schrodinger.application.matsci.qeschema.qeschema.documents module

schrodinger.application.matsci.qeschema.qeschema.documents.requires_xml_data(method)[source]

A decorator for XML document methods that require XML data to be loaded.

schrodinger.application.matsci.qeschema.qeschema.documents.removeprefix(s, prefix)[source]
class schrodinger.application.matsci.qeschema.qeschema.documents.XmlDocument(source=None, schema=None)[source]

Bases: object

Base class for a generic XML document based on an XSD schema. The schema associated is used for checking types, validation of the XML data and for lookup of default values. XML data is loaded into memory into an ElementTree structure. Data files can be also in JSON or YAML format, in these cases the data source is converted to XML when loading.

Parameters

  • source – can be a xmlschema.XMLResource instance or a file-like object or a file path or an URL of a resource or a string containing the XML data.

  • schema – can be a xmlschema.XMLSchema instance or a file-like object or a file path or an URL of a resource or a string containing the XSD schema.

Variables

  • SEARCH_PATHS – the sequence of search paths used by fetch_schema for fetching schemas.

  • root – the root element of the XML tree.

  • filename – the filepath of the data source file.

  • format – the format of the data source file (XML, JSON, YAML).

  • errors – the list of detected validation errors.

  • schema – the XMLSchema instance associated with the document.

SEARCH_PATHS = ('.',)
DEFAULT_SCHEMA = None
__init__(source=None, schema=None)[source]
property namespaces

XML data namespaces map, a dictionary that maps prefixes to URI. An empty dictionary if the XML data file is not loaded or it doesn’t contain any namespace declaration.

classmethod fetch_schema(filename)[source]
read(filename, validation='strict', **kwargs)[source]

Reads XML data from a file encoded in XML, JSON or YAML format.

Parameters

  • filename – filepath of the data source file.

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options to pass to the encoding method of the schema instance in case of a non-XML data source.

from_xml(source, validation='strict', **kwargs)[source]

Load XML data. Data is validated against the schema.

Parameters

  • source – a filepath to an XML file or a string containing XML data.

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options for creating the xmlschema.XMLResource instance used for reading the XML data.

Returns

a couple with the root element of the XML ElementTree a list containing the detected errors.

from_json(source, validation='strict', **kwargs)[source]

Load JSON encoded data. Data is converted to an XML ElementTree structure and validated against the schema.

Parameters

  • source – a filepath to a JSON file or a string containing JSON data.

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options to pass to the encoding method of the schema instance.

Returns

the root element of the XML ElementTree data structure and a list containing the detected errors.

Raise

an xmlschema.XMLSchemaValidationError if validation is strict and at least an error is found.

from_yaml(source, validation='strict', **kwargs)[source]

Converts a YAML encoded file to an XML ElementTree structure. Data is validated against the schema during conversion.

Parameters

  • source – a filepath to a YAML file or a string containing YAML data.

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options to pass to the encoding method of the schema instance.

Returns

a couple with the root element of the XML ElementTree and a list containing the detected errors.

from_dict(data, validation='strict', **kwargs)[source]

Converts a Python object to an XML ElementTree structure. Object data is validated against the schema during conversion.

Parameters

  • data – filepath of the data source file.

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options to pass to the encoding method of the schema instance.

Returns

a couple with the root element of the XML ElementTree and a list containing the detected errors.

write(filename, output_format='xml', validation='strict', **kwargs)[source]

Write loaded XML data to a file. Binds the document to saved file if it’s not already bound to another file.

Parameters

  • filename – filepath of the destination file.

  • output_format – the data format of the output file.

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options for the decoding method of the schema instance.

to_dict(validation='strict', **kwargs)[source]

Converts loaded XML data to a nested dictionary.

Parameters

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options for the decoding method of the schema instance.

Returns

a dictionary.

to_json(filename=None, validation='strict', **kwargs)[source]

Converts loaded XML data to a JSON string or file.

Parameters

  • filename – filepath of the destination file. Binds the document to this file if it’s not already bound to another file.

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options for the decoding method of the schema instance.

to_yaml(filename=None, validation='strict', **kwargs)[source]

Converts loaded XML data to YAML string or file.

Parameters

  • filename – filepath of the destination file. Binds the document to this file if it’s not already bound to another file.

