Module pcs
source code
Module for the manipulation of pseudo-contact shift data.
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centre(pos=None,
atom_id=None,
pipe=None,
verbosity=1,
ave_pos=False,
force=False)
Specify the atom in the loaded structure corresponding to the
paramagnetic centre. |
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check_pipe_setup(pipe=None,
pcs_id=None,
sequence=False,
N=False,
tensors=False,
pcs=False,
paramag_centre=False)
Check that the current data pipe has been setup sufficiently. |
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copy(pipe_from=None,
pipe_to=None,
align_id=None,
back_calc=True)
Copy the PCS data from one data pipe to another. |
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corr_plot(format=None,
title=None,
subtitle=None,
file=None,
dir=None,
force=False)
Generate a correlation plot of the measured vs. |
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delete(align_id=None)
Delete the PCS data corresponding to the alignment ID. |
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display(align_id=None,
bc=False)
Display the PCS data corresponding to the alignment ID. |
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bool
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opt_uses_pcs(align_id)
Determine if the PCS data for the given alignment ID is needed for
optimisation. |
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q_factors(spin_id=None,
sim_index=None,
verbosity=1)
Calculate the Q factors for the PCS data. |
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read(align_id=None,
file=None,
dir=None,
file_data=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,
data_col=None,
error_col=None,
sep=None,
spin_id=None)
Read the PCS data from file. |
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tuple of (numpy rank-2 float64 array, numpy rank-2 float64 array,
numpy rank-2 float64 array, list of float, list of float, numpy
rank-1 int32 array)
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return_pcs_data(sim_index=None,
verbosity=0)
Set up the data structures for optimisation using PCSs as base data
sets. |
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structural_noise(align_id=None,
rmsd=0.2,
sim_num=1000,
file=None,
dir=None,
force=False)
Determine the PCS error due to structural noise via simulation. |
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weight(align_id=None,
spin_id=None,
weight=1.0)
Set optimisation weights on the PCS data. |
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write(align_id=None,
file=None,
dir=None,
bc=False,
force=False)
Display the PCS data corresponding to the alignment ID. |
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__package__ = ' pipe_control '
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Imports:
deepcopy,
ceil,
floor,
pi,
sqrt,
array,
eye,
float64,
int32,
ones,
std,
zeros,
norm,
multivariate_normal,
sys,
warn,
ave_pcs_tensor,
pcs_tensor,
is_float,
RelaxError,
RelaxNoAlignError,
RelaxNoPdbError,
RelaxNoPCSError,
RelaxNoSequenceError,
open_write_file,
write_data,
periodic_table,
pcs_constant,
write_xy_data,
write_xy_header,
read_spin_data,
write_spin_data,
RelaxWarning,
RelaxNoSpinWarning,
pipes,
get_tensor_index,
get_tensor_object,
opt_uses_align_data,
opt_uses_tensor,
exists_mol_res_spin_data,
generate_spin_id_unique,
is_pseudoatom,
return_spin,
spin_loop,
check_pipe
Back calculate the PCS from the alignment tensor.
- Parameters:
align_id (str) - The alignment tensor ID string.
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centre(pos=None,
atom_id=None,
pipe=None,
verbosity=1,
ave_pos=False,
force=False)
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Specify the atom in the loaded structure corresponding to the
paramagnetic centre.
- Parameters:
pos (list of float) - The atomic position. If set, the atom_id string will be ignored.
atom_id (str) - The atom identification string.
pipe (None or str) - An alternative data pipe to extract the paramagnetic centre from.
verbosity (int) - The amount of information to print out. The bigger the number,
the more information.
ave_pos (bool) - A flag which if True causes the atomic positions from multiple
models to be averaged.
force - A flag which if True will cause the current PCS centre to be
overwritten.
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check_pipe_setup(pipe=None,
pcs_id=None,
sequence=False,
N=False,
tensors=False,
pcs=False,
paramag_centre=False)
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Check that the current data pipe has been setup sufficiently.
