schrodinger.application.matsci.qexsd.qespresso.documents module

class schrodinger.application.matsci.qexsd.qespresso.documents.QeDocument(xsd_file, input_builder)

Bases: schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmldocument.XmlDocument

Abstract class for XML schema based configurations.

__init__(xsd_file, input_builder)

Initialize self. See help(type(self)) for accurate signature.

read_qe_input(filename)

Map from a Fortran input to XML old parameters to correspondent parameter in XML schema.

Parameters:filename –
Returns:
write_qe_input(filename)

Write the XML configuration to a Fortran input.

Parameters:filename –
Returns:
get_input_path()
get_qe_input(use_defaults=True)
load_fortran_input(filename)
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.qexsd.qespresso.documents', '__doc__': '\n Abstract class for XML schema based configurations.\n ', '__init__': <function QeDocument.__init__>, 'read_qe_input': <function QeDocument.read_qe_input>, 'write_qe_input': <function QeDocument.write_qe_input>, 'get_input_path': <function QeDocument.get_input_path>, 'get_qe_input': <function QeDocument.get_qe_input>, 'load_fortran_input': <function QeDocument.load_fortran_input>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__getitem__(section)
__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.qexsd.qespresso.documents'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

extra_validations(xlm_tree)

Hook for ad-hoc validations of dependencies between parameters that are not explainable with the XSD schema.

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()

Build an ElementTree object from a dictionary

get(qualified_name)
iter(tag=None)
parse_json(filename)

Build an ElementTree object representing a YAML file

parse_xml(filename)

Return an ElementTree object representing an XML file

parse_yaml(filename)

Build an ElementTree object representing a YAML file

read(filename, data_format='XML')

Read configuration from a text file in a specific data format.

Parameters:
  • filename – Name of the text file containing the configuration
  • data_format – Input file data format (XML, JSON or YAML)
read_string(text)
to_dict()
to_json()

Converts the configuration to to json.

validate(filename=None)
write(filename, output_format='XML')

Write configuration to a text file in a specific data format.

Parameters:
  • filename –
  • output_format –
Returns:
class schrodinger.application.matsci.qexsd.qespresso.documents.PwDocument

Bases: schrodinger.application.matsci.qexsd.qespresso.documents.QeDocument

Class to manage PW XML documents.

__init__()

Initialize self. See help(type(self)) for accurate signature.

get_input_path()
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.qexsd.qespresso.documents', '__doc__': '\n Class to manage PW XML documents.\n ', '__init__': <function PwDocument.__init__>, 'get_input_path': <function PwDocument.get_input_path>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__getitem__(section)
__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.qexsd.qespresso.documents'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

extra_validations(xlm_tree)

Hook for ad-hoc validations of dependencies between parameters that are not explainable with the XSD schema.

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()

Build an ElementTree object from a dictionary

get(qualified_name)
get_qe_input(use_defaults=True)
iter(tag=None)
load_fortran_input(filename)
parse_json(filename)

Build an ElementTree object representing a YAML file

parse_xml(filename)

Return an ElementTree object representing an XML file

parse_yaml(filename)

Build an ElementTree object representing a YAML file

read(filename, data_format='XML')

Read configuration from a text file in a specific data format.

Parameters:
  • filename – Name of the text file containing the configuration
  • data_format – Input file data format (XML, JSON or YAML)
read_qe_input(filename)

Map from a Fortran input to XML old parameters to correspondent parameter in XML schema.

Parameters:filename –
Returns:
read_string(text)
to_dict()
to_json()

Converts the configuration to to json.

validate(filename=None)
write(filename, output_format='XML')

Write configuration to a text file in a specific data format.

Parameters:
  • filename –
  • output_format –
Returns:
write_qe_input(filename)

Write the XML configuration to a Fortran input.

Parameters:filename –
Returns:
class schrodinger.application.matsci.qexsd.qespresso.documents.PhononDocument

Bases: schrodinger.application.matsci.qexsd.qespresso.documents.QeDocument

Class to manage Phonon XML documents.

__init__()

Initialize self. See help(type(self)) for accurate signature.

get_input_path()
get_qe_input(use_defaults=False)

overrides get_qe_input calling super get_qe_input with use_defaults set to False. :param use_defaults: :return: the input as obtained from its input builder

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.qexsd.qespresso.documents', '__doc__': '\n Class to manage Phonon XML documents.\n ', '__init__': <function PhononDocument.__init__>, 'get_input_path': <function PhononDocument.get_input_path>, 'get_qe_input': <function PhononDocument.get_qe_input>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__getitem__(section)
__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.qexsd.qespresso.documents'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

extra_validations(xlm_tree)

Hook for ad-hoc validations of dependencies between parameters that are not explainable with the XSD schema.

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()

Build an ElementTree object from a dictionary

get(qualified_name)
iter(tag=None)
load_fortran_input(filename)
parse_json(filename)

Build an ElementTree object representing a YAML file

parse_xml(filename)

Return an ElementTree object representing an XML file

parse_yaml(filename)

Build an ElementTree object representing a YAML file

read(filename, data_format='XML')

Read configuration from a text file in a specific data format.

Parameters:
  • filename – Name of the text file containing the configuration
  • data_format – Input file data format (XML, JSON or YAML)
read_qe_input(filename)

Map from a Fortran input to XML old parameters to correspondent parameter in XML schema.

Parameters:filename –
Returns:
read_string(text)
to_dict()
to_json()

Converts the configuration to to json.

validate(filename=None)
write(filename, output_format='XML')

Write configuration to a text file in a specific data format.

