diff --git a/README.md b/README.md
index 9ee41fe0dd5710248f24c75f52a7c43a9cbd1e69..e81cadce51b1a9bffeb9d6f081ef9e8a3e4a7a3a 100644
--- a/README.md
+++ b/README.md
@@ -80,12 +80,11 @@ and navigate to `build/viewer`
### Code generation
**CIF schemas**
+Install CIFTools `npm install ciftools -g`
- export NODE_PATH="build/src"; node build/src/apps/schema-generator/schema-from-cif-dic.js -ts -o src/mol-io/reader/cif/schema/mmcif.ts --fieldNamesPath data/mmcif-field-names.csv --name mmCIF
-
- export NODE_PATH="build/src"; node build/src/apps/schema-generator/schema-from-cif-dic.js -ts -o src/mol-io/reader/cif/schema/ccd.ts --fieldNamesPath data/ccd-field-names.csv --name CCD
-
- export NODE_PATH="build/src"; node build/src/apps/schema-generator/schema-from-cif-dic.js -ts -o src/mol-io/reader/cif/schema/bird.ts --fieldNamesPath data/bird-field-names.csv --name BIRD
+ cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/mmcif.ts -p mmCIF
+ cifschema -mip ../../../../mol-data-o src/mol-io/reader/cif/schema/ccd.ts -p CCD
+ cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/bird.ts -p BIRD
**GraphQL schemas**
diff --git a/src/mol-io/reader/cif/schema/bird.ts b/src/mol-io/reader/cif/schema/bird.ts
index f35b02eb04004d9b981e2e50e5e3870d5d6f8303..29e5b0e4373c7ef39e11f0226b39a84777f83f42 100644
--- a/src/mol-io/reader/cif/schema/bird.ts
+++ b/src/mol-io/reader/cif/schema/bird.ts
@@ -1,9 +1,9 @@
/**
- * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
- * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.309, IHM 0.141, CARB draft.
+ * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.311, IHM 1.0, CARB draft.
*
- * @author mol-star package (src/apps/schema-generator/generate)
+ * @author molstar/ciftools package
*/
import { Database, Column } from '../../../../mol-data/db'
@@ -84,6 +84,10 @@ export const BIRD_Schema = {
* corresponding to the chemical definition for the molecule.
*/
chem_comp_id: str,
+ /**
+ * Special details about this molecule.
+ */
+ compound_details: str,
/**
* Description of this molecule.
*/
diff --git a/src/mol-io/reader/cif/schema/ccd.ts b/src/mol-io/reader/cif/schema/ccd.ts
index f65c958b4fcac4b040d474b221db867f9ecb0254..a4ee2576f384cc0816832e8b3d8d0f9134d0eda0 100644
--- a/src/mol-io/reader/cif/schema/ccd.ts
+++ b/src/mol-io/reader/cif/schema/ccd.ts
@@ -1,9 +1,9 @@
/**
- * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
- * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.309, IHM 0.141, CARB draft.
+ * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.311, IHM 1.0, CARB draft.
*
- * @author mol-star package (src/apps/schema-generator/generate)
+ * @author molstar/ciftools package
*/
import { Database, Column } from '../../../../mol-data/db'
@@ -167,6 +167,10 @@ export const CCD_Schema = {
* Date component was last modified.
*/
pdbx_modified_date: str,
+ /**
+ * This data item holds the current release status for the component.
+ */
+ pdbx_release_status: Aliased<'REL' | 'HOLD' | 'HPUB' | 'OBS' | 'DEL' | 'REF_ONLY'>(str),
/**
* This data item identifies the deposition site that processed
* this chemical component defintion.
diff --git a/src/mol-io/reader/cif/schema/mmcif.ts b/src/mol-io/reader/cif/schema/mmcif.ts
index 347fbb0766c622398254fc9285b773ef66c4ba46..10a092bb9de104cc6f6c8e2513fb7a8d344e3aa7 100644
--- a/src/mol-io/reader/cif/schema/mmcif.ts
+++ b/src/mol-io/reader/cif/schema/mmcif.ts
@@ -1,9 +1,9 @@
/**
- * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
- * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.310, IHM 0.141, CARB draft.
+ * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.311, IHM 1.0, CARB draft.
*
- * @author mol-star package (src/apps/schema-generator/generate)
+ * @author molstar/ciftools package
*/
import { Database, Column } from '../../../../mol-data/db'
@@ -590,7 +590,8 @@ export const mmCIF_Schema = {
*/
entity_poly_seq: {
/**
- * This data item is a pointer to _entity.id in the ENTITY category.
+ * This data item is a pointer to _entity_poly.entity_id in the
+ * ENTITY_POLY category.
*/
entity_id: str,
/**
@@ -2137,15 +2138,11 @@ export const mmCIF_Schema = {
*/
asym_id: str,
/**
- * The leading residue index for the sequence segment modeled using this starting model.
- * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category.
+ * The identifier for the polymeric segment modeled using this starting model.
+ * This data item is a pointer to _ihm_entity_poly_segment.id in the
+ * IHM_ENTITY_POLY_SEGMENT category.
*/
- seq_id_begin: int,
- /**
- * The trailing residue index for the sequence segment modeled using this starting model.
- * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category.
- */
- seq_id_end: int,
+ entity_poly_segment_id: int,
/**
* The source of the starting model.
*/
@@ -2180,7 +2177,7 @@ export const mmCIF_Schema = {
/**
* A unique identifier for the starting comparative model.
*/
- ordinal_id: int,
+ id: int,
/**
* The identifier for the starting structural model.
* This data item is a pointer to _ihm_starting_model_details.starting_model_id
@@ -2244,7 +2241,7 @@ export const mmCIF_Schema = {
/**
* A unique identifier for the entry.
*/
- ordinal_id: int,
+ id: int,
/**
* A unique identifier for the distinct molecular entities.
* This data item is a pointer to _entity_poly_seq.entity_id in the ENTITY_POLY category.
@@ -2293,25 +2290,46 @@ export const mmCIF_Schema = {
details: str,
},
/**
- * Data items in the IHM_MODEL_REPRESENTATION category records the
- * details about the architecture and representation of structural
- * models created by the integrative model building tasks. This
- * category handles the multi-scale model representation, if employed.
+ * Data items in the IHM_MODEL_REPRESENTATION category lists the
+ * various mono or multi-scale model representations used in the
+ * integrative modeling study.
*/
ihm_model_representation: {
/**
- * A unique identifier for the model details record.
+ * A unique identifier for the model representation.
*/
- ordinal_id: int,
+ id: int,
+ /**
+ * Name/brief description for the model representation.
+ */
+ name: str,
+ /**
+ * Additional details about the model representation.
+ */
+ details: str,
+ },
+ /**
+ * Data items in the IHM_MODEL_REPRESENTATION_DETAILS category records the
+ * details about the architecture and representation of structural
+ * models involved in the integrative modeling study.
+ */
+ ihm_model_representation_details: {
+ /**
+ * A unique identifier for the category.
+ */
+ id: int,
/**
* An identifier that collects or groups together a set of representations.
- * This data item may be used to identify a complete model representation.
+ * This data item is a pointer to _ihm_model_representation.id in the
+ * IHM_MODEL_REPRESENTATION category.
*/
representation_id: int,
/**
- * An identifier for the residue range segment within the structural model.
+ * The identifier for the polymeric segment in the representation.
+ * This data item is a pointer to _ihm_entity_poly_segment.id in the
+ * IHM_ENTITY_POLY_SEGMENT category.
*/
- segment_id: int,
+ entity_poly_segment_id: int,
/**
* A unique identifier distinct molecular entities.
* This data item is a pointer to _entity.id in the
@@ -2328,16 +2346,6 @@ export const mmCIF_Schema = {
* STRUCT_ASYM category.
*/
entity_asym_id: str,
- /**
- * The leading residue index for the sequence segment modeled using this starting model.
- * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category.
- */
- seq_id_begin: int,
- /**
- * The trailing residue index for the sequence segment modeled using this starting model.
- * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category.
- */
- seq_id_end: int,
/**
* The primitive object used to model this segment.
