Class Palmer

Instance Methods

__init__(self, relax)

create(self, run=None, dir=None, force=0, binary='modelfree4', 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, binary='modelfree4')
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, binary='modelfree4', 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.

binary:  The name of the executable Modelfree program file.

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.

If you would like to use a different Modelfree executable file, change the keyword argument
'binary' to the appropriate file name.  If the file is not located within the environment's
path, include the full path infront of the binary file name.

execute(self, run=None, dir=None, force=0, binary='modelfree4')

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.

binary:  The name of the executable Modelfree program file.


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'.


If you would like to use a different Modelfree executable file, change the keyword argument
'binary' to the appropriate file name.  If the file is not located within the environment's
path, include the full path in front of the binary 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'.