class CompoundXref(
six.with_metaclass(ChemblModelMetaClass, ChemblCoreAbstractModel)):
molecule = models.ForeignKey(MoleculeDictionary,
db_column='molregno',
help_text=u'Foreign key to compounds table')
xref_src_db = models.ForeignKey(
XrefSource,
db_column='xref_src_db',
help_text=u'Name of the database that this cross reference links to')
xref_id = ChemblCharField(
max_length=330,
unique=True,
help_text=u'Identifier for the entry in the cross-referenced database')
xref_name = ChemblCharField(
max_length=150,
blank=True,
null=True,
help_text=
u'Name for the entry in the cross-referenced database, where applicable'
)
cmpd_xref_id = ChemblPositiveIntegerField(primary_key=True, length=9)
class Meta(ChemblCoreAbstractModel.Meta):
pass
class ResearchCompanies(
six.with_metaclass(ChemblModelMetaClass, ChemblCoreAbstractModel)):
co_stem_id = ChemblAutoField(primary_key=True,
length=9,
help_text=u'Primary key.')
res_stem = models.ForeignKey(
ResearchStem,
blank=True,
null=True,
help_text=u'Foreign key to research_stem table.')
company = ChemblCharField(
max_length=100,
blank=True,
null=True,
help_text=
u'Name of current company associated with this research code stem.')
country = ChemblCharField(
max_length=50,
blank=True,
null=True,
help_text=u'Country in which the company uses this research code stem.'
) # TODO: should have a constraint
previous_company = ChemblCharField(
max_length=100,
blank=True,
null=True,
help_text=
u'Previous name of the company associated with this research code stem (e.g., if the company has undergone acquisitions/mergers).'
)
class Meta(ChemblCoreAbstractModel.Meta):
unique_together = (("res_stem", "company"), )
class MoleculeSynonyms(
six.with_metaclass(ChemblModelMetaClass, ChemblCoreAbstractModel)):
molecule = models.ForeignKey(
MoleculeDictionary,
db_column='molregno',
help_text=u'Foreign key to molecule_dictionary')
synonyms = ChemblCharField(max_length=200,
db_index=True,
blank=True,
null=True,
help_text=u'Synonym for the compound')
syn_type = ChemblCharField(
max_length=50,
help_text=
u'Type of name/synonym (e.g., TRADE_NAME, RESEARCH_CODE, USAN)')
molsyn_id = ChemblAutoField(primary_key=True,
length=9,
help_text=u'Primary key.')
res_stem = models.ForeignKey(
ResearchStem,
blank=True,
null=True,
help_text=
u'Foreign key to the research_stem table. Where a synonym is a research code, this links to further information about the company associated with that code.'
)
molecule_synonym = ChemblCharField(max_length=200,
blank=True,
null=True,
help_text=u'Synonym for the compound')
class Meta(ChemblCoreAbstractModel.Meta):
unique_together = (("molecule", "synonyms", "syn_type"), )
class RecordSynonyms(
six.with_metaclass(ChemblModelMetaClass, ChemblCoreAbstractModel)):
rec_syn_id = ChemblAutoField(primary_key=True,
length=9,
help_text=u'Primary key.')
record = models.ForeignKey(CompoundRecords)
record_synonym = ChemblCharField(
max_length=200,
blank=True,
null=True,
help_text=u'Synonym for the compound record')
syn_type = ChemblCharField(
max_length=50,
help_text=
u'Type of name/synonym (e.g., TRADE_NAME, RESEARCH_CODE, USAN)')
res_stem = models.ForeignKey(
ResearchStem,
blank=True,
null=True,
help_text=
u'Foreign key to the research_stem table. Where a synonym is a research code, this links to further information about the company associated with that code.'
)
canonical_synonym = ChemblCharField(
max_length=200,
blank=True,
null=True,
help_text=u'Canonical synonym for the compound record')
removed = ChemblNullBooleanField(
default=0,
help_text=
"Indicates whether the synonym has been removed (1) from the database")
class Meta(ChemblCoreAbstractModel.Meta):
unique_together = (("record", "record_synonym", "syn_type"), )
class StructuralAlerts(
six.with_metaclass(ChemblModelMetaClass, ChemblCoreAbstractModel)):
ALERT_SET_ID_CHOICES = (
(1, '1'),
(2, '2'),
(3, '3'),
(4, '4'),
(5, '5'),
(6, '6'),
(7, '7'),
(8, '8'),
)
alert_id = ChemblPositiveIntegerField(
primary_key=True,
length=9,
help_text=u'Primary key. Unique identifier for the structural alert')
alert_set = models.ForeignKey(
StructuralAlertSets,
choices=ALERT_SET_ID_CHOICES,
help_text=
u'Foreign key to structural_alert_sets table indicating which set this particular alert comes from'
)
alert_name = ChemblCharField(max_length=100,
help_text=u'A name for the structural alert')
smarts = ChemblCharField(
max_length=4000,
help_text=
u'SMARTS defining the structural feature that is considered to be an alert'
)
class Meta(ChemblCoreAbstractModel.Meta):
pass #unique_together = ( ("alert_set", "alert_name", "smarts"), )
class Biotherapeutics(
six.with_metaclass(ChemblModelMetaClass, ChemblCoreAbstractModel)):
molecule = models.OneToOneField(
MoleculeDictionary,
primary_key=True,
db_column='molregno',
help_text=u'Foreign key to molecule_dictionary')
description = ChemblCharField(
max_length=2000,
blank=True,
null=True,
help_text=u'Description of the biotherapeutic.')
helm_notation = ChemblCharField(
max_length=4000,
blank=True,
null=True,
help_text=
u'Sequence notation generated according to the HELM standard (http://www.openhelm.org/home). Currently for peptides only'
)
bio_component_sequences = models.ManyToManyField(
'BioComponentSequences',
through="BiotherapeuticComponents",
blank=True)
class Meta(ChemblCoreAbstractModel.Meta):
pass
class UcStructure(six.with_metaclass(ChemblModelMetaClass, ChemblAbstractModel)):
uci = ChemblCharField(primary_key=True, max_length=20, help_text=u'UniChem Identifier')
standardinchi = ChemblCharField(max_length=4000, unique=True, blank=True, null=True, help_text=u'The standard Inchi assigned to this UCI')
standardinchikey = ChemblCharField(max_length=30, unique=True, blank=True, null=True, help_text=u'The Standard Inchi Key generated from the Standard Inchi field.')
