From ef1ccd4286fb2757bb81a3d1ca444be5044fd2f8 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Fri, 21 Jun 2019 12:44:28 -0700
Subject: [PATCH] cif schema updates
---
README.md | 2 +-
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 | 85 ++++++++++++++++++++++++++-
4 files changed, 85 insertions(+), 6 deletions(-)
diff --git a/README.md b/README.md
index bea25cde6..65283ff68 100644
--- a/README.md
+++ b/README.md
@@ -85,7 +85,7 @@ and navigate to `build/viewer`
Install CIFTools `npm install ciftools -g`
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/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 29e5b0e43..ff10cb3d5 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) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
- * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.311, IHM 1.0, CARB draft.
+ * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.312, IHM 1.0, CARB draft.
*
* @author molstar/ciftools package
*/
diff --git a/src/mol-io/reader/cif/schema/ccd.ts b/src/mol-io/reader/cif/schema/ccd.ts
index a4ee2576f..4c8314a2d 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) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
- * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.311, IHM 1.0, CARB draft.
+ * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.312, IHM 1.0, CARB draft.
*
* @author molstar/ciftools package
*/
diff --git a/src/mol-io/reader/cif/schema/mmcif.ts b/src/mol-io/reader/cif/schema/mmcif.ts
index 10a092bb9..7fa520eee 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) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
- * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.311, IHM 1.0, CARB draft.
+ * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.312, IHM 1.0, CARB draft.
*
* @author molstar/ciftools package
*/
@@ -1549,6 +1549,85 @@ export const mmCIF_Schema = {
*/
program_version: str,
},
+ /**
+ * Data items in the PDBX_UNOBS_OR_ZERO_OCC_RESIDUES category list the
+ * residues within the entry that are not observed or have zero occupancy.
+ */
+ pdbx_unobs_or_zero_occ_residues: {
+ /**
+ * The value of _pdbx_unobs_or_zero_occ_residues.id must uniquely identify
+ * each item in the PDBX_UNOBS_OR_ZERO_OCC_RESIDUES list.
+ *
+ * This is an integer serial number.
+ */
+ id: int,
+ /**
+ * The value of polymer flag indicates whether the unobserved or
+ * zero occupancy residue is part of a polymer chain or not
+ */
+ polymer_flag: Aliased<'Y' | 'N'>(str),
+ /**
+ * The value of occupancy flag indicates whether the residue
+ * is unobserved (= 1) or the coordinates have an occupancy of zero (=0)
+ */
+ occupancy_flag: Aliased<'1' | '0'>(int),
+ /**
+ * Part of the identifier for the unobserved or zero occupancy residue.
+ *
+ * This data item is a pointer to _atom_site.pdbx_PDB_model_num in the
+ * ATOM_SITE category.
+ */
+ PDB_model_num: int,
+ /**
+ * Part of the identifier for the unobserved or zero occupancy residue.
+ *
+ * This data item is a pointer to _atom_site.auth_asym_id in the
+ * ATOM_SITE category.
+ */
+ auth_asym_id: str,
+ /**
+ * Part of the identifier for the unobserved or zero occupancy residue.
+ *
+ * This data item is a pointer to _atom_site.auth_comp_id in the
+ * ATOM_SITE category.
+ */
+ auth_comp_id: str,
+ /**
+ * Part of the identifier for the unobserved or zero occupancy residue.
+ *
+ * This data item is a pointer to _atom_site.auth_seq_id in the
+ * ATOM_SITE category.
+ */
+ auth_seq_id: str,
+ /**
+ * Part of the identifier for the unobserved or zero occupancy residue.
+ *
+ * This data item is a pointer to _atom_site.pdbx_PDB_ins_code in the
+ * ATOM_SITE category.
+ */
+ PDB_ins_code: str,
+ /**
+ * Part of the identifier for the unobserved or zero occupancy residue.
+ *
+ * This data item is a pointer to _atom_site.label_asym_id in the
+ * ATOM_SITE category.
+ */
+ label_asym_id: str,
+ /**
+ * Part of the identifier for the unobserved or zero occupancy residue.
+ *
+ * This data item is a pointer to _atom_site.label_comp_id in the
+ * ATOM_SITE category.
+ */
+ label_comp_id: str,
+ /**
+ * Part of the identifier for the unobserved or zero occupancy residue.
+ *
+ * This data item is a pointer to _atom_site.label_seq_id in the
+ * ATOM_SITE category.
+ */
+ label_seq_id: int,
+ },
/**
* Data items in the PDBX_STRUCT_MOD_RESIDUE category list the
* modified polymer components in the entry and provide some
@@ -2079,10 +2158,10 @@ export const mmCIF_Schema = {
pdbx_end_seq_num: int,
},
/**
- * Data items in the PDBX_ENTITY_DESCRIPTOR category provide
+ * Data items in the PDBX_ENTITY_BRANCH_DESCRIPTOR category provide
* string descriptors of entity chemical structure.
*/
- pdbx_entity_descriptor: {
+ pdbx_entity_branch_descriptor: {
/**
* This data item is a pointer to _entity_poly.entity_id in the ENTITY
* category.
--
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