models.py

from __future__ import unicode_literals

from django.db import models
from django.forms import ModelForm

from .ws import get_pubmed_info, get_epo_info, get_uniprot_info, get_taxonomy_info

class Bibliography(models.Model):
    """
    Bibliography data table
    """
    SOURCES = (
        ('PM', 'PubMed article'),
        ('PT', 'Patent')
    )
    source = models.CharField('Bibliographic type', max_length=2, choices=SOURCES)
    id_source = models.CharField('Bibliographic ID', max_length=25)
    title = models.CharField('Title', max_length=300)
    journal_name = models.CharField('Journal name', max_length=50, null=True)
    authors_list = models.CharField('Authors list', max_length=500)
    biblio_year = models.PositiveSmallIntegerField('Year')
    cytotox = models.BooleanField('Cytotoxicity data', default=False)
    in_silico = models.BooleanField('in silico study performed', default=False)
    in_vitro = models.BooleanField('in vitro study performed', default=False)
    in_vivo = models.BooleanField('in vivo study performed', default=False)
    in_cellulo = models.BooleanField('in cellulo study performed', default=False)
    pharmacokinetic = models.BooleanField('pharmacokinetic study performed', default=False)
    xray = models.BooleanField('contains xray data', default=False)

    def get_absolute_url(self):
        return reverse('bibliography-detail', args=[str(self.id)])

    def save(self, *args, **kwargs):
        if self.source == 'PM':
            info = get_pubmed_info(self.id_source)
        else:
            info = get_epo_info(self.id_source)
        self.title = info['title']
        self.journal_name = info['journal_name']
        self.authors_list = info['authors_list']
        self.biblio_year = info['biblio_year']
        super(Bibliography, self).save(*args, **kwargs)

    class Meta:
        verbose_name_plural = "bibliographies"

class BibliographyForm(ModelForm):
    class Meta:
        model = Bibliography
        exclude = ['title','journal_name', 'authors_list', 'biblio_year']

class Taxonomy(models.Model):
    taxonomy_id = models.DecimalField('NCBI TaxID', unique=True, max_digits=9, decimal_places=0)
    name = models.CharField('Organism name', max_length=200)

    def save(self, *args, **kwargs):
        info = get_taxonomy_info(self.taxonomy_id)
        self.name = info['scientific_name']
        super(Taxonomy, self).save(*args, **kwargs)

    class Meta:
        verbose_name_plural = "taxonomies"

class MolecularFunction(models.Model):
    go_id = models.CharField('Gene Ontology ID', unique=True, max_length=10) # GO term id format: 'GO:0000000' 
    description = models.CharField('description', max_length=500)

class Protein(models.Model):
    uniprot_id = models.CharField('Uniprot ID', unique=True, max_length=10)
    recommended_name_long = models.CharField('Uniprot Recommended Name (long)', max_length=75)
    short_name = models.CharField('Short name', max_length=50)
    gene_name = models.CharField('Gene name', unique=True, max_length=30)
    entry_name = models.CharField('Entry name', max_length=30)
    organism = models.ForeignKey('Taxonomy')
    molecular_functions = models.ManyToManyField(MolecularFunction)

    def save(self, *args, **kwargs):
        info = get_uniprot_info(self.uniprot_id)
        self.recommended_name_long = info['recommended_name']
        self.gene_name = info['gene']
        self.entry_name = info['entry_name']
        try:
            taxonomy = Taxonomy.objects.get(taxonomy_id=info['organism'])
        except Taxonomy.DoesNotExist:
            tax_info = get_taxonomy_info(info['organism'])
            taxonomy = Taxonomy()
            taxonomy.taxonomy_id = info['organism']
            taxonomy.save()
        self.organism = taxonomy
        super(Protein, self).save(*args, **kwargs)

class Domain(models.Model):
    pfam_acc = models.CharField('Pfam Accession', max_length=10, unique=True) 
    pfam_id = models.CharField('Pfam Family Identifier', max_length=20) 
    pfam_description = models.CharField('Pfam Description', max_length=100)
    domainfamily = models.CharField('Domain family', max_length=25)  #TODO: what is this field? check database contents

