__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)
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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 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.
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