From 2205e2965bb6167a3f4df4ca750d21bdcdcc00e7 Mon Sep 17 00:00:00 2001 From: Dennis Piehl Date: Wed, 31 Jul 2024 14:56:41 -0400 Subject: [PATCH] RO-4209: Update polymer instance features with ligand interaction enumerations --- ...col-pdbx_core_polymer_entity_instance.json | 42 +++++++++++++++++-- .../schema_def-pdbx_core-ANY.json | 14 ++++++- ...col-pdbx_core_polymer_entity_instance.json | 6 +++ ...col-pdbx_core_polymer_entity_instance.json | 42 +++++++++++++++++-- 4 files changed, 97 insertions(+), 7 deletions(-) diff --git a/schemas/exchange/min-meta/json-min-db-pdbx_core-col-pdbx_core_polymer_entity_instance.json b/schemas/exchange/min-meta/json-min-db-pdbx_core-col-pdbx_core_polymer_entity_instance.json index 115e64e..682bb95 100644 --- a/schemas/exchange/min-meta/json-min-db-pdbx_core-col-pdbx_core_polymer_entity_instance.json +++ b/schemas/exchange/min-meta/json-min-db-pdbx_core-col-pdbx_core_polymer_entity_instance.json @@ -863,6 +863,9 @@ "HELX_RH_3T_P", "HELX_RH_AL_P", "HELX_RH_PI_P", + "LIGAND_COVALENT_LINKAGE", + "LIGAND_INTERACTION", + "LIGAND_METAL_COORDINATION_LINKAGE", "MA_QA_METRIC_LOCAL_TYPE_CONTACT_PROBABILITY", "MA_QA_METRIC_LOCAL_TYPE_DISTANCE", "MA_QA_METRIC_LOCAL_TYPE_ENERGY", @@ -974,6 +977,21 @@ "detail": "Right-handed pi helix (protein)", "name": "Right-handed pi helix (protein)" }, + { + "value": "LIGAND_COVALENT_LINKAGE", + "detail": "Covalent ligand linkages with macromolecular target", + "name": "Covalent Ligand Linkages" + }, + { + "value": "LIGAND_INTERACTION", + "detail": "Ligand interactions with macromolecular target (includes covalent, metal coordination, and non-bonded interactions)", + "name": "Ligand Interactions" + }, + { + "value": "LIGAND_METAL_COORDINATION_LINKAGE", + "detail": "Metal coordination ligand linkages with macromolecular target", + "name": "Metal Coordination Ligand Linkages" + }, { "value": "MA_QA_METRIC_LOCAL_TYPE_CONTACT_PROBABILITY", "detail": "the contact probability of a pairwise interaction", @@ -1541,6 +1559,9 @@ "HELX_RH_3T_P", "HELX_RH_AL_P", "HELX_RH_PI_P", + "LIGAND_COVALENT_LINKAGE", + "LIGAND_INTERACTION", + "LIGAND_METAL_COORDINATION_LINKAGE", "MA_QA_METRIC_LOCAL_TYPE_CONTACT_PROBABILITY", "MA_QA_METRIC_LOCAL_TYPE_DISTANCE", "MA_QA_METRIC_LOCAL_TYPE_ENERGY", @@ -1656,6 +1677,21 @@ "detail": "Right-handed pi helix (protein)", "name": "Right-handed pi helix (protein)" }, + { + "value": "LIGAND_COVALENT_LINKAGE", + "detail": "Covalent ligand linkages with macromolecular target", + "name": "Covalent Ligand Linkages" + }, + { + "value": "LIGAND_INTERACTION", + "detail": "Ligand interactions with macromolecular target (includes covalent, metal coordination, and non-bonded interactions)", + "name": "Ligand Interactions" + }, + { + "value": "LIGAND_METAL_COORDINATION_LINKAGE", + "detail": "Metal coordination ligand linkages with macromolecular target", + "name": "Metal Coordination Ligand Linkages" + }, { "value": "MA_QA_METRIC_LOCAL_TYPE_CONTACT_PROBABILITY", "detail": "the contact probability of a pairwise interaction", @@ -2419,7 +2455,7 @@ ], "$id": "https://github.com/rcsb/py-rcsb.db/tree/master/rcsb.db/data/json-schema/json-schema-min-pdbx_core_polymer_entity_instance.json", "$schema": "http://json-schema.org/draft-04/schema#", - "title": "schema: pdbx_core collection: pdbx_core_polymer_entity_instance version: 10.0.1", - "description": "RCSB Exchange Database JSON schema derived from the pdbx_core content type schema. This schema supports collection pdbx_core_polymer_entity_instance version 10.0.1. This schema is hosted in repository