@rcsb/rcsb-saguaro-app 6.0.0-development.1 → 6.0.0-development.2

package/lib/RcsbAnnotationConfig/RcsbResidueConfig.ac.json

@@ -0,0 +1,685 @@
+{
+    "provenance_color_code": {
+        "external": "#DB9128",
+        "rcsb_pdb": "#325880",
+        "rcsb_link": "#5e94c3",
+        "csm": "#1abdcf"
+    },
+    "merge": [
+        {
+            "merged_types": ["UNOBSERVED_RESIDUE_XYZ", "UNOBSERVED_ATOM_XYZ"],
+            "type": "UNOBSERVED",
+            "title": "UNMODELED",
+            "display": "block"
+        },
+        {
+            "merged_types": ["TOPOLOGICAL_DOMAIN", "TRANSMEMBRANE_REGION", "INTRAMEMBRANE_REGION"],
+            "type": "MEMBRANE_TOPOLOGY",
+            "title": "MEMBRANE TOPOLOGY",
+            "display": "block"
+        }, {
+            "merged_types": ["INITIATOR_METHIONINE", "CHAIN", "SIGNAL_PEPTIDE"],
+            "type": "MOLECULE_PROCESSING",
+            "title": "MOLECULE PROCESSING",
+            "display": "block"
+        }, {
+            "merged_types": ["HELIX_P", "HELX_LH_PP_P", "HELX_RH_AL_P", "HELX_RH_3_T_P", "HELX_RH_PI_P"],
+            "type": "HELIX",
+            "title": "HELIX",
+            "display": "block"
+        }, {
+            "merged_types": ["SHEET", "STRN"],
+            "type": "SHEET",
+            "title": "SHEET",
+            "display": "block"
+        }, {
+            "merged_types": ["BEND", "TURN_TY_1_P"],
+            "type": "TURN",
+            "title": "TURN",
+            "display": "block"
+        }, {
+            "merged_types": ["SCOP_2_FAMILY", "SCOP_2_SUPERFAMILY", "SCOP_2_B_SUPERFAMILY", "SCOP"],
+            "type": "ALL_SCOP",
+            "title": "SCOP",
+            "display": "block"
+        }
+    ],
+    "external_data_order": [
+        "PFAM",
+        "CATH",
+        "ALL_SCOP",
+        "SCOP",
+        "SCOP_2_B_SUPERFAMILY",
+        "SCOP2_FAMILY",
+        "SCOP2_SUPERFAMILY",
+        "ECOD",
+        "IMGT_ANTIBODY_DESCRIPTION",
+        "IMGT_ANTIBODY_DOMAIN_NAME",
+        "IMGT_ANTIBODY_GENE_ALLELE_NAME",
+        "IMGT_ANTIBODY_ORGANISM_NAME",
+        "IMGT_ANTIBODY_PROTEIN_NAME",
+        "IMGT_ANTIBODY_RECEPTOR_DESCRIPTION",
+        "IMGT_ANTIBODY_RECEPTOR_TYPE",
+        "SABDAB_ANTIBODY_ANTIGEN_NAME",
+        "SABDAB_ANTIBODY_NAME",
+        "SABDAB_ANTIBODY_TARGET",
+        "SABDAB_ANTIBODY_HEAVY_CHAIN_SUBCLASS",
+        "SABDAB_ANTIBODY_LIGHT_CHAIN_SUBCLASS",
+        "SABDAB_ANTIBODY_LIGHT_CHAIN_TYPE",
+        "MOLECULE_PROCESSING",
+        "MEMBRANE_TOPOLOGY",
+        "MEMBRANE_SEGMENT",
+        "CHAIN",
+        "INITIATOR_METHIONINE",
+        "SEQUENCE_VARIANT",
+        "GLYCOSYLATION_SITE",
+        "LIPID_MOIETY_BINDING_REGION",
+        "CROSS_LINK",
+        "DISULFIDE_BOND",
+        "METAL_ION_BINDING_SITE",
+        "NUCLEOTIDE_PHOSPHATE_BINDING_REGION",
+        "DNA_BINDING_REGION",
+        "ACTIVE_SITE",
+        "MODIFIED_RESIDUE",
+        "MUTAGENESIS_SITE",
+        "SEQUENCE_CONFLICT",
+        "SITE",
+        "SHORT_SEQUENCE_MOTIF",
+        "ZINC_FINGER_REGION",
+        "PROPEPTIDE",
+        "TRANSMEMBRANE_REGION",
+        "INTRAMEMBRANE_REGION",
+        "TOPOLOGICAL_DOMAIN",
+        "COILED_COIL_REGION",
+        "REPEAT",
+        "DOMAIN",
+        "REGION_OF_INTEREST",
+        "COMPOSITIONALLY_BIASED_REGION",
+        "SPLICE_VARIANT",
+        "NON_TERMINAL_RESIDUE",
+        "TURN",
+        "SIGNAL_PEPTIDE",
+        "CARD_MODEL",
+        "CALCIUM_BINDING_REGION",
+        "PEPTIDE"
+    ],
+    "instance_order": [
+        "SECONDARY_STRUCTURE",
+        "HELIX_P",
+        "SHEET",
