diff --git a/modules/mol/base/doc/editors.rst b/modules/mol/base/doc/editors.rst index c4241b8cad54deaa1ef7701601aa2e50f752d0b7..c9b78b26b35dd9cda438c0360cc070abdd300efc 100644 --- a/modules/mol/base/doc/editors.rst +++ b/modules/mol/base/doc/editors.rst @@ -67,7 +67,9 @@ The basic functionality of editors is implemented in the EditorBase class. :type residue_name: string :returns: :class:`ResidueHandle` - .. method:: InsertAtom(residue, atom_name, pos, element="", occupancy=1.0, b_factor=0.0, is_hetatm=False) + .. method:: InsertAtom(residue, atom_name, pos, + element="", occupancy=1.0, b_factor=0.0, + is_hetatm=False) Insert new atom and add it to residue. For atoms with alternative atom locations use :meth:`InsertAltAtom`. If the element parameter is a valid @@ -85,7 +87,7 @@ The basic functionality of editors is implemented in the EditorBase class. module rely on proper naming. :type atom_name: string :param pos: is the position of the atom in global coordinates - :type pos: :class:`geom.Vec3` + :type pos: :class:`~ost.geom.Vec3` :param element: is the atom's element. If set to a a valid element, atom properties such as mass, charge, radius are set based on default values for that element. If the element @@ -100,6 +102,74 @@ The basic functionality of editors is implemented in the EditorBase class. :type is_hetatm: bool :returns: :class:`AtomHandle` + .. method:: AddTorsion(name, atom1, atom2, atom3, atom4) + + Add a named torsion to the entity. The atoms must have bonds between + atom1-atom2-atom3-atom4. + + :param name: The torsion name, e.g. PHI or PSI + :type name: :class:`str` + + :param atom1: First atom. must be valid + :type atom1: :class:`AtomHandle` + + :param atom2: Second atom. must be valid + :type atom2: :class:`AtomHandle` + + :param atom3: Third atom. must be valid + :type atom3: :class:`AtomHandle` + + :param atom4: Fourth atom. must be valid + :type atom4: :class:`AtomHandle` + + .. method:: DeleteAtom(atom) + + Deletes the atom from the entity and removes all bonds and torsions this + atom is involved. + + :param atom: A valid atom + :type atom: :class:`EntityHandle` + + .. method:: DeleteAllAtoms(residue) + + Deletes all atoms of this residue from the entity and remove all bonds and + torsions for where an atom of the residue is involved. + + :type residue: :class:`ResidueHandle` + :param residue: A valid residue + + + :type atom: The atom to be deleted + + :type atom: :class:`EntityHandle` + + .. method:: DeleteResidue(residue) + + Deletes the residue, it's atoms and removes all bonds and torsion where one + atom of the residue is involved + + :type residue: :class:`ResidueHandle` + :param residue: A valid residue + + .. method:: DeleteChain(chain) + + Delete the given chain, and all its residues + + :param chain: `A valid chain` + :type chain: :class:`ChainHandle` + + .. method:: ReorderResidues(chain) + ReorderResidues() + + Reorder residues of the chain (the entity) such that their residues numbers + are continuously increasing. This function might be useful in cases of PDB + files that do not list the residues from N to C terminus but rather use the + residue number to describe their position in the chain. + + :param chain: `A valid chain` + :type chain: :class:`ChainHandle` + + Editor for the External Coordinate System -------------------------------------------------------------------------------- @@ -135,7 +205,7 @@ euclidian space. :param atom: must be a valid atom handle :type atom: :class:`ost.mol.AtomHandle` :param pos: The new position - :type pos: :class:`geom.Vec3` + :type pos: :class:`~ost.geom.Vec3` .. method:: SetOriginalAtomPos(atom, pos) @@ -146,7 +216,7 @@ euclidian space. :param atom: must be a valid atom handle :type atom: :class:`ost.mol.AtomHandle` :param pos: The new untransformed position - :type pos: :class:`geom.Vec3` + :type pos: :class:`~ost.geom.Vec3` Editor for the Internal Coordinate System -------------------------------------------------------------------------------- @@ -176,7 +246,7 @@ using an :class:`ICSEditor` is undefined and vice versa. to buffered, the external coordinates remain unchanged. If set to unbuffered, the external coordinates are immediately recalculated. - :see: :meth:`UpdateICS` + :see: :meth:`UpdateXCS` :param torsion: A valid torsion