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2017-3 Schrodinger Python API
Package schrodinger :: Package application :: Package matsci :: Module amorphous :: Class Initiator
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Class Initiator

object --+    
         |    
BaseMoiety --+
             |
            Initiator

A group that starts the whole polymer off - can have multiple grow points, which means that multiple chains will radiate from this group (a dendrimer).

Note that the concept of an "Initiator" can be a bit fungible. It can either be the actual intiator moiety that starts the whole polymer, or it may be a partially built polymer that still needs additional chains added to it.

Instance Methods [hide private]
 
__init__(self, *args, **kwargs)
Overrides the parent init method to allow the parial_polymer keyword parameter.
 
completePolymer(self, chain_terminator, chain_namer, clash_fixer)
Tack on an existing chain to each grow point
(schrodinger.structure.Structure, int)
fillBranchPoints(self, chain_terminator, chain_branch_points, chain_namer, clash_fixer)
Tack on an existing chain to each of our branch points - each point has a percent chance of getting a chain added to it as long as its generation is less than the generation limit
 
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, *args, **kwargs)
(Constructor)

 

Overrides the parent init method to allow the parial_polymer keyword parameter.

Parameters:
  • partial_polymer (bool) - If True, this Initiator is actually a partially built polymer that is going to just act like an initiator.
Overrides: object.__init__

completePolymer(self, chain_terminator, chain_namer, clash_fixer)

 

Tack on an existing chain to each grow point

Parameters:
  • chain_terminator (Terminator) - A Terminator object that stores the existing chain to add
  • chain_namer (function) - A function that should be called on each chain that will be added to the existing polymer. The purpose of this function should be to add chain name data to the added structure.
  • clash_fixer (function) - A function to call on the polymer when any new chain is added in order to fix any clashes caused by the new chain

fillBranchPoints(self, chain_terminator, chain_branch_points, chain_namer, clash_fixer)

 

Tack on an existing chain to each of our branch points - each point has a percent chance of getting a chain added to it as long as its generation is less than the generation limit

Parameters:
  • chain_terminator (Terminator) - A Terminator object that stores the existing chain to add
  • chain_branch_points (list) - A list of atom indexes in the chain_terminator structure that are branch points
  • chain_namer (function) - A function that should be called on each chain that will be added to the existing polymer. The purpose of this function should be to add chain name data to the added structure.
  • clash_fixer (function) - A function to call on the polymer when any new chain is added in order to fix any clashes caused by the new chain
Returns: (schrodinger.structure.Structure, int)
The new polymer structure with additional branching, plus the number of new branches that were added

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2017-3 Schrodinger Python API
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