Module selection

Module for selecting and deselecting spins.

Functions

bool boolean_deselect(current=None, boolean=None)
Return the new boolean deselection result using the current selection.

bool boolean_select(current=None, boolean=None)
Return the new boolean selection result using the current selection.

desel_all()
Deselect all spins.

desel_interatom(spin_id1=None, spin_id2=None, boolean='AND', change_all=False)
Deselect specific interatomic data containers.

desel_read(file=None, dir=None, file_data=None, spin_id_col=None, mol_name_col=None, res_num_col=None, res_name_col=None, spin_num_col=None, spin_name_col=None, sep=None, spin_id=None, boolean='AND', change_all=False)
Deselect the spins contained in the given file.

desel_spin(spin_id=None, boolean='AND', change_all=False)
Deselect specific spins.

display(sep=None, mol_name_flag=True, res_num_flag=True, res_name_flag=True, spin_num_flag=True, spin_name_flag=True)
Display the current spin selections.

is_mol_selected(selection=None)
Query if the molecule is selected.

is_res_selected(selection=None)
Query if the residue is selected.

is_spin_selected(selection=None)
Query if the spin is selected.

reverse(spin_id=None)
Reversal of spin selections.

sel_all()
Select all residues.

sel_domain(domain_id=None, boolean='OR', change_all=False)
Select all spins and interatomic data containers of the given domain.

sel_interatom(spin_id1=None, spin_id2=None, boolean='OR', change_all=False)
Select specific interatomic data containers.

sel_read(file=None, dir=None, file_data=None, spin_id_col=None, mol_name_col=None, res_num_col=None, res_name_col=None, spin_num_col=None, spin_name_col=None, sep=None, spin_id=None, boolean='OR', change_all=False)
Select the spins contained in the given file.

sel_spin(spin_id=None, boolean='OR', change_all=False)
Select specific spins.

Variables

uf_tables = Uf_tables()

boolean_doc = Desc_container("Boolean operators")

table = uf_tables.add_table(label= "table: bool operators", ca...

__package__ = 'pipe_control'

Imports: sys, warn, RelaxError, RelaxNoDomainError, RelaxNoSequenceError, Selection, spin_id_to_data_list, read_spin_data, write_spin_data, RelaxNoSpinWarning, interatomic_loop, check_mol_res_spin_data, exists_mol_res_spin_data, generate_spin_id_unique, return_spin, spin_loop, check_pipe, Uf_tables, Desc_container

Function Details

boolean_deselect(current=None, boolean=None)

Return the new boolean deselection result using the current selection.

Parameters:

• current (bool) - The current selection state.
• boolean (str) - The boolean operator used to select with. It can be one of 'OR', 'NOR', 'AND', 'NAND', 'XOR', or 'XNOR'.

Returns: bool

The new selection state.

boolean_select(current=None, boolean=None)

Return the new boolean selection result using the current selection.

Parameters:

• current (bool) - The current selection state.
• boolean (str) - The boolean operator used to select with. It can be one of 'OR', 'NOR', 'AND', 'NAND', 'XOR', or 'XNOR'.

Returns: bool

The new selection state.

desel_all()

Deselect all spins.

Raises:

• RelaxNoSequenceError - If no molecule/residue/spins sequence data exists.

desel_interatom(spin_id1=None, spin_id2=None, boolean='AND', change_all=False)

Deselect specific interatomic data containers.

Parameters:

• spin_id1 (str or None) - The spin ID string of the first spin of the pair.
• spin_id2 (str or None) - The spin ID string of the second spin of the pair.
• boolean (str) - The boolean operator used to deselect the spin systems with. It can be one of 'OR', 'NOR', 'AND', 'NAND', 'XOR', or 'XNOR'. This will be ignored if the change_all flag is set.
• change_all (bool) - A flag which if True will cause all spins not specified in the file to be selected. Only the boolean operator 'AND' is compatible with this flag set to True (all others will be ignored).