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options for the decoding method of the schema instance.

iter(tag=None)[source]
find(path, namespaces=None)[source]

Find first matching element by tag name or path.

Parameters

  • path – is a string having either an element tag or an XPath,

  • namespaces – is an optional mapping from namespace prefix to full name.

Returns

the first matching element, or None if no element was found

findall(path, namespaces=None)[source]

Find all matching subelements by tag name or path.

Parameters

  • path – is a string having either an element tag or an XPath,

  • namespaces – is an optional mapping from namespace prefix to full name.

Returns

the first matching element, or None if no element was found

class schrodinger.application.matsci.qeschema.qeschema.documents.QeDocument(source=None, schema=None, input_builder=None)[source]

Bases: schrodinger.application.matsci.qeschema.qeschema.documents.XmlDocument

Abstract base class for schema-based XML documents of Quantum ESPRESSO applications.

SEARCH_PATHS = ('/scr/buildbot/savedbuilds/2022-2/NB/build-128/internal/lib/python3.8/site-packages/schrodinger/application/matsci/qeschema/qeschema/schemas', '/scr/buildbot/savedbuilds/2022-2/NB/build-128/internal/lib/python3.8/site-packages/schrodinger/application/matsci/qeschema/qeschema/schemas/releases', '.')
DEFAULT_INPUT_BUILDER = None
__init__(source=None, schema=None, input_builder=None)[source]
property input_path

The path to XML input section.

property output_path

The path to XML input section.

write_fortran_input(filename)[source]

Converts the XML input data to a Fortran namelist input and writes it to a file.

Parameters

filename – the pathname of the file to use to save the Fortran namelist.

get_fortran_input(use_defaults=True)[source]

Converts the XML input data to a Fortran namelist input.

Parameters

use_defaults – use the defaults of the XSD schema to fill missing values.

Returns

a string.

DEFAULT_SCHEMA = None
classmethod fetch_schema(filename)
find(path, namespaces=None)

Find first matching element by tag name or path.

Parameters

  • path – is a string having either an element tag or an XPath,

  • namespaces – is an optional mapping from namespace prefix to full name.

Returns

the first matching element, or None if no element was found

findall(path, namespaces=None)

Find all matching subelements by tag name or path.

Parameters

  • path – is a string having either an element tag or an XPath,

  • namespaces – is an optional mapping from namespace prefix to full name.

Returns

the first matching element, or None if no element was found

from_dict(data, validation='strict', **kwargs)

Converts a Python object to an XML ElementTree structure. Object data is validated against the schema during conversion.

Parameters

  • data – filepath of the data source file.

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options to pass to the encoding method of the schema instance.

Returns

a couple with the root element of the XML ElementTree and a list containing the detected errors.

from_json(source, validation='strict', **kwargs)

Load JSON encoded data. Data is converted to an XML ElementTree structure and validated against the schema.

Parameters

  • source – a filepath to a JSON file or a string containing JSON data.

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options to pass to the encoding method of the schema instance.

Returns

the root element of the XML ElementTree data structure and a list containing the detected errors.

Raise

an xmlschema.XMLSchemaValidationError if validation is strict and at least an error is found.

from_xml(source, validation='strict', **kwargs)

Load XML data. Data is validated against the schema.

Parameters

  • source – a filepath to an XML file or a string containing XML data.

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options for creating the xmlschema.XMLResource instance used for reading the XML data.

Returns

a couple with the root element of the XML ElementTree a list containing the detected errors.

from_yaml(source, validation='strict', **kwargs)

Converts a YAML encoded file to an XML ElementTree structure. Data is validated against the schema during conversion.

Parameters

  • source – a filepath to a YAML file or a string containing YAML data.

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options to pass to the encoding method of the schema instance.

Returns

a couple with the root element of the XML ElementTree and a list containing the detected errors.

iter(tag=None)
property namespaces

XML data namespaces map, a dictionary that maps prefixes to URI. An empty dictionary if the XML data file is not loaded or it doesn’t contain any namespace declaration.

read(filename, validation='strict', **kwargs)

Reads XML data from a file encoded in XML, JSON or YAML format.

Parameters

  • filename – filepath of the data source file.

