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

Class Cascader

object --+        
         |        
BaseMoiety --+    
             |    
    Terminator --+
                 |
                Cascader


A group that ends a chain but starts multiple new chains

Cascaders are drawn as:
        R2
        |
    R1-stuff-R2
and stored as:
              cascader
                  |
    marker-head-stuff-cascader
where cascader is an atom property added to the R2 marker atoms

Instance Methods

[hide private]

__init__(self, *args, **kwargs)
Create a Terminator object

findBackbone(self)
Find the set of atoms that creates the shortest distance (number of bonds) between the head and each cascade points.

findHead(self)
Find the head atom, but also mark cascader atoms that will start new points

readFromStructure(self, struct)
Overrides the parent method to add and read Cascader-specific properties.

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

setAsFragment(self)
Prepare Cascader information for in-cell grow.

Inherited from Terminator: getCouplerAndGrower, getCouplerElement, getNextStructure

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

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

Class Methods

[hide private]

write(cls, generations, filename, struct, *args)
Over-ride the parent class method to add generations as a property to the structure.

Class Variables

[hide private]

Inherited from BaseMoiety: bond_length_cache

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, *args, **kwargs)
(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__

(inherited documentation)

findBackbone(self)

Find the set of atoms that creates the shortest distance (number of bonds) between the head and each cascade points. These are considered backbone atoms.

Backbone atoms are marked with a backbone atom property.