class ProteinDomainComplex(models.Model):
    protein_id = models.ForeignKey('Protein')
    domain_id = models.ForeignKey('Domain')
    ppc_copy_nb = models.IntegerField('Number of copies of the protein in the complex')
    
    class Meta:
        verbose_name_plural = "complexes"

class ProteinDomainBoundComplex(ProteinDomainComplex):
    ppp_copy_nb_per_p = models.IntegerField('Number of copies of the protein in the pocket')
    pockets_nb = models.IntegerField('Total number of pockets in the complex')
    class Meta:
        verbose_name_plural = "bound complexes"
    
class ProteinDomainPartnerComplex(ProteinDomainComplex):
    class Meta:
        verbose_name_plural = "partner complexes"

class Symmetry(models.Model):
    code = models.CharField('Symmetry code', max_length=2)
    description = models.CharField('Description', max_length=300)

    class Meta:
        verbose_name_plural = "symmetries"

class Ppi(models.Model):
    ppi_id = models.IntegerField('PPI identifier')
    complex_id = models.ForeignKey(ProteinDomainComplex)
    cc_nb = models.IntegerField('Number of copies of the complex in the PPI', default=1)
    pdb_id = models.CharField('PDB ID', max_length=4)
    symmetry_id = models.ForeignKey(Symmetry)

class Disease(models.Model):
    ppi_id = models.ForeignKey(Ppi)
    disease_name = models.CharField('Disease', max_length=30) # is there any database/nomenclature for diseases?


