Package Biskit :: Module IcmCad :: Class IcmCad

Class IcmCad

CAD calculation

Calculate ContactAreaDifference between a reference structure and one or many other structures. Described in Abagyan and Totrov, 1997.

Example usage

>>> x = IcmCad( ref_model, [ m1, m2 ], verbose=1 )
>>> result = x.run()

IcmCad writes temporary pdb files, calls the icmbrowser program, and parses the result from the STDOUT pipe. The result values are then in x.result (if x is the IcmCad instance). As recommended, the value is multiplied by factor 1.8 which puts it into a range from 0 (identical) to 100 (completely different). This scaling is not recommended for docking solutions.

To Do: Not speed-optimized!

it should be possible to pipe the PDB-files directly into icmbrowser instead of writing temporary files to disc
Abagyan and Totrov mention a c-library available -- the best solution would hence be to wrap this c-library in python...

Note: Command configuration in: biskit/external/defaults/exe_icmbrowser.da

Instance Methods

[hide private]

__init__(self, ref_model, models, **kw)

__prepareModel(self, model, f_out)
Prepare a model that ICM likes.

prepare(self)
Overrides Executor method.

cleanup(self)
Tidy up the mess you created.

[str] parse_icm(self, output)
Extract CAD value from icm output.

isFailed(self)
Overrides Executor method

finish(self)
Overrides Executor method

[str] generateInp(self)
Has to be overridden to support head / segment / tail structure.

Class Variables

[hide private]

inp_head = """ call _startup read pdb unix cat \"%(f_ref)s\" co...

inp_tail = "quit\n"

inp_calc = """ read pdb unix cat \"%(f_pdb)s\" copy a_ \"mol2\"...

Method Details

[hide private]

init(self, ref_model, models, **kw)
(Constructor)

source code

Parameters:

ref_model (PDBModel) - reference
models ([PDBModel]) - structures to be compared with reference

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_out)

source code

Prepare a model that ICM likes.

consecutive numbering of residues
no chain identifier

Parameters:

model (PDBModel) - model
f_out (str) - name of pdb file to write

prepare(self)

source code

Overrides Executor method.

cleanup(self)

source code

Tidy up the mess you created.

parse_icm(self, output)

source code

Extract CAD value from icm output.

Parameters:

output ([str]) - STDOUT result of ICM run

Returns: [str]: ICM result

Raises:

IcmCadError - if no result

isFailed(self)

source code

Overrides Executor method

finish(self)

source code

Overrides Executor method

generateInp(self)

source code

Has to be overridden to support head / segment / tail structure. Replace formatstr place holders in inp by fields of this class.

Returns: [str]: ICM input script

Raises:

TemplateError - if template not found

Class Variable Details

[hide private]

inp_head

Value:

"""
call _startup
read pdb unix cat \"%(f_ref)s\"
copy a_ \"mol1\"
"""

inp_tail

Value:

"quit\n"

inp_calc

Value:

"""
read pdb unix cat \"%(f_pdb)s\"
copy a_ \"mol2\" delete
1.8*Cad( a_mol1./* a_mol2./* )
"""

Class IcmCad

CAD calculation

Example usage

__init__(self, ref_model, models, **kw) (Constructor)

__prepareModel(self, model, f_out)

prepare(self)

cleanup(self)

parse_icm(self, output)

isFailed(self)

finish(self)

generateInp(self)

inp_head

inp_tail

inp_calc

init(self, ref_model, models, **kw)
(Constructor)