CIF_COD_MOLECULE

Version: 0.001 (2022-09-19)

COD_MOLECULE_POLYMER

Category contains data items for calculated polymer properties.

_cod_molecule_is_polymer

This code signals whether the entry represents a part of a polymeric compound.

Values:

Default value: 'no'

COD_MOLECULE_ATOM

Data items from this category are used to describe details of atoms of restored molecules. Data items belonging to this category are written by the cif_molecule script from svn://www.crystallography.net/cod-tools repository. Data items belonging to this category are read by the cif_bonds_angles and some other scripts from svn://saulius-grazulis.lt/atomclasses repository.

Examples:

loop_
 _cod_molecule_atom_label
 _cod_molecule_atom_orig_label
 _cod_molecule_atom_symmetry
 _cod_molecule_atom_symop_id
 _cod_molecule_atom_symop_xyz
 _cod_molecule_atom_transl_id
 _cod_molecule_atom_transl_x
 _cod_molecule_atom_transl_y
 _cod_molecule_atom_transl_z
 _cod_molecule_atom_mult
 _cod_molecule_atom_mult_ratio

 Sr Sr 1_555 1 x,y,z 555 0 0 0 4 1

_cod_molecule_atom_label

Label of an atom, restored from asymmetric unit using symmetry operators.

_cod_molecule_atom_orig_label

Label denoting the original atom, from which symmetrically equivalent atom was restored.

_cod_molecule_atom_symmetry

Description of transformation applied to the original atom, producing the symmetry equivalent, in the form S_ABC, where S is the number of the symmetry operator, given in the _symmetry_equiv_pos_as_xyz list, and A-5, B-5 and C-5 denote the translation along the x, y and z axes respectively.

_cod_molecule_atom_symop_id

Number of the symmetry operator from the _symmetry_equiv_pos_as_xyz list, that was used to produce the symmetry equivalent of the original atom.

_cod_molecule_atom_symop_xyz

Symmetry operator, that was used to produce the symmetry equivalent of the original atom.

_cod_molecule_atom_transl_id

Translation identifier in the form of 'ABC', where A-5, B-5 and C-5 denotes translation along x, y and z axes respectively.

_cod_molecule_atom_transl_x

Translation along the x axis.

_cod_molecule_atom_transl_y

Translation along the y axis.

_cod_molecule_atom_transl_z

Translation along the z axis.

_cod_molecule_atom_mult

Number of total crystal symmetry operators divided by site's multiplicity ratio, as given in _cod_molecule_atom_mult_ratio.

_cod_molecule_atom_mult_ratio

Multiplicity ratio: number of crystal symmetry operators that map this atom site to itself.

_cod_molecule_atom_assembly

A code which identifies a cluster of atoms in the restored molecule that show long-range positional disorder but are locally ordered. Within each such cluster of atoms, _cod_molecule_atom_group is used to identify the sites that are simultaneously occupied. This field is only needed if there is more than one cluster of disordered atoms showing independent local order.

_cod_molecule_atom_group

A code which identifies a group of positionally disordered atom sites that are locally simultaneously occupied. Atoms that are positionally disordered over two or more sites (e.g. the hydrogen atoms of a methyl group that exists in two orientations) can be assigned to two or more groups. Sites belonging to the same group are simultaneously occupied, but those belonging to different groups are not.

COD_MOLECULE_TRANSFORM

Data items from this category are used to list symmetry operators mapping an original atom to each of its symmetry equivalents. Data items belonging to this category are written by the cif_molecule script from svn://www.crystallography.net/cod-tools repository. Data items belonging to this category are read by the cif_bonds_angles and some other scripts from svn://saulius-grazulis.lt/atomclasses repository.

Examples:

loop_
 _cod_molecule_transform_label
 _cod_molecule_transform_symop

 C1 x,y,z
 C3 x,y,z
 O1 x,y,z
 O2 x,y,z
 O5 x,y,z
 O7 x,y,z
 D3_4_555 x-0.5,-y-0.5,z-0.5

_cod_molecule_transform_label

Label of an atom restored from the asymmetric unit using symmetry operators.

_cod_molecule_transform_symop

Symmetry operator that maps the original atom to its symmetry equivalent.

COD_MOLECULE_SPACE_GROUP

Data items from the COD_MOLECULE_SPACE_GROUP category record the space group information of the input crystal structure.

_cod_molecule_space_group_IT_number

The number of the space group that the molecule was crystallised in. This number is derived from symmetry information provided in the input file and follows the conventions described in the International Tables for Crystallography, Volume A.