mmCIF File Format
--------------------------------------------------------------------------------
.. currentmodule:: ost.io
The mmCIF file format is a container for structural entities provided by the
PDB. Here we describe how to load those files and how to deal with information
provided above the legacy PDB format (:class:`MMCifInfo`,
:class:`MMCifInfoCitation`, :class:`MMCifInfoTransOp`,
:class:`MMCifInfoBioUnit`, :class:`MMCifInfoStructDetails`,
:class:`MMCifInfoObsolete`, :class:`MMCifInfoStructRef`,
:class:`MMCifInfoStructRefSeq`, :class:`MMCifInfoStructRefSeqDif`,
:class:`MMCifInfoRevisions`, :class:`MMCifInfoEntityBranchLink`).
Loading mmCIF Files
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. autofunction:: ost.io.LoadMMCIF
Categories Available
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
The following categories of a mmCIF file are considered by the reader:
* ``atom_site``: Used to build the :class:`~ost.mol.EntityHandle`
* ``entity``: Involved in setting :class:`~ost.mol.ChainType` of chains
* ``entity_poly``: Involved in setting :class:`~ost.mol.ChainType` of chains
* ``citation``: Goes into :class:`MMCifInfoCitation`
* ``citation_author``: Goes into :class:`MMCifInfoCitation`
* ``exptl``: Goes into :class:`MMCifInfo` as :attr:`~MMCifInfo.method`.
* ``refine``: Goes into :class:`MMCifInfo` as :attr:`~MMCifInfo.resolution`,
:attr:`~MMCifInfo.r_free` and :attr:`~MMCifInfo.r_work`.
* ``pdbx_struct_assembly``: Used for :class:`MMCifInfoBioUnit`.
* ``pdbx_struct_assembly_gen``: Used for :class:`MMCifInfoBioUnit`.
* ``pdbx_struct_oper_list``: Used for :class:`MMCifInfoBioUnit`.
* ``struct``: Details about a structure, stored in
:class:`MMCifInfoStructDetails`.
* ``struct_conf``: Stores secondary structure information (practically helices)
in the :class:`~ost.mol.EntityHandle`
* ``struct_sheet_range``: Stores secondary structure information for sheets in
the :class:`~ost.mol.EntityHandle`
* ``pdbx_database_PDB_obs_spr``: Verbose information on obsoleted/ superseded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`
* ``database_pdb_rev`` (mmCIF dictionary version < 5) stored in
:class:`MMCifInfoRevisions`
* ``pdbx_audit_revision_history`` and ``pdbx_audit_revision_details``
(mmCIF dictionary version >= 5) used to fill :class:`MMCifInfoRevisions`
* ``pdbx_entity_branch`` and ``pdbx_entity_branch_link`` used for
:class:`MMCifInfoEntityBranchLink`, a list of links is available by
:meth:`~MMCifInfo.GetEntityBranchLinks`
Notes:
* Structures in mmCIF format can have two chain names. The "new" chain name
extracted from ``atom_site.label_asym_id`` is used to name the chains in the
:class:`~ost.mol.EntityHandle`. The "old" (author provided) chain name is
extracted from ``atom_site.auth_asym_id`` for the first atom of the chain.
It is added as string property named "pdb_auth_chain_name" to the
:class:`~ost.mol.ChainHandle`. The mapping is also stored in
:class:`MMCifInfo` as :meth:`~MMCifInfo.GetMMCifPDBChainTr` and
:meth:`~MMCifInfo.GetPDBMMCifChainTr` if SEQRES records are read in
:func:`~ost.io.LoadMMCIF` and a non-empty SEQRES record exists for that chain
(this should exclude ligands and water).
* Molecular entities in mmCIF are identified by an ``entity.id``. Each chain is
mapped to an ID in :class:`MMCifInfo` as :meth:`~MMCifInfo.GetMMCifEntityIdTr`.
Info Classes
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Information from mmCIF files that goes beyond structural data, is kept in a
special container, the :class:`MMCifInfo` class. Here is a detailed description
of the annotation available.
.. class:: MMCifInfo
This is the container for all bits of non-molecular data pulled from a mmCIF
file.
.. attribute:: citations
Stores a list of citations (:class:`MMCifInfoCitation`).
