diff --git a/modules/io/doc/mmcif.rst b/modules/io/doc/mmcif.rst
index 7fba2f5c6df41b711f56bc8e8426c99b174ce5a2..ed3ebb395136b95d00b27d1694de8f2e7d91c358 100644
--- a/modules/io/doc/mmcif.rst
+++ b/modules/io/doc/mmcif.rst
@@ -122,6 +122,8 @@ of the annotation available.
Also available as :meth:`GetRevisions`. May be extended by
:meth:`AddRevision`.
+ :type: :class:`MMCifInfoRevisions`
+
.. method:: AddCitation(citation)
Add a citation to the citation list of an info object.
@@ -246,14 +248,8 @@ of the annotation available.
.. method:: AddRevision(num, date, status)
- Add a new iteration to the history.
-
- :param num: database_pdb_rev.num
- :type num: :class:`int`
- :param date: database_pdb_rev.date
- :type date: :class:`str`
- :param status: database_pdb_rev.status
- :type status: :class:`str`
+ Add a new iteration to the revision history.
+ See :meth:`MMCifInfoRevisions.AddRevision`.
.. method:: GetRevisions()
@@ -262,9 +258,7 @@ of the annotation available.
.. method:: SetRevisionsDateOriginal(date)
Set the date, when this entry first entered the PDB.
-
- :param date: database_pdb_rev.date_original
- :type date: :class:`str`
+ See :meth:`MMCifInfoRevisions.SetDateOriginal`.
.. class:: MMCifInfoCitation
@@ -654,7 +648,7 @@ of the annotation available.
Since this function is at the moment mainly used to create biounits from
mmCIF files to be saved as PDBs, the function assumes that the
- :ref:`ChainType` properties are set correctly.
+ :class:`ChainType` properties are set correctly.
:param asu: Asymmetric unit to work on. Should be created from a mmCIF
file.
@@ -662,7 +656,7 @@ of the annotation available.
:param seqres: If set to a valid sequence list, the length of the seqres
records will be used to determine if a certain chain has the minimally
required length.
- :type seqres: :class:'~ost.seq.SequenceList'
+ :type seqres: :class:`~ost.seq.SequenceList`
:param min_polymer_size: The minimal number of residues a polymer needs to
get its own chain. Everything below that number will be sorted into the
ligand chain.
@@ -919,7 +913,7 @@ of the annotation available.
The starting point (1-based) and end point of the aligned range in the
deposited sequence, respectively.
- :type: :class:`int`
+ :type: :class:`int`
.. attribute:: db_begin
db_end
@@ -927,16 +921,16 @@ of the annotation available.
The starting point (1-based) and end point of the aligned range in the
database sequence, respectively.
- :type: :class:`int`
+ :type: :class:`int`
.. attribute:: difs
List of differences between the deposited sequence and the sequence in the
database.
- .. attribute:: chain_name
-
- Chain name of the polymer in the mmCIF file.
+ .. attribute:: chain_name
+
+ Chain name of the polymer in the mmCIF file.
.. class:: MMCifInfoStructRefSeqDif
@@ -946,7 +940,7 @@ of the annotation available.
.. attribute:: rnum
The residue number (1-based) of the residue in the deposited sequence
-
+
:type: :class:`int`
.. attribute:: details
@@ -961,77 +955,72 @@ of the annotation available.
Revision history of a PDB entry. If you find a '?' somewhere, this means
'not set'.
- .. attribute:: date_original
+ .. attribute:: date_original
- The date when this entry was seen in PDB for the very first time. This is
- not necessarily the release date.
+ The date when this entry was seen in PDB for the very first time. This is
+ not necessarily the release date. Expected format 'yyyy-mm-dd'.
- :type: :class:`str`
-
- .. attribute:: first_release
-
- Index + 1 of the revision releasing this entry. If the value is 0, was not
- set yet.
-
- :type: :class:`int`
-
- .. method:: SetDateOriginal(date)
-
- Set the date, when this entry first entered the PDB.