Raises:

• RelaxNoSequenceError - If no molecule/residue/spins sequence data exists.
• RelaxError - If the boolean operator is unknown.

desel_read(file=None, dir=None, file_data=None, spin_id_col=None, mol_name_col=None, res_num_col=None, res_name_col=None, spin_num_col=None, spin_name_col=None, sep=None, spin_id=None, boolean='AND', change_all=False)

Deselect the spins contained in the given file.

Parameters:

• file (str) - The name of the file to open.
• dir (str or None) - The directory containing the file (defaults to the current directory if None).
• file_data (list of lists) - An alternative opening a file, if the data already exists in the correct format. The format is a list of lists where the first index corresponds to the row and the second the column.
• spin_id_col (int or None) - The column containing the spin ID strings. If supplied, the mol_name_col, res_name_col, res_num_col, spin_name_col, and spin_num_col arguments must be none.
• mol_name_col (int or None) - The column containing the molecule name information. If supplied, spin_id_col must be None.
• res_name_col (int or None) - The column containing the residue name information. If supplied, spin_id_col must be None.
• res_num_col (int or None) - The column containing the residue number information. If supplied, spin_id_col must be None.
• spin_name_col (int or None) - The column containing the spin name information. If supplied, spin_id_col must be None.
• spin_num_col (int or None) - The column containing the spin number information. If supplied, spin_id_col must be None.
• sep (str or None) - The column separator which, if None, defaults to whitespace.
• spin_id (None or str) - The spin ID string used to restrict data loading to a subset of all spins.
• boolean (str) - The boolean operator used to deselect the spin systems with. It can be one of 'OR', 'NOR', 'AND', 'NAND', 'XOR', or 'XNOR'. This will be ignored if the change_all flag is set.
• change_all (bool) - A flag which if True will cause all spins not specified in the file to be selected. Only the boolean operator 'AND' is compatible with this flag set to True (all others will be ignored).

Raises:

• RelaxNoSequenceError - If no molecule/residue/spins sequence data exists.
• RelaxError - If the boolean operator is unknown.

desel_spin(spin_id=None, boolean='AND', change_all=False)

Deselect specific spins.

Parameters:

• spin_id (str or None) - The spin identification string.
• boolean (str) - The boolean operator used to deselect the spin systems with. It can be one of 'OR', 'NOR', 'AND', 'NAND', 'XOR', or 'XNOR'. This will be ignored if the change_all flag is set.
• change_all (bool) - A flag which if True will cause all spins not specified in the file to be selected. Only the boolean operator 'AND' is compatible with this flag set to True (all others will be ignored).

Raises:

• RelaxNoSequenceError - If no molecule/residue/spins sequence data exists.
• RelaxError - If the boolean operator is unknown.

display(sep=None, mol_name_flag=True, res_num_flag=True, res_name_flag=True, spin_num_flag=True, spin_name_flag=True)

Display the current spin selections.

Parameters:

• sep (str or None) - The column seperator which, if None, defaults to whitespace.
• mol_name_flag (bool) - A flag which if True will cause the molecule name column to be written.
• res_num_flag (bool) - A flag which if True will cause the residue number column to be written.
• res_name_flag (bool) - A flag which if True will cause the residue name column to be written.
• spin_name_flag (bool) - A flag which if True will cause the spin name column to be written.
• spin_num_flag (bool) - A flag which if True will cause the spin number column to be written.

is_mol_selected(selection=None)

Query if the molecule is selected.

Parameters:

• selection (str) - The molecule ID string.

is_res_selected(selection=None)

Query if the residue is selected.

Parameters:

• selection (str) - The residue ID string.

is_spin_selected(selection=None)

Query if the spin is selected.

Parameters:

• selection (str) - The molecule ID string.

reverse(spin_id=None)

Reversal of spin selections.

Parameters:

• spin_id (str or None) - The spin identification string.

Raises:

• RelaxNoSequenceError - If no molecule/residue/spins sequence data exists.

sel_all()

Select all residues.

