structure
Modules:
| Name | Description |
|---|---|
categories |
|
collection |
Collection of structure data blocks. |
item |
|
Modules
categories
Modules:
| Name | Description |
|---|---|
atom_site_aniso |
|
atom_sites |
|
cell |
|
geom |
|
space_group |
|
space_group_wyckoff |
|
Modules
atom_site_aniso
Modules:
| Name | Description |
|---|---|
default |
Anisotropic ADP category. |
factory |
Atom-site-aniso factory — delegates entirely to |
Classes
Modules
default
Anisotropic ADP category.
Defines :class:AtomSiteAniso items and
:class:AtomSiteAnisoCollection used alongside :class:AtomSites to
hold anisotropic displacement parameters.
Classes:
| Name | Description |
|---|---|
AtomSiteAniso |
Single atom site anisotropic ADP entry. |
AtomSiteAnisoCollection |
Collection of :class: |
AtomSiteAniso()
Single atom site anisotropic ADP entry.
Each entry mirrors an :class:AtomSite by label and holds six
tensor components whose physical meaning (B or U) is determined by
atom_site.adp_type.
Methods:
| Name | Description |
|---|---|
__str__ |
Human-readable representation of this component. |
__repr__ |
Return the developer representation of this object. |
__getattr__ |
Raise a descriptive error for unknown attribute access. |
__setattr__ |
Set an attribute with access-control diagnostics. |
help |
Print parameters, other properties, and methods. |
from_cif |
Populate this item from a CIF block. |
Attributes:
| Name | Type | Description |
|---|---|---|
label |
StringDescriptor
|
Label matching the parent atom_site entry. |
adp_11 |
Parameter
|
Anisotropic ADP tensor component (1,1) in Ų. |
adp_22 |
Parameter
|
Anisotropic ADP tensor component (2,2) in Ų. |
adp_33 |
Parameter
|
Anisotropic ADP tensor component (3,3) in Ų. |
adp_12 |
Parameter
|
Anisotropic ADP tensor component (1,2) in Ų. |
adp_13 |
Parameter
|
Anisotropic ADP tensor component (1,3) in Ų. |
adp_23 |
Parameter
|
Anisotropic ADP tensor component (2,3) in Ų. |
unique_name |
str
|
Fully qualified name: datablock, category, entry. |
parameters |
list
|
All GenericDescriptorBase instances on this item. |
as_cif |
str
|
Return CIF representation of this object. |
label
property
writable
Label matching the parent atom_site entry.
adp_11
property
writable
Anisotropic ADP tensor component (1,1) in Ų.
adp_22
property
writable
Anisotropic ADP tensor component (2,2) in Ų.
adp_33
property
writable
Anisotropic ADP tensor component (3,3) in Ų.
adp_12
property
writable
Anisotropic ADP tensor component (1,2) in Ų.
adp_13
property
writable
Anisotropic ADP tensor component (1,3) in Ų.
adp_23
property
writable
Anisotropic ADP tensor component (2,3) in Ų.
unique_name
property
Fully qualified name: datablock, category, entry.
parameters
property
All GenericDescriptorBase instances on this item.
as_cif
property
Return CIF representation of this object.
__str__()
Human-readable representation of this component.
__repr__()
Return the developer representation of this object.
__getattr__(key)
Raise a descriptive error for unknown attribute access.
__setattr__(key, value)
Set an attribute with access-control diagnostics.
help()
Print parameters, other properties, and methods.
from_cif(block, idx=0)
Populate this item from a CIF block.
AtomSiteAnisoCollection()
Collection of :class:AtomSiteAniso instances.
Methods:
| Name | Description |
|---|---|
__str__ |
Human-readable representation of this component. |
__repr__ |
Return the developer representation of this object. |
__getattr__ |
Raise a descriptive error for unknown attribute access. |
__setattr__ |
Set an attribute with access-control diagnostics. |
help |
Print a summary of public attributes and contained items. |
__getitem__ |
Return an item by name or positional index. |
__setitem__ |
Insert or replace an item under the given identity key. |
__delitem__ |
Delete an item by key or raise |
__contains__ |
Check whether an item with the given key exists. |
__iter__ |
Iterate over items in insertion order. |
__len__ |
Return the number of items in the collection. |
remove |
Remove an item by its key. |
keys |
Yield keys for all items in insertion order. |
values |
Yield items in insertion order. |
items |
Yield |
from_cif |
Populate this collection from a CIF block. |
add |
Insert or replace a pre-built item into the collection. |
create |
Create a new item with the given attributes and add it. |
Attributes:
| Name | Type | Description |
|---|---|---|
unique_name |
str | None
|
Return None; collections have no unique name. |
parameters |
list
|
All parameters from all items in this collection. |
as_cif |
str
|
Return CIF representation of this object. |
names |
list[str | None]
|
List of all item keys in the collection. |
scalar_descriptors |
list
|
Collection-level descriptors serialized outside the loop. |
unique_name
property
Return None; collections have no unique name.
parameters
property
All parameters from all items in this collection.
as_cif
property
Return CIF representation of this object.
names
property
List of all item keys in the collection.
scalar_descriptors
property
Collection-level descriptors serialized outside the loop.
__str__()
Human-readable representation of this component.
__repr__()
Return the developer representation of this object.
__getattr__(key)
Raise a descriptive error for unknown attribute access.
__setattr__(key, value)
Set an attribute with access-control diagnostics.
help()
Print a summary of public attributes and contained items.
__getitem__(key)
Return an item by name or positional index.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
key
|
str | int
|
Identity key (str) or zero-based positional index (int). |
required |
Returns:
| Type | Description |
|---|---|
GuardedBase
|
The item matching the given key or index. |
Raises:
| Type | Description |
|---|---|
TypeError
|
If key is neither |
__setitem__(name, item)
Insert or replace an item under the given identity key.
__delitem__(name)
Delete an item by key or raise KeyError if missing.
__contains__(name)
Check whether an item with the given key exists.
__iter__()
Iterate over items in insertion order.
__len__()
Return the number of items in the collection.
remove(name)
Remove an item by its key.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
name
|
str
|
Identity key of the item to remove. |
required |
keys()
Yield keys for all items in insertion order.
values()
Yield items in insertion order.
items()
Yield (key, item) pairs in insertion order.
from_cif(block)
Populate this collection from a CIF block.
add(item)
Insert or replace a pre-built item into the collection.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
item
|
object
|
A |
required |
create(**kwargs)
Create a new item with the given attributes and add it.
A default instance of the collection's item type is created,
then each keyword argument is applied via setattr.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
**kwargs
|
object
|
Attribute names and values for the new item. |
{}
|
factory
Atom-site-aniso factory — delegates entirely to FactoryBase.
Classes:
| Name | Description |
|---|---|
AtomSiteAnisoFactory |
Create atom-site-aniso collections by tag. |
AtomSiteAnisoFactory
Create atom-site-aniso collections by tag.
