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Class: ChemAtomNmrDistrib


    nD chemical shift distribution matrix. The atoms on the axes are defined by the chemAtomNmrRefs link, the referencing by the refPoints refValues, and valuePerPoint arrays.

    The distribution is normalised and the values must sum to 1.0. The shifts to which the individual points belong are defined so that for each dimension point i collects the  shifts from
    refValue + valuePerPoint*( i-refPoint) to refValue + valuePerPoint*( i+1-refPoint).
Attributes
Link Attributes
Attribute Methods
Link Attribute Methods
Class Methods
Factory Methods
Other Methods
Appendix

Inheritance:


Details:

Parent: link chemCompNmrRef to class ChemCompNmrRef
Main key: serial
Mandatory Attributes: refPoints, refValues, shape, valuesPerPoint, refAtoms
Known Subclasses: None
Children: None
Constructor: newObj = ChemAtomNmrDistrib( chemCompNmrRef,refPoints=value, refValues=value, shape=value, valuesPerPoint=value, refAtoms=value, ... )

Attributes (in package)

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Attribute Type Multiplicity Description
data Float 0..* Matrix data as packed list.  
defaultValue Float 1..1 default value of data in matrix. Used instead of values that are not explicitly set.  
ndim PositiveInt 1..1 Derived. Number of matrix dimensions  
refPoints Float 2..* Reference points - one for each dimension  
refValues Float 2..* Reference values - shift value at the reference point for each dimension  
serial Int 1..1 Serial number of object. Serves as object main key. Serial numbers of deleted objects are not re-used. Serial numbers can only be set by the implementation. Values are in practice always positive, since negative values are interpreted as a signal to set the next free serial  
shape NonNegativeInt 1..* Matrix shape, slowest moving index first. SIze in first dimension (only) may be zero.  
size NonNegativeInt 1..1 Derived. Matrix size - product of dimensions sizes  
valuesPerPoint Float 2..* Width of a matrix row in ppm. One for each dimension  

Inherited Attributes (not in package): applicationDataclassNamefieldNamesinConstructorisDeletedmetaclasspackageNamepackageShortNamequalifiedName

Link Attributes (in package)

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Attribute Type Multiplicity Description
chemCompNmrRef ChemCompNmrRef 1..1 (Parent link). parent link  
parent ChemCompNmrRef 1..1 link to parent object - synonym for chemCompNmrRef  
refAtoms ChemAtomNmrRef 2..* Atom references for chemical shifts in shiftDistribution  

Inherited Attributes (not in package): accessactiveAccessroottopObject

Attribute Methods (in package)

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Attribute Method Return Parameters Comment
data
getData Float Tuple -
setData - Float List
defaultValue
getDefaultValue Float -
setDefaultValue - Float
ndim
getNdim PositiveInt - non-std.
refPoints
getRefPoints Float Tuple -
setRefPoints - Float List
addRefPoint - Float
removeRefPoint - Float
refValues
getRefValues Float Tuple -
setRefValues - Float List
addRefValue - Float
removeRefValue - Float
serial
getSerial Int -
setSerial - Int
shape
getShape NonNegativeInt Tuple -
setShape - NonNegativeInt List
size
getSize NonNegativeInt - non-std.
valuesPerPoint
getValuesPerPoint Float Tuple -
setValuesPerPoint - Float List
addValuePerPoint - Float
removeValuePerPoint - Float

Link Attribute Methods (in package)

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Attribute Method Return Parameters Comment
chemCompNmrRef
getChemCompNmrRef ChemCompNmrRef -
parent
getParent ChemCompNmrRef -
refAtoms
getRefAtoms ChemAtomNmrRef Tuple -
setRefAtoms - ChemAtomNmrRef List
findFirstRefAtom ChemAtomNmrRef keyword=value pairs
findAllRefAtoms ChemAtomNmrRef List keyword=value pairs

Class Methods (in package)

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Method Return Parameters Comment
checkValid - Boolean
checkAllValid - Boolean
getByKey ChemAtomNmrDistrib memops.api.Implementation.MemopsObject, Any List static
getFullKey Any List Boolean
getLocalKey Any -
get Any String
set - String, Any

Factory Methods (in package)

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Method Return Parameters
None

Other Methods (in package)

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Method Return Parameters Comment
getPointValue Float Int List non-std. get value of matrix at position 'point'. Point is converted as for self.pointToIndex.
getSubmatrixData Float List Int List, Int List non-std. get data (packed linear array)  for submatrix of shape 'shape' with 'point' as the corner with the smallest index values. point is convered as for self.pointToIndex. 'shape values that are omitted or set to zero are reset to the (rest of the) dimension size.
indexToPoint Int List Int non-std. Converts array index to equivalent point
pointToIndex Int Int List non-std. converts point to equivalent array index. Point is padded to matrix dimension with zeros. negative index values -i in point are treated as eqal to (size-i).
removeSlice - Int non-std. Remove slice of matrix in slowest verying dimension at offset index.
resetData - - non-std. Reset data to default values and free memory used.
setPointValue - Int List, Float non-std. set value of matrix at position 'point'. Point is converted as for self.pointToIndex.
setSubmatrixData - Int List, Int List, Float List non-std. set data for submatrix of shape 'shape' with 'point' as the corner with the smallest index values to 'values' (packed linear array). Point is converted as for self.pointToIndex.  shape values that are omitted or set to zero are reset to the (rest of the) dimension size.
sizeFirstDim - Int non-std. Change size in first (slowest) dimension, truncating or padding with self.defaultValue as necessary.

Appendix

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guid:

www.ccpn.ac.uk_Fogh_2010-05-14-15:28:22_00001

isImplicit:

False

Tag

Value
repositoryId $Id: $

Tag

Value
repositoryTag $Name: $

Special constructor code:

None

Special destructor code:

None

Special postDestructor code:

None

Constraint name:

consistent_matrix_size
Constraint code: len(self.refPoints) == self.ndim

Constraint name:

consistent_number_of_reference_atoms
Constraint code: len(self.refPoints) == len(self.refAtoms)

Constraint name:

consistent_number_valuesPerPoint
Constraint code: len(self.valuesPerPoint) == self.ndim

Constraint name:

consistent_referencing_dimension
Constraint code: len(self.refPoints) == len(self.refValues)

Constraint name:

nd_distribution_is_normalised
Constraint code: isValid = False

ll = self.data
if ll:
  floatTolerance = 1.0e-5

  if abs(sum(ll)-1.0) <= floatTolerance:
    isValid = True

Constraint name:

numbers_are_positive
Constraint code: data= self.data
isValid = (not data or min(data) >= 0)
Known inward one-way links: None
  Data Model Version 2.1.2
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  Autogenerated by  PyApiDocGen  revision 1.3   on  Mon Mar 2 17:24:35 2015    from data model package  ccp.api.nmr.NmrReference.ChemAtomNmrDistrib   revision ?  
  Work done by the CCPN team.
www.ccpn.ac.uk