Author: bugman
Date: Mon Feb 22 16:36:13 2010
New Revision: 10822
URL: http://svn.gna.org/viewcvs/relax?rev=10822&view=rev
Log:
Completed the Stereochem_analysis.__init__() docstring, adding all the epydoc
tags.
Modified:
1.3/auto_analyses/stereochem_analysis.py
Modified: 1.3/auto_analyses/stereochem_analysis.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/auto_analyses/stereochem_analysis.py?rev=10822&r1=10821&r2=10822&view=diff
==============================================================================
--- 1.3/auto_analyses/stereochem_analysis.py (original)
+++ 1.3/auto_analyses/stereochem_analysis.py Mon Feb 22 16:36:13 2010
@@ -67,7 +67,65 @@
"""Class for performing the relative stereochemistry analysis."""
def __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_id_col=None, rdc_mol_name_col=None,
rdc_res_num_col=None, rdc_res_name_col=None, rdc_spin_num_col=None,
rdc_spin_name_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):
- """Set up the analysis."""
+ """Set up for the stereochemistry analysis.
+
+ @keyword stage: Stage of analysis (see the module
docstring above for the options).
+ @type stage: int
+ @keyword results_dir: The optional directory to place all
results files into.
+ @type results_dir: None or str
+ @keyword num_ens: Number of ensembles.
+ @type num_ens: int
+ @keyword num_models: Ensemble size.
+ @type num_models: int
+ @keyword configs: All the configurations.
+ @type configs: list of str
+ @keyword snapshot_dir: Snapshot directories (corresponding to
the configurations).
+ @type snapshot_dir: list of str
+ @keyword snapshot_min: The number of the first snapshots
(corresponding to the configurations).
+ @type snapshot_min: list of int
+ @keyword snapshot_max: The number of the last snapshots
(corresponding to the configurations).
+ @type snapshot_max: list of int
+ @keyword pseudo: 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"]]].
+ @type pseudo: list of list of str and list of str
+ @keyword noe_file: The name of the NOE restraint file.
+ @type noe_file: str
+ @keyword noe_norm: The NOE normalisation factor (equal to
the sum of all NOEs squared).
+ @type noe_norm: float
+ @keyword rdc_name: The label for this RDC data set.
+ @type rdc_name: str
+ @keyword rdc_file: The name of the RDC file.
+ @type rdc_file: str
+ @keyword rdc_spin_id_col: The spin ID column of the RDC file.
+ @type rdc_spin_id_col: None or int
+ @keyword rdc_mol_name_col: The molecule name column of the RDC file.
+ @type rdc_mol_name_col: None or int
+ @keyword rdc_res_num_col: The residue number column of the RDC
file.
+ @type rdc_res_num_col: None or int
+ @keyword rdc_res_name_col: The residue name column of the RDC file.
+ @type rdc_res_name_col: None or int
+ @keyword rdc_spin_num_col: The spin number column of the RDC file.
+ @type rdc_spin_num_col: None or int
+ @keyword rdc_spin_name_col: The spin name column of the RDC file.
+ @type rdc_spin_name_col: None or int
+ @keyword rdc_data_col: The data column of the RDC file.
+ @type rdc_data_col: int
+ @keyword rdc_error_col: The error column of the RDC file.
+ @type rdc_error_col: int
+ @keyword bond_length: The bond length value in meters.
+ @type bond_length: float
+ @keyword log: Log file output flag (only for certain
stages).
+ @type log: bool
+ @keyword bucket_num: Number of buckets for the distribution
plots.
+ @type bucket_num: int
+ @keyword lower_lim_noe: Distribution plot limits.
+ @type lower_lim_noe: int
+ @keyword upper_lim_noe: Distribution plot limits.
+ @type upper_lim_noe: int
+ @keyword lower_lim_rdc: Distribution plot limits.
+ @type lower_lim_rdc: int
+ @keyword upper_lim_rdc: Distribution plot limits.
+ @type upper_lim_rdc: int
+ """
# Store all the args.
self.stage = stage
r10822 - /1.3/auto_analyses/stereochem_analysis.py