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pynmrstar 2.4.4

PyNMR-STAR provides tools for reading, writing, modifying, and interacting with NMR-STAR files. Maintained by the BMRB.

Latest Version: 2.5

PyNMRSTAR
=========

A Python module for reading, writing, and manipulating NMR-STAR files.
|Build Status|

Python versions supported: 2.6, 2.7, 3.3, 3.4, 3.5, and 3.6

====

Command line tools
~~~~~~~~~~~~~~~~~~

We have developed several command line tools to ease certain common
actions performed against NMR-STAR files. If you are looking for
information on those please go `here <cmdline readme.md="">`__.

====

PyNMRSTAR Overview
~~~~~~~~~~~~~~~~~~

This module provides Entry, Saveframe, and Loop objects. Use python's
built in help function for documentation.

There are eight module variables you can set to control our behavior.

- Setting bmrb.VERBOSE to True will print some of what is going on to
the terminal.

- Setting bmrb.RAISE\_PARSE\_WARNINGS to True will raise an exception
if the parser encounters something problematic. Normally warnings are
suppressed.

- In addition, if you want to ignore some parse warnings but allow the
rest, you can specify warnings to ignore by adding the warning to
ignore to the "WARNINGS\_TO\_IGNORE" list.

Here are descriptions of the parse warnings that can be suppressed:

- "tag-only-loop": A loop with no data was found.
- "empty-loop": A loop with no tags or values was found.
- "tag-not-in-schema": A tag was found in the entry that was not
present in the schema.
- "invalid-null-value": A tag for which the schema disallows null
values had a null value.
- "bad-multiline": A tag with an improper multi-line value was found.
Multiline values should look like this:

.. code:: code

;
The multi-line
value here.
;

but the tag looked like this:

.. code:: code

; The multi-line
value here.
;

- Setting SKIP\_EMPTY\_LOOPS to True will suppress the printing of
empty loops when calling **str** methods.

- Adding key->value pairs to STR\_CONVERSION\_DICT will automatically
convert tags whose value matches "key" to the string "value" when
printing. This allows you to set the default conversion value for
Booleans or other objects.

- Setting bmrb.ALLOW\_V2\_ENTRIES will allow parsing of NMR-STAR
version 2.1 entries. Most other methods will not operate correctly on
parsed 2.1 entries. This is only to allow you parse and access the
data in these entries - nothing else. Only set this if you have a
really good reason to. Attempting to print a 2.1 entry will 'work'
but tags that were after loops will be moved to before loops.

- Setting bmrb.DONT\_SHOW\_COMMENTS to True will supress the printing
of comments before saveframes.

- Setting bmrb.CONVERT\_DATATYPES to True will automatically convert
the data loaded from the file into the corresponding python type as
determined by loading the standard BMRB schema. This would mean that
all floats will be represented as decimal.Decimal objects, all
integers will be python int objects, strings and vars will remain
strings, and dates will become datetime.date objects. When printing
str() is called on all objects. Other that converting uppercase "E"s
in scientific notation floats to lowercase "e"s this should not cause
any change in the way re-printed NMR-STAR objects are displayed.

Some errors will be detected and exceptions raised, but this does not
implement a full validator (at least at present).

Call directly (rather than importing) to run a self-test.

Variables
---------

- ``ALLOW_V2_ENTRIES``: False
- ``CONVERT_DATATYPES``: False
- ``DONT_SHOW_COMMENTS``: False
- ``RAISE_PARSE_WARNINGS``: False
- ``SKIP_EMPTY_LOOPS``: False
- ``STR_CONVERSION_DICT``: {None: '.'}
- ``VERBOSE``: False
- ``WARNINGS_TO_IGNORE``: []

