eefxPot
index
/home/schwitrs/bzr-repo/xplor-python3/bin.Linux_x86_64/eefxPot.py


An implicit solvent energy for solution and membrane
environments. 
 
Author: Ye Tian
 
References:
 
   Y. Tian, C.D. Schwieters, S.J. Opella, and F.M. Marassi,
   ``A Practical Implicit Solvent Potential for NMR Structure
   Calculation ,'' J. Magn. Res. 243, 54-64 (2014) PMID: 24747742.
  
   Ye Tian, C.D. Schwieters, S.J. Opella and F.M. Marassi, ``A
   Practical Implicit Membrane Potential for NMR Structure
   Calculations of Membrane Proteins,'' Biophys J. 109, 574-585
   (2015) PMID: 26244739.
  
   Ye Tian, C.D. Schwieters, S.J. Opella, and F.M. Marassi,
   ``High quality NMR structures: a new force field with
   implicit water and membrane solvation for Xplor-NIH,''
   J. Biomol. NMR 67, 35-49 (2017) PMID: 28035651.
 
Based on:
 
   Lazaridis & Karplus Proteins 35, 133 (1999).
   Lazaridis  Proteins 52, 176 (2003).
 
 
Constructor:
 
  EEFxPot(instanceName,
          groupAssignment,
          slvParams,
          groupIndices,
          vdwParams,
          resExclusions,
          nbfixParams,
          defaultSelection)
 
  instanceName is a user-specified identifier, groupAssignment is an
  array which specifies which group index each atom belongs to,
  slvParams is a dictionary containing EEFx parameters for each atom
  type, vdwParams is a map of atom chemical types to a list of a tuple
  of (eps, sigma, eps14, sigma14), where epsilon is a vdw well depth
  (unused in this term) and sigma is the equilibrium interatomic
  distance. The 14 versions are special values to use for atoms which
  are separated by three covalent bonds. resExclusions is a dictionary
  which contains pairs of atom names whose interactions are not to be
  computed. Normally, the interatomic distance at which the energy
  becomes nonzero is computed using the types of the two atoms
  involved, but exceptions to this rule can be specified by
  nbfixParams which is a dictionary with keys consisting of chemical
  types separated by the '*' character. The values in the dictionary
  is the tuple of VDW parameters (A,B, A14, B14). From these values
  sigma and sigma14 are computed. defaultSelection is an optional
  argument specifying an atomSel.AtomSel. The effective selection for
  each selection specified in a selectionPair is the intersection of that
  which is explicitly specified and defaultSelection.
  
 this term should
  compute interactions for.
 
Methods: FIX: to be completed
 
  typedef Pair<String,String> StringPair;
 
  const int numAtoms; // number of atoms when term created
  float_type elecEnergy;
  float_type solvEnergy;
  float_type vdwEnergy;
  EEFx_ElecPot elecPot;
  EEFx_SolvPot solvPot;
  EEFx_VDWPot  vdwPot;
  bool staleGradient;
 
  float_type calcEnergy();
 
  float_type calcEnergyAndDerivs(DerivList*);
      
  void setTemperature(const float_type& temperature);
 
  testGroupCutoffDist() - helper function to test that cutoffDist is larger
                          than the maximum current distance between group
                          centroid and its furthest atom.
 
  String showParam() const;
 
  Simulation* simulation() const { return sim; };
 
  ACCESSOR(verbose,Verbose,bool);
  MODACCESSOR(cutoffDist,CutoffDist,float_type);
  MODACCESSOR(moveTol,MoveTol,float_type);
  MODACCESSOR(profileN,ProfileN,int);
  MODACCESSOR(a,A,float_type);
  MODACCESSOR(thickness,Thickness,float_type);
  MODACCESSOR(e14Factor,E14Factor,float_type);
 
 
Accessors
 
 The following parameters can be set [defaults in square brackets]
 
    scale             - scale factor for energy.
 
    moveTol           - size of atomic displacement above which
                        recalculation of the nonbond list is
                        recalculated.
 
    collectAtomEnergies - if set to True, atom per-atom energies will be 
                          computed. Is False by default because of extra 
                          computational cost.
 
    verbose           - a boolean describing whether or not to print
                        detailed information on the neighbor lists [False].
 
 the above quantities may be retrieved using the member function form
 quantity(), while they are set using the form setQuantity(value).
 
 
  bool E14FullScale;
  void setE14FullScale(bool v);
 