created = ChemblDateField(blank=True, null=True, help_text=u'Date this record was first created')
username = ChemblCharField(max_length=20, blank=True, null=True, help_text=u'Name of user who created this record.')
fikhb = ChemblCharField(max_length=14, db_index=True, blank=True, null=True, help_text=u'First InchKey Hash Block. 14 letters that appear at the start of the InChiKey. Denotes the connectivity of the inchi')
class Meta:
app_label = 'unistruct'
managed = False
class UcXref(six.with_metaclass(ChemblModelMetaClass, ChemblAbstractModel)):
uci = models.OneToOneField(UcStructure, primary_key=True, db_column='uci', help_text=u'Foreign key to UCI in UC_STRUCTURE')
src = models.OneToOneField(UcSource, primary_key=True, help_text=u'Foreign key to SRC_ID in UC_SOURCE')
src_compound_id = ChemblCharField(primary_key=True, max_length=400, help_text=u'ID of compound as defined in source.')
assignment = ChemblNullableBooleanField(help_text=u'Flag to indicate whether this assignment of src_compound_id to UCI is CURRENT [1], or is OBSOLETE [0]. ie is this assignment true in the current release.')
last_release_u_when_current = ChemblNoLimitDecimalField(blank=True, null=True, help_text=u'For obsolete assignments, UniChem release number where ASSIGNMENT was last CURRENT. Note, this release number refers to the release_u, ie the release number assigned by unichem')
created = ChemblDateField(blank=True, null=True, help_text=u'Date this record was first created.')
lastupdated = ChemblDateField(blank=True, null=True, help_text=u'Date this record was last updated [NB Only update permitted is the changing of CURRENT to OBSOLETE together with the changing of last_release_when_current from null to a version number]')
userstamp = ChemblCharField(max_length=20, blank=True, null=True, help_text=u'User who last updated this record.')
aux_src = ChemblCharField(max_length=4000, blank=True, null=True, help_text=u'Auxiliary information associated with this src_compound_id')
class Meta:
unique_together = (("uci", "src", "src_compound_id"),)
app_label = 'unistruct'
managed = False
class UcRelease(six.with_metaclass(ChemblModelMetaClass, ChemblAbstractModel)):
src = models.OneToOneField(UcSource, primary_key=True, help_text=u'Foreign key to SRC_ID in UC_SOURCE')
release_u = ChemblNoLimitDecimalField(primary_key=True, help_text=u'The UniChem assigned release number of this data release, for this source - may be different to release numbers or dates assigned by the source')
created = ChemblDateField(blank=True, null=True, help_text=u'The date that this record was created.')
src_release_number = ChemblNoLimitDecimalField(blank=True, null=True, help_text=u'The release number (if any) assigned by the source (src) for this data release.')
src_release_date = ChemblDateField(blank=True, null=True, help_text=u'The release date, if no SRC_RELEASE_NUMBER available, as supplied by the source src.')
userstamp = ChemblCharField(max_length=20, blank=True, null=True, help_text=u'The user who created this record.')
records_without_comments = ChemblPositiveIntegerField(length=38, blank=True, null=True, help_text=u'Number of records loaded without comments.')
records_with_comments = ChemblPositiveIntegerField(length=38, blank=True, null=True, help_text=u'Number of records loaded with comments. Comments in UC_RELEASE_LOGs.')
records_ignored = ChemblPositiveIntegerField(length=38, blank=True, null=True, help_text=u'Number of records ignored (ie: NOT loaded). Comments in UC_RELEASE_LOGs.')
number_of_new_ucis = ChemblPositiveIntegerField(length=38, blank=True, null=True, help_text=u'Number of new UCIs generated when this release was loaded.')
uc_load_index = ChemblPositiveIntegerField(length=38, blank=True, null=True, help_text=u'Data Release Load Number (order in which data releases were loaded into UniChem)')
misc = ChemblCharField(max_length=4000, blank=True, null=True)
class Meta:
unique_together = (("src", "release_u"),)
app_label = 'unistruct'
managed = False
class StructuralAlertSets(
six.with_metaclass(ChemblModelMetaClass, ChemblCoreAbstractModel)):
ALERT_SET_ID_CHOICES = (
(1, '1'),
(2, '2'),
(3, '3'),
(4, '4'),
(5, '5'),
(6, '6'),
(7, '7'),
(8, '8'),
)
PRIORITY_CHOICES = (
(1, '1'),
(2, '2'),
(3, '3'),
(4, '4'),
(5, '5'),
(6, '6'),
(7, '7'),
(8, '8'),
)
SET_NAME_CHOICES = (
('BMS', 'BMS'),
('Dundee', 'Dundee'),
('Glaxo', 'Glaxo'),
('Inpharmatica', 'Inpharmatica'),
('LINT', 'LINT'),
('MLSMR', 'MLSMR'),
('PAINS', 'PAINS'),
('SureChEMBL', 'SureChEMBL'),
)
alert_set_id = ChemblPositiveIntegerField(
primary_key=True,
length=9,
choices=ALERT_SET_ID_CHOICES,
help_text=u'Unique ID for the structural alert set')
set_name = ChemblCharField(
max_length=100,
unique=True,
choices=SET_NAME_CHOICES,
help_text=u'Name (or origin) of the structural alert set')
priority = ChemblPositiveIntegerField(
length=2,
choices=PRIORITY_CHOICES,
help_text=
u'Priority assigned to the structural alert set for display on the ChEMBL interface (priorities >=4 are shown by default).'
