Package schrodinger :: Package analysis :: Module reaction :: Class ReagentNode

Class ReagentNode

object --+        
         |        
      Node --+    
             |    
     RouteNode --+
                 |
                ReagentNode

A node representing a starting material in a synthetic route. Unlike RouteNode, it cannot have any reaction instances. Reagent nodes are identified by an index and a reagent class.

Reagents may optionally have a filename or a smiles or a list of smiles as a source of reagent molecules. If none of these is provided, the object can try to find a reagent file based on the reagent class alone.

Instance Methods

[hide private]

__init__(self, index, reagent_class, filename=None, smiles=None, smiles_list=None)
x.__init__(...) initializes x; see help(type(x)) for signature

__str__(self)
str(x)

str

findReagentFile(self)
First, look for structure files matching <reagent_class>.* in the CWD.

_getNodeData(self, specific)

Inherited from RouteNode: checkReactions, depth, getReactionSet, getStartingNodes, getTreeData, isStartingMaterial, setReactionInstance, steps, write

Inherited from Node: treeAsString

Inherited from Node (private): _asStringList

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

Properties

[hide private]

Inherited from RouteNode: precursors, reaction, reaction_instance

Inherited from object: __class__

Method Details

[hide private]

init(self, index, reagent_class, filename=None, smiles=None, smiles_list=None)
(Constructor)

x.__init__(...) initializes x; see help(type(x)) for signature

Parameters:

index (int)
smiles (str or NoneType)
smiles_list (list of str or NoneType)
reagent_class (str)
filename (str or NoneType)

Overrides: object.__init__

str(self)
(Informal representation operator)

str(x)

Overrides: object.__str__: (inherited documentation)

findReagentFile(self)

First, look for structure files matching <reagent_class>.* in the CWD. If one is found, return it. If multiple matches are found, an exception is raised. If none are found, look for <reagent_class>.smi in the mmshare data directory and return it if it exists, or None otherwise.

Returns: str: path to reagent file, or None if not found

_getNodeData(self, specific)

Overrides: RouteNode._getNodeData

Class ReagentNode

__init__(self, index, reagent_class, filename=None, smiles=None, smiles_list=None) (Constructor)

__str__(self) (Informal representation operator)

findReagentFile(self)

_getNodeData(self, specific)

init(self, index, reagent_class, filename=None, smiles=None, smiles_list=None)
(Constructor)

str(self)
(Informal representation operator)