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Topology.dic
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#\#CIF_2.0
################################################################################
# #
# Topology CIF dictionary #
# #
################################################################################
data_TOPOLOGY_CIF
_dictionary.title TOPOLOGY_CIF
_dictionary.class Instance
_dictionary.version 0.9.6
_dictionary.date 2024-05-15
_dictionary.uri
https://raw.githubusercontent.com/COMCIFS/TopoCif/master/Topology.dic
_dictionary.ddl_conformance 4.1.0
_dictionary.namespace CifCore
_description.text
;
The Topology CIF dictionary provides data items for describing crystal
structure topology.
;
save_TOPOLOGY
_definition.id TOPOLOGY
_definition.scope Category
_definition.class Head
_definition.update 2024-05-15
_description.text
;
This category is the parent of all categories in the dictionary.
;
_name.category_id TOPOLOGY_CIF
_name.object_id TOPOLOGY
_import.get
[{'file':cif_core.dic 'mode':Full 'save':CIF_CORE_HEAD}]
save_
save_TOPOL
_definition.id TOPOL
_definition.scope Category
_definition.class Set
_definition.update 2021-09-27
_description.text
;
The TOPOL category covers data on connectivity
between atoms and structural groups and the
related structural properties as calculated from
the ATOM, CELL and SPACE_GROUP data.
;
_name.category_id TOPOLOGY
_name.object_id TOPOL
loop_
_description_example.case
_description_example.detail
;
[ex 1]
;
;
Example 1
;
;
[ex 2]
;
;
Example 2
;
;
[ex 3]
;
;
Example 3
;
;
[ex 4]
;
;
Example 4
;
;
[ex 5]
;
;
Example 5
;
;
[ex 6]
;
;
Example 6
;
;
[ex 7]
;
;
Example 7
;
save_
save_topol.special_details
_definition.id '_topol.special_details'
_definition.update 2021-09-14
_description.text
;
A description of topological information not covered by the
existing data items in the topology categories.
;
_name.category_id topol
_name.object_id special_details
_type.purpose Describe
_type.source Assigned
_type.container Single
_type.contents Text
save_
save_TOPOL_ATOM
_definition.id TOPOL_ATOM
_definition.scope Category
_definition.class Loop
_definition.update 2021-08-29
_description.text
;
The TOPOL_ATOM category provides information on the atoms of the initial
structure that compose links or nodes of a net. The _topol_atom.atom_label
value must match a value for _atom_site.label.
;
_name.category_id TOPOLOGY
_name.object_id TOPOL_ATOM
_category_key.name '_topol_atom.id'
save_
save_topol_atom.atom_label
_definition.id '_topol_atom.atom_label'
_definition.update 2021-11-16
_description.text
;
A pointer to an atom that is associated with a link or a node
(not including link end-point atoms). It must coincide with a
value given for _atom_site.label.
;
_name.category_id topol_atom
_name.object_id atom_label
_name.linked_item_id '_atom_site.label'
_type.purpose Link
_type.source Related
_type.container Single
_type.contents Word
save_
save_topol_atom.element_symbol
_definition.id '_topol_atom.element_symbol'
_definition.update 2021-09-05
_description.text
;
The element symbol for this atom, written in accordance with
the IUPAC systematic nomenclature for periodic elements. This should be
a single element symbol found on the official IUPAC Periodic Table.
For example: 'C', 'H', or 'Co', without isotope or charge.
Data items in the ATOM_SITE category that do not correspond to elements
of the periodic table should be represented here as '.'.
;
_name.category_id topol_atom
_name.object_id element_symbol
_type.purpose Encode
_type.source Assigned
_type.container Single
_type.contents Text
save_
save_topol_atom.id
_definition.id '_topol_atom.id'
_definition.update 2021-10-08
_description.text
;
The unique identifier of a topological "atom" that
is associated with a link or node.
;
_name.category_id topol_atom
_name.object_id id
_type.purpose Key
_type.source Assigned
_type.container Single
_type.contents Integer
_enumeration.range 1:
_units.code none
save_
save_topol_atom.link_id
_definition.id '_topol_atom.link_id'
_definition.update 2021-10-08
_description.text
;
The link associated with this atom, if applicable.
It must match a value provided for _topol_link.id. Note that this
association is in a bridging or molecular linker sense, not
the end points of the link. For example, a net may
specify a link that is composed of a carbonyl CO group or an
aromatic ring, representing those groups for the purposes of the net.