)
class Meta(ChemblCoreAbstractModel.Meta):
pass
class CompoundStructures(
six.with_metaclass(ChemblModelMetaClass, ChemblCoreAbstractModel)):
molecule = models.OneToOneField(
MoleculeDictionary,
primary_key=True,
db_column='molregno',
help_text=
u'Internal Primary Key for the compound structure and foreign key to molecule_dictionary table'
)
molfile = ChemblTextField(
blank=True,
null=True,
help_text=u'MDL Connection table representation of compound')
standard_inchi = ChemblCharField(
max_length=4000,
db_index=True,
unique=True,
blank=True,
null=True,
help_text=u'IUPAC standard InChI for the compound')
standard_inchi_key = ChemblCharField(
max_length=27,
db_index=True,
help_text=u'IUPAC standard InChI key for the compound')
canonical_smiles = ChemblCharField(
max_length=4000,
db_index=True,
blank=True,
null=True,
help_text=u'Canonical smiles, generated using pipeline pilot')
structure_exclude_flag = ChemblBooleanField(
default=False,
help_text=
u'Indicates whether the structure for this compound should be hidden from users (e.g., organometallic compounds with bad valence etc)'
)
class Meta(ChemblCoreAbstractModel.Meta):
pass
class BioComponentSequences(
six.with_metaclass(ChemblModelMetaClass, ChemblCoreAbstractModel)):
component_id = ChemblAutoField(
primary_key=True,
length=9,
help_text=
u'Primary key. Unique identifier for each of the molecular components of biotherapeutics in ChEMBL (e.g., antibody chains, recombinant proteins, synthetic peptides).'
)
component_type = ChemblCharField(
max_length=50,
help_text=u"Type of molecular component (e.g., 'PROTEIN','DNA','RNA')."
) # TODO: add constraint, is always PROTEIN now... this should be similar to compound sequences!!!
description = ChemblCharField(
max_length=200,
blank=True,
null=True,
help_text=u'Description/name of molecular component.')
sequence = ChemblTextField(
blank=True,
null=True,
help_text=u'Sequence of the biotherapeutic component.')
sequence_md5sum = ChemblCharField(
max_length=32,
blank=True,
null=True,
help_text=u'MD5 checksum of the sequence.')
tax_id = ChemblPositiveIntegerField(
length=11,
blank=True,
null=True,
help_text=
u'NCBI tax ID for the species from which the sequence is derived. May be null for humanized monoclonal antibodies, synthetic peptides etc.'
)
organism = ChemblCharField(
max_length=150,
blank=True,
null=True,
help_text=u'Name of the species from which the sequence is derived.')
updated_on = ChemblDateField(blank=True, null=True)
updated_by = ChemblCharField(max_length=100, blank=True, null=True)
insert_date = ChemblDateField(blank=True, null=True)
accession = ChemblCharField(max_length=25, blank=True, null=True)
db_source = ChemblCharField(max_length=25, blank=True, null=True)
db_version = ChemblCharField(max_length=10, blank=True, null=True)
class Meta(ChemblCoreAbstractModel.Meta):
pass
class StructuralAlerts(
six.with_metaclass(ChemblModelMetaClass, ChemblCoreAbstractModel)):
alert_id = ChemblPositiveIntegerField(
primary_key=True,
length=9,
help_text=u'Primary key. Unique identifier for the structural alert')
alertset = models.ForeignKey(
StructuralAlertSets,
db_column='alert_set_id',
help_text=
u'Foreign key to structural_alert_sets table indicating which set this particular alert comes from'
)
alert_name = ChemblCharField(max_length=100,
help_text=u'A name for the structural alert')
smarts = ChemblCharField(
max_length=4000,
help_text=
u'SMARTS defining the structural feature that is considered to be an alert'
)
class Meta(ChemblCoreAbstractModel.Meta):
pass # unique_together = (("alert_set", "alert_name", "smarts"),)
class ResearchStem(
six.with_metaclass(ChemblModelMetaClass, ChemblCoreAbstractModel)):
res_stem_id = ChemblAutoField(
primary_key=True,
length=9,
help_text=u'Primary key. Unique ID for each research code stem.')
research_stem = ChemblCharField(
max_length=20,
unique=True,
blank=True,
null=True,
help_text=u'The actual stem/prefix used in the research code.')
class Meta(ChemblCoreAbstractModel.Meta):
pass
class StructuralAlertSets(
six.with_metaclass(ChemblModelMetaClass, ChemblCoreAbstractModel)):
alert_set_id = ChemblPositiveIntegerField(
primary_key=True,
length=9,
help_text=u'Unique ID for the structural alert set')
set_name = ChemblCharField(
max_length=100,
unique=True,
help_text=u'Name (or origin) of the structural alert set')
priority = ChemblPositiveIntegerField(
length=2,
help_text=
u'Priority assigned to the structural alert set for display on the ChEMBL interface (priorities >=4 are shown by default).'
)
class Meta(ChemblCoreAbstractModel.Meta):
pass
class CompoundRecords(
six.with_metaclass(ChemblModelMetaClass, ChemblCoreAbstractModel)):
SRC_COMPOUND_ID_VERSION_CHOICES = (
(1, '1'),
(2, '2'),
(3, '3'),
(4, '4'),
(5, '5'),
(6, '6'),
(7, '7'),
(8, '8'),
)
record_id = ChemblAutoField(primary_key=True,
length=9,
help_text=u'Unique ID for a compound/record')
molecule = models.ForeignKey(
MoleculeDictionary,
blank=True,
null=True,
db_column='molregno',
help_text=u'Foreign key to compounds table (compound structure)')
doc = models.ForeignKey(Docs, help_text=u'Foreign key to documents table')
compound_key = ChemblCharField(
max_length=250,
db_index=True,
blank=True,
null=True,
help_text=
u'Key text identifying this compound in the scientific document')
compound_name = ChemblCharField(
max_length=4000,
blank=True,
null=True,
help_text=u'Name of this compound recorded in the scientific document')
filename = ChemblCharField(max_length=250, blank=True, null=True)
updated_by = ChemblCharField(max_length=100, blank=True, null=True)
updated_on = ChemblDateField(blank=True, null=True)
src = models.ForeignKey(Source, help_text=u'Foreign key to source table')
src_compound_id = ChemblCharField(
max_length=150,
db_index=True,
blank=True,
null=True,
help_text=
u'Identifier for the compound in the source database (e.g., pubchem SID)'
)
removed = ChemblNullBooleanField(default=0)
src_compound_id_version = ChemblPositiveIntegerField(
length=3,
blank=True,
null=True,
choices=SRC_COMPOUND_ID_VERSION_CHOICES)
curated = ChemblBooleanField(
default=False,
help_text=
u'Can be marked as curated if the entry has been mapped to a molregno other than that given by the original structure, and hence care should be taken when updating'
)
products = models.ManyToManyField('Products',
through="Formulations",
null=True,
blank=True)
assays = models.ManyToManyField('Assays',
through="Activities",
null=True,
blank=True)
class Meta(ChemblCoreAbstractModel.Meta):
pass
class UcSource(six.with_metaclass(ChemblModelMetaClass, ChemblAbstractModel)):
NUMBER_OR_DATE_CHOICES = (
('date', 'date'),
('number', 'number'),
)
SRC_CLASS_CHOICES = (
(1, '1'),
(2, '2'),
(3, '3'),
)
src_id = ChemblPositiveIntegerField(length=2, primary_key=True, help_text=u'Unique ID for source (generated by UniChem, ie: an internal ID)')
name = ChemblCharField(max_length=50, blank=True, null=True, help_text=u'Name of source')
description = ChemblCharField(max_length=2000, blank=True, null=True, help_text=u'Description of this source.')
current_release_u = ChemblPositiveIntegerField(length=2, blank=True, null=True, help_text=u'Current unichem release number (assigned by unichem) of this source')
created = ChemblDateField(blank=True, null=True, help_text=u'Date this record was created')
last_updated = ChemblDateField(blank=True, null=True, help_text=u'Date this record was last updated')
userstamp = ChemblCharField(max_length=20, blank=True, null=True, help_text=u'The user who last updated this record')
number_or_date = ChemblCharField(max_length=20, blank=True, null=True, choices=NUMBER_OR_DATE_CHOICES, help_text=u'Does this source version data releases by date or by number')
name_long = ChemblCharField(max_length=2000, blank=True, null=True, help_text=u'Name of Source. Longer form for presentation.')
src_details = ChemblCharField(max_length=2000, blank=True, null=True, help_text=u'Technical details of how the data was/is obtained from the source. Note, more detailed info for each release can be found in UC_RELEASE.MISC')
src_url = ChemblCharField(max_length=2000, blank=True, null=True, help_text=u'The Home Page URL for the source')
base_id_url = ChemblCharField(max_length=2000, blank=True, null=True, help_text=u"The base url for the src_compound_id in the source. If 'null', then this source does not support direct links to src_compound_id pages. If not null, simply append src_compound_id to end of this string to create full url if base_id_url available = 1. If base_url_id_available = 0, then a more complex manipulation of base_id_url and src_compound_id is required (managed in interface)")
base_id_url_available = ChemblNullableBooleanField(help_text=u"May the src_compound_id simply be appended to the base_url_id to create a valid url to a unique page for the src_compound_id ? 1 = yes, 0 = no, a more complex manipulation may be required to create the url. This field ignorred in interface if base_url_id is 'null'")
aux_required = ChemblNullableBooleanField(help_text=u'Auxilliary information for each src-compound_id is required to be captured at load time for this source [col4 of input file], and stored in UC_XREF.AUX_SRC')
aux_for_url = ChemblNullableBooleanField(help_text=u'Does the auxiliary information get used to create the URL instead of the src_compound_id ?')
aux_description = ChemblCharField(max_length=4000, blank=True, null=True, help_text=u'If Auxiliary information is required (ie: if 1 in AUX_REQUIRED field), what is it required FOR, and how should it be processed ? Note: if AUX_FOR_URL = 1, then aux information is used to create the URL instead of the src_compound_id')
private = ChemblPositiveIntegerField(length=38, blank=True, null=True, help_text=u'A flag to indicate whether data from this source is private (1) or can be made public (0)')
name_label = ChemblCharField(max_length=200, blank=True, null=True, help_text=u'The name of the source, with spacing and case of text as in the source itself. Suitable for use as a label in hyperlinks. Always less than 30 characters.')
src_class = ChemblPositiveIntegerField(length=38, blank=True, null=True, choices=SRC_CLASS_CHOICES, help_text=u'Class of the source. FK to UC_SRC_CLASS.CLASS_ID')
keys_only = ChemblNullableBooleanField(help_text=u'Source has only InChIKeys, as InChIs are not made available. 1=yes, 0 or null = no')
update_min = ChemblPositiveIntegerField(length=38, blank=True, null=True, help_text=u'The minimum number of days before which an update can be expected. Do not bother trying to update this source if days from last release is smaller than this.')
update_opt = ChemblPositiveIntegerField(length=38, blank=True, null=True, help_text=u'The optimal number of days between releases (ie: you can expect a new release to be available if the days since the last release equals this number) ')
update_max = ChemblPositiveIntegerField(length=38, blank=True, null=True, help_text=u'The maximum number of days after which an update can be considered very overdue.')
update_j = ChemblNullableBooleanField(help_text=u'Are incremental updates appropriate for this source (1=yes, 0=no)')
update_comments = ChemblCharField(max_length=500, blank=True, null=True, help_text=u'A comment on the reasons behind the settings used for other UPDATE_ columns in this table.')
synonyms = ChemblPositiveIntegerField(length=38, blank=True, null=True, help_text=u'The number of synonyms captured from this source, and available in UC_SYNONYMS table.')
class Meta:
app_label = 'unistruct'
managed = False
class CompoundRecords(
six.with_metaclass(ChemblModelMetaClass, ChemblCoreAbstractModel)):
SRC_COMPOUND_ID_VERSION_CHOICES = (
(1, '1'),
(2, '2'),
(3, '3'),
(4, '4'),
(5, '5'),
(6, '6'),
(7, '7'),
(8, '8'),
)
record_id = ChemblAutoField(primary_key=True,
length=9,
help_text=u'Unique ID for a compound/record')
molecule = models.ForeignKey(
MoleculeDictionary,
blank=True,
null=True,
db_column='molregno',
help_text=u'Foreign key to compounds table (compound structure)')
doc = models.ForeignKey(Docs, help_text=u'Foreign key to documents table')
compound_key = ChemblCharField(
max_length=250,
db_index=True,
blank=True,
null=True,
help_text=
u'Key text identifying this compound in the scientific document')
compound_name = ChemblCharField(
max_length=4000,
blank=True,
null=True,
help_text=u'Name of this compound recorded in the scientific document')
filename = ChemblCharField(max_length=250, blank=True, null=True)
updated_by = ChemblCharField(max_length=100, blank=True, null=True)
updated_on = ChemblDateField(blank=True, null=True)
src = models.ForeignKey(Source, help_text=u'Foreign key to source table')
src_compound_id = ChemblCharField(
max_length=150,
db_index=True,
blank=True,
null=True,
help_text=
u'Identifier for the compound in the source database (e.g., pubchem SID)'
)
removed = ChemblNullBooleanField(default=0)
src_compound_id_version = ChemblPositiveIntegerField(
length=3,
blank=True,
null=True,
choices=SRC_COMPOUND_ID_VERSION_CHOICES)
curated = ChemblBooleanField(
default=False,
help_text=
u'Can be marked as curated if the entry has been mapped to a molregno other than that given by the original structure, and hence care should be taken when updating'
)
load_date = ChemblDateField(blank=True,
null=True,
default=datetime.date.today)
ridx = ChemblCharField(
max_length=600,
default=u'CLD0',
help_text=u'The Depositor Defined Reference Identifier.')