*/
@@ -2362,31 +2370,33 @@ export const mmCIF_Schema = {
model_object_count: int,
},
/**
- * Data items in the IHM_STRUCT_ASSEMBLY category records the
- * details of the structural assemblies and used in the
- * IHM modeling.
+ * Data items in the IHM_STRUCT_ASSEMBLY_DETAILS category records
+ * the details of the structural assemblies and used in the
+ * integrative modeling.
*/
- ihm_struct_assembly: {
+ ihm_struct_assembly_details: {
/**
* A unique identifier for the structural assembly description.
*/
- ordinal_id: int,
+ id: int,
/**
* An identifier for the structural assembly.
* This data item will remain the same for all components
* of an assembly.
+ * This data item is a pointer to _ihm_struct_assembly.id
+ * in the IHM_STRUCT_ASSEMBLY category.
*/
assembly_id: int,
/**
* The parent of this assembly in a hierarchy.
- * This data item is an internal category pointer to
- * _ihm_struct_assembly.assembly_id
+ * This data item is a pointer to _ihm_struct_assembly.id in the
+ * IHM_STRUCT_ASSEMBLY category.
* This data item should point to the assembly id of the immediate
* parent in a hierarchy.
* By convention, the full assembly (top of hierarchy) is assigned parent id 0 (zero).
* In case of assemblies that do not conform to a hierarchy,
- * _ihm_struct_assembly.parent_assembly_id is the same as
- * _ihm_struct_assembly.assembly_id indicating a self-parent.
+ * _ihm_struct_assembly_details.parent_assembly_id is the same as
+ * _ihm_struct_assembly_details.assembly_id indicating a self-parent.
*/
parent_assembly_id: int,
/**
@@ -2406,47 +2416,62 @@ export const mmCIF_Schema = {
*/
asym_id: str,
/**
- * The starting residue index for the sequence segment of the entity instance
- * that is part of the assembly.
- * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category.
- */
- seq_id_begin: int,
- /**
- * The ending residue index for the sequence segment of the entity instance
- * that is part of the assembly.
- * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category.
+ * The identifier for the polymeric segment in the assembly.
+ * This data item is a pointer to _ihm_entity_poly_segment.id in the
+ * IHM_ENTITY_POLY_SEGMENT category.
*/
- seq_id_end: int,
+ entity_poly_segment_id: int,
},
/**
- * Data items in the IHM_STRUCT_ASSEMBLY_DETAILS category provides
- * additional details regarding the structure assembly.
+ * Data items in the IHM_STRUCT_ASSEMBLY category lists
+ * all the structural assemblies used in the integrative
+ * modeling study.
*/
- ihm_struct_assembly_details: {
+ ihm_struct_assembly: {
/**
* A unique identifier for the structural assembly.
*/
- assembly_id: int,
+ id: int,
/**
* A name for the structural assembly.
*/
- assembly_name: str,
+ name: str,
/**
* Description of the structural assembly.
*/
- assembly_description: str,
+ description: str,
},
/**
- * Data items in the IHM_MODELING_PROTOCOL category records the
- * step-wise details of the integrative modeling workflow.
+ * Data items in the IHM_MODELING_PROTOCOL category lists all
+ * modeling protocols used in the integrative modeling study.
*/
ihm_modeling_protocol: {
+ /**
+ * A unique identifier for the modeling protocol.
+ */
+ id: int,
+ /**
+ * Number of independent steps in the modeling protocol.
+ */
+ num_steps: int,
+ /**
+ * The name for the modeling protocol.
+ */
+ protocol_name: str,
+ },
+ /**
+ * Data items in the IHM_MODELING_PROTOCOL_DETAILS category records the
+ * step-wise details of the integrative modeling workflow.
+ */
+ ihm_modeling_protocol_details: {
/**
* A unique identifier for the modeling protocol/step combination.
*/
- ordinal_id: int,
+ id: int,
/**
* An index for the modeling protocol carried out.
+ * This data item is a pointer to _ihm_modeling_protocol.id in the
+ * IHM_MODELING_PROTOCOL category.
*/
protocol_id: int,
/**
@@ -2457,7 +2482,7 @@ export const mmCIF_Schema = {
* An index for the structural assembly being modeled.
