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generic_distance_restraint.dic
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## Preliminary definitions for describing generic distance restraints as requested in Issue 47
## on Github (https://github.com/ihmwg/IHM-dictionary/issues/47)
## Distance restraints are derived between selected features, which can be atoms, residues or
## a range of contiguous residues.
################################
## IHM_FEATURE_SELECTION_ATOM ##
################################
save_ihm_feature_selection_atom
_category.description
; Data items in the IHM_FEATURE_SELECTION_ATOM category provides the defintions
required to select specific atoms.
;
_category.id ihm_feature_selection_atom
_category.mandatory_code no
loop_
_category_key.name '_ihm_feature_selection_atom.ordinal_id'
loop_
_category_group.id 'inclusive_group'
'ihm_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 -
;
;
loop_
_ihm_feature_selection_atom.ordinal_id
_ihm_feature_selection_atom.feature_id
_ihm_feature_selection_atom.entity_id
_ihm_feature_selection_atom.asym_id
_ihm_feature_selection_atom.seq_id
_ihm_feature_selection_atom.comp_id
_ihm_feature_selection_atom.atom_id
1 1 3 C 17 LYS CB
2 2 3 C 206 LYS CB
3 3 3 C 38 LYS CB
4 4 3 C 400 LYS CB
5 5 3 C 400 LYS CB
6 6 3 C 400 LYS CB
7 7 3 C 735 LYS CB
8 8 3 C 735 LYS CB
9 9 3 C 865 LYS CB
10 10 3 C 865 LYS CB
11 11 4 D 103 LYS CB
12 12 4 D 103 LYS CB
# ... abbreviated ...
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_pdbx_category_context.type CONTRIBUTED
_pdbx_category_context.category_id ihm_feature_selection_atom
save_
save__ihm_feature_selection_atom.ordinal_id
_item_description.description
; A unique identifier for the category.
;
_item.name '_ihm_feature_selection_atom.ordinal_id'
_item.category_id ihm_feature_selection_atom
_item.mandatory_code yes
_item_type.code int
save_
save__ihm_feature_selection_atom.feature_id
_item_description.description
; An identifier for the selected atom feature.
;
_item.name '_ihm_feature_selection_atom.feature_id'
_item.category_id ihm_feature_selection_atom
_item.mandatory_code yes
_item_type.code int
save_
save__ihm_feature_selection_atom.entity_id
_item_description.description
; The entity identifier of the atom.
This data item is a pointer to _entity_poly_seq.entity_id in the ENTITY_POLY_SEQ category.
;
_item.name '_ihm_feature_selection_atom.entity_id'
_item.category_id ihm_feature_selection_atom
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_ihm_feature_selection_atom.entity_id'
_item_linked.parent_name '_entity_poly_seq.entity_id'
save_
save__ihm_feature_selection_atom.asym_id
_item_description.description
; An asym/strand identifier of the atom.
This data item is a pointer to _struct_asym.id in the
STRUCT_ASYM category.
;
_item.name '_ihm_feature_selection_atom.asym_id'
_item.category_id ihm_feature_selection_atom
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_ihm_feature_selection_atom.asym_id'
_item_linked.parent_name '_struct_asym.id'
save_
save__ihm_feature_selection_atom.comp_id
_item_description.description
; The component identifier of the atom.
This data item is a pointer to _entity_poly_seq.mon_id in the ENTITY_POLY_SEQ category.
;
_item.name '_ihm_feature_selection_atom.comp_id'
_item.category_id ihm_feature_selection_atom
_item.mandatory_code yes
_item_type.code ucode
_item_linked.child_name '_ihm_feature_selection_atom.comp_id'
_item_linked.parent_name '_entity_poly_seq.mon_id'
save_
save__ihm_feature_selection_atom.seq_id
_item_description.description
; The sequence index of the residue to which the atom belongs.
This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category.
;
_item.name '_ihm_feature_selection_atom.seq_id'
_item.category_id ihm_feature_selection_atom
_item.mandatory_code yes
_item_type.code int
_item_linked.child_name '_ihm_feature_selection_atom.seq_id'
_item_linked.parent_name '_entity_poly_seq.num'
save_
save__ihm_feature_selection_atom.atom_id
_item_description.description
; The identifier of the atom.
This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category.
