Class Palmer

Instance Methods

__init__(self, relax)

create(self, run=None, dir=None, force=0, diff_search='none', sims=0, sim_type='pred', trim=0, steps=20, constraints=1, nucleus='15N', atom1='N', atom2='H')
Function for creating the Modelfree4 input files.

execute(self, run=None, dir=None, force=0)
Function for executing Modelfree4.

extract(self, run=None, dir=None)
Function for extracting data from the Modelfree4 'mfout' star formatted file.

Method Details

create(self, run=None, dir=None, force=0, diff_search='none', sims=0, sim_type='pred', trim=0, steps=20, constraints=1, nucleus='15N', atom1='N', atom2='H')

Function for creating the Modelfree4 input files.

Keyword Arguments
~~~~~~~~~~~~~~~~~

run:  The name of the run.

dir:  The directory to place the files.  The default is the value of 'run'.

force:  A flag which if set to 1 will cause the results file to be overwritten if it already
exists.

diff_search:  See the Modelfree4 manual for 'diffusion_search'.

sims:  The number of Monte Carlo simulations.

sim_type:  See the Modelfree4 manual.

trim:  See the Modelfree4 manual.

steps:  See the Modelfree4 manual.

constraints:  A flag specifying whether the parameters should be constrained.  The default
is to turn constraints on (constraints=1).

nucleus:  A three letter string describing the nucleus type, ie 15N, 13C, etc.

atom1:  The symbol of the X nucleus in the pdb file.

atom2:  The symbol of the H nucleus in the pdb file.


Description
~~~~~~~~~~~

The following files are created

    'dir/mfin',
    'dir/mfdata',
    'dir/mfpar',
    'dir/mfmodel',
    'dir/run.sh'.

The file 'run/run.sh' contains the single command,

'modelfree4 -i mfin -d mfdata -p mfpar -m mfmodel -o mfout -e out',

which can be used to execute modelfree4.

execute(self, run=None, dir=None, force=0)

Function for executing Modelfree4.

Keyword Arguments
~~~~~~~~~~~~~~~~~

run:  The name of the run.

dir:  The directory to place the files.  The default is the value of 'run'.

force:  A flag which if set to 1 will cause the results file to be overwritten if it already
exists.


Description
~~~~~~~~~~~

Modelfree 4 will be executed as

$ modelfree4 -i mfin -d mfdata -p mfpar -m mfmodel -o mfout -e out

If a PDB file is loaded and non-isotropic diffusion is selected, then the file name will be
placed on the command line as '-s pdb_file_name'.

extract(self, run=None, dir=None)

Function for extracting data from the Modelfree4 'mfout' star formatted file.

Keyword Arguments
~~~~~~~~~~~~~~~~~

run:  The name of the run.

dir:  The directory where the file 'mfout' is found.  The default is the value of 'run'.