From 1767bf40ea83003e98087d818f7e6e48e1275446 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Thu, 12 Jul 2018 14:30:48 -0700
Subject: [PATCH] updated mmcif schema and annotated one more item as list-type
(thanks @valasatava for the pointer)
---
src/apps/schema-generator/util/cif-dic.ts | 1 +
src/mol-io/reader/cif/schema/mmcif.ts | 18 +++++++++---------
2 files changed, 10 insertions(+), 9 deletions(-)
diff --git a/src/apps/schema-generator/util/cif-dic.ts b/src/apps/schema-generator/util/cif-dic.ts
index ca190ae4a..bd48670c4 100644
--- a/src/apps/schema-generator/util/cif-dic.ts
+++ b/src/apps/schema-generator/util/cif-dic.ts
@@ -155,6 +155,7 @@ const COMMA_SEPARATED_LIST_FIELDS = [
'_em_diffraction.tilt_angle_list', // 20,40,50,55
'_em_entity_assembly.entity_id_list',
'_entity.pdbx_ec',
+ '_entity_poly.pdbx_strand_id', // A,B
'_pdbx_depui_entry_details.experimental_methods',
'_pdbx_depui_entry_details.requested_accession_types',
'_pdbx_soln_scatter_model.software_list', // INSIGHT II, HOMOLOGY, DISCOVERY, BIOPOLYMER, DELPHI
diff --git a/src/mol-io/reader/cif/schema/mmcif.ts b/src/mol-io/reader/cif/schema/mmcif.ts
index 9cb22fed0..4e664e087 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 5.293, IHM 0.130.
+ * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.296, IHM 0.132.
*
* @author mol-star package (src/apps/schema-generator/generate)
*/
@@ -80,25 +80,25 @@ export const mmCIF_Schema = {
pdbx_aromatic_flag: Aliased<'Y' | 'N'>(str),
},
entity: {
+ details: str,
+ formula_weight: float,
id: str,
- type: Aliased<'polymer' | 'non-polymer' | 'macrolide' | 'water'>(str),
src_method: Aliased<'nat' | 'man' | 'syn'>(str),
- formula_weight: float,
+ type: Aliased<'polymer' | 'non-polymer' | 'macrolide' | 'water'>(str),
pdbx_description: str,
pdbx_number_of_molecules: float,
pdbx_mutation: str,
pdbx_fragment: str,
pdbx_ec: List(',', x => x),
- details: str,
},
entity_poly: {
entity_id: str,
- type: str,
nstd_linkage: Aliased<'no' | 'n' | 'yes' | 'y'>(str),
nstd_monomer: Aliased<'no' | 'n' | 'yes' | 'y'>(str),
+ type: Aliased<'polypeptide(D)' | 'polypeptide(L)' | 'polydeoxyribonucleotide' | 'polyribonucleotide' | 'polysaccharide(D)' | 'polysaccharide(L)' | 'polydeoxyribonucleotide/polyribonucleotide hybrid' | 'cyclic-pseudo-peptide' | 'peptide nucleic acid' | 'other'>(str),
+ pdbx_strand_id: List(',', x => x),
pdbx_seq_one_letter_code: str,
pdbx_seq_one_letter_code_can: str,
- pdbx_strand_id: str,
pdbx_target_identifier: str,
},
entity_poly_seq: {
@@ -119,11 +119,11 @@ export const mmCIF_Schema = {
title: str,
},
struct_asym: {
- id: str,
+ details: str,
entity_id: str,
+ id: str,
pdbx_modified: str,
pdbx_blank_PDB_chainid_flag: Aliased<'Y' | 'N'>(str),
- details: str,
},
struct_conf: {
beg_label_asym_id: str,
@@ -338,7 +338,7 @@ export const mmCIF_Schema = {
asym_id: str,
seq_id_begin: int,
seq_id_end: int,
- starting_model_source: Aliased<'comparative model' | 'experimental model' | 'integrative model' | 'other ab initio models'>(str),
+ starting_model_source: Aliased<'comparative model' | 'experimental model' | 'integrative model' | 'ab initio model' | 'other'>(str),
starting_model_auth_asym_id: str,
starting_model_sequence_offset: int,
dataset_list_id: int,
--
GitLab