def define_tdoc_struct_ref_seq_dif():
table_name='struct_ref_seq_dif'
comment='Table that provides a mechanism for indicating and annotating point differences in the alignment of the macromolecular sequence with the reference sequence; mmCIF category: struct_ref_seq_dif'
column_defs = [
Column.define(
"pdbx_ordinal",
builtin_types.int8,
comment='A unique identifier for a record in the table',
nullok=False
),
Column.define(
"align_id",
builtin_types.text,
comment='A pointer to the alignment in the struct_ref_seq table',
nullok=False
),
Column.define(
"seq_num",
builtin_types.int8,
comment='The position in the macromolecular sequence with the point difference',
nullok=True
),
Column.define(
"mon_id",
builtin_types.text,
comment='The monomer type in the macromolecular sequence with the point difference',
nullok=True
),
Column.define(
"db_mon_id",
builtin_types.text,
comment='The monomer type in the reference database sequence with the point difference',
nullok=True
),
Column.define(
"details",
builtin_types.text,
comment='Additional details about the special aspects of the point difference',
nullok=True
),
Column.define(
"structure_id",
builtin_types.text,
comment='Structure identifier',
nullok=False
),
# HT: to use for Chaise
Column.define(
"Align_RID",
builtin_types.text,
comment='Identifier to the alignment RID',
nullok=False
)
]
key_defs = [
Key.define(["structure_id", "pdbx_ordinal"], constraint_names=[["PDB", "struct_ref_seq_dif_primary_key"]] ),
Key.define(["RID"], constraint_names=[["PDB", "struct_ref_seq_dif_RID_key"]] )
]
# @brinda: add fk pseudo-definition
fkey_defs = [
# HT: it own fk to Entry table
ForeignKey.define(["structure_id"], "PDB", "entry", ["id"],
constraint_names=[["PDB", "struct_ref_seq_dif_structure_id_fkey"]],
on_update="CASCADE",
on_delete="NO ACTION"
),
# HT: In annotation, apply domain_filter to filter the RID list by constraining structure_id
ForeignKey.define(["Align_RID", "structure_id", "align_id"], "PDB", "struct_ref_seq", ["RID", "structure_id", "align_id"],
constraint_names=[["PDB", "struct_ref_seq_dif_struct_ref_seq_combo1_fkey"]],
on_update="CASCADE",
on_delete="NO ACTION"
),
ForeignKey.define(["details"], "Vocab", "struct_ref_seq_dif_details", ["Name"],
constraint_names=[ ["Vocab", "struct_ref_seq_dif_details_fkey"] ],
on_update="CASCADE",
on_delete="NO ACTION"
)
]
table_def = Table.define(
table_name,
column_defs,
key_defs=key_defs,
fkey_defs=fkey_defs,
comment=comment,
provide_system=True
)
return table_def
config.acls.update(acls)
catalog.applyCatalogConfig(config)
for fname in monarch_files:
print('Importing {fname}...'.format(fname=fname))
tname = os.path.splitext(os.path.basename(fname))[0]
pk = 'pk'
col_defs = [Column.define(pk, builtin_types.int8)]
key_defs = [Key.define([pk])]
with open(fname) as tsvfile:
reader = csv.DictReader(tsvfile, delimiter='\t')
for cname in reader.fieldnames:
col_defs.append(Column.define(cname, builtin_types.text))
tab_def = Table.define(tname, column_defs=col_defs, key_defs=key_defs, acls=acls, provide_system=False)
print('Creating table {tname}...'.format(tname=tname))
try:
public.create_table(catalog, tab_def)
except HTTPError as e:
print(e)
print(e.response.text)
exit(1)
# Now to import data...
pb = catalog.getPathBuilder()
table = pb.public.tables[tname]
print('Importing data into {tname}'.format(tname=tname))
print(table.uri)
def define_tdoc_struct_ref_seq():
table_name='struct_ref_seq'
comment='Table that provides a mechanism for indicating and annotating the regions of alignment between the macromolecular sequence of an entity in the integrative model and the sequence in the reference database; mmCIF category: struct_ref_seq'
column_defs = [
Column.define(
"align_id",
builtin_types.text,
comment='A unique identifier for a record in the table',
nullok=False
),
Column.define(
"ref_id",
builtin_types.text,
comment='A pointer to the reference in the struct_ref table',
nullok=False
),
Column.define(
"db_align_beg",
builtin_types.int8,
comment='The sequence position in the referenced database entry at which the alignment begins',
nullok=False
),
Column.define(
"db_align_end",
builtin_types.int8,
comment='The sequence position in the referenced database entry at which the alignment ends',
nullok=False
),
Column.define(
"seq_align_beg",
builtin_types.int8,
comment='The position in the macromolecular entity sequence at which the alignment begins',
nullok=False
),
Column.define(
"seq_align_end",
builtin_types.int8,
comment='The position in the macromolecular entity sequence at which the alignment ends',
nullok=False
),
Column.define(
"details",
builtin_types.text,
comment='Additional details about the alignment',
nullok=True
),
Column.define(
"structure_id",
builtin_types.text,
comment='Structure identifier',
nullok=False
),
# HT: to use for Chaise
Column.define(
"Ref_RID",
builtin_types.text,
comment='Identifier to the reference RID',
nullok=False
)
]
key_defs = [
Key.define(["structure_id", "align_id"], constraint_names=[["PDB", "struct_ref_seq_primary_key"]] ),
Key.define(["RID"], constraint_names=[["PDB", "struct_ref_seq_RID_key"]] ),
Key.define(["RID", "structure_id", "align_id"], constraint_names=[["PDB", "struct_ref_seq_combo1_key"]] )
]
# @brinda: add fk pseudo-definition
fkey_defs = [
# HT: it own fk to Entry table
ForeignKey.define(["structure_id"], "PDB", "entry", ["id"],
constraint_names=[["PDB", "struct_ref_seq_structure_id_fkey"]],
on_update="CASCADE",
on_delete="NO ACTION"
),
# HT: In annotation, apply domain_filter to filter the RID list by constraining structure_id
ForeignKey.define(["Ref_RID", "structure_id", "ref_id"], "PDB", "struct_ref", ["RID", "structure_id", "id"],
constraint_names=[["PDB", "struct_ref_seq_struct_ref_combo1_fkey"]],
on_update="CASCADE",
on_delete="NO ACTION"
)
]
table_def = Table.define(
table_name,
column_defs,
key_defs=key_defs,
fkey_defs=fkey_defs,
comment=comment,
provide_system=True
)
return table_def
def define_tdoc_ihm_derived_dihedral_restraint():
table_name = 'ihm_derived_dihedral_restraint'
comment = 'Details of dihedral restraints used in integrative modeling; can be uploaded as CSV/TSV file above; mmCIF category: ihm_derived_dihedral_restraint'
column_defs = [
Column.define("id",
builtin_types.int8,
comment='An identifier for the dihedral restraint',
nullok=False),
Column.define("group_id",
builtin_types.int8,
comment='An identifier to group the dihedral restraints',
nullok=True),
Column.define(
"feature_id_1",
builtin_types.int8,
comment=
'The feature identifier for the first partner in the dihedral restraint',
nullok=False),
Column.define(
"feature_id_2",
builtin_types.int8,
comment=
'The feature identifier for the second partner in the dihedral restraint',
nullok=False),
Column.define(
"feature_id_3",
builtin_types.int8,
comment=
'The feature identifier for the third partner in the dihedral restraint',
nullok=False),
Column.define(
"feature_id_4",
builtin_types.int8,
comment=
'The feature identifier for the fourth partner in the dihedral restraint',
nullok=False),
Column.define(
"group_conditionality",
builtin_types.text,
comment=
'If a group of dihedrals are restrained together, this data item defines the conditionality based on which the restraint is applied in the modeling',
nullok=True),
Column.define(
"dihedral_lower_limit",
builtin_types.float8,
comment=
'The lower limit to the threshold applied to this dihedral restraint',
nullok=True),
Column.define(
"dihedral_upper_limit",
builtin_types.float8,
comment=
'The upper limit to the threshold applied to this dihedral restraint',
nullok=True),
Column.define(
"dihedral_lower_limit_esd",
builtin_types.float8,
comment=
'The estimated standard deviation of the lower limit dihedral threshold applied',
nullok=True),
Column.define(
"dihedral_upper_limit_esd",