* This is an indicator to whether the whole assembly is modeled
* or if only a subset of the structural assembly is modeled.
- * This data item is a pointer to _ihm_struct_assembly.assembly_id in the
+ * This data item is a pointer to _ihm_struct_assembly.id in the
* IHM_STRUCT_ASSEMBLY category. The IHM_STRUCT_ASSEMBLY category provides the
* details regarding the different structural assemblies used in the modeling.
* The default value for this data item is "1", indicating that the entire
@@ -2466,7 +2491,7 @@ export const mmCIF_Schema = {
struct_assembly_id: int,
/**
* An index for the dataset group being used in the modeling protocol.
- * This data item is a pointer to the _ihm_dataset_group.group_id in the
+ * This data item is a pointer to the _ihm_dataset_group.id in the
* IHM_DATASET_GROUP category.
*/
dataset_group_id: int,
@@ -2474,10 +2499,6 @@ export const mmCIF_Schema = {
* A textual description of the structural assembly being modeled.
*/
struct_assembly_description: str,
- /**
- * The name for the modeling protocol.
- */
- protocol_name: str,
/**
* The name or type of the modeling step.
*/
@@ -2506,6 +2527,17 @@ export const mmCIF_Schema = {
* A flag to indicate if the modeling involves an ensemble ordered by time or other order.
*/
ordered_flag: Aliased<'YES' | 'NO'>(str),
+ /**
+ * The file id corresponding to the script used in the modeling protocol step.
+ * This data item is a pointer to _ihm_external_files.id in the IHM_EXTERNAL_FILES category.
+ */
+ script_file_id: int,
+ /**
+ * Identifier to the software used in the modeling protocol step.
+ * This data item is a pointer to the _software.pdbx_ordinal in the
+ * SOFTWARE category.
+ */
+ software_id: int,
},
/**
* Data items in the IHM_MULTI_STATE_MODELING category records the
@@ -2513,24 +2545,23 @@ export const mmCIF_Schema = {
*/
ihm_multi_state_modeling: {
/**
- * A unique identifier for the multiple states being described.
- */
- ordinal_id: int,
- /**
- * An identifier for the particular state in the multi-state modeling.
+ * A unique identifier for a particular state in the multi-state modeling.
*/
state_id: int,
/**
* An identifier for a collections of states in the multi-state modeling.
- * If the states do not need to be grouped into collections, then
- * _ihm_multi_state_modeling.state_group_id is the same as
- * _ihm_multi_state_modeling.state_id.
+ * This data item can be used when structural models belong to diffent
+ * multi-state modeling types.
*/
state_group_id: int,
/**
* A fraction representing the population of the particular state.
*/
population_fraction: float,
+ /**
+ * The standard deviation of the population fraction.
+ */
+ population_fraction_sd: float,
/**
* The type that the multiple states being modeled belong to.
*/
@@ -2539,14 +2570,6 @@ export const mmCIF_Schema = {
* A descriptive name for the state.
*/
state_name: str,
- /**
- * The model group id corresponding to the particular state in the multi-state model.
- * This data item is a pointer to _ihm_model_list.model_group_id in the
- * IHM_MODEL_LIST category.
- * If there is only a single model corresponding to a particular state, then the
- * _ihm_model_list.model_group_id is the same as the _ihm_model_list.model_id.
- */
- model_group_id: int,
/**
* The type of multi-state modeling experiment carried out.
*/
@@ -2569,7 +2592,7 @@ export const mmCIF_Schema = {
/**
* An identifier for the modeling protocol, whose post modeling analysis
* is being carried out.
- * This data item is a pointer to the _ihm_modeling_protocol.protocol_id
+ * This data item is a pointer to the _ihm_modeling_protocol.id
* in the IHM_MODELING_PROTOCOL category.
*/
protocol_id: int,
@@ -2622,8 +2645,8 @@ export const mmCIF_Schema = {
post_process_id: int,
/**
* An identifier for the cluster or group of models being deposited.
- * This data item is a pointer to the _ihm_model_list.model_group_id
- * in the IHM_MODEL_LIST category.
+ * This data item is a pointer to the _ihm_model_group.id
+ * in the IHM_MODEL_GROUP category.
