From 0fb6ed11f6863fe9dc8fbb1921d2c76dce520321 Mon Sep 17 00:00:00 2001
From: Alexander Rose <alex.rose@rcsb.org>
Date: Tue, 26 Jun 2018 20:15:50 -0700
Subject: [PATCH] added some missing ihm fields
---
data/mmcif-field-names.csv | 4 +++
src/mol-io/reader/cif/schema/mmcif.ts | 36 +++++++++++++++------------
2 files changed, 24 insertions(+), 16 deletions(-)
diff --git a/data/mmcif-field-names.csv b/data/mmcif-field-names.csv
index 45b870d17..9b27261b1 100644
--- a/data/mmcif-field-names.csv
+++ b/data/mmcif-field-names.csv
@@ -365,10 +365,12 @@ ihm_cross_link_restraint.group_id
ihm_cross_link_restraint.entity_id_1
ihm_cross_link_restraint.asym_id_1
ihm_cross_link_restraint.seq_id_1
+ihm_cross_link_restraint.atom_id_1
ihm_cross_link_restraint.comp_id_1
ihm_cross_link_restraint.entity_id_2
ihm_cross_link_restraint.asym_id_2
ihm_cross_link_restraint.seq_id_2
+ihm_cross_link_restraint.atom_id_2
ihm_cross_link_restraint.comp_id_2
ihm_cross_link_restraint.restraint_type
ihm_cross_link_restraint.conditional_crosslink_flag
@@ -434,6 +436,7 @@ ihm_3dem_restraint.model_id
ihm_3dem_restraint.cross_correlation_coefficient
ihm_predicted_contact_restraint.id
+ihm_predicted_contact_restraint.group_id
ihm_predicted_contact_restraint.entity_id_1
ihm_predicted_contact_restraint.asym_id_1
ihm_predicted_contact_restraint.seq_id_1
@@ -445,6 +448,7 @@ ihm_predicted_contact_restraint.seq_id_2
ihm_predicted_contact_restraint.comp_id_2
ihm_predicted_contact_restraint.atom_id_2
ihm_predicted_contact_restraint.restraint_type
+ihm_predicted_contact_restraint.distance_lower_limit
ihm_predicted_contact_restraint.distance_upper_limit
ihm_predicted_contact_restraint.probability
ihm_predicted_contact_restraint.model_granularity
diff --git a/src/mol-io/reader/cif/schema/mmcif.ts b/src/mol-io/reader/cif/schema/mmcif.ts
index 19ac89f35..b87bee82a 100644
--- a/src/mol-io/reader/cif/schema/mmcif.ts
+++ b/src/mol-io/reader/cif/schema/mmcif.ts
@@ -21,11 +21,6 @@ const Vector = Schema.Vector;
const List = Schema.List;
export const mmCIF_Schema = {
- atom_sites: {
- entry_id: str,
- fract_transf_matrix: Matrix(3, 3),
- fract_transf_vector: Vector(3)
- },
atom_site: {
auth_asym_id: str,
auth_atom_id: str,
@@ -50,6 +45,11 @@ export const mmCIF_Schema = {
pdbx_formal_charge: int,
ihm_model_id: int,
},
+ atom_sites: {
+ entry_id: str,
+ fract_transf_matrix: Matrix(3, 3),
+ fract_transf_vector: Vector(3),
+ },
cell: {
angle_alpha: float,
angle_beta: float,
@@ -80,11 +80,11 @@ export const mmCIF_Schema = {
pdbx_aromatic_flag: Aliased<'Y' | 'N'>(str),
},
entity: {
+ details: str,
+ formula_weight: float,
id: str,
src_method: Aliased<'nat' | 'man' | 'syn'>(str),
type: Aliased<'polymer' | 'non-polymer' | 'macrolide' | 'water'>(str),
- details: str,
- formula_weight: float,
pdbx_description: str,
pdbx_number_of_molecules: float,
pdbx_mutation: str,
@@ -93,9 +93,9 @@ export const mmCIF_Schema = {
},
entity_poly_seq: {
entity_id: str,
- num: int,
+ hetero: Aliased<'no' | 'n' | 'yes' | 'y'>(str),
mon_id: str,
- hetero: Aliased<'no' | 'n' | 'yes' | 'y'>(str)
+ num: int,
},
entry: {
id: str,
@@ -182,6 +182,13 @@ export const mmCIF_Schema = {
text: List(',', x => x),
pdbx_keywords: str,
},
+ struct_ncs_oper: {
+ code: Aliased<'given' | 'generate'>(str),
+ details: str,
+ id: str,
+ matrix: Matrix(3, 3),
+ vector: Vector(3),
+ },
struct_sheet_range: {
beg_label_asym_id: str,
beg_label_comp_id: str,
@@ -409,13 +416,6 @@ export const mmCIF_Schema = {
experiment_type: Aliased<'Fraction of bulk' | 'Single molecule'>(str),
details: str,
},
- struct_ncs_oper: {
- id: str,
- code: str,
- matrix: Matrix(3, 3),
- vector: Vector(3),
- details: str
- },
ihm_modeling_post_process: {
id: int,
protocol_id: int,
@@ -509,6 +509,7 @@ export const mmCIF_Schema = {
},
ihm_predicted_contact_restraint: {
id: int,
+ group_id: int,
entity_id_1: str,
entity_id_2: str,
asym_id_1: str,
@@ -519,6 +520,7 @@ export const mmCIF_Schema = {
seq_id_2: int,
atom_id_1: str,
atom_id_2: str,
+ distance_lower_limit: float,
distance_upper_limit: float,
probability: float,
restraint_type: Aliased<'lower bound' | 'upper bound' | 'lower and upper bound'>(str),
@@ -551,6 +553,8 @@ export const mmCIF_Schema = {
comp_id_2: str,
seq_id_1: int,
seq_id_2: int,
+ atom_id_1: str,
+ atom_id_2: str,
restraint_type: Aliased<'harmonic' | 'upper bound' | 'lower bound'>(str),
conditional_crosslink_flag: Aliased<'ALL' | 'ANY'>(str),
model_granularity: Aliased<'by-residue' | 'by-feature' | 'by-atom'>(str),
--
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