Package auto_analyses :: Module stereochem_analysis
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Module stereochem_analysis

source code

Determination of relative stereochemistry in organic molecules.

The analysis is preformed by using multiple ensembles of structures, randomly sampled from a given set of structures. The discrimination is performed by comparing the sets of ensembles using NOE violations and RDC Q factors.

This script is split into multiple stages:

  1. The random sampling of the snapshots to generate the N ensembles (NUM_ENS, usually 10,000 to 100,000) of M members (NUM_MODELS, usually ~10). The original snapshot files are expected to be named the SNAPSHOT_DIR + CONFIG + a number from SNAPSHOT_MIN to SNAPSHOT_MAX + ".pdb", e.g. "snapshots/R647.pdb". The ensembles will be placed into the "ensembles" directory.
  2. The NOE violation analysis.
  3. The superimposition of ensembles. For each ensemble, Molmol is used for superimposition using the fit to first algorithm. The superimposed ensembles will be placed into the "ensembles_superimposed" directory. This stage is not necessary for the NOE analysis.
  4. The RDC Q factor analysis.
  5. Generation of Grace graphs.
  6. Final ordering of ensembles using the combined RDC and NOE Q factors, whereby the NOE Q factor is defined as:
       Q^2 = U / sum(NOE_i^2),

    where U is the quadratic flat bottom well potential - the NOE violation in Angstrom^2. The denominator is the sum of all squared NOEs - this must be given as the value of NOE_NORM. The combined Q is given by:

       Q_total^2 = Q_NOE^2 + Q_RDC^2.
Classes [hide private]
Class for performing the relative stereochemistry analysis.
Variables [hide private]
  status = Status()
  __package__ = 'auto_analyses'

Imports: dep_check, pi, sqrt, F_OK, access, getcwd, sep, randint, search, PIPE, Popen, sys, write_xy_data, write_xy_header, dipolar_constant, g1H, g13C, Interpreter, RelaxError, mkdir_nofail, Status