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options to pass to the encoding method of the schema instance in case of a non-XML data source.

to_dict(validation='strict', **kwargs)

Converts loaded XML data to a nested dictionary.

Parameters

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options for the decoding method of the schema instance.

Returns

a dictionary.

to_json(filename=None, validation='strict', **kwargs)

Converts loaded XML data to a JSON string or file.

Parameters

  • filename – filepath of the destination file. Binds the document to this file if it’s not already bound to another file.

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options for the decoding method of the schema instance.

to_yaml(filename=None, validation='strict', **kwargs)

Converts loaded XML data to YAML string or file.

Parameters

  • filename – filepath of the destination file. Binds the document to this file if it’s not already bound to another file.

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options for the decoding method of the schema instance.

write(filename, output_format='xml', validation='strict', **kwargs)

Write loaded XML data to a file. Binds the document to saved file if it’s not already bound to another file.

Parameters

  • filename – filepath of the destination file.

  • output_format – the data format of the output file.

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options for the decoding method of the schema instance.

class schrodinger.application.matsci.qeschema.qeschema.documents.PwDocument(source=None, schema=None, input_builder=None)[source]

Bases: schrodinger.application.matsci.qeschema.qeschema.documents.QeDocument

Class to manage PW XML documents.

DEFAULT_SCHEMA = 'qes.xsd'
DEFAULT_INPUT_BUILDER

alias of schrodinger.application.matsci.qeschema.qeschema.converters.PwInputConverter

get_atomic_positions()[source]

Gets atomic symbols and atomic positions from XML output data.

Returns

the list of atomic symbols and a nested list containing the coordinates

get_cell_parameters()[source]

Gets cell parameters from an XML output data.

Returns

a nested list containing the cell vectors in Bohr atomic units

get_stress()[source]

Gets stress tensor from the XML output data, if present.

Returns

nested list containing the stress tensor in C order

get_forces()[source]

Gets forces from the XML output data, if present.

Returns

the list of atomic symbols plus a nested list with the forces in atomic units

get_k_points()[source]

Extracts the k_points list from the XML output data.

Returns

nested list with k_points

get_ks_eigenvalues()[source]

Extracts the eigenvalues from the XML output data.

Returns

nested list of KS eigenvalues for each k_point in Hartree Units

get_total_energy()[source]

Extracts the total energy from the XML output data.

Returns

total energy in Hartree Units

SEARCH_PATHS = ('/scr/buildbot/savedbuilds/2022-2/NB/build-128/internal/lib/python3.8/site-packages/schrodinger/application/matsci/qeschema/qeschema/schemas', '/scr/buildbot/savedbuilds/2022-2/NB/build-128/internal/lib/python3.8/site-packages/schrodinger/application/matsci/qeschema/qeschema/schemas/releases', '.')
__init__(source=None, schema=None, input_builder=None)
classmethod fetch_schema(filename)
find(path, namespaces=None)

Find first matching element by tag name or path.

Parameters

  • path – is a string having either an element tag or an XPath,

  • namespaces – is an optional mapping from namespace prefix to full name.

Returns

the first matching element, or None if no element was found

findall(path, namespaces=None)

Find all matching subelements by tag name or path.

Parameters

  • path – is a string having either an element tag or an XPath,

  • namespaces – is an optional mapping from namespace prefix to full name.

Returns

the first matching element, or None if no element was found

from_dict(data, validation='strict', **kwargs)

Converts a Python object to an XML ElementTree structure. Object data is validated against the schema during conversion.

Parameters

  • data – filepath of the data source file.

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options to pass to the encoding method of the schema instance.

Returns

a couple with the root element of the XML ElementTree and a list containing the detected errors.

from_json(source, validation='strict', **kwargs)

Load JSON encoded data. Data is converted to an XML ElementTree structure and validated against the schema.

Parameters

  • source – a filepath to a JSON file or a string containing JSON data.

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options to pass to the encoding method of the schema instance.

Returns

the root element of the XML ElementTree data structure and a list containing the detected errors.

Raise

an xmlschema.XMLSchemaValidationError if validation is strict and at least an error is found.

from_xml(source, validation='strict', **kwargs)

Load XML data. Data is validated against the schema.

Parameters

  • source – a filepath to an XML file or a string containing XML data.

