Module interatomic

Module for the manipulation of the interatomic data structures in the relax data store.

Functions

copy(pipe_from=None, pipe_to=None, spin_id1=None, spin_id2=None, verbose=True)
Copy the interatomic data from one data pipe to another.

consistent_interatomic_data(pipe1=None, pipe2=None)
Check that the interatomic data is consistent between two data pipes.

data.interatomic.InteratomContainer instance create_interatom(spin_id1=None, spin_id2=None, pipe=None)
Create and return the interatomic data container for the two spins.

bool exists_data(pipe=None)
Determine if any interatomic data exists.

bool id_match(spin_id=None, interatom=None, pipe=None)
Test if the spin ID matches one of the two spins of the given container.

interatomic_loop(selection1=None, selection2=None, pipe=None, selected=True)
Generator function for looping over all the interatomic data containers.

data.interatomic.InteratomContainer instance or None return_interatom(spin_id1=None, spin_id2=None, pipe=None)
Return the list of interatomic data containers for the two spins.

list of data.interatomic.InteratomContainer instances return_interatom_list(spin_id=None, pipe=None)
Return the list of interatomic data containers for the given spin.

Variables

__package__ = 'generic_fns'

Imports: deepcopy, search, sys, pipes, Selection, count_spins, return_spin, spin_loop, RelaxError, RelaxInteratomError, RelaxInteratomInconsistentError, RelaxNoInteratomError, RelaxNoSpinError, write_data

Function Details

copy(pipe_from=None, pipe_to=None, spin_id1=None, spin_id2=None, verbose=True)

Copy the interatomic data from one data pipe to another.

Parameters:

• pipe_from (str) - The data pipe to copy the interatomic data from. This defaults to the current data pipe.
• pipe_to (str) - The data pipe to copy the interatomic data to. This defaults to the current data pipe.
• spin_id1 (str) - The spin ID string of the first atom.
• spin_id2 (str) - The spin ID string of the second atom.
• verbose (bool) - A flag which if True will cause info about each spin pair to be printed out.

consistent_interatomic_data(pipe1=None, pipe2=None)

Check that the interatomic data is consistent between two data pipes.

Parameters:

• pipe1 (str) - The name of the first data pipe to compare.
• pipe2 (str) - The name of the second data pipe to compare.

Raises:

• RelaxError - If the data is inconsistent.

create_interatom(spin_id1=None, spin_id2=None, pipe=None)

Create and return the interatomic data container for the two spins.

Parameters:

• spin_id1 (str) - The spin ID string of the first atom.
• spin_id2 (str) - The spin ID string of the second atom.
• pipe (str or None) - The data pipe to create the interatomic data container for. This defaults to the current data pipe if not supplied.

Returns: data.interatomic.InteratomContainer instance

The newly created interatomic data container.

exists_data(pipe=None)

Determine if any interatomic data exists.

Parameters:

• pipe (str) - The data pipe in which the interatomic data will be checked for.

Returns: bool

The answer to the question about the existence of data.

id_match(spin_id=None, interatom=None, pipe=None)

Test if the spin ID matches one of the two spins of the given container.

Parameters:

• spin_id (str) - The spin ID string of the first atom.
• interatom (InteratomContainer instance) - The interatomic data container.
• pipe (str or None) - The data pipe containing the interatomic data container. Defaults to the current data pipe.

Returns: bool

True if the spin ID matches one of the two spins, False otherwise.

interatomic_loop(selection1=None, selection2=None, pipe=None, selected=True)

Generator function for looping over all the interatomic data containers.

Parameters:

• selection1 (str) - The optional spin ID selection of the first atom.
• selection2 (str) - The optional spin ID selection of the second atom.
• pipe (str) - The data pipe containing the spin. Defaults to the current data pipe.
• selected (bool) - A flag which if True will only return selected interatomic data containers.

return_interatom(spin_id1=None, spin_id2=None, pipe=None)

Return the list of interatomic data containers for the two spins.

Parameters:

• spin_id1 (str) - The spin ID string of the first atom.
• spin_id2 (str) - The spin ID string of the second atom.
• pipe (str or None) - The data pipe holding the container. Defaults to the current data pipe.

Returns: data.interatomic.InteratomContainer instance or None

The matching interatomic data container, if it exists.

return_interatom_list(spin_id=None, pipe=None)

Return the list of interatomic data containers for the given spin.

Parameters:

• spin_id (str) - The spin ID string.
• pipe (str or None) - The data pipe holding the container. This defaults to the current data pipe.

Returns: list of data.interatomic.InteratomContainer instances

The list of matching interatomic data containers, if any exist.