Detailed Description
Master class for parsing input files and suggesting settings
Definition at line 62 of file psize.py.
Member Function Documentation
def getConstant |
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name |
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Get a constant value; raises KeyError if constant not found
Definition at line 136 of file psize.py.
def parseInput |
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filename |
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Parse input structure file in PDB or PQR format
Definition at line 85 of file psize.py.
def parseLines |
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lines |
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def parseString |
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self, |
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structure |
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Parse the input structure as a string in PDB or PQR format
Definition at line 80 of file psize.py.
def printResults |
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Return a string with the formatted results
Definition at line 268 of file psize.py.
def runPsize |
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filename |
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Parse input PQR file and set parameters
Definition at line 263 of file psize.py.
Set up all of the things calculated individually above
Definition at line 223 of file psize.py.
def setCenter |
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maxlen, |
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minlen |
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def setCoarseGridDims |
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self, |
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olen |
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Compute coarse mesh dimensions
Definition at line 148 of file psize.py.
def setConstant |
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name, |
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value |
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Set a constant to a value; returns 0 if constant not found
Definition at line 128 of file psize.py.
def setFineGridDims |
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olen, |
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clen |
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Compute fine mesh dimensions
Definition at line 154 of file psize.py.
def setFineGridPoints |
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self, |
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flen |
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Compute mesh grid points, assuming 4 levels in MG hierarchy
Definition at line 168 of file psize.py.
def setFocus |
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flen, |
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np, |
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clen |
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Calculate the number of levels of focusing required for
each processor subdomain
Definition at line 210 of file psize.py.
def setLength |
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maxlen, |
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minlen |
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Compute molecule dimensions
Definition at line 140 of file psize.py.
def setProcGrid |
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n, |
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nsmall |
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Calculate the number of processors required to span each
dimension
Definition at line 200 of file psize.py.
def setSmallest |
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n |
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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
Definition at line 178 of file psize.py.
The documentation for this class was generated from the following file: