rdkit.Chem.rdDistGeom.EmbedParameters

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(...)