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Fix doc spacing error in NXpdb. There is still a manual build error
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further in to be investigated. -- HJB
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@yayahjb
yayahjb committed Aug 8, 2017
1 parent 529a527 commit afbbe88
Showing 1 changed file with 94 additions and 94 deletions.
188 changes: 94 additions & 94 deletions base_classes/NXpdb.nxdl.xml
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Expand Up @@ -22,113 +22,113 @@
# For further information, see http://www.nexusformat.org
-->
<definition xmlns="http://definition.nexusformat.org/nxdl/3.1"
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"
>
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"
>

<!--
The ignoreExtra* attributes are used in the definition to
avoid warning messages that would be generated from
unexpected groups, fields, and attributes.
Since no groups or attributes are declared here, _every_
child of this class would generate a warning message without this
attribute being set to "true".
-->
<!--
The ignoreExtra* attributes are used in the definition to
avoid warning messages that would be generated from
unexpected groups, fields, and attributes.
Since no groups or attributes are declared here, _every_
child of this class would generate a warning message without this
attribute being set to "true".
-->

<doc>
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).
<doc>
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"]
=====================================================================================

</doc>
<!-- any content is purely optional -->
<!--
NOTE
=====
As with NXcollection, NXpdb is an unvalidated class, do not add
any subgroups in this nxdl file.
See: https://github.com/nexusformat/definitions/issues/259
-->
</doc>
<!-- any content is purely optional -->
<!--
NOTE
=====
As with NXcollection, NXpdb is an unvalidated class, do not add
any subgroups in this nxdl file.
See: https://github.com/nexusformat/definitions/issues/259
-->
</definition>

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