Class Sequence

Instance Methods

__init__(self, relax)

add(self, run=None, res_num=None, res_name=None, select=1)
Function for adding a residue onto the sequence.

copy(self, run1=None, run2=None)
Function for copying the sequence from run1 to run2.

delete(self, run=None)
Function for deleting the sequence.

display(self, run=None)
Function for displaying the sequence.

read(self, run=None, file=None, dir=None, num_col=0, name_col=1, sep=None)
Function for reading sequence data.

sort(self, run=None)
Function for numerically sorting the sequence by residue number.

write(self, run=None, file=None, dir=None, force=0)
Function for writing the sequence to a file.

Method Details

add(self, run=None, res_num=None, res_name=None, select=1)

Function for adding a residue onto the sequence.

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

run:  The name of the run.

res_num:  The residue number.

res_name:  The name of the residue.

select:  A flag specifying if the residue should be selected.


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

Using this function a new sequence can be generated without having to load the sequence from
a file.  However if the sequence already exists, the new residue will be added to the end.
The same residue number cannot be used more than once.


Examples
~~~~~~~~

The following sequence of commands will generate the sequence 1 ALA, 2 GLY, 3 LYS and assign
it to the run 'm3':

relax> run = 'm3'
relax> sequence.add(run, 1, 'ALA')
relax> sequence.add(run, 2, 'GLY')
relax> sequence.add(run, 3, 'LYS')

copy(self, run1=None, run2=None)

Function for copying the sequence from run1 to run2.

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

run1:  The name of the run to copy the sequence from.

run2:  The name of the run to copy the sequence to.


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

This function will copy the sequence from 'run1' to 'run2'.  'run1' must contain sequence
information, while 'run2' must have no sequence loaded.


Examples
~~~~~~~~

To copy the sequence from the run 'm1' to the run 'm2', type:

relax> sequence.copy('m1', 'm2')
relax> sequence.copy(run1='m1', run2='m2')

delete(self, run=None)

Function for deleting the sequence.

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

run:  The name of the run.


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

This function has the same effect as using the 'delete' function to delete all residue
specific data.

display(self, run=None)

Function for displaying the sequence.

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

run:  The name of the run.

read(self, run=None, file=None, dir=None, num_col=0, name_col=1, sep=None)

Function for reading sequence data.

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

run:  The name of the run.

file:  The name of the file containing the sequence data.

dir:  The directory where the file is located.

num_col:  The residue number column (the default is 0, ie the first column).

name_col:  The residue name column (the default is 1).

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


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

If no directory is given, the file will be assumed to be in the current working directory.


Examples
~~~~~~~~

The following commands will read the sequence data out of a file called 'seq' where the
residue numbers and names are in the first and second columns respectively and assign it to
the run 'm1'.

relax> sequence.read('m1', 'seq')
relax> sequence.read('m1', 'seq', num_col=0, name_col=1)
relax> sequence.read(run='m1', file='seq', num_col=0, name_col=1, sep=None)


The following commands will read the sequence out of the file 'noe.out' which also contains
the NOE values.

relax> sequence.read('m1', 'noe.out')
relax> sequence.read('m1', 'noe.out', num_col=0, name_col=1)
relax> sequence.read(run='m1', file='noe.out', num_col=0, name_col=1)


The following commands will read the sequence out of the file 'noe.600.out' where the
residue numbers are in the second column, the names are in the sixth column and the columns
are separated by commas and assign it to the run 'm5'.

relax> sequence.read('m5', 'noe.600.out', num_col=1, name_col=5, sep=',')
relax> sequence.read(run='m5', file='noe.600.out', num_col=1, name_col=5, sep=',')

sort(self, run=None)

Function for numerically sorting the sequence by residue number.

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

run:  The name of the run.

write(self, run=None, file=None, dir=None, force=0)

Function for writing the sequence to a file.

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

run:  The name of the run.

file:  The name of the file.

dir:  The directory name.

force:  A flag which, if set to 1, will cause the file to be overwritten.


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

If no directory name is given, the file will be placed in the current working directory.