Author: tlinnet
Date: Thu Dec 5 22:48:13 2013
New Revision: 21798
URL: http://svn.gna.org/viewcvs/relax?rev=21798&view=rev
Log:
Created the back end function for the read_spins function.
Work in progress for Support Request #3044,
(https://gna.org/support/index.php?3044) - Load spins from SPARKY list.
Modified:
trunk/pipe_control/spectrum.py
Modified: trunk/pipe_control/spectrum.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/spectrum.py?rev=21798&r1=21797&r2=21798&view=diff
==============================================================================
--- trunk/pipe_control/spectrum.py (original)
+++ trunk/pipe_control/spectrum.py Thu Dec 5 22:48:13 2013
@@ -37,7 +37,7 @@
from lib.statistics import std
from lib.warnings import RelaxWarning, RelaxNoSpinWarning
from pipe_control import pipes
-from pipe_control.mol_res_spin import check_mol_res_spin_data,
generate_spin_id_unique, return_spin, spin_loop
+from pipe_control.mol_res_spin import check_mol_res_spin_data, create_spin,
generate_spin_id_unique, return_spin, spin_loop
def __errors_height_no_repl():
@@ -609,6 +609,57 @@
write_data(out=sys.stdout, headings=["Spin_ID", "Intensity"],
data=data)
+def read_spins(file=None, dir=None, dim=1, 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, verbose=True):
+ """Read the peak intensity data.
+
+ @keyword file: The name of the file containing the peak
intensities.
+ @type file: str
+ @keyword dir: The directory where the file is located.
+ @type dir: str
+ @keyword dim: The dimension of the peak list to associate the
data with.
+ @type dim: int
+ @keyword spin_id_col: The column containing the spin ID strings (used
by the generic intensity file format). If supplied, the mol_name_col,
res_name_col, res_num_col, spin_name_col, and spin_num_col arguments must be
none.
+ @type spin_id_col: int or None
+ @keyword mol_name_col: The column containing the molecule name
information (used by the generic intensity file format). If supplied,
spin_id_col must be None.
+ @type mol_name_col: int or None
+ @keyword res_name_col: The column containing the residue name
information (used by the generic intensity file format). If supplied,
spin_id_col must be None.
+ @type res_name_col: int or None
+ @keyword res_num_col: The column containing the residue number
information (used by the generic intensity file format). If supplied,
spin_id_col must be None.
+ @type res_num_col: int or None
+ @keyword spin_name_col: The column containing the spin name information
(used by the generic intensity file format). If supplied, spin_id_col must
be None.
+ @type spin_name_col: int or None
+ @keyword spin_num_col: The column containing the spin number
information (used by the generic intensity file format). If supplied,
spin_id_col must be None.
+ @type spin_num_col: int or None
+ @keyword sep: The column separator which, if None, defaults to
whitespace.
+ @type sep: str or None
+ @keyword spin_id: The spin ID string used to restrict data loading
to a subset of all spins. If 'auto' is provided for a NMRPipe seriesTab
formatted file, the ID's are auto generated in form of Z_Ai.
+ @type spin_id: None or str
+ @keyword verbose: A flag which if True will cause all relaxation
data loaded to be printed out.
+ @type verbose: bool
+ """
+
+ # Data checks.
+ pipes.test()
+
+ # Check the file name.
+ if file == None:
+ raise RelaxError("The file name must be supplied.")
+
+ # Read the peak list data.
+ peak_list = read_peak_list(file=file, dir=dir, spin_id_col=spin_id_col,
mol_name_col=mol_name_col, res_num_col=res_num_col,
res_name_col=res_name_col, spin_num_col=spin_num_col,
spin_name_col=spin_name_col, sep=sep, spin_id=spin_id)
+
+ # Loop over the peak_list.
+ for assign in peak_list:
+ mol_name = assign.mol_names[dim-1]
+ res_num = assign.res_nums[dim-1]
+ res_name = assign.res_names[dim-1]
+ spin_num = assign.spin_nums[dim-1]
+ spin_name = assign.spin_names[dim-1]
+ # Create the spin
+ create_spin(spin_num=spin_num, spin_name=spin_name, res_num=res_num,
res_name=res_name, mol_name=mol_name)
+
+ # Test that data exists.
+ check_mol_res_spin_data()
def replicated(spectrum_ids=None):
"""Set which spectra are replicates.
r21798 - /trunk/pipe_control/spectrum.py