.. auto-generated by dev_tools.docs.nxdl from the NXDL source base_classes/NXpdb.nxdl.xml -- DO NOT EDIT

.. index::
    ! NXpdb (base class)
    ! pdb (base class)
    see: pdb (base class); NXpdb

.. _NXpdb:

=====
NXpdb
=====

..
    Contributors List

    .. |contrib_name| replace:: Pete R Jemian|prjemian|https://avatars.githubusercontent.com/u/2279984?v=4|2022-01-28

    .. |contrib_name| replace:: Herbert J. Bernstein|yayahjb|https://avatars.githubusercontent.com/u/4448769?v=4|2018-10-26

    .. |contrib_name| replace:: Tobias Richter|zjttoefs|https://avatars.githubusercontent.com/u/856440?v=4|2018-03-14

**Status**:

  base class, extends :ref:`NXobject`

**Description**:

  .. collapse:: A NeXus transliteration of a PDB file, to be validated only as a PDB ...

      A NeXus transliteration of a PDB file, to be validated only as a PDB
      rather than in NeXus.

      Use :ref:`NXpdb` to incorporate the information in an arbitrary
      PDB into a NeXus file.

      The main suggestion is to use this as a container
      class for a PDB entry to describe a sample in NXsample,
      but it may be more appropriate to place this higher in the
      hierarchy, say in NXentry.

      The structure has to follow the structure of a PDB
      with each PDB data block mapped to a NeXus group of class NXpdb,
      using a lowercase version of the data block name as the name
      of the NeXus group, each PDB category in that data block
      mapped to a NeXus group of class NXpdb and with each PDB column
      mapped to a NeXus field.  Each column in a looped PDB category
      should always be presented as a 1-dimensional array.  The columns 
      in an unlooped PDB category should be presented as scalar values.  
      If a PDB category specifies particular units for columns, the same 
      units should beused for the corresponding fields.

      A PDB entry is unambigous when all information is carried as text.
      All text data should be presented as quoted strings, with the quote
      marks except for the null values "." or "?"

      For clarity in NXpdb form, numeric data may be presented using the
      numeric types specified in the mmCIF dictionary.  In that case,
      if a PDB null value, "." or "?", is contained in a numeric column, the
      IEEE nan should be used for "?" and the IEEE inf should be used for ".".

      An arbitrary DDL2 CIF file can be represented in NeXus using NXpdb.  
      However, if save frames are required, an NXpdb_class  attribute with the
      value "CBF_cbfsf" is required for each NeXus group representing a save
      frame.  NXpdb attributes are not required for other CIF components,
      but may be used to provide internal documentation.

      The nesting of NXpdb groups and datasets that correspond to a CIF with
      two categories and one saveframe, including the NXpdb_class attribues is::

      	(datablock1):NXpdb
      	   @NXpdb_class:CBF_cbfdb
      	   (category1):NXpdb
      	     @NXpdb_class:CBF_cbfcat
      	      (column_name1):[...]
      	      (column_name2):[...]
      	      (column_name3):[...]
      	      ...
      	   (category2):NXpdb
      	      @NXpdb_class:CBF_cbfcat
      	      (column_name4):[...]
      	      (column_name5):[...]
      	      (column_name6):[...]
      	      ...
      	   (saveframe1):NXpdb
      	      @NXpdb_class:CBF_cbfsf
      	      (category3):NXpdb
      	        @NXpdb_class:CBF_cbfcat
      	        (column_name7):[...]
      	        (column_name8):[...]
      	        (column_name9):[...]
      	         ...
      	      ...
      	   ...

      For example, a PDB entry that begins::

      	data_1YVA
      	#
      	 _entry.id   1YVA
      	#
      	_audit_conform.dict_name       mmcif_pdbx.dic
      	_audit_conform.dict_version    5.279
      	_audit_conform.dict_location   http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
      	#
      	loop_
      	_database_2.database_id
      	_database_2.database_code
      	PDB   1YVA
      	RCSB  RCSB031959
      	WWPDB D_1000031959
      	#

      would produce::

      	sample:NXsample
      	   1yva:NXpdb
      	     entry:NXpdb
      		 id:"1YVA"
      	     audit_conform:NXpdb
      		 dict_name:"mmcif_pdbx.dic"
      		 dict_version:"5.279"
      		 dict_location:"http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic"
      	     database_2:NXpdb
      		 database_id:["PDB","RCSB","WWPDB"]
      		 database_code:["1YVA","RCSB031959","D_1000031959"]

      another example is the following excerpt from pdb entry 9ins, giving the sequences
      of the two chains::

      	loop_
      	_entity_poly.entity_id
      	_entity_poly.nstd_linkage
      	_entity_poly.nstd_monomer
      	_entity_poly.pdbx_seq_one_letter_code 
      	_entity_poly.pdbx_seq_one_letter_code_can
      	_entity_poly.type
      	1 no no GIVEQCCTSICSLYQLENYCN GIVEQCCTSICSLYQLENYCN polypeptide(L)
      	2 no no FVNQHLCGSHLVEALYLVCGERGFFYTPKA FVNQHLCGSHLVEALYLVCGERGFFYTPKA
      	polypeptide(L)

      which converts to::

      	entity_poly:NXpdb
      	  @NXpdb_class:CBF_cbfcat
      	  entity_id:["1", "2"]
      	  nstd_linkage:["no", "no"]
      	  nstd_monomer:["no", "no"]
      	  pdbx_seq_one_letter_code:["GIVEQCCTSICSLYQLENYCN","FVNQHLCGSHLVEALYLVCGERGFFYTPKA"]
      	  pdbx_seq_one_letter_code_can:["GIVEQCCTSICSLYQLENYCN","FVNQHLCGSHLVEALYLVCGERGFFYTPKA"]
      	  type:["polypeptide(L)", "polypeptide(L)"]


**Symbols**:

  No symbol table

**Groups cited**:
  none

**Structure**:


**NXDL Source**:
  https://github.com/nexusformat/definitions/blob/main/base_classes/NXpdb.nxdl.xml