Author: bugman
Date: Wed Nov 14 18:05:52 2012
New Revision: 17975
URL: http://svn.gna.org/viewcvs/relax?rev=17975&view=rev
Log:
Implemented the rdc.copy and pcs.copy user function backends.
This code is copied from the relax_data.copy user function and has been
tailored to the different
data types.
Modified:
trunk/generic_fns/pcs.py
trunk/generic_fns/rdc.py
Modified: trunk/generic_fns/pcs.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/pcs.py?rev=17975&r1=17974&r2=17975&view=diff
==============================================================================
--- trunk/generic_fns/pcs.py (original)
+++ trunk/generic_fns/pcs.py Wed Nov 14 18:05:52 2012
@@ -33,10 +33,10 @@
# relax module imports.
from generic_fns import grace, pipes
from generic_fns.align_tensor import get_tensor_index
-from generic_fns.mol_res_spin import exists_mol_res_spin_data,
generate_spin_id, return_spin, spin_loop
+from generic_fns.mol_res_spin import exists_mol_res_spin_data,
generate_spin_id, return_spin, spin_index_loop, spin_loop
from maths_fns.pcs import ave_pcs_tensor
from physical_constants import g1H, pcs_constant
-from relax_errors import RelaxError, RelaxNoPdbError, RelaxNoSequenceError
+from relax_errors import RelaxError, RelaxAlignError, RelaxNoAlignError,
RelaxNoPdbError, RelaxNoSequenceError, RelaxPCSError
from relax_io import open_write_file, read_spin_data, write_spin_data
from relax_warnings import RelaxWarning, RelaxNoSpinWarning
@@ -200,6 +200,98 @@
if verbosity:
print("\nUsing all paramagnetic positions.")
cdp.paramagnetic_centre = full_pos_list
+
+
+def copy(pipe_from=None, pipe_to=None, align_id=None):
+ """Copy the PCS data from one data pipe to another.
+
+ @keyword pipe_from: The data pipe to copy the PCS data from. This
defaults to the current data pipe.
+ @type pipe_from: str
+ @keyword pipe_to: The data pipe to copy the PCS data to. This
defaults to the current data pipe.
+ @type pipe_to: str
+ @param align_id: The alignment ID string.
+ @type align_id: str
+ """
+
+ # Defaults.
+ if pipe_from == None and pipe_to == None:
+ raise RelaxError("The pipe_from and pipe_to arguments cannot both be
set to None.")
+ elif pipe_from == None:
+ pipe_from = pipes.cdp_name()
+ elif pipe_to == None:
+ pipe_to = pipes.cdp_name()
+
+ # Test if the pipe_from and pipe_to data pipes exist.
+ pipes.test(pipe_from)
+ pipes.test(pipe_to)
+
+ # Get the data pipes.
+ dp_from = pipes.get_pipe(pipe_from)
+ dp_to = pipes.get_pipe(pipe_to)
+
+ # Test if pipe_from contains sequence data.
+ if not exists_mol_res_spin_data(pipe_from):
+ raise RelaxNoSequenceError
+
+ # Test if pipe_to contains sequence data.
+ if not exists_mol_res_spin_data(pipe_to):
+ raise RelaxNoSequenceError
+
+ # Test if alignment ID string exists for pipe_from.
+ if align_id and (not hasattr(dp_from, 'align_ids') or align_id not in
dp_from.align_ids):
+ raise RelaxNoAlignError(align_id, pipe_from)
+
+ # Test if PCS data for the alignment ID exists.
+ if not hasattr(dp_from, 'pcs_ids'):
+ raise RelaxError("No PCS data exists.")
+ elif align_id and align_id not in dp_from.pcs_ids:
+ raise RelaxNoPCSError(align_id)
+
+ # The IDs.
+ if align_id == None:
+ align_ids = dp_from.align_ids
+ else:
+ align_ids = [align_id]
+
+ # Init target pipe global structures.
+ if not hasattr(dp_to, 'align_ids'):
+ dp_to.align_ids = []
+ if not hasattr(dp_to, 'pcs_ids'):
+ dp_to.pcs_ids = []
+
+ # Loop over the align IDs.
+ for align_id in align_ids:
+ # Test if PCS ID string exists for pipe_to.
+ if align_id in dp_to.pcs_ids:
+ raise RelaxPCSError(align_id)
+
+ # Copy the global data.
+ dp_to.align_ids.append(align_id)
+ dp_to.pcs_ids.append(align_id)
+
+ # Spin loop.
+ for mol_index, res_index, spin_index in spin_index_loop():
+ # Alias the spin containers.
+ spin_from =
dp_from.mol[mol_index].res[res_index].spin[spin_index]
+ spin_to = dp_to.mol[mol_index].res[res_index].spin[spin_index]
+
+ # No data or errors.
+ if (not hasattr(spin_from, 'pcs') or not align_id in
spin_from.pcs) and (not hasattr(spin_from, 'pcs_err') or not align_id in
spin_from.pcs_err):
+ continue
+
+ # Initialise the spin data if necessary.
+ if hasattr(spin_from, 'pcs') and not hasattr(spin_to, 'pcs'):
+ spin_to.pcs = {}
+ if hasattr(spin_from, 'pcs_err') and not hasattr(spin_to,
'pcs_err'):
+ spin_to.pcs_err = {}
+
+ # Copy the value and error from pipe_from.