Methods:
| Name | Description |
|---|---|
__init_subclass__ |
Give each subclass its own independent registry and rules. |
register |
Class decorator to register a concrete class. |
supported_tags |
Return list of all supported tags. |
default_tag |
Resolve the default tag for a given experimental context. |
create |
Instantiate a registered class by tag. |
create_default_for |
Instantiate the default class for a given context. |
supported_for |
Return classes matching conditions and/or calculator. |
show_supported |
Pretty-print a table of supported types. |
__init_subclass__(**kwargs)
Give each subclass its own independent registry and rules.
register(klass)
classmethod
Class decorator to register a concrete class.
Usage::
@SomeFactory.register class MyClass(SomeBase): type_info = TypeInfo(...)
Returns the class unmodified.
supported_tags()
classmethod
Return list of all supported tags.
default_tag(**conditions)
classmethod
Resolve the default tag for a given experimental context.
Uses largest-subset matching: the rule whose key is the
biggest subset of the given conditions wins. A rule with an
empty key (frozenset()) acts as a universal fallback.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
**conditions
|
object
|
Experimental-axis values, e.g.
|
{}
|
Returns:
| Type | Description |
|---|---|
str
|
The resolved default tag string. |
Raises:
| Type | Description |
|---|---|
ValueError
|
If no rule matches the given conditions. |
create(tag, **kwargs)
classmethod
Instantiate a registered class by tag.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
tag
|
str
|
|
required |
**kwargs
|
object
|
Forwarded to the class constructor. |
{}
|
Returns:
| Type | Description |
|---|---|
object
|
A new instance of the registered class. |
Raises:
| Type | Description |
|---|---|
ValueError
|
If tag is not in the registry. |
create_default_for(**conditions)
classmethod
Instantiate the default class for a given context.
Combines default_tag(**conditions) with create(tag).
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
**conditions
|
object
|
Experimental-axis values. |
{}
|
Returns:
| Type | Description |
|---|---|
object
|
A new instance of the default class. |
supported_for(*, calculator=None, sample_form=None, scattering_type=None, beam_mode=None, radiation_probe=None)
classmethod
Return classes matching conditions and/or calculator.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
calculator
|
object
|
Optional |
None
|
sample_form
|
object
|
Optional |
None
|
scattering_type
|
object
|
Optional |
None
|
beam_mode
|
object
|
Optional |
None
|
radiation_probe
|
object
|
Optional |
None
|
Returns:
| Type | Description |
|---|---|
list[type]
|
Classes matching the given conditions. |
show_supported(*, calculator=None, sample_form=None, scattering_type=None, beam_mode=None, radiation_probe=None)
classmethod
Pretty-print a table of supported types.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
calculator
|
object
|
Optional |
None
|
sample_form
|
object
|
Optional |
None
|
scattering_type
|
object
|
Optional |
None
|
beam_mode
|
object
|
Optional |
None
|
radiation_probe
|
object
|
Optional |
None
|
atom_sites
Modules:
| Name | Description |
|---|---|
default |
Atom site category. |
enums |
Enumeration for ADP type values. |
factory |
Atom-sites factory — delegates entirely to |
Classes
Modules
default
Atom site category.
Defines :class:AtomSite items and :class:AtomSites collection used
in crystallographic structures.
Classes:
| Name | Description |
|---|---|
AtomSite |
Single atom site with fractional coordinates and ADP. |
AtomSites |
Collection of :class: |
AtomSite()
Single atom site with fractional coordinates and ADP.
Attributes are represented by descriptors to support validation and CIF serialization.
Methods:
| Name | Description |
|---|---|
__str__ |
Human-readable representation of this component. |
__repr__ |
Return the developer representation of this object. |
__getattr__ |
Raise a descriptive error for unknown attribute access. |
__setattr__ |
Set an attribute with access-control diagnostics. |
help |
Print parameters, other properties, and methods. |
from_cif |
Populate this item from a CIF block. |
Attributes:
| Name | Type | Description |
|---|---|---|
label |
StringDescriptor
|
Unique identifier for the atom site. |
type_symbol |
StringDescriptor
|
Chemical symbol of the atom at this site. |
adp_type |
EnumDescriptor
|
ADP type used (e.g., Biso, Uiso, Uani, Bani). |
wyckoff_letter |
StringDescriptor
|
Wyckoff letter for the atom site symmetry position. |
multiplicity |
IntegerDescriptor
|
Read-only site multiplicity derived from the Wyckoff position. |
fract_x |
Parameter
|
Fractional x-coordinate of the atom site within the unit cell. |
fract_y |
Parameter
|
Fractional y-coordinate of the atom site within the unit cell. |
fract_z |
Parameter
|
Fractional z-coordinate of the atom site within the unit cell. |
occupancy |
Parameter
|
Occupancy fraction of the atom type at this site. |
adp_iso |
Parameter
|
Isotropic ADP for the atom site (Ų). |
adp_iso_as_b |
float
|
Return the isotropic ADP as a B-factor value. |
unique_name |
str
|
Fully qualified name: datablock, category, entry. |
parameters |
list
|
All GenericDescriptorBase instances on this item. |
as_cif |
str
|
Return CIF representation of this object. |
label
property
writable
Unique identifier for the atom site.
Reading this property returns the underlying
StringDescriptor object. Assigning to it updates the
parameter value.
type_symbol
property
writable
Chemical symbol of the atom at this site.
Reading this property returns the underlying
StringDescriptor object. Assigning to it updates the
parameter value.
adp_type
property
writable
ADP type used (e.g., Biso, Uiso, Uani, Bani).
Reading this property returns the underlying EnumDescriptor
object. Assigning to it updates the parameter value.
wyckoff_letter
property
writable
Wyckoff letter for the atom site symmetry position.
Reading this property returns the underlying
StringDescriptor object. Assigning to it updates the
parameter value.
multiplicity
property
Read-only site multiplicity derived from the Wyckoff position.
Populated by Wyckoff detection; value is None when the
space group is untabulated. There is no public setter.
fract_x
property
writable
Fractional x-coordinate of the atom site within the unit cell.
Reading this property returns the underlying Parameter
object. Assigning to it updates the parameter value.
fract_y
property
writable
Fractional y-coordinate of the atom site within the unit cell.
Reading this property returns the underlying Parameter
object. Assigning to it updates the parameter value.
fract_z
property
writable
Fractional z-coordinate of the atom site within the unit cell.
Reading this property returns the underlying Parameter
object. Assigning to it updates the parameter value.
occupancy
property
writable
Occupancy fraction of the atom type at this site.
Reading this property returns the underlying Parameter
object. Assigning to it updates the parameter value.
adp_iso
property
writable
Isotropic ADP for the atom site (Ų).
Reading this property returns the underlying Parameter
object. Assigning to it updates the parameter value.
adp_iso_as_b
property
Return the isotropic ADP as a B-factor value.