Raises:

• RelaxNoSequenceError - If no molecule/residue/spins sequence data exists.

sel_domain(domain_id=None, boolean='OR', change_all=False)

Select all spins and interatomic data containers of the given domain.

Parameters:

• domain_id (str or None) - The domain ID string.
• boolean (str) - The boolean operator used to select the spin systems with. It can be one of 'OR', 'NOR', 'AND', 'NAND', 'XOR', or 'XNOR'. This will be ignored if the change_all flag is set.
• change_all (bool) - A flag which if True will cause all spins and interatomic data containers outside of the domain to be deselected.

sel_interatom(spin_id1=None, spin_id2=None, boolean='OR', change_all=False)

Select specific interatomic data containers.

Parameters:

• spin_id1 (str or None) - The spin ID string of the first spin of the pair.
• spin_id2 (str or None) - The spin ID string of the second spin of the pair.
• boolean (str) - The boolean operator used to select the spin systems with. It can be one of 'OR', 'NOR', 'AND', 'NAND', 'XOR', or 'XNOR'. This will be ignored if the change_all flag is set.
• change_all (bool) - A flag which if True will cause all spins not specified in the file to be deselected. Only the boolean operator 'OR' is compatible with this flag set to True (all others will be ignored).

Raises:

• RelaxNoSequenceError - If no molecule/residue/spins sequence data exists.
• RelaxError - If the boolean operator is unknown.

sel_read(file=None, dir=None, file_data=None, spin_id_col=None, mol_name_col=None, res_num_col=None, res_name_col=None, spin_num_col=None, spin_name_col=None, sep=None, spin_id=None, boolean='OR', change_all=False)

Select the spins contained in the given file.

Parameters:

• file (str) - The name of the file to open.
• dir (str or None) - The directory containing the file (defaults to the current directory if None).
• file_data (list of lists) - An alternative opening a file, if the data already exists in the correct format. The format is a list of lists where the first index corresponds to the row and the second the column.
• spin_id_col (int or None) - The column containing the spin ID strings. If supplied, the mol_name_col, res_name_col, res_num_col, spin_name_col, and spin_num_col arguments must be none.
• mol_name_col (int or None) - The column containing the molecule name information. If supplied, spin_id_col must be None.
• res_name_col (int or None) - The column containing the residue name information. If supplied, spin_id_col must be None.
• res_num_col (int or None) - The column containing the residue number information. If supplied, spin_id_col must be None.
• spin_name_col (int or None) - The column containing the spin name information. If supplied, spin_id_col must be None.
• spin_num_col (int or None) - The column containing the spin number information. If supplied, spin_id_col must be None.
• sep (str or None) - The column separator which, if None, defaults to whitespace.
• spin_id (None or str) - The spin ID string used to restrict data loading to a subset of all spins.
• boolean (str) - The boolean operator used to select the spin systems with. It can be one of 'OR', 'NOR', 'AND', 'NAND', 'XOR', or 'XNOR'. This will be ignored if the change_all flag is set.
• change_all (bool) - A flag which if True will cause all spins not specified in the file to be deselected. Only the boolean operator 'OR' is compatible with this flag set to True (all others will be ignored).

Raises:

• RelaxNoSequenceError - If no molecule/residue/spins sequence data exists.
• RelaxError - If the boolean operator is unknown.

sel_spin(spin_id=None, boolean='OR', change_all=False)

Select specific spins.

Parameters:

• spin_id (str or None) - The spin identification string.
• boolean (str) - The boolean operator used to select the spin systems with. It can be one of 'OR', 'NOR', 'AND', 'NAND', 'XOR', or 'XNOR'. This will be ignored if the change_all flag is set.
• change_all (bool) - A flag which if True will cause all spins not specified in the file to be deselected. Only the boolean operator 'OR' is compatible with this flag set to True (all others will be ignored).

Raises:

• RelaxNoSequenceError - If no molecule/residue/spins sequence data exists.
• RelaxError - If the boolean operator is unknown.

Variables Details

table

Value:

uf_tables.add_table(label= "table: bool operators", caption= "Boolean 
operators and their effects on selections")