;
_name.category_id topol_atom
_name.object_id link_id
_name.linked_item_id '_topol_link.id'
_type.purpose Link
_type.source Related
_type.container Single
_type.contents Integer
_enumeration.range 1:
_units.code none
save_
save_topol_atom.node_id
_definition.id '_topol_atom.node_id'
_definition.update 2021-10-08
_description.text
;
The node associated with this atom, if applicable.
It must match a value provided for _topol_node.id.
;
_name.category_id topol_atom
_name.object_id node_id
_name.linked_item_id '_topol_node.id'
_type.purpose Link
_type.source Related
_type.container Single
_type.contents Integer
_enumeration.range 1:
_units.code none
save_
save_topol_atom.symop_id
_definition.id '_topol_atom.symop_id'
_definition.update 2021-11-16
_description.text
;
The identifier of the symmetry operation that is to be
applied to the coordinates of the atom given by
_topol_atom.atom_label before addition of
the translations given by _topol_atom.translation.
The value must match a value of _space_group_symop.id.
If this item is omitted or assigned to '.', the identity
operation is assumed.
;
_name.category_id topol_atom
_name.object_id symop_id
_name.linked_item_id '_space_group_symop.id'
_type.purpose Link
_type.source Derived
_type.container Single
_type.contents Integer
_enumeration.range 1:192
_enumeration.default 1
_units.code none
save_
save_topol_atom.translation
_definition.id '_topol_atom.translation'
_definition.update 2021-10-21
_description.text
;
The lattice translation vector that must be added to the
coordinates after application of the symmetry operation specified by
_topol_atom.symop_id to generate the atom belonging to
a link or a node. For example, if the symmetry operation
referred to by _topol_atom.symop_id is
(x-1/2,y+1/2,z), _topol_atom.translation is [0,-1,0]
and the original position is (0.2,0.7,1.0) in fractional coordinates,
then the resultant position is (-0.3,0.2,1.0). Alternatively,
_topol_atom.translation_x,
_topol_atom.translation_y, and
_topol_atom.translation_z data items may be used to
describe separate components of the vector for CIF1 compatibility.
If this item is omitted or
assigned to '.' it is assumed to be equal to [0,0,0].
;
_name.category_id topol_atom
_name.object_id translation
_type.purpose Number
_type.source Derived
_type.container Matrix
_type.dimension '[3]'
_type.contents Integer
_enumeration.default [0 0 0]
_units.code none
save_
save_topol_atom.translation_x
_definition.id '_topol_atom.translation_x'
_definition.update 2021-10-21
_description.text
;
The x component of the vector of lattice translations that is added
to the coordinates after application of the symmetry operation given by
_topol_atom.symop_id to generate an atom belonging to a link or a node.
Default value is 0.
;
_name.category_id topol_atom
_name.object_id translation_x
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Integer
_enumeration.default 0
_units.code none
save_
save_topol_atom.translation_y
_definition.id '_topol_atom.translation_y'
_definition.update 2021-10-21
_description.text
;
The y component of the vector of lattice translations that is added
to the coordinates after application of the symmetry operation given by
_topol_atom.symop_id to generate an atom belonging to a link or a node.
Default value is 0.
;
_name.category_id topol_atom
_name.object_id translation_y
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Integer
_enumeration.default 0
_units.code none
save_
save_topol_atom.translation_z
_definition.id '_topol_atom.translation_z'
_definition.update 2021-10-21
_description.text
;
The z component of the vector of lattice translations that is added
to the coordinates after application of the symmetry operation given by
_topol_atom.symop_id to generate an atom belonging to a link or a node.
Default value is 0.
;
_name.category_id topol_atom
_name.object_id translation_z
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Integer
_enumeration.default 0
_units.code none
save_
save_TOPOL_ENTANGL
_definition.id TOPOL_ENTANGL
_definition.scope Category
_definition.class Set
_definition.update 2018-01-30
_description.text
;
The TOPOL_ENTANGL category describes entanglements in the
underlying net. This category is a placeholder for future development
of descriptions of entanglement.
;
_name.category_id TOPOLOGY
_name.object_id TOPOL_ENTANGL
save_
save_TOPOL_LINK
_definition.id TOPOL_LINK
_definition.scope Category
_definition.class Loop
_definition.update 2021-10-11
_description.text
;
The TOPOL_LINK category describes the crystal structure
connectivity and encodes the weighted colored
symmetry-labeled quotient graph, from which the whole
periodic net describing the overall topology of the crystal
structure can be restored. The definition of
symmetry-labeled quotient graph was given by Klein (1996)
and examples of weights and colors for the graph edges and
vertices are provided by Blatov (2006). The
connections described in TOPOL_LINK may correspond to any
vectors in the structure, not just bonds or contacts. The two end-point
references are to nodes listed in TOPOL_NODE using
_topol_link.node_id_1 and _topol_link.node_id_2.