Also available as :meth:`GetCitations`.
.. attribute:: biounits
Stores a list of biounits (:class:`MMCifInfoBioUnit`).
Also available as :meth:`GetBioUnits`.
.. attribute:: method
Stores the experimental method used to create the structure.
Also available as :meth:`GetMethod`. May also be modified by
:meth:`SetMethod`.
.. attribute:: resolution
Stores the resolution of the crystal structure. Set to 0 if no value in
loaded mmCIF file.
Also available as :meth:`GetResolution`. May also be modified by
:meth:`SetResolution`.
.. attribute:: r_free
Stores the R-free value of the crystal structure. Set to 0 if no value in
loaded mmCIF file.
Also available as :meth:`GetRFree`. May also be modified by
:meth:`SetRFree`.
.. attribute:: r_work
Stores the R-work value of the crystal structure. Set to 0 if no value in
loaded mmCIF file.
Also available as :meth:`GetRWork`. May also be modified by
:meth:`SetRWork`.
.. attribute:: operations
Stores the operations needed to transform a crystal structure into a
bio unit.
Also available as :meth:`GetOperations`. May also be modified by
:meth:`AddOperation`.
.. attribute:: struct_details
Stores details about the structure in a :class:`MMCifInfoStructDetails`
object.
Also available as :meth:`GetStructDetails`. May also be modified by
:meth:`SetStructDetails`.
.. attribute:: struct_refs
Lists all links to external databases in the mmCIF file.
.. attribute:: revisions
Stores a simple history of a PDB entry.
Also available as :meth:`GetRevisions`. May be extended by
:meth:`AddRevision`.
:type: :class:`MMCifInfoRevisions`
.. attribute:: obsolete
Stores information about obsoleted / superseded entries.
Also available as :meth:`GetObsoleteInfo`. May also be modified by
:meth:`SetObsoleteInfo`.
:type: :class:`MMCifInfoObsolete`
.. method:: AddCitation(citation)
Add a citation to the citation list of an info object.
:param citation: Citation to be added.
:type citation: :class:`MMCifInfoCitation`
.. method:: AddAuthorsToCitation(id, authors)
Adds a list of authors to a specific citation.
:param id: Identifier of the citation.
:type id: :class:`str`
:param authors: List of authors.
:type authors: :class:`~ost.StringList`
.. method:: GetCitations()
See :attr:`citations`
.. method:: AddBioUnit(biounit)
Add a bio unit to the bio unit list of an info object. If the
:attr:`id <MMCifInfoBioUnit.id>` of ``biounit`` already exists in the set
of assemblies, both will be merged. This means that
:attr:`chain <MMCifInfoBioUnit.chains>` and
:attr:`operations <MMCifInfoBioUnit.operations>` lists will be concatenated
and the interval lists
(:attr:`operationsintervalls <MMCifInfoBioUnit.operationsintervalls>`,
:attr:`chainintervalls <MMCifInfoBioUnit.chainintervalls>`) will be updated.
:param biounit: Bio unit to be added.
:type biounit: :class:`MMCifInfoBioUnit`
.. method:: GetBioUnits()
See :attr:`biounits`
.. method:: SetMethod(method)
See :attr:`method`
.. method:: GetMethod()
See :attr:`method`
.. method:: SetResolution(resolution)
See :attr:`resolution`
.. method:: GetResolution()
See :attr:`resolution`
.. method:: AddOperation(operation)
See :attr:`operations`
.. method:: GetOperations()
See :attr:`operations`
.. method:: SetStructDetails(details)
See :attr:`struct_details`
.. method:: GetStructDetails()
.. method:: AddMMCifPDBChainTr(cif_chain_id, pdb_chain_id)
Set up a translation for a certain mmCIF chain name to the traditional PDB
chain name.
:param cif_chain_id: atom_site.label_asym_id
:type cif_chain_id: :class:`str`
:param pdb_chain_id: atom_site.auth_asym_id
:type pdb_chain_id: :class:`str`
.. method:: GetMMCifPDBChainTr(cif_chain_id)
Get the translation of a certain mmCIF chain name to the traditional PDB
chain name.
