Subsections


select.read

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Synopsis

Select the spins contained in a file.

Defaults

select.read(file=None, dir=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)

Keyword arguments

file: The name of the file containing the list of spins to select.

dir: The directory where the file is located.

spin_id_col: The spin ID string column (an alternative to the mol, res, and spin name and number columns).

mol_name_col: The molecule name column (alternative to the spin_id_col).

res_num_col: The residue number column (alternative to the spin_id_col).

res_name_col: The residue name column (alternative to the spin_id_col).

spin_num_col: The spin number column (alternative to the spin_id_col).

spin_name_col: The spin name column (alternative to the spin_id_col).

sep: The column separator (the default is white space).

spin_id: The spin ID string to restrict the loading of data to certain spin subsets.

boolean: The boolean operator specifying how spins should be selected.

change_all: A flag specifying if all other spins should be changed.

Description

The spin system can be identified in the file using two different formats. The first is the spin ID string column which can include the molecule name, the residue name and number, and the spin name and number. Alternatively the molecule name, residue number, residue name, spin number and/or spin name columns can be supplied allowing this information to be in separate columns. Note that the numbering of columns starts at one. The spin ID string can be used to restrict the reading to certain spin types, for example only 15N spins when only residue information is in the file.

Empty lines and lines beginning with a hash are ignored.

The `change all' flag default is False meaning that all spins currently either selected or deselected will remain that way. Setting this to True will cause all spins not specified in the file to be deselected.

Boolean operators

The boolean operator can be used to change how spin systems or interatomic data containers are selected. The allowed values are: `OR', `NOR', `AND', `NAND', `XOR', `XNOR'. The following table details how the selections will occur for the different boolean operators.

Please see Table 17.1 on page [*].

Prompt examples

To select all residues listed with residue numbers in the first column of the file `isolated_peaks', type one of:

[numbers=none]
relax> select.read('isolated_peaks', res_num_col=1)

[numbers=none]
relax> select.read(file='isolated_peaks', res_num_col=1)

To select the spins in the second column of the relaxation data file `r1.600' while deselecting all other spins, for example type:

[numbers=none]
relax> select.read('r1.600', spin_num_col=2, change_all=True)

[numbers=none]
relax> select.read(file='r1.600', spin_num_col=2, change_all=True)


The relax user manual (PDF), created 2016-10-28.