Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Estimate bond distances in template tool #1099

Merged
merged 3 commits into from
Aug 16, 2022
Merged

Estimate bond distances in template tool #1099

Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
5a58231
Estimate bond distances for monodentate and haptic
aerkiaga Aug 15, 2022
667d3d3
Merge branch 'master' into template-bond-distances
aerkiaga Aug 15, 2022
d1db92c
Extend bond distance calculation to all ligands
aerkiaga Aug 15, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
19 changes: 19 additions & 0 deletions avogadro/qtplugins/templatetool/templatetool.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -397,6 +397,25 @@ void TemplateTool::atomLeftClick(QMouseEvent *e)
moleculeLigandOutVector += newPos - m_molecule->atomPosition3d(moleculeCenterIndex);
}

// Estimate and try to realize bond distances
Vector3 displacement(0.0, 0.0, 0.0);
for (size_t i = 0; i < templateLigandIndices.size(); i++) {
unsigned char ligandAtomicNumber = templateMolecule.atomicNumber(templateLigandIndices[i]);
ligandAtomicNumber = (ligandAtomicNumber == 0)? 6 : ligandAtomicNumber;
// Estimate as the sum of covalent radii
double bondDistance = Elements::radiusCovalent(ligandAtomicNumber)
+ Elements::radiusCovalent(m_molecule->atomicNumber(moleculeCenterIndex));
Vector3 inVector = templateMolecule.atomPosition3d(templateDummyIndex)
- templateMolecule.atomPosition3d(templateLigandIndices[i]);
Vector3 correctionVector = inVector;
correctionVector.normalize();
correctionVector *= bondDistance - inVector.norm();
displacement += correctionVector;
}
displacement *= 1.0 / templateLigandIndices.size();
Vector3 newPos = templateMolecule.atomPosition3d(templateDummyIndex) + displacement;
templateMolecule.setAtomPosition3d(templateDummyIndex, newPos);

// Translate template so dummy atom is brought to center atom
for (size_t i = 0; i < templateMolecule.atomCount(); i++) {
if (i != templateDummyIndex) {
Expand Down