A tool to find hydrogen bonds present between two sets of
molecules.
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__init__(self,
atomsel1,
atomsel2,
tol=0.01,
*args,
**kwargs)
Initialize frame slicing information. |
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isOrthogonal(self,
box,
tol) |
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getClosestDistance(self,
atoms1,
atoms2,
pbc) |
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doFrameInit(self,
frame)
Initialize data that requires a frame instance for reference. |
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updatePositions(self,
st,
frame) |
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getHydrophobicResidueIndex(self,
st) |
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labelProtRes(self,
atm_idx) |
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labelProtAtm(self,
atm_idx) |
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processFrame(self,
frame)
Collect data for the provided frame. |
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processPiCationFrame(self,
frame) |
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processPiPiFrame(self,
frame) |
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processHydrophobicFrame(self,
frame) |
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getFrameResults(self)
For each frame, return a list of (acceptor, donor) integer tuples,
each value being a 1-based atom index into the overall simulation
structure. |
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getResults(self)
Return results for all values and frames as a numpy array with the
first index across analyses. |
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getAllBonds(self)
Return a set of all hydrogen bonds found by the analysis. |
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Inherited from analysistool.AnalysisTool :
getDataLabels ,
getLabel ,
plot ,
plot2D ,
postProcess ,
setSlice ,
shouldProcessFrame
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