cidx = ChemblCharField(
max_length=600,
default=u'CLD0',
help_text=u'The Depositor Defined Compound Identifier.')
job_id = ChemblPositiveIntegerField(
length=38,
default=0,
help_text=u'The JOB_ID assigned to this record when first inserted.')
log_id = ChemblPositiveIntegerField(length=38, default=0)
molregno_fixed = ChemblIntegerField(
length=38,
blank=True,
null=True,
help_text=
u"The molregno associated with this record has been fixed by curators: Do not update automatically. null = not fixed. '1' = Fixed"
)
molregno_comment = ChemblCharField(
max_length=3000,
blank=True,
null=True,
help_text=u'The reason why this molregno is associated with this record'
)
molregno_sv = ChemblNoLimitDecimalField(
blank=True,
null=True,
help_text=u'The version of the standardizer protocol used')
products = models.ManyToManyField('Products',
through="Formulations",
blank=True)
assays = models.ManyToManyField('Assays', through="Activities", blank=True)
def __str__(self):
return 'Compound Record {0} for Molecule {1}, name {2}, key {3}'.format(
self.record_id, self.molecule.chembl_id if self.molecule else '',
self.compound_name, self.compound_key)
class Meta(ChemblCoreAbstractModel.Meta):
pass
class CompoundProperties(
six.with_metaclass(ChemblModelMetaClass, ChemblCoreAbstractModel)):
MOLECULAR_SPECIES_CHOICES = (
('ACID', 'ACID'),
('BASE', 'BASE'),
('ZWITTERION', 'ZWITTERION'),
('NEUTRAL', 'NEUTRAL'),
)
NUM_RO5_VIOLATIONS_CHOICES = (
(0, '0'),
(1, '1'),
(2, '2'),
(3, '3'),
(4, '4'),
)
RO3_PASS_CHOICES = (
('Y', 'Y'),
('N', 'N'),
)
molecule = models.OneToOneField(
MoleculeDictionary,
primary_key=True,
db_column='molregno',
help_text=u'Foreign key to compounds table (compound structure)')
mw_freebase = ChemblPositiveDecimalField(
db_index=True,
blank=True,
null=True,
decimal_places=2,
max_digits=9,
help_text=u'Molecular weight of parent compound')
alogp = models.DecimalField(db_index=True,
blank=True,
null=True,
decimal_places=2,
max_digits=9,
help_text=u'Calculated ALogP')
hba = ChemblPositiveIntegerField(
length=3,
db_index=True,
blank=True,
null=True,
help_text=u'Number hydrogen bond acceptors')
hbd = ChemblPositiveIntegerField(length=3,
db_index=True,
blank=True,
null=True,
help_text=u'Number hydrogen bond donors')
psa = ChemblPositiveDecimalField(db_index=True,
blank=True,
null=True,
decimal_places=2,
max_digits=9,
help_text=u'Polar surface area')
rtb = ChemblPositiveIntegerField(length=3,
db_index=True,
blank=True,
null=True,
help_text=u'Number rotatable bonds')
ro3_pass = ChemblCharField(
max_length=3,
blank=True,
null=True,
choices=RO3_PASS_CHOICES,
help_text=
u'Indicates whether the compound passes the rule-of-three (mw < 300, logP < 3 etc)'
)
num_ro5_violations = ChemblPositiveIntegerField(
length=1,
db_index=True,
blank=True,
null=True,
choices=NUM_RO5_VIOLATIONS_CHOICES,
help_text=
u"Number of violations of Lipinski's rule-of-five, using HBA and HBD definitions"
)
acd_most_apka = models.DecimalField(
blank=True,
null=True,
max_digits=9,
decimal_places=2,
help_text=u'The most acidic pKa calculated using ACDlabs v12.01')
acd_most_bpka = ChemblPositiveDecimalField(
blank=True,
null=True,
max_digits=9,
decimal_places=2,
help_text=u'The most basic pKa calculated using ACDlabs v12.01')
acd_logp = models.DecimalField(
blank=True,
null=True,
max_digits=9,
decimal_places=2,
help_text=
u'The calculated octanol/water partition coefficient using ACDlabs v12.01'
)
acd_logd = models.DecimalField(
blank=True,
null=True,
max_digits=9,
decimal_places=2,
help_text=
u'The calculated octanol/water distribution coefficient at pH7.4 using ACDlabs v12.01'
)
molecular_species = ChemblCharField(
max_length=50,
blank=True,
null=True,
choices=MOLECULAR_SPECIES_CHOICES,
help_text=u'Indicates whether the compound is an acid/base/neutral')
full_mwt = ChemblPositiveDecimalField(
blank=True,
null=True,
max_digits=9,
decimal_places=2,
help_text=u'Molecular weight of the full compound including any salts')
aromatic_rings = ChemblPositiveIntegerField(
length=3, blank=True, null=True, help_text=u'Number of aromatic rings')
heavy_atoms = ChemblPositiveIntegerField(
length=3,
blank=True,
null=True,
help_text=u'Number of heavy (non-hydrogen) atoms')
qed_weighted = ChemblPositiveDecimalField(
blank=True,
null=True,
max_digits=3,
decimal_places=2,
help_text=
u'Weighted quantitative estimate of drug likeness (as defined by Bickerton et al., Nature Chem 2012)'
)
updated_on = ChemblDateField(
blank=True,
null=True,
help_text=u'Shows date properties were last recalculated')
mw_monoisotopic = ChemblPositiveDecimalField(
blank=True,
null=True,
max_digits=11,
decimal_places=4,
help_text=u'Monoisotopic parent molecular weight')
full_molformula = ChemblCharField(
max_length=100,
blank=True,
null=True,
help_text=
u'Molecular formula for the full compound (including any salt)')
hba_lipinski = ChemblPositiveIntegerField(
length=3,
blank=True,
null=True,
help_text=
u"Number of hydrogen bond acceptors calculated according to Lipinski's original rules (i.e., N + O count))"
)
hbd_lipinski = ChemblPositiveIntegerField(