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options for creating the xmlschema.XMLResource instance used for reading the XML data.

Returns

a couple with the root element of the XML ElementTree a list containing the detected errors.

from_yaml(source, validation='strict', **kwargs)

Converts a YAML encoded file to an XML ElementTree structure. Data is validated against the schema during conversion.

Parameters

  • source – a filepath to a YAML file or a string containing YAML data.

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options to pass to the encoding method of the schema instance.

Returns

a couple with the root element of the XML ElementTree and a list containing the detected errors.

get_fortran_input(use_defaults=True)

Converts the XML input data to a Fortran namelist input.

Parameters

use_defaults – use the defaults of the XSD schema to fill missing values.

Returns

a string.

property input_path

The path to XML input section.

iter(tag=None)
property namespaces

XML data namespaces map, a dictionary that maps prefixes to URI. An empty dictionary if the XML data file is not loaded or it doesn’t contain any namespace declaration.

property output_path

The path to XML input section.

read(filename, validation='strict', **kwargs)

Reads XML data from a file encoded in XML, JSON or YAML format.

Parameters

  • filename – filepath of the data source file.

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options to pass to the encoding method of the schema instance in case of a non-XML data source.

to_dict(validation='strict', **kwargs)

Converts loaded XML data to a nested dictionary.

Parameters

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options for the decoding method of the schema instance.

Returns

a dictionary.

to_json(filename=None, validation='strict', **kwargs)

Converts loaded XML data to a JSON string or file.

Parameters

  • filename – filepath of the destination file. Binds the document to this file if it’s not already bound to another file.

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options for the decoding method of the schema instance.

to_yaml(filename=None, validation='strict', **kwargs)

Converts loaded XML data to YAML string or file.

Parameters

  • filename – filepath of the destination file. Binds the document to this file if it’s not already bound to another file.

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options for the decoding method of the schema instance.

write(filename, output_format='xml', validation='strict', **kwargs)

Write loaded XML data to a file. Binds the document to saved file if it’s not already bound to another file.

Parameters

  • filename – filepath of the destination file.

  • output_format – the data format of the output file.

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options for the decoding method of the schema instance.

write_fortran_input(filename)

Converts the XML input data to a Fortran namelist input and writes it to a file.

Parameters

filename – the pathname of the file to use to save the Fortran namelist.

class schrodinger.application.matsci.qeschema.qeschema.documents.PhononDocument(source=None, schema=None, input_builder=None)[source]

Bases: schrodinger.application.matsci.qeschema.qeschema.documents.QeDocument

Class to manage Phonon XML documents.

DEFAULT_SCHEMA = 'ph_xmlschema.xsd'
DEFAULT_INPUT_BUILDER

alias of schrodinger.application.matsci.qeschema.qeschema.converters.PhononInputConverter

property input_path

The path to XML input section.

property output_path

The path to XML input section.

get_fortran_input(use_defaults=False)[source]

Overrides get_fortran_input() setting use_defaults optional argument to False.

Parameters

use_defaults –

Returns

the input as obtained from its input builder

SEARCH_PATHS = ('/scr/buildbot/savedbuilds/2022-2/NB/build-128/internal/lib/python3.8/site-packages/schrodinger/application/matsci/qeschema/qeschema/schemas', '/scr/buildbot/savedbuilds/2022-2/NB/build-128/internal/lib/python3.8/site-packages/schrodinger/application/matsci/qeschema/qeschema/schemas/releases', '.')
__init__(source=None, schema=None, input_builder=None)
classmethod fetch_schema(filename)
find(path, namespaces=None)

Find first matching element by tag name or path.

Parameters

  • path – is a string having either an element tag or an XPath,

  • namespaces – is an optional mapping from namespace prefix to full name.

Returns

the first matching element, or None if no element was found

findall(path, namespaces=None)

Find all matching subelements by tag name or path.

Parameters

  • path – is a string having either an element tag or an XPath,

  • namespaces – is an optional mapping from namespace prefix to full name.

Returns

the first matching element, or None if no element was found

from_dict(data, validation='strict', **kwargs)

Converts a Python object to an XML ElementTree structure. Object data is validated against the schema during conversion.

Parameters

  • data – filepath of the data source file.

