Public Member Functions | Data Fields

Psize Class Reference

Public Member Functions

def __init__
def parseString
def parseInput
def parseLines
def setConstant
def getConstant
def setLength
def setCoarseGridDims
def setFineGridDims
def setCenter
def setFineGridPoints
def setSmallest
def setProcGrid
def setFocus
def setAll
def getMax
def getMin
def getCharge
def getLength
def getCoarseGridDims
def getFineGridDims
def getCenter
def getFineGridPoints
def getSmallest
def getProcGrid
def getFocus
def runPsize
def printResults

Data Fields

 constants
 minlen
 maxlen
 q
 gotatom
 gothet
 olen
 cen
 clen
 flen
 n
 np
 nsmall
 nfocus

Detailed Description

Master class for parsing input files and suggesting settings

Definition at line 62 of file psize.py.


Member Function Documentation

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

Definition at line 136 of file psize.py.

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

Definition at line 85 of file psize.py.

def parseLines (   self,
  lines 
)
Parse the lines 

Definition at line 90 of file psize.py.

def parseString (   self,
  structure 
)
Parse the input structure as a string in PDB or PQR format 

Definition at line 80 of file psize.py.

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

Definition at line 268 of file psize.py.

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

Definition at line 263 of file psize.py.

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

Definition at line 223 of file psize.py.

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

Definition at line 162 of file psize.py.

def setCoarseGridDims (   self,
  olen 
)
Compute coarse mesh dimensions 

Definition at line 148 of file psize.py.

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

Definition at line 128 of file psize.py.

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

Definition at line 154 of file psize.py.

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

Definition at line 168 of file psize.py.

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

Definition at line 210 of file psize.py.

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

Definition at line 140 of file psize.py.

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

Definition at line 200 of file psize.py.

def 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 

Definition at line 178 of file psize.py.


The documentation for this class was generated from the following file: