CDPL.Biomol.ResidueDictionary Class Reference

Global dictionary for the lookup of meta-data associated with the residues in biological macromolecules. More...

Inheritance diagram for CDPL.Biomol.ResidueDictionary:

Classes
class	Entry
	A single residue dictionary entry. More...

Public Member Functions
None	__init__ ()
	Initializes the ResidueDictionary instance.
None	__init__ (ResidueDictionary dict)
	Initializes a copy of the ResidueDictionary instance dict. More...
int	getObjectID ()
	Returns the numeric identifier (ID) of the wrapped C++ class instance. More...
None	addEntry (Entry entry)
	Adds (or overwrites) the dictionary entry entry by moving its data. More...
bool	containsEntry (str code)
	Tells whether the dictionary contains an entry for the residue with three-letter code code. More...
None	removeEntry (str code)
	Removes the dictionary entry for the residue with three-letter code code. More...
Entry	getEntry (str code)
	Returns the dictionary entry for the residue with three-letter code code. More...
None	clear ()
	Removes all entries from the dictionary.
int	getNumEntries ()
	Returns the number of entries in the dictionary. More...
list	getEntries ()
None	loadDefaults ()
	Loads the built-in default residue dictionary entries.
ResidueDictionary	assign (ResidueDictionary dict)
	Replaces the current state of self with a copy of the state of the ResidueDictionary instance dict. More...
str	getReplacedCode (str code)
str	getReplacedByCode (str code)
str	getParentCode (str code)
str	getOneLetterCode (str code)
bool	isObsolete (str code)
str	getName (str code)
int	getType (str code)
Chem.MolecularGraph	getStructure (str code)

Static Public Member Functions
None	set (ResidueDictionary dict)
	Replaces the process-wide default dictionary by dict. More...
ResidueDictionary	get ()
	Returns the process-wide default dictionary (lazily initialized on first call). More...
bool	isStdResidue (str code)
	Tells whether the residue with three-letter code code is a standard biopolymer residue (amino acid or nucleotide). More...

Properties
	objectID = property(getObjectID)
	numEntries = property(getNumEntries)
	entries = property(getEntries)

Detailed Description

Global dictionary for the lookup of meta-data associated with the residues in biological macromolecules.

Constructor & Destructor Documentation

__init__()

None CDPL.Biomol.ResidueDictionary.__init__

(

ResidueDictionary

dict

)

Initializes a copy of the ResidueDictionary instance dict.

Parameters

dict	The ResidueDictionary instance to copy.

Member Function Documentation

getObjectID()

int CDPL.Biomol.ResidueDictionary.getObjectID

(

)

Returns the numeric identifier (ID) of the wrapped C++ class instance.

Different Python ResidueDictionary instances may reference the same underlying C++ class instance. The commonly used Python expression a is not b thus cannot tell reliably whether the two ResidueDictionary instances a and b reference different C++ objects. The numeric identifier returned by this method allows to correctly implement such an identity test via the simple expression a.getObjectID() != b.getObjectID().

Returns

The numeric ID of the internally referenced C++ class instance.

addEntry()

None CDPL.Biomol.ResidueDictionary.addEntry

(

Entry

entry

)

Adds (or overwrites) the dictionary entry entry by moving its data.

Parameters

entry

The entry to add.

Since

1.2

containsEntry()

bool CDPL.Biomol.ResidueDictionary.containsEntry

(

str

code

)

Tells whether the dictionary contains an entry for the residue with three-letter code code.

Parameters

code	The residue three-letter code.

Returns

True if a matching entry exists, and False otherwise.

removeEntry()

None CDPL.Biomol.ResidueDictionary.removeEntry

(

str

code

)

Removes the dictionary entry for the residue with three-letter code code.

Parameters

code	The residue three-letter code.

getEntry()

Entry CDPL.Biomol.ResidueDictionary.getEntry

(

str

code

)

Returns the dictionary entry for the residue with three-letter code code.

Parameters

code	The residue three-letter code.

Returns

A reference to the matching entry (or to an empty default-constructed entry if no matching entry exists).

getNumEntries()

int CDPL.Biomol.ResidueDictionary.getNumEntries

(

)

Returns the number of entries in the dictionary.

Returns

The entry count.

getEntries()

list CDPL.Biomol.ResidueDictionary.getEntries

(

)

Returns

assign()

ResidueDictionary CDPL.Biomol.ResidueDictionary.assign

(

ResidueDictionary

dict

)

Replaces the current state of self with a copy of the state of the ResidueDictionary instance dict.

Parameters

dict	The ResidueDictionary instance to copy.

Returns

self

set()

None CDPL.Biomol.ResidueDictionary.set ( ResidueDictionary  dict )

static

Replaces the process-wide default dictionary by dict.

Parameters

dict	The new default dictionary (a nullptr resets to the built-in default).

get()

ResidueDictionary CDPL.Biomol.ResidueDictionary.get ( )

static

Returns the process-wide default dictionary (lazily initialized on first call).

Returns

A reference to the default-dictionary shared reference.

getReplacedCode()

str CDPL.Biomol.ResidueDictionary.getReplacedCode

(

str

code

)

Parameters

arg1
code

Returns

getReplacedByCode()

str CDPL.Biomol.ResidueDictionary.getReplacedByCode

(

str

code

)

Parameters

arg1
code

Returns

getParentCode()

str CDPL.Biomol.ResidueDictionary.getParentCode

(

str

code

)

Parameters

arg1
code

Returns

getOneLetterCode()

str CDPL.Biomol.ResidueDictionary.getOneLetterCode

(

str

code

)

Parameters

arg1
code

Returns

isObsolete()

bool CDPL.Biomol.ResidueDictionary.isObsolete

(

str

code

)

Parameters

arg1
code

Returns

getName()

str CDPL.Biomol.ResidueDictionary.getName

(

str

code

)

Parameters

arg1
code

Returns

isStdResidue()

bool CDPL.Biomol.ResidueDictionary.isStdResidue ( str  code )

static

Tells whether the residue with three-letter code code is a standard biopolymer residue (amino acid or nucleotide).

Parameters

code	The residue three-letter code.

Returns

True if the residue is a standard biopolymer residue, and False otherwise.

getType()

int CDPL.Biomol.ResidueDictionary.getType

(

str

code

)

Parameters

arg1
code

Returns

getStructure()

Chem.MolecularGraph CDPL.Biomol.ResidueDictionary.getStructure

(

str

code

)

Parameters

arg1
code

Returns