Biskit :: Dock :: ContactSlave :: ContactSlave :: Class ContactSlave

Class ContactSlave

Calculate contact matrix and some scores for complexes. ContactMaster creates several instances of this class, each on one node.

Instance Methods

[hide private]

str version(self)
Version of Dock.Complex

initialize(self, params)
Copy the parameters that ContactMaster is passing in as dict into fields of this class.

reportError(self, msg, soln)
Report any errors to log

1|0 __containsAny(self, lst_or_dic, *items)
Check if dictionary or list contains items.

1|0 requested(self, c, *keys)
Determine the keys in an info dictionary of a complex that need to be calculated or updated

pickleError(self, o)
Pickle object to disc.

calcContacts(self, soln, c)
Calculate contact matrices and fraction of native contacts, residue- and atom-based, with different distance cutoffs.

calcReducedContacts(self, soln, c)
Get contact matrices and/or fnarc from reduced-atom models.

calcInterfaceRms(self, soln, c)
RMS between this and reference interface atoms after superposition.

calcProsa(self, soln, c)
Prosa2003 energy score

calcPairScore(self, soln, c)
calculate contact pair score

calcConservation(self, soln, c, method)
calculate conservation score

calcFoldX(self, soln, c)
calculate fold-X binding energies

{int:str} go(self, cmplxDic)
Obtain contact matrix for all complexes.

Method Details

[hide private]

version(self)

source code

Version of Dock.Complex

Returns: str: version of class

initialize(self, params)

source code

Copy the parameters that ContactMaster is passing in as dict into fields of this class.

Parameters:

params (dict) - defined in ContactMaster

reportError(self, msg, soln)

source code

Report any errors to log

Parameters:

msg (str) - error message
soln (int) - solution number for complex giving the error

__containsAny(self, lst_or_dic, *items)

source code

Check if dictionary or list contains items.

Parameters:

lst_or_dic (list OR dict) - lokk for items in this
items (any) - items to look for

Returns: 1|0: result of test

requested(self, c, *keys)

source code

Determine the keys in an info dictionary of a complex that need to be calculated or updated

Parameters:

c (Complex) - Complex
keys (str OR [str]) - key or keys for c.infos dict

Returns: 1|0: 1 if the given value should be calculated for the given complex

pickleError(self, o)

source code

Pickle object to disc.

Parameters:

o (any) - object to pickle

calcContacts(self, soln, c)

source code

Calculate contact matrices and fraction of native contacts, residue- and atom-based, with different distance cutoffs.

Parameters:

soln (int) - solution number
c (Complex) - Complex

calcReducedContacts(self, soln, c)

source code

Get contact matrices and/or fnarc from reduced-atom models.

Parameters:

soln (int) - solution number
c (Complex) - Complex

calcInterfaceRms(self, soln, c)

source code

RMS between this and reference interface atoms after superposition.

rms_if_bb, considers backbone of interface residues (10 A cutoff) (same as used for CAPRI)
rms_if, considers all atoms of more tightly defined interf. residues (correlates better with fraction of native contacts)

Parameters:

soln (int) - solution number
c (Complex) - Complex

calcProsa(self, soln, c)

source code

Prosa2003 energy score

Parameters:

soln (int) - solution number
c (Complex) - Complex

calcPairScore(self, soln, c)

source code

calculate contact pair score

Parameters:

soln (int) - solution number
c (Complex) - Complex

calcConservation(self, soln, c, method)

source code

calculate conservation score

Parameters:

soln (int) - solution number
c (Complex) - Complex
method (str) - scoring method to use see Complex.conservationScore

calcFoldX(self, soln, c)

source code

calculate fold-X binding energies

Parameters:

soln (int) - solution number
c (Complex) - Complex

go(self, cmplxDic)

source code

Obtain contact matrix for all complexes.

Parameters:

cmplxDic ({int:Complex}) - dictionary of complexes:

                {soln:Complex, soln:Complex, ...}

Returns: {int:str}

similar dictionary with Complex.info['soln'] as keys and file names of matrices as value:

 soln : fname, soln : fname ....}