__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,
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)
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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) - The bond length value in meters.
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.
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