+        "UNOBSERVED",
+        "UNOBSERVED_RESIDUE_XYZ",
+        "UNOBSERVED_ATOM_XYZ",
+        "ZERO_OCCUPANCY_RESIDUE_XYZ",
+        "ZERO_OCCUPANCY_ATOM_XYZ",
+        "RAMACHANDRAN_OUTLIER",
+        "ANGLE_OUTLIER",
+        "BOND_OUTLIER",
+        "ROTAMER_OUTLIER",
+        "RSRZ_OUTLIER",
+        "RSCC_OUTLIER",
+        "RSRCC_OUTLIER",
+        "MOGUL_ANGLE_OUTLIER",
+        "MOGUL_BOND_OUTLIER",
+        "STEREO_OUTLIER",
+        "CIS_PEPTIDE",
+        "BINDING_SITE",
+        "ASA_UNBOUND",
+        "ASA_BOUND",
+        "BURIAL_FRACTION",
+        "BURIED_RESIDUES",
+        "DISULFIDE_BRIDGE",
+        "COVALENT_BOND",
+        "METAL_COORDINATION",
+        "HYDROGEN_BOND"
+    ],
+    "entity_order": [
+        "ARTIFACT",
+        "MUTATION",
+        "MODIFIED_MONOMER",
+        "HYDROPATHY",
+        "DISORDER",
+        "DISORDER_BINDING"
+    ],
+    "config": [{
+            "type": "CARD_MODEL",
+            "color": "#4d901b",
+            "display": "block",
+            "title": "CARD"
+        }, {
+            "type": "ECOD",
+            "color": "#42d0b1",
+            "display": "block",
+            "title": "ECOD"
+        }, {
+            "type": "IMGT_ANTIBODY_DOMAIN_NAME",
+            "color": "#3c0d7f",
+            "display": "block",
+            "title": "ANTIBODY DOMAIN"
+        }, {
+            "type": "SABDAB_ANTIBODY_HEAVY_CHAIN_SUBCLASS",
+            "color": "#4c9f0d",
+            "display": "block",
+            "title": "ANTIBODY HEAVY CHAIN",
+            "ignore": true
+        }, {
+            "type": "SABDAB_ANTIBODY_LIGHT_CHAIN_SUBCLASS",
+            "color": "#4c9f0d",
+            "display": "block",
+            "title": "ANTIBODY HEAVY CHAIN",
+            "ignore": true
+        }, {
+            "type": "SABDAB_ANTIBODY_LIGHT_CHAIN_TYPE",
+            "color": "#4c9f0d",
+            "display": "block",
+            "title": "ANTIBODY HEAVY CHAIN",
+            "ignore": true
+        }, {
+            "type": "IMGT_ANTIBODY_DESCRIPTION",
+            "color": "#bf5c0d",
+            "display": "block",
+            "title": "ANTIBODY DESCRIPTION",
+            "ignore": true
+        }, {
+            "type": "IMGT_ANTIBODY_GENE_ALLELE_NAME",
+            "color": "#bf5c0d",
+            "display": "block",
+            "title": "ANTIBODY GENE NAME",
+            "ignore": true
+        }, {
+            "type": "IMGT_ANTIBODY_ORGANISM_NAME",
+            "color": "#bf5c0d",
+            "display": "block",
+            "title": "ANTIBODY ORGANISM NAME",
+            "ignore": true
+        }, {
+            "type": "IMGT_ANTIBODY_PROTEIN_NAME",
+            "color": "#bf5c0d",
+            "display": "block",
+            "title": "ANTIBODY PROTEIN NAME",
+            "ignore": true
+        }, {
+            "type": "IMGT_ANTIBODY_RECEPTOR_DESCRIPTION",
+            "color": "#bf5c0d",
+            "display": "block",
+            "title": "ANTIBODY RECEPTOR DESCRIPTION",
+            "ignore": true
+        }, {
+            "type": "IMGT_ANTIBODY_RECEPTOR_TYPE",
+            "color": "#bf5c0d",
+            "display": "block",
+            "title": "ANTIBODY RECEPTOR TYPE",
+            "ignore": true
+        }, {
+            "type": "SABDAB_ANTIBODY_ANTIGEN_NAME",
+            "color": "#bf5c0d",
+            "display": "block",
+            "title": "ANTIBODY ANTIGEN NAME",
+            "ignore": true
+        }, {
+            "type": "SABDAB_ANTIBODY_NAME",
+            "color": "#bf5c0d",
+            "display": "block",
+            "title": "ANTIBODY NAME",
