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Merge pull request #10 from rcsb/ro-4209
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RO-4209: Update polymer instance features with ligand interaction enumerations
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@piehld
piehld authored Aug 14, 2024
2 parents cceafdd + 2205e29 commit 5c63cc0
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Showing 4 changed files with 97 additions and 7 deletions.
42 changes: 39 additions & 3 deletions schemas/exchange/min-meta/json-min-db-pdbx_core-col-pdbx_core_polymer_entity_instance.json
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Expand Up @@ -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",
Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -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"
}
14 changes: 13 additions & 1 deletion schemas/exchange/schema_mapping/schema_def-pdbx_core-ANY.json
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Expand Up @@ -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",
Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -99952,7 +99964,7 @@
},
{
"NAME": "pdbx_core_polymer_entity_instance",
"VERSION": "10.0.1"
"VERSION": "10.0.2"
},
{
"NAME": "pdbx_core_nonpolymer_entity_instance",
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6 changes: 6 additions & 0 deletions schemas/exchange/working/bson-min-db-pdbx_core-col-pdbx_core_polymer_entity_instance.json
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Expand Up @@ -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",
Expand Down Expand Up @@ -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",
Expand Down
42 changes: 39 additions & 3 deletions schemas/exchange/working/json-min-db-pdbx_core-col-pdbx_core_polymer_entity_instance.json
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Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -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"
}

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