When adp_type is Uiso or Uani the stored U value is
converted to B via B = 8π²U. Otherwise the stored value is
returned unchanged.
Returns:
| Type | Description |
|---|---|
float
|
Equivalent B_iso value. |
unique_name
property
Fully qualified name: datablock, category, entry.
parameters
property
All GenericDescriptorBase instances on this item.
as_cif
property
Return CIF representation of this object.
__str__()
Human-readable representation of this component.
__repr__()
Return the developer representation of this object.
__getattr__(key)
Raise a descriptive error for unknown attribute access.
__setattr__(key, value)
Set an attribute with access-control diagnostics.
help()
Print parameters, other properties, and methods.
from_cif(block, idx=0)
Populate this item from a CIF block.
AtomSites()
Collection of :class:AtomSite instances.
Methods:
| Name | Description |
|---|---|
__str__ |
Human-readable representation of this component. |
__repr__ |
Return the developer representation of this object. |
__getattr__ |
Raise a descriptive error for unknown attribute access. |
__setattr__ |
Set an attribute with access-control diagnostics. |
help |
Print a summary of public attributes and contained items. |
__getitem__ |
Return an item by name or positional index. |
__setitem__ |
Insert or replace an item under the given identity key. |
__delitem__ |
Delete an item by key or raise |
__contains__ |
Check whether an item with the given key exists. |
__iter__ |
Iterate over items in insertion order. |
__len__ |
Return the number of items in the collection. |
remove |
Remove an item by its key. |
keys |
Yield keys for all items in insertion order. |
values |
Yield items in insertion order. |
items |
Yield |
from_cif |
Populate this collection from a CIF block. |
add |
Insert or replace a pre-built item into the collection. |
create |
Create a new item with the given attributes and add it. |
Attributes:
| Name | Type | Description |
|---|---|---|
unique_name |
str | None
|
Return None; collections have no unique name. |
parameters |
list
|
All parameters from all items in this collection. |
as_cif |
str
|
Return CIF representation of this object. |
names |
list[str | None]
|
List of all item keys in the collection. |
scalar_descriptors |
list
|
Collection-level descriptors serialized outside the loop. |
unique_name
property
Return None; collections have no unique name.
parameters
property
All parameters from all items in this collection.
as_cif
property
Return CIF representation of this object.
names
property
List of all item keys in the collection.
scalar_descriptors
property
Collection-level descriptors serialized outside the loop.
__str__()
Human-readable representation of this component.
__repr__()
Return the developer representation of this object.
__getattr__(key)
Raise a descriptive error for unknown attribute access.
__setattr__(key, value)
Set an attribute with access-control diagnostics.
help()
Print a summary of public attributes and contained items.
__getitem__(key)
Return an item by name or positional index.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
key
|
str | int
|
Identity key (str) or zero-based positional index (int). |
required |
Returns:
| Type | Description |
|---|---|
GuardedBase
|
The item matching the given key or index. |
Raises:
| Type | Description |
|---|---|
TypeError
|
If key is neither |
__setitem__(name, item)
Insert or replace an item under the given identity key.
__delitem__(name)
Delete an item by key or raise KeyError if missing.
__contains__(name)
Check whether an item with the given key exists.
__iter__()
Iterate over items in insertion order.
__len__()
Return the number of items in the collection.
remove(name)
Remove an item by its key.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
name
|
str
|
Identity key of the item to remove. |
required |
keys()
Yield keys for all items in insertion order.
values()
Yield items in insertion order.
items()
Yield (key, item) pairs in insertion order.
from_cif(block)
Populate this collection from a CIF block.
add(item)
Insert or replace a pre-built item into the collection.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
item
|
object
|
A |
required |
create(**kwargs)
Create a new item with the given attributes and add it.
A default instance of the collection's item type is created,
then each keyword argument is applied via setattr.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
**kwargs
|
object
|
Attribute names and values for the new item. |
{}
|
enums
Enumeration for ADP type values.
Classes:
| Name | Description |
|---|---|
AdpTypeEnum |
Atomic displacement parameter type. |
AdpTypeEnum
Atomic displacement parameter type.
Methods:
| Name | Description |
|---|---|
default |
Return the default ADP type (BISO). |
description |
Return a human-readable description of this ADP type. |
default()
classmethod
Return the default ADP type (BISO).
description()
Return a human-readable description of this ADP type.
factory
Atom-sites factory — delegates entirely to FactoryBase.
Classes:
| Name | Description |
|---|---|
AtomSitesFactory |
Create atom-sites collections by tag. |
AtomSitesFactory
Create atom-sites collections by tag.
Methods:
| Name | Description |
|---|---|
__init_subclass__ |
Give each subclass its own independent registry and rules. |
register |
Class decorator to register a concrete class. |
supported_tags |
Return list of all supported tags. |
default_tag |
Resolve the default tag for a given experimental context. |
create |
Instantiate a registered class by tag. |
create_default_for |
Instantiate the default class for a given context. |
supported_for |
Return classes matching conditions and/or calculator. |
show_supported |
Pretty-print a table of supported types. |
__init_subclass__(**kwargs)
Give each subclass its own independent registry and rules.
register(klass)
classmethod
Class decorator to register a concrete class.
Usage::
@SomeFactory.register class MyClass(SomeBase): type_info = TypeInfo(...)
Returns the class unmodified.
supported_tags()
classmethod
Return list of all supported tags.
default_tag(**conditions)
classmethod
Resolve the default tag for a given experimental context.
Uses largest-subset matching: the rule whose key is the
biggest subset of the given conditions wins. A rule with an
empty key (frozenset()) acts as a universal fallback.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
**conditions
|
object
|
Experimental-axis values, e.g.
|
{}
|
Returns:
| Type | Description |
|---|---|
str
|
The resolved default tag string. |
Raises:
| Type | Description |
|---|---|
ValueError
|
If no rule matches the given conditions. |
create(tag, **kwargs)
classmethod
Instantiate a registered class by tag.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
tag
|
str
|
|
required |
**kwargs
|
object
|
Forwarded to the class constructor. |
{}
|
Returns:
| Type | Description |
|---|---|
object
|
A new instance of the registered class. |
Raises:
| Type | Description |
|---|---|
ValueError
|
If tag is not in the registry. |
create_default_for(**conditions)
classmethod
Instantiate the default class for a given context.
Combines default_tag(**conditions) with create(tag).
