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2016-3 Schrodinger Python API
Package schrodinger :: Package application :: Package matsci :: Module rxn_path :: Class ReactionCoords
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Class ReactionCoords

object --+
         |
        ReactionCoords

Manage reaction coordinates.

Instance Methods [hide private]
 
__init__(self)
Create a ReactionCoords instance.
schrodinger.structure.Structure, schrodinger.structure.Structure
getNormalOrdering(self, reactant, product, logger=None)
Attempt to normalize the atomic ordering between reactants and products.
schrodinger.structure.Structure, schrodinger.structure.Structure
makeRxnComplex(self, reactant, product, vdwscale, logger=None)
For certain bimolecular reactions preprocess reactants and products into reaction complexes.
 
collectInternals(self, reactant, product, rinternals, pinternals, logger=None)
Find the redundant internal coordinates by merging the coordinates defined in the reactant and product.
 
getReactionInternals(self, rinternals, pinternals, reactioninternals)
Determine the reactive redundant internal coordinates.
list of ints, float
runSuperposition(self, reactant, product, reactioninternals, logger=None)
Superpose the product structure on to the reactant structure using the non-reactive atoms, i.e.
list of float
getCartesianCoords(self, astructure)
Get the Cartesian coordinates of a structure as a 3N dimensional list of floats.
 
prepare(self, reactant, product, interpolation, norxncomplex, vdwscale, samplepoints, logger=None)
Prepare reaction coordinates.

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

Class Variables [hide private]
  REACTIONBONDTHRESH = 0.05
  REACTIONANGLETHRESH = 1.0
  REACTIONDIHEDRALTHRESH = 1.0
  REVOLUTION = 360
  HALFREVOLUTION = 180
  REVOLUTIONTHRESH = 10
  REACTANTPREFIX = 'pre-'
  PRODUCTPREFIX = 'post-'
Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self)
(Constructor)

 

Create a ReactionCoords instance.

Overrides: object.__init__

getNormalOrdering(self, reactant, product, logger=None)

 

Attempt to normalize the atomic ordering between reactants and products.

Parameters:
  • reactant (schrodinger.structure.Structure) - the reactant
  • product (schrodinger.structure.Structure) - the product
  • logger (logging.getLogger) - output logger
Returns: schrodinger.structure.Structure, schrodinger.structure.Structure
newreactant, newproduct, if defined specifies the reordered reactant and product structures

makeRxnComplex(self, reactant, product, vdwscale, logger=None)

 

For certain bimolecular reactions preprocess reactants and products into reaction complexes.

Parameters:
  • reactant (schrodinger.structure.Structure) - reactant
  • product (schrodinger.structure.Structure) - product
  • vdwscale (float) - scales the intermolecular distance
  • logger (logging.getLogger) - output logger
Returns: schrodinger.structure.Structure, schrodinger.structure.Structure
newreactant, newproduct, if defined specifies the reactant and product structures in the created reaction complex

collectInternals(self, reactant, product, rinternals, pinternals, logger=None)

 

Find the redundant internal coordinates by merging the coordinates defined in the reactant and product.

Parameters:
  • reactant (schrodinger.structure.Structure) - reactant
  • product (schrodinger.structure.Structure) - product
  • rinternals (InternalCoords) - reactant internal coordinates
  • pinternals (InternalCoords) - product internal coordinates
  • logger (logging.getLogger) - output logger

getReactionInternals(self, rinternals, pinternals, reactioninternals)

 

Determine the reactive redundant internal coordinates.

Parameters:
  • rinternals (InternalCoords) - reactant internal coordinates
  • pinternals (InternalCoords) - product internal coordinates
  • reactioninternals (InternalCoords) - reaction internal coordinates

runSuperposition(self, reactant, product, reactioninternals, logger=None)

 

Superpose the product structure on to the reactant structure using the non-reactive atoms, i.e. those that do not define any reactive redundant internal coordinate.

Parameters:
  • reactant (schrodinger.structure.Structure) - reactant
  • product (schrodinger.structure.Structure) - product
  • reactioninternals (InternalCoords) - reaction internal coordinates
  • logger (logging.getLogger) - output logger
Returns: list of ints, float
tosuperpose, armsd, atom indicies used to superpose and the final RMSD

getCartesianCoords(self, astructure)

 

Get the Cartesian coordinates of a structure as a 3N dimensional list of floats.

Parameters:
  • astructure (schrodinger.structure.Structure) - structure
Returns: list of float
cartesians, the 3N Cartesian coordinates ordered like [x1, y1, z1, x2, ..., zN]

prepare(self, reactant, product, interpolation, norxncomplex, vdwscale, samplepoints, logger=None)

 

Prepare reaction coordinates.

Parameters:
  • reactant (schrodinger.structure.Structure) - reactant
  • product (schrodinger.structure.Structure) - product
  • interpolation (str) - coordinate system used for interpolating
  • norxncomplex (boolean) - disable preprocessing into a reaction complex
  • vdwscale (float) - scales the intermolecular distance
  • samplepoints (list of float) - reaction path sample points
  • logger (logging.getLogger) - output logger

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2016-3 Schrodinger Python API
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