+            "ignore": true
+        }, {
+            "type": "SABDAB_ANTIBODY_TARGET",
+            "color": "#bf5c0d",
+            "display": "block",
+            "title": "ANTIBODY TARGET",
+            "ignore": true
+        }, {
+            "type": "HOMOLOGY MODELLING",
+            "color": "#2fcc5d",
+            "display": "block",
+            "title": "HOMOLOGY MODELS"
+        }, {
+            "type": "DISORDER_BINDING",
+            "display": "area",
+            "color": {
+                "thresholds": [0.5],
+                "colors": ["#8484FF", "#FF8484"]
+            },
+            "height": 45,
+            "title": "DISORDERED BINDING",
+            "domain": [0, 1]
+        }, {
+            "type": "HYDROPATHY",
+            "display": "area",
+            "color": {
+                "thresholds": [0],
+                "colors": ["#8484FF", "#FF8484"]
+            },
+            "height": 45,
+            "title": "HYDROPATHY"
+        }, {
+            "type": "DISORDER",
+            "display": "area",
+            "color": {
+                "thresholds": [0.5],
+                "colors": ["#8484FF", "#FF8484"]
+            },
+            "height": 45,
+            "title": "DISORDER",
+            "domain": [0, 1]
+        }, {
+            "type": "SEQUENCE_VARIANT",
+            "display": "composite",
+            "color": "#ff6666",
+            "title": "GENOME VARIANT"
+        }, {
+            "type": "ZINC_FINGER_REGION",
+            "display": "block",
+            "color": "#66ff66",
+            "title": "ZINC FINGER"
+        }, {
+            "type": "NUCLEOTIDE_PHOSPHATE_BINDING_REGION",
+            "display": "block",
+            "color": "#ffcc00",
+            "title": "NUCLEOTIDE BINDING"
+        }, {
+            "type": "DNA_BINDING_REGION",
+            "display": "block",
+            "color": "#ff5c9f",
+            "title": "DNA BINDING"
+        }, {
+            "type": "ACTIVE_SITE",
+            "display": "pin",
+            "color": "#ff88cc",
+            "title": "ACTIVE SITE"
+        }, {
+            "type": "COMPOSITIONALLY_BIASED_REGION",
+            "display": "block",
+            "color": "#D58874",
+            "title": "COMPOSITIONAL BIAS"
+        }, {
+            "type": "BINDING_SITE",
+            "display": "pin",
+            "color": "#984657",
+            "title": "BINDING SITE",
+            "key": "name",
+            "addToType": ["feature_id"]
+        }, {
+            "type": "MUTAGENESIS_SITE",
+            "display": "composite",
+            "color": "#b82a80",
+            "title": "MUTAGENESIS"
+        }, {
+            "type": "SEQUENCE_CONFLICT",
+            "display": "composite",
+            "color": "#e80368",
+            "title": "CONFLICT"
+        }, {
+            "type": "METAL_ION_BINDING_SITE",
+            "display": "pin",
+            "color": "#41a754",
+            "title": "METAL BINDING"
+        }, {
+            "type": "CROSS_LINK",
+            "display": "pin",
+            "color": "#0a39af",
+            "title": "CROSS-LINK"
+        }, {
+            "type": "INITIATOR_METHIONINE",
+            "display": "pin",
+            "color": "#e2916d",
+            "title": "INITIATOR METHIONINE"
+        }, {
+            "type": "MODIFIED_RESIDUE",
+            "display": "pin",
+            "color": "#44b8fd",
+            "title": "MODIFIED RESIDUE"
+        }, {
+            "type": "TURN",
+            "display": "block",
+            "color": "#155870",
+            "title": "TURN"
+        }, {
+            "type": "CHAIN",