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
**conditions
|
object
|
Experimental-axis values. |
{}
|
Returns:
| Type | Description |
|---|---|
object
|
A new instance of the default class. |
supported_for(*, calculator=None, sample_form=None, scattering_type=None, beam_mode=None, radiation_probe=None)
classmethod
Return classes matching conditions and/or calculator.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
calculator
|
object
|
Optional |
None
|
sample_form
|
object
|
Optional |
None
|
scattering_type
|
object
|
Optional |
None
|
beam_mode
|
object
|
Optional |
None
|
radiation_probe
|
object
|
Optional |
None
|
Returns:
| Type | Description |
|---|---|
list[type]
|
Classes matching the given conditions. |
show_supported(*, calculator=None, sample_form=None, scattering_type=None, beam_mode=None, radiation_probe=None)
classmethod
Pretty-print a table of supported types.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
calculator
|
object
|
Optional |
None
|
sample_form
|
object
|
Optional |
None
|
scattering_type
|
object
|
Optional |
None
|
beam_mode
|
object
|
Optional |
None
|
radiation_probe
|
object
|
Optional |
None
|
cell
Modules:
| Name | Description |
|---|---|
default |
Unit cell parameters category for structures. |
factory |
Cell factory — delegates entirely to |
Classes
Modules
default
Unit cell parameters category for structures.
Classes:
| Name | Description |
|---|---|
Cell |
Unit cell with lengths a, b, c and angles alpha, beta, gamma. |
Cell()
Unit cell with lengths a, b, c and angles alpha, beta, gamma.
All six lattice parameters are exposed as :class:Parameter
descriptors supporting validation, fitting and CIF serialization.
Methods:
| Name | Description |
|---|---|
__str__ |
Human-readable representation of this component. |
__repr__ |
Return the developer representation of this object. |
__getattr__ |
Raise a descriptive error for unknown attribute access. |
__setattr__ |
Set an attribute with access-control diagnostics. |
help |
Print parameters, other properties, and methods. |
from_cif |
Populate this item from a CIF block. |
Attributes:
| Name | Type | Description |
|---|---|---|
length_a |
Parameter
|
Length of the a axis of the unit cell (Å). |
length_b |
Parameter
|
Length of the b axis of the unit cell (Å). |
length_c |
Parameter
|
Length of the c axis of the unit cell (Å). |
angle_alpha |
Parameter
|
Angle between edges b and c (deg). |
angle_beta |
Parameter
|
Angle between edges a and c (deg). |
angle_gamma |
Parameter
|
Angle between edges a and b (deg). |
unique_name |
str
|
Fully qualified name: datablock, category, entry. |
parameters |
list
|
All GenericDescriptorBase instances on this item. |
as_cif |
str
|
Return CIF representation of this object. |
length_a
property
writable
Length of the a axis of the unit cell (Å).
Reading this property returns the underlying Parameter
object. Assigning to it updates the parameter value.
length_b
property
writable
Length of the b axis of the unit cell (Å).
Reading this property returns the underlying Parameter
object. Assigning to it updates the parameter value.
length_c
property
writable
Length of the c axis of the unit cell (Å).
Reading this property returns the underlying Parameter
object. Assigning to it updates the parameter value.
angle_alpha
property
writable
Angle between edges b and c (deg).
Reading this property returns the underlying Parameter
object. Assigning to it updates the parameter value.
angle_beta
property
writable
Angle between edges a and c (deg).
Reading this property returns the underlying Parameter
object. Assigning to it updates the parameter value.
angle_gamma
property
writable
Angle between edges a and b (deg).
Reading this property returns the underlying Parameter
object. Assigning to it updates the parameter value.
unique_name
property
Fully qualified name: datablock, category, entry.
parameters
property
All GenericDescriptorBase instances on this item.
as_cif
property
Return CIF representation of this object.
__str__()
Human-readable representation of this component.
__repr__()
Return the developer representation of this object.
__getattr__(key)
Raise a descriptive error for unknown attribute access.
__setattr__(key, value)
Set an attribute with access-control diagnostics.
help()
Print parameters, other properties, and methods.
from_cif(block, idx=0)
Populate this item from a CIF block.
factory
Cell factory — delegates entirely to FactoryBase.
Classes:
| Name | Description |
|---|---|
CellFactory |
Create unit-cell categories by tag. |
CellFactory
Create unit-cell categories by tag.
Methods:
| Name | Description |
|---|---|
__init_subclass__ |
Give each subclass its own independent registry and rules. |
register |
Class decorator to register a concrete class. |
supported_tags |
Return list of all supported tags. |
default_tag |
Resolve the default tag for a given experimental context. |
create |
Instantiate a registered class by tag. |
create_default_for |
Instantiate the default class for a given context. |
supported_for |
Return classes matching conditions and/or calculator. |
show_supported |
Pretty-print a table of supported types. |
__init_subclass__(**kwargs)
Give each subclass its own independent registry and rules.
register(klass)
classmethod
Class decorator to register a concrete class.
Usage::
@SomeFactory.register class MyClass(SomeBase): type_info = TypeInfo(...)
Returns the class unmodified.
supported_tags()
classmethod
Return list of all supported tags.
default_tag(**conditions)
classmethod
Resolve the default tag for a given experimental context.
Uses largest-subset matching: the rule whose key is the
biggest subset of the given conditions wins. A rule with an
empty key (frozenset()) acts as a universal fallback.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
**conditions
|
object
|
Experimental-axis values, e.g.
|
{}
|
Returns:
| Type | Description |
|---|---|
str
|
The resolved default tag string. |
Raises:
| Type | Description |
|---|---|
ValueError
|
If no rule matches the given conditions. |
create(tag, **kwargs)
classmethod
Instantiate a registered class by tag.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
tag
|
str
|
|
required |
**kwargs
|
object
|
Forwarded to the class constructor. |
{}
|
Returns:
| Type | Description |
|---|---|
object
|
A new instance of the registered class. |
Raises:
| Type | Description |
|---|---|
ValueError
|
If tag is not in the registry. |
create_default_for(**conditions)
classmethod
Instantiate the default class for a given context.
Combines default_tag(**conditions) with create(tag).
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
**conditions
|
object
|
Experimental-axis values. |
{}
|
Returns:
| Type | Description |
|---|---|
object
|
A new instance of the default class. |
supported_for(*, calculator=None, sample_form=None, scattering_type=None, beam_mode=None, radiation_probe=None)
classmethod
Return classes matching conditions and/or calculator.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
calculator
|
object
|
Optional |
None
|
sample_form
|
object
|
Optional |
None
|
scattering_type
|
object
|
Optional |
None
|
beam_mode
|
object
|
Optional |
None
|
radiation_probe
|
object
|
Optional |
None
|
Returns:
| Type | Description |
|---|---|
list[type]
|
Classes matching the given conditions. |
show_supported(*, calculator=None, sample_form=None, scattering_type=None, beam_mode=None, radiation_probe=None)
classmethod
Pretty-print a table of supported types.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
calculator
|
object
|
Optional |
None
|
sample_form
|
object
|
Optional |
None
|
scattering_type
|
object
|
Optional |
None
|
beam_mode
|
object
|
Optional |
None
|
radiation_probe
|
object
|
Optional |
None
|
geom
Modules:
| Name | Description |
|---|---|
default |
Per-structure bond-generation cutoffs (standard cif_core |
factory |
Geom factory — delegates entirely to |
Classes
Modules
default
Per-structure bond-generation cutoffs (standard cif_core _geom).
