Class Stereochem_analysis

Class for performing the relative stereochemistry analysis.

Instance Methods

__init__(self, stage=1, results_dir=None, num_ens=10000, num_models=10, configs=None, snapshot_dir='snapshots', snapshot_min=None, snapshot_max=None, pseudo=None, noe_file=None, noe_norm=None, rdc_name=None, rdc_file=None, rdc_spin_id1_col=None, rdc_spin_id2_col=None, rdc_data_col=None, rdc_error_col=None, bond_length=None, bond_length_file=None, log=None, bucket_num=200, lower_lim_noe=0.0, upper_lim_noe=600.0, lower_lim_rdc=0.0, upper_lim_rdc=1.0)
Set up for the stereochemistry analysis.

run(self)
Execute the given stage of the analysis.

combined_q(self)
Calculate the combined Q factor.

generate_distribution(self, values, lower=0.0, upper=200.0, inc=None)
Create the distribution data structure.

grace_plots(self)
Generate grace plots of the results.

noe_viol(self)
NOE violation calculations.

rdc_analysis(self)
Perform the RDC part of the analysis.

sample(self)
Generate the ensembles by random sampling of the snapshots.

superimpose(self)
Superimpose the ensembles using fit to first in Molmol.

Method Details

__init__(self, stage=1, results_dir=None, num_ens=10000, num_models=10, configs=None, snapshot_dir='snapshots', snapshot_min=None, snapshot_max=None, pseudo=None, noe_file=None, noe_norm=None, rdc_name=None, rdc_file=None, rdc_spin_id1_col=None, rdc_spin_id2_col=None, rdc_data_col=None, rdc_error_col=None, bond_length=None, bond_length_file=None, log=None, bucket_num=200, lower_lim_noe=0.0, upper_lim_noe=600.0, lower_lim_rdc=0.0, upper_lim_rdc=1.0)
(Constructor)

Set up for the stereochemistry analysis.

Parameters:

• stage (int) - Stage of analysis (see the module docstring above for the options).
• results_dir (None or str) - The optional directory to place all results files into.
• num_ens (int) - Number of ensembles.
• num_models (int) - Ensemble size.
• configs (list of str) - All the configurations.
• snapshot_dir (list of str) - Snapshot directories (corresponding to the configurations).
• snapshot_min (list of int) - The number of the first snapshots (corresponding to the configurations).
• snapshot_max (list of int) - The number of the last snapshots (corresponding to the configurations).
• pseudo (list of list of str and list of str) - The list of pseudo-atoms. Each element is a list of the pseudo-atom name and a list of all those atoms forming the pseudo-atom. For example, pseudo = [["Q7", ["@H16", "@H17", "@H18"]], ["Q9", ["@H20", "@H21", "@H22"]]].
• noe_file (str) - The name of the NOE restraint file.
• noe_norm (float) - The NOE normalisation factor (equal to the sum of all NOEs squared).
• rdc_name (str) - The label for this RDC data set.
• rdc_file (str) - The name of the RDC file.
• rdc_spin_id1_col (None or int) - The spin ID column of the first spin in the RDC file.
• rdc_spin_id2_col (None or int) - The spin ID column of the second spin in the RDC file.
• rdc_data_col (int) - The data column of the RDC file.
• rdc_error_col (int) - The error column of the RDC file.
• bond_length (float or None) - The bond length value in meters. This overrides the bond_length_file argument.
• bond_length_file (float or None) - The file of bond lengths for each atom pair in meters. The first and second columns must be the spin ID strings and the third column must contain the data.
• log (bool) - Log file output flag (only for certain stages).
• bucket_num (int) - Number of buckets for the distribution plots.
• lower_lim_noe (int) - Distribution plot limits.
• upper_lim_noe (int) - Distribution plot limits.
• lower_lim_rdc (int) - Distribution plot limits.
• upper_lim_rdc (int) - Distribution plot limits.

combined_q(self)

Calculate the combined Q factor.

The combined Q is defined as:

   Q_total^2 = Q_NOE^2 + Q_RDC^2,

and the NOE Q factor as:

   Q^2 = U / sum(NOE_i^2),

where U is the quadratic flat bottom well potential - the NOE violation in Angstrom^2.