Input/Output for the BornProfiler modules — bornprofiler.io

The module contains functions and classes to handle common functionality to read and write files.

class bornprofiler.bpio.PQRReader(filename, **kwargs)

Naive implementation of a PQR reader.

class bornprofiler.bpio.RunParameters(filename, *omissions, **defaults)

All parameters for a BornProfiler or APBSmem run are stored in a INI-style file.

This class accesses these parameters and can create a template with the default values.

The class guarantees that all parameters exist; if needed they are populated with default values. Hence it is always possible to access a parameter without having to check if it is there.

Parameters:

• zmem : membrane centre (A)
• lmem : membrane thickness (A)
• Vmem : cytosolic potential in kT/e (untested)
• pdie : protein dielectric
• sdie: solvent dielectric
• mdie: membrane dielectric
• Rtop : exclusion cylinder top
• Rbot : exclusion cylinder bottom
• x0_R : exclusion zone centre in X, None selects the default
• y0_R : exclusion zone centre in Y, None selects the default
• dx_R : shift centre of the exclusion zone in X
• dy_R : shift centre of the exclusion zone in Y
• cdie : dielectric in the channel (e.g. SDIE)
• headgroup_l : thicknes of headgroup region
• headgroup_die : dielectric for headgroup region
• temperature : temperature
• conc : ionic strength in mol/l
• … and more

Reads and parses the configuration file for a job.

get_apbsmem_kwargs(*args, **kwargs)

Return a dict with kwargs appropriate for membrane.APBSmem.

Default values can be supplied in kwargs. This method picks unique parameter keys from the relevant sections of the run parameters file (i.e. bornprofile, membrane, and environment).

If args are provided, then either a single value corresponding to the key or a list of such values is returned instead.

get_apbsnomem_kwargs(*args, **kwargs)

Return a dict with kwargs appropriate for membrane.APBSnomem.

Default values can be supplied in kwargs. This method picks unique parameter keys from the relevant sections of the run parameters file (i.e. bornprofile and environment).

If args are provided, then either a single value corresponding to the key or a list of such values is returned instead.

get_bornprofile_kwargs(*args, **kwargs)

Return a dict with kwargs appropriate for bornprofile.

Default values can be supplied in kwargs. This method picks unique parameter keys from the relevant sections of the run parameters file (i.e. bornprofile, membrane, and environment).

If args are provided, then either a single value corresponding to the key or a list of such values is returned instead.

get_bornprofilenomem_kwargs(*args, **kwargs)

Return a dict with kwargs appropriate for bornprofilenomem.

Default values can be supplied in kwargs. This method picks unique parameter keys from the relevant sections of the run parameters file (i.e. bornprofile, membrane, and environment).

If args are provided, then either a single value corresponding to the key or a list of such values is returned instead.

write(filename=None)

Write the current parameters to filename.

bornprofiler.bpio.float_or_None(s)

Return s as float or None when x == “None”.

bornprofiler.bpio.path(s)

Return s with user expansion.

bornprofiler.bpio.readPoints(filename)

Read coordinates from either data file or pdb.

Returns (N,3) array.

bornprofiler.bpio.readPointsDat(filename)

Read points from a simple data file.

Example::

# comment x y z x y z …

bornprofiler.bpio.readPointsPDB(filename)

Read points form a PDB formatted file.

Takes x,y,z from any ATOM or HETATM record.

bornprofiler.bpio.read_dat_to_array(datfile)

Reads the dat file into a (4,N) numpy array

bornprofiler.bpio.read_template(filename)

Return filename as one string.

filename can be one of the template files.