Functions
---------

def ``clean_value(value)``
~~~~~~~~~~~~~~~~~~~~~~~~~~

Automatically quotes the value in the appropriate way. Don't quote
values you send to this method or they will show up in another set of
quotes as part of the actual data. E.g.:

clean\_value('"e. coli"') returns ''"e. coli"''

while

clean\_value("e. coli") returns "'e. coli'"

This will automatically be called on all values when you use a str()
method (so don't call it before inserting values into tags or loops).

Be mindful of the value of STR\_CONVERSION\_DICT as it will effect the
way the value is converted to a string.

def ``delete_empty_saveframes(entry_object, tags_to_ignore=['sf_category', 'sf_framecode'], allowed_null_values=['.', '?', None])``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

This method will delete all empty saveframes in an entry (the loops in
the saveframe must also be empty for the saveframe to be deleted).
"Empty" means no values in tags, not no tags present.

def ``diff(entry1, entry2)``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Prints the differences between two entries. Non-equal entries will
always be detected, but specific differences detected depends on order
of entries. ### def ``enable_nef_defaults()``

Sets the module variables such that our behavior matches the NEF
standard. Specifically, suppress printing empty loops by default and
convert True -> "true" and False -> "false" when printing. ### def
``enable_nmrstar_defaults()``

Sets the module variables such that our behavior matches the BMRB
standard (NMR-STAR). This is the default behavior of this module. This
method only exists to revert after calling enable\_nef\_defaults().

def ``validate(entry_to_validate, schema=None)``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Prints a validation report of an entry.

Classes
-------

class ``Entry()``
~~~~~~~~~~~~~~~~~

An OO representation of a BMRB entry. You can initialize this object
several ways; (e.g. from a file, from the official database, from
scratch) see the class methods below.

Methods:

def ``__init__()``
^^^^^^^^^^^^^^^^^^

You should not directly instantiate an Entry using this method. Instead
use the class methods:" Entry.from\_database() Entry.from\_file()
Entry.from\_string() Entry.from\_scratch() Entry.from\_json()

def ``add_saveframe(frame)``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Add a saveframe to the entry.

def ``compare(other)``
^^^^^^^^^^^^^^^^^^^^^^

Returns the differences between two entries as a list. Otherwise returns
1 if different and 0 if equal. Non-equal entries will always be
detected, but specific differences detected depends on order of entries.

def ``frame_dict()``
^^^^^^^^^^^^^^^^^^^^

Returns a dictionary of saveframe name -> saveframe object

def ``from_database(cls, entry_num)``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Create an entry corresponding to the most up to date entry on the public
BMRB server. (Requires ability to initiate outbound HTTP connections.)

def ``from_file(cls, the_file)``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Create an entry by loading in a file. If the\_file starts with http://,
https://, or ftp:// then we will use those protocols to attempt to open
the file.

def ``from_json(cls, json_dict)``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Create an entry from JSON (serialized or unserialized JSON).

def ``from_scratch(cls, entry_id)``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Create an empty entry that you can programatically add to. You must pass
a value corresponding to the Entry ID. (The unique identifier "xxx" from
"data\_xxx".)

def ``from_string(cls, the_string)``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Create an entry by parsing a string.

def ``get_json(serialize=True)``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Returns the entry in JSON format. If serialize is set to False a
dictionary representation of the entry that is serializeable is
returned.

def ``get_loops_by_category(value)``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Allows fetching loops by category.

def ``get_saveframe_by_name(frame)``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Allows fetching a saveframe by name.

def ``get_saveframes_by_category(value)``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Allows fetching saveframes by category.

def ``get_saveframes_by_tag_and_value(tag_name, value)``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Allows fetching saveframe(s) by tag and tag value.

def ``get_tag(tag, whole_tag=False)``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Given a tag (E.g. \_Assigned\_chem\_shift\_list.Data\_file\_name) return
a list of all values for that tag. Specify whole\_tag=True and the
[tag\_name, tag\_value (,tag\_linenumber)] pair will be returned.

def ``get_tags(tags)``
^^^^^^^^^^^^^^^^^^^^^^

Given a list of tags, get all of the tags and return the results in a
dictionary.

def ``nef_string()``
^^^^^^^^^^^^^^^^^^^^

Returns a string representation of the entry in NEF.

