Package rdkit :: Package Chem :: Module rdDistGeom :: Class EmbedParameters
[hide private]
[frames] | no frames]

Class EmbedParameters

 object --+    
          |    
??.instance --+
              |
             EmbedParameters

Parameters controlling embedding

Instance Methods [hide private]
 
__init__(...)
__init__( (object)arg1) -> None :
 
__reduce__(...)
helper for pickle

Inherited from unreachable.instance: __new__

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

Class Variables [hide private]
  __instance_size__ = 96
Properties [hide private]
  boxSizeMult
determines the size of the box used for random coordinates
  clearConfs
clear all existing conformations on the molecule
  enforceChirality
enforce correct chirilaty if chiral centers are present
  ignoreSmoothingFailures
try and embed the molecule if if triangle smoothing of the bounds matrix fails
  maxIterations
maximum number of embedding attempts to use for a single conformation
  numThreads
number of threads to use when embedding multiple conformations
  numZeroFail
fail embedding if we have at least this many zero eigenvalues
  onlyHeavyAtomsForRMS
Only consider heavy atoms when doing RMS filtering
  optimizerForceTol
the tolerance to be used during the distance-geometry force field minimization
  pruneRmsThresh
used to filter multiple conformations: keep only conformations that are at least this far apart from each other
  randNegEig
if the embedding yields a negative eigenvalue, pick coordinates that correspond to this component at random
  randomSeed
seed for the random number generator
  useBasicKnowledge
impose basic-knowledge constraints such as flat rings
  useExpTorsionAnglePrefs
impose experimental torsion angle preferences
  useRandomCoords
start the embedding from random coordinates instead of using eigenvalues of the distance matrix
  verbose
be verbose about configuration

Inherited from object: __class__

Method Details [hide private]

__init__(...)
(Constructor)

 

__init__( (object)arg1) -> None :

    C++ signature :
        void __init__(_object*)

Overrides: object.__init__

__reduce__(...)

 
helper for pickle

Overrides: object.__reduce__
(inherited documentation)

Property Details [hide private]

boxSizeMult

determines the size of the box used for random coordinates

Get Method:
unreachable(...)
Set Method:
unreachable(...)

clearConfs

clear all existing conformations on the molecule

Get Method:
unreachable(...)
Set Method:
unreachable(...)

enforceChirality

enforce correct chirilaty if chiral centers are present

Get Method:
unreachable(...)
Set Method:
unreachable(...)

ignoreSmoothingFailures

try and embed the molecule if if triangle smoothing of the bounds matrix fails

Get Method:
unreachable(...)
Set Method:
unreachable(...)

maxIterations

maximum number of embedding attempts to use for a single conformation

Get Method:
unreachable(...)
Set Method:
unreachable(...)

numThreads

number of threads to use when embedding multiple conformations

Get Method:
unreachable(...)
Set Method:
unreachable(...)

numZeroFail

fail embedding if we have at least this many zero eigenvalues

Get Method:
unreachable(...)
Set Method:
unreachable(...)

onlyHeavyAtomsForRMS

Only consider heavy atoms when doing RMS filtering

Get Method:
unreachable(...)
Set Method:
unreachable(...)

optimizerForceTol

the tolerance to be used during the distance-geometry force field minimization

Get Method:
unreachable(...)
Set Method:
unreachable(...)

pruneRmsThresh

used to filter multiple conformations: keep only conformations that are at least this far apart from each other

Get Method:
unreachable(...)
Set Method:
unreachable(...)

randNegEig

if the embedding yields a negative eigenvalue, pick coordinates that correspond to this component at random

Get Method:
unreachable(...)
Set Method:
unreachable(...)

randomSeed

seed for the random number generator

Get Method:
unreachable(...)
Set Method:
unreachable(...)

useBasicKnowledge

impose basic-knowledge constraints such as flat rings

Get Method:
unreachable(...)
Set Method:
unreachable(...)

useExpTorsionAnglePrefs

impose experimental torsion angle preferences

Get Method:
unreachable(...)
Set Method:
unreachable(...)

useRandomCoords

start the embedding from random coordinates instead of using eigenvalues of the distance matrix

Get Method:
unreachable(...)
Set Method:
unreachable(...)

verbose

be verbose about configuration

Get Method:
unreachable(...)
Set Method:
unreachable(...)