*/
model_group_id: int,
/**
@@ -2670,57 +2693,79 @@ export const mmCIF_Schema = {
* details of the models being deposited.
*/
ihm_model_list: {
- /**
- * A unique identifier for the model / model group combination.
- */
- ordinal_id: int,
/**
* A unique identifier for the structural model being deposited.
*/
model_id: int,
/**
- * An identifier to group structural models into collections or sets.
+ * A decsriptive name for the model.
+ */
+ model_name: str,
+ /**
+ * An identifier to the structure assembly corresponding to the model.
+ * This data item is a pointer to the _ihm_struct_assembly.id
+ * in the IHM_STRUCT_ASSEMBLY category.
+ */
+ assembly_id: int,
+ /**
+ * An identifier to the modeling protocol that produced the model.
+ * This data item is a pointer to the _ihm_modeling_protocol.id
+ * in the IHM_MODELING_PROTOCOL category.
+ */
+ protocol_id: int,
+ /**
+ * An identifier to the multi-scale model representation id of the model.
+ * This data item is a pointer to the _ihm_model_representation.id
+ * in the IHM_MODEL_REPRESENTATION category.
+ */
+ representation_id: int,
+ },
+ /**
+ * IHM_MODEL_GROUP category defines collections or groups of integrative
+ * structural models.
+ */
+ ihm_model_group: {
+ /**
+ * A unique identifier for a collection or group of structural models.
* This data item can be used to group models into structural clusters
* or using other criteria based on experimental data or other
* relationships such as those belonging to the same state or time stamp.
* An ensemble of models and its representative can either be grouped together
- * or can be separate groups in the ihm_model_list table. The choice between
+ * or can be separate groups in the ihm_model_group table. The choice between
* the two options should be decided based on how the modeling was carried out
* and how the representative was chosen. If the representative is a member of
* the ensemble (i.e., best scoring model), then it is recommended that the
* representative and the ensemble belong to the same model group. If the
* representative is calculated from the ensemble (i.e., centroid), then it is
* recommended that the representative be separated into a different group.
- * If the models do not need to be grouped into collections, then the
- * _ihm_model_list.model_group_id is the same as _ihm_model_list.model_id.
*/
- model_group_id: int,
- /**
- * A decsriptive name for the model.
- */
- model_name: str,
+ id: int,
/**
- * A decsriptive name for the model group.
+ * A name for the collection of models.
*/
- model_group_name: str,
+ name: str,
/**
- * An identifier to the structure assembly corresponding to the model.
- * This data item is a pointer to the _ihm_struct_assembly.assembly_id
- * in the IHM_STRUCT_ASSEMBLY category.
+ * Additional details about the collection of models.
*/
- assembly_id: int,
+ details: str,
+ },
+ /**
+ * IHM_MODEL_GROUP_LINK category provides the list of models present in
+ * a particular model group.
+ */
+ ihm_model_group_link: {
/**
- * An identifier to the modeling protocol that produced the model.
- * This data item is a pointer to the _ihm_modeling_protocol.protocol_id
- * in the IHM_MODELING_PROTOCOL category.
+ * An identifier for the structural model.
+ * This data item is a pointer to _ihm_model_list.model_id in the
+ * IHM_MODEL_LIST category.
*/
- protocol_id: int,
+ model_id: int,
/**
- * An identifier to the multi-scale model representation id of the model.
- * This data item is a pointer to the _ihm_model_representation.representation_id
- * in the IHM_MODEL_REPRESENTATION category.
+ * An identifier for the structural model group.
+ * This data item is a pointer to _ihm_model_group.id in the
+ * IHM_MODEL_GROUP category.
*/
- representation_id: int,
+ group_id: int,
},
/**
* Data items in the IHM_MODEL_REPRESENTATIVE category record the
@@ -2733,8 +2778,8 @@ export const mmCIF_Schema = {
id: int,
/**
* The model group identifier corresponding to the representative model.
- * This data item is a pointer to _ihm_model_list.model_group_id in the
- * IHM_MODEL_LIST category.
+ * This data item is a pointer to _ihm_model_group.id in the
+ * IHM_MODEL_GROUP category.