def ``normalize(schema=None)``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Sorts saveframes, loops, and tags according to the schema provided (or
BMRB default if none provided) and according to the assigned ID.

def ``print_tree()``
^^^^^^^^^^^^^^^^^^^^

Prints a summary, tree style, of the frames and loops in the entry.

def ``rename_saveframe(original_name, new_name)``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Renames a saveframe and updates all pointers to that saveframe in the
entry with the new name.

def ``validate(validate_schema=True, schema=None, validate_star=True)``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Validate an entry in a variety of ways. Returns a list of errors found.
0-length list indicates no errors found. By default all validation modes
are enabled.

validate\_schema - Determines if the entry is validated against the
NMR-STAR schema. You can pass your own custom schema if desired,
otherwise the schema will be fetched from the BMRB servers.

validate\_star - Determines if the STAR syntax checks are ran.

class ``Saveframe()``
~~~~~~~~~~~~~~~~~~~~~

A saveframe object. Create using the class methods, see below.

Methods:

def ``__init__()``
^^^^^^^^^^^^^^^^^^

Don't use this directly. Use the class methods to construct:
Saveframe.from\_scratch() Saveframe.from\_string()
Saveframe.from\_template() Saveframe.from\_file() and
Saveframe.from\_json()

def ``add_loop(loop_to_add)``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Add a loop to the saveframe loops.

def ``add_tag(name, value, linenum=None, update=False)``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Add a tag to the tag list. Does a bit of validation and parsing. Set
update to true to update a tag if it exists rather than raise an
exception.

def ``add_tags(tag_list, update=False)``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Adds multiple tags to the list. Input should be a list of tuples that
are either [key, value] or [key]. In the latter case the value will be
set to ".". Set update to true to update a tag if it exists rather than
raise an exception.

def ``compare(other)``
^^^^^^^^^^^^^^^^^^^^^^

Returns the differences between two saveframes as a list. Non-equal
saveframes will always be detected, but specific differences detected
depends on order of saveframes.

def ``delete_tag(tag)``
^^^^^^^^^^^^^^^^^^^^^^^

Deletes a tag from the saveframe based on tag name.

def ``from_file(cls, the_file, csv=False)``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Create a saveframe by loading in a file. Specify csv=True is the file is
a CSV file. If the\_file starts with http://, https://, or ftp:// then
we will use those protocols to attempt to open the file.

def ``from_json(cls, json_dict)``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Create a saveframe from JSON (serialized or unserialized JSON).

def ``from_scratch(cls, sf_name, tag_prefix=None, source=from_scratch())``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Create an empty saveframe that you can programatically add to. You may
also pass the tag prefix as the second argument. If you do not pass the
tag prefix it will be set the first time you add a tag.

def ``from_string(cls, the_string, csv=False)``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Create a saveframe by parsing a string. Specify csv=True is the string
is in CSV format and not NMR-STAR format.

def ``from_template(cls, category, name=None, all_tags=False, schema=None)``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Create a saveframe that has all of the tags and loops from the schema
present. No values will be assigned. Specify the category when calling
this method. Optionally also provide the name of the saveframe as the
'name' argument.

The optional argument 'all\_tags' forces all tags to be included rather
than just the mandatory tags.

def ``get_data_as_csv(header=True, show_category=True)``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Return the data contained in the loops, properly CSVd, as a string. Set
header to False omit the header. Set show\_category to False to omit the
loop category from the headers.

def ``get_json(serialize=True)``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Returns the saveframe in JSON format. If serialize is set to False a
dictionary representation of the saveframe that is serializeable is
returned.

def ``get_loop_by_category(name)``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Return a loop based on the loop name (category).

def ``get_tag(query, whole_tag=False)``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Allows fetching the value of a tag by tag name. Specify whole\_tag=True
and the [tag\_name, tag\_value] pair will be returned.

def ``loop_dict()``
^^^^^^^^^^^^^^^^^^^

Returns a hash of loop category -> loop.

def ``loop_iterator()``
^^^^^^^^^^^^^^^^^^^^^^^

Returns an iterator for saveframe loops.

def ``print_tree()``
^^^^^^^^^^^^^^^^^^^^

Prints a summary, tree style, of the loops in the saveframe.

def ``set_tag_prefix(tag_prefix)``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Set the tag prefix for this saveframe.

def ``sort_tags(schema=None)``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Sort the tags so they are in the same order as a BMRB schema. Will
automatically use the standard schema if none is provided.

def ``tag_iterator()``
^^^^^^^^^^^^^^^^^^^^^^

Returns an iterator for saveframe tags.

def ``validate(validate_schema=True, schema=None, validate_star=True)``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Validate a saveframe in a variety of ways. Returns a list of errors
found. 0-length list indicates no errors found. By default all
validation modes are enabled.

validate\_schema - Determines if the entry is validated against the
NMR-STAR schema. You can pass your own custom schema if desired,
otherwise the schema will be fetched from the BMRB servers.

validate\_star - Determines if the STAR syntax checks are ran.

class ``Schema()``
~~~~~~~~~~~~~~~~~~