In the case of multiple nets, _topol_link.net_id is required. Other
items in this category are optional. If the link itself represents
atoms (as in the case of a molecular linker), the atoms comprising the
link must be referenced by _topol_atom.link_id.
References: Klein, H.-J. (1996). Systematic generation of models
for crystal structures. Math. Model. Sci. Comput. 6, 325-330;
Blatov, V. A. (2006). A method for hierarchical comparative
analysis of crystal structures. Acta Cryst. A62, 356-364,
DOI:10.1107/S0108767306025591.
;
_name.category_id TOPOLOGY
_name.object_id TOPOL_LINK
_category_key.name '_topol_link.id'
save_
save_topol_link.distance
_definition.id '_topol_link.distance'
_definition.update 2018-01-30
_description.text
;
The link length in angstroms.
;
_name.category_id topol_link
_name.object_id distance
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0.:
_units.code angstroms
save_
save_topol_link.distance_su
_definition.id '_topol_link.distance_su'
_definition.update 2023-07-11
_description.text
;
Standard uncertainty of _topol_link.distance.
;
_name.category_id topol_link
_name.object_id distance_su
_name.linked_item_id '_topol_link.distance'
_type.purpose SU
_type.source Related
_type.container Single
_type.contents Real
_units.code angstroms
save_
save_topol_link.id
_definition.id '_topol_link.id'
_definition.update 2021-10-08
_description.text
;
The identifier of the link.
;
_name.category_id topol_link
_name.object_id id
_type.purpose Key
_type.source Assigned
_type.container Single
_type.contents Integer
_enumeration.range 1:
_units.code none
save_
save_topol_link.label
_definition.id '_topol_link.label'
_definition.update 2021-09-12
_description.text
;
An optional not necessarily unique label for this link.
;
_name.category_id topol_link
_name.object_id label
_type.purpose Encode
_type.source Assigned
_type.container Single
_type.contents Text
save_
save_topol_link.multiplicity
_definition.id '_topol_link.multiplicity'
_definition.update 2021-10-08
_description.text
;
The number of these links in the unit cell.
;
_name.category_id topol_link
_name.object_id multiplicity
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Integer
_enumeration.range 1:
_units.code none
save_
save_topol_link.net_id
_definition.id '_topol_link.net_id'
_definition.update 2021-10-08
_description.text
;
The identifier of the net, to which this node belongs.
;
_name.category_id topol_link
_name.object_id net_id
_name.linked_item_id '_topol_net.id'
_type.purpose Link
_type.source Related
_type.container Single
_type.contents Integer
_enumeration.range 1:
_units.code none
save_
save_topol_link.node_id_1
_definition.id '_topol_link.node_id_1'
_definition.update 2021-10-11
_description.text
;
The identifier of the first node associated with a link
This must match a _topol_node.id value.
;
_name.category_id topol_link
_name.object_id node_id_1
_name.linked_item_id '_topol_node.id'
_type.purpose Link
_type.source Related
_type.container Single
_type.contents Integer
_enumeration.range 1:
_units.code none
save_
save_topol_link.node_id_2
_definition.id '_topol_link.node_id_2'
_definition.update 2021-10-11
_description.text
;
The identifier of the second node associated with a link
This must match a _topol_node.id value.
;
_name.category_id topol_link
_name.object_id node_id_2
_name.linked_item_id '_topol_node.id'
_type.purpose Link
_type.source Related
_type.container Single
_type.contents Integer
_enumeration.range 1:
_units.code none
save_
save_topol_link.order
_definition.id '_topol_link.order'
_definition.update 2021-10-08
_description.text
;
The number of electron pairs participating in the bond
described by _topol_link.type.
;
_name.category_id topol_link
_name.object_id order
_type.purpose Number
_type.source Assigned
_type.container Single
_type.contents Real
_units.code none
save_
save_topol_link.special_details
_definition.id '_topol_link.special_details'
_definition.update 2021-09-14
_description.text
;
Information about the link that is not expressed using other
data items, for example, bond subtypes and explanations
of links with _topol_link.type of 'sb'.
;
_name.category_id topol_link
_name.object_id special_details
_type.purpose Describe
_type.source Assigned
_type.container Single
_type.contents Text
save_
save_topol_link.symop_id_1
_definition.id '_topol_link.symop_id_1'
_definition.update 2021-11-16
_description.text
;
The identifier of the symmetry operation that is to be
applied to the coordinates of the node given by
_topol_link.node_id_1 before addition of
the translations given by _topol_link.translation_1.