class Compound(models.Model):
    canonical_smile = models.CharField('Canonical Smile', unique=True, max_length=250)
    #TODO index this table on canonical_smile
    is_macrocycle = models.BooleanField('Contains one or more macrocycles') 
    aromatic_ratio = models.DecimalField('Aromatic ratio', max_digits=3, decimal_places=2)
    balaban_index = models.DecimalField('Balaban index', max_digits=3, decimal_places=2)  
    fsp3 = models.DecimalField('Fsp3', max_digits=3, decimal_places=2)
    dh_Petitjean = models.DecimalField('Dh Petitjean', max_digits=4, decimal_places=2) 
    diam_graph_non_h_petitjean = models.IntegerField('Diameter for the molecular graph for heavy atoms (Petitjean)') 
    gc_molar_refractivity = models.DecimalField('GC Molar Refractivity', max_digits=5, decimal_places=2)
    g_petitjean = models.DecimalField('G Petitjean', max_digits=3, decimal_places=2)
    ig_petitjean = models.DecimalField('Ig Petitjean', max_digits=3, decimal_places=2)
    log_d = models.DecimalField('LogD (Partition coefficient octanol-1/water, with pKa information)', max_digits=4, decimal_places=2)
    a_log_p = models.DecimalField('ALogP (Partition coefficient octanol-1/water)', max_digits=4, decimal_places=2)
    mean_atom_vol_vdw = models.DecimalField('Mean atom volume computed with VdW radii', max_digits=4, decimal_places=2)
    molecular_weight = models.DecimalField('Molecular weight', max_digits=6, decimal_places=2)
    nb_acceptor_h = models.IntegerField('Number of hydrogen bond acceptors')
    nb_aliphatic_amines = models.IntegerField('Number of aliphatics amines')
    nb_aromatic_bonds = models.IntegerField('Number of aromatic bonds')
    nb_aromatic_ether = models.IntegerField('Number of aromatic ethers')
    nb_aromatic_sssr = models.IntegerField('Number of aromatic Smallest Set of System Rings (SSSR)')
    nb_atom = models.IntegerField('Number of atoms') 
    nb_atom_non_h = models.IntegerField('Number of non hydrogen atoms') 
    nb_benzene_like_rings = models.IntegerField('Number of benzene-like rings')
    nb_bonds = models.IntegerField('Number of bonds')
    nb_bonds_non_h = models.IntegerField('Number of bonds not involving a hydrogen')  
    nb_br = models.IntegerField('Number of Bromine atoms')  
    nb_c = models.IntegerField('Number of Carbon atoms')  
    nb_chiral_centers = models.IntegerField('Number of chiral centers')  
    nb_circuits = models.IntegerField('Number of circuits')  
    nb_cl = models.IntegerField('Number of Chlorine atoms')  
    nb_csp2 = models.IntegerField('Number of sp2-hybridized carbon atoms')  
    nb_csp3 = models.IntegerField('Number of sp3-hybridized carbon atoms')  
    nb_donor_h = models.IntegerField('Number of hydrogen bond donors')  
    nb_double_bonds = models.IntegerField('Number of double bonds')  
    nb_f = models.IntegerField('Number of fluorine atoms')  
    nb_i = models.IntegerField('Number of iodine atoms')  
    nb_multiple_bonds = models.IntegerField('Number of multiple bonds')  
    nb_n = models.IntegerField('Number of nitrogen atoms')
    nb_o = models.IntegerField('Number of oxygen atoms')  
    nb_rings = models.IntegerField('Number of rings')  
    nb_rotatable_bonds = models.IntegerField('Number of rotatable bonds')  
    radius_graph_non_h_petitjean = models.IntegerField('Radius for the molecular graph for heavy atoms (Petitjean)')  
    randic_index = models.DecimalField('Randic index', max_digits=4, decimal_places=2)  
    rdf070m = models.DecimalField('RDF070m, radial distribution function weighted by the atomic masses at 7Å', max_digits=5, decimal_places=2)  
    rotatable_bond_fraction = models.DecimalField('Fraction of rotatable bonds', max_digits=3, decimal_places=2)  
    sum_atom_polar = models.DecimalField('Sum of atomic polarizabilities', max_digits=5, decimal_places=2)  
    sum_atom_vol_vdw = models.DecimalField('Sum of atom volumes computed with VdW radii', max_digits=6, decimal_places=2)  
    surface_vdw_petitjean = models.DecimalField('Van der Waals surface area (Petitjean)', max_digits=6, decimal_places=2)  
    thickness_petitjean = models.DecimalField('Thickness (Petitjean)', max_digits=4, decimal_places=2)  
    tpsa = models.DecimalField('Topological Polar Surface Area (TPSA)', max_digits=5, decimal_places=2)  
    ui = models.DecimalField('Unsaturation index', max_digits=4, decimal_places=2)  
    vol_vdw_petitjean = models.DecimalField('Van der Waals volume (Petitjean)', max_digits=7, decimal_places=2)  
    wiener_index = models.IntegerField('Wiener index')  
    common_name = models.CharField('Common name', unique=True, max_length=20, blank=True, null=True)  
    pubchem_id = models.CharField('Pubchem ID', unique=True, max_length=10, blank=True, null=True)  
    chemspider_id = models.CharField('Chemspider ID', unique=True, max_length=10, blank=True, null=True)  
    chembl_id = models.CharField('Chembl ID', unique=True, max_length=30, blank=True, null=True)  
    iupac_name = models.CharField('IUPAC name', unique=True, max_length=255, blank=True, null=True)  
    mddr_compound_id = models.ForeignKey('MDDRCompoundImport', blank=True, null=True)  


class MDDRCompoundImport(models.Model):
    mddr_compound_id = models.IntegerField('MDDR compound ID')  
    mddr_name = models.CharField('MDDR name', max_length=40)  
    dvpmt_phase = models.CharField('Development phase', max_length=20)  
    canonical_smile = models.CharField('Canonical Smile', max_length=500, unique=True, blank=True, null=True)  
    #TODO index this table on canonical_smile
    db_import_date = models.DecimalField('MDDR release year/month', max_digits=6, decimal_places=0)  

    class Meta:
        # over multiple releases of the MDDR database, the same compound can evolve in its development phase
        # the same compound can have different names and development phases in the same MDDR release
        unique_together = (('mddr_compound_id', 'mddr_name', 'dvpmt_phase'),)


class MDDRCompoundActivityClass(models.Model):
    mddr_compound_id = models.ForeignKey(MDDRCompoundImport)  
    activity_class = models.CharField('Activity Class', max_length=100)  

    class Meta:
        unique_together = (('mddr_compound_id', 'activity_class'),)


class MDDRSimilarity(models.Model):
    canonical_smile_ippidb = models.CharField('Canonical Smile for IPPIDB compound', max_length=500, unique=True, blank=True, null=True)
    canonical_smile_mddr = models.CharField('Canonical Smile for MDDR Compound', max_length=500, unique=True, blank=True, null=True)
    tanimoto = models.DecimalField('Tanimoto', max_digits=6, decimal_places=5)  

    class Meta:
        unique_together = (('canonical_smile_ippidb', 'canonical_smile_mddr'),)