;
_item.name '_ihm_feature_selection_atom.atom_id'
_item.category_id ihm_feature_selection_atom
_item.mandatory_code no
_item_type.code atcode
_item_linked.child_name '_ihm_feature_selection_atom.atom_id'
_item_linked.parent_name '_chem_comp_atom.atom_id'
save_
###################################
## IHM_FEATURE_SELECTION_RESIDUE ##
###################################
save_ihm_feature_selection_residue
_category.description
; Data items in the IHM_FEATURE_SELECTION_RESIDUE category provides the defintions
required to select a specific residue or a set of residues that may or may not be
in a contiguous range.
;
_category.id ihm_feature_selection_residue
_category.mandatory_code no
loop_
_category_key.name '_ihm_feature_selection_residue.ordinal_id'
loop_
_category_group.id 'inclusive_group'
'ihm_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 -
;
;
loop_
_ihm_feature_selection_residue.ordinal_id
_ihm_feature_selection_residue.feature_id
_ihm_feature_selection_residue.entity_id
_ihm_feature_selection_residue.asym_id
_ihm_feature_selection_residue.seq_id_begin
_ihm_feature_selection_residue.comp_id_begin
_ihm_feature_selection_residue.seq_id_end
_ihm_feature_selection_residue.comp_id_end
1 1 3 C 17 LYS 17 LYS # Single residue selection
2 2 3 C 206 LYS 206 LYS
3 3 3 C 38 THR 54 ALA # Residue range selection
4 4 3 C 400 LEU 428 PHE
5 5 3 C 429 GLN 429 GLN
6 6 3 C 461 LEU 478 ARG
7 7 3 C 735 ASP 735 ASP
8 8 3 C 865 SER 891 VAL
# ... abbreviated ...
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_pdbx_category_context.type CONTRIBUTED
_pdbx_category_context.category_id ihm_feature_selection_residue
save_
save__ihm_feature_selection_residue.ordinal_id
_item_description.description
; A unique identifier for the category.
;
_item.name '_ihm_feature_selection_residue.ordinal_id'
_item.category_id ihm_feature_selection_residue
_item.mandatory_code yes
_item_type.code int
save_
save__ihm_feature_selection_residue.feature_id
_item_description.description
; An identifier for the selected residue / residue range feature.
;
_item.name '_ihm_feature_selection_residue.feature_id'
_item.category_id ihm_feature_selection_residue
_item.mandatory_code yes
_item_type.code int
save_
save__ihm_feature_selection_residue.entity_id
_item_description.description
; The entity identifier for residue / residue range.
This data item is a pointer to _entity_poly_seq.entity_id in the ENTITY_POLY_SEQ category.
;
_item.name '_ihm_feature_selection_residue.entity_id'
_item.category_id ihm_feature_selection_residue
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_ihm_feature_selection_residue.entity_id'
_item_linked.parent_name '_entity_poly_seq.entity_id'
save_
save__ihm_feature_selection_residue.asym_id
_item_description.description
; An asym/strand identifier for the residue / residue range.
This data item is a pointer to _struct_asym.id in the
STRUCT_ASYM category.
;
_item.name '_ihm_feature_selection_residue.asym_id'
_item.category_id ihm_feature_selection_residue
_item.mandatory_code yes
_item_type.code code
_item_linked.child_name '_ihm_feature_selection_residue.asym_id'
_item_linked.parent_name '_struct_asym.id'
save_
save__ihm_feature_selection_residue.comp_id_begin
_item_description.description
; The component identifier of the beginning residue / residue range.
This data item is a pointer to _entity_poly_seq.mon_id in the ENTITY_POLY_SEQ category.
;
_item.name '_ihm_feature_selection_residue.comp_id_begin'
_item.category_id ihm_feature_selection_residue
_item.mandatory_code no
_item_type.code ucode
_item_linked.child_name '_ihm_feature_selection_residue.comp_id_begin'
_item_linked.parent_name '_entity_poly_seq.mon_id'
save_
save__ihm_feature_selection_residue.comp_id_end
_item_description.description
; The component identifier of the ending residue / residue range.
This data item is a pointer to _entity_poly_seq.mon_id in the ENTITY_POLY_SEQ category.
