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__init__(self)
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parseString(self,
structure)
Parse the input structure as a string in PDB or PQR format
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parseInput(self,
filename)
Parse input structure file in PDB or PQR format
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parseLines(self,
lines)
Parse the lines
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setConstant(self,
name,
value)
Set a constant to a value; returns 0 if constant not found
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getConstant(self,
name)
Get a constant value; raises KeyError if constant not found
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setLength(self,
maxlen,
minlen)
Compute molecule dimensions
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setCoarseGridDims(self,
olen)
Compute coarse mesh dimensions
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setFineGridDims(self,
olen,
clen)
Compute fine mesh dimensions
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setCenter(self,
maxlen,
minlen)
Compute molecule center
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setFineGridPoints(self,
flen)
Compute mesh grid points, assuming 4 levels in MG hierarchy
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setSmallest(self,
n)
Compute parallel division in case memory requirement above ceiling
Find the smallest dimension and see if the number of grid points in
that dimension will fit below the memory ceiling Reduce nsmall until
an nsmall^3 domain will fit into memory
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setProcGrid(self,
n,
nsmall)
Calculate the number of processors required to span each
dimension
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setFocus(self,
flen,
np,
clen)
Calculate the number of levels of focusing required for each
processor subdomain
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setAll(self)
Set up all of the things calculated individually above
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getMax(self)
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getMin(self)
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getCharge(self)
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getLength(self)
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getCoarseGridDims(self)
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getFineGridDims(self)
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getCenter(self)
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getFineGridPoints(self)
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getSmallest(self)
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getProcGrid(self)
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getFocus(self)
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runPsize(self,
filename)
Parse input PQR file and set parameters
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printResults(self)
Return a string with the formatted results
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