"""
class TestActivityDescription(models.Model):
    complex_id = models.ForeignKey(Complex)
    biblio_id = models.ForeignKey(Biblio)
    idppi = models.ForeignKey(Ppi, models.DO_NOTHING, ='IDPPI', blank=True, null=True)  
    testnameactivity = models.CharField(='TestNameActivity', max_length=40)  
    isprimary = models.CharField(='IsPrimary', max_length=1)  
    protboundconstruct = models.CharField(='ProtBoundConstruct', max_length=11)  
    testtype = models.CharField(='TestType', max_length=5)  
    testmodulationtype = models.CharField(='TestModulationType', max_length=13)  
    nbactivescmpdstot = models.IntegerField(='NbActivesCmpdsTot')  
    conccmpds = models.DecimalField(='ConcCmpds', max_digits=7, decimal_places=3, blank=True, null=True)  
    protocol = models.TextField(='Protocol', blank=True, null=True)  
    concproteinbound = models.DecimalField(='ConcProteinBound', max_digits=7, decimal_places=3, blank=True, null=True)  
    concprotein2 = models.DecimalField(='ConcProtein2', max_digits=7, decimal_places=3, blank=True, null=True)  
    controlepos = models.CharField(='ControlePos', max_length=50, blank=True, null=True)  
    controleneg = models.CharField(='ControleNeg', max_length=50, blank=True, null=True)  
    cellline = models.CharField(='CellLine', max_length=50, blank=True, null=True)  
    pepseq = models.CharField(='PepSeq', max_length=100, blank=True, null=True)  
    marker = models.CharField(='Marker', max_length=35, blank=True, null=True)  






class Actionevidencetest(models.Model):
    idcmpdaction = models.ForeignKey('Cmpdaction', models.DO_NOTHING, ='IDCmpdAction')  
    idtestactivity = models.ForeignKey('Testactivitydescription', models.DO_NOTHING, ='IDTestActivity')  
    nbcopycompound = models.IntegerField(='NbCopyCompound', blank=True, null=True)  

    class Meta:
#        managed = False
        db_table = 'actionEvidenceTest'
        unique_together = (('idcmpdaction', 'idtestactivity'),)


class Actionevidencexray(models.Model):
    idcmpdaction = models.ForeignKey('Cmpdaction', models.DO_NOTHING, ='IDCmpdAction')  
    codepdb = models.CharField(='CodePDB', max_length=4)  
    nbcopycompound = models.IntegerField(='NbCopyCompound')  
    idbindingsite = models.ForeignKey('Bindingsite', models.DO_NOTHING, ='IDBindingSite')  
    idbiblio = models.ForeignKey('Biblio', models.DO_NOTHING, ='IDBiblio', blank=True, null=True)  

    class Meta:
#        managed = False
        db_table = 'actionEvidenceXRay'
        unique_together = (('idcmpdaction', 'codepdb'),)


class Cmpdaction(models.Model):
    idcmpdaction = models.AutoField(='IDCmpdAction', primary_key=True)  
    idcomplexebound = models.ForeignKey('Complexe', models.DO_NOTHING, ='IDComplexeBound')  
    idcompound = models.ForeignKey('Compound', models.DO_NOTHING, ='IDCompound')  
    activationmode = models.CharField(='ActivationMode', max_length=11)  
    modulationtype = models.CharField(='ModulationType', max_length=10)  

    class Meta:
#        managed = False
        db_table = 'cmpdAction'