The value must match a value of _space_group_symop.id.
If this item is omitted or assigned to '.', the identity
operation is assumed.
;
_name.category_id topol_link
_name.object_id symop_id_1
_name.linked_item_id '_space_group_symop.id'
_type.purpose Link
_type.source Derived
_type.container Single
_type.contents Integer
_enumeration.range 1:192
_enumeration.default 1
_units.code none
save_
save_topol_link.symop_id_2
_definition.id '_topol_link.symop_id_2'
_definition.update 2021-11-16
_description.text
;
The identifier of the symmetry operation that is to be
applied to the coordinates of the node given by
_topol_link.node_id_2 before addition of
the translations given by _topol_link.translation_2.
The value must match a value of _space_group_symop.id.
If this item is omitted or assigned to '.', the identity
operation is assumed.
;
_name.category_id topol_link
_name.object_id symop_id_2
_name.linked_item_id '_space_group_symop.id'
_type.purpose Link
_type.source Derived
_type.container Single
_type.contents Integer
_enumeration.range 1:192
_enumeration.default 1
_units.code none
save_
save_topol_link.translation_1
_definition.id '_topol_link.translation_1'
_definition.update 2021-10-21
_description.text
;
The lattice translation vector that must be added to the
coordinates after application of the symmetry operation given by
_topol_link.symop_id_1 to generate the node used in
calculating the link. For example, if the symmetry operation
referred to by _topol_link.symop_id_1 is
(x-1/2,y+1/2,z), _topol_link.translation_1 is [0,-1,0]
and the original position is (0.2,0.7,1.0) in fractional coordinates,
then the resultant position is (-0.3,0.2,1.0). Alternatively,
_topol_link.translation_1_x,
_topol_link.translation_1_y, and
_topol_link.translation_1_z data items may be used to
describe separate components of the vector.
;
_name.category_id topol_link
_name.object_id translation_1
_type.purpose Number
_type.source Derived
_type.container Matrix
_type.dimension '[3]'
_type.contents Integer
_enumeration.default [0 0 0]
_units.code none
save_
save_topol_link.translation_1_x
_definition.id '_topol_link.translation_1_x'
_definition.update 2021-10-21
_description.text
;
The x component of the vector of lattice translations that is added
to the coordinates after application of the symmetry operation given by
_topol_link.symop_id_1 to generate the node used in
calculating the link.
;
_name.category_id topol_link
_name.object_id translation_1_x
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Integer
_enumeration.default 0
_units.code none
save_
save_topol_link.translation_1_y
_definition.id '_topol_link.translation_1_y'
_definition.update 2021-10-21
_description.text
;
The y component of the vector of lattice translations that is added
to the coordinates after application of the symmetry operation given by
_topol_link.symop_id_1 to generate the node used in
calculating the link.
;
_name.category_id topol_link
_name.object_id translation_1_y
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Integer
_enumeration.default 0
_units.code none
save_
save_topol_link.translation_1_z
_definition.id '_topol_link.translation_1_z'
_definition.update 2021-10-21
_description.text
;
The z component of the vector of lattice translations that is added
to the coordinates after application of the symmetry operation given by
_topol_link.symop_id_1 to generate the node used in
calculating the link.
;
_name.category_id topol_link
_name.object_id translation_1_z
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Integer
_enumeration.default 0
_units.code none
save_
save_topol_link.translation_2
_definition.id '_topol_link.translation_2'
_definition.update 2021-10-21
_description.text
;
The lattice translation vector that must be added to the
coordinates after application of the symmetry operation given by
_topol_link.symop_id_2 to generate the node used in
calculating the link. For example, if the symmetry operation
referred to by _topol_link.symop_id_2 is
(x-1/2,y+1/2,z), _topol_link.translation_2 is [0,-1,0]
and the original position is (0.2,0.7,1.0) in fractional coordinates,
then the resultant position is (-0.3,0.2,1.0). Alternatively,
_topol_link.translation_2_x,
_topol_link.translation_2_y, and
_topol_link.translation_2_z data items may be used to
describe separate components of the vector.
;
_name.category_id topol_link
_name.object_id translation_2
_type.purpose Number
_type.source Derived
_type.container Matrix
_type.dimension '[3]'
_type.contents Integer
_enumeration.default [0 0 0]
_units.code none
save_
save_topol_link.translation_2_x
_definition.id '_topol_link.translation_2_x'
_definition.update 2021-10-21
_description.text
;
The x component of the vector of lattice translations that is added
to the coordinates after application of the symmetry operation given by
_topol_link.symop_id_2 to generate the node used in
calculating the link.