+            "display": "block",
+            "color": "#ad9c5e",
+            "title": "CHAIN"
+        }, {
+            "type": "DOMAIN",
+            "display": "block",
+            "color": "#715e76",
+            "title": "DOMAIN"
+        }, {
+            "type": "SITE",
+            "display": "composite",
+            "color": "#b5748d",
+            "title": "SITE"
+        }, {
+            "type": "SHORT_SEQUENCE_MOTIF",
+            "display": "block",
+            "color": "#6a508e",
+            "title": "LINEAR MOTIF"
+        }, {
+            "type": "SPLICE_VARIANT",
+            "display": "block",
+            "color": "#f03634",
+            "title": "SEQUENCE SPLICING"
+        }, {
+            "type": "LIPID_MOIETY_BINDING_REGION",
+            "display": "pin",
+            "color": "#06cb7a",
+            "title": "LIPIDATION"
+        }, {
+            "type": "REGION_OF_INTEREST",
+            "display": "block",
+            "color": "#6797be",
+            "title": "REGION"
+        }, {
+            "type": "PROPEPTIDE",
+            "display": "block",
+            "color": "#94d687",
+            "title": "PROPEPTIDE"
+        }, {
+            "type": "UNOBSERVED_RESIDUE_XYZ",
+            "display": "block",
+            "color": "#cccccc",
+            "title": "UNMODELED RESIDUE"
+        }, {
+            "type": "ANGLE_OUTLIER",
+            "display": "area",
+            "color": "#aa33aa",
+            "height": 45,
+            "title": "ANGLE OUTLIER",
+            "transformToNumerical": true
+        }, {
+            "type": "ROTAMER_OUTLIER",
+            "display": "pin",
+            "color": "#33aaaa",
+            "title": "ROTAMER OUTLIER"
+        }, {
+            "type": "RAMACHANDRAN_OUTLIER",
+            "display": "pin",
+            "color": "#cc3333",
+            "title": "RAMACHANDRAN OUTLIER"
+        }, {
+            "type": "RSRCC_OUTLIER",
+            "display": "pin",
+            "color": "#cc33cc",
+            "title": "RSRCC OUTLIER"
+        }, {
+            "type": "BOND_OUTLIER",
+            "display": "area",
+            "color": "#33aa33",
+            "height": 45,
+            "title": "BOND OUTLIER",
+            "transformToNumerical": true
+        }, {
+            "type": "MOGUL_BOND_OUTLIER",
+            "display": "area",
+            "color": "#fcd303",
+            "height": 45,
+            "title": "MOGUL-BOND OUTLIER",
+            "transformToNumerical": true
+        }, {
+            "type": "MOGUL_ANGLE_OUTLIER",
+            "display": "area",
+            "color": "#d303fc",
+            "height": 45,
+            "title": "MOGUL-ANGLE OUTLIER",
+            "transformToNumerical": true
+        }, {
+            "type": "MUTATION",
+            "display": "pin",
+            "color": "#ebae56",
+            "title": "MUTATION"
+        }, {
+            "type": "mutation",
+            "display": "pin",
+            "color": "#ebae56",
+            "title": "MUTATION"
+        }, {
+            "type": "HELIX_P",
+            "display": "block",
+            "color": "#e43372",
+            "title": "HELIX"
+        }, {
+            "type": "HELX_LH_PP_P",
+            "display": "block",
+            "color": "#e43372",
+            "title": "HELIX"
+        }, {
+            "type": "HELX_RH_AL_P",
+            "display": "block",
+            "color": "#e43372",
+            "title": "HELIX"
+        }, {
+            "type": "HELX_RH_3_T_P",
+            "display": "block",
+            "color": "#e43372",
+            "title": "HELIX"
