From 57ed9a42260321c353e6def7c86486a1ff04824c Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Wed, 12 Feb 2020 18:50:52 -0800
Subject: [PATCH] updated cif schemas
---
README.md | 1 +
data/cif-core.csv | 60 ------------------------
src/mol-io/reader/cif/schema/bird.ts | 6 +--
src/mol-io/reader/cif/schema/ccd.ts | 4 +-
src/mol-io/reader/cif/schema/cif-core.ts | 12 ++---
src/mol-io/reader/cif/schema/mmcif.ts | 40 ++++++++--------
6 files changed, 32 insertions(+), 91 deletions(-)
delete mode 100644 data/cif-core.csv
diff --git a/README.md b/README.md
index 91d48e5e5..966b03ca7 100644
--- a/README.md
+++ b/README.md
@@ -91,6 +91,7 @@ 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/bird.ts -p BIRD
+ cifschema -mip ../../../../mol-data -o src/mol-io/reader/cif/schema/cif-core.ts -p CifCore -aa
**GraphQL schemas**
diff --git a/data/cif-core.csv b/data/cif-core.csv
deleted file mode 100644
index 25ce0320c..000000000
--- a/data/cif-core.csv
+++ /dev/null
@@ -1,60 +0,0 @@
-audit.block_doi
-
-database_code.depnum_ccdc_archive
-
-chemical.name_systematic
-chemical.name_common
-chemical.melting_point
-
-chemical_formula.moiety
-chemical_formula.sum
-chemical_formula.weight
-
-atom_type.symbol
-atom_type.description
-
-atom_type_scat.dispersion_real
-atom_type_scat.dispersion_imag
-atom_type_scat.source
-
-space_group.crystal_system
-space_group.name_H-M_full
-space_group_symop.operation_xyz
-
-cell.length_a
-cell.length_b
-cell.length_c
-cell.angle_alpha
-cell.angle_beta
-cell.angle_gamma
-cell.volume
-cell.formula_units_Z
-
-atom_site.label
-atom_site.type_symbol
-atom_site.fract_x
-atom_site.fract_y
-atom_site.fract_z
-atom_site.U_iso_or_equiv
-atom_site.adp_type
-atom_site.occupancy
-atom_site.calc_flag
-atom_site.refinement_flags
-atom_site.disorder_assembly
-atom_site.disorder_group
-
-atom_site.site_symmetry_multiplicity
-
-atom_site_aniso.label
-atom_site_aniso.U_11
-atom_site_aniso.U_22
-atom_site_aniso.U_33
-atom_site_aniso.U_23
-atom_site_aniso.U_13
-atom_site_aniso.U_12
-
-geom_bond.atom_site_label_1
-geom_bond.atom_site_label_2
-geom_bond.distance
-geom_bond.site_symmetry_2
-geom_bond.publ_flag
\ No newline at end of file
diff --git a/src/mol-io/reader/cif/schema/bird.ts b/src/mol-io/reader/cif/schema/bird.ts
index 6a1912e5f..195cdc7d6 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.
+ * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
- * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.320, IHM 1.05, CARB draft.
+ * Code-generated 'BIRD' schema file. Dictionary versions: mmCIF 5.323, IHM 1.07, CARB draft.
*
* @author molstar/ciftools package
*/
@@ -78,7 +78,7 @@ export const BIRD_Schema = {
/**
* Defines how this entity is represented in PDB data files.
*/
- represent_as: Aliased<'polymer' | 'single molecule'>(str),
+ represent_as: Aliased<'polymer' | 'single molecule' | 'branched'>(str),
/**
* For entities represented as single molecules, the identifier
* corresponding to the chemical definition for the molecule.
diff --git a/src/mol-io/reader/cif/schema/ccd.ts b/src/mol-io/reader/cif/schema/ccd.ts
index ba7162129..11aa912e9 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.
+ * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
- * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.320, IHM 1.05, CARB draft.
+ * Code-generated 'CCD' schema file. Dictionary versions: mmCIF 5.323, IHM 1.07, CARB draft.