- Parameters:
pipe (None or str) - The data pipe to check, defaulting to the current pipe.
pcs_id (None or str) - The PCS ID string to check for in cdp.pcs_ids.
sequence (bool) - A flag which when True will invoke the sequence data check.
N (bool) - A flag which if True will check that cdp.N is set.
tensors (bool) - A flag which if True will check that alignment tensors exist.
pcs (bool) - A flag which if True will check that PCSs exist.
paramag_centre (bool) - A flag which if True will check that the paramagnetic centre has
been set.
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copy(pipe_from=None,
pipe_to=None,
align_id=None,
back_calc=True)
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Copy the PCS data from one data pipe to another.
- Parameters:
pipe_from (str) - The data pipe to copy the PCS data from. This defaults to the
current data pipe.
pipe_to (str) - The data pipe to copy the PCS data to. This defaults to the
current data pipe.
align_id (str) - The alignment ID string.
back_calc (bool) - A flag which if True will cause any back-calculated RDCs present
to also be copied with the real values and errors.
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corr_plot(format=None,
title=None,
subtitle=None,
file=None,
dir=None,
force=False)
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Generate a correlation plot of the measured vs. back-calculated
PCSs.
- Parameters:
format (str or None) - The format for the plot file. The following values are accepted:
'grace', a Grace plot; None, a plain text file.
title (None or str) - The title for the plot, overriding the default.
subtitle (None or str) - The subtitle for the plot, overriding the default.
file (str or file object) - The file name or object to write to.
dir (str) - The name of the directory to place the file into (defaults to the
current directory).
force (bool) - A flag which if True will cause any pre-existing file to be
overwritten.
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Delete the PCS data corresponding to the alignment ID.
- Parameters:
align_id (str or None) - The alignment tensor ID string. If not specified, all data will
be deleted.
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Display the PCS data corresponding to the alignment ID.
- Parameters:
align_id (str) - The alignment tensor ID string.
bc (bool) - The back-calculation flag which if True will cause the
back-calculated rather than measured data to be displayed.
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Determine if the PCS data for the given alignment ID is needed for
optimisation.
- Parameters:
align_id (str) - The alignment ID string.
- Returns: bool
- True if the PCS data is to be used for optimisation, False
otherwise.
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q_factors(spin_id=None,
sim_index=None,
verbosity=1)
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Calculate the Q factors for the PCS data.
- Parameters:
spin_id (None or str) - The spin ID string used to restrict the Q factor calculation to a
subset of all spins.
sim_index (None or int) - The optional Monte Carlo simulation index.
verbosity (int) - A flag specifying the amount of information to print. The higher
the value, the greater the verbosity.
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read(align_id=None,
file=None,
dir=None,
file_data=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,
data_col=None,
error_col=None,
sep=None,
spin_id=None)
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Read the PCS data from file.
- Parameters:
align_id (str) - The alignment tensor ID string.
file (str) - The name of the file to open.
dir (str or None) - The directory containing the file (defaults to the current
directory if None).
file_data (list of lists) - An alternative opening a file, if the data already exists in the
correct format. The format is a list of lists where the first
index corresponds to the row and the second the column.
spin_id_col (int or None) - The column containing the spin ID strings. If supplied, the
mol_name_col, res_name_col, res_num_col, spin_name_col, and
spin_num_col arguments must be none.
mol_name_col (int or None) - The column containing the molecule name information. If
supplied, spin_id_col must be None.
res_name_col (int or None) - The column containing the residue name information. If supplied,
spin_id_col must be None.
res_num_col (int or None) - The column containing the residue number information. If
supplied, spin_id_col must be None.
spin_name_col (int or None) - The column containing the spin name information. If supplied,
spin_id_col must be None.
spin_num_col (int or None) - The column containing the spin number information. If supplied,
spin_id_col must be None.
data_col (int or None) - The column containing the PCS data in Hz.
error_col (int or None) - The column containing the PCS errors.
sep (str or None) - The column separator which, if None, defaults to whitespace.
spin_id (None or str) - The spin ID string used to restrict data loading to a subset of
all spins.
