diff --git a/modules/conop/doc/aminoacid.rst b/modules/conop/doc/aminoacid.rst index fe42a4c631b746b19992ed085cc1eb0b1185076e..9751631723150af30d849154f03f253ee4ba2c26 100644 --- a/modules/conop/doc/aminoacid.rst +++ b/modules/conop/doc/aminoacid.rst @@ -69,7 +69,7 @@ Converter functions Whether the set is empty, i.e. doesn't contain any amino acids. -Maping functions +Mapping functions -------------------------------------------------------------------------------- The following functions help to convert one residue into another by reusing as @@ -79,11 +79,16 @@ to standard amino acids. .. function:: CopyResidue(src_res, dst_res, editor) - Copies the atoms of ``src_res`` to ``dst_res`` using the residue names of + Copies the atoms of ``src_res`` to ``dst_res`` using the residue names as guide to decide which of the atoms should be copied. If ``src_res`` and ``dst_res`` have the same name, or ``src_res`` is a modified version of - ``dst_res``, CopyConserved will be called, otherwise CopyNonConserved will - be called. + ``dst_res`` (i.e. have the same single letter code), CopyConserved will be + called, otherwise CopyNonConserved will be called. + + :param src_res: The source residue + :type src_res: :class:`~mol.ResidueHandle` + :param dst_res: The destination residue + :type dst_res: :class:`~mol.ResidueHandle` :returns: true if the residue could be copied, false if not. @@ -93,13 +98,13 @@ to standard amino acids. amino acid of ``src_res`` (or ``src_res`` itself) are identical to ``dst_res``. If ``src_res`` and ``dst_res`` are identical, all heavy atoms are copied - ``to dst_res``. If ``src_res`` is a modified version of ``dst_res`` and the + to ``dst_res``. If ``src_res`` is a modified version of ``dst_res`` and the modification is a pure addition (e.g. the phosphate group of phosphoserine), the modification is stripped off and all other heavy atoms are copied to ``dst_res``. If the modification is not a pure addition, only the backbone heavy atoms are copied to ``dst_res``. - Additionally, the selenium atom of MSE is converted to sulphur. + Additionally, the selenium atom of ``MSE`` is converted to sulphur. :param src_res: The source residue :type src_res: :class:`~mol.ResidueHandle` @@ -111,7 +116,8 @@ to standard amino acids. .. function:: CopyNonConserved(src_res, dst_res, editor) - Copies the heavy backbone atoms of ``src_res`` to ``dst_res``. + Copies the heavy backbone atoms and Cbeta (except for ``GLY``) of ``src_res`` + to ``dst_res``. :param src_res: The source residue :type src_res: :class:`~mol.ResidueHandle`