Python: module waterRefineTools

waterRefineTools

Tools for explicit water refinement with additional NMR restraints along the lines of the RECOORD work: Aart J. Nederveen, Jurgen F. Doreleijers, Wim Vranken, Zachary Miller, Chris A.E.M. Spronk, Sander B. Nabuurs, Peter Guentert, Miron Livny, John L. Markley, Michael Nilges, Eldon L. Ulrich, Robert Kaptein and Alexandre M.J.J. Bonvin, ``RECOORD: a REcalculated COORdinates Database of 500+ proteins from the PDB using restraints from the BioMagResBank,'' Proteins 59, 662-672 (2005)..

Classes

atomSelAction.PyAtomSelAction(atomSelAction.Base)

GetBounds
RenumberResids

class GetBounds(atomSelAction.PyAtomSelAction)

compute Cartesian bounds of atom selection.
The method bounds() returns a tuple of
(xmin,xmax,ymin,ymax,zmin,zmax)

Method resolution order:: GetBounds; atomSelAction.PyAtomSelAction; atomSelAction.Base; builtins.object

Methods defined here:

__init__(s): Initialize self. See help(type(self)) for accurate signature.

bounds(s)

init(s, sel)

run(s, sim, index)

Methods inherited from atomSelAction.PyAtomSelAction:

__repr__ = _swig_repr(self)

pyXplorHelp(self, *args, **kwargs) -> 'String'

Static methods inherited from atomSelAction.PyAtomSelAction:

__swig_destroy__ = delete_PyAtomSelAction(...)

Data descriptors inherited from atomSelAction.PyAtomSelAction:

thisown: The membership flag

Methods inherited from atomSelAction.Base:

finish_unused(self, *args, **kwargs) -> 'void'

init_unused(self, *args, **kwargs) -> 'void'

returnMethodName(self, *args, **kwargs) -> 'String'

Data descriptors inherited from atomSelAction.Base:

__dict__: dictionary for instance variables (if defined)

__weakref__: list of weak references to the object (if defined)

class RenumberResids(atomSelAction.PyAtomSelAction)

Method resolution order:: RenumberResids; atomSelAction.PyAtomSelAction; atomSelAction.Base; builtins.object

Methods defined here:

__init__(s): Initialize self. See help(type(self)) for accurate signature.

init(s, sel)

run(s, sim, index)

Methods inherited from atomSelAction.PyAtomSelAction:

__repr__ = _swig_repr(self)

pyXplorHelp(self, *args, **kwargs) -> 'String'

Static methods inherited from atomSelAction.PyAtomSelAction:

__swig_destroy__ = delete_PyAtomSelAction(...)

Data descriptors inherited from atomSelAction.PyAtomSelAction:

thisown: The membership flag

Methods inherited from atomSelAction.Base:

finish_unused(self, *args, **kwargs) -> 'void'

init_unused(self, *args, **kwargs) -> 'void'

returnMethodName(self, *args, **kwargs) -> 'String'

Data descriptors inherited from atomSelAction.Base:

__dict__: dictionary for instance variables (if defined)

__weakref__: list of weak references to the object (if defined)

Functions

buildShell(thickness=8.0, pw_dist=4.0, dyncount=1, waterBoxPDB='TOPPAR:waterRef/boxtyp20.pdb', waterBoxLength=18.856, waterDiam=2.4, waterResname='WAT'): water soaking protocol from Aria 1.2 (M. Nilges and J. Linge)

options:
thickness -  max initial water-protein(heavy atom) distance
pw_dist   -  min initial water-protein(heavy atom) distance
dyncount  -  iteration number - used to generate a unique segment name

refine(heatingParams=[], highTempParams=[], coolingParams=[], potList=[], outFilename='waterRefine.pdb', rigidRegions=(), fixedRegions=(), keepWaters=False, waterResname='TIP3'): An implementation of the water refinement protocol from Aria 1.2. M.
Nilges and J. Linge. This version can accommodate additional NMR
restraints, such as dipolar coupling, etc.

heatingParams
highTempParams
coolingParams  - lists of ramped parameters to use during the heating,
                 high-temperature and cooling phases of the refinement
                 protocol.

potList      - potential terms to use in water refinement. To these are
               added the following terms: ELEC, VDW, BOND, ANGL, IMPR,
               DIHE.

rigidRegions - selections of atoms which do not move relative to
               each other.

fixedRegions - selections of atoms which do not move at all.

outFilename  - name of pdb file written after water refinement.

keepWaters   - if True, do not delete water molecules when writing out
               pdb files.

waterResname - residue name of water molecules [default: 'TIP3']

segidCountMap(cnt): Given an integer return a character or throw an exception if out of
range. The map looks like:
0..9 --> '0'..'9'
10..35 --> 'A'..'Z'