Classes:
| Name | Description |
|---|---|
Geom |
Bond-generation cutoffs for a structure (cif_core |
Geom()
Bond-generation cutoffs for a structure (cif_core _geom).
Methods:
| Name | Description |
|---|---|
__str__ |
Human-readable representation of this component. |
__repr__ |
Return the developer representation of this object. |
__getattr__ |
Raise a descriptive error for unknown attribute access. |
__setattr__ |
Set an attribute with access-control diagnostics. |
help |
Print parameters, other properties, and methods. |
from_cif |
Populate this item from a CIF block. |
Attributes:
| Name | Type | Description |
|---|---|---|
min_bond_distance_cutoff |
NumericDescriptor
|
Minimum permitted bonded distance (angstrom). |
bond_distance_incr |
NumericDescriptor
|
Increment added to the summed bonding radii (angstrom). |
as_cif |
str
|
Return CIF representation of this geom category. |
unique_name |
str
|
Fully qualified name: datablock, category, entry. |
parameters |
list
|
All GenericDescriptorBase instances on this item. |
min_bond_distance_cutoff
property
writable
Minimum permitted bonded distance (angstrom).
bond_distance_incr
property
writable
Increment added to the summed bonding radii (angstrom).
as_cif
property
Return CIF representation of this geom category.
unique_name
property
Fully qualified name: datablock, category, entry.
parameters
property
All GenericDescriptorBase instances on this item.
__str__()
Human-readable representation of this component.
__repr__()
Return the developer representation of this object.
__getattr__(key)
Raise a descriptive error for unknown attribute access.
__setattr__(key, value)
Set an attribute with access-control diagnostics.
help()
Print parameters, other properties, and methods.
from_cif(block, idx=0)
Populate this item from a CIF block.
factory
Geom factory — delegates entirely to FactoryBase.
Classes:
| Name | Description |
|---|---|
GeomFactory |
Create bond-geometry-cutoff categories by tag. |
GeomFactory
Create bond-geometry-cutoff categories by tag.
Methods:
| Name | Description |
|---|---|
__init_subclass__ |
Give each subclass its own independent registry and rules. |
register |
Class decorator to register a concrete class. |
supported_tags |
Return list of all supported tags. |
default_tag |
Resolve the default tag for a given experimental context. |
create |
Instantiate a registered class by tag. |
create_default_for |
Instantiate the default class for a given context. |
supported_for |
Return classes matching conditions and/or calculator. |
show_supported |
Pretty-print a table of supported types. |
__init_subclass__(**kwargs)
Give each subclass its own independent registry and rules.
register(klass)
classmethod
Class decorator to register a concrete class.
Usage::
@SomeFactory.register class MyClass(SomeBase): type_info = TypeInfo(...)
Returns the class unmodified.
supported_tags()
classmethod
Return list of all supported tags.
default_tag(**conditions)
classmethod
Resolve the default tag for a given experimental context.
Uses largest-subset matching: the rule whose key is the
biggest subset of the given conditions wins. A rule with an
empty key (frozenset()) acts as a universal fallback.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
**conditions
|
object
|
Experimental-axis values, e.g.
|
{}
|
Returns:
| Type | Description |
|---|---|
str
|
The resolved default tag string. |
Raises:
| Type | Description |
|---|---|
ValueError
|
If no rule matches the given conditions. |
create(tag, **kwargs)
classmethod
Instantiate a registered class by tag.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
tag
|
str
|
|
required |
**kwargs
|
object
|
Forwarded to the class constructor. |
{}
|
Returns:
| Type | Description |
|---|---|
object
|
A new instance of the registered class. |
Raises:
| Type | Description |
|---|---|
ValueError
|
If tag is not in the registry. |
create_default_for(**conditions)
classmethod
Instantiate the default class for a given context.
Combines default_tag(**conditions) with create(tag).
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
**conditions
|
object
|
Experimental-axis values. |
{}
|
Returns:
| Type | Description |
|---|---|
object
|
A new instance of the default class. |
supported_for(*, calculator=None, sample_form=None, scattering_type=None, beam_mode=None, radiation_probe=None)
classmethod
Return classes matching conditions and/or calculator.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
calculator
|
object
|
Optional |
None
|
sample_form
|
object
|
Optional |
None
|
scattering_type
|
object
|
Optional |
None
|
beam_mode
|
object
|
Optional |
None
|
radiation_probe
|
object
|
Optional |
None
|
Returns:
| Type | Description |
|---|---|
list[type]
|
Classes matching the given conditions. |
show_supported(*, calculator=None, sample_form=None, scattering_type=None, beam_mode=None, radiation_probe=None)
classmethod
Pretty-print a table of supported types.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
calculator
|
object
|
Optional |
None
|
sample_form
|
object
|
Optional |
None
|
scattering_type
|
object
|
Optional |
None
|
beam_mode
|
object
|
Optional |
None
|
radiation_probe
|
object
|
Optional |
None
|
space_group
Modules:
| Name | Description |
|---|---|
default |
Space group category for crystallographic structures. |
factory |
Space-group factory — delegates entirely to |
Classes
Modules
default
Space group category for crystallographic structures.
Classes:
| Name | Description |
|---|---|
SpaceGroup |
Space group with H-M symbol and IT coordinate system code. |
SpaceGroup()
Space group with H-M symbol and IT coordinate system code.
Holds the space-group symbol (name_h_m) and the International
Tables coordinate-system qualifier (it_coordinate_system_code).
Changing the symbol automatically resets the coordinate-system code
to the first allowed value for the new group.
Methods:
| Name | Description |
|---|---|
__str__ |
Human-readable representation of this component. |
__repr__ |
Return the developer representation of this object. |
__getattr__ |
Raise a descriptive error for unknown attribute access. |
__setattr__ |
Set an attribute with access-control diagnostics. |
help |
Print parameters, other properties, and methods. |
from_cif |
Populate this item from a CIF block. |
Attributes:
| Name | Type | Description |
|---|---|---|
name_h_m |
StringDescriptor
|
Hermann-Mauguin symbol of the space group. |
it_coordinate_system_code |
StringDescriptor
|
A qualifier identifying which setting in IT is used. |
crystal_system |
str
|
Crystal system derived from the H-M symbol. |
unique_name |
str
|
Fully qualified name: datablock, category, entry. |
parameters |
list
|
All GenericDescriptorBase instances on this item. |
as_cif |
str
|
Return CIF representation of this object. |
name_h_m
property
writable
Hermann-Mauguin symbol of the space group.
Reading this property returns the underlying
StringDescriptor object. Assigning to it updates the
parameter value.
it_coordinate_system_code
property
writable
A qualifier identifying which setting in IT is used.
