAtom("CA");
if ( (caa != 0) && (cab != 0)
&& ( !limit_to_selection
|| (caa->isSelected() || cab->isSelected())))
{
push_back(AtomPair(caa, cab));
}
}
//
return size();
}
Size AtomBijection::assignBackboneAtoms(AtomContainer& A, AtomContainer& B, bool limit_to_selection)
{
// Delete old bijection.
clear();
// Extract all residues in A and B
ResidueList rla(residues(A));
ResidueList rlb(residues(B));
// Walk over the residues in parallel
ResidueList::iterator ita(rla.begin());
ResidueList::iterator itb(rlb.begin());
for (; ita != rla.end() && itb != rlb.end(); ++ita, ++itb)
{
// If the two residues do have backbone atoms (CA, C, N, O, H)
// map then onto each other.
Atom* a = (*ita)->getAtom("CA");
Atom* b = (*itb)->getAtom("CA");
if ( (a != 0) && (b != 0)
&& ( !limit_to_selection
|| (a->isSelected() || b->isSelected())))
{
push_back(AtomPair(a, b));
}
a = (*ita)->getAtom("C");
b = (*itb)->getAtom("C");
if ( (a != 0) && (b != 0)
&& ( !limit_to_selection
|| (a->isSelected() || b->isSelected())))
{
push_back(AtomPair(a, b));
}
a = (*ita)->getAtom("N");
b = (*itb)->getAtom("N");
if ( (a != 0) && (b != 0)
&& ( !limit_to_selection
|| (a->isSelected() || b->isSelected())))
{
push_back(AtomPair(a, b));
}
a = (*ita)->getAtom("O");
b = (*itb)->getAtom("O");
if ( (a != 0) && (b != 0)
&& ( !limit_to_selection
|| (a->isSelected() || b->isSelected())))
{
push_back(AtomPair(a, b));
}
a = (*ita)->getAtom("H");
b = (*itb)->getAtom("H");
if ( (a != 0) && (b != 0)
&& ( !limit_to_selection
|| (a->isSelected() || b->isSelected())))
{
push_back(AtomPair(a, b));
}
}
//
return size();
}
Size AtomBijection::assignAtomsByProperty(AtomContainer& A, AtomContainer& B)
{
// Delete old bijection.
clear();
// Map in order -- first atom of A onto
// first atom of B and so on.
AtomIterator ai(A.beginAtom());
AtomIterator bi(B.beginAtom());
for (; +ai && +bi; ++ai, ++bi)
{
if ( ai->hasProperty("ATOMBIJECTION_RMSD_SELECTION") || bi->hasProperty("ATOMBIJECTION_RMSD_SELECTION"))
{
push_back(std::pair<Atom*, Atom*>(&*ai, &*bi));
}
}
return size();
}
} // namespace BALL
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