*/
model_group_id: int,
/**
@@ -2773,31 +2818,48 @@ export const mmCIF_Schema = {
database_hosted: Aliased<'YES' | 'NO'>(str),
},
/**
- * Category provides a mechanism to group datasets.
+ * Category to define groups or collections of input datasets.
*/
ihm_dataset_group: {
/**
- * A unique identifier for the entry.
+ * A unique identifier for the dataset group.
*/
- ordinal_id: int,
+ id: int,
/**
- * An identifier for the dataset group.
+ * A name for the dataset group.
*/
- group_id: int,
+ name: str,
/**
- * An identifier to the dataset. This data item is a pointer to
- * _ihm_dataset_list.id in the IHM_DATASET_LIST category.
+ * The application / utilization of the dataset group in modeling.
+ */
+ application: Aliased<'restraint' | 'validation' | 'filter' | 'representation' | 'sampling' | 'other'>(str),
+ /**
+ * Additional details regarding the dataset group.
+ */
+ details: str,
+ },
+ /**
+ * IHM_DATASET_GROUP_LINK category provides the list of datasets present in
+ * a particular group.
+ */
+ ihm_dataset_group_link: {
+ /**
+ * An identifier for the dataset.
+ * This data item is a pointer to _ihm_dataset_list.id in the
+ * IHM_DATASET_LIST category.
*/
dataset_list_id: int,
+ /**
+ * An identifier for the dataset group.
+ * This data item is a pointer to _ihm_dataset_group.id in the
+ * IHM_DATASET_GROUP category.
+ */
+ group_id: int,
},
/**
* Category holds information about related datasets, where one is derived from the other.
*/
ihm_related_datasets: {
- /**
- * A unique identifier for the entry.
- */
- ordinal_id: int,
/**
* The dataset list id corresponding to the derived dataset.
* This data item is a pointer to _ihm_dataset_list.id in the
@@ -2978,15 +3040,12 @@ export const mmCIF_Schema = {
*/
entity_id: str,
/**
- * The leading sequence index corresponding to this localization density.
- * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY category.
+ * The identifier for the polymeric segment corresponding to this
+ * localization density.
+ * This data item is a pointer to _ihm_entity_poly_segment.id in the
+ * IHM_ENTITY_POLY_SEGMENT category.
*/
- seq_id_begin: int,
- /**
- * The trailing sequence index corresponding to this localization density.
- * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY category.
- */
- seq_id_end: int,
+ entity_poly_segment_id: int,
/**
* An asym/strand identifier corresponding to this localization density.
* This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category.
@@ -3053,17 +3112,15 @@ export const mmCIF_Schema = {
*/
seq_id_2: int,
/**
- * The atom id of the first partner in the predicted contact.
- * This data item is a pointer to _chem_comp_atom.atom_id in the
- * CHEM_COMP_ATOM category.
+ * If _ihm_predicted_contact_restraint.model_granularity is by-residue, then indicate the atom
+ * used to represent the first monomer partner in three-dimension. Default is the C-alpha atom.
*/
- atom_id_1: str,
+ rep_atom_1: Aliased<'CA' | 'CB'>(str),
/**
- * The atom id of the second partner in the predicted contact.
- * This data item is a pointer to _chem_comp_atom.atom_id in the
- * CHEM_COMP_ATOM category.
+ * If _ihm_predicted_contact_restraint.model_granularity is by-residue, then indicate the atom
+ * used to represent the second monomer partner in three-dimension. Default is the C-alpha atom.
*/
- atom_id_2: str,
+ rep_atom_2: Aliased<'CA' | 'CB'>(str),
/**
* The lower limit to the distance threshold applied to this predicted contact restraint
* in the integrative modeling task.
@@ -3086,7 +3143,7 @@ export const mmCIF_Schema = {
/**
* The granularity of the predicted contact as applied to the multi-scale model.
*/
- model_granularity: Aliased<'by-residue' | 'by-feature' | 'by-atom'>(str),
+ model_granularity: Aliased<'by-residue' | 'by-feature'>(str),
/**
* Identifier to the predicted contacts dataset.
