Package nMOLDYN :: Package Analysis :: Module Analysis :: Class Analysis
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Class Analysis

source code

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.

Instance Methods [hide private]
 
__init__(self, parameters=None, statusBar=None)
The constructor.
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setInputParameters(self, parameters)
Sets the input parameters dictionnary.
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dict
parseInputParameters(self)
Parses the input parameters stored in |parameters| dictionnary.
source code
 
buildTimeInfo(self)
Builds some attributes related to the frame selection string.
source code
 
preLoadTrajectory(self, structure, differentiation=1) source code
 
saveAnalysis(self, filename)
Saves the settings of an analysis to an output file.
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dict
runAnalysis(self)
Runs an analysis.
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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
analysisTime(self, time)
Converts a time in second in days, hours, minutes and seconds.
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an instance of MMTK.ParticleProperties.ParticledScalar
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
subsetSelection(self, universe, selection)
Returns a MMTK collection of atoms that matches |selection| selection string.
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instance of MMTK.Collections.Collection
deuterationSelection(self, universe, selection)
Returns a MMTK collection of atoms that matches |selection| selection string.
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list
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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__buildGroup(self, g, gSelection, gLevel) source code
Python set for |selectionMode| = 'subset' or 'deuteration' and dict for |selectionMode| = 'group'
__parseExpressionSelectionString(self, universe, selectionString, selectionMode)
Parses a nMOLDYN selection string that starts with 'expression' keyword.
source code
Python set for |selectionMode| = 'subset' or 'deuteration' and dict for |selectionMode| = 'group'
__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
__parseObjectSelectionString(self, universe, selectionString)
Parses a selection string.
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list
__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.
source code
list
__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
__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.
source code
list
__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.
source code
list
__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.
source code
list
__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.
source code
list
__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
__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.
source code
Method Details [hide private]

__init__(self, parameters=None, statusBar=None)
(Constructor)

source code 

The constructor.

Parameters:
  • parameters (dict) - a dictionnary that contains parameters of the selected analysis.
  • statusBar (instance of nMOLDYN.GUI.Widgets.StatusBar) - if not None, an instance of nMOLDYN.GUI.Widgets.StatusBar. Will attach a status bar to the selected analysis.

parseInputParameters(self)

source code 

Parses the input parameters stored in |parameters| dictionnary.

Returns: dict
a dictionnary of the parsed parameters.

buildTimeInfo(self)

source code 

Builds some attributes related to the frame selection string. They will be used to define at which times a given analysis should be run.

saveAnalysis(self, filename)

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Saves the settings of an analysis to an output file.

Parameters:
  • filename - the name of the output file. If the extension is '.nmi' the output file will be a nMOLDYN input script otherwise the output file will be a nMOLDYN autostart script.

runAnalysis(self)

source code 

Runs an analysis.

Returns: dict
a dictionnary of the form {'days' : d, 'hours' : h, 'minutes' : m, 'seconds' : s} specifying the time the analysis took in dayx, hours, minutes and seconds.

updateJobProgress(self, norm)

source code 

Check the progress of the running analysis and displays periodically on the console and the logfile how far is the analysis. Called each time a step of an analysis loop is achieved.

Parameters:
  • norm - the maximum number of steps of the analysis.

analysisTime(self, time)

source code 

Converts a time in second in days, hours, minutes and seconds.

Parameters:
  • time (integer.) - the time (in seconds) to convert.
Returns: dict
a dictionnary of the form {'days' : d, 'hours' : h, 'minutes' : m, 'seconds' : s} where d, h, m and s are integers resulting respectively from the conversion of |time| in days, hours, minutes and seconds.

weightingScheme(self, universe, atoms, deuter, scheme='equal')

source code 

Returns the weights of |atoms| MMTK collection of |universe| MMTK universe using the weighting scheme |scheme|.

Parameters:
  • universe (instance of MMTK.Universe) - the MMTK universe.
  • atoms (instance of MMTK.Collections.Collection) - the atoms to take into account when defining the weights.
  • deuter (instance of MMTK.Collections.Collection) - the hydrogen atoms that will be parametrized as deuterium atoms.
  • scheme (string) - a string equal to 'equal', 'mass', 'coherent' , 'incoherent' or 'atomicNumber' that specifies the weighting scheme to use.
Returns: an instance of MMTK.ParticleProperties.ParticledScalar
the weights of the selected atoms.

subsetSelection(self, universe, selection)

source code 

Returns a MMTK collection of atoms that matches |selection| selection string. Used to apply an analysis to a subset of atoms.

Parameters:
  • universe (instance of MMTK.Universe) - the universe on which the selection will be performed.
  • selection (string) - the selection string that will define the atoms to select.
Returns: instance of MMTK.Collections.Collection
a MMTK Collection of the atoms that matches |selection| selection string.

deuterationSelection(self, universe, selection)

source code 

Returns a MMTK collection of atoms that matches |selection| selection string. Used to switch the parameters of a subset (or all) of hydrogen atoms to the parameters of deuterium in order to simulate deuterated system.

Parameters:
  • universe (instance of MMTK.Universe) - the universe on which the selection will be performed.
  • selection (string) - the selection string that will define the atoms to select.
Returns: instance of MMTK.Collections.Collection
a MMTK Collection of the atoms that matches |selection| selection string.

groupSelection(self, universe, selection)

source code 

Returns a list of MMTK collections where each collection defines a group on which will be applied collectively an analysis.