:param cif_chain_id: atom_site.label_asym_id
:type cif_chain_id: :class:`str`
:returns: atom_site.auth_asym_id as :class:`str` (empty if no mapping)
.. method:: AddPDBMMCifChainTr(pdb_chain_id, cif_chain_id)
Set up a translation for a certain PDB chain name to the mmCIF chain name.
:param pdb_chain_id: atom_site.auth_asym_id
:type pdb_chain_id: :class:`str`
:param cif_chain_id: atom_site.label_asym_id
:type cif_chain_id: :class:`str`
.. method:: GetPDBMMCifChainTr(pdb_chain_id)
Get the translation of a certain PDB chain name to the mmCIF chain name.
:param pdb_chain_id: atom_site.auth_asym_id
:type pdb_chain_id: :class:`str`
:returns: atom_site.label_asym_id as :class:`str` (empty if no mapping)
.. method:: AddMMCifEntityIdTr(cif_chain_id, entity_id)
Set up a translation for a certain mmCIF chain name to the mmCIF entity ID.
:param cif_chain_id: atom_site.label_asym_id
:type cif_chain_id: :class:`str`
:param entity_id: atom_site.label_entity_id
:type entity_id: :class:`str`
.. method:: GetMMCifEntityIdTr(cif_chain_id)
Get the translation of a certain mmCIF chain name to the mmCIF entity ID.
:param cif_chain_id: atom_site.label_asym_id
:type cif_chain_id: :class:`str`
:returns: atom_site.label_entity_id as :class:`str` (empty if no mapping)
.. method:: AddRevision(num, date, status, major=-1, minor=-1)
Add a new iteration to the revision history.
See :meth:`MMCifInfoRevisions.AddRevision`.
.. method:: GetRevisions()
See :attr:`revisions`
.. method:: SetRevisionsDateOriginal(date)
Set the date, when this entry first entered the PDB. Ignored if it was set
in the past. See :meth:`MMCifInfoRevisions.SetDateOriginal`.
.. method:: GetObsoleteInfo()
See :attr:`obsolete`
.. method:: SetObsoleteInfo()
See :attr:`obsolete`
.. method:: GetEntityBranchLinks()
Get bond information for branched entities. Returns all
:class:`MMCifInfoEntityBranchLink` objects in one list. Chain and residue
information is available by the stored
:class:`AtomHandles <ost.mol.AtomHandle>` of each entry.
.. method:: AddEntityBranchLink(chain_name, atom1, atom2, bond_order)
Add bond information for a branched entity.
:param chain_name: Chain the bond belongs to
:type chain_name: :class:`str`
:param atom1: First atom of the bond
:type atom1: :class:`~ost.mol.AtomHandle`
:param atom2: Second atom of the bond
:type atom2: :class:`~ost.mol.AtomHandle`
:param bond_order: bond order (e.g. 1=single, 2=double, 3=triple)
:type bond_order: :class:`int`
:returns: Nothing
.. method:: ConnectBranchLinks()
Establish all bonds stored for branched entities.
.. class:: MMCifInfoCitation
This stores citation information from an input file.
.. attribute:: id
Stores an internal identifier for a citation. If not provided, resembles an
empty string.
Also available as :meth:`GetID`. May also be modified by :meth:`SetID`.
.. attribute:: cas
Stores a Chemical Abstract Service identifier if available. If not
provided, resembles an empty string.
Also available as :meth:`GetCAS`. May also be modified by :meth:`SetCas`.
.. attribute:: isbn
Stores the ISBN code, presumably for cited books. If not
provided, resembles an empty string.
Also available as :meth:`GetISBN`. May also be modified by :meth:`SetISBN`.
.. attribute:: published_in
Stores the book or journal title of a publication. Should take the full
title, no abbreviations. If not provided, resembles an empty string.
Also available as :meth:`GetPublishedIn`. May also be modified by
:meth:`SetPublishedIn`.
.. attribute:: volume
Supposed to store volume information for journals. Since the volume number
is not always a simple integer, it is stored as a string. If not provided,
resembles an empty string.
Also available as :meth:`GetVolume`. May also be modified by
:meth:`SetVolume`.
.. attribute:: page_first
Stores the first page of a publication. Since the page numbers are not
always a simple integers, they are stored as strings. If not provided,
resembles empty strings.