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options to pass to the encoding method of the schema instance.

Returns

a couple with the root element of the XML ElementTree and a list containing the detected errors.

from_json(source, validation='strict', **kwargs)

Load JSON encoded data. Data is converted to an XML ElementTree structure and validated against the schema.

Parameters

  • source – a filepath to a JSON file or a string containing JSON data.

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options to pass to the encoding method of the schema instance.

Returns

the root element of the XML ElementTree data structure and a list containing the detected errors.

Raise

an xmlschema.XMLSchemaValidationError if validation is strict and at least an error is found.

from_xml(source, validation='strict', **kwargs)

Load XML data. Data is validated against the schema.

Parameters

  • source – a filepath to an XML file or a string containing XML data.

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options for creating the xmlschema.XMLResource instance used for reading the XML data.

Returns

a couple with the root element of the XML ElementTree a list containing the detected errors.

from_yaml(source, validation='strict', **kwargs)

Converts a YAML encoded file to an XML ElementTree structure. Data is validated against the schema during conversion.

Parameters

  • source – a filepath to a YAML file or a string containing YAML data.

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options to pass to the encoding method of the schema instance.

Returns

a couple with the root element of the XML ElementTree and a list containing the detected errors.

iter(tag=None)
property namespaces

XML data namespaces map, a dictionary that maps prefixes to URI. An empty dictionary if the XML data file is not loaded or it doesn’t contain any namespace declaration.

read(filename, validation='strict', **kwargs)

Reads XML data from a file encoded in XML, JSON or YAML format.

Parameters

  • filename – filepath of the data source file.

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options to pass to the encoding method of the schema instance in case of a non-XML data source.

to_dict(validation='strict', **kwargs)

Converts loaded XML data to a nested dictionary.

Parameters

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options for the decoding method of the schema instance.

Returns

a dictionary.

to_json(filename=None, validation='strict', **kwargs)

Converts loaded XML data to a JSON string or file.

Parameters

  • filename – filepath of the destination file. Binds the document to this file if it’s not already bound to another file.

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options for the decoding method of the schema instance.

to_yaml(filename=None, validation='strict', **kwargs)

Converts loaded XML data to YAML string or file.

Parameters

  • filename – filepath of the destination file. Binds the document to this file if it’s not already bound to another file.

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options for the decoding method of the schema instance.

write(filename, output_format='xml', validation='strict', **kwargs)

Write loaded XML data to a file. Binds the document to saved file if it’s not already bound to another file.

Parameters

  • filename – filepath of the destination file.

  • output_format – the data format of the output file.

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options for the decoding method of the schema instance.

write_fortran_input(filename)

Converts the XML input data to a Fortran namelist input and writes it to a file.

Parameters

filename – the pathname of the file to use to save the Fortran namelist.

class schrodinger.application.matsci.qeschema.qeschema.documents.NebDocument(source=None, schema=None, input_builder=None)[source]

Bases: schrodinger.application.matsci.qeschema.qeschema.documents.QeDocument

Class to manage NEB XML documents.

DEFAULT_SCHEMA = 'qes_neb.xsd'
DEFAULT_INPUT_BUILDER

alias of schrodinger.application.matsci.qeschema.qeschema.converters.NebInputConverter

SEARCH_PATHS = ('/scr/buildbot/savedbuilds/2022-2/NB/build-128/internal/lib/python3.8/site-packages/schrodinger/application/matsci/qeschema/qeschema/schemas', '/scr/buildbot/savedbuilds/2022-2/NB/build-128/internal/lib/python3.8/site-packages/schrodinger/application/matsci/qeschema/qeschema/schemas/releases', '.')
__init__(source=None, schema=None, input_builder=None)
classmethod fetch_schema(filename)
find(path, namespaces=None)

Find first matching element by tag name or path.

Parameters

  • path – is a string having either an element tag or an XPath,

  • namespaces – is an optional mapping from namespace prefix to full name.

Returns

the first matching element, or None if no element was found

findall(path, namespaces=None)

Find all matching subelements by tag name or path.

Parameters

  • path – is a string having either an element tag or an XPath,

  • namespaces – is an optional mapping from namespace prefix to full name.

