Biskit :: Fold_X :: Fold_X :: Class Fold_X

Class Fold_X

Run fold_X with given PDBModel

Returns a dictionary with energy terms.

Example usage

>>> x = Fold_X( model, verbose=1 )
>>> result = x.run()

Energy terms (kcal/mol)

This is the order of the energy terms in the output file. There are two additional values that are unlabeled in the output (version 2.5.2). The first is the entropy cost of making a complex. This is zero if not 'AnalyseComplex' is run. The final value are the number of residues.

We'll try to keep the energy labels of Fold-X version 1 of possible. :

 ene    - total energy   
 bb_hb  - Backbone Hbond 
 sc_hb  - Sidechain Hbond           
 vw     - Van der Waals  
 el     - Electrostatics 
 sol_p  - Solvation Polar           
 sol_h  - Solvation Hydrophobic  
 vwcl   - Van de Waals clashes   
 sc     - entropy side chain     
 mc     - entropy main chain     
 sloop  - sloop_entropy  
 mloop  - mloop_entropy  
 cis    - cis_bond       
 tcl    - torsional clash           
 bbcl   - backbone clash 
 dip    - helix dipole   
 wtbr   - water bridge   
 disu   - disulfide      
 el_kon - electrostatic kon      
 p_cov  - partial covalent bonds
      ( - complex entropy )
      ( - number of residues )

Reference

http://foldx.embl.de for more info

Note: September 11 - 2006: Tested with Fold-X 2.5.2

Instance Methods

[hide private]

__init__(self, model, **kw)

__prepareModel(self, model, f_pdb_out)
Prepare model for fold_X and write to file:

prepare(self)
Write a Fold-X compatible pdb file to disc.

cleanup(self)
Remove files created for and by the calculation.

dict parse_foldx(self)
Extract energies from output.

isFailed(self)

finish(self)

Method Details

[hide private]

init(self, model, **kw)
(Constructor)

source code

Parameters:

model (PDBModel) - reference PDBModel

kw (

key=value pairs :
 debug    - 0|1, keep all temporary files (default: 0)
 verbose  - 0|1, print progress messages to log (log != STDOUT)
 node     - str, host for calculation (None->local) NOT TESTED
                 (default: None)
 nice     - int, nice level (default: 0)
 log      - Biskit.LogFile, program log (None->STOUT) (default: None)

) - additional key=value parameters for Executor:

__prepareModel(self, model, f_pdb_out)

source code

Prepare model for fold_X and write to file:

 - remove all hydrogens but H
 - rename H to HN
 - rename H1 to HN (remove H2 and H3)
 - ( terminal oxygens should be OXT )
 - sort atoms according to self.aminoAcidDict

Parameters:

model (PDBModel) - reference PDBModel
f_pdb_out (str) - remaned pdb file name

Raises:

Fold_XError - if preparation fail

prepare(self)

source code

Write a Fold-X compatible pdb file to disc.

: Note: Overrides Executor method.

cleanup(self)

source code

Remove files created for and by the calculation.

parse_foldx(self)

source code

Extract energies from output.

Returns: dict: dictionary with energy terms as keys

isFailed(self)

source code

: Note: Overrides Executor method

finish(self)

source code

: Note: Overrides Executor method

Class Fold_X

Run fold_X with given PDBModel

Example usage

Energy terms (kcal/mol)

Reference

__init__(self, model, **kw) (Constructor)

__prepareModel(self, model, f_pdb_out)

prepare(self)

cleanup(self)

parse_foldx(self)

isFailed(self)

finish(self)

init(self, model, **kw)
(Constructor)