builtin_types.float8,
comment=
'The estimated standard deviation of the upper limit dihedral threshold applied',
nullok=True),
Column.define(
"probability",
builtin_types.float8,
comment='The probability that the dihedral restraint is correct',
nullok=True),
Column.define("restraint_type",
builtin_types.text,
comment='The type of dihedral restraint applied',
nullok=False),
Column.define(
"dihedral_threshold_mean",
builtin_types.float8,
comment='The dihedral threshold mean applied to the restraint',
nullok=True),
Column.define(
"dihedral_threshold_mean_esd",
builtin_types.float8,
comment=
'The estimated standard deviation of the dihedral threshold mean applied to the restraint',
nullok=True),
Column.define(
"dataset_list_id",
builtin_types.int8,
comment=
'Identifier to the input data from which the dihedral restraint is derived',
nullok=False),
Column.define(
"Entry_Related_File",
builtin_types.text,
comment=
'A reference to the uploaded restraint file in the table Entry_Related_File.id.',
nullok=True),
Column.define("structure_id",
builtin_types.text,
comment='Structure identifier',
nullok=False),
# HT: to use for Chaise
Column.define("Feature_Id_1_RID",
builtin_types.text,
comment='Identifier to the feature 1 RID',
nullok=False),
Column.define("Feature_Id_2_RID",
builtin_types.text,
comment='Identifier to the feature 2 RID',
nullok=False),
Column.define("Feature_Id_3_RID",
builtin_types.text,
comment='Identifier to the feature 3 RID',
nullok=False),
Column.define("Feature_Id_4_RID",
builtin_types.text,
comment='Identifier to the feature 4 RID',
nullok=False),
Column.define("Dataset_List_RID",
builtin_types.text,
comment='Identifier to the dataset list RID',
nullok=False)
]
#BV: This is a leaf table; so no combo1/combo2 keys required
key_defs = [
Key.define(["structure_id", "id"],
constraint_names=[[
"PDB", "ihm_derived_dihedral_restraint_primary_key"
]]),
Key.define(["RID"],
constraint_names=[[
"PDB", "ihm_derived_dihedral_restraint_RID_key"
]]),
]
# @brinda: add fk pseudo-definition
fkey_defs = [
# HT: it own fk to Entry table
ForeignKey.define(
["structure_id"],
"PDB",
"entry", ["id"],
constraint_names=[[
"PDB", "ihm_derived_dihedral_restraint_structure_id_fkey"
]],
on_update="CASCADE",
on_delete="NO ACTION"),
# HT: In annotation, apply domain_filter to filter the RID list by constraining structure_id
ForeignKey.define(
["Feature_Id_1_RID", "structure_id", "feature_id_1"],
"PDB",
"ihm_feature_list", ["RID", "structure_id", "feature_id"],
constraint_names=[[
"PDB",
"ihm_derived_dihedral_restraint_ihm_feature_list_1_combo1_fkey"
]],
on_update="CASCADE",
on_delete="NO ACTION"),
ForeignKey.define(
["Feature_Id_2_RID", "structure_id", "feature_id_2"],
"PDB",
"ihm_feature_list", ["RID", "structure_id", "feature_id"],
constraint_names=[[
"PDB",
"ihm_derived_dihedral_restraint_ihm_feature_list_2_combo1_fkey"
]],
on_update="CASCADE",
on_delete="NO ACTION"),
ForeignKey.define(
["Feature_Id_3_RID", "structure_id", "feature_id_3"],
"PDB",
"ihm_feature_list", ["RID", "structure_id", "feature_id"],
constraint_names=[[
"PDB",
"ihm_derived_dihedral_restraint_ihm_feature_list_3_combo1_fkey"
]],
on_update="CASCADE",
on_delete="NO ACTION"),
ForeignKey.define(
["Feature_Id_4_RID", "structure_id", "feature_id_4"],
"PDB",
"ihm_feature_list", ["RID", "structure_id", "feature_id"],
constraint_names=[[
"PDB",
"ihm_derived_dihedral_restraint_ihm_feature_list_4_combo1_fkey"
]],
on_update="CASCADE",
on_delete="NO ACTION"),
ForeignKey.define(
["Dataset_List_RID", "structure_id", "dataset_list_id"],
"PDB",
"ihm_dataset_list", ["RID", "structure_id", "id"],
constraint_names=[[
"PDB",
"ihm_derived_dihedral_restraint_ihm_dataset_list_combo1_fkey"
]],
on_update="CASCADE",
on_delete="NO ACTION"),
ForeignKey.define(
["group_conditionality"],
"Vocab",
"ihm_derived_dihedral_restraint_group_conditionality", ["Name"],
constraint_names=[[
"Vocab",
"ihm_derived_dihedral_restraint_group_conditionality_fkey"
]],
on_update="CASCADE",
on_delete="NO ACTION"),
ForeignKey.define(
["restraint_type"],
"Vocab",
"ihm_derived_dihedral_restraint_restraint_type", ["Name"],
constraint_names=[[
"Vocab", "ihm_derived_dihedral_restraint_restraint_type_fkey"
]],
on_update="CASCADE",
on_delete="NO ACTION"),
ForeignKey.define(
["Entry_Related_File"],
"PDB",
"Entry_Related_File", ["RID"],
constraint_names=[[
"PDB", "ihm_derived_dihedral_restraint_Entry_Related_File_fkey"
]],
on_update="CASCADE",
on_delete="NO ACTION")
]
table_def = Table.define(table_name,
column_defs,
key_defs=key_defs,
fkey_defs=fkey_defs,
comment=comment,
provide_system=True)
return table_def