diff --git a/base_classes/NXpdb.nxdl.xml b/base_classes/NXpdb.nxdl.xml index 3ab07fff61..e3d7dbd9bb 100644 --- a/base_classes/NXpdb.nxdl.xml +++ b/base_classes/NXpdb.nxdl.xml @@ -22,113 +22,113 @@ # For further information, see http://www.nexusformat.org --> + category="base" + name="NXpdb" + version="1.0" + type="group" + extends="NXobject" + ignoreExtraGroups="true" + ignoreExtraFields="true" + ignoreExtraAttributes="true" + xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" + xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd" + > - + - - A NeXus transliteration of a PDB file, to be validated only as a PDB - rather than as a NeXus file (similar to the handling of NXcollection). + + A NeXus transliteration of a PDB file, to be validated only as a PDB + rather than as a NeXus file (similar to the handling of NXcollection). - Use :ref:`NXpdb` to incorporate the information in an arbitrary - PDB into a NeXus file. - - The original suggestion is to use this as a container - class for a PDB entry to be used to describe a sample in NXsample - in a data collection, but in other cases it may be more - appropriate to place this higher, say in NXentry. - - For NeXus validation, :ref:`NXpdb` will always generate - a warning since it is always an optional group. - Anything (groups, fields, or attributes) placed in - an :ref:`NXcollection` group will not be validated. + Use :ref:`NXpdb` to incorporate the information in an arbitrary + PDB into a NeXus file. + + The original suggestion is to use this as a container + class for a PDB entry to be used to describe a sample in NXsample + in a data collection, but in other cases it may be more + appropriate to place this higher, say in NXentry. + + For NeXus validation, :ref:`NXpdb` will always generate + a warning since it is always an optional group. + Anything (groups, fields, or attributes) placed in + an :ref:`NXcollection` group will not be validated. - The recommended structure is 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 mappred - mapped to a NeXus group of class NXpdb and with each PDB column - mapped to a NeXus field. The columns in a looped PDB category - should always be presented as arrays. 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 be - used for the corresponding fields. + The recommended structure is 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 mappred + mapped to a NeXus group of class NXpdb and with each PDB column + mapped to a NeXus field. The columns in a looped PDB category + should always be presented as arrays. 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 be + used for the corresponding fields. - All text data should be presented as quoted strings, with the quote - marks except for the null values "." or "?". + All text data should be presented as quoted strings, with the quote + marks except for the null values "." or "?". - 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 ".". + 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 ".". - For example, a PDB entry that begins + 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 - # + 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: + 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"] - - ===================================================================================== + 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"] + + ===================================================================================== - - - - - + + + + +