length=3,
blank=True,
null=True,
help_text=
u"Number of hydrogen bond donors calculated according to Lipinski's original rules (i.e., NH + OH count)"
)
num_lipinski_ro5_violations = ChemblPositiveIntegerField(
length=1,
blank=True,
null=True,
choices=NUM_RO5_VIOLATIONS_CHOICES,
help_text=
u"Number of violations of Lipinski's rule of five using HBA_LIPINSKI and HBD_LIPINSKI counts"
)
class Meta(ChemblCoreAbstractModel.Meta):
pass
class MoleculeBrowseDrugs(
six.with_metaclass(ChemblModelMetaClass, ChemblCoreAbstractModel)):
AVAILABILITY_TYPE_CHOICES = (
(-2, -2),
(-1, -1),
(0, 0),
(1, 1),
(2, 2),
)
CHIRALITY_CHOICES = (
(-1, -1),
(0, 0),
(1, 1),
(2, 2),
)
DEVELOPMENT_PHASE_CHOICES = (
(0, 0),
(1, 1),
(2, 2),
(3, 3),
(4, 4),
)
parent = models.OneToOneField('MoleculeDictionary',
primary_key=True,
db_column='parent_molregno')
chembl = models.OneToOneField(
ChemblIdLookup,
blank=True,
null=False,
help_text=
u'ChEMBL identifier for this compound (for use on web interface etc)')
synonyms = ChemblCharField(max_length=4000, blank=True, null=True)
development_phase = ChemblPositiveIntegerField(
length=1, blank=True, null=True, choices=DEVELOPMENT_PHASE_CHOICES)
research_codes = ChemblCharField(max_length=600, blank=True, null=True)
applicants = ChemblCharField(max_length=2000, blank=True, null=True)
usan_stem = ChemblCharField(max_length=600, blank=True, null=True)
usan_year = ChemblPositiveIntegerField(length=4, blank=True, null=True)
first_approval = ChemblPositiveIntegerField(length=4,
blank=True,
null=True)
atc_code = ChemblCharField(max_length=2000, blank=True, null=True)
drug_type = ChemblIntegerField(length=2, blank=True, null=True)
rule_of_five = ChemblNullableBooleanField()
first_in_class = ChemblNullableBooleanField()
chirality = ChemblIntegerField(length=1,
blank=True,
null=True,
choices=CHIRALITY_CHOICES)
prodrug = ChemblNullableBooleanField()
oral = ChemblNullableBooleanField()
parenteral = ChemblNullableBooleanField()
topical = ChemblNullableBooleanField()
black_box = ChemblNullableBooleanField()
availability_type = ChemblIntegerField(length=1,
blank=True,
null=True,
choices=AVAILABILITY_TYPE_CHOICES)
usan_stem_definition = ChemblCharField(max_length=2000,
blank=True,
null=True)
indication_class = ChemblCharField(max_length=2000, blank=True, null=True)
usan_stem_substem = ChemblCharField(max_length=300, blank=True, null=True)
atc_code_description = ChemblCharField(max_length=2000,
blank=True,
null=True)
ob_patent = ChemblCharField(max_length=120, blank=True, null=True)
sc_patent = ChemblCharField(max_length=180, blank=True, null=True)
withdrawn_year = ChemblPositiveIntegerField(length=4,
blank=True,
null=True)
withdrawn_country = ChemblCharField(max_length=2000, blank=True, null=True)
withdrawn_reason = ChemblCharField(max_length=2000, blank=True, null=True)
withdrawn_class = ChemblCharField(max_length=1000, blank=True, null=True)
class Meta(ChemblCoreAbstractModel.Meta):
pass
class MoleculeDictionary(
six.with_metaclass(ChemblModelMetaClass, ChemblCoreAbstractModel)):
AVAILABILITY_TYPE_CHOICES = (
(-2, '-2'),
(-1, '-1'),
(0, '0'),
(1, '1'),
(2, '2'),
)
CHIRALITY_CHOICES = (
(-1, '-1'),
(0, '0'),
(1, '1'),
(2, '2'),
)
MAX_PHASE_CHOICES = (
(0, '0'),
(1, '1'),
(2, '2'),
(3, '3'),
(4, '4'),
)
MOLECULE_TYPE_CHOICES = (
('Antibody', 'Antibody'),
('Cell', 'Cell'),
('Enzyme', 'Enzyme'),
('Oligonucleotide', 'Oligonucleotide'),
('Oligosaccharide', 'Oligosaccharide'),
('Protein', 'Protein'),
('Small molecule', 'Small molecule'),
('Unclassified', 'Unclassified'),
('Unknown', 'Unknown'),
)
NOMERGE_REASON_CHOICES = (
('GSK', 'GSK'),
('PARENT', 'PARENT'),
('PDBE', 'PDBE'),
('SALT', 'SALT'),
)
STRUCTURE_TYPE_CHOICES = (
('NONE', 'NONE'),
('MOL', 'MOL'),
('SEQ', 'SEQ'),
('BOTH', 'BOTH'),
)
@property
def compoundImage(self):
if hasattr(self, 'compoundimages'):
return self.compoundimages
return None
@property
def compoundMol(self):
if hasattr(self, 'compoundmols'):
return self.compoundmols
return None
@property
def compoundProperty(self):
if hasattr(self, 'compoundproperties'):
return self.compoundproperties
return None
@property
def compoundStructure(self):
if hasattr(self, 'compoundstructures'):
return self.compoundstructures
return None
@property
def moleculeHierarchy(self):
if hasattr(self, 'moleculehierarchy'):
return self.moleculehierarchy
return None
molregno = ChemblAutoField(
primary_key=True,
length=9,
help_text=u'Internal Primary Key for the molecule')
pref_name = ChemblCharField(max_length=255,
db_index=True,
blank=True,
null=True,
help_text=u'Preferred name for the molecule')
chembl = models.OneToOneField(
ChemblIdLookup,
blank=True,
null=False,
help_text=
u'ChEMBL identifier for this compound (for use on web interface etc)'
) # This combination of null and blank is actually very important!
max_phase = ChemblPositiveIntegerField(
length=1,
db_index=True,
default=0,
choices=MAX_PHASE_CHOICES,
help_text=
u'Maximum phase of development reached for the compound (4 = approved). Null where max phase has not yet been assigned.'
