Base class for all analysis defined in nMOLDYN.
The class Analysis is an abstract-base-class that defines attributes
and methods common to all the analysis available in nMOLDYN. To set up an
analysis object, use one of its subclass.
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setInputParameters(self,
parameters)
Sets the input parameters dictionnary. |
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dict
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preLoadTrajectory(self,
structure,
differentiation=1) |
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dict
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updateJobProgress(self,
norm)
Check the progress of the running analysis and displays periodically
on the console and the logfile how far is the analysis. |
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buildJobInfo(self)
Display on the console and in the log file the main ifnormation about
the analysis to run. |
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dict
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an instance of MMTK.ParticleProperties.ParticledScalar
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weightingScheme(self,
universe,
atoms,
deuter,
scheme='equal')
Returns the weights of |atoms| MMTK collection of |universe| MMTK
universe using the weighting scheme |scheme|. |
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instance of MMTK.Collections.Collection
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subsetSelection(self,
universe,
selection)
Returns a MMTK collection of atoms that matches |selection| selection
string. |
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instance of MMTK.Collections.Collection
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list
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groupSelection(self,
universe,
selection)
Returns a list of MMTK collections where each collection defines a
group on which will be applied collectively an analysis. |
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Python set for |selectionMode| = 'subset' or 'deuteration' and dict
for |selectionMode| = 'group'
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Python set for |selectionMode| = 'subset' or 'deuteration' and dict
for |selectionMode| = 'group'
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__parseFileSelectionString(self,
universe,
selectionString,
selectionMode)
Parses a nMOLDYN Selection file (nms file) in order to perform a
subset, a deuteration or a group selection. |
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set
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list
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__retrieveAtomIndexes(self,
universe,
objectClass,
objectName,
selectionKeyword,
selectionValue)
Retrieves the MMTK index of the atoms matching |objectClass| MMTK
chemical object class, |objectName| nMOLDYN name, |selectionKeyword|
selection keyword and |selectionValue| selection value. |
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list
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__allClassParser(self,
universe,
selectionKeyword,
selectionValue)
Retrieves the MMTK indexes of the atoms whose nMOLDYN name is '*'
matching |selectionKeyword| selection keyword and |selectionValue|
selection value. |
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list
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__atomParser(self,
universe,
objectName,
selectionKeyword,
selectionValue)
Retrieves the MMTK index of the atoms whose MMTK chemical object
class is 'Atom' matching |objectName| nMOLDYN name,
|selectionKeyword| selection keyword and |selectionValue| selection
value. |
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list
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__atomClusterParser(self,
universe,
objectName,
selectionKeyword,
selectionValue)
Retrieves the MMTK index of the atoms whose MMTK chemical object
class is 'AtomCluster' matching |objectName| nMOLDYN name,
|selectionKeyword| selection keyword and |selectionValue| selection
value. |
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list
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__moleculeParser(self,
universe,
objectName,
selectionKeyword,
selectionValue)
Retrieves the MMTK index of the atoms whose MMTK chemical object
class is 'Molecule' matching |objectName| nMOLDYN name,
|selectionKeyword| selection keyword and |selectionValue| selection
value. |
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list
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__nucleotideChainParser(self,
universe,
objectName,
selectionKeyword,
selectionValue)
Retrieves the MMTK index of the atoms whose MMTK chemical object
class is 'NucleotideChain' matching |objectName| nMOLDYN name,
|selectionKeyword| selection keyword and |selectionValue| selection
value. |
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list
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__peptideChainParser(self,
universe,
objectName,
selectionKeyword,
selectionValue)
Retrieves the MMTK index of the atoms whose MMTK chemical object
class is 'PeptideChain' matching |objectName| nMOLDYN name,
|selectionKeyword| selection keyword and |selectionValue| selection
value. |
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list
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__proteinParser(self,
universe,
objectName,
selectionKeyword,
selectionValue)
Retrieves the MMTK index of the atoms whose MMTK chemical object
class is 'Protein' matching |objectName| nMOLDYN name,
|selectionKeyword| selection keyword and |selectionValue| selection
value. |
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