404 Extend CL validation and imports

backend/protzilla/constants/cif_columns.py

@@ -0,0 +1,63 @@
+from enum import StrEnum
+
+
+ATOM_SITE_PREFIX = "_atom_site."
+
+
+class ATOM_SITE_COLUMNS(StrEnum):
+    """
+    Enum containing all column names that should be present in
+    the _atom_site. table for mmCIF files from PDB or AFDB
+    """
+
+    ID = f"{ATOM_SITE_PREFIX}id"
+    TYPE_SYMBOL = f"{ATOM_SITE_PREFIX}type_symbol"
+    LABEL_ATOM_ID = f"{ATOM_SITE_PREFIX}label_atom_id"
+    LABEL_ALT_ID = f"{ATOM_SITE_PREFIX}label_alt_id"
+    LABEL_COMP_ID = f"{ATOM_SITE_PREFIX}label_comp_id"
+    LABEL_ASYM_ID = f"{ATOM_SITE_PREFIX}label_asym_id"
+    LABEL_ENTITY_ID = f"{ATOM_SITE_PREFIX}label_entity_id"
+    LABEL_SEQ_ID = f"{ATOM_SITE_PREFIX}label_seq_id"
+    PDBX_PDB_INS_CODE = f"{ATOM_SITE_PREFIX}pdbx_PDB_ins_code"
+    CARTN_X = f"{ATOM_SITE_PREFIX}Cartn_x"
+    CARTN_Y = f"{ATOM_SITE_PREFIX}Cartn_y"
+    CARTN_Z = f"{ATOM_SITE_PREFIX}Cartn_z"
+    OCCUPANCY = f"{ATOM_SITE_PREFIX}occupancy"
+    B_ISO_OR_EQUIV = f"{ATOM_SITE_PREFIX}B_iso_or_equiv"
+    PDBX_FORMAL_CHARGE = f"{ATOM_SITE_PREFIX}pdbx_formal_charge"
+    AUTH_SEQ_ID = f"{ATOM_SITE_PREFIX}auth_seq_id"
+    AUTH_COMP_ID = f"{ATOM_SITE_PREFIX}auth_comp_id"
+    AUTH_ASYM_ID = f"{ATOM_SITE_PREFIX}auth_asym_id"
+    AUTH_ATOM_ID = f"{ATOM_SITE_PREFIX}auth_atom_id"
+    PDBX_PDB_MODEL_NUM = f"{ATOM_SITE_PREFIX}pdbx_PDB_model_num"
+
+
+ATOM_SITE_LABEL_COMP_ID = ATOM_SITE_COLUMNS.LABEL_COMP_ID
+
+ATOM_SITE_COLUMNS_NUMERIC = [
+    ATOM_SITE_COLUMNS.ID,
+    ATOM_SITE_COLUMNS.LABEL_SEQ_ID,
+    ATOM_SITE_COLUMNS.CARTN_X,
+    ATOM_SITE_COLUMNS.CARTN_Y,
+    ATOM_SITE_COLUMNS.CARTN_Z,
+    ATOM_SITE_COLUMNS.OCCUPANCY,
+    ATOM_SITE_COLUMNS.B_ISO_OR_EQUIV,
+    ATOM_SITE_COLUMNS.AUTH_SEQ_ID,
+]
+
+CHEM_COMP_PREFIX = "_chem_comp."
+
+
+class CHEM_COMP_COLUMNS(StrEnum):
+    """
+    Enum containing all column names that should be present in
+    the _chem_comp. table for mmCIF files from PDB or AFDB
+    """
+
+    ID = f"{CHEM_COMP_PREFIX}id"
+    TYPE = f"{CHEM_COMP_PREFIX}type"
+    MON_NSTD_FLAG = f"{CHEM_COMP_PREFIX}mon_nstd_flag"
+    NAME = f"{CHEM_COMP_PREFIX}name"
+    PDBX_SYNONYMS = f"{CHEM_COMP_PREFIX}pdbx_synonyms"
+    FORMULA = f"{CHEM_COMP_PREFIX}formula"
+    FORMULA_WEIGHT = f"{CHEM_COMP_PREFIX}formula_weight"

backend/protzilla/constants/data_types.py

@@ -23,7 +23,7 @@ class DataKey(StrEnum):
     GENE_MAPPING_DF = "gene_mapping_df"
     CIF_DF = "cif_df"
     AMINO_ACID_SEQUENCES_DF = "amino_acid_sequences_df"
-    PAE_DF = "pae_df"  # pae = predicted aligned error
+    PAE_MATRIX = "pae_matrix"  # pae = predicted aligned error
     PLDDT_DF = "plddt_df"  # plddt = predicted local distance difference test
     CROSSLINKING_DF = "crosslinking_df"
     CONFIDENCE_DF = "confidence_df"

backend/protzilla/constants/option_types.py

@@ -60,6 +60,13 @@ class PValueColumnName(StrEnum):
     ptm = "PTM"
 
 
+class CrosslinkingValidationCriterion(Enum):
+    manual_bounds = "Manual Bounds (set below)"
+    max_pae = "CL length +/- maximum PAE between sites"
+    min_pae = "CL length +/- minimum PAE between sites"
+    plddt_adjusted = "plDDT adjusted"
+
+
 FC_SIGNIFICANCE_COLUMNS = ["Protein ID", "fc_z_score", "fc_significance"]
 CORRECTED_P_VALUES_COLUMNS = [
     "Protein ID",