  MODACCESSOR(poreR,PoreR,float_type);
  MODACCESSOR(bicelleR,bicelleR,float_type);
        
  float_type rms(){return -1;};
  violations() - returns vdwPot().violations()
  int numRestraints() const {return -1;};
  void setIMMx(bool v);
  bool IMMx() const { return IMMx_; }
  void useCDIE(bool v);
  bool IMMx_pore_,IMMx_bicelle_,IMMx_micelle_;
  void setIMMx_pore(bool v);
  void setIMMx_bicelle(bool v);
  void setIMMx_micelle(bool v);
  bool IMMx_pore()    const { return IMMx_pore_; }
  bool IMMx_bicelle() const { return IMMx_bicelle_; }
  bool IMMx_micelle() const { return IMMx_micelle_; }
 
  void useGROUp(bool inpV);
 
  void setMicelleX(const float_type& x){sqmicX=x*x;};
  void setMicelleY(const float_type& y){sqmicY=y*y;};
  void setMicelleZ(const float_type& z){sqmicZ=z*z;};
 
//Gouy-Chapmen energy;
  float_type gcEnergy;
  float_type voltEnergy;
  void setGCvalence(const float_type& valence);
  void setGCconc(const float_type& concentration);
  void setGCfraction(const float_type& fraction);
  void setGCoffset(const float_type& offset);
  void setGCvoltage(const float_type& voltage);
  void setIMMx_GC(bool v);
  bool IMMx_GC() const { return IMMx_GC_; }
  void setIMMx_volt(bool v);
  bool IMMx_volt() const { return IMMx_volt_; }
 
  void printTotalE();
  atomInfo(atomIndex) - return string giving info abour atom specified
                        by index.
  atomEnergies        - return a per-atom array with each element a
                        structure containing the following members:
                           Evdw, Eelec, Eslv, Egc, Evolt
 
public:
 
  typedef Pair<AtomSel,AtomSel> SelectionPair;
 
  CDSList<SelectionPair>  selPairs;
  CDSList<float_type>     selPairWeights;
  CDSList<float_type>     selPairEnergies;
  CDSList<CDSVector<bool> > selPairIncludeA;
  CDSList<CDSVector<bool> > selPairIncludeB;
 
  const CDSList<SelectionPair>& selectionPairs() const { return selPairs; }
  int numSelectionPairs() const { return selPairs.size(); }
  void addSelectionPair(const AtomSel&,
                        const AtomSel&);
  void setSelectionPairWeight(const int index,
                              const float_type& val);
  float_type selectionPairWeight(const int index) const;
  float_type selectionPairEnergy(const int index);
 
 
  void deleteSelectionPair(const int& index);
  void resetSelectionPairs();
 
struct EEFxAtomEnergies {
 float_type Evdw;
 float_type Eelec;
 float_type Eslv;
 float_type Egc;
 float_type Evolt;
 
 void clear() {
  Evdw = Eelec = Eslv = Egc = Evolt = 0.;
 }
};
 
class EEFxPot;
 
class EEFx_ElecPot: public Pot {
  EEFxPot& eefxPot;
  EEFx_ElecPot& operator=(const EEFx_ElecPot&);
public:
  EEFx_ElecPot(EEFxPot& pot);
 
  float_type calcEnergy();
 
  float_type calcEnergyAndDerivs(DerivList*);
 
  float_type rms() { return -1; }
  float_type violations() { return -1; }
  int numRestraints() const { return -1; }
};
 
class EEFx_SolvPot: public Pot {
  EEFxPot& eefxPot;
  EEFx_SolvPot& operator=(const EEFx_SolvPot&);
public:
  EEFx_SolvPot(EEFxPot& pot);
 
  float_type calcEnergy();
 
  float_type calcEnergyAndDerivs(DerivList*);
 
  float_type rms() { return -1; }
  float_type violations() { return -1; }
  int numRestraints() const { return -1; }
};
 
class EEFx_VDWPot: public Pot {
  EEFxPot& eefxPot;
  EEFx_VDWPot& operator=(const EEFx_VDWPot&);
public:
  EEFx_VDWPot(EEFxPot& pot);
 
  float_type calcEnergy();
 
  float_type calcEnergyAndDerivs(DerivList*);
 
  float_type rms() { return -1; }
  violations() - number of atomic clashes within threshold
  bumps(idx=-1)- returns a list of VDWBump records containing the
                 identity of clashing atoms, with members:
 
                  atomi, atomj, - clashing atom.Atoms
                  dist          - the distance between them
                  dist0         - 1/2 ( sigma_i + sigma_j )
 
                 The idx argument specifies which selection pair to report on
                 (an index into the pot.selPairs member). A value of -1
