diff --git a/modules/conop/doc/functions.rst b/modules/conop/doc/functions.rst index 49c9d0fc0ce0c39a7d179152f75d809b82bd8293..7b3618a9f3bc15ba5d5dcdc4318bc1d0f5096012 100644 --- a/modules/conop/doc/functions.rst +++ b/modules/conop/doc/functions.rst @@ -7,10 +7,10 @@ Conop Functions AssignBackboneTorsions(chain) AssignBackboneTorsions(residues) - Assigns the backbone torsions PHI, PSI and OMEGA. The backbone atoms - are required to be connected for the torsions to be added. In addition, - only residues for which :meth:`~ost.mol.ResidueHandle.IsPeptideLinking` - returns True are considered. + Assigns the backbone torsions PHI, PSI and OMEGA. The backbone atoms are + required to be connected for the torsions to be added. In addition, only + residues for which :attr:`~ost.mol.ResidueHandle.peptide_linking` is True are + considered. The first signature assigns the torsions to *res*, assuming prev is the amino acid before, and *next* is the amino acid next to *res*. diff --git a/modules/mol/base/doc/entity.rst b/modules/mol/base/doc/entity.rst index c3dd84b4043662d7387622ae648ca3bcce419091..6c89358fcd0b5fbf1cd54fd3d436b4fec2515273 100644 --- a/modules/mol/base/doc/entity.rst +++ b/modules/mol/base/doc/entity.rst @@ -545,7 +545,16 @@ The Handle Classes Whether the residue is considered to be part of a protein. This is set when loading a structure if the residue forms a feasible peptide bond to the previous or next residue (see :meth:`~ost.conop.IsBondFeasible`). Also - available as :meth:`IsProtein`, :meth:`SetIsProtein`. + available as :meth:`IsProtein`, :meth:`SetIsProtein`. In contrast to + :meth:`IsPeptideLinking` this excludes residues which are not connected to + neighbouring residues such as CA-only residues or badly positioned ones. + + .. attribute:: peptide_linking + + Whether residue can form peptide bonds. This is determined based on + :attr:`chem_class` which is set when loading the structure. + + :type: :class:`bool` .. attribute:: index @@ -569,9 +578,7 @@ The Handle Classes .. method:: IsPeptideLinking() - :return: True, if residue can form peptide bonds (determined based on - :attr:`chem_class` set when loading the structure). - :rtype: :class:`bool` + See :attr:`peptide_linking` .. method:: GetChain() diff --git a/modules/mol/base/doc/query.rst b/modules/mol/base/doc/query.rst index baa08d3fe07315eb5d2e05f9ccb3232dd1d44baa..d187296d4a9ed93b51d9694c2d0b9b0c05338bf1 100644 --- a/modules/mol/base/doc/query.rst +++ b/modules/mol/base/doc/query.rst @@ -192,11 +192,11 @@ all beta sheets or "coil" for any type of coil. **rindex** (int): :attr:`Index<ResidueHandle.index>` of residue handle in chain. This index is the same for views and handles. -**peptide** (bool): Whether the residue is :meth:`peptide linking -<ResidueHandle.IsPeptideLinking>`. +**peptide** (bool): Whether the residue is :attr:`peptide linking +<ResidueHandle.peptide_linking>`. **protein** (bool): Whether the residue is considered to be -:attr:`part of a protein <ResidueHandle.is_protein>`. +:attr:`part of a connected protein <ResidueHandle.is_protein>`. **rbfac** (float): average B (temperature) factor of residue