Also available as :meth:`GetPageFirst`. May also be modified by
:meth:`SetPageFirst`.
.. attribute:: page_last
Stores the last page of a publication. Since the page numbers are not
always a simple integers, they are stored as strings. If not provided,
resembles empty strings.
Also available as :meth:`GetPageLast`. May also be modified by
:meth:`SetPageLast`.
.. attribute:: doi
Stores the Document Object Identifier as used by doi.org for a cited
document. If not provided, resembles an empty string.
Also available as :meth:`GetDOI`. May also be modified by :meth:`SetDOI`.
.. attribute:: pubmed
Stores the PubMed accession number. If not provided, is set to 0.
Also available as :meth:`GetPubMed`. May also be modified by
:meth:`SetPubmed`.
.. attribute:: year
Stores the publication year. If not provided, is set to 0.
Also available as :meth:`GetYear`. May also be modified by :meth:`SetYear`.
.. attribute:: title
Stores a title. If not provided, is set to an empty string.
Also available as :meth:`GetTitle`. May also be modified by
:meth:`SetTitle`.
.. attribute:: book_publisher
Name of publisher of the citation, relevant for books and book chapters.
Also available as :meth:`GetBookPublisher` and :meth:`SetBookPublisher`.
.. attribute:: book_publisher_city
City of the publisher of the citation, relevant for books and book
chapters.
Also available as :meth:`GetBookPublisherCity` and
:meth:`SetBookPublisherCity`.
.. attribute:: citation_type
Defines where a citation was published. Either journal, book or unknown.
Also available as :meth:`GetCitationType`. May also be modified by
:meth:`SetCitationType` with values from :class:`MMCifInfoCType`. For
conveinience setters :meth:`SetCitationTypeJournal`,
:meth:`SetCitationTypeBook` and :meth:`SetCitationTypeUnknown` exist.
For checking the type of a citation, :meth:`IsCitationTypeJournal`,
:meth:`IsCitationTypeBook` and :meth:`IsCitationTypeUnknown` can be used.
.. attribute:: authors
Stores a :class:`~ost.StringList` of authors.
Also available as :meth:`GetAuthorList`. May also be modified by
:meth:`SetAuthorList`.
.. method:: GetCAS()
See :attr:`cas`
.. method:: SetCAS(cas)
See :attr:`cas`
.. method:: GetISBN()
See :attr:`isbn`
.. method:: SetISBN(isbn)
See :attr:`isbn`
.. method:: GetPublishedIn()
See :attr:`published_in`
.. method:: SetPublishedIn(title)
See :attr:`published_in`
.. method:: GetVolume()
See :attr:`volume`
.. method:: SetVolume(volume)
See :attr:`volume`
.. method:: GetPageFirst()
See :attr:`page_first`
.. method:: SetPageFirst(first)
See :attr:`page_first`
.. method:: GetPageLast()
See :attr:`page_last`
.. method:: SetPageLast(last)
See :attr:`page_last`
.. method:: GetDOI()
See :attr:`doi`
.. method:: SetDOI(doi)
See :attr:`doi`
.. method:: GetPubMed()
See :attr:`pubmed`
.. method:: SetPubMed(no)
See :attr:`pubmed`
.. method:: GetYear()
See :attr:`year`
.. method:: SetYear(year)
See :attr:`year`
.. method:: GetTitle()
See :attr:`title`
.. method:: SetTitle(title)
See :attr:`title`
.. method:: GetBookPublisher
See :attr:`book_publisher`
.. method:: SetBookPublisher
See :attr:`book_publisher`
.. method:: GetBookPublisherCity
See :attr:`book_publisher_city`
.. method:: SetBookPublisherCity
See :attr:`book_publisher_city`
.. method:: GetCitationType()
See :attr:`citation_type`
.. method:: SetCitationType(publication_type)
See :attr:`citation_type`
.. method:: SetCitationTypeJournal()
See :attr:`citation_type`
.. method:: SetCitationTypeBook()
See :attr:`citation_type`
.. method:: SetCitationTypeUnknown()
See :attr:`citation_type`
.. method:: IsCitationTypeJournal()
See :attr:`citation_type`
.. method:: IsCitationTypeBook()
See :attr:`citation_type`
.. method:: IsCitationTypeUnknown()
See :attr:`citation_type`
.. method:: GetAuthorList()
See :attr:`authors`
.. method:: SetAuthorList(list)
See :attr:`authors`
.. class:: MMCifInfoTransOp
This stores operations needed to transform an :class:`~ost.mol.EntityHandle`
into a bio unit.