+ print spin_from
+ print spin_to
+ if hasattr(spin_from, 'pcs'):
+ spin_to.pcs[align_id] = spin_from.pcs[align_id]
+ if hasattr(spin_from, 'pcs_err'):
+ spin_to.pcs_err[align_id] = spin_from.pcs_err[align_id]
def corr_plot(format=None, file=None, dir=None, force=False):
Modified: trunk/generic_fns/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/rdc.py?rev=17975&r1=17974&r2=17975&view=diff
==============================================================================
--- trunk/generic_fns/rdc.py (original)
+++ trunk/generic_fns/rdc.py Wed Nov 14 18:05:52 2012
@@ -36,10 +36,10 @@
from generic_fns import grace, pipes
from generic_fns.align_tensor import get_tensor_index
from generic_fns.interatomic import create_interatom, interatomic_loop,
return_interatom
-from generic_fns.mol_res_spin import exists_mol_res_spin_data,
generate_spin_id, return_spin, spin_loop
+from generic_fns.mol_res_spin import exists_mol_res_spin_data,
generate_spin_id, return_spin, spin_index_loop, spin_loop
from maths_fns.rdc import ave_rdc_tensor
from physical_constants import dipolar_constant, return_gyromagnetic_ratio
-from relax_errors import RelaxError, RelaxNoRDCError, RelaxNoSequenceError,
RelaxSpinTypeError
+from relax_errors import RelaxError, RelaxAlignError, RelaxNoAlignError,
RelaxNoRDCError, RelaxNoSequenceError, RelaxSpinTypeError
from relax_io import extract_data, open_write_file, strip, write_data
from relax_warnings import RelaxWarning
@@ -149,6 +149,96 @@
# Return the converted value.
return value * factor
+
+
+def copy(pipe_from=None, pipe_to=None, align_id=None):
+ """Copy the RDC data from one data pipe to another.
+
+ @keyword pipe_from: The data pipe to copy the RDC data from. This
defaults to the current data pipe.
+ @type pipe_from: str
+ @keyword pipe_to: The data pipe to copy the RDC data to. This
defaults to the current data pipe.
+ @type pipe_to: str
+ @param align_id: The alignment ID string.
+ @type align_id: str
+ """
+
+ # Defaults.
+ if pipe_from == None and pipe_to == None:
+ raise RelaxError("The pipe_from and pipe_to arguments cannot both be
set to None.")
+ elif pipe_from == None:
+ pipe_from = pipes.cdp_name()
+ elif pipe_to == None:
+ pipe_to = pipes.cdp_name()
+
+ # Test if the pipe_from and pipe_to data pipes exist.
+ pipes.test(pipe_from)
+ pipes.test(pipe_to)
+
+ # Get the data pipes.
+ dp_from = pipes.get_pipe(pipe_from)
+ dp_to = pipes.get_pipe(pipe_to)
+
+ # Test if pipe_from contains sequence data.
+ if not exists_mol_res_spin_data(pipe_from):
+ raise RelaxNoSequenceError
+
+ # Test if pipe_to contains sequence data.
+ if not exists_mol_res_spin_data(pipe_to):
+ raise RelaxNoSequenceError
+
+ # Test if alignment ID string exists for pipe_from.
+ if align_id and (not hasattr(dp_from, 'align_ids') or align_id not in
dp_from.align_ids):
+ raise RelaxNoAlignError(align_id, pipe_from)
+
+ # Test if RDC data for the alignment ID exists.
+ if not hasattr(dp_from, 'rdc_ids'):
+ raise RelaxError("No RDC data exists.")
+ elif align_id and align_id not in dp_from.rdc_ids:
+ raise RelaxNoRDCError(align_id)
+
+ # The IDs.
+ if align_id == None:
+ align_ids = dp_from.align_ids
+ else:
+ align_ids = [align_id]
+
+ # Init target pipe global structures.
+ if not hasattr(dp_to, 'align_ids'):
+ dp_to.align_ids = []
+ if not hasattr(dp_to, 'rdc_ids'):
+ dp_to.rdc_ids = []
+
+ # Loop over the align IDs.
+ for align_id in align_ids:
+ # Test if RDC ID string exists for pipe_to.
+ if align_id in dp_to.rdc_ids:
+ raise RelaxRDCError(align_id)
+
+ # Copy the global data.
+ dp_to.align_ids.append(align_id)
+ dp_to.rdc_ids.append(align_id)
+
+ # Spin loop.
+ for mol_index, res_index, spin_index in spin_index_loop():
+ # Alias the spin containers.
+ spin_from =
dp_from.mol[mol_index].res[res_index].spin[spin_index]
+ spin_to = dp_to.mol[mol_index].res[res_index].spin[spin_index]
+
+ # No data or errors.
+ if (not hasattr(spin_from, 'rdc') or not align_id in
spin_from.rdc) and (not hasattr(spin_from, 'rdc_err') or not align_id in
spin_from.rdc_err):
+ continue
+
+ # Initialise the spin data if necessary.
+ if hasattr(spin_from, 'rdc') and not hasattr(spin_to, 'rdc'):
+ spin_to.rdc = {}
+ if hasattr(spin_from, 'rdc_err') and not hasattr(spin_to,
'rdc_err'):
+ spin_to.rdc_err = {}
+
+ # Copy the value and error from pipe_from.
+ if hasattr(spin_from, 'rdc'):
+ spin_to.rdc[align_id] = spin_from.rdc[align_id]
+ if hasattr(spin_from, 'rdc_err'):
+ spin_to.rdc_err[align_id] = spin_from.rdc_err[align_id]
def corr_plot(format=None, file=None, dir=None, force=False):
r17975 - in /trunk/generic_fns: pcs.py rdc.py