class Cmpdactiveresult(models.Model):
    idcompound = models.ForeignKey('Compound', models.DO_NOTHING, ='IDCompound')  
    idtestactivity = models.ForeignKey('Testactivitydescription', models.DO_NOTHING, ='IDTestActivity')  
    activitytype = models.CharField(='ActivityType', max_length=5)  
    activity = models.DecimalField(='Activity', max_digits=4, decimal_places=2)  
    pourcentinhib = models.IntegerField(='PourcentInhib', blank=True, null=True)  

    class Meta:
#        managed = False
        db_table = 'cmpdActiveResult'
        unique_together = (('idcompound', 'idtestactivity', 'activitytype'),)


class Cmpdcytotoxresult(models.Model):
    idcompound = models.ForeignKey('Compound', models.DO_NOTHING, ='IDCompound')  
    idtestcytotox = models.ForeignKey('Testcytotoxdescription', models.DO_NOTHING, ='IDTestCytotox')  
    toxicity = models.CharField(='Toxicity', max_length=1)  

    class Meta:
#        managed = False
        db_table = 'cmpdCytotoxResult'
        unique_together = (('idcompound', 'idtestcytotox'),)


class Cmpdinactiveresult(models.Model):
    idtestactivity = models.ForeignKey('Testactivitydescription', models.DO_NOTHING, ='IDTestActivity')  
    idcompound = models.ForeignKey('Compound', models.DO_NOTHING, ='IDCompound')  
    pourcentinhib = models.IntegerField(='PourcentInhib', blank=True, null=True)  

    class Meta:
#        managed = False
        db_table = 'cmpdInactiveResult'
        unique_together = (('idtestactivity', 'idcompound'),)


class Cmpdpkresult(models.Model):
    idcompound = models.ForeignKey('Compound', models.DO_NOTHING, ='IDCompound')  
    idtestpk = models.ForeignKey('Testpkdescription', models.DO_NOTHING, ='IDTestPK')  
    tolerated = models.CharField(='Tolerated', max_length=1)  
    auc = models.IntegerField(='AUC', blank=True, null=True)  
    clearance = models.DecimalField(='Clearance', max_digits=7, decimal_places=3, blank=True, null=True)  
    cmax = models.DecimalField(='Cmax', max_digits=7, decimal_places=3, blank=True, null=True)  
    oralbioavailability = models.IntegerField(='OralBioavailability', blank=True, null=True)  
    tdemi = models.IntegerField(='Tdemi', blank=True, null=True)  
    tmax = models.IntegerField(='Tmax', blank=True, null=True)  
    voldistribution = models.DecimalField(='VolDistribution', max_digits=5, decimal_places=2, blank=True, null=True)  

    class Meta:
#        managed = False
        db_table = 'cmpdPKResult'
        unique_together = (('idcompound', 'idtestpk'),)



    class Meta:
#        managed = False
        db_table = 'disease'
        unique_together = (('idppi', 'disease'),)


class DjangoMigrations(models.Model):
    app = models.CharField(max_length=255)
    name = models.CharField(max_length=255)
    applied = models.DateTimeField()

    class Meta:
#        managed = False
        db_table = 'django_migrations'


class Domain(models.Model):
    iddomain = models.AutoField(='IDDomain', primary_key=True)  
    pfamid = models.CharField(='PfamID', max_length=20)  
    pfamnumaccession = models.CharField(='PfamNumAccession', unique=True, max_length=10)  
    domaindescription = models.CharField(='DomainDescription', max_length=100)  
    domainfamily = models.CharField(='DomainFamily', max_length=25)  

    class Meta:
#        managed = False
        db_table = 'domain'

class Mddrsimilarity(models.Model):
    idcompound = models.ForeignKey(Compound, models.DO_NOTHING, ='IDCompound')  
    idmddrcompound = models.ForeignKey(Mddrcompound, models.DO_NOTHING, ='IDMDDRCompound')  
    versionmddr = models.CharField(='VersionMDDR', max_length=7)  
    tanimoto = models.DecimalField(='Tanimoto', max_digits=6, decimal_places=5)  