Returns

the first matching element, or None if no element was found

from_dict(data, validation='strict', **kwargs)

Converts a Python object to an XML ElementTree structure. Object data is validated against the schema during conversion.

Parameters

  • data – filepath of the data source file.

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options to pass to the encoding method of the schema instance.

Returns

a couple with the root element of the XML ElementTree and a list containing the detected errors.

from_json(source, validation='strict', **kwargs)

Load JSON encoded data. Data is converted to an XML ElementTree structure and validated against the schema.

Parameters

  • source – a filepath to a JSON file or a string containing JSON data.

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options to pass to the encoding method of the schema instance.

Returns

the root element of the XML ElementTree data structure and a list containing the detected errors.

Raise

an xmlschema.XMLSchemaValidationError if validation is strict and at least an error is found.

from_xml(source, validation='strict', **kwargs)

Load XML data. Data is validated against the schema.

Parameters

  • source – a filepath to an XML file or a string containing XML data.

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options for creating the xmlschema.XMLResource instance used for reading the XML data.

Returns

a couple with the root element of the XML ElementTree a list containing the detected errors.

from_yaml(source, validation='strict', **kwargs)

Converts a YAML encoded file to an XML ElementTree structure. Data is validated against the schema during conversion.

Parameters

  • source – a filepath to a YAML file or a string containing YAML data.

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options to pass to the encoding method of the schema instance.

Returns

a couple with the root element of the XML ElementTree and a list containing the detected errors.

get_fortran_input(use_defaults=True)

Converts the XML input data to a Fortran namelist input.

Parameters

use_defaults – use the defaults of the XSD schema to fill missing values.

Returns

a string.

property input_path

The path to XML input section.

iter(tag=None)
property namespaces

XML data namespaces map, a dictionary that maps prefixes to URI. An empty dictionary if the XML data file is not loaded or it doesn’t contain any namespace declaration.

property output_path

The path to XML input section.

read(filename, validation='strict', **kwargs)

Reads XML data from a file encoded in XML, JSON or YAML format.

Parameters

  • filename – filepath of the data source file.

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options to pass to the encoding method of the schema instance in case of a non-XML data source.

to_dict(validation='strict', **kwargs)

Converts loaded XML data to a nested dictionary.

Parameters

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options for the decoding method of the schema instance.

Returns

a dictionary.

to_json(filename=None, validation='strict', **kwargs)

Converts loaded XML data to a JSON string or file.

Parameters

  • filename – filepath of the destination file. Binds the document to this file if it’s not already bound to another file.

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options for the decoding method of the schema instance.

to_yaml(filename=None, validation='strict', **kwargs)

Converts loaded XML data to YAML string or file.

Parameters

  • filename – filepath of the destination file. Binds the document to this file if it’s not already bound to another file.

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options for the decoding method of the schema instance.

write(filename, output_format='xml', validation='strict', **kwargs)

Write loaded XML data to a file. Binds the document to saved file if it’s not already bound to another file.

Parameters

  • filename – filepath of the destination file.

  • output_format – the data format of the output file.

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options for the decoding method of the schema instance.

write_fortran_input(filename)

Converts the XML input data to a Fortran namelist input and writes it to a file.

Parameters

filename – the pathname of the file to use to save the Fortran namelist.

class schrodinger.application.matsci.qeschema.qeschema.documents.TdDocument(source=None, schema=None, input_builder=None)[source]

Bases: schrodinger.application.matsci.qeschema.qeschema.documents.QeDocument

Class to manage TDDFPT XML documents.

DEFAULT_SCHEMA = 'tddfpt.xsd'
DEFAULT_INPUT_BUILDER

alias of schrodinger.application.matsci.qeschema.qeschema.converters.TdInputConverter

SEARCH_PATHS = ('/scr/buildbot/savedbuilds/2022-2/NB/build-128/internal/lib/python3.8/site-packages/schrodinger/application/matsci/qeschema/qeschema/schemas', '/scr/buildbot/savedbuilds/2022-2/NB/build-128/internal/lib/python3.8/site-packages/schrodinger/application/matsci/qeschema/qeschema/schemas/releases', '.')
__init__(source=None, schema=None, input_builder=None)
classmethod fetch_schema(filename)
find(path, namespaces=None)

Find first matching element by tag name or path.

