Class Select

Instance Methods

__init__(self, relax)

all(self, run=None)
Function for selecting all residues.

read(self, run=None, file=None, dir=None, boolean='OR', change_all=0, column=0)
Function for selecting the residues contained in a file.

res(self, run=None, num=None, name=None, boolean='OR', change_all=0)
Function for selecting specific residues.

reverse(self, run=None)
Function for the reversal of the residue selection.

Class Variables

__boolean_doc = '\n Boolean operators\n ~~~~~~~~...

Method Details

all(self, run=None)

Function for selecting all residues.

Keyword Arguments
~~~~~~~~~~~~~~~~~

run:  The name of the run(s).  By supplying a single string, array of strings, or None, a
single run, multiple runs, or all runs will be selected respectively.


Examples
~~~~~~~~

To select all residues for all runs type:

relax> select.all()


To select all residues for the run 'srls_m1', type:

relax> select.all('srls_m1')
relax> select.all(run='srls_m1')

read(self, run=None, file=None, dir=None, boolean='OR', change_all=0, column=0)

Function for selecting the residues contained in a file.

Keyword Arguments
~~~~~~~~~~~~~~~~~

run:  The name of the run(s).  By supplying a single string, array of strings, or None, a
single run, multiple runs, or all runs will be selected respectively.

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

dir:  The directory where the file is located.

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

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

column:  The column containing the residue numbers (defaulting to 0, the first column).


Description
~~~~~~~~~~~

Empty lines and lines beginning with a hash are ignored.

The 'change_all' flag argument default is zero meaning that all residues currently either
selected or unselected will remain that way.  Setting the argument to 1 will cause all
residues not specified in the file to be unselected.


Examples
~~~~~~~~

To select all residues in the file 'isolated_peaks', type one of:

relax> select.read('noe', 'isolated_peaks')
relax> select.read(run='noe', file='isolated_peaks')

To select the residues in the second column of the relaxation data file 'r1.600' while
deselecting all other residues, type one of: 

relax> select.read('test', 'r1.600', change_all=1, column=1)
relax> select.read(run='test', file='r1.600', change_all=1, column=1)



Boolean operators
~~~~~~~~~~~~~~~~~

The 'boolean' keyword argument can be used to change how spin systems 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.
__________________________________________________________
|                    |   |   |   |   |   |   |   |   |   |
| Spin system        | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 |
|____________________|___|___|___|___|___|___|___|___|___|
|                    |   |   |   |   |   |   |   |   |   |
| Original selection | 0 | 1 | 1 | 1 | 1 | 0 | 1 | 0 | 1 |
|                    |   |   |   |   |   |   |   |   |   |
| New selection      | 0 | 1 | 1 | 1 | 1 | 1 | 0 | 0 | 0 |
|____________________|___|___|___|___|___|___|___|___|___|
|                    |   |   |   |   |   |   |   |   |   |
| OR                 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 0 | 1 |
|                    |   |   |   |   |   |   |   |   |   |
| NOR                | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 |
|                    |   |   |   |   |   |   |   |   |   |
| AND                | 0 | 1 | 1 | 1 | 1 | 0 | 0 | 0 | 0 |
|                    |   |   |   |   |   |   |   |   |   |
| NAND               | 1 | 0 | 0 | 0 | 0 | 1 | 1 | 1 | 1 |
|                    |   |   |   |   |   |   |   |   |   |
| XOR                | 0 | 0 | 0 | 0 | 0 | 1 | 1 | 0 | 1 |
|                    |   |   |   |   |   |   |   |   |   |
| XNOR               | 1 | 1 | 1 | 1 | 1 | 0 | 0 | 1 | 0 |
|____________________|___|___|___|___|___|___|___|___|___|

res(self, run=None, num=None, name=None, boolean='OR', change_all=0)

Function for selecting specific residues.

Keyword Arguments
~~~~~~~~~~~~~~~~~

run:  The name of the run(s).  By supplying a single string, array of strings, or None, a
single run, multiple runs, or all runs will be selected respectively.

num:  The residue number.

name:  The residue name.

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

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


Description
~~~~~~~~~~~

The residue number can be either an integer for selecting a single residue or a python
regular expression, in string form, for selecting multiple residues.  For details about
using regular expression, see the python documentation for the module 're'.

The residue name argument must be a string.  Regular expression is also allowed.

The 'change_all' flag argument default is zero meaning that all residues currently either
selected or unselected will remain that way.  Setting the argument to 1 will cause all
residues not specified by 'num' or 'name' to become unselected.


Examples
~~~~~~~~

To select only glycines and alanines for the run 'm3', assuming they have been loaded with
the names GLY and ALA, type:

relax> select.res(run='m3', name='GLY|ALA', change_all=1)
relax> select.res(run='m3', name='[GA]L[YA]', change_all=1)

To select residue 5 CYS in addition to the currently selected residues, type:

relax> select.res('m3', 5)
relax> select.res('m3', 5, 'CYS')
relax> select.res('m3', '5')
relax> select.res('m3', '5', 'CYS')
relax> select.res(run='m3', num='5', name='CYS')

reverse(self, run=None)

Function for the reversal of the residue selection.

Keyword Arguments
~~~~~~~~~~~~~~~~~

run:  The name of the run(s).  By supplying a single string, array of strings, or None, a
single run, multiple runs, or all runs will be selected respectively.


Examples
~~~~~~~~

To unselect all currently selected residues and select those which are unselected type:

relax> select.reverse()

Class Variable Details

__boolean_doc

Value:

'''
        Boolean operators
        ~~~~~~~~~~~~~~~~~

        The \'boolean\' keyword argument can be used to change how spi
n systems are selected.  The
        allowed values are: \'OR\', \'NOR\', \'AND\', \'NAND\', \'XOR\
', \'XNOR\'.  The following table details
...