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ITG2e: after author proof corrections #80

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173905b
Dictionary file Topology.dic amended to accommodate proof corrections
Feb 20, 2024
7286e0a
Dictionary file Topology.dic amended to accommodate proof correct…
nautolycus Feb 20, 2024
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183 changes: 64 additions & 119 deletions Topology.dic
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Original file line number Diff line number Diff line change
Expand Up @@ -9,8 +9,8 @@ data_TOPOLOGY_CIF

_dictionary.title TOPOLOGY_CIF
_dictionary.class Instance
_dictionary.version 0.9.6
_dictionary.date 2024-02-13
_dictionary.version 0.9.7
_dictionary.date 2024-02-20
_dictionary.uri
https://raw.githubusercontent.com/COMCIFS/TopoCif/master/Topology.dic
_dictionary.ddl_conformance 4.1.0
Expand Down Expand Up @@ -54,51 +54,8 @@ save_TOPOL
_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
;
_import.get
[{'file':topo_examples.cif 'save':topol_examples}]

save_

Expand Down Expand Up @@ -169,7 +126,7 @@ save_topol_atom.element_symbol
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 '.'.
of the Periodic Table should be represented here as '.'.
;
_name.category_id topol_atom
_name.object_id element_symbol
Expand Down Expand Up @@ -288,9 +245,9 @@ save_topol_atom.translation
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_y and
_topol_atom.translation_z data items may be used to
describe separate components of the vector for CIF1 compatibility.
describe separate components of the vector for CIF 1 compatibility.
If this item is omitted or
assigned to '.' it is assumed to be equal to [0,0,0].
;
Expand Down Expand Up @@ -398,7 +355,7 @@ save_TOPOL_LINK
_description.text
;
The TOPOL_LINK category describes the crystal structure
connectivity and encodes the weighted colored
connectivity and encodes the weighted coloured
symmetry-labeled quotient graph, from which the whole
periodic net describing the overall topology of the crystal
structure can be restored. The definition of
Expand All @@ -408,8 +365,7 @@ save_TOPOL_LINK
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
_topol_link.node_id_1 and _topol_link.node_id_2. 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.
Expand Down Expand Up @@ -519,26 +475,6 @@ save_topol_link.multiplicity

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'
Expand Down Expand Up @@ -688,7 +624,7 @@ save_topol_link.translation_1
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_y and
_topol_link.translation_1_z data items may be used to
describe separate components of the vector.
;
Expand Down Expand Up @@ -785,7 +721,7 @@ save_topol_link.translation_2
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_y and
_topol_link.translation_2_z data items may be used to
describe separate components of the vector.
;
Expand Down Expand Up @@ -954,6 +890,7 @@ save_TOPOL_NET

Reference: Delgado-Friedrichs, O., Foster, M. D., O'Keeffe, M.,
Proserpio, D. M., Treacy, M. M. J. & Yaghi, O. M. (2005).
What do we know about three-periodic nets?
J. Solid State Chem. 178, 2533-2554,
DOI:10.1016/j.jssc.2005.06.037.
;
Expand All @@ -977,7 +914,8 @@ save_topol_net.genus
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,
(2005). Crystal nets as graphs: Terminology and definitions.
J. Solid State Chem. 178, 2480-2485,
DOI:10.1016/j.jssc.2005.06.011.
;
_name.category_id topol_net
Expand Down Expand Up @@ -1027,24 +965,6 @@ save_topol_net.label

save_

save_topol_net.overall_topology

_definition.id '_topol_net.overall_topology'
_definition.update 2018-01-30
_description.text
;
The overall topology symbol in an arbitrary form.
;
_name.category_id topol_net
_name.object_id overall_topology
_type.purpose Describe
_type.source Assigned
_type.container Single
_type.contents Text
_description_example.case 'face-centered cubic topology'

save_

save_topol_net.overall_topology_epinet

_definition.id '_topol_net.overall_topology_EPINET'
Expand All @@ -1070,7 +990,7 @@ save_topol_net.overall_topology_iza
_definition.update 2018-01-30
_description.text
;
The three-letters symbol for a Zeolite Framework Types that has
The three-letter symbol for a Zeolite Framework Types that has
been approved by the Structure Commission of the International
Zeolite Association (IZA-SC).