Reading this property returns the underlying
StringDescriptor object. Assigning to it updates the
parameter value.
crystal_system
property
Crystal system derived from the H-M symbol.
unique_name
property
Fully qualified name: datablock, category, entry.
parameters
property
All GenericDescriptorBase instances on this item.
as_cif
property
Return CIF representation of this object.
__str__()
Human-readable representation of this component.
__repr__()
Return the developer representation of this object.
__getattr__(key)
Raise a descriptive error for unknown attribute access.
__setattr__(key, value)
Set an attribute with access-control diagnostics.
help()
Print parameters, other properties, and methods.
from_cif(block, idx=0)
Populate this item from a CIF block.
factory
Space-group factory — delegates entirely to FactoryBase.
Classes:
| Name | Description |
|---|---|
SpaceGroupFactory |
Create space-group categories by tag. |
SpaceGroupFactory
Create space-group categories by tag.
Methods:
| Name | Description |
|---|---|
__init_subclass__ |
Give each subclass its own independent registry and rules. |
register |
Class decorator to register a concrete class. |
supported_tags |
Return list of all supported tags. |
default_tag |
Resolve the default tag for a given experimental context. |
create |
Instantiate a registered class by tag. |
create_default_for |
Instantiate the default class for a given context. |
supported_for |
Return classes matching conditions and/or calculator. |
show_supported |
Pretty-print a table of supported types. |
__init_subclass__(**kwargs)
Give each subclass its own independent registry and rules.
register(klass)
classmethod
Class decorator to register a concrete class.
Usage::
@SomeFactory.register class MyClass(SomeBase): type_info = TypeInfo(...)
Returns the class unmodified.
supported_tags()
classmethod
Return list of all supported tags.
default_tag(**conditions)
classmethod
Resolve the default tag for a given experimental context.
Uses largest-subset matching: the rule whose key is the
biggest subset of the given conditions wins. A rule with an
empty key (frozenset()) acts as a universal fallback.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
**conditions
|
object
|
Experimental-axis values, e.g.
|
{}
|
Returns:
| Type | Description |
|---|---|
str
|
The resolved default tag string. |
Raises:
| Type | Description |
|---|---|
ValueError
|
If no rule matches the given conditions. |
create(tag, **kwargs)
classmethod
Instantiate a registered class by tag.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
tag
|
str
|
|
required |
**kwargs
|
object
|
Forwarded to the class constructor. |
{}
|
Returns:
| Type | Description |
|---|---|
object
|
A new instance of the registered class. |
Raises:
| Type | Description |
|---|---|
ValueError
|
If tag is not in the registry. |
create_default_for(**conditions)
classmethod
Instantiate the default class for a given context.
Combines default_tag(**conditions) with create(tag).
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
**conditions
|
object
|
Experimental-axis values. |
{}
|
Returns:
| Type | Description |
|---|---|
object
|
A new instance of the default class. |
supported_for(*, calculator=None, sample_form=None, scattering_type=None, beam_mode=None, radiation_probe=None)
classmethod
Return classes matching conditions and/or calculator.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
calculator
|
object
|
Optional |
None
|
sample_form
|
object
|
Optional |
None
|
scattering_type
|
object
|
Optional |
None
|
beam_mode
|
object
|
Optional |
None
|
radiation_probe
|
object
|
Optional |
None
|
Returns:
| Type | Description |
|---|---|
list[type]
|
Classes matching the given conditions. |
show_supported(*, calculator=None, sample_form=None, scattering_type=None, beam_mode=None, radiation_probe=None)
classmethod
Pretty-print a table of supported types.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
calculator
|
object
|
Optional |
None
|
sample_form
|
object
|
Optional |
None
|
scattering_type
|
object
|
Optional |
None
|
beam_mode
|
object
|
Optional |
None
|
radiation_probe
|
object
|
Optional |
None
|
space_group_wyckoff
Modules:
| Name | Description |
|---|---|
default |
Derived space-group Wyckoff category. |
factory |
Space-group Wyckoff factory — delegates entirely to |
Classes
Modules
default
Derived space-group Wyckoff category.
Defines :class:SpaceGroupWyckoff items and the read-only
:class:SpaceGroupWyckoffCollection. Rows are derived from the bundled
space-group table for the structure's current space group; they are not
user-edited. Structure rebuilds the collection when the space group
changes via
:meth:SpaceGroupWyckoffCollection._replace_from_space_group.
Classes:
| Name | Description |
|---|---|
SpaceGroupWyckoff |
A single Wyckoff position of the space group (all fields read-only). |
SpaceGroupWyckoffCollection |
Read-only collection of derived Wyckoff positions. |
SpaceGroupWyckoff()
A single Wyckoff position of the space group (all fields read-only).
Methods:
| Name | Description |
|---|---|
__str__ |
Human-readable representation of this component. |
__repr__ |
Return the developer representation of this object. |
__getattr__ |
Raise a descriptive error for unknown attribute access. |
__setattr__ |
Set an attribute with access-control diagnostics. |
help |
Print parameters, other properties, and methods. |
from_cif |
Populate this item from a CIF block. |
Attributes:
| Name | Type | Description |
|---|---|---|
id |
StringDescriptor
|
Read-only Wyckoff-position identifier. |
letter |
StringDescriptor
|
Read-only Wyckoff letter. |
multiplicity |
IntegerDescriptor
|
Read-only multiplicity. |
site_symmetry |
StringDescriptor
|
Read-only site-symmetry symbol. |
coords_xyz |
StringDescriptor
|
Read-only orbit coordinates. |
unique_name |
str
|
Fully qualified name: datablock, category, entry. |
parameters |
list
|
All GenericDescriptorBase instances on this item. |
as_cif |
str
|
Return CIF representation of this object. |
id
property
Read-only Wyckoff-position identifier.
letter
property
Read-only Wyckoff letter.
multiplicity
property
Read-only multiplicity.
site_symmetry
property
Read-only site-symmetry symbol.
coords_xyz
property
Read-only orbit coordinates.
unique_name
property
Fully qualified name: datablock, category, entry.
parameters
property
All GenericDescriptorBase instances on this item.
as_cif
property
Return CIF representation of this object.
__str__()
Human-readable representation of this component.
__repr__()
Return the developer representation of this object.
__getattr__(key)
Raise a descriptive error for unknown attribute access.
__setattr__(key, value)
Set an attribute with access-control diagnostics.
help()
Print parameters, other properties, and methods.
from_cif(block, idx=0)
Populate this item from a CIF block.
SpaceGroupWyckoffCollection()
Read-only collection of derived Wyckoff positions.