A BMRB schema. Used to validate STAR files.

Methods:

def ``__init__(schema_file=None)``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Initialize a BMRB schema. With no arguments the most up-to-date schema
will be fetched from the BMRB FTP site. Otherwise pass a URL or a file
to load a schema from using the schema\_file keyword argument.

def ``add_tag(tag, tag_type, null_allowed, sf_category, loop_flag, after=None)``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Adds the specified tag to the tag dictionary. You must provide:

1) The full tag as such: "\_Entry\_interview.Sf\_category"
2) The tag type which is one of the following: "INTEGER" "FLOAT"
"CHAR(len)" "VARCHAR(len)" "TEXT" "DATETIME year to day"
3) A python True/False that indicates whether null values are allowed.
4) The sf\_category of the parent saveframe.
5) A True/False value which indicates if this tag is a loop tag.
6) Optional: The tag to order this tag behind when normalizing
saveframes.

def ``convert_tag(tag, value, linenum=None)``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Converts the provided tag from string to the appropriate type as
specified in this schema.

def ``string_representation(search=None)``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Prints all the tags in the schema if search is not specified and prints
the tags that contain the search string if it is.

def ``val_type(tag, value, category=None, linenum=None)``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Validates that a tag matches the type it should have according to this
schema.

class ``Loop()``
~~~~~~~~~~~~~~~~

A BMRB loop object. Create using the class methods, see below.

Methods:

def ``__init__()``
^^^^^^^^^^^^^^^^^^

You should not directly instantiate a Loop using this method. Instead
use the class methods: Loop.from\_scratch() Loop.from\_string()
Loop.from\_template() Loop.from\_file() Loop.from\_json()

def ``add_column(name, ignore_duplicates=False)``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Add a column to the column list. Does a bit of validation and parsing.
Set ignore\_duplicates to true to ignore attempts to add the same tag
more than once rather than raise an exception.

You can also pass a list of column names to add more than one column at
a time.

Note that adding a column only adds a new tag to the list of tags
present in this loop. It does not automatically add a column of None
values to the data array if the loop is already populated with data.

def ``add_data(the_list, rearrange=False)``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Add a list to the data field. Items in list can be any type, they will
be converted to string and formatted correctly. The list must have the
same cardinality as the column names or you must set the rearrange
variable to true and have already set all the columns in the loop.
Rearrange will break a longer list into rows based on the number of
columns.

def ``add_data_by_column(column_id, value)``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Add data to the loop one element at a time, based on column. Useful when
adding data from SANS parsers.

def ``clear_data()``
^^^^^^^^^^^^^^^^^^^^

Erases all data in this loop. Does not erase the data columns or loop
category.

def ``compare(other)``
^^^^^^^^^^^^^^^^^^^^^^

Returns the differences between two loops as a list. Order of loops
being compared does not make a difference on the specific errors
detected.

def ``delete_data_by_tag_value(tag, value, index_tag=None)``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Deletes all rows which contain the provided value in the provided
column. If index\_tag is provided, that column is renumbered starting
with 1. Returns the deleted rows.

def ``filter(tag_list, ignore_missing_tags=False)``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Returns a new loop containing only the specified tags. Specify
ignore\_missing\_tags=True to bypass missing tags rather than raising an
error.

def ``from_file(cls, the_file, csv=False)``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Create a saveframe by loading in a file. Specify csv=True if the file is
a CSV file. If the\_file starts with http://, https://, or ftp:// then
we will use those protocols to attempt to open the file.

def ``from_json(cls, json_dict)``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Create a loop from JSON (serialized or unserialized JSON).

def ``from_scratch(cls, category=None, source=from_scratch())``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Create an empty saveframe that you can programatically add to. You may
also pass the tag prefix as the second argument. If you do not pass the
tag prefix it will be set the first time you add a tag.

def ``from_string(cls, the_string, csv=False)``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Create a saveframe by parsing a string. Specify csv=True is the string
is in CSV format and not NMR-STAR format.

def ``from_template(cls, tag_prefix, all_tags=False, schema=None)``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Create a loop that has all of the tags from the schema present. No
values will be assigned. Specify the tag prefix of the loop.

The optional argument all\_tags forces all tags to be included rather
than just the mandatory tags.

def ``get_columns()``
^^^^^^^^^^^^^^^^^^^^^

Return the columns for this entry with the category included. Throws
ValueError if the category was never set.

def ``get_data_as_csv(header=True, show_category=True)``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Return the data contained in the loops, properly CSVd, as a string. Set
header to False to omit the header. Set show\_category to false to omit
the loop category from the headers.

def ``get_data_by_tag(tags=None)``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Identical to get\_tag but wraps the results in a list even if only
fetching one tag. Primarily exists for legacy code.

def ``get_json(serialize=True)``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Returns the loop in JSON format. If serialize is set to False a
dictionary representation of the loop that is serializeable is returned.

def ``get_tag(tags=None, whole_tag=False)``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Provided a tag name (or a list of tag names), or ordinals corresponding
to columns, return the selected tags by row as a list of lists.

def ``print_tree()``
^^^^^^^^^^^^^^^^^^^^

Prints a summary, tree style, of the loop.

def ``renumber_rows(index_tag, start_value=1, maintain_ordering=False)``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Renumber a given column incrementally. Set start\_value to initial value
if 1 is not acceptable. Set maintain\_ordering to preserve sequence with
offset.

E.g. 2,3,3,5 would become 1,2,2,4.

def ``set_category(category)``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Set the category of the loop. Useful if you didn't know the category at
loop creation time.

def ``sort_rows(tags, key=None)``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Sort the data in the rows by their values for a given column or columns.
Specify the columns using their names or ordinals. Accepts a list or an
int/float. By default we will sort numerically. If that fails we do a
string sort. Supply a function as key and we will order the elements
based on the keys it provides. See the help for sorted() for more
details. If you provide multiple columns to sort by, they are
interpreted as increasing order of sort priority.

def ``sort_tags(schema=None)``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Rearranges the columns and data in the loop to match the order from the
schema. Uses the BMRB schema unless one is provided.

def ``validate(validate_schema=True, schema=None, validate_star=True, category=None)``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Validate a loop in a variety of ways. Returns a list of errors found.
0-length list indicates no errors found. By default all validation modes
are enabled.

validate\_schema - Determines if the entry is validated against the
NMR-STAR schema. You can pass your own custom schema if desired,
otherwise the schema will be fetched from the BMRB servers.

validate\_star - Determines if the STAR syntax checks are ran.

.. |Build Status| image:: https://travis-ci.org/uwbmrb/PyNMRSTAR.svg?branch=v2
:target: https://travis-ci.org/uwbmrb/PyNMRSTAR  
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