PrimaryKeyConstraint(biomolecules.c.biomolecule_id,
deferrable=True,
initially='deferred')
Index('idx_biomolecules_structures_id',
biomolecules.c.structure_id,
biomolecules.c.assembly_serial,
unique=True)
Index('idx_biomolecules_path', biomolecules.c.path, postgresql_using='gist')
comments = {
"table":
"Stores the biological assemblies that are generated from an asymmetric unit.",
"columns": {
"biomolecule_id": "Primary key.",
"structure_id": "Primary key of the parent structure.",
"path": "ptree path in the form PDB/assembly serial number.",
"assembly_serial":
"Serial number of the assembly. Can be > 1 if asymmetric unit contains more than one biological assembly.",
"assembly_type": "Assembly type of the biomolecule, e.g. Monomeric.",
"conformational_state_bm":
"Bit mask of the conformational state of the biomolecule.",
"structural_interaction_bm":
"Bit mask of the kinds of structural interactions that are present.",
"num_chains": "Number of chains in biological assembly.",
"num_ligands": "Number of ligands in biological assembly.",
"num_atoms": "Number of atoms in biological assembly."
}
}
comment_on_table_elements(biomolecules, comments)
pi_groups_comments = {
"table": "Contains the non-ring pi groups found in structures.",
"columns": {
"pi_id": "Primary Key of the pi system.",
"biomolecule_id": "Foreign key of the parent biomolecule.",
"pi_serial": "Pi system serial number inside the parent biomolecule.",
#"pi_number": "Number of the pi system inside the residue it is part of.",
"size": "Number of atoms in the pi group.",
"centroid": "The Centroid of the pi group as vector3d type.",
"normal": "The normal of the pi group as vector3d type.",
#"is_hetero_aromatic": "True if the aromatic ring contains atoms other than carbon."
}
}
comment_on_table_elements(pi_groups, pi_groups_comments)
## table to hold pi group atoms
CURRENT_BIOMOL_MAX = app.config.get('schema', 'current_biomol_max')
PI_GROUP_PARTITION_SIZE = app.config.get(
'schema', 'pi_group_partition_size') # In terms of biomolecules
PI_GROUP_INS_RULE_DDL = """
CREATE OR REPLACE RULE {rule} AS
ON INSERT TO {schema}.{master_table}
WHERE (biomolecule_id > {part_bound_low} AND biomolecule_id <= {part_bound_high})
DO INSTEAD INSERT INTO {schema}.{table} VALUES (NEW.*)
"""
## pi group to residues map
pi_group_res = Table('pi_group_residues',
"pdb":
"PDB 4-letter code.",
"title":
"Title of the PDB deposition.",
"authors":
"Concatenated string of author names.",
"method":
"Method used in the experiment (exptl.method).",
"deposition_date":
"Date the entry first entered the PDB database in the form yyyy-mm-dd. Taken from the PDB HEADER record (database_PDB_rev.date_original).",
"modified_date":
"Date the latest PDB revision took place. Taken from the REVDAT record (database_PDB_rev.date).",
"resolution":
"Smallest value for the interplanar spacings for the reflection dataused in the refinement in angstroms. This is called the highest resolution (refine.ls_d_res_high).",
"r_factor":
"Residual factor R for reflections* that satisfy the reflns.observed_criterion were included in the refinement (when the refinement included the calculation of a free R factor) (refine.ls_R_factor_R_work).",
"r_free":
"Residual factor R for reflections that satisfy the reflns.observed_criterion that were used as test reflections (i.e. were excluded from the refinement) (refine.ls_R_factor_R_free).",
"ph":
"pH at which the crystal was grown (exptl_crystal_grow.pH).",
"dpi":
"Diffraction-component Precision Index.",
"dpi_theoretical_min":
"Theoretical minimum of the DPI.",
"num_biomolecules":
"Number of biological assemblies in the asymmetric unit.",
}
}
comment_on_table_elements(structures, comments)
"ring_serial":
"Aromatic ring serial number inside the parent biomolecule.",
"ring_number":
"Number of the aromatic ring inside the residue it is part of.",
"size":
"Number of atoms in the aromatic ring.",
"centroid":
"The Centroid of the aromatic ring as vector3d type.",
"normal":
"The normal of the aromatic ring as vector3d type.",
"is_hetero_aromatic":
"True if the aromatic ring contains atoms other than carbon."