+ :type: :class:`str`
- :param date: database_pdb_rev.date_original
- :type date: :class:`str`
+ .. attribute:: first_release
- .. method:: GetDateOriginal()
+ Index + 1 of the revision releasing this entry. If the value is 0, was not
+ set yet.
- Retrieve database_pdb_rev.date_original.
+ :type: :class:`int`
- :returns: database_pdb_rev.date_original as :class:`str` in format 'yyyy-mm-dd'
+ .. method:: AddRevision(num, date, status)
- .. method:: AddRevision(int num, String date, String status)
+ Add a new iteration to the history.
- Add a new iteration to the history.
+ :param num: See :meth:`GetNum`
+ :type num: :class:`int`
+ :param date: See :meth:`GetDate`
+ :type date: :class:`str`
+ :param status: See :meth:`GetStatus`
+ :type status: :class:`str`
- :param num: database_pdb_rev.num
- :type num: :class:`int`
- :param date: database_pdb_rev.date
- :type date: :class:`str`
- :param status: database_pdb_rev.status
- :type status: :class:`str`
+ :raises: Exception if *num* is <= the last added iteration.
- .. method:: GetSize()
+ .. method:: GetSize()
- :returns: Number of revisions as :class:`int`
+ :return: Number of revisions (valid revision indices are in [0, number-1]).
+ :rtype: :class:`int`
- .. method:: GetDate(i)
+ .. method:: GetDate(i)
- :param i: Index of revision
- :type i: :class:`int`
- :returns: database_pdb_rev.date as :class:`str`
+ :param i: Index of revision
+ :type i: :class:`int`
+ :return: Date the PDB revision took place. Expected format 'yyyy-mm-dd'.
+ :rtype: :class:`str`
- .. method:: GetNum(i)
+ .. method:: GetNum(i)
- :param i: Index of revision
- :type i: :class:`int`
- :returns: database_pdb_rev.num as :class:`int`
+ :param i: Index of revision
+ :type i: :class:`int`
+ :return: Unique identifier of revision (assigned in increasing order)
+ :rtype: :class:`int`
- .. method:: GetStatus(i)
+ .. method:: GetStatus(i)
- :param i: Index of revision
- :type i: :class:`int`
- :returns: database_pdb_rev.status as :class:`str`
+ :param i: Index of revision
+ :type i: :class:`int`
+ :return: The status of this revision.
+ :rtype: :class:`str`
- .. method:: GetLastDate()
+ .. method:: GetLastDate()
- The date of the latest revision.
+ :return: Date of the latest revision.
+ :rtype: :class:`str`
- :returns: date as :class:`str`
+ .. method:: SetDateOriginal(date)
+ GetDateOriginal()
- .. method:: GetFirstRelease()
+ See :attr:`date_original`
- Points to the revision releasing the entry.
+ .. method:: GetFirstRelease()
- :returns: Index as :class:`int`
+ See :attr:`first_release`
.. LocalWords: cas isbn pubmed asu seqres conop ConnectAll casp COMPND OBSLTE
.. LocalWords: SPRSDE pdb func autofunction exptl attr pdbx oper conf spr dif
diff --git a/modules/io/src/mol/mmcif_info.hh b/modules/io/src/mol/mmcif_info.hh
index 8054c160f5386130bc94d181b7a04c81258c6b22..6f9b3ed317c5bed68c27c0ebc1569420fbbfb987 100644
--- a/modules/io/src/mol/mmcif_info.hh
+++ b/modules/io/src/mol/mmcif_info.hh
@@ -699,7 +699,7 @@ public:
/// \param status status of the revision
void AddRevision(int num, String date, String status)
{
- if (num_.size() && (num_.back() > num)) {
+ if (num_.size() && (num_.back() >= num)) {
std::stringstream ss;
ss << "'num' component of 'database_pdb_rev' category has to increase ";
ss << "with every revision, last was ";