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

Add formal charge to atom property tables #839

Merged
merged 1 commit into from
Mar 12, 2022
Merged

Add formal charge to atom property tables #839

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
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
36 changes: 22 additions & 14 deletions avogadro/qtplugins/propertytables/propertymodel.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -30,13 +30,18 @@ using std::vector;

using SecondaryStructure = Avogadro::Core::Residue::SecondaryStructure;

const int AtomColumns = 6; // element, valence, x, y, z, color
const int BondColumns = 5; // type, atom 1, atom 2, bond order, length
const int AngleColumns = 5; // type, atom 1, atom 2, atom 3, angle
const int TorsionColumns = 6; // type, atom 1, atom 2, atom 3, atom 4, dihedral
const int ResidueColumns =
6; // name, number, chain, secondary structure, heterogen, color
const int ConformerColumns = 2; // number, energy
// element, valence, formal charge, x, y, z, color TODO: partial charge
const int AtomColumns = 7;
// type, atom 1, atom 2, bond order, length
const int BondColumns = 5;
// type, atom 1, atom 2, atom 3, angle
const int AngleColumns = 5;
// type, atom 1, atom 2, atom 3, atom 4, dihedral
const int TorsionColumns = 6;
// name, number, chain, secondary structure, heterogen, color
const int ResidueColumns = 6;
// number, energy, ??
const int ConformerColumns = 2;

inline double distance(Vector3 v1, Vector3 v2)
{
Expand Down Expand Up @@ -96,18 +101,17 @@ int PropertyModel::columnCount(const QModelIndex& parent) const
Q_UNUSED(parent);
switch (m_type) {
case AtomType:
return AtomColumns; // element, valence, X, Y, Z, color
return AtomColumns; // see above
case BondType:
return BondColumns; // type, atom 1, atom 2, order, length
return BondColumns; // see above
case AngleType:
return AngleColumns; // type, atom 1, atom 2, atom 3, angle
return AngleColumns; // see above
case TorsionType:
return TorsionColumns; // type, atom 1, atom 2, atom 3, atom 4, dihedral
return TorsionColumns;
case ResidueType:
return ResidueColumns; // name, number, chain, secondary structure,
// heterogen, color
return ResidueColumns;
case ConformerType:
return ConformerColumns; // number, energy
return ConformerColumns;
}
return 0;
}
Expand Down Expand Up @@ -194,6 +198,8 @@ QVariant PropertyModel::data(const QModelIndex& index, int role) const
return Core::Elements::symbol(m_molecule->atomicNumber(row));
case AtomDataValence:
return QVariant::fromValue(m_molecule->bonds(row).size());
case AtomDataFormalCharge:
return m_molecule->formalCharge(row);
case AtomDataX:
return QString("%L1").arg(m_molecule->atomPosition3d(row).x(), 0, 'f',
4);
Expand Down Expand Up @@ -349,6 +355,8 @@ QVariant PropertyModel::headerData(int section, Qt::Orientation orientation,
return tr("Element");
case AtomDataValence:
return tr("Valence");
case AtomDataFormalCharge:
return tr("Formal Charge");
case AtomDataX:
return tr("X (Å)");
case AtomDataY:
Expand Down
1 change: 1 addition & 0 deletions avogadro/qtplugins/propertytables/propertymodel.h
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -85,6 +85,7 @@ public slots:
{
AtomDataElement = 0,
AtomDataValence,
AtomDataFormalCharge,
AtomDataX,
AtomDataY,
AtomDataZ,
Expand Down