}
}
comment_on_table_elements(aromatic_rings, aromatic_ring_comments)
aromatic_ring_atoms = Table('aromatic_ring_atoms',
metadata,
Column('aromatic_ring_atom_id',
Integer,
primary_key=True),
Column('aromatic_ring_id', Integer,
nullable=False),
Column('atom_id', Integer, nullable=False),
schema=schema)
Index('idx_aromatic_ring_atoms_aromatic_ring_id',
aromatic_ring_atoms.c.aromatic_ring_id)
Index('idx_aromatic_ring_atoms_atom_id', aromatic_ring_atoms.c.atom_id)
"chain_end_id": "Primary key of the second chain.",
"path":
"ptree path in the form PDB/assembly serial number/I:PDB chain bgn ID-PDB chain end ID",
"num_res_bgn":
"Number of residues of the first chain that are part of this interface.",
"num_res_end":
"Number of residues of the second chain that are part of this interface.",
"is_quaternary":
"True if both chains are at identity, i.e. exist in the asymmetric unit.",
"has_mod_res":
"True if at least one modified residue if part of the interface.",
"has_missing_atoms": "True if at least one residue has missing atoms."
}
}
comment_on_table_elements(interfaces, interface_comments)
interface_peptide_pairs = Table('interface_peptide_pairs',
metadata,
Column('interface_id',
Integer,
autoincrement=False),
Column('residue_bgn_id',
Integer,
autoincrement=False),
Column('residue_end_id',
Integer,
autoincrement=False),
schema=schema)
PrimaryKeyConstraint(interface_peptide_pairs.c.interface_id,
{
"prot_fragment_id": "Primary key of the protein fragment.",
"biomolecule_id": "Primary key of the biomolecule the secondary structure fragment belongs to.",
"chain_id": "Primary key of the chain the secondary structure belongs to.",
"path": "ptree",
"sstruct_serial": "Secondary structure serial number inside the chain.",
"sstruct": "Secondary structure DSSP type.",
"fragment_size": "Number of residues that form the protein fragment.",
"fragment_seq": "Fragment one-letter-code sequence.",
"prot_fragment_nterm_id": "N-terminal protein fragment neighbour.",
"prot_fragment_cterm_id": "C-terminal protein fragment neighbour.",
"completeness": "Simple measure to quantify the completeness of the protein fragment: is is the number of its residues that are in CREDO divided by the size of the fragment."
}
}
comment_on_table_elements(prot_fragments, prot_fragment_comments)
prot_fragment_residues = Table('prot_fragment_residues', metadata,
Column('prot_fragment_id', Integer, nullable=False),
Column('residue_id', Integer, nullable=False),
schema=schema)
PrimaryKeyConstraint(prot_fragment_residues.c.prot_fragment_id,
prot_fragment_residues.c.residue_id, deferrable=True,
initially='deferred')
Index('idx_prot_fragment_residues_residue_id', prot_fragment_residues.c.residue_id)
prot_fragment_residue_comments = {
"table": "Mapping between protein fragments and residues in CREDO - The database contains only residue interacting with other entities though, so some residues are missing.",
"columns":
{
"residue_id": "Primary key.",
"biomolecule_id": "Primary key of the parent biomolecule.",
"chain_id": "Primary key of the parent chain.",
"path":
"ptree path in the form PDB/assembly serial number/PDB chain ID/PDB residue name[residue insertion code]`PDB residue number.",
"res_name": "Three-letter name of the residue.",
"res_num": "PDB residue number.",
"ins_code": "PDB insertion code.",
"entity_type_bm":
"Entity type bitmask (the bits are solvent, ligand, saccharide, rna, dna, protein).",
"is_disordered": "True if the residue has disordered atoms.",
"is_incomplete": "True if the residue has missing atoms."
}
}
comment_on_table_elements(residues, residue_comments)
### create the table partitions for the different polymer residue types
# polypeptide residues
peptides = Table(
'peptides',
metadata,
Column('residue_id', Integer, nullable=False),
Column('biomolecule_id', Integer, nullable=False),
Column('chain_id', Integer, nullable=False),
Column('path', PTree, nullable=False),
Column('res_name', String(3), nullable=False),
Column('res_num', Integer, nullable=False),
Column('ins_code', String(1), nullable=False), # ' '
Column('entity_type_bm', Integer, nullable=False),
"is_covalent": "",
"is_vdw_clash": "",
"is_vdw": "",
"is_proximal": "",
"is_hbond": "",
"is_weak_hbond": "",
"is_xbond": "",
"is_ionic": "",
"is_metal_complex": "",
"is_aromatic": "",
"is_hydrophobic": "",
"is_carbonyl": ""
}
}
comment_on_table_elements(contacts, comments)
create_partition_insert_trigger(contacts, CONTACTS_PARTITION_SIZE)
# create new paritions for every 5000 biomolecules
partitions = range(0, CURRENT_BIOMOL_MAX + CONTACTS_PARTITION_SIZE,
CONTACTS_PARTITION_SIZE)
for part_bound_low, part_bound_high in zip(partitions[:-1], partitions[1:]):
tablename = 'contacts_biomol_le_{0}'.format(part_bound_high)
rulename = tablename + '_insert'
partition = Table(
tablename,
metadata,
Column('contact_id', Integer, primary_key=True, nullable=False),
Column('biomolecule_id', Integer, nullable=False),
"chain_seq":
"Sequence of the polymer.",
"chain_seq_md5":
"MD5 Hash of the chain sequence.",
"rotation":
"Rotation matrix.",
"translation":
"Translation vector.",
"is_at_identity":
"True if the chain is at identity, i.e. no transformation was performed.",
"has_disordered_regions":
"True if the chain contains at least one disordered region (unobserved residues)."
