diff --git a/modules/io/doc/mmcif.rst b/modules/io/doc/mmcif.rst index 1cd557a5f30bf4d441c43d22e3e23565bdd0ed14..1c7d17c98ed50a92261d15ba90175914fd39d1ed 100644 --- a/modules/io/doc/mmcif.rst +++ b/modules/io/doc/mmcif.rst @@ -45,8 +45,8 @@ The following categories of a mmCIF file are considered by the reader: * ``pdbx_database_PDB_obs_spr``: Verbose information on obsoleted/ superseded entries, stored in :class:`MMCifInfoObsolete` * ``struct_ref`` stored in :class:`MMCifInfoStructRef` -* ``struct_ref_seq`` stored in :class:`MMCifInfoStructRefSeqDif` -* ``struct_ref_seq_dif`` stored in :class:`MMCifInfoStructRefDif` +* ``struct_ref_seq`` stored in :class:`MMCifInfoStructRefSeq` +* ``struct_ref_seq_dif`` stored in :class:`MMCifInfoStructRefSeqDif` * ``database_pdb_rev`` (mmCIF dictionary version < 5) stored in :class:`MMCifInfoRevisions` * ``pdbx_audit_revision_history`` and ``pdbx_audit_revision_details`` @@ -140,7 +140,7 @@ of the annotation available. :meth:`SetMethod`. Some PDB entries have multiple experimental methods. This function - only a single one of them. + returns only a single one of them. .. attribute:: resolution @@ -194,7 +194,11 @@ of the annotation available. .. attribute:: struct_refs - Lists all links to external databases in the mmCIF file. + Lists all links to external databases in the mmCIF file as a + list of :class:`MMCifInfoStructRef`. + + Also available as :meth:`GetStructRefs`. May also be modified by + :meth:`SetStructRefs`. .. attribute:: revisions @@ -287,6 +291,16 @@ of the annotation available. .. method:: GetStructDetails() + See :attr:`struct_details` + + .. method:: SetStructRef(refs) + + See :attr:`struct_refs` + + .. method:: GetStructRef() + + See :attr:`struct_refs` + .. method:: AddMMCifPDBChainTr(cif_chain_id, pdb_chain_id) Set up a translation for a certain mmCIF chain name to the traditional PDB @@ -1141,16 +1155,22 @@ of the annotation available. :attr:`db_name`. :type: :class:`str` + + .. attribute:: aligned_seqs + + List of aligned sequences (all entries of the struct_ref_seq category + mapping to this struct_ref) as :class:`MMCifInfoStructRefSeq`. + + Also available as :meth:`GetAlignedSeqs`. .. method:: GetAlignedSeq(name) - Returns the aligned sequence for the given name, None if the sequence does + Returns the aligned sequence for the given name, None if the sequence does not exist. - - .. attribute:: aligned_seqs - List of aligned sequences (all entries of the struct_ref_seq category - mapping to this struct_ref). + .. method:: GetAlignedSeqs() + + See :attr:`aligned_seqs` .. class:: MMCifInfoStructRefSeq @@ -1181,8 +1201,8 @@ of the annotation available. .. attribute:: difs - List of differences between the deposited sequence and the sequence in the - database. + List of differences (:class:`MMCifInfoStructRefSeqDif`) between the + deposited sequence and the sequence in the database. .. attribute:: chain_name @@ -1193,12 +1213,19 @@ of the annotation available. A particular difference between the deposited sequence and the sequence in the database. - .. attribute:: rnum + .. attribute:: seq_rnum The residue number (1-based) of the residue in the deposited sequence :type: :class:`int` + .. attribute:: db_rnum + + The number of the residue in the database sequence or '?' if + 'struct_ref_seq_dif.pdbx_seq_db_seq_num' was missing. + + :type: :class:`str` + .. attribute:: details A textual description of the difference, e.g. point mutation,