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'