.. attribute:: id
A unique identifier. If not provided, resembles an empty string.
Also available as :meth:`GetID`. May also be modified by
:meth:`SetID`.
.. attribute:: type
Describes the operation. If not provided, resembles an empty string.
Also available as :meth:`GetType`. May also be modified by
:meth:`SetType`.
.. attribute:: translation
The translational vector. Also available as :meth:`GetVector`. May also be
modified by :meth:`SetVector`.
.. attribute:: rotation
The rotational matrix. Also available as :meth:`GetMatrix`. May also be
modified by :meth:`SetMatrix`.
.. method:: GetID()
See :attr:`id`
.. method:: SetID(id)
See :attr:`id`
.. method:: GetType()
See :attr:`type`
.. method:: SetType(type)
See :attr:`type`
.. method:: GetVector()
See :attr:`translation`
.. method:: SetVector(x, y, z)
See :attr:`translation`
.. method:: GetMatrix()
See :attr:`rotation`
.. method:: SetMatrix(i00,i01, i02, i10,i11, i12, i20,i21, i22)
See :attr:`rotation`
.. class:: MMCifInfoBioUnit
This stores information how a structure is to be assembled to form the
bio unit.
.. attribute:: id
The id of a bio unit as given by the original mmCIF file.
Also available as :meth:`GetID`. May also be modified by :meth:`SetID`.
:type: :class:`str`
.. attribute:: details
Special aspects of the biological assembly. If not provided, resembles an
empty string.
Also available as :meth:`GetDetails`. May also be modified by
:meth:`SetDetails`.
.. attribute:: method_details
Details about the method used to determine this biological assembly.
Also available as :meth:`GetMethodDetails`. May also be modified by
:meth:`SetMethodDetails`.
.. attribute:: chains
Chains involved in this bio unit. If not provided, resembles an empty list.
Also available as :meth:`GetChainList`. May also be modified by
:meth:`AddChain` or :meth:`SetChainList`.
.. attribute:: chainintervals
List of intervals on the chain list. Needed if there a several sets of
chains and transformations to create the bio unit. Comes as a list of
tuples. First component is the start, second is the right border of the
interval.
Also available as :meth:`GetChainIntervalList`. Is automatically modified by
:meth:`AddChain`, :meth:`SetChainList` and :meth:`MMCifInfo.AddBioUnit`.
.. attribute:: operations
Translations and rotations needed to create the bio unit. Filled with
objects of class :class:`MMCifInfoTransOp`.
Also available as :meth:`GetOperations`. May be modified by
:meth:`AddOperations`
.. attribute:: operationsintervalls
List of intervals on the operations list. Needed if there a several sets of
chains and transformations to create the bio unit. Comes as a list of
tuples. First component is the start, second is the right border of the
interval.
Also available as :meth:`GetOperationsIntervalList`. Is automatically
modified by :meth:`AddOperations` and :meth:`MMCifInfo.AddBioUnit`.
.. method:: GetID()
See :attr:`id`
.. method:: SetID(id)
See :attr:`id`
.. method:: GetDetails()
See :attr:`details`
.. method:: SetDetails(details)
See :attr:`details`
.. method:: GetMethodDetails()
See :attr:`method_details`
.. method:: SetMethodDetails(details)
See :attr:`method_details`
.. method:: GetChainList()
See :attr:`chains`
.. method:: SetChainList(chains)
See :attr:`chains`, also resets :attr:`chainintervalls` to contain only one
interval enclosing the whole chain list.
:param chains: List of chain names.
:type chains: :class:`~ost.StringList`
.. method:: AddChain(chain name)
See :attr:`chains`, also extends the right border of the last entry in
:attr:`chainintervalls`.
.. method:: GetChainIntervalList()
See :attr:`chainintervals`
.. method:: GetOperations()
See :attr:`operations`
.. method:: AddOperations(list of operations)
See :attr:`operations`, also extends the right border of the last entry in
:attr:`operationsintervalls`.