Expand All @@ -1097,7 +1017,9 @@ save_topol_net.overall_topology_rcsr
by O'Keeffe et al. (2008).

Reference: O'Keeffe, M., Peskov, M. A., Ramsden, S. J. & Yaghi, O. M.
(2008). Acc. Chem. Res. 41, 1782-1789, DOI:10.1021/ar800124u.
(2008). The Reticular Chemistry Structure Resource (RCSR) Database of,
and Symbols for, Crystal Nets. Acc. Chem. Res. 41, 1782-1789,
DOI:10.1021/ar800124u.
;
_name.category_id topol_net
_name.object_id overall_topology_RCSR
Expand All @@ -1118,8 +1040,9 @@ save_topol_net.overall_topology_sp
The overall topology symbol according to the nomenclature of
Fischer for sphere packings described by Koch et al. (2006).

Reference: Koch, E., Fischer, W. & Sowa, H. (2006). Acta Cryst.
A62, 152-167, DOI:10.1107/S010876730600362X.
Reference: Koch, E., Fischer, W. & Sowa, H. (2006). Interpenetration
of homogeneous sphere packings and of two-periodic layers of spheres.
Acta Cryst. A62, 152-167, DOI:10.1107/S010876730600362X.
;
_name.category_id topol_net
_name.object_id overall_topology_SP
Expand All @@ -1142,12 +1065,13 @@ save_topol_net.overall_topology_topos
(coordination numbers) of all independent nodes; D is one of the letters
C (chain), L (layer) or T (three-periodic) designating the dimensionality
of the net; and n enumerates non-isomorphic nets with a given ND sequence.
For finite (molecular) graphs the symbols NMK-n are used, where k is the
For finite (molecular) graphs the symbols NMk-n are used, where k is the
number of vertices (atoms) in the graph.

Reference: Aman, F., Asiri, A. M., Siddiqui, W. A., Arshad, M. N.,
Ashraf, A., Zakharov, N. S. & Blatov, V. A. (2014). Cryst. Eng. Comm,
16, 1963-1970, DOI:10.1039/C3CE42218F.
Ashraf, A., Zakharov, N. S. & Blatov, V. A. (2014). Multilevel
topological description of molecular packings in 1,2-benzothiazines.
Cryst. Eng. Comm, 16, 1963-1970, DOI:10.1039/C3CE42218F.
;
_name.category_id topol_net
_name.object_id overall_topology_TOPOS
Expand Down Expand Up @@ -1281,11 +1205,9 @@ save_TOPOL_NODE
_description.text
;
The TOPOL_NODE category, along with TOPOL_ATOM, describes the topological
properties, position, and chemical composition
of the nodes of the underlying net. The TOPOL_NODE category is optional.
It is only required for polyatomic nodes or in cases where the
label given to the node is different from _atom_site.label. Data items
_topol_node.fract_x, _topol_node.fract_y, and _topol_node.fract_z must be
properties, position and chemical composition
of the nodes of the underlying net. Data items
_topol_node.fract_x, _topol_node.fract_y and _topol_node.fract_z must be
present only if the node's position cannot be derived from
other data items in TOPOL_NODE or TOPOL_ATOM.
Fractional coordinates can be given in other
Expand All @@ -1294,6 +1216,8 @@ save_TOPOL_NODE
In the case of multiple nets, _topol_node.net_id is also required.

