cls.DrugBankAnnotation.CDrugBankAnnotation Class Reference

Drugs associated with a protein. More...

Public Member Functions
def	__init__ (s, dbp)
	Constructor. More...
def	SetFilter (s, fltType, fltLst)
	Set a filter. More...
def	ClearFilter (s, fltType)
	Stop filtering of a certain filter type. More...
def	ClearFilters (s)
	Stop any filtering. More...
def	GetPossibleGroups (s)
	Get valid names for drug classes. More...
def	GetPossibleActions (s)
	Get valid names for mechanisms of drug interactions with partners. More...
def	GetPossibleAffectedOrganisms (s)
	Get valid organism names where the drug is targeting the drug partner. More...
def	GetPossibleBondTypes (s)
	Get valid names for drug-related function of drug partner. More...
def	GetPossibleKnownActions (s)
	Get valid tokens if knowledge exists on how the drug works. More...
def	GetDrugs (s, upAcc)
	Get drugs affecting a protein. More...
def	GetPartnersByDrugName (s, drugName)
	Get protein which are in physical contact with a drug. More...

Detailed Description

Drugs associated with a protein.

Proteins are encoded by UniProt accession numbers, as they are reported by
the DrugBank XML file. The class allows filtering for certain types of
drugs and drug/protein relationships. (Proteins are always called
'partners' in DrugBank terms, and they differ between four types of drug
related proteins, see container class CDrugPartnerPair for more
information on this.

Constructor & Destructor Documentation

__init__()

def cls.DrugBankAnnotation.CDrugBankAnnotation.__init__	(		s,
			dbp
	)

Constructor.

    @param dbp  Instance of cls.DrugBankParser.CDrugBankParser, loaded
    with data.

Member Function Documentation

ClearFilter()

def cls.DrugBankAnnotation.CDrugBankAnnotation.ClearFilter	(		s,
			fltType
	)

Stop filtering of a certain filter type.

Parameters

fltType

One of the global variables defined here, DBFLT_*.

Returns

See SetFilter.

ClearFilters()

def cls.DrugBankAnnotation.CDrugBankAnnotation.ClearFilters

(

s

)

Stop any filtering.

GetDrugs()

def cls.DrugBankAnnotation.CDrugBankAnnotation.GetDrugs	(		s,
			upAcc
	)

Get drugs affecting a protein.

    Drugs are reported Based on the filters set by the method
    @ref SetFilter. If no filter has been set, all drugs
    assicated with the protein are reported.

    @param upAcc  UniProtKB accession number, eg. 'P35372'.
    @return  A list of drugs and their relationships to the protein in
    question, stored in an instance of CDrugPartnerPairList.

GetPartnersByDrugName()

def cls.DrugBankAnnotation.CDrugBankAnnotation.GetPartnersByDrugName	(		s,
			drugName
	)

Get protein which are in physical contact with a drug.

    This interface is rather preliminary, since we do not use this
    direction of information flow.
    @param drugName  (@c String) Drug name to be queried.
    @return A @c List of triplets, (cls.DrugBankPartner.CDrugBankPartner,
    cls.DrugBankDrug.CDrugBankDrug, cls.DrugBankDrug.CDrugBankDrugPartner)
    which are filtered by the currently active set of filter rules.

GetPossibleActions()

def cls.DrugBankAnnotation.CDrugBankAnnotation.GetPossibleActions

(

s

)

Get valid names for mechanisms of drug interactions with partners.

    @return (@c List) Drug action names, eg. 'inhibitor'.

GetPossibleAffectedOrganisms()

def cls.DrugBankAnnotation.CDrugBankAnnotation.GetPossibleAffectedOrganisms

(

s

)

Get valid organism names where the drug is targeting the drug partner.

Returns

(List) Organism names which are affected by a drug, eg. 'Humans and other mammals', or 'Human Herpes Virus'.

GetPossibleBondTypes()

def cls.DrugBankAnnotation.CDrugBankAnnotation.GetPossibleBondTypes

(

s

)

Get valid names for drug-related function of drug partner.

    This is implied in the schema file.
    @return (@c List) Partner types, eg. 'enzyme', 'transporter', etc.

GetPossibleGroups()

def cls.DrugBankAnnotation.CDrugBankAnnotation.GetPossibleGroups

(

s

)

Get valid names for drug classes.

    These tokens are hard coded in the schema file.
    @return (@c List) Drug group names, eg. 'approved'.

GetPossibleKnownActions()

def cls.DrugBankAnnotation.CDrugBankAnnotation.GetPossibleKnownActions

(

s

)

Get valid tokens if knowledge exists on how the drug works.

    These strings are listed in the schema file.
    @return (@c List) Drug/target specific knowledge names, eg. 'yes'.

SetFilter()

def cls.DrugBankAnnotation.CDrugBankAnnotation.SetFilter	(		s,
			fltType,
			fltLst
	)

Set a filter.

    Briefly, filtering works as inclusive AND. There are multiple types of
    filters that can be applied, see @c DBFLT_* globals. First, if a
    filter is not set, then all data related to this filter type will be
    reported. Second, if a filter is set, only these drugs will be
    reported that are tagged with at least one (!) of the filter names set
    here. Third, a combination of filters is always a logical 'and'.
    @param fltType  One of the global variables defined here, @c DBFLT_*.
    @param fltLst  @c List of names to be filtered for. (If this is an
    empty list, the filter is disabled. Use ClearFilter for this, though.)
    @return @c False, if the @c fltType or @c fltLst included invalid
    data; @c True, otherwise.

---

The documentation for this class was generated from the following file:

• cls/DrugBankAnnotation.py