Crystallographic data (Models)

Schema overview

../_images/crys_schema.jpg

[Explain schema]

Model details

class viewer.models.Project(*args, **kwargs)

Django model for holding information about a project. This is used on the Targets level, adding a new project for each target, and saving a list of users that can access a target during the authentication step

Parameters

  • title (CharField) – The title of the project

  • init_date (DateTimeField) – The date the project was initiated (autofield)

  • user_id (ManyToManyField) – Links to the User model

class viewer.models.Target(*args, **kwargs)

Django model to define a Target - a protein.

Parameters

  • title (CharField) – The name of the target

  • init_date (DateTimeField) – The date the target was initiated (autofield)

  • project_id (ManyToManyField) – Links targets to projects for authentication

  • uniprot_id (Charfield) – Optional field where a uniprot id can be stored

  • metadata (FileField) – Optional file upload defining metadata about the target - can be used to add custom site labels

  • zip_archive (FileField) – Link to zip file created from targets uploaded with the loader

class viewer.models.Protein(*args, **kwargs)

Django model for holding information about a protein. A protein is a protein structure which has a unique set of 3D coordinates, rather than a target, which is a set of protein objects of the same protein. A Molecule object is also linked to a protein, so that a complete structure is comprised of the molecule and protein in separate parts in fragalysis.

Parameters

  • code (CharField) – A unique name for the protein (e.g. NUDT5A-x0001_1)

  • target_id (ForeignKey) – Foreign key linking the protein to it’s target

  • apo_holo (NullBooleanField) – 0 for apo (ligand removed), 1 for holo (ligand in tact)

  • prot_type (CharField) –

    protein type - from a pre-defined list and determined by file extension on upload (defined in loader.config.get_prot_choices):

    prot_choices = ( (APO, “Apo”, “_apo.pdb”, “APO”), (STRIPPED, “Stripped”, “_no_buffer_altlocs.pdb”, “STRIPPED”), (TLEAPED, “Tleaped”, “_tleap.pdb”, “TLEAP”), (CHUNKED, “Chunked”, “_chunk.pdb”, “CHUNK”), (BOUND, “Bound”, ‘_bound.pdb’, “BOUND”) )

  • pdb_info (FileField) – File link to apo pdb structure - pdb file with ligand removed

  • bound_info (FileField) – File link to bound state structure - same as apo pdb but with ligand in-tact

  • cif_info (FileField) – File link to cif file for ligand restraints (optional)

  • mtz_info (FileField) – File link to uploaded mtz file (optional)

  • map_info (FileField) – File link to uploaded map file (optional)

  • aligned (NullBooleanField) – Bool - 1 if aligned, 0 if not

  • aligned_to (ForeignKey (self)) – Foreign key to another instance of a protein to which this protein is aligned (optional)

  • has_eds (NullBooleanField) – Bool - 1 if has ED, 0 it not (optional)

class viewer.models.Compound(*args, **kwargs)

Django model for holding information about a compound, which is a unique 2D molecule

Parameters

  • inchi (CharField) – The inchi key of the compound

  • long_inchi (TextField) – For historical reasons, the inchifield cannot be removed, but has a max limit of 255 characters. If the inchi key for a compound is longer than this, it is stored in the long_inchi field, and the inchi key is concatenated to the first 255 characters. (optional) TODO: Use a method to get the inchi key

  • smiles (Charfield) – The SMILES string representation of the compound

  • current_identifier (Charfield) – The identifier for this compound that is used in Fragalysis to represent it’s 3D molecule (optional)

  • all_identifiers (TextField) – A comma separated list of all identifiers that have been used in the past to represent this 2D compound

  • project_id (ManyToManyField) – Many to Many foreign key relationship to all projects that this compound is associated to (prevents duplication of compounds across multiple targets)

  • mol_log_p (FloatField) – Computed LogP value (from rdkit)

  • mol_wt (FloatField) – Computed molecular weight (Da) (from rdkit)

  • tpsa (FloatField) – Computed Topological Polar Surface Area (from rdkit)

  • heavy_atom_count (IntegerField) – Computed heavy (non-hydrogen) atom count (from rdkit)

  • heavy_atom_mol_wt (FloatField) – Computed molecular weight of all heavy (non-hydrogen) atoms (from rdkit)

  • nhoh_count (IntegerField) – Computed number of hydroxylamine groups (from rdkit)

  • no_count (IntegerField) – Computed number of nitroso groups (from rdkit)

  • num_h_acceptors (IntegerField) – Computed number of hydrogen-bond acceptor groups (from rdkit)

  • num_h_donors (IntegerField) – Computed number of hydrogen-bond donor groups (from rdkit)

  • num_het_atoms (IntegerField) – Computed number of heterogeneous atoms (from rdkit)

  • num_rot_bonds (IntegerField) – Computed number of rotatable bonds (from rdkit)

  • num_val_electrons (IntegerField) – Computed number of valence electrons (from rdkit)

  • ring_count (IntegerField) – Computed number of rings in the molecule (from rdkit)

  • inspirations (ManyToManyField) – Foreign key link to any number of 3D Molecules that inspired the design of this compound

  • description (TextField) – A description of the compound added by a user (optional)

  • comments (TextField) – A free-text comments field (optional)

class viewer.models.Molecule(*args, **kwargs)

Django model for holding information about a Molecule. A molecule is linked to a compound, and represents the unique 3D coordinates for that molecule. Note a compound can be linked to multiple molecules, each with a different 3D structure, but the same 2D structure

Parameters

  • smiles (CharField) – The smiles string of the molecule. (optional) TODO: Check if this is needed…

  • lig_id (CharField) – The ligand ID from the pdb file it originated from (e.g. LIG 1 A) (optional)

  • chain_id (CharField) – The chain from the protein structure pdb file that this ligand is from (e.g. A) (optional)

  • mol_type (CharField) –

    molecule type - from a pre-defined list and determined by file extension on upload (defined in loader.config.get_mol_choices): mol_choices = ( (PROASIS, “Proasis molecule”, “.mol”, “MOL”), (SDF, “Sdf molecule”, “.sdf”, “SDF”), (HYDROGEN, “Hydrogens added “, “_h.mol”, “H_MOL”), (

    HYDROGEN_AM1_CHARGES, “Mol2 format with Hydrogens and AM1 BCC”, “.mol2”, “MOL2”,

    ), )

  • sdf_info (TextField) – The 3D coordinates for the molecule in MDL (mol file) format. Taken directly from the uploaded file

  • rscc (FloatField) – The RSCC score of the molecule 3D coordinates vs. PANDDA event map (optional)

  • occupancy (FloatField) – The occupancy (electron density) of the molecule (optional)

  • x_com (FloatField) – x-coordinate for centre of mass (optional)

  • y_com (FloatField) – y-coordinate for centre of mass (optional)

  • z_com (FloatField) – z-coordinate for centre of mass (optional)

  • rmsd (FloatField) – RMSD of this molecule compared to ? (optional - unused)

  • prot_id (ForeignKey) – Foreign key link to the associated protein (apo) that this ligand was pulled from

  • cmpd_id (ForeignKey) – Foreign key link to the associated 2D compound

  • history (HistoricalRecords) – Tracks the changes made to an instance of this model over time