Parameters:
  • universe (instance of MMTK.Universe) - the universe on which the selection will be performed.
  • selection (string) - the selection string that will define the contents of each group.
Returns: list
a list of MMTK Collection where each collection defines a group..

__parseExpressionSelectionString(self, universe, selectionString, selectionMode)

source code 

Parses a nMOLDYN selection string that starts with 'expression' keyword.

Parameters:
  • universe (instance of MMTK.Universe) - the universe on which the selection will be performed.
  • selectionString (string) - the selection string to parse.
  • selectionMode (string) - a string being one of 'subset', 'deuteration' or 'group' that will specify which kind of selection should be performed.
Returns: Python set for |selectionMode| = 'subset' or 'deuteration' and dict for |selectionMode| = 'group'
will depend on |selectionMode|.

__parseFileSelectionString(self, universe, selectionString, selectionMode)

source code 

Parses a nMOLDYN Selection file (nms file) in order to perform a subset, a deuteration or a group selection.

Parameters:
  • universe (instance of MMTK.Universe) - the universe on which the selection will be performed.
  • selectionString (string) - the selection string to parse.
  • selectionMode (string) - a string being one of 'subset', 'deuteration' or 'group' that will specify which kind of selection should be performed.
Returns: Python set for |selectionMode| = 'subset' or 'deuteration' and dict for |selectionMode| = 'group'
will depend on |selectionMode|.

__parseObjectSelectionString(self, universe, selectionString)

source code 

Parses a selection string.

Parameters:
  • universe (instance of MMTK.Universe) - the universe on which the selection will be performed.
  • selectionString (string) - the selection strin to parse.
Returns: set
a set of the atoms that match |selectionString| selection string.

__retrieveAtomIndexes(self, universe, objectClass, objectName, selectionKeyword, selectionValue)

source code 

Retrieves the MMTK index of the atoms matching |objectClass| MMTK chemical object class, |objectName| nMOLDYN name, |selectionKeyword| selection keyword and |selectionValue| selection value.

Parameters:
  • universe (instance of MMTK.Universe) - the universe on which the selection will be performed.
  • objectClass (string) - the MMTK chemical object to match.
  • objectName (string) - the nMOLDYN name to match.
  • selectionKeyword (string) - the selection keyword to match.
  • selectionValue (string) - the selection value to match.
Returns: list
a list of MMTK indexes of the selected atoms.

__allClassParser(self, universe, selectionKeyword, selectionValue)

source code 

Retrieves the MMTK indexes of the atoms whose nMOLDYN name is '*' matching |selectionKeyword| selection keyword and |selectionValue| selection value.

Parameters:
  • universe (instance of MMTK.Universe) - the universe on which the selection will be performed.
  • selectionKeyword (string) - the selection keyword to match.
  • selectionValue (string) - the selection value to match.
Returns: list
a list of MMTK indexes of the selected atoms.

__atomParser(self, universe, objectName, selectionKeyword, selectionValue)

source code 

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.

Parameters:
  • universe (instance of MMTK.Universe) - the universe on which the selection will be performed.
  • objectName (string) - the nMOLDYN name to match.
  • selectionKeyword (string) - the selection keyword to match.
  • selectionValue (string) - the selection value to match.
Returns: list
a list of MMTK indexes of the selected atoms.

__atomClusterParser(self, universe, objectName, selectionKeyword, selectionValue)

source code 

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.

Parameters:
  • universe (instance of MMTK.Universe) - the universe on which the selection will be performed.
  • objectName (string) - the nMOLDYN name to match.
  • selectionKeyword (string) - the selection keyword to match.
  • selectionValue (string) - the selection value to match.
Returns: list
a list of MMTK indexes of the selected atoms.

__moleculeParser(self, universe, objectName, selectionKeyword, selectionValue)

source code 

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.

Parameters:
  • universe (instance of MMTK.Universe) - the universe on which the selection will be performed.
  • objectName (string) - the nMOLDYN name to match.
  • selectionKeyword (string) - the selection keyword to match.
  • selectionValue (string) - the selection value to match.
Returns: list
a list of MMTK indexes of the selected atoms.

__nucleotideChainParser(self, universe, objectName, selectionKeyword, selectionValue)

source code 

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.

Parameters:
  • universe (instance of MMTK.Universe) - the universe on which the selection will be performed.
  • objectName (string) - the nMOLDYN name to match.
  • selectionKeyword (string) - the selection keyword to match.
  • selectionValue (string) - the selection value to match.
Returns: list
a list of MMTK indexes of the selected atoms.

__peptideChainParser(self, universe, objectName, selectionKeyword, selectionValue)

source code 

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.

Parameters:
  • universe (instance of MMTK.Universe) - the universe on which the selection will be performed.
  • objectName (string) - the nMOLDYN name to match.
  • selectionKeyword (string) - the selection keyword to match.
  • selectionValue (string) - the selection value to match.
Returns: list
a list of MMTK indexes of the selected atoms.

__proteinParser(self, universe, objectName, selectionKeyword, selectionValue)

source code 

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.

Parameters:
  • universe (instance of MMTK.Universe) - the universe on which the selection will be performed.
  • objectName (string) - the nMOLDYN name to match.
  • selectionKeyword (string) - the selection keyword to match.
  • selectionValue (string) - the selection value to match.
Returns: list
a list of MMTK indexes of the selected atoms.