psize | index /home/todd/release/pdb2pqr/psize.py

`# You may need to edit the above to point to your version of Python 2.0`

Modules

``

string | sys |  |

Classes

``

Psize

class Psize
`` |

Methods defined here:

__init__(self)

getCenter(self)

getCharge(self)

getCoarseGridDims(self)

getConstant(self, name)
  `Get a constant value; raises KeyError if constant not found`

getFineGridDims(self)

getFineGridPoints(self)

getFocus(self)

getLength(self)

getMax(self)

getMin(self)

getProcGrid(self)

getSmallest(self)

parseInput(self, filename)
  `Parse input structure file in PDB or PQR format`

printResults(self)
  `Return a string with the formatted results`

runPsize(self, filename)
  `Parse input PQR file and set parameters`

setAll(self)
  `Set up all of the things calculated individually above`

setCenter(self, maxlen, minlen)
  `Compute molecule center`

setCoarseGridDims(self, olen)
  `Compute coarse mesh dimensions`

setConstant(self, name, value)
  `Set a constant to a value; returns 0 if constant not found`

setFineGridDims(self, olen, clen)
  `Compute fine mesh dimensions`

setFineGridPoints(self, flen)
  `Compute mesh grid points, assuming 4 levels in MG hierarchy`

setFocus(self, flen, np, clen)
  `Calculate the number of levels of focusing required for each
  processor subdomain`

setLength(self, maxlen, minlen)
  `Compute molecule dimensions`

setProcGrid(self, n, nsmall)
  `Calculate the number of processors required to span each
  dimension`

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`

Data and non-method functions defined here:

__doc__ = None

__module__ = 'psize'

Functions

``

log(...)
  `log(x) -> the natural logarithm (base e) of x.`

main()

usage()

Data
`` |  | __file__ = './psize.pyc' __name__ = 'psize' stdout = <open file '<stdout>', mode 'w'>