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return_pcs_data(sim_index=None,
verbosity=0)
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Set up the data structures for optimisation using PCSs as base data
sets.
- Parameters:
sim_index (None or int) - The index of the simulation to optimise. This should be None if
normal optimisation is desired.
verbosity (int) - A flag specifying the amount of information to print. The higher
the value, the greater the verbosity.
- Returns: tuple of (numpy rank-2 float64 array, numpy rank-2 float64 array,
numpy rank-2 float64 array, list of float, list of float, numpy
rank-1 int32 array)
- The assembled data structures for using PCSs as the base data for
optimisation. These include:
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the PCS values.
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the unit vectors connecting the paramagnetic centre (the
electron spin) to the spin.
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the PCS weight.
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the experimental temperatures.
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the spectrometer frequencies.
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pseudo_flags, the list of flags indicating if the interatomic
data contains a pseudo-atom (as 1's and 0's).
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set_errors(align_id=None,
spin_id=None,
sd=None)
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Set the PCS errors if not already present.
- Parameters:
align_id (str) - The optional alignment tensor ID string.
spin_id (None or str) - The optional spin ID string.
sd (float or int.) - The PCS standard deviation in ppm.
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Make sure that the spin systems are properly set up for pseudo-atoms
and PCSs.
All spin data containers which are a member of a pseudo-atom will be
deselected.
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structural_noise(align_id=None,
rmsd=0.2,
sim_num=1000,
file=None,
dir=None,
force=False)
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Determine the PCS error due to structural noise via simulation.
For the simulation the following must already be set up in the current
data pipe:
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The position of the paramagnetic centre.
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The alignment and magnetic susceptibility tensor.
The protocol for the simulation is as follows:
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The lanthanide or paramagnetic centre position will be fixed. Its
motion is assumed to be on the femto- to pico- and nanosecond
timescales. Hence the motion is averaged over the evolution of the
PCS and can be ignored.
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The positions of the nuclear spins will be randomised N times using a
multivariate normal distribution.
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The PCS for the randomised position will be back calculated.
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The PCS standard deviation will be calculated from the N randomised
PCS values.
The standard deviation will both be stored in the spin container data
structure in the relax data store as well as being added to the already
present PCS error (using variance addition). This will then be used in
any optimisations involving the PCS.
If the alignment ID string is not supplied, the procedure will be
applied to the PCS data from all alignments.
- Parameters:
align_id (str) - The alignment tensor ID string.
rmsd (float) - The atomic position RMSD, in Angstrom, to randomise the spin
positions with for the simulations.
sim_num (int) - The number of simulations, N, to perform to determine the
structural noise component of the PCS errors.
file (None or str) - The optional name of the Grace file to plot the structural errors
verses the paramagnetic centre to spin distances.
dir (None or str) - The directory name to place the Grace file into.
force (bool) - A flag which if True will cause any pre-existing file to be
overwritten.
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weight(align_id=None,
spin_id=None,
weight=1.0)
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Set optimisation weights on the PCS data.
- Parameters:
align_id (str) - The alignment tensor ID string.
spin_id (None or str) - The spin ID string.
weight (float or int.) - The optimisation weight. The higher the value, the more
importance the PCS will have.
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write(align_id=None,
file=None,
dir=None,
bc=False,
force=False)
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Display the PCS data corresponding to the alignment ID.
- Parameters:
align_id (str) - The alignment tensor ID string.
file (str or file object) - The file name or object to write to.
dir (str) - The name of the directory to place the file into (defaults to the
current directory).
bc (bool) - The back-calculation flag which if True will cause the
back-calculated rather than measured data to be written.
force (bool) - A flag which if True will cause any pre-existing file to be
overwritten.
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