From ea02fe832f769244196bd4f8856dce64934afa66 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Wed, 19 Sep 2018 18:20:20 -0700
Subject: [PATCH] wip, carbohydrate related schema additions
---
data/mmcif-field-names.csv | 37 +++++++++++++++
src/mol-io/reader/cif/schema/bird.ts | 2 +-
src/mol-io/reader/cif/schema/ccd.ts | 2 +-
src/mol-io/reader/cif/schema/mmcif.ts | 66 ++++++++++++++++++++++++++-
4 files changed, 104 insertions(+), 3 deletions(-)
diff --git a/data/mmcif-field-names.csv b/data/mmcif-field-names.csv
index 68893eed5..e7d8b64c4 100644
--- a/data/mmcif-field-names.csv
+++ b/data/mmcif-field-names.csv
@@ -41,6 +41,12 @@ chem_comp_bond.atom_id_1
chem_comp_bond.atom_id_2
chem_comp_bond.value_order
+pdbx_chem_comp_identifier.comp_id
+pdbx_chem_comp_identifier.type
+pdbx_chem_comp_identifier.program
+pdbx_chem_comp_identifier.program_version
+pdbx_chem_comp_identifier.identifier
+
cell.entry_id
cell.length_a
cell.length_b
@@ -76,6 +82,37 @@ entity_poly_seq.num
entity_poly_seq.mon_id
entity_poly_seq.hetero
+pdbx_entity_branch.entity_id
+pdbx_entity_branch.type
+
+pdbx_entity_branch_list.entity_id
+pdbx_entity_branch_list.comp_id
+pdbx_entity_branch_list.num
+pdbx_entity_branch_list.component_comp_id
+pdbx_entity_branch_list.hetero
+
+pdbx_entity_branch_link.link_id
+pdbx_entity_branch_link.entity_id
+pdbx_entity_branch_link.entity_branch_list_num_1
+pdbx_entity_branch_link.comp_id_1
+pdbx_entity_branch_link.atom_id_1
+pdbx_entity_branch_link.leaving_atom_id_1
+pdbx_entity_branch_link.atom_stereo_config_1
+pdbx_entity_branch_link.entity_branch_list_num_2
+pdbx_entity_branch_link.comp_id_2
+pdbx_entity_branch_link.atom_id_2
+pdbx_entity_branch_link.leaving_atom_id_2
+pdbx_entity_branch_link.atom_stereo_config_2
+pdbx_entity_branch_link.value_order
+pdbx_entity_branch_link.details
+
+pdbx_entity_descriptor.ordinal
+pdbx_entity_descriptor.entity_id
+pdbx_entity_descriptor.descriptor
+pdbx_entity_descriptor.type
+pdbx_entity_descriptor.program
+pdbx_entity_descriptor.program_version
+
entry.id
exptl.entry_id
diff --git a/src/mol-io/reader/cif/schema/bird.ts b/src/mol-io/reader/cif/schema/bird.ts
index 0614e8410..5cf18d466 100644
--- a/src/mol-io/reader/cif/schema/bird.ts
+++ b/src/mol-io/reader/cif/schema/bird.ts
@@ -1,7 +1,7 @@
/**
* Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
- * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.298, IHM 0.134.
+ * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.299, IHM 0.134.
*
* @author mol-star package (src/apps/schema-generator/generate)
*/
diff --git a/src/mol-io/reader/cif/schema/ccd.ts b/src/mol-io/reader/cif/schema/ccd.ts
index 3a5e0d2c0..06a77ba67 100644
--- a/src/mol-io/reader/cif/schema/ccd.ts
+++ b/src/mol-io/reader/cif/schema/ccd.ts
@@ -1,7 +1,7 @@
/**
* Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
- * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.298, IHM 0.134.
+ * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.299, IHM 0.134.
*
* @author mol-star package (src/apps/schema-generator/generate)
*/
diff --git a/src/mol-io/reader/cif/schema/mmcif.ts b/src/mol-io/reader/cif/schema/mmcif.ts
index 526cb248b..c40dc4159 100644
--- a/src/mol-io/reader/cif/schema/mmcif.ts
+++ b/src/mol-io/reader/cif/schema/mmcif.ts
@@ -1,7 +1,7 @@
/**
* Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
- * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.298, IHM 0.134.
+ * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.299, IHM 0.134.
*
* @author mol-star package (src/apps/schema-generator/generate)
*/
@@ -1470,6 +1470,36 @@ export const mmCIF_Schema = {
*/
'space_group_name_H-M': str,
},
+ /**
+ * Data items in the CHEM_COMP_IDENTIFIER category provide
+ * identifiers for chemical components.
+ */
+ pdbx_chem_comp_identifier: {
+ /**
+ * This data item is a pointer to _chem_comp.id in the CHEM_COMP
+ * category.
+ */
+ comp_id: str,
+ /**
+ * This data item contains the identifier value for this
+ * component.
+ */
+ identifier: str,
+ /**
+ * This data item contains the identifier type.
+ */
+ type: Aliased<'COMMON NAME' | 'SYSTEMATIC NAME' | 'CAS REGISTRY NUMBER' | 'PUBCHEM Identifier' | 'MDL Identifier' | 'SYNONYM'>(str),
+ /**
+ * This data item contains the name of the program
+ * or library used to compute the identifier.
+ */
+ program: str,
+ /**
+ * This data item contains the version of the program
+ * or library used to compute the identifier.
+ */
+ program_version: str,
+ },
/**
* Data items in the PDBX_STRUCT_MOD_RESIDUE category list the
* modified polymer components in the entry and provide some
@@ -1886,6 +1916,40 @@ export const mmCIF_Schema = {
*/
details: str,
},
+ /**
+ * Data items in the PDBX_ENTITY_DESCRIPTOR category provide
+ * string descriptors of entity chemical structure.
+ */
+ pdbx_entity_descriptor: {
+ /**
+ * This data item is a pointer to _entity_poly.entity_id in the ENTITY
+ * category.
+ */
+ entity_id: str,
+ /**
+ * This data item contains the descriptor value for this
+ * entity.
+ */
+ descriptor: str,
+ /**
+ * This data item contains the descriptor type.
+ */
+ type: Aliased<'LINUCS' | 'IUPAC' | 'IUPAC Abbreviated'>(str),
+ /**
+ * This data item contains the name of the program
+ * or library used to compute the descriptor.
+ */
+ program: str,
+ /**
+ * This data item contains the version of the program
+ * or library used to compute the descriptor.
+ */
+ program_version: str,
+ /**
+ * Ordinal index for this category.
+ */
+ ordinal: int,
+ },
/**
* Data items in the IHM_STARTING_MODEL_DETAILS category records the
* details about structural models used as starting inputs in
--
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