// Paste oriented model to target model
void Fragment::pasteOrientedModel(Vec3<double> origin, Model* target)
{
Messenger::enter("Fragment::pasteOrientedModel");
// Translate model to correct origin
orientedModel_.translateSelectionLocal(origin, true);
// Select all atoms except any anchor atoms
orientedModel_.selectAll();
orientedModel_.deselectElement(0);
// Paste to the target model, bonding the anchor and linkPartners if a bond was there before
Clipboard clip;
clip.copySelection(&orientedModel_);
clip.pasteToModel(target, false);
// Translate orientedModel_ back to its previous position
orientedModel_.translateSelectionLocal(-origin, true);
orientedModel_.selectNone();
Messenger::exit("Fragment::pasteOrientedModel");
}
// Paste anchored model to target model
void Fragment::pasteAnchoredModel(Atom* anchorpoint, bool replace, int& replacebond, Model* target, bool adjustbond)
{
Messenger::enter("Fragment::pasteAnchoredModel");
// Set up anchored model in correct geometry - have we a valid attachment point?
if (!anchoredModel(anchorpoint, replace, replacebond))
{
Messenger::exit("Fragment::pasteAnchoredModel");
return;
}
// Get pointers to link and partner atoms, determine if there was a bond there, and then delete link atom
Bond::BondType bt = Bond::nBondTypes;
Atom* linkPartner = NULL, *linkAtom;
if (masterLinkPartner_ != NULL)
{
linkPartner = anchoredModel_.atom(masterLinkPartner_->id());
bt = (masterLinkAtom_->findBond(masterLinkPartner_) == NULL ? Bond::nBondTypes : masterLinkAtom_->findBond(masterLinkPartner_)->type());
}
linkAtom = anchoredModel_.atom(masterLinkAtom_->id());
anchoredModel_.deleteAtom(linkAtom);
// Remove any other anchorpoints, and translate model to correct position relative to anchor
anchoredModel_.selectElement(0);
anchoredModel_.selectionDelete();
anchoredModel_.selectAll();
anchoredModel_.translateSelectionLocal(anchorpoint->r());
// If we are to replace a hydrogen in the target model, delete it first
if (replace && (anchorpoint->nBonds() != 0))
{
// For safety, clamp range of replaced atom id (shouldn't be necessary)
if (replacebond >= anchorpoint->nBonds()) replacebond = 0;
// Grab atom along n'th bond
RefListItem<Bond,int>* ri = anchorpoint->bond(replacebond);
target->deleteAtom(ri->item->partner(anchorpoint));
}
// Paste to the target model, bonding the anchor and linkPartners if a bond was there before
Clipboard clip;
clip.copyAll(&anchoredModel_);
// Translate to adjust bond length if requested
if (adjustbond)
{
Vec3<double> delta = linkPartner->r() - anchorpoint->r();
double original = delta.magAndNormalise();
delta *= (ElementMap::atomicRadius(linkPartner) + ElementMap::atomicRadius(anchorpoint)) - original;
clip.translate(delta);
}
clip.pasteToModel(target, false);
if (bt != Bond::nBondTypes) target->bondAtoms(anchorpoint->id(), target->nAtoms() - anchoredModel_.nAtoms() + linkPartner->id(), bt);
// Since we've physically altered anchoredModel_, re-copy it
anchoredModel_.copy(masterModel_);
linkAtom = anchoredModel_.atom(masterLinkAtom_->id());
anchoredModel_.markAll();
anchoredModel_.translateSelectionLocal(-linkAtom->r(), true);
Messenger::exit("Fragment::pasteAnchoredModel");
}