int BondedPairFilter::get_value_index(
Model *m, const ParticleIndexPair &pip) const {
if (!Bonded::get_is_setup(m, pip[0]) || !Bonded::get_is_setup(m, pip[1])) {
return false;
}
Bonded ba(m, pip[0]);
Bonded bb(m, pip[1]);
Bond bd = get_bond(ba, bb);
return bd != Bond();
}
void CHARMMPatch::apply(CHARMMResidueTopology *res) const {
if (res->get_patched()) {
IMP_THROW("Cannot patch an already-patched residue", ValueException);
}
check_empty_patch(this);
// Copy or update atoms
for (base::Vector<CHARMMAtomTopology>::const_iterator it = atoms_.begin();
it != atoms_.end(); ++it) {
try {
res->get_atom(it->get_name()) = *it;
}
catch (base::ValueException &) {
res->add_atom(*it);
}
}
// Delete atoms
for (base::Vector<std::string>::const_iterator it = deleted_atoms_.begin();
it != deleted_atoms_.end(); ++it) {
try {
res->remove_atom(*it);
}
catch (base::ValueException &) {
// ignore atoms that don't exist to start with
}
}
// Add angles/bonds/dihedrals/impropers
for (unsigned int i = 0; i < get_number_of_bonds(); ++i) {
res->add_bond(get_bond(i));
}
for (unsigned int i = 0; i < get_number_of_angles(); ++i) {
res->add_angle(get_angle(i));
}
for (unsigned int i = 0; i < get_number_of_dihedrals(); ++i) {
res->add_dihedral(get_dihedral(i));
}
for (unsigned int i = 0; i < get_number_of_impropers(); ++i) {
res->add_improper(get_improper(i));
}
// Add internal coordinates
for (unsigned int i = 0; i < get_number_of_internal_coordinates(); ++i) {
res->add_internal_coordinate(get_internal_coordinate(i));
}
res->set_patched(true);
}
void Bonded::show(std::ostream &out) const {
if (*this == Bonded()) {
out << "Null Bonded";
return;
}
out << "Particle " << get_particle()->get_name() << " is bonded to ";
for (unsigned int i = 0; i < get_number_of_bonds(); ++i) {
Bond b = get_bond(i);
if (b.get_bonded(0) == *this) {
out << b.get_bonded(1).get_particle()->get_name();
} else {
out << b.get_bonded(0).get_particle()->get_name();
}
out << " ";
}
}
void CHARMMPatch::apply(CHARMMResidueTopology *res1,
CHARMMResidueTopology *res2) const
{
if (res1->get_patched()) {
IMP_THROW("Cannot patch an already-patched residue", ValueException);
}
if (res2->get_patched()) {
IMP_THROW("Cannot patch an already-patched residue", ValueException);
}
check_empty_patch(this);
// Extra checks for the commonly-used CHARMM DISU patch
if (get_type() == "DISU"
&& (res1->get_type() != "CYS" || res2->get_type() != "CYS")) {
IMP_WARN("Applying a DISU patch to two residues that are not both 'CYS' "
"(they are " << *res1 << " and " << *res2 << "). This is "
"probably not what was intended.");
}
// Copy or update atoms
for (base::Vector<CHARMMAtomTopology>::const_iterator it = atoms_.begin();
it != atoms_.end(); ++it) {
std::pair<CHARMMResidueTopology *, CHARMMAtomTopology> resatom =
handle_two_patch_atom(*it, res1, res2);
try {
resatom.first->get_atom(resatom.second.get_name()) = resatom.second;
} catch (ValueException &e) {
resatom.first->add_atom(resatom.second);
}
}
// Delete atoms
for (base::Vector<std::string>::const_iterator it = deleted_atoms_.begin();
it != deleted_atoms_.end(); ++it) {
std::pair<CHARMMResidueTopology *, CHARMMAtomTopology> resatom =
handle_two_patch_atom(*it, res1, res2);
try {
resatom.first->remove_atom(resatom.second.get_name());
} catch (ValueException &e) {
// ignore atoms that don't exist to start with
}
}
// Add angles/bonds/dihedrals/impropers
for (unsigned int i = 0; i < get_number_of_bonds(); ++i) {
CHARMMResidueTopology *res =
get_two_patch_residue_for_bond(get_bond(i), res1, res2);
res->add_bond(CHARMMBond(handle_two_patch_bond(get_bond(i), res1,
res2, res)));
}
for (unsigned int i = 0; i < get_number_of_angles(); ++i) {
CHARMMResidueTopology *res =
get_two_patch_residue_for_bond(get_angle(i), res1, res2);
res->add_angle(CHARMMAngle(handle_two_patch_bond(get_angle(i), res1, res2,
res)));
}
for (unsigned int i = 0; i < get_number_of_dihedrals(); ++i) {
CHARMMResidueTopology *res =
get_two_patch_residue_for_bond(get_dihedral(i), res1, res2);
res->add_dihedral(CHARMMDihedral(handle_two_patch_bond(get_dihedral(i),
res1, res2, res)));
}
for (unsigned int i = 0; i < get_number_of_impropers(); ++i) {
CHARMMResidueTopology *res =
get_two_patch_residue_for_bond(get_improper(i), res1, res2);
res->add_improper(CHARMMDihedral(handle_two_patch_bond(get_improper(i),
res1, res2, res)));
}
// Add internal coordinates
for (unsigned int i = 0; i < get_number_of_internal_coordinates(); ++i) {
CHARMMInternalCoordinate ic = get_internal_coordinate(i);
CHARMMResidueTopology *res =
get_two_patch_residue_for_bond(get_internal_coordinate(i),
res1, res2);
res->add_internal_coordinate(
CHARMMInternalCoordinate(handle_two_patch_bond(ic, res1,
res2, res),
ic.get_first_distance(), ic.get_first_angle(),
ic.get_dihedral(), ic.get_second_angle(),
ic.get_second_distance(), ic.get_improper()));
}
res1->set_patched(true);
res2->set_patched(true);
}