;
_item.name '_ihm_feature_selection_residue.comp_id_end'
_item.category_id ihm_feature_selection_residue
_item.mandatory_code no
_item_type.code ucode
_item_linked.child_name '_ihm_feature_selection_residue.comp_id_end'
_item_linked.parent_name '_entity_poly_seq.mon_id'
save_
save__ihm_feature_selection_residue.seq_id_begin
_item_description.description
; The sequence index of the beginning residue / residue range.
This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category.
;
_item.name '_ihm_feature_selection_residue.seq_id_begin'
_item.category_id ihm_feature_selection_residue
_item.mandatory_code yes
_item_type.code int
_item_linked.child_name '_ihm_feature_selection_residue.seq_id_begin'
_item_linked.parent_name '_entity_poly_seq.num'
save_
save__ihm_feature_selection_residue.seq_id_end
_item_description.description
; The sequence index of the ending residue / residue range.
This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category.
;
_item.name '_ihm_feature_selection_residue.seq_id_end'
_item.category_id ihm_feature_selection_residue
_item.mandatory_code yes
_item_type.code int
_item_linked.child_name '_ihm_feature_selection_residue.seq_id_end'
_item_linked.parent_name '_entity_poly_seq.num'
save_
####################################
## IHM_DERIVED_DISTANCE_RESTRAINT ##
####################################
save_ihm_derived_distance_restraint
_category.description
; Data items in the IHM_DERIVED_DISTANCE_RESTRAINT category records the
list of distance restraints used in the integrative modeling experiment.
These distance redistance restraints may be derived from various kinds of experiments.
;
_category.id ihm_derived_distance_restraint
_category.mandatory_code no
loop_
_category_key.name '_ihm_derived_distance_restraint.id'
loop_
_category_group.id 'inclusive_group'
'ihm_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 -
;
;
loop_
_ihm_derived_distance_restraint.id
_ihm_derived_distance_restraint.feature_id_1
_ihm_derived_distance_restraint.feature_type_1
_ihm_derived_distance_restraint.feature_id_2
_ihm_derived_distance_restraint.feature_type_2
_ihm_derived_distance_restraint.restraint_type
_ihm_derived_distance_restraint.distance_upper_limit
_ihm_derived_distance_restraint.probability
_ihm_derived_distance_restraint.dataset_list_id
1 7 'residue' 21 'residue' 'upper bound' 8.0 0.8 1
2 16 'residue' 19 'residue' 'upper bound' 8.0 0.5 1
3 8 'residue' 40 'residue' 'upper bound' 8.0 0.8 1
4 35 'residue' 43 'residue' 'upper bound' 8.0 0.6 1
5 23 'residue' 45 'residue' 'upper bound' 8.0 0.7 1
6 86 'residue' 94 'residue' 'upper bound' 8.0 0.7 1
7 63 'residue' 80 'residue' 'upper bound' 8.0 0.5 1
8 15 'residue' 33 'residue' 'upper bound' 8.0 0.5 1
9 41 'residue' 52 'residue' 'upper bound' 8.0 0.9 1
# ... abbreviated ...
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
_pdbx_category_context.type CONTRIBUTED
_pdbx_category_context.category_id ihm_derived_distance_restraint
save_
save__ihm_derived_distance_restraint.id
_item_description.description
; A unique identifier for the derived distance restraint.
;
_item.name '_ihm_derived_distance_restraint.id'
_item.category_id ihm_derived_distance_restraint
_item.mandatory_code yes
_item_type.code int
save_
save__ihm_derived_distance_restraint.group_id
_item_description.description
; An identifier to group the distance restraints.
;
_item.name '_ihm_derived_distance_restraint.group_id'
_item.category_id ihm_derived_distance_restraint
_item.mandatory_code no
_item_type.code int
save_
save__ihm_derived_distance_restraint.feature_id_1
_item_description.description
; The feature identifier for the first partner in the distance restraint.
This is a child of either _ihm_feature_selection_atom.feature_id or
ihm_feature_selection_residue.feature_id depending on the data in
_ihm_derived_distance_restraint.feature_type_1.
;
_item.name '_ihm_derived_distance_restraint.feature_id_1'
_item.category_id ihm_derived_distance_restraint
_item.mandatory_code yes
_item_type.code int
save_
save__ihm_derived_distance_restraint.feature_id_2
_item_description.description
; The feature identifier for the second partner in the distance restraint.