* This data item is a pointer to the _ihm_dataset_list.id in the
@@ -3296,7 +3353,7 @@ export const mmCIF_Schema = {
/**
* A unique identifier for the restraint/model combination.
*/
- ordinal_id: int,
+ id: int,
/**
* An identifier for the crosslink restraint between a pair of residues.
* This data item is a pointer to _ihm_cross_link_restraint.id in the
@@ -3373,7 +3430,7 @@ export const mmCIF_Schema = {
/**
* An indicator to whether the whole assembly that is modeled is fit into the image
* or if only a subset of the structural assembly is fit into the image.
- * This data item is a pointer to _ihm_struct_assembly.assembly_id in the
+ * This data item is a pointer to _ihm_struct_assembly.id in the
* IHM_STRUCT_ASSEMBLY category. The IHM_STRUCT_ASSEMBLY category provides the
* details regarding the different structural assemblies used in the modeling.
* The default value for this data item is "1" indicating that the entire assembly
@@ -3407,7 +3464,7 @@ export const mmCIF_Schema = {
/**
* A unique identifier for the 2dem class average fitting data.
*/
- ordinal_id: int,
+ id: int,
/**
* Identifier to the 2dem class average restraint.
* This data item is a pointer to the _ihm_2dem_class_average_restraint.id in the
@@ -3442,7 +3499,7 @@ export const mmCIF_Schema = {
/**
* A unique identifier for the 3DEM restraint description.
*/
- ordinal_id: int,
+ id: int,
/**
* Identifier to the 3DEM map used.
* This data item is a pointer to the _ihm_dataset_list.id in the
@@ -3458,7 +3515,7 @@ export const mmCIF_Schema = {
/**
* An indicator to whether the whole assembly that is modeled is fit into the 3DEM map
* or if only a subset of the structural assembly is fit into the map.
- * This data item is a pointer to _ihm_struct_assembly.assembly_id in the
+ * This data item is a pointer to _ihm_struct_assembly.id in the
* IHM_STRUCT_ASSEMBLY category. The IHM_STRUCT_ASSEMBLY category provides the
* details regarding the different structural assemblies used in the modeling.
* The default value for this data item is "1" indicating that the entire assembly
@@ -3490,7 +3547,7 @@ export const mmCIF_Schema = {
/**
* A unique identifier for the SAS restraint description.
*/
- ordinal_id: int,
+ id: int,
/**
* Identifier to the SAS data used.
* This data item is a pointer to the _ihm_dataset_list.id in the
@@ -3506,7 +3563,7 @@ export const mmCIF_Schema = {
/**
* An indicator to whether the whole assembly that is modeled is fit into the SAS data
* or if only a subset of the structural assembly is fit into the data.
- * This data item is a pointer to _ihm_struct_assembly.assembly_id in the
+ * This data item is a pointer to _ihm_struct_assembly.id in the
* IHM_STRUCT_ASSEMBLY category. The IHM_STRUCT_ASSEMBLY category provides the
* details regarding the different structural assemblies used in the modeling.
* The default value for this data item is "1" indicating that the entire assembly
@@ -3587,13 +3644,13 @@ export const mmCIF_Schema = {
atom_id: str,
/**
* The component identifier corresponding to this coordinate position.
- * This data item is a pointer to _chem_comp.id in the CHEM_COMP category.
+ * This data item is a pointer to _chem_comp.id in the
+ * CHEM_COMP category.
*/
comp_id: str,
/**
* The sequence index corresponding this to coordinate position.
- *
- * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY category.
+ * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category.
*/
seq_id: int,
/**
@@ -3627,7 +3684,7 @@ export const mmCIF_Schema = {
/**
* A unique identifier for this pseudo atom / sphere object.
*/
- ordinal_id: int,
+ id: int,
/**
* The entity identifier corresponding to this sphere object.
* This data item is a pointer to _entity.id in the ENTITY category.
@@ -3635,12 +3692,12 @@ export const mmCIF_Schema = {
entity_id: str,
/**
* The leading sequence index corresponding to this sphere object.
- * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY category.
+ * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category.
*/
seq_id_begin: int,
/**
* The trailing sequence index corresponding to this sphere object.
- * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY category.
+ * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category.
*/
seq_id_end: int,
/**
@@ -3684,7 +3741,7 @@ export const mmCIF_Schema = {
/**
* A unique identifier for this gaussian object in the model.
*/
- ordinal_id: int,
+ id: int,
/**
* The entity identifier corresponding to this gaussian object.
* This data item is a pointer to _entity.id in the ENTITY category.
@@ -3692,12 +3749,12 @@ export const mmCIF_Schema = {
entity_id: str,
/**
* The leading sequence index corresponding to this gaussian object.
- * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY category.
+ * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category.
*/
seq_id_begin: int,
/**
* The trailing sequence index corresponding to this gaussian object.
- * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY category.
+ * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category.
*/
seq_id_end: int,
/**
@@ -3740,7 +3797,7 @@ export const mmCIF_Schema = {
/**
* A unique identifier for this gaussian object.
*/
- ordinal_id: int,
+ id: int,
/**
* The entity identifier corresponding to this gaussian object.
* This data item is a pointer to _entity.id in the ENTITY category.
@@ -3748,12 +3805,12 @@ export const mmCIF_Schema = {
entity_id: str,
/**
* The leading sequence index corresponding to this gaussian object.
- * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY category.
+ * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category.
*/
seq_id_begin: int,
/**
* The trailing sequence index corresponding to this gaussian object.
- * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY category.
+ * This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category.
*/
seq_id_end: int,
/**
@@ -4065,6 +4122,11 @@ export const mmCIF_Schema = {
* PDBX_ENTITY_BRANCH_LIST category.
*/
num: int,
+ /**
+ * This data item is a pointer to _atom_site.pdbx_auth_asym_id in the
+ * ATOM_SITE category.
+ */
+ auth_asym_id: str,
/**
* This data item is a pointer to _atom_site.pdbx_auth_seq_id in the
* ATOM_SITE category.
diff --git a/src/mol-model-formats/structure/mmcif/parser.ts b/src/mol-model-formats/structure/mmcif/parser.ts
index 4691e52c5ebcd5f28f91f7a94ac5008ec4072f27..0721e70eb72d970d603ce0357c24d7110db514b8 100644
--- a/src/mol-model-formats/structure/mmcif/parser.ts
+++ b/src/mol-model-formats/structure/mmcif/parser.ts
@@ -329,6 +329,17 @@ function splitTable<T extends Table<any>>(table: T, col: Column<number>) {
return ret;
}
+function getModelGroupName(model_id: number, format: mmCIF_Format) {
+ const { ihm_model_group, ihm_model_group_link } = format.data;
+
+ const link = Table.pickRow(ihm_model_group_link, i => ihm_model_group_link.model_id.value(i) === model_id)
+ if (link) {
+ const group = Table.pickRow(ihm_model_group, i => ihm_model_group.id.value(i) === link.group_id)
+ if (group) return group.name
+ }
+ return ''
+}
+
async function readIHM(ctx: RuntimeContext, format: mmCIF_Format, formatData: FormatData) {
// when `atom_site.ihm_model_id` is undefined fall back to `atom_site.pdbx_PDB_model_num`
const atom_sites_modelColumn = format.data.atom_site.ihm_model_id.isDefined ? format.data.atom_site.ihm_model_id : format.data.atom_site.pdbx_PDB_model_num
@@ -345,7 +356,7 @@ async function readIHM(ctx: RuntimeContext, format: mmCIF_Format, formatData: Fo
const models: Model[] = [];
- const { model_id, model_name, model_group_name } = ihm_model_list;
+ const { model_id, model_name } = ihm_model_list;
for (let i = 0; i < ihm_model_list._rowCount; i++) {
const id = model_id.value(i);
@@ -364,7 +375,7 @@ async function readIHM(ctx: RuntimeContext, format: mmCIF_Format, formatData: Fo
const data: IHMData = {
model_id: id,
model_name: model_name.value(i),
- model_group_name: model_group_name.value(i),
+ model_group_name: getModelGroupName(id, format),
entities: entities,
atom_site,
atom_site_sourceIndex,