+        }, {
+            "type": "HELX_RH_PI_P",
+            "display": "block",
+            "color": "#e43372",
+            "title": "HELIX"
+        }, {
+            "type": "BEND",
+            "display": "block",
+            "color": "#65cbf3",
+            "title": "BEND"
+        }, {
+            "type": "TURN_TY_1_P",
+            "display": "block",
+            "color": "#0053d6",
+            "title": "TURN"
+        }, {
+            "type": "SHEET",
+            "display": "block",
+            "color": "#f1d23b",
+            "title": "BETA STRAND"
+        }, {
+            "type": "STRN",
+            "display": "block",
+            "color": "#f1d23b",
+            "title": "BETA STRAND"
+        }, {
+            "type": "CATH",
+            "display": "block",
+            "color": "#e4ad56",
+            "title": "CATH"
+        }, {
+            "type": "SCOP",
+            "display": "block",
+            "color": "#455d5a",
+            "title": "SCOP"
+        }, {
+            "type": "SCOP_2_FAMILY",
+            "display": "block",
+            "color": "#455d5a",
+            "title": "SCOP FAMILY"
+        }, {
+            "type": "SCOP_2_B_SUPERFAMILY",
+            "display": "block",
+            "color": "#455d5a",
+            "title": "SCOP SUPERFAMILY"
+        }, {
+            "type": "SCOP_2_SUPERFAMILY",
+            "display": "block",
+            "color": "#455d5a",
+            "title": "SCOP SUPERFAMILY"
+        }, {
+            "type": "PFAM",
+            "display": "block",
+            "color": "#ECACA6",
+            "title": "PFAM"
+        }, {
+            "type": "RSRZ_OUTLIER",
+            "display": "pin",
+            "color": "#3333aa",
+            "title": "RSRZ OUTLIER"
+        }, {
+            "type": "RSCC_OUTLIER",
+            "display": "pin",
+            "color": "#63339a",
+            "title": "RSCC OUTLIER"
+        }, {
+            "type": "UNOBSERVED_ATOM_XYZ",
+            "display": "block",
+            "color": "#b2997f",
+            "title": "UNMODELED ATOM"
+        }, {
+            "type": "ZERO_OCCUPANCY_ATOM_XYZ",
+            "display": "composite",
+            "color": "#aca86a",
+            "title": "ZERO OCCUPANCY ATOM"
+        }, {
+            "type": "CIS_PEPTIDE",
+            "display": "bond",
+            "color": "#761e47",
+            "title": "CIS-PEPTIDE"
+        }, {
+            "type": "HYDROGEN_BOND",
+            "display": "bond",
+            "color": "#76Ae47",
+            "title": "HYDROGEN BOND",
+            "ignore": true
+        }, {
+            "type": "ARTIFACT",
+            "display": "block",
+            "color": "#4c3f0f",
+            "title": "ARTIFACT"
+        }, {
+            "type": "ARTIFACT",
+            "display": "block",
+            "color": "#4c3f0f",
+            "title": "ARTIFACT"
+        }, {
+            "type": "TOPOLOGICAL_DOMAIN",
+            "display": "block",
+            "color": "#853faf",
+            "title": "TOPOLOGICAL DOMAIN"
+        }, {
+            "type": "INTRAMEMBRANE_REGION",
+            "display": "block",
+            "color": "#c58f0f",
+            "title": "INTRAMEMBRANE REGION"
+        }, {
+            "type": "TRANSMEMBRANE_REGION",
+            "display": "block",
+            "color": "#8fc50f",
+            "title": "TRANSMEMBRANE REGION"
+        }, {
+            "type": "REPEAT",
+            "display": "block",
+            "color": "#2ea37b",
+            "title": "REPEAT"
+        }, {
+            "type": "SIGNAL_PEPTIDE",
+            "display": "block",