.. method:: GetOperationsIntervalList()
See :attr:`operationsintervalls`
.. function:: PDBize(asu, seqres=None, min_polymer_size=10, transformation=False)
Returns the biological assembly (bio unit) for an entity. The new entity
created is well suited to be saved as a PDB file. Therefore the function
tries to meet the requirements of single-character chain names. The
following measures are taken.
- All ligands are put into one chain (_)
- Water is put into one chain (-)
- Each polymer gets its own chain, named A-Z 0-9 a-z.
- The description of non-polymer chains will be put into a generic string
property called description on the residue level.
- Ligands that resemble a polymer but have less than *min_polymer_size*
residues are assigned the same numeric residue number. The residues are
distinguished by insertion code.
- Sometimes bio units exceed the coordinate system storable in a PDB file.
In that case, the box around the entity will be aligned to the lower
left corner of the coordinate system.
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
:class:`~ost.mol.ChainType` properties are set correctly.
:param asu: Asymmetric unit to work on. Should be created from a mmCIF
file.
:type asu: :class:`~ost.mol.EntityHandle`
: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`
: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.
:type min_polymer_size: int
:param transformation: If set, return the transformation matrix used to
move the bounding box of the bio unit to the lower left corner.
:type transformation: :class:`bool`
.. class:: MMCifInfoStructDetails
Holds details about the structure.
.. attribute:: entry_id
Identifier for a curtain data block. If not provided, resembles an empty
string.
Also available as :meth:`GetEntryID`. May also be modified by
:meth:`SetEntryID`.
.. attribute:: title
Set a title for the structure.
Also available as :meth:`GetTitle`. May also be modified by
:meth:`SetTitle`.
.. attribute:: casp_flag
Tells whether this structure was a target in some competition.
Also available as :meth:`GetCASPFlag`. May also be modified by
:meth:`SetCASPFlag`.
.. attribute:: descriptor
Descriptor for an NDB structure or the unstructured content of a PDB COMPND
record.
Also available as :meth:`GetDescriptor`. May also be modified by
:meth:`SetDescriptor`.
.. attribute:: mass
Molecular mass of a molecule.
Also available as :meth:`GetMass`. May also be modified by
:meth:`SetMass`.
.. attribute:: mass_method
Method used to determine the molecular weight.
Also available as :meth:`GetMassMethod`. May also be modified by
:meth:`SetMassMethod`.
.. attribute:: model_details
Details about how the structure was determined.
Also available as :meth:`GetModelDetails`. May also be modified by
:meth:`SetModelDetails`.
.. attribute:: model_type_details
Details about how the type of the structure was determined.
Also available as :meth:`GetModelTypeDetails`. May also be modified by
:meth:`SetModelTypeDetails`.
.. method:: GetEntryID()
See :attr:`entry_id`
.. method:: SetEntryID(id)
See :attr:`entry_id`
.. method:: GetTitle()
See :attr:`title`
.. method:: SetTitle(title)
See :attr:`title`
.. method:: GetCASPFlag()
See :attr:`casp_flag`
.. method:: SetCASPFlag(flag)
See :attr:`casp_flag`
.. method:: GetDescriptor()
See :attr:`descriptor`
.. method:: SetDescriptor(descriptor)
See :attr:`descriptor`
.. method:: GetMass()
See :attr:`mass`
.. method:: SetMass(mass)
See :attr:`mass`
.. method:: GetMassMethod()
See :attr:`mass_method`
.. method:: SetMassMethod(method)
See :attr:`mass_method`
.. method:: GetModelDetails()
See :attr:`model_details`
.. method:: SetModelDetails(details)
See :attr:`model_details`
.. method:: GetModelTypeDetails()
See :attr:`model_type_details`
.. method:: SetModelTypeDetails(details)
See :attr:`model_type_details`
.. class:: MMCifInfoObsolete
Holds details on obsolete / superseded structures. The data is
available both in the obsolete and in the replacement entries.
.. attribute:: date
When was the entry replaced?
Also available as :meth:`GetDate`. May also be modified by
:meth:`SetDate`.
.. attribute:: id
Type of change. Either *Obsolete* or *Supersede*. Returns a string starting
upper case. Has to be set via ``OBSLTE`` or ``SPRSDE``.
