diff --git a/modules/mol/base/doc/entity.rst b/modules/mol/base/doc/entity.rst index 0bbf46aa1543a450778dde420eb38abab400c270..197d41091f16f66775a40a9a87252e6bd856f593 100644 --- a/modules/mol/base/doc/entity.rst +++ b/modules/mol/base/doc/entity.rst @@ -98,19 +98,28 @@ The Handle Classes :type: float - .. attribute:: center_of_mass - - Center of mass. Also available as :meth:`GetCenterOfMass` - - :type: :class:`~ost.geom.Vec3` - .. attribute:: center_of_atoms + + Center of atoms, that is the average atom position of the entity. + Use :attr:`center_of_mass` for the the mass-weighted center of the entity. + Also available as :meth:`GetCenterOfAtoms`. + + :type: :class:`~ost.geom.Vec3` + + .. attribute:: center_of_mass - Center of atoms (not mass-weighted). Also available as - :meth:`GetCenterOfAtoms`. + Center of mass of the entity. + Also available as :meth:`GetCenterOfMass` :type: :class:`~ost.geom.Vec3` + .. attribute:: geometric_center + + Mid-point of the axis aligned bounding box of the entity. + Also available as :meth:`GetGeometricCenter` + + :type: Vec3 + .. attribute:: positions Equivalent to calling :meth:`GetPositions` with *sort_by_index = True*. This @@ -286,29 +295,21 @@ The Handle Classes alternative atom positions are not handled yet. + .. method:: GetMass() + + See :attr:`mass` + .. method:: GetCenterOfAtoms() - - Get center of atoms, that is the average atom position of the entity. Use - :meth:`GetCenterOfMass` to calculate the mass-weighted center of the entity. - - :returns: :class:`~ost.geom.Vec3` - + + See :attr:`center_of_atoms` + .. method:: GetCenterOfMass() - - Calculates the center of mass of the entity. Use :meth:`GetCenterOfAtoms` - to calculate the non-mass-weighted center of the entity. - - :returns: :class:`~ost.geom.Vec3` - + + See :attr:`center_of_mass` + .. method:: GetGeometricCenter() - - Calculates the mid-point of the axis aligned bounding box of the entity. - - :returns: :class:`~ost.geom.Vec3` - - .. method:: GetMass() - - See :attr:`mass` + + See :attr:`geometric_center` .. method:: GetPositions(sort_by_index=True) @@ -367,10 +368,17 @@ The Handle Classes .. attribute:: center_of_mass - Center of mass. Also available as :meth:`GetCenterOfMass` + Center of mass. Also available as :meth:`GetCenterOfMass`. :type: :class:`~ost.geom.Vec3` + .. attribute:: geometric_center + + Mid-point of the axis aligned bounding box of the chain. + Also available as :meth:`GetGeometricCenter` + + :type: Vec3 + .. attribute:: description Details about the chain. Not categorised, just text. @@ -641,6 +649,12 @@ The Handle Classes :type: :class:`~ost.geom.Vec3` + .. attribute:: geometric_center + + Mid-point of the axis aligned bounding box of the residue. + + :type: Vec3 + .. attribute:: chain The chain this residue belongs to. Read-only. Also available as @@ -851,6 +865,10 @@ The Handle Classes See :attr:`center_of_mass` + .. method:: GetGeometricCenter() + + See :attr:`geometric_center` + .. method:: GetChain() See :attr:`chain` @@ -1332,9 +1350,23 @@ The View Classes .. attribute:: bounds - Axis-aligned bounding box of the entity view. Read-only. - - :type: :class:`ost.geom.AlignedCuboid` + See :attr:`EntityHandle.bounds` + + .. attribute:: mass + + See :attr:`EntityHandle.mass` + + .. attribute:: center_of_atoms + + See :attr:`EntityHandle.center_of_atoms` + + .. attribute:: center_of_mass + + See :attr:`EntityHandle.center_of_mass` + + .. attribute:: geometric_center + + See :attr:`EntityHandle.geometric_center` .. attribute:: valid @@ -1695,24 +1727,17 @@ The View Classes :type: float + .. attribute:: center_of_atoms + + See :attr:`ChainHandle.center_of_atoms` + .. attribute:: center_of_mass - Center of mass. Also available as :meth:`GetCenterOfMass` - - :type: :class:`~ost.geom.Vec3` - - .. attribute:: center_of_atoms - - Center of atoms (not mass weighted). Also available as - :meth:`GetCenterOfAtoms`. - - :type: :class:`~ost.geom.Vec3` + See :attr:`ChainHandle.center_of_mass` .. attribute:: geometric_center - Mid-point of the axis aligned bounding box of the entity. - - :type: Vec3 + See :attr:`ChainHandle.geometric_center` .. attribute:: valid @@ -1860,6 +1885,7 @@ The View Classes mass center_of_atoms center_of_mass + geometric_center phi_torsion psi_torsion chem_class @@ -1919,6 +1945,7 @@ The View Classes GetMass GetCenterOfAtoms GetCenterOfMass + GetGeometricCenter GetPhiTorsion GetPsiTorsion GetChemClass @@ -1976,10 +2003,6 @@ The View Classes .. method:: GetIndex() See :attr:`index` - - .. method:: GetGeometricCenter() - - See :attr:`geometric_center` .. method:: Select(query, flags=0)