diff --git a/modules/mol/base/doc/entity.rst b/modules/mol/base/doc/entity.rst index 192d3e27a51275c5ba09d7323f5630d83b3cc482..6d036a70bf3e287cad950c7b55734d6e915f75fb 100644 --- a/modules/mol/base/doc/entity.rst +++ b/modules/mol/base/doc/entity.rst @@ -534,6 +534,8 @@ The Handle Classes .. attribute:: sec_structure The secondary structure of the residue. + + :type: :class:`SecStructure` .. attribute:: is_ligand @@ -1755,7 +1757,7 @@ here. ``CHAINTYPE_POLY_PEPTIDE_D``, ``CHAINTYPE_POLY_PEPTIDE_L``, ``CHAINTYPE_POLY_DN``, ``CHAINTYPE_POLY_RN``, ``CHAINTYPE_POLY_SAC_D``, ``CHAINTYPE_POLY_SAC_L``, ``CHAINTYPE_POLY_DN_RN``, - ``CHAINTYPE_UNKNOWN``, ``CHAINTYPE_N_CHAINTYPES`` + ``CHAINTYPE_UNKNOWN``, ``CHAINTYPE_N_CHAINTYPES`` Where ``CHAINTYPE_N_CHAINTYPES`` holds the number of different types available. @@ -1795,3 +1797,49 @@ ViewAddFlags * ``CHECK_DUPLICATES`` - If set, it will be checked that no duplicates are created when adding a new handle + +SecStructure +-------------------------------------------------------------------------------- + +.. class:: SecStructure(type) + + Defines a secondary structure type following the types defined by DSSP. + + :param type: Type to be set for this object. + :type type: :class:`SecStructure.Type` / :class:`str` + + .. method:: IsHelical + + :return: True, if the set type is any type of helix (i.e. ALPHA_HELIX, + PI_HELIX or THREE_TEN_HELIX) + + .. method:: IsExtended + + :return: True, if the set type is any type of beta sheet (i.e. EXTENDED, + BETA_BRIDGE) + + .. method:: IsCoil + + :return: True, if the set type is any type of coil (i.e. TURN, BEND or COIL) + + .. method:: __str__ + + :return: The character corresponding to the set type (see + :class:`SecStructure.Type`) + +.. class:: SecStructure.Type + + Enumerates all popssible secondary structure types distinguished by DSSP. + Their values with the corresponding character code are listed here: + + .. hlist:: + :columns: 2 + + * ALPHA_HELIX = 'H' + * PI_HELIX = 'I' + * THREE_TEN_HELIX = 'G' + * EXTENDED = 'E' + * BETA_BRIDGE = 'B' + * TURN = 'T' + * BEND = 'S' + * COIL = 'C' diff --git a/modules/mol/base/doc/query.rst b/modules/mol/base/doc/query.rst index d187296d4a9ed93b51d9694c2d0b9b0c05338bf1..8d5a6328658829756c9d227e76061c3efd043d55 100644 --- a/modules/mol/base/doc/query.rst +++ b/modules/mol/base/doc/query.rst @@ -187,7 +187,7 @@ numeric part is honored. **rtype** (str): Residue type as given by the DSSP code (e.g. "H" for alpha helix, "E" for extended), "helix" for all helix types, "ext" or "strand" for -all beta sheets or "coil" for any type of coil. +all beta sheets or "coil" for any type of coil (see :class:`SecStructure`). **rindex** (int): :attr:`Index<ResidueHandle.index>` of residue handle in chain. This index is the same for views and handles.