Also available as :meth:`GetID`. May also be modified by
:meth:`SetID`.
.. attribute:: pdb_id
ID of the replacing entry.
Also available as :meth:`GetPDBID`. May also be modified by
:meth:`SetPDBID`.
.. attribute:: replace_pdb_id
ID of the replaced entry.
Also available as :meth:`GetReplacedPDBID`. May also be modified by
:meth:`SetReplacedPDBID`.
.. method:: GetDate()
See :attr:`date`
.. method:: SetDate(date)
See :attr:`date`
.. method:: GetID()
See :attr:`id`
.. method:: SetID(id)
See :attr:`id`
.. method:: GetPDBID()
See :attr:`pdb_id`
.. method:: SetPDBID(flag)
See :attr:`pdb_id`
.. method:: GetReplacedPDBID()
See :attr:`replace_pdb_id`
.. method:: SetReplacedPDBID(descriptor)
See :attr:`replace_pdb_id`
.. class:: MMCifInfoStructRef
Holds the information of the struct_ref category. The category describes the
link of polymers in the mmCIF file to sequences stored in external databases
such as UniProt. The related categories ``struct_ref_seq`` and
``struct_ref_seq_dif`` also list differences between the sequences of the
deposited structure and the sequences in the database. Two prominent examples
of such differences are point mutations and/or expression tags.
.. attribute:: db_name
Name of the external database, for example UNP for UniProt.
:type: :class:`str`
.. attribute:: db_id
Name of the reference sequence in the database pointed to by :attr:`db_name`.
:type: :class:`str`
.. attribute:: db_access
Alternative accession code for the sequence in the database pointed to by
:attr:`db_name`.
:type: :class:`str`
.. method:: GetAlignedSeq(name)
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).
.. class:: MMCifInfoStructRefSeq
An aligned range of residues between a sequence in a reference database and the
deposited sequence.
.. attribute:: align_id
Uniquely identifies every struct_ref_seq item in the mmCIF file.
:type: :class:`str`
.. attribute:: seq_begin
seq_end
The starting point (1-based) and end point of the aligned range in the
deposited sequence, respectively.
:type: :class:`int`
.. attribute:: db_begin
db_end
The starting point (1-based) and end point of the aligned range in the
database sequence, respectively.
: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.
.. class:: MMCifInfoStructRefSeqDif
A particular difference between the deposited sequence and the sequence in
the database.
.. attribute:: rnum
The residue number (1-based) of the residue in the deposited sequence
:type: :class:`int`
.. attribute:: details
A textual description of the difference, e.g. point mutation,
expression tag, purification artifact.
:type: :class:`str`
.. class:: MMCifInfoRevisions
Revision history of a PDB entry. If you find a '?' somewhere, this means
'not set'.
.. attribute:: date_original
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. Set first time we encounter a :meth:`GetStatus` value of
"full release" (mmCIF versions < 5) or "Initial release" (current mmCIF).
:type: :class:`int`
.. method:: AddRevision(num, date, status, major=-1, minor=-1)
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 major: See :meth:`GetMajor`
:type major: :class:`int`
:param minor: See :meth:`GetMinor`
:type minor: :class:`int`
:raises: Exception if *num* is <= the last added iteration.
.. method:: GetSize()
:return: Number of revisions (valid revision indices are in [0, number-1]).
:rtype: :class:`int`
.. method:: GetDate(i)
:param i: Index of revision
:type i: :class:`int`
:return: Date the PDB revision took place. Expected format 'yyyy-mm-dd'.
:rtype: :class:`str`
:raises: Exception if *i* out of bounds.
.. method:: GetNum(i)
:param i: Index of revision
:type i: :class:`int`
:return: Unique identifier of revision (assigned in increasing order)
:rtype: :class:`int`
:raises: Exception if *i* out of bounds.
.. method:: GetStatus(i)
:param i: Index of revision
:type i: :class:`int`
:return: The status of this revision.
:rtype: :class:`str`
:raises: Exception if *i* out of bounds.
.. method:: GetMajor(i)
:param i: Index of revision
:type i: :class:`int`
:return: The major version of this revision (-1 if not set).
:rtype: :class:`int`
:raises: Exception if *i* out of bounds.