}
}
comment_on_table_elements(chains, chain_comments)
## chain subsets: polypeptides, oligonucleotides and polysaccharides
# polypeptides are chains where the type in mmCIF is polypeptide
polypeptides = Table('polypeptides',
metadata,
Column('chain_id', Integer, nullable=False),
Column('is_wildtype',
Boolean(create_constraint=False),
DefaultClause('false'),
nullable=False),
Column('is_human',
Boolean(create_constraint=False),
DefaultClause('false'),
nullable=False),
"is_acceptor": "",
"is_aromatic": "",
"is_weak_acceptor": "",
"is_weak_donor": "",
"is_hydrophobe": "",
"is_metal": "",
"is_pos_ionisable": "",
"is_neg_ionisable": "",
"is_xbond_donor": "",
"is_xbond_acceptor": "",
"is_carbonyl_oxygen": "",
"is_carbonyl_carbon": ""
}
}
comment_on_table_elements(atoms, comments)
create_partition_insert_trigger(atoms, ATOMS_PARTITION_SIZE)
# create new paritions for every X biomolecules
partitions = range(0, CURRENT_BIOMOL_MAX + ATOMS_PARTITION_SIZE,
ATOMS_PARTITION_SIZE)
for part_bound_low, part_bound_high in zip(partitions[:-1], partitions[1:]):
tablename = 'atoms_biomol_le_{0}'.format(part_bound_high)
rulename = tablename + '_insert'
partition = Table(
tablename,
metadata,
Column('atom_id', Integer, primary_key=True),
Column('biomolecule_id', Integer, nullable=False),
from credovi.util.sqlalchemy import comment_on_table_elements
xrefs = Table('xrefs',
metadata,
Column('xref_id', Integer, nullable=False),
Column('entity_type', String(12), nullable=False),
Column('entity_id', Integer, nullable=False),
Column('source', String(32), nullable=False),
Column('xref', String(64), nullable=False),
Column('description', Text),
schema=schema)
PrimaryKeyConstraint(xrefs.c.xref_id, deferrable=True, initially='deferred')
Index('idx_xrefs_entity_type', xrefs.c.entity_type, xrefs.c.entity_id)
Index('idx_xrefs_xref', xrefs.c.source, xrefs.c.xref)
comments = {
"table":
"Contains cross references between entities in CREDO and external databases.",
"columns": {
"xref_id": "Primary key of the cross reference.",
"entity_id": "Primary key of the CREDO entity.",
"entity_type": "Type of the CREDO entity, e.g. Ligand.",
"source": "Name of the external database.",
"xref": "cross reference in the external database.",
"description": "Further description of the cross reference."
}
}
comment_on_table_elements(xrefs, comments)
"groove_id": "",
"biomolecule_id": "Primary key of the parent biomolecule.",
"chain_prot_id": "Primary key of the polypeptide chain.",
"chain_nuc_id": "Primary key of the oligonucleotide chain.",
"path":
"ptree path in the form PDB/assembly serial number/G:PDB chain prot ID-PDB chain nuc ID",
"num_res_prot": "Number of polypetide residues that are interacting.",
"num_res_nuc":
"Number of oligonucleotide residues that are interacting.",
"nucleic_acid_type":
"Type of the nucleic acid, either DNA/RNA or hybrid.",
"has_missing_atoms": "True if at least one residue has missing atoms."
}
}
comment_on_table_elements(grooves, groove_comments)
groove_residue_pairs = Table('groove_residue_pairs',
metadata,
Column('groove_id',
Integer,
autoincrement=False,
primary_key=True),
Column('residue_prot_id',
Integer,
autoincrement=False,
primary_key=True),
Column('residue_nuc_id',
Integer,
autoincrement=False,
primary_key=True),