Reference: Blatov, V. A., O'Keeffe, M. & Proserpio, D. M. (2010).
Vertex-, face-, point-, Schl\"afli-, and Delaney-symbols in nets,
polyhedra and tilings: recommended terminology.
Cryst. Eng. Comm. 12, 44-48, DOI:10.1039/B910671E.
;
_name.category_id TOPOLOGY
Expand Down Expand Up @@ -1335,7 +1259,7 @@ save_topol_node.coordination_sequence_plain
_definition.update 2021-07-28
_description.text
;
A CIF1-compatible alternative representation of the coordination sequence
A CIF 1 compatible alternative representation of the coordination sequence
as plain text, as a quoted string of white-space-separated numbers.
;
_name.category_id topol_node
Expand All @@ -1355,7 +1279,7 @@ save_topol_node.extended_point_symbol
_definition.update 2021-10-20
_description.text
;
The extended point symbol of a N-coordinated node lists all shortest
The extended point symbol of an N-coordinated node lists all shortest
circuits for each of the N(N-1)/2 angles (pairs of edges) incident to
the node. It is written as A(a).B(b)... where A, B, ... designate sizes of
circuits, which meet at angles A, B, ..., and a, b, ... designate numbers
Expand All @@ -1375,13 +1299,13 @@ save_topol_node.extended_point_symbol
_description_example.case
_description_example.detail
6(2).6(2).6(2).6(2).6(2).6(2)
'ES for a vertex in the diamond structure'
'extended symbol for a vertex in the diamond structure'
4.6(2).4.8(3).6(2).6(2)
'ES for one vertex of feldspar net'
'extended symbol for one vertex of feldspar net'
7(2).9(2).7(3).7(3).7(3).7(3)
'ES for the vertex of qzd net'
'extended symbol for the vertex of qzd net'
4.4.4.4.6(3).6(3).6(5).6(5).6(5).6(5)
'ES for the vertex of 5-c sqp net'
'extended symbol for the vertex of 5-c sqp net'

save_

Expand Down Expand Up @@ -1639,10 +1563,14 @@ save_topol_node.vertex_symbol
loop_
_description_example.case
_description_example.detail
6(2).6(2).6(2).6(2).6(2).6(2) 'Vertex symbol for diamond'
4.6(2).4.8.6.6(2) 'VS for one vertex of feldspar net'
7(2).*.7(3).7(3).7(3).7(3) 'VS for the vertex of qzd net'
4.4.4.4.6.6.6(5).6(5).6(5).6(5) 'VS for the vertex of 5-c sqp net'
6(2).6(2).6(2).6(2).6(2).6(2)
'vertex symbol for diamond'
4.6(2).4.8.6.6(2)
'vertex symbol for one vertex of feldspar net'
7(2).*.7(3).7(3).7(3).7(3)
'vertex symbol for the vertex of qzd net'
4.4.4.4.6.6.6(5).6(5).6(5).6(5)
'vertex symbol for the vertex of 5-c sqp net'

save_

Expand Down Expand Up @@ -1677,7 +1605,7 @@ save_TOPOL_TILING
;
The TOPOL_TILING category describes the natural tiling
corresponding to the underlying net. A tiling is a
partition of crystal space using generalised polyhedra, and a
partition of crystal space using generalized polyhedra, and a
natural tiling is one for which tiles are the smallest possible
that conserve the full symmetry of the net and for which the
faces are all locally strong rings. This means that there is no
Expand All @@ -1688,7 +1616,8 @@ save_TOPOL_TILING
the number of faces of a given size in the tile.

Reference: Blatov, V. A., Delgado-Friedrichs, O., O'Keeffe M. &
Proserpio D. M. (2007). Acta Cryst. A63, 418-425,
Proserpio D. M. (2007). Three-periodic nets and tilings: natural
tilings for nets. Acta Cryst. A63, 418-425,
DOI:10.1107/S0108767307038287.
;
_name.category_id TOPOLOGY
Expand All @@ -1704,10 +1633,12 @@ save_topol_tiling.d_size
_description.text
;
The number of distinct (not symmetry-related) chambers in the
tiling as expressed by the Delaney Dress symbol or just D-symbol,
tiling as expressed by the Delaney-Dress symbol or just D-symbol,
as a measure of the complexity of the tiling (D-size).

Reference: Blatov, V. A., O'Keeffe, M. & Proserpio, D. M. (2010).
Vertex-, face-, point-, Schl\"afli-, and Delaney-symbols in nets,
polyhedra and tilings: recommended terminology.
Cryst. Eng. Comm. 12, 44-48, DOI:10.1039/B910671E.
;
_name.category_id topol_tiling
Expand Down Expand Up @@ -2038,4 +1969,18 @@ save_

Changed the _type.source attribute of all SU data items to 'Related'.
(A. Vaitkus)
;
0.9.7 2024-02-20
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;
Removed _topol_link.net_id and _topol_net.overall_topology in line
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with proof corrections of draft chapters 3.9 and 4.9 by Blatov et al.
(B. McMahon)

Replaced example placeholders in TOPOL category by _import.get of
associated topo_examples.cif file.
(B. McMahon)

Made various small style and punctuation changes to prepare for
publication in International Tables Volume G.
(B. McMahon)
;
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