)
therapeutic_flag = ChemblBooleanField(
db_index=True,
default=False,
help_text=
u'Indicates that a drug has a therapeutic application (as opposed to e.g., an imaging agent, additive etc).'
)
dosed_ingredient = ChemblBooleanField(
default=False,
help_text=
u'Indicates that the drug is dosed in this form (e.g., a particular salt)'
)
structure_key = ChemblCharField(
max_length=27,
db_index=True,
unique=True,
blank=True,
null=True,
help_text=
u'Unique key for the structure/sequence (e.g., inchi_key or sequence md5sum) to help enforce non-redundancy.'
)
structure_type = ChemblCharField(
max_length=10,
default='MOL',
choices=STRUCTURE_TYPE_CHOICES,
novalidate_default=True,
help_text=
u'Indications whether the molecule has a small molecule structure or a protein sequence (MOL indicates an entry in the compound_structures table, SEQ indications an entry in the protein_therapeutics table, NONE indicates an entry in neither table, e.g., structure unknown)'
)
chebi_id = ChemblPositiveIntegerField(
length=9,
unique=True,
blank=True,
null=True,
help_text=
u'Assigned ChEBI ID for the compound, where it is a small molecule.')
chebi_par_id = ChemblPositiveIntegerField(
length=9,
blank=True,
null=True,
help_text=
u'Preferred ChEBI ID for the compound (where different from assigned)')
insert_date = ChemblDateField(
blank=False, null=True, default=datetime.date.today
) # blank is false because it has default value
molfile_update = ChemblDateField(blank=True, null=True)
downgraded = ChemblBooleanField(default=False)
downgrade_reason = ChemblCharField(max_length=2000, blank=True, null=True)
replacement_mrn = ChemblPositiveIntegerField(length=9,
blank=True,
null=True)
checked_by = ChemblCharField(max_length=2000, blank=True, null=True)
nomerge = ChemblBooleanField(
default=False,
help_text=
u"Flag to show that this entry shouldn't be merged with others of the same structure (when set to 1)"
)
nomerge_reason = ChemblCharField(
max_length=200,
blank=True,
null=True,
choices=NOMERGE_REASON_CHOICES,
help_text=
u'Reason for entry not being merged with others of the same structure (e.g., known to be a stereoisomer)'
)
molecule_type = ChemblCharField(
max_length=30,
blank=True,
null=True,
choices=MOLECULE_TYPE_CHOICES,
help_text=
u'Type of molecule (Small molecule, Protein, Antibody, Oligosaccharide, Oligonucleotide, Cell, Unknown)'
)
first_approval = ChemblPositiveIntegerField(
length=4,
blank=True,
null=True,
help_text=u'Earliest known approval year for the molecule'
) # TODO: should be date!
oral = ChemblBooleanField(
default=False,
help_text=
u'Indicates whether the drug is known to be administered orally.')
parenteral = ChemblBooleanField(
default=False,
help_text=
u'Indicates whether the drug is known to be administered parenterally')
topical = ChemblBooleanField(
default=False,
help_text=
u'Indicates whether the drug is known to be administered topically.')
black_box_warning = ChemblNullBooleanField(
default=0,
help_text=u'Indicates that the drug has a black box warning')
natural_product = ChemblNullBooleanField(
default=(-1),
help_text=
u'Indicates whether the compound is natural product-derived (currently curated only for drugs)'
)
first_in_class = ChemblNullBooleanField(
default=(-1),
help_text=
u'Indicates whether this is known to be the first compound of its class (e.g., acting on a particular target).'
)
chirality = ChemblIntegerField(
length=1,
default=(-1),
choices=CHIRALITY_CHOICES,
help_text=
u'Shows whether a drug is dosed as a racemic mixture (0), single stereoisomer (1) or is an achiral molecule (2)'
)
prodrug = ChemblNullBooleanField(
default=(-1),
help_text=
u'Indicates that the molecule is a pro-drug (see molecule hierarchy for active component, where known)'
)
inorganic_flag = ChemblNullBooleanField(
default=0,
help_text=
u'Indicates whether the molecule is inorganic (i.e., containing only metal atoms and <2 carbon atoms)'
)
usan_year = ChemblPositiveIntegerField(
length=4,
blank=True,
null=True,
help_text=
u'The year in which the application for a USAN/INN name was made')
availability_type = ChemblIntegerField(
length=1,
blank=True,
null=True,
choices=AVAILABILITY_TYPE_CHOICES,
help_text=
u'The availability type for the drug (0 = discontinued, 1 = prescription only, 2 = over the counter)'
)
usan_stem = ChemblCharField(
max_length=50,
blank=True,
null=True,
help_text=
u'Where the compound has been assigned a USAN name, this indicates the stem, as described in the USAN_STEM table.'