Methods:
| Name | Description |
|---|---|
add |
Reject public mutation; the collection is derived (read-only). |
create |
Reject public mutation; the collection is derived (read-only). |
remove |
Reject public mutation; the collection is derived (read-only). |
__setitem__ |
Reject item assignment; the collection is derived (read-only). |
__delitem__ |
Reject item deletion; the collection is derived (read-only). |
from_cif |
Ignore incoming CIF values for this derived category. |
__str__ |
Human-readable representation of this component. |
__repr__ |
Return the developer representation of this object. |
__getattr__ |
Raise a descriptive error for unknown attribute access. |
__setattr__ |
Set an attribute with access-control diagnostics. |
help |
Print a summary of public attributes and contained items. |
__getitem__ |
Return an item by name or positional index. |
__contains__ |
Check whether an item with the given key exists. |
__iter__ |
Iterate over items in insertion order. |
__len__ |
Return the number of items in the collection. |
keys |
Yield keys for all items in insertion order. |
values |
Yield items in insertion order. |
items |
Yield |
Attributes:
| Name | Type | Description |
|---|---|---|
unique_name |
str | None
|
Return None; collections have no unique name. |
parameters |
list
|
All parameters from all items in this collection. |
as_cif |
str
|
Return CIF representation of this object. |
names |
list[str | None]
|
List of all item keys in the collection. |
scalar_descriptors |
list
|
Collection-level descriptors serialized outside the loop. |
unique_name
property
Return None; collections have no unique name.
parameters
property
All parameters from all items in this collection.
as_cif
property
Return CIF representation of this object.
names
property
List of all item keys in the collection.
scalar_descriptors
property
Collection-level descriptors serialized outside the loop.
add(item)
Reject public mutation; the collection is derived (read-only).
create(**kwargs)
Reject public mutation; the collection is derived (read-only).
remove(name)
Reject public mutation; the collection is derived (read-only).
__setitem__(name, item)
Reject item assignment; the collection is derived (read-only).
__delitem__(name)
Reject item deletion; the collection is derived (read-only).
from_cif(block)
Ignore incoming CIF values for this derived category.
The Wyckoff table is derived from the structure's space group
and is never read back from a CIF file: any
_space_group_Wyckoff.* loop in incoming CIF (for example a
hand-edited project file) is discarded and the table is rebuilt
from the space group on the next update.
__str__()
Human-readable representation of this component.
__repr__()
Return the developer representation of this object.
__getattr__(key)
Raise a descriptive error for unknown attribute access.
__setattr__(key, value)
Set an attribute with access-control diagnostics.
help()
Print a summary of public attributes and contained items.
__getitem__(key)
Return an item by name or positional index.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
key
|
str | int
|
Identity key (str) or zero-based positional index (int). |
required |
Returns:
| Type | Description |
|---|---|
GuardedBase
|
The item matching the given key or index. |
Raises:
| Type | Description |
|---|---|
TypeError
|
If key is neither |
__contains__(name)
Check whether an item with the given key exists.
__iter__()
Iterate over items in insertion order.
__len__()
Return the number of items in the collection.
keys()
Yield keys for all items in insertion order.
values()
Yield items in insertion order.
items()
Yield (key, item) pairs in insertion order.
factory
Space-group Wyckoff factory — delegates entirely to FactoryBase.
Classes:
| Name | Description |
|---|---|
SpaceGroupWyckoffFactory |
Create space-group Wyckoff collections by tag. |
SpaceGroupWyckoffFactory
Create space-group Wyckoff collections by tag.
Methods:
| Name | Description |
|---|---|
__init_subclass__ |
Give each subclass its own independent registry and rules. |
register |
Class decorator to register a concrete class. |
supported_tags |
Return list of all supported tags. |
default_tag |
Resolve the default tag for a given experimental context. |
create |
Instantiate a registered class by tag. |
create_default_for |
Instantiate the default class for a given context. |
supported_for |
Return classes matching conditions and/or calculator. |
show_supported |
Pretty-print a table of supported types. |
__init_subclass__(**kwargs)
Give each subclass its own independent registry and rules.
register(klass)
classmethod
Class decorator to register a concrete class.
Usage::
@SomeFactory.register class MyClass(SomeBase): type_info = TypeInfo(...)
Returns the class unmodified.
supported_tags()
classmethod
Return list of all supported tags.
default_tag(**conditions)
classmethod
Resolve the default tag for a given experimental context.
Uses largest-subset matching: the rule whose key is the
biggest subset of the given conditions wins. A rule with an
empty key (frozenset()) acts as a universal fallback.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
**conditions
|
object
|
Experimental-axis values, e.g.
|
{}
|
Returns:
| Type | Description |
|---|---|
str
|
The resolved default tag string. |
Raises:
| Type | Description |
|---|---|
ValueError
|
If no rule matches the given conditions. |
create(tag, **kwargs)
classmethod
Instantiate a registered class by tag.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
tag
|
str
|
|
required |
**kwargs
|
object
|
Forwarded to the class constructor. |
{}
|
Returns:
| Type | Description |
|---|---|
object
|
A new instance of the registered class. |
Raises:
| Type | Description |
|---|---|
ValueError
|
If tag is not in the registry. |
create_default_for(**conditions)
classmethod
Instantiate the default class for a given context.
Combines default_tag(**conditions) with create(tag).
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
**conditions
|
object
|
Experimental-axis values. |
{}
|
Returns:
| Type | Description |
|---|---|
object
|
A new instance of the default class. |
supported_for(*, calculator=None, sample_form=None, scattering_type=None, beam_mode=None, radiation_probe=None)
classmethod
Return classes matching conditions and/or calculator.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
calculator
|
object
|
Optional |
None
|
sample_form
|
object
|
Optional |
None
|
scattering_type
|
object
|
Optional |
None
|
beam_mode
|
object
|
Optional |
None
|
radiation_probe
|
object
|
Optional |
None
|
Returns:
| Type | Description |
|---|---|
list[type]
|
Classes matching the given conditions. |
show_supported(*, calculator=None, sample_form=None, scattering_type=None, beam_mode=None, radiation_probe=None)
classmethod
Pretty-print a table of supported types.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
calculator
|
object
|
Optional |
None
|
sample_form
|
object
|
Optional |
None
|
scattering_type
|
object
|
Optional |
None
|
beam_mode
|
object
|
Optional |
None
|
radiation_probe
|
object
|
Optional |
None
|
collection
Collection of structure data blocks.
Classes:
| Name | Description |
|---|---|
Structures |
Ordered collection of :class: |
Classes
Structures()
Ordered collection of :class:Structure instances.
Provides convenience add_from_* methods that mirror the
:class:StructureFactory classmethods plus a bare :meth:add for
inserting pre-built structures.