*
* @author molstar/ciftools package
*/
diff --git a/src/mol-io/reader/cif/schema/cif-core.ts b/src/mol-io/reader/cif/schema/cif-core.ts
index ddde84aaa..e3de62df5 100644
--- a/src/mol-io/reader/cif/schema/cif-core.ts
+++ b/src/mol-io/reader/cif/schema/cif-core.ts
@@ -1,7 +1,7 @@
/**
- * Copyright (c) 2017-2019 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
- * Code-generated 'cifCore' schema file. Dictionary versions: CifCore 3.0.11.
+ * Code-generated 'CifCore' schema file. Dictionary versions: CifCore 3.0.11.
*
* @author molstar/ciftools package
*/
@@ -14,7 +14,7 @@ const int = Schema.int;
const float = Schema.float;
const str = Schema.str;
-export const cifCore_Schema = {
+export const CifCore_Schema = {
/**
* The CATEGORY of data items used to describe the parameters of
* the crystal unit cell and their measurement.
@@ -585,7 +585,7 @@ export const cifCore_Schema = {
},
}
-export const cifCore_Aliases = {
+export const CifCore_Aliases = {
'space_group.name_H-M_full': [
'symmetry_space_group_name_H-M',
],
@@ -633,5 +633,5 @@ export const cifCore_Aliases = {
],
}
-export type cifCore_Schema = typeof cifCore_Schema;
-export interface cifCore_Database extends Database<cifCore_Schema> {}
\ No newline at end of file
+export type CifCore_Schema = typeof CifCore_Schema;
+export interface CifCore_Database extends Database<CifCore_Schema> {}
\ No newline at end of file
diff --git a/src/mol-io/reader/cif/schema/mmcif.ts b/src/mol-io/reader/cif/schema/mmcif.ts
index d52d5763e..b653ea77e 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.
+ * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
- * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.320, IHM 1.05, CARB draft.
+ * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.323, IHM 1.07, CARB draft.
*
* @author molstar/ciftools package
*/
@@ -1880,6 +1880,23 @@ export const mmCIF_Schema = {
*/
name: str,
},
+ /**
+ * PDBX_CHEM_COMP_SYNONYMS holds chemical name and synonym correspondences.
+ */
+ pdbx_chem_comp_synonyms: {
+ /**
+ * The synonym of this particular chemical component.
+ */
+ name: str,
+ /**
+ * The chemical component for which this synonym applies.
+ */
+ comp_id: str,
+ /**
+ * The provenance of this synonym.
+ */
+ provenance: Aliased<'AUTHOR' | 'DRUGBANK' | 'CHEBI' | 'CHEMBL' | 'PDB' | 'PUBCHEM'>(str),
+ },
/**
* Data items in the CHEM_COMP_IDENTIFIER category provide
* identifiers for chemical components.
@@ -3665,7 +3682,7 @@ export const mmCIF_Schema = {
/**
* The type of crosslinker used.
*/
- linker_type: Aliased<'EDC' | 'DSS' | 'EGS' | 'BS3' | 'BS2G' | 'DST' | 'sulfo-SDA' | 'sulfo-SMCC' | 'DSSO' | 'DSG' | 'BSP' | 'BMSO' | 'DHSO' | 'Other'>(str),
+ linker_type: Aliased<'EDC' | 'DSS' | 'EGS' | 'BS3' | 'BS2G' | 'DST' | 'sulfo-SDA' | 'sulfo-SMCC' | 'DSSO' | 'DSG' | 'BSP' | 'BMSO' | 'DHSO' | 'CYS' | 'Other'>(str),
/**
* Identifier to the crosslinking dataset.
* This data item is a pointer to the _ihm_dataset_list.id in the
@@ -4584,23 +4601,6 @@ export const mmCIF_Schema = {
*/
auth_mon_id: str,
},
- /**
- * PDBX_CHEM_COMP_SYNONYMS holds chemical name and synonym correspondences.
- */
- pdbx_chem_comp_synonyms: {
- /**
- * The synonym of this particular chemical component.
- */
- name: str,
- /**
- * The chemical component for which this synonym applies.
- */
- comp_id: str,
- /**
- * The provenance of this synonym.
- */
- provenance: Aliased<'AUTHOR' | 'DRUGBANK' | 'CHEBI' | 'CHEMBL' | 'PDB' | 'PUBCHEM'>(str),
- },
/**
* PDBX_CHEM_COMP_RELATED describes the relationship between two chemical components.
*/
--
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