This is a child of either _ihm_feature_selection_atom.feature_id or
ihm_feature_selection_residue.feature_id depending on the data in
_ihm_derived_distance_restraint.feature_type_2.
;
_item.name '_ihm_derived_distance_restraint.feature_id_2'
_item.category_id ihm_derived_distance_restraint
_item.mandatory_code yes
_item_type.code int
save_
save__ihm_derived_distance_restraint.feature_type_1
_item_description.description
; The type of feature for the first partner in the distance restraint.
;
_item.name '_ihm_derived_distance_restraint.feature_type_1'
_item.category_id ihm_derived_distance_restraint
_item.mandatory_code yes
_item_type.code line
loop_
_item_enumeration.value
_item_enumeration.detail
'atom' 'feature is an atom or a set of atoms'
'residue' 'feature is a residue or a set of residues, each represented by the alpha carbon atom'
'residue range' 'feature is a set of residues in a contiguous range, each represented by the alpha carbon atom'
save_
save__ihm_derived_distance_restraint.feature_type_2
_item_description.description
; The type of feature for the second partner in the distance restraint.
;
_item.name '_ihm_derived_distance_restraint.feature_type_2'
_item.category_id ihm_derived_distance_restraint
_item.mandatory_code yes
_item_type.code line
loop_
_item_enumeration.value
_item_enumeration.detail
'atom' 'feature is an atom or a set of atoms'
'residue' 'feature is a residue or a set of residues, each represented by the alpha carbon atom'
'residue range' 'feature is a set of residues in a contiguous range, each represented by the alpha carbon atom'
save_
save__ihm_derived_distance_restraint.conditionality
_item_description.description
; If the feature is a set of atoms or a set of residues, the conditionality
based on which the restraint in applied in the modeling.
;
_item.name '_ihm_derived_distance_restraint.conditionality'
_item.category_id ihm_derived_distance_restraint
_item.mandatory_code no
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
'ALL' 'All distances among the group of atoms or residues are restrained'
'ANY' 'Any one of the distances among the group of atoms or residues could be satisfied'
save_
save__ihm_derived_distance_restraint.distance_lower_limit
_item_description.description
; The lower limit to the distance threshold applied to this distance restraint
in the intergrative modeling task.
;
_item.name '_ihm_derived_distance_restraint.distance_lower_limit'
_item.category_id ihm_derived_distance_restraint
_item.mandatory_code no
_item_type.code float
_item_units.code angstroms
save_
save__ihm_derived_distance_restraint.distance_upper_limit
_item_description.description
; The upper limit to the distance threshold applied to this distance restraint
in the intergrative modeling task.
;
_item.name '_ihm_derived_distance_restraint.distance_upper_limit'
_item.category_id ihm_derived_distance_restraint
_item.mandatory_code no
_item_type.code float
_item_units.code angstroms
save_
save__ihm_derived_distance_restraint.probability
_item_description.description
; The real number that indicates the probability that the distance restraint
is correct. This number should fall between 0.0 and 1.0.
;
_item.name '_ihm_derived_distance_restraint.probability'
_item.category_id ihm_derived_distance_restraint
_item.mandatory_code no
_item_type.code float
loop_
_item_range.minimum
_item_range.maximum
0.0 0.0
0.0 1.0
1.0 1.0
save_
save__ihm_derived_distance_restraint.restraint_type
_item_description.description
; The type of distance restraint applied.
;
_item.name '_ihm_derived_distance_restraint.restraint_type'
_item.category_id ihm_derived_distance_restraint
_item.mandatory_code yes
_item_type.code line
loop_
_item_enumeration.value
'lower bound'
'upper bound'
'lower and upper bound'
save_
save__ihm_derived_distance_restraint.dataset_list_id
_item_description.description
; Identifier to the input data from which the distance restraint is derived.
This data item is a pointer to the _ihm_dataset_list.id in the
IHM_DATASET_LIST category.
;
_item.name '_ihm_derived_distance_restraint.dataset_list_id'
_item.category_id ihm_derived_distance_restraint
_item.mandatory_code yes
_item_type.code int
_item_linked.child_name '_ihm_derived_distance_restraint.dataset_list_id'
_item_linked.parent_name '_ihm_dataset_list.id'
save_