.. method:: GetMinor(i)
:param i: Index of revision
:type i: :class:`int`
:return: The minor version of this revision (-1 if not set).
:rtype: :class:`int`
:raises: Exception if *i* out of bounds.
.. method:: GetLastDate()
:return: Date of the latest revision ('?' if no revision set).
:rtype: :class:`str`
.. method:: GetLastMajor()
:return: Major version of the latest revision (-1 if not set).
:rtype: :class:`int`
.. method:: GetLastMinor()
:return: Minor version of the latest revision (-1 if not set).
:rtype: :class:`int`
.. method:: SetDateOriginal(date)
GetDateOriginal()
See :attr:`date_original`
.. method:: GetFirstRelease()
See :attr:`first_release`
.. class:: MMCifInfoEntityBranchLink
Data from ``pdbx_entity_branch``, most specifically
``pdbx_entity_branch_link``. That is connectivity information for branched
entities, e.g. carbohydrates/ oligosaccharides.
:class:`Conop Processors <ost.conop.Processor>` can not easily connect them so
we use this information in :meth:`LoadMMCIF` to do that.
.. attribute:: atom1
The first atom of the bond. Corresponds to ``entity_branch_link.atom_id_1``,
``entity_branch_link.comp_id_1`` and
``entity_branch_link.entity_branch_list_num_1``. Also available via
:meth:`GetAtom1` and :meth:`SetAtom1`.
:type: :class:`~ost.mol.AtomHandle`
.. attribute:: atom2
The second atom of the bond. Corresponds to ``entity_branch_link.atom_id_2``,
``entity_branch_link.comp_id_2`` and
``entity_branch_link.entity_branch_list_num_2``. Also available via
:meth:`GetAtom2` and :meth:`SetAtom2`.
:type: :class:`~ost.mol.AtomHandle`
.. attribute:: bond_order
Order of a bond (e.g. 1=single, 2=double, 3=triple). Corresponds to
``entity_branch_link.value_order``. Also available via :meth:`GetBondOrder`
and :meth:`SetBondOrder`.
:type: :class:`int`
.. method:: ConnectBranchLink(editor)
Establish a bond between :attr:`atom1` and :attr:`atom2` of a
:class:`MMCifInfoEntityBranchLink`.
:param editor: The editor instance to call for connecting the atoms.
:type editor: :class:`~ost.mol.XCSEditor`
:returns: Nothing
.. method:: GetEntityBranchChainNames
Get a list of chain names which contain branched entities.
:returns: :class:`list` of :class:`str`
.. method:: GetAtom1
See :attr:`atom1`
.. method:: GetAtom2
See :attr:`atom2`
.. method:: GetBondOrder
See :attr:`bond_order`
.. method:: SetAtom1
See :attr:`atom1`
.. method:: SetAtom2
See :attr:`atom2`
.. method:: SetBondOrder
See :attr:`bond_order`
.. LocalWords: cas isbn pubmed asu seqres conop ConnectAll casp COMPND OBSLTE
.. LocalWords: SPRSDE pdb func autofunction exptl attr pdbx oper conf spr dif
.. LocalWords: biounits biounit uniprot UNP seqs AddMMCifPDBChainTr cif asym
.. LocalWords: auth GetMMCifPDBChainTr AddPDBCMMCifhainTr GetPDBMMCifChainTr
.. LocalWords: GetRevisions AddRevision SetRevisionsDateOriginal GetSize
.. LocalWords: GetNum num GetStatus GetLastDate GetFirstRelease storable
.. LocalWords: cas isbn pubmed asu seqres conop casp COMPND OBSLTE LoadMMCIF
.. LocalWords: SetChainList MMCifInfoTransOp ChainTypes MMCifInfoStructRef
.. LocalWords: MMCifInfoRevisions bool difs MMCifInfoStructRefSeqDif rnum
.. LocalWords: SetDateOriginal GetDateOriginal yyyy operationsintervalls
.. LocalWords: chainintervalls GetChainIntervalList GetMethodDetails GetAtom
.. LocalWords: GetOperationsIntervalList SetMethodDetails oligosaccharides
.. LocalWords: SetAtom GetBondOrder SetBondOrder MMCifInfoEntityBranchLink