Parameters

  • path – is a string having either an element tag or an XPath,

  • namespaces – is an optional mapping from namespace prefix to full name.

Returns

the first matching element, or None if no element was found

findall(path, namespaces=None)

Find all matching subelements by tag name or path.

Parameters

  • path – is a string having either an element tag or an XPath,

  • namespaces – is an optional mapping from namespace prefix to full name.

Returns

the first matching element, or None if no element was found

from_dict(data, validation='strict', **kwargs)

Converts a Python object to an XML ElementTree structure. Object data is validated against the schema during conversion.

Parameters

  • data – filepath of the data source file.

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options to pass to the encoding method of the schema instance.

Returns

a couple with the root element of the XML ElementTree and a list containing the detected errors.

from_json(source, validation='strict', **kwargs)

Load JSON encoded data. Data is converted to an XML ElementTree structure and validated against the schema.

Parameters

  • source – a filepath to a JSON file or a string containing JSON data.

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options to pass to the encoding method of the schema instance.

Returns

the root element of the XML ElementTree data structure and a list containing the detected errors.

Raise

an xmlschema.XMLSchemaValidationError if validation is strict and at least an error is found.

from_xml(source, validation='strict', **kwargs)

Load XML data. Data is validated against the schema.

Parameters

  • source – a filepath to an XML file or a string containing XML data.

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options for creating the xmlschema.XMLResource instance used for reading the XML data.

Returns

a couple with the root element of the XML ElementTree a list containing the detected errors.

from_yaml(source, validation='strict', **kwargs)

Converts a YAML encoded file to an XML ElementTree structure. Data is validated against the schema during conversion.

Parameters

  • source – a filepath to a YAML file or a string containing YAML data.

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options to pass to the encoding method of the schema instance.

Returns

a couple with the root element of the XML ElementTree and a list containing the detected errors.

get_fortran_input(use_defaults=True)

Converts the XML input data to a Fortran namelist input.

Parameters

use_defaults – use the defaults of the XSD schema to fill missing values.

Returns

a string.

property input_path

The path to XML input section.

iter(tag=None)
property namespaces

XML data namespaces map, a dictionary that maps prefixes to URI. An empty dictionary if the XML data file is not loaded or it doesn’t contain any namespace declaration.

property output_path

The path to XML input section.

read(filename, validation='strict', **kwargs)

Reads XML data from a file encoded in XML, JSON or YAML format.

Parameters

  • filename – filepath of the data source file.

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options to pass to the encoding method of the schema instance in case of a non-XML data source.

to_dict(validation='strict', **kwargs)

Converts loaded XML data to a nested dictionary.

Parameters

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options for the decoding method of the schema instance.

Returns

a dictionary.

to_json(filename=None, validation='strict', **kwargs)

Converts loaded XML data to a JSON string or file.

Parameters

  • filename – filepath of the destination file. Binds the document to this file if it’s not already bound to another file.

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options for the decoding method of the schema instance.

to_yaml(filename=None, validation='strict', **kwargs)

Converts loaded XML data to YAML string or file.

Parameters

  • filename – filepath of the destination file. Binds the document to this file if it’s not already bound to another file.

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options for the decoding method of the schema instance.

write(filename, output_format='xml', validation='strict', **kwargs)

Write loaded XML data to a file. Binds the document to saved file if it’s not already bound to another file.

Parameters

  • filename – filepath of the destination file.

  • output_format – the data format of the output file.

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options for the decoding method of the schema instance.

write_fortran_input(filename)

Converts the XML input data to a Fortran namelist input and writes it to a file.

Parameters

filename – the pathname of the file to use to save the Fortran namelist.

class schrodinger.application.matsci.qeschema.qeschema.documents.TdSpectrumDocument(source=None, schema=None, input_builder=None)[source]

Bases: schrodinger.application.matsci.qeschema.qeschema.documents.QeDocument

Class to manage turbo-spectrum XML inputs

SEARCH_PATHS = ('/scr/buildbot/savedbuilds/2022-2/NB/build-128/internal/lib/python3.8/site-packages/schrodinger/application/matsci/qeschema/qeschema/schemas', '/scr/buildbot/savedbuilds/2022-2/NB/build-128/internal/lib/python3.8/site-packages/schrodinger/application/matsci/qeschema/qeschema/schemas/releases', '.')
__init__(source=None, schema=None, input_builder=None)
classmethod fetch_schema(filename)
find(path, namespaces=None)

Find first matching element by tag name or path.