    class Meta:
#        managed = False
        db_table = 'mDDRSimilarity'
        unique_together = (('idcompound', 'idmddrcompound', 'versionmddr'),)


class Ppi(models.Model):
    idppi = models.AutoField(='IDPPI', primary_key=True)  
    idcomplexe1 = models.ForeignKey(Complexe, models.DO_NOTHING, ='IDComplexe1', related_name='cplx_id_1')  
    idcomplexe2 = models.ForeignKey(Complexe, models.DO_NOTHING, ='IDComplexe2', related_name='cplx_id_2')  
    idbindingsite1 = models.ForeignKey(Bindingsite, models.DO_NOTHING, ='IDBindingSite1', related_name='bs_id_1') 
    idbindingsite2 = models.ForeignKey(Bindingsite, models.DO_NOTHING, ='IDBindingSite2', related_name='bs_id_2')  
    family = models.CharField(='Family', max_length=25)  

    class Meta:
#        managed = False
        db_table = 'ppi'
        unique_together = (('idcomplexe1', 'idcomplexe2', 'idbindingsite1', 'idbindingsite2'),)


class Protein(models.Model):
    idprotein = models.AutoField(='IDProtein', primary_key=True)  
    numuniprot = models.CharField(='NumUniprot', unique=True, max_length=10)  
    protnamelg = models.CharField(='ProtNameLg', max_length=75)  
    protnamesh = models.CharField(='ProtNameSh', max_length=50)  
    protalias = models.CharField(='ProtAlias', unique=True, max_length=30)  
    protnamesp = models.CharField(='ProtNameSp', max_length=30)  
    organism = models.CharField(='Organism', max_length=80)  

    class Meta:
#        managed = False
        db_table = 'protein'


class Refcmpdbiblio(models.Model):
    idcompound = models.ForeignKey(Compound, models.DO_NOTHING, ='IDCompound')  
    idbiblio = models.ForeignKey(Biblio, models.DO_NOTHING, ='IDBiblio')  
    cmpdnameinbiblio = models.CharField(='CmpdNameInBiblio', max_length=20, blank=True, null=True)  

    class Meta:
#        managed = False
        db_table = 'refCmpdBiblio'
        unique_together = (('idcompound', 'idbiblio'),)


class Refproteinfonction(models.Model):
    idprotein = models.ForeignKey(Protein, models.DO_NOTHING, ='IDProtein')  
    protfonctionsp = models.CharField(='ProtFonctionSP', max_length=200)  

    class Meta:
#        managed = False
        db_table = 'refProteinFonction'
        unique_together = (('protfonctionsp', 'idprotein'),)



    class Meta:
#        managed = False
        db_table = 'testActivityDescription'


class Testcytotoxdescription(models.Model):
    idtestcytotox = models.AutoField(='IDTestCytotox', primary_key=True)  
    idbiblio = models.ForeignKey(Biblio, models.DO_NOTHING, ='IDBiblio')  
    testnamecytotox = models.CharField(='TestNameCytotox', max_length=40)  
    cellline = models.CharField(='CellLine', max_length=50)  
    conccmpd = models.DecimalField(='ConcCmpd', max_digits=7, decimal_places=3, blank=True, null=True)  

    class Meta:
#        managed = False
        db_table = 'testCytotoxDescription'


class Testpkdescription(models.Model):
    idtestpk = models.AutoField(='IDTestPK', primary_key=True)  
    idbiblio = models.ForeignKey(Biblio, models.DO_NOTHING, ='IDBiblio')  
    testnamepk = models.CharField(='TestNamePK', max_length=40)  
    animal = models.CharField(='Animal', max_length=100)  
    administrationmode = models.CharField(='AdministrationMode', max_length=2, blank=True, null=True)  
    concentration = models.DecimalField(='Concentration', max_digits=7, decimal_places=3, blank=True, null=True)  
    dose = models.DecimalField(='Dose', max_digits=7, decimal_places=2, blank=True, null=True)  
    doseinterval = models.IntegerField(='DoseInterval', blank=True, null=True)  

    class Meta:
#        managed = False
        db_table = 'testPKDescription'
"""