;
_name.category_id topol_link
_name.object_id translation_2_x
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Integer
_enumeration.default 0
_units.code none
save_
save_topol_link.translation_2_y
_definition.id '_topol_link.translation_2_y'
_definition.update 2021-10-21
_description.text
;
The y component of the vector of lattice translations that is added
to the coordinates after application of the symmetry operation given by
_topol_link.symop_id_2 to generate the node used in
calculating the link.
;
_name.category_id topol_link
_name.object_id translation_2_y
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Integer
_enumeration.default 0
_units.code none
save_
save_topol_link.translation_2_z
_definition.id '_topol_link.translation_2_z'
_definition.update 2021-10-21
_description.text
;
The z component of the vector of lattice translations that is added
to the coordinates after application of the symmetry operation given by
_topol_link.symop_id_2 to generate the node used in
calculating the link.
;
_name.category_id topol_link
_name.object_id translation_2_z
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Integer
_enumeration.default 0
_units.code none
save_
save_topol_link.type
_definition.id '_topol_link.type'
_definition.update 2021-09-17
_description.text
;
The chemical bond type associated with the connection between the
two sites. If no bond exists, use an undelimited period character.
If the bond type is unknown, use ? or leave out the data item. The
number of electron pairs participating in the bond can be indicated
using _topol_link.order. The value 'sb' or 'gl' should be used for
any case where the connection is not a bond between two atoms.
;
_name.category_id topol_link
_name.object_id type
_type.purpose State
_type.source Assigned
_type.container Single
_type.contents Code
loop_
_enumeration_set.state
_enumeration_set.detail
ar 'aromatic bond'
v 'valence bond'
pi 'pi bond'
hb 'hydrogen bond'
vw 'van der Waals contact'
sb 'special bond type described in _topol_link.special_details'
gl 'generic link'
save_
save_topol_link.voronoi_solid_angle
_definition.id '_topol_link.Voronoi_solid_angle'
_definition.update 2021-09-15
_description.text
;
The solid angle fraction of the interatomic contact A-X, which is
the percentage of the sphere of unit radius cut by the pyramid with the
basal face of the Voronoi polyhedron of A or X, the two atoms defining
the contact. The total solid angle (the whole sphere) is equal to 100.
The face used is that corresponding to the A-X interatomic contact.
;
_name.category_id topol_link
_name.object_id Voronoi_solid_angle
_type.purpose Measurand
_type.source Derived
_type.container Single
_type.contents Real
_enumeration.range 0:50
_units.code none
save_
save_topol_link.voronoi_solid_angle_su
_definition.id '_topol_link.Voronoi_solid_angle_su'
_definition.update 2023-07-11
_description.text
;
Standard uncertainty of _topol_link.Voronoi_solid_angle.
;
_name.category_id topol_link
_name.object_id Voronoi_solid_angle_su
_name.linked_item_id '_topol_link.Voronoi_solid_angle'
_type.purpose SU
_type.source Related
_type.container Single
_type.contents Real
_units.code none
save_
save_TOPOL_NET
_definition.id TOPOL_NET
_definition.scope Category
_definition.class Loop
_definition.update 2021-09-15
_description.text
;
The TOPOL_NET category describes an atomic network or underlying net.
Reference: Delgado-Friedrichs, O., Foster, M. D., O'Keeffe, M.,
Proserpio, D. M., Treacy, M. M. J. & Yaghi, O. M. (2005).
J. Solid State Chem. 178, 2533-2554,
DOI:10.1016/j.jssc.2005.06.037.
;
_name.category_id TOPOLOGY
_name.object_id TOPOL_NET
_category_key.name '_topol_net.id'
save_
save_topol_net.genus
_definition.id '_topol_net.genus'
_definition.update 2021-10-08
_description.text
;
The genus of the underlying net, defined as the cyclomatic number of
its own quotient graph: g = 1 + e - v, where e and v are the number
of edges and vertices in the quotient graph. The quotient graph is
a finite graph that contains all of the information of the periodic
net: the vertices of the graph are the vertices of a translational
repeat unit and the edges are all the edges of the repeat unit.
Reference: Delgado-Friedrichs, O. & O'Keeffe, M.
(2005). J. Solid State Chem. 178, 2480-2485,
DOI:10.1016/j.jssc.2005.06.011.
;
_name.category_id topol_net
_name.object_id genus
_type.purpose Number
_type.source Derived
_type.container Single
_type.contents Integer
_units.code none
save_
save_topol_net.id
_definition.id '_topol_net.id'
_definition.update 2021-10-08
_description.text
;
The unique integer identifier for this net, generally