Data Item _pdbx_nonpoly_atom_coordination.geometry

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General

Item name: _pdbx_nonpoly_atom_coordination.geometry_generic
Category name: pdbx_nonpoly_atom_coordination
Attribute name: geometry_generic
Required in PDB entries: yes
Used in current PDB entries: No

Item Description

This data item translates the geometry output from a software program (for example, FindGeo or MetalCoord) into a unified naming scheme. As software programs sometimes have different names for the same geometry (for instance, 'tetrahedral' and 'tetrahedron' correspond to the same geometry), this data item provides a name for the geometry that is consistent regardless of the provenance to enhance findability.

Data Type

Data type code: line
Data type detail: char item types / multi-word items ...
Primitive data type code: char
Regular expression: [][ \t_(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*

Controlled Vocabulary

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Allowed Value	Details
ball
bent
cubic
cubic with vacancy
cuboctahedral
dodecahedral
hexagonal bipyramidal
hexagonal bipyramidal with vacancy
hexagonal planar
irregular
linear
linear bicapped
linear monocapped
octahedral
octahedral bicapped
octahedral monocapped
octahedral monocapped with vacancy
paired octahedral
penta trigonal planar
penta trigonal planar i
penta trigonal planar i i
penta trigonal planar v
pentagonal antiprismatic
pentagonal bipyramidal
pentagonal bipyramidal with vacancy
pentagonal prismatic
pyramidal
sandwich 4 2
sandwich 4 3
sandwich 4h 2
sandwich 4h 3
sandwich 4h 4
sandwich 4h 4h
sandwich 5 1
sandwich 5 2
sandwich 5 3
sandwich 5 4
sandwich 5 4 i
sandwich 5 4h
sandwich 5 4h v
sandwich 5 5
sandwich 5 5 4
sandwich 5 5 i
sandwich 5 5 star
sandwich 5 5 v
sandwich 5 5 v i
sandwich 5 5 v v
sandwich 5 5 v v 3d
sandwich 5 5o
sandwich 5 capped 1
sandwich 5 hexagonal pyramidal
sandwich 5 pentagonal pyramidal
sandwich 5 square pyramidal
sandwich 5 square pyramidal monocapped
sandwich 5 tricapped i
sandwich 5 tricapped v
sandwich 5h 3
sandwich 6 1
sandwich 6 2
sandwich 6 3
sandwich 6 4
sandwich 6 5
sandwich 6 5 v
sandwich 6 6
sandwich 6 6 triangle
sandwich 6 6 v
sandwich 6 trigonal pyramidal
sandwich 7 1
sandwich 7 2
sandwich 7 3
sandwich 7 5
sandwich 8 3
sandwich 8 4
sandwich 8 5
sandwich 8 5 i
sandwich 8 8
sandwich 8 8 i
sandwich 8 8 v
sandwich c5 5 i
seamine
square antiprismatic
square antiprismatic bicapped
square antiprismatic monocapped
square antiprismatic with vacancy
square non-planar
square planar
square planar bicapped
square planar monocapped
square pyramidal
square pyramidal with vacancy
t shape
tetrahedral
trigonal bipyramidal
trigonal bipyramidal with vacancy
trigonal planar
trigonal planar bicapped
trigonal planar monocapped
trigonal planar tricapped
trigonal prism tricapped
trigonal prismatic
trigonal prismatic all face capped
trigonal prismatic bicapped
trigonal prismatic monocapped
trigonal prismatic monocapped with vacancy
trigonal prismatic with vacancy
trigonal pyramidal

Controlled Vocabulary at Deposition