)
polymer_flag = ChemblNullableBooleanField(
help_text=
u'Indicates whether a molecule is a small molecule polymer (e.g., polistyrex)'
)
usan_substem = ChemblCharField(
max_length=50,
blank=True,
null=True,
help_text=
u'Where the compound has been assigned a USAN name, this indicates the substem'
)
usan_stem_definition = ChemblCharField(
max_length=1000,
blank=True,
null=True,
help_text=u'Definition of the USAN stem')
indication_class = ChemblCharField(
max_length=1000,
blank=True,
null=True,
help_text=
u'Indication class(es) assigned to a drug in the USP dictionary')
products = models.ManyToManyField('Products',
through="Formulations",
blank=True)
docs = models.ManyToManyField('Docs',
through="CompoundRecords",
blank=True)
assays = models.ManyToManyField('Assays', through="Activities", blank=True)
withdrawn_flag = ChemblBooleanField(
default=False,
help_text=
"Flag indicating whether the drug has been withdrawn in at least one country (not necessarily in the US)"
)
withdrawn_year = ChemblPositiveIntegerField(
length=4,
blank=True,
null=True,
help_text=u'Year the drug was first withdrawn in any country')
withdrawn_country = ChemblCharField(
max_length=2000,
blank=True,
null=True,
help_text=u'List of countries/regions where the drug has been withdrawn'
)
withdrawn_reason = ChemblCharField(
max_length=2000,
blank=True,
null=True,
help_text=u'Reasons for withdrawal (e.g., safety)')
withdrawn_class = ChemblCharField(max_length=1000, blank=True, null=True)
def __str__(self):
return 'Molecule {0} ({1}) {2}'.format(self.molregno, self.chembl_id,
self.pref_name)
class Meta(ChemblCoreAbstractModel.Meta):
pass
class RecordDrugProperties(
six.with_metaclass(ChemblModelMetaClass, ChemblCoreAbstractModel)):
AVAILABILITY_TYPE_CHOICES = (
(-2, '-2'),
(-1, '-1'),
(0, '0'),
(1, '1'),
(2, '2'),
)
CHIRALITY_CHOICES = (
(-1, '-1'),
(0, '0'),
(1, '1'),
(2, '2'),
)
MAX_PHASE_CHOICES = (
(0, '0'),
(1, '1'),
(2, '2'),
(3, '3'),
(4, '4'),
)
MOLECULE_TYPE_CHOICES = (
('Antibody', 'Antibody'),
('Cell', 'Cell'),
('Enzyme', 'Enzyme'),
('Oligonucleotide', 'Oligonucleotide'),
('Oligosaccharide', 'Oligosaccharide'),
('Protein', 'Protein'),
('Small molecule', 'Small molecule'),
('Unclassified', 'Unclassified'),
('Unknown', 'Unknown'),
)
record = models.OneToOneField(CompoundRecords, primary_key=True)
max_phase = ChemblPositiveIntegerField(
length=1,
db_index=True,
default=0,
choices=MAX_PHASE_CHOICES,
help_text=
u'Maximum phase of development reached for the compound (4 = approved). Null where max phase has not yet been assigned.'
)
molecule_type = ChemblCharField(
max_length=30,
blank=True,
null=True,
choices=MOLECULE_TYPE_CHOICES,
help_text=
u'Type of molecule (Small molecule, Protein, Antibody, Oligosaccharide, Oligonucleotide, Cell, Unknown)'
)
first_approval = ChemblPositiveIntegerField(
length=4,
blank=True,
null=True,
help_text=u'Earliest known approval year for the molecule'
) # TODO: should be date!
oral = ChemblNullableBooleanField(
default=False,
help_text=
u'Indicates whether the drug is known to be administered orally.')
parenteral = ChemblNullableBooleanField(
default=False,
help_text=
u'Indicates whether the drug is known to be administered parenterally')
topical = ChemblNullableBooleanField(
default=False,
help_text=
u'Indicates whether the drug is known to be administered topically.')
black_box_warning = ChemblNullableBooleanField(
default=0,
help_text=u'Indicates that the drug has a black box warning')
first_in_class = ChemblNullBooleanField(
default=(-1),
help_text=
u'Indicates whether this is known to be the first compound of its class (e.g., acting on a particular target).'
)
chirality = ChemblIntegerField(
length=1,
default=(-1),
choices=CHIRALITY_CHOICES,
help_text=
u'Shows whether a drug is dosed as a racemic mixture (0), single stereoisomer (1) or is an achiral molecule (2)'
)
prodrug = ChemblNullableBooleanField(
default=False,
help_text=
u'Indicates that the molecule is a pro-drug (see molecule hierarchy for active component, where known)'
)
therapeutic_flag = ChemblNullableBooleanField(
db_index=True,
default=False,
help_text=
u'Indicates that a drug has a therapeutic application (as opposed to e.g., an imaging agent, additive etc).'
)
natural_product = ChemblNullBooleanField(
default=(-1),
help_text=
u'Indicates whether the compound is natural product-derived (currently curated only for drugs)'
)
inorganic_flag = ChemblNullableBooleanField(
default=0,
help_text=
u'Indicates whether the molecule is inorganic (i.e., containing only metal atoms and <2 carbon atoms)'
)
applicants = ChemblCharField(max_length=1000, blank=True, null=True)
usan_stem = ChemblCharField(
max_length=50,
blank=True,
null=True,
help_text=
u'Where the compound has been assigned a USAN name, this indicates the stem, as described in the USAN_STEM table.'
)
usan_year = ChemblPositiveIntegerField(
length=4,
blank=True,
null=True,
help_text=
u'The year in which the application for a USAN/INN name was made')
availability_type = ChemblIntegerField(
length=1,
blank=True,
null=True,
choices=AVAILABILITY_TYPE_CHOICES,
help_text=
u'The availability type for the drug (0 = discontinued, 1 = prescription only, 2 = over the counter)'
)
usan_substem = ChemblCharField(
max_length=50,
blank=True,
null=True,
help_text=
u'Where the compound has been assigned a USAN name, this indicates the substem'
)
indication_class = ChemblCharField(
max_length=1000,
blank=True,
null=True,
help_text=
u'Indication class(es) assigned to a drug in the USP dictionary')
usan_stem_definition = ChemblCharField(
max_length=1000,
blank=True,
null=True,
help_text=u'Definition of the USAN stem')
polymer_flag = ChemblNullableBooleanField(
help_text=
u'Indicates whether a molecule is a small molecule polymer (e.g., polistyrex)'
)
withdrawn_flag = ChemblPositiveIntegerField(length=1,
blank=True,
null=True)
withdrawn_year = ChemblPositiveIntegerField(length=4,
blank=True,
null=True)
withdrawn_country = ChemblCharField(max_length=1000, blank=True, null=True)
withdrawn_reason = ChemblCharField(max_length=1000, blank=True, null=True)
withdrawn_class = ChemblCharField(max_length=1000, blank=True, null=True)
class Meta(ChemblCoreAbstractModel.Meta):
pass