Methods:
| Name | Description |
|---|---|
create |
Create a minimal structure and add it to the collection. |
add_from_cif_str |
Create a structure from CIF content and add it. |
add_from_cif_path |
Create a structure from a CIF file and add it. |
show_names |
List all structure names in the collection. |
show_params |
Show parameters of all structures in the collection. |
__str__ |
Human-readable representation of this component. |
__repr__ |
Return the developer representation of this object. |
__getattr__ |
Raise a descriptive error for unknown attribute access. |
__setattr__ |
Set an attribute with access-control diagnostics. |
help |
Print a summary of public attributes and contained items. |
__getitem__ |
Return an item by name or positional index. |
__setitem__ |
Insert or replace an item under the given identity key. |
__delitem__ |
Delete an item by key or raise |
__contains__ |
Check whether an item with the given key exists. |
__iter__ |
Iterate over items in insertion order. |
__len__ |
Return the number of items in the collection. |
remove |
Remove an item by its key. |
keys |
Yield keys for all items in insertion order. |
values |
Yield items in insertion order. |
items |
Yield |
add |
Add a pre-built item to the collection. |
Attributes:
| Name | Type | Description |
|---|---|---|
unique_name |
str | None
|
Return None; collections have no unique name. |
parameters |
list
|
All parameters from all datablocks in this collection. |
as_cif |
str
|
Return CIF representation of this object. |
names |
list[str | None]
|
List of all item keys in the collection. |
fittable_parameters |
list
|
All Parameters not blocked by constraints or symmetry. |
free_parameters |
list
|
All fittable parameters that are currently marked as free. |
Attributes
unique_name
property
Return None; collections have no unique name.
parameters
property
All parameters from all datablocks in this collection.
as_cif
property
Return CIF representation of this object.
names
property
List of all item keys in the collection.
fittable_parameters
property
All Parameters not blocked by constraints or symmetry.
free_parameters
property
All fittable parameters that are currently marked as free.
Functions
create(*, name)
Create a minimal structure and add it to the collection.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
name
|
str
|
Identifier for the new structure. |
required |
add_from_cif_str(cif_str)
Create a structure from CIF content and add it.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
cif_str
|
str
|
CIF file content as a string. |
required |
add_from_cif_path(cif_path)
Create a structure from a CIF file and add it.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
cif_path
|
str
|
Filesystem path to a CIF file. |
required |
show_names()
List all structure names in the collection.
show_params()
Show parameters of all structures in the collection.
__str__()
Human-readable representation of this component.
__repr__()
Return the developer representation of this object.
__getattr__(key)
Raise a descriptive error for unknown attribute access.
__setattr__(key, value)
Set an attribute with access-control diagnostics.
help()
Print a summary of public attributes and contained items.
__getitem__(key)
Return an item by name or positional index.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
key
|
str | int
|
Identity key (str) or zero-based positional index (int). |
required |
Returns:
| Type | Description |
|---|---|
GuardedBase
|
The item matching the given key or index. |
Raises:
| Type | Description |
|---|---|
TypeError
|
If key is neither |
__setitem__(name, item)
Insert or replace an item under the given identity key.
__delitem__(name)
Delete an item by key or raise KeyError if missing.
__contains__(name)
Check whether an item with the given key exists.
__iter__()
Iterate over items in insertion order.
__len__()
Return the number of items in the collection.
remove(name)
Remove an item by its key.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
name
|
str
|
Identity key of the item to remove. |
required |
keys()
Yield keys for all items in insertion order.
values()
Yield items in insertion order.
items()
Yield (key, item) pairs in insertion order.
add(item)
Add a pre-built item to the collection.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
item
|
object
|
A |
required |
item
Modules:
| Name | Description |
|---|---|
base |
Structure datablock item. |
factory |
Factory for creating structure instances from various inputs. |
Modules
base
Structure datablock item.
Classes:
| Name | Description |
|---|---|
Structure |
Structure datablock item. |
Classes
Structure(*, name)
Structure datablock item.
Methods:
| Name | Description |
|---|---|
show_as_cif |
Render the CIF text for this structure in the terminal. |
__str__ |
Human-readable representation of this component. |
__repr__ |
Developer-oriented representation of this component. |
__getattr__ |
Raise a descriptive error for unknown attribute access. |
__setattr__ |
Set an attribute with access-control diagnostics. |
help |
Print a summary of public attributes and categories. |
Attributes:
| Name | Type | Description |
|---|---|---|
name |
str
|
Name identifier for this structure. |
cell |
Cell
|
Unit-cell category for this structure. |
space_group |
SpaceGroup
|
Space-group category for this structure. |
atom_sites |
AtomSites
|
Atom-sites collection for this structure. |
atom_site_aniso |
AtomSiteAnisoCollection
|
Anisotropic-ADP collection for this structure. |
geom |
Geom
|
Bond-geometry cutoffs for this structure. |
space_group_wyckoff |
SpaceGroupWyckoffCollection
|
Read-only Wyckoff table derived from the current space group. |
unique_name |
str | None
|
Unique name of this datablock item (from identity). |
parameters |
list
|
All parameters from all owned categories. |
as_cif |
str
|
Return CIF representation of this object. |
categories |
list
|
All category objects owned by this object, sorted by priority. |
name
property
writable
Name identifier for this structure.
Returns:
| Type | Description |
|---|---|
str
|
The structure's name. |
cell
property
writable
Unit-cell category for this structure.
space_group
property
writable
Space-group category for this structure.
atom_sites
property
writable
Atom-sites collection for this structure.
atom_site_aniso
property
writable
Anisotropic-ADP collection for this structure.
geom
property
writable
Bond-geometry cutoffs for this structure.
space_group_wyckoff
property
Read-only Wyckoff table derived from the current space group.
unique_name
property
Unique name of this datablock item (from identity).
parameters
property
All parameters from all owned categories.
as_cif
property
Return CIF representation of this object.
categories
property
All category objects owned by this object, sorted by priority.
show_as_cif()
Render the CIF text for this structure in the terminal.
__str__()
Human-readable representation of this component.
__repr__()
Developer-oriented representation of this component.
__getattr__(key)
Raise a descriptive error for unknown attribute access.
__setattr__(key, value)
Set an attribute with access-control diagnostics.
help()
Print a summary of public attributes and categories.
Functions
factory
Factory for creating structure instances from various inputs.
Provides individual class methods for each creation pathway:
from_scratch, from_cif_path, or from_cif_str.
Classes:
| Name | Description |
|---|---|
StructureFactory |
Create :class: |
Classes
StructureFactory()
Create :class:Structure instances from supported inputs.
Methods:
| Name | Description |
|---|---|
from_scratch |
Create a minimal default structure. |
from_cif_str |
Create a structure by parsing a CIF string. |
from_cif_path |
Create a structure by reading and parsing a CIF file. |
from_scratch(*, name)
classmethod
Create a minimal default structure.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
name
|
str
|
Identifier for the new structure. |
required |
Returns:
| Type | Description |
|---|---|
Structure
|
An empty structure with default categories. |
from_cif_str(cif_str)
classmethod
Create a structure by parsing a CIF string.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
cif_str
|
str
|
Raw CIF content. |
required |
Returns:
| Type | Description |
|---|---|
Structure
|
A populated structure instance. |
from_cif_path(cif_path)
classmethod
Create a structure by reading and parsing a CIF file.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
cif_path
|
str
|
Filesystem path to a CIF file. |
required |
Returns:
| Type | Description |
|---|---|
Structure
|
A populated structure instance. |