Package schrodinger :: Package application :: Package matsci :: Module amorphous :: Class Terminator

Class Terminator

object --+    
         |    
BaseMoiety --+
             |
            Terminator

Known Subclasses:

Cascader

A unit that terminates a chain

Note that the concept of an "Terminator" can be a bit fungible. It can either be the actual terminator moiety that ends a polymer chain, or it may be an already built chain that will be tacked on to some initiation point.

Instance Methods

[hide private]

__init__(self, struct, markers=None, name=None)
Create a Terminator object

findHead(self)
Find and store the index of the head atom

getNextStructure(self, *args)
Get a copy of this structure to add to a chain

getCouplerElement(self, *args)
Get the element of the coupler (head) atom

AttachmentAtoms

getCouplerAndGrower(self, *args)
Get the coupler and grower atoms and markers.

getPDBName(self)
Get a PDB residue-like name for this moiety

Inherited from BaseMoiety: addToChain, alignToVector, checkRequiredProperties, determineCouplerLocation, finalizeSideGroup, findAttachedAtomIndex, findBackbone2BranchingPoint, findRotatableBonds, findSideGroup, getBondLength, getStructureForCoupling, markBackboneAtom, moveHeadToOrigin, readFromStructure, setAsFragment

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Class Methods

[hide private]

Inherited from BaseMoiety: write

Class Variables

[hide private]

Inherited from BaseMoiety: bond_length_cache

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, struct, markers=None, name=None)
(Constructor)


Create a Terminator object

Terminators drawn by the user as:
    R1-stuff
And stored as:
    marker-head-stuff

where marker is the R1 atom, head is the atom it is bound to, and stuff
is everything else.

@type struct: L{schrodinger.structure.Structure}
@param struct: The structure of this Moiety

@type markers: list
@param markers: A list of the indexes of the Rx atoms

@type name: str
@param name: The name of this moiety - gets added to each atom as an
atom property

Parameters:

struct - The structure of this Moiety
markers - A list of the indexes of the Rx atoms. If not supplied, information will be read from the structure properties

Overrides: object.__init__

getCouplerAndGrower(self, *args)

Get the coupler and grower atoms and markers. The latter is None because Terminators have no grow points

Returns: AttachmentAtoms: The atoms indexes of the coupler, grower and marker atoms

Class Terminator

__init__(self, struct, markers=None, name=None) (Constructor)

getCouplerAndGrower(self, *args)

init(self, struct, markers=None, name=None)
(Constructor)