https://github.com/rcsb/py-rcsb.db/tree/master/rcsb.db/data/json-schema/json-schema-min-pdbx_core_polymer_entity_instance.json and follows JSON schema specification version 4", - "$comment": "schema_version: 10.0.1" + "title": "schema: pdbx_core collection: pdbx_core_polymer_entity_instance version: 10.0.2", + "description": "RCSB Exchange Database JSON schema derived from the pdbx_core content type schema. This schema supports collection pdbx_core_polymer_entity_instance version 10.0.2. This schema is hosted in repository https://github.com/rcsb/py-rcsb.db/tree/master/rcsb.db/data/json-schema/json-schema-min-pdbx_core_polymer_entity_instance.json and follows JSON schema specification version 4", + "$comment": "schema_version: 10.0.2" } \ No newline at end of file diff --git a/schemas/exchange/schema_mapping/schema_def-pdbx_core-ANY.json b/schemas/exchange/schema_mapping/schema_def-pdbx_core-ANY.json index c3e4311..3b0558f 100644 --- a/schemas/exchange/schema_mapping/schema_def-pdbx_core-ANY.json +++ b/schemas/exchange/schema_mapping/schema_def-pdbx_core-ANY.json @@ -65585,6 +65585,9 @@ "HELX_RH_3T_P", "HELX_RH_AL_P", "HELX_RH_PI_P", + "LIGAND_COVALENT_LINKAGE", + "LIGAND_INTERACTION", + "LIGAND_METAL_COORDINATION_LINKAGE", "MA_QA_METRIC_LOCAL_TYPE_CONTACT_PROBABILITY", "MA_QA_METRIC_LOCAL_TYPE_DISTANCE", "MA_QA_METRIC_LOCAL_TYPE_ENERGY", @@ -66069,6 +66072,9 @@ "HELX_RH_3T_P", "HELX_RH_AL_P", "HELX_RH_PI_P", + "LIGAND_COVALENT_LINKAGE", + "LIGAND_INTERACTION", + "LIGAND_METAL_COORDINATION_LINKAGE", "MA_QA_METRIC_LOCAL_TYPE_CONTACT_PROBABILITY", "MA_QA_METRIC_LOCAL_TYPE_DISTANCE", "MA_QA_METRIC_LOCAL_TYPE_ENERGY", @@ -80998,6 +81004,9 @@ "HELX_RH_3T_P", "HELX_RH_AL_P", "HELX_RH_PI_P", + "LIGAND_COVALENT_LINKAGE", + "LIGAND_INTERACTION", + "LIGAND_METAL_COORDINATION_LINKAGE", "MA_QA_METRIC_LOCAL_TYPE_CONTACT_PROBABILITY", "MA_QA_METRIC_LOCAL_TYPE_DISTANCE", "MA_QA_METRIC_LOCAL_TYPE_ENERGY", @@ -81463,6 +81472,9 @@ "HELX_RH_3T_P", "HELX_RH_AL_P", "HELX_RH_PI_P", + "LIGAND_COVALENT_LINKAGE", + "LIGAND_INTERACTION", + "LIGAND_METAL_COORDINATION_LINKAGE", "MA_QA_METRIC_LOCAL_TYPE_CONTACT_PROBABILITY", "MA_QA_METRIC_LOCAL_TYPE_DISTANCE", "MA_QA_METRIC_LOCAL_TYPE_ENERGY", @@ -99952,7 +99964,7 @@ }, { "NAME": "pdbx_core_polymer_entity_instance", - "VERSION": "10.0.1" + "VERSION": "10.0.2" }, { "NAME": "pdbx_core_nonpolymer_entity_instance", diff --git a/schemas/exchange/working/bson-min-db-pdbx_core-col-pdbx_core_polymer_entity_instance.json b/schemas/exchange/working/bson-min-db-pdbx_core-col-pdbx_core_polymer_entity_instance.json index 8507c0c..3eb7c3d 100644 --- a/schemas/exchange/working/bson-min-db-pdbx_core-col-pdbx_core_polymer_entity_instance.json +++ b/schemas/exchange/working/bson-min-db-pdbx_core-col-pdbx_core_polymer_entity_instance.json @@ -225,6 +225,9 @@ "HELX_RH_3T_P", "HELX_RH_AL_P", "HELX_RH_PI_P", + "LIGAND_COVALENT_LINKAGE", + "LIGAND_INTERACTION", + "LIGAND_METAL_COORDINATION_LINKAGE", "MA_QA_METRIC_LOCAL_TYPE_CONTACT_PROBABILITY", "MA_QA_METRIC_LOCAL_TYPE_DISTANCE", "MA_QA_METRIC_LOCAL_TYPE_ENERGY", @@ -396,6 +399,9 @@ "HELX_RH_3T_P", "HELX_RH_AL_P", "HELX_RH_PI_P", + "LIGAND_COVALENT_LINKAGE", + "LIGAND_INTERACTION", + "LIGAND_METAL_COORDINATION_LINKAGE", "MA_QA_METRIC_LOCAL_TYPE_CONTACT_PROBABILITY", "MA_QA_METRIC_LOCAL_TYPE_DISTANCE", "MA_QA_METRIC_LOCAL_TYPE_ENERGY", diff --git a/schemas/exchange/working/json-min-db-pdbx_core-col-pdbx_core_polymer_entity_instance.json b/schemas/exchange/working/json-min-db-pdbx_core-col-pdbx_core_polymer_entity_instance.json index 115e64e..682bb95 100644 --- a/schemas/exchange/working/json-min-db-pdbx_core-col-pdbx_core_polymer_entity_instance.json +++ b/schemas/exchange/working/json-min-db-pdbx_core-col-pdbx_core_polymer_entity_instance.json @@ -863,6 +863,9 @@ "HELX_RH_3T_P", "HELX_RH_AL_P", "HELX_RH_PI_P", + "LIGAND_COVALENT_LINKAGE", + "LIGAND_INTERACTION", + "LIGAND_METAL_COORDINATION_LINKAGE", "MA_QA_METRIC_LOCAL_TYPE_CONTACT_PROBABILITY", "MA_QA_METRIC_LOCAL_TYPE_DISTANCE", "MA_QA_METRIC_LOCAL_TYPE_ENERGY", @@ -974,6 +977,21 @@ "detail": "Right-handed pi helix (protein)", "name": "Right-handed pi helix (protein)" }, + { + "value": "LIGAND_COVALENT_LINKAGE", + "detail": "Covalent ligand linkages with macromolecular target", + "name": "Covalent Ligand Linkages" + }, + { + "value": "LIGAND_INTERACTION", + "detail": "Ligand interactions with macromolecular target (includes covalent, metal coordination, and non-bonded interactions)", + "name": "Ligand Interactions" + }, + { + "value": "LIGAND_METAL_COORDINATION_LINKAGE", + "detail": "Metal coordination ligand linkages with macromolecular target", + "name": "Metal Coordination Ligand Linkages" + }, { "value": "MA_QA_METRIC_LOCAL_TYPE_CONTACT_PROBABILITY", "detail": "the contact probability of a pairwise interaction", @@ -1541,6 +1559,9 @@ "HELX_RH_3T_P", "HELX_RH_AL_P", "HELX_RH_PI_P", + "LIGAND_COVALENT_LINKAGE", + "LIGAND_INTERACTION", + "LIGAND_METAL_COORDINATION_LINKAGE", "MA_QA_METRIC_LOCAL_TYPE_CONTACT_PROBABILITY", "MA_QA_METRIC_LOCAL_TYPE_DISTANCE", "MA_QA_METRIC_LOCAL_TYPE_ENERGY", @@ -1656,6 +1677,21 @@ "detail": "Right-handed pi helix (protein)", "name": "Right-handed pi helix (protein)" }, + { + "value": "LIGAND_COVALENT_LINKAGE", + "detail": "Covalent ligand linkages with macromolecular target", + "name": "Covalent Ligand Linkages" + }, + { + "value": "LIGAND_INTERACTION", + "detail": "Ligand interactions with macromolecular target (includes covalent, metal coordination, and non-bonded interactions)", + "name": "Ligand Interactions" + }, + { + "value": "LIGAND_METAL_COORDINATION_LINKAGE", + "detail": "Metal coordination ligand linkages with macromolecular target", + "name": "Metal Coordination Ligand Linkages" + }, { "value": "MA_QA_METRIC_LOCAL_TYPE_CONTACT_PROBABILITY", "detail": "the contact probability of a pairwise interaction", @@ -2419,7 +2455,7 @@ ], "$id": "https://github.com/rcsb/py-rcsb.db/tree/master/rcsb.db/data/json-schema/json-schema-min-pdbx_core_polymer_entity_instance.json", "$schema": "http://json-schema.org/draft-04/schema#", - "title": "schema: pdbx_core collection: pdbx_core_polymer_entity_instance version: 10.0.1", - "description": "RCSB Exchange Database JSON schema derived from the pdbx_core content type schema. This schema supports collection pdbx_core_polymer_entity_instance version 10.0.1. This schema is hosted in repository https://github.com/rcsb/py-rcsb.db/tree/master/rcsb.db/data/json-schema/json-schema-min-pdbx_core_polymer_entity_instance.json and follows JSON schema specification version 4", - "$comment": "schema_version: 10.0.1" + "title": "schema: pdbx_core collection: pdbx_core_polymer_entity_instance version: 10.0.2", + "description": "RCSB Exchange Database JSON schema derived from the pdbx_core content type schema. This schema supports collection pdbx_core_polymer_entity_instance version 10.0.2. This schema is hosted in repository https://github.com/rcsb/py-rcsb.db/tree/master/rcsb.db/data/json-schema/json-schema-min-pdbx_core_polymer_entity_instance.json and follows JSON schema specification version 4", + "$comment": "schema_version: 10.0.2" } \ No newline at end of file