Parameters:
  • filename –
  • output_format –
Returns:
write_qe_input(filename)

Write the XML configuration to a Fortran input.

Parameters:filename –
Returns:
class schrodinger.application.matsci.qexsd.qespresso.documents.NebDocument

Bases: schrodinger.application.matsci.qexsd.qespresso.documents.QeDocument

Class to manage NEB XML documents.

__init__()

Initialize self. See help(type(self)) for accurate signature.

get_input_path()
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.qexsd.qespresso.documents', '__doc__': '\n Class to manage NEB XML documents.\n ', '__init__': <function NebDocument.__init__>, 'get_input_path': <function NebDocument.get_input_path>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__getitem__(section)
__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.qexsd.qespresso.documents'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

extra_validations(xlm_tree)

Hook for ad-hoc validations of dependencies between parameters that are not explainable with the XSD schema.

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()

Build an ElementTree object from a dictionary

get(qualified_name)
get_qe_input(use_defaults=True)
iter(tag=None)
load_fortran_input(filename)
parse_json(filename)

Build an ElementTree object representing a YAML file

parse_xml(filename)

Return an ElementTree object representing an XML file

parse_yaml(filename)

Build an ElementTree object representing a YAML file

read(filename, data_format='XML')

Read configuration from a text file in a specific data format.

Parameters:
  • filename – Name of the text file containing the configuration
  • data_format – Input file data format (XML, JSON or YAML)
read_qe_input(filename)

Map from a Fortran input to XML old parameters to correspondent parameter in XML schema.

Parameters:filename –
Returns:
read_string(text)
to_dict()
to_json()

Converts the configuration to to json.

validate(filename=None)
write(filename, output_format='XML')

Write configuration to a text file in a specific data format.

Parameters:
  • filename –
  • output_format –
Returns:
write_qe_input(filename)

Write the XML configuration to a Fortran input.

Parameters:filename –
Returns:
class schrodinger.application.matsci.qexsd.qespresso.documents.TdDocument

Bases: schrodinger.application.matsci.qexsd.qespresso.documents.QeDocument

Class to manage TDDFPT

__init__()

Initialize self. See help(type(self)) for accurate signature.

get_input_path()
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.qexsd.qespresso.documents', '__doc__': '\n Class to manage TDDFPT\n ', '__init__': <function TdDocument.__init__>, 'get_input_path': <function TdDocument.get_input_path>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__getitem__(section)
__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.qexsd.qespresso.documents'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

extra_validations(xlm_tree)

Hook for ad-hoc validations of dependencies between parameters that are not explainable with the XSD schema.

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()

Build an ElementTree object from a dictionary

get(qualified_name)
get_qe_input(use_defaults=True)
iter(tag=None)
load_fortran_input(filename)
parse_json(filename)

Build an ElementTree object representing a YAML file

parse_xml(filename)

Return an ElementTree object representing an XML file

parse_yaml(filename)

Build an ElementTree object representing a YAML file

read(filename, data_format='XML')

Read configuration from a text file in a specific data format.

Parameters:
  • filename – Name of the text file containing the configuration
  • data_format – Input file data format (XML, JSON or YAML)
read_qe_input(filename)

Map from a Fortran input to XML old parameters to correspondent parameter in XML schema.

Parameters:filename –
Returns:
read_string(text)
to_dict()
to_json()

Converts the configuration to to json.

validate(filename=None)
write(filename, output_format='XML')

Write configuration to a text file in a specific data format.

Parameters:
  • filename –
  • output_format –
Returns:
write_qe_input(filename)

Write the XML configuration to a Fortran input.

Parameters:filename –
Returns:
class schrodinger.application.matsci.qexsd.qespresso.documents.SpectrumDocument

Bases: schrodinger.application.matsci.qexsd.qespresso.documents.QeDocument

Class to manage turbo-spectrum inputs

__init__()

Initialize self. See help(type(self)) for accurate signature.

get_input_path()
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.qexsd.qespresso.documents', '__doc__': '\n Class to manage turbo-spectrum inputs\n ', '__init__': <function SpectrumDocument.__init__>, 'get_input_path': <function SpectrumDocument.get_input_path>})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__getitem__(section)
__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.qexsd.qespresso.documents'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

extra_validations(xlm_tree)

Hook for ad-hoc validations of dependencies between parameters that are not explainable with the XSD schema.

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()

Build an ElementTree object from a dictionary

get(qualified_name)
get_qe_input(use_defaults=True)
iter(tag=None)
load_fortran_input(filename)
parse_json(filename)

Build an ElementTree object representing a YAML file

parse_xml(filename)

Return an ElementTree object representing an XML file

parse_yaml(filename)

Build an ElementTree object representing a YAML file

read(filename, data_format='XML')

Read configuration from a text file in a specific data format.

Parameters:
  • filename – Name of the text file containing the configuration
  • data_format – Input file data format (XML, JSON or YAML)
read_qe_input(filename)

Map from a Fortran input to XML old parameters to correspondent parameter in XML schema.

Parameters:filename –
Returns:
read_string(text)
to_dict()
to_json()

Converts the configuration to to json.

validate(filename=None)
write(filename, output_format='XML')

Write configuration to a text file in a specific data format.

Parameters:
  • filename –
  • output_format –
Returns:
write_qe_input(filename)

Write the XML configuration to a Fortran input.

Parameters:filename –
Returns: