From fbfcedf3df52f6a9ef849fe86b48f12aec8a567a Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Thu, 17 Jan 2019 16:18:20 -0800
Subject: [PATCH] updated cif schemas
---
src/apps/schema-generator/schema-from-cif-dic.ts | 2 +-
src/mol-io/reader/cif/schema/bird.ts | 4 ++--
src/mol-io/reader/cif/schema/ccd.ts | 4 ++--
src/mol-io/reader/cif/schema/mmcif.ts | 7 +++----
4 files changed, 8 insertions(+), 9 deletions(-)
diff --git a/src/apps/schema-generator/schema-from-cif-dic.ts b/src/apps/schema-generator/schema-from-cif-dic.ts
index 88bd34a8f..5fd4d778e 100644
--- a/src/apps/schema-generator/schema-from-cif-dic.ts
+++ b/src/apps/schema-generator/schema-from-cif-dic.ts
@@ -97,7 +97,7 @@ const IHM_DIC_URL = 'https://raw.githubusercontent.com/ihmwg/IHM-dictionary/mast
const CARB_BRANCH_DIC_PATH = `${DIC_DIR}/entity_branch-extension.dic`
const CARB_BRANCH_DIC_URL = 'https://raw.githubusercontent.com/pdbxmmcifwg/carbohydrate-extension/master/dict/entity_branch-extension.dic'
const CARB_COMP_DIC_PATH = `${DIC_DIR}/chem_comp-extension.dic`
-const CARB_COMP_DIC_URL = 'https://raw.githubusercontent.com/pdbxmmcifwg/carbohydrate-extension/master/dict/chem_comp-extension.txt'
+const CARB_COMP_DIC_URL = 'https://raw.githubusercontent.com/pdbxmmcifwg/carbohydrate-extension/master/dict/chem_comp-extension.dic'
const parser = new argparse.ArgumentParser({
addHelp: true,
diff --git a/src/mol-io/reader/cif/schema/bird.ts b/src/mol-io/reader/cif/schema/bird.ts
index a4398188b..b6a895004 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 5.300, IHM 0.136, CARB draft.
+ * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.303, IHM 0.139, CARB draft.
*
* @author mol-star package (src/apps/schema-generator/generate)
*/
@@ -483,7 +483,7 @@ export const BIRD_Schema = {
/**
* An identifier for the wwPDB site creating or modifying the molecule.
*/
- processing_site: str,
+ processing_site: Aliased<'RCSB' | 'PDBe' | 'PDBJ' | 'BMRB'>(str),
/**
* The action associated with this audit record.
*/
diff --git a/src/mol-io/reader/cif/schema/ccd.ts b/src/mol-io/reader/cif/schema/ccd.ts
index d8d61e76b..7086e69b7 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 5.300, IHM 0.136, CARB draft.
+ * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.303, IHM 0.139, CARB draft.
*
* @author mol-star package (src/apps/schema-generator/generate)
*/
@@ -378,7 +378,7 @@ export const CCD_Schema = {
/**
* This data item contains the identifier type.
*/
- type: Aliased<'COMMON NAME' | 'SYSTEMATIC NAME' | 'CAS REGISTRY NUMBER' | 'PUBCHEM Identifier' | 'MDL Identifier' | 'SYNONYM'>(str),
+ type: Aliased<'COMMON NAME' | 'SYSTEMATIC NAME' | 'CAS REGISTRY NUMBER' | 'PUBCHEM Identifier' | 'MDL Identifier' | 'SYNONYM' | 'CONDENSED IUPAC CARB SYMBOL' | 'IUPAC CARB SYMBOL' | 'SNFG CARB SYMBOL'>(str),
/**
* This data item contains the name of the program
* or library used to compute the identifier.
diff --git a/src/mol-io/reader/cif/schema/mmcif.ts b/src/mol-io/reader/cif/schema/mmcif.ts
index 6f18cc2aa..94ef98f33 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 5.300, IHM 0.136, CARB draft.
+ * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.303, IHM 0.139, CARB draft.
*
* @author mol-star package (src/apps/schema-generator/generate)
*/
@@ -3687,12 +3687,11 @@ export const mmCIF_Schema = {
/**
* The type of feature.
*/
- feature_type: Aliased<'atom' | 'residue' | 'residue range'>(str),
+ feature_type: Aliased<'atom' | 'residue' | 'residue range' | 'ligand' | 'pseudo site'>(str),
/**
* The type of entity.
- * This data item is a pointer to _entity.type in the ENTITY category.
*/
- entity_type: Aliased<'polymer' | 'non-polymer' | 'macrolide' | 'water'>(str),
+ entity_type: Aliased<'polymer' | 'non-polymer' | 'water' | 'other'>(str),
},
/**
* Data items in the IHM_POLY_RESIDUE_FEATURE category provides the defintions
--
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