Parameters

  • path – is a string having either an element tag or an XPath,

  • namespaces – is an optional mapping from namespace prefix to full name.

Returns

the first matching element, or None if no element was found

findall(path, namespaces=None)

Find all matching subelements by tag name or path.

Parameters

  • path – is a string having either an element tag or an XPath,

  • namespaces – is an optional mapping from namespace prefix to full name.

Returns

the first matching element, or None if no element was found

from_dict(data, validation='strict', **kwargs)

Converts a Python object to an XML ElementTree structure. Object data is validated against the schema during conversion.

Parameters

  • data – filepath of the data source file.

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options to pass to the encoding method of the schema instance.

Returns

a couple with the root element of the XML ElementTree and a list containing the detected errors.

from_json(source, validation='strict', **kwargs)

Load JSON encoded data. Data is converted to an XML ElementTree structure and validated against the schema.

Parameters

  • source – a filepath to a JSON file or a string containing JSON data.

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options to pass to the encoding method of the schema instance.

Returns

the root element of the XML ElementTree data structure and a list containing the detected errors.

Raise

an xmlschema.XMLSchemaValidationError if validation is strict and at least an error is found.

from_xml(source, validation='strict', **kwargs)

Load XML data. Data is validated against the schema.

Parameters

  • source – a filepath to an XML file or a string containing XML data.

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options for creating the xmlschema.XMLResource instance used for reading the XML data.

Returns

a couple with the root element of the XML ElementTree a list containing the detected errors.

from_yaml(source, validation='strict', **kwargs)

Converts a YAML encoded file to an XML ElementTree structure. Data is validated against the schema during conversion.

Parameters

  • source – a filepath to a YAML file or a string containing YAML data.

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options to pass to the encoding method of the schema instance.

Returns

a couple with the root element of the XML ElementTree and a list containing the detected errors.

get_fortran_input(use_defaults=True)

Converts the XML input data to a Fortran namelist input.

Parameters

use_defaults – use the defaults of the XSD schema to fill missing values.

Returns

a string.

iter(tag=None)
property namespaces

XML data namespaces map, a dictionary that maps prefixes to URI. An empty dictionary if the XML data file is not loaded or it doesn’t contain any namespace declaration.

property output_path

The path to XML input section.

read(filename, validation='strict', **kwargs)

Reads XML data from a file encoded in XML, JSON or YAML format.

Parameters

  • filename – filepath of the data source file.

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options to pass to the encoding method of the schema instance in case of a non-XML data source.

to_dict(validation='strict', **kwargs)

Converts loaded XML data to a nested dictionary.

Parameters

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options for the decoding method of the schema instance.

Returns

a dictionary.

to_json(filename=None, validation='strict', **kwargs)

Converts loaded XML data to a JSON string or file.

Parameters

  • filename – filepath of the destination file. Binds the document to this file if it’s not already bound to another file.

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options for the decoding method of the schema instance.

to_yaml(filename=None, validation='strict', **kwargs)

Converts loaded XML data to YAML string or file.

Parameters

  • filename – filepath of the destination file. Binds the document to this file if it’s not already bound to another file.

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options for the decoding method of the schema instance.

write(filename, output_format='xml', validation='strict', **kwargs)

Write loaded XML data to a file. Binds the document to saved file if it’s not already bound to another file.

Parameters

  • filename – filepath of the destination file.

  • output_format – the data format of the output file.

  • validation – validation mode, can be ‘strict’, ‘lax’ or ‘skip’.

  • kwargs – other options for the decoding method of the schema instance.

write_fortran_input(filename)

Converts the XML input data to a Fortran namelist input and writes it to a file.

Parameters

filename – the pathname of the file to use to save the Fortran namelist.

DEFAULT_SCHEMA = 'qes_spectrum.xsd'
DEFAULT_INPUT_BUILDER

alias of schrodinger.application.matsci.qeschema.qeschema.converters.TdSpectrumInputConverter

property input_path

The path to XML input section.