+            "color": "#2ea3bb",
+            "title": "SIGNAL PEPTIDE"
+        }, {
+            "type": "COILED_COIL_REGION",
+            "display": "block",
+            "color": "#a2ac85",
+            "title": "COILED COIL REGION"
+        }, {
+            "type": "DISULFIDE_BRIDGE",
+            "display": "bond",
+            "color": "#6a534a",
+            "title": "DISULFIDE BRIDGE"
+        }, {
+            "type": "GLYCOSYLATION_SITE",
+            "display": "pin",
+            "color": "#6af34a",
+            "title": "GLYCOSYLATION"
+        }, {
+            "type": "NON_TERMINAL_RESIDUE",
+            "display": "pin",
+            "color": "#6af3fa",
+            "title": "NON-TERMINAL RESIDUE"
+        }, {
+            "type": "MODIFIED_MONOMER",
+            "display": "composite",
+            "color": "#458756",
+            "title": "MODIFIED MONOMER"
+        }, {
+            "type": "MODIFIED_MONOMER",
+            "display": "composite",
+            "color": "#458756",
+            "title": "MODIFIED MONOMER"
+        }, {
+            "type": "ZERO_OCCUPANCY_RESIDUE_XYZ",
+            "display": "composite",
+            "color": "#fca86a",
+            "title": "ZERO OCCUPANCY RESIDUE"
+        }, {
+            "type": "METAL_COORDINATION",
+            "display": "bond",
+            "color": "#aaaada",
+            "title": "METAL COORDINATION"
+        }, {
+            "type": "COVALENT_BOND",
+            "display": "bond",
+            "color": "#aadaaa",
+            "title": "COVALENT BOND"
+        }, {
+            "type": "MEMBRANE_SEGMENT",
+            "display": "block",
+            "color": "#8fc50f",
+            "title": "MEMBRANE SEGMENT",
+            "displayCooccurrence": true
+        }, {
+            "type": "CALCIUM_BINDING_REGION",
+            "display": "block",
+            "color": "#c58f0f",
+            "title": "CALCIUM BINDING"
+        }, {
+            "type": "PEPTIDE",
+            "display": "block",
+            "color": "#cf53df",
+            "title": "PEPTIDE"
+        }, {
+            "type": "STEREO_OUTLIER",
+            "display": "pin",
+            "color": "#cfdf53",
+            "title": "STEREO OUTLIER"
+        }, {
+            "type": "ASA_UNBOUND",
+            "display": "area",
+            "color": {
+                "thresholds": [50],
+                "colors": ["#8484FF", "#FF8484"]
+            },
+            "height": 45,
+            "title": "ASA UNBOUND"
+        }, {
+            "type": "ASA_BOUND",
+            "display": "area",
+            "color": {
+                "thresholds": [50],
+                "colors": ["#8484FF", "#FF8484"]
+            },
+            "height": 45,
+            "title": "ASA BOUND"
+        }, {
+            "type": "BURIAL_FRACTION",
+            "display": "block-area",
+            "color": {
+                "colors": "#8484FF",
+                "thresholds": [0.00001, 0.2, 0.4, 0.6, 0.8]
+            },
+            "title": "BURIAL FRACTION"
+        }, {
+            "type": "BURIED_RESIDUES",
+            "display": "block-area",
+            "color": {
+                "colors": "#44AA44",
+                "thresholds": [0.000001]
+            },
+            "title": "BURIED RESIDUES"
+        }, {
+            "type": "MA_QA_METRIC_LOCAL_TYPE_PLDDT",
+            "display": "block-area",
+            "color": {
+                "colors": ["#ff7d45", "#ffdb13", "#65cbf3", "#0053d6"],
+                "thresholds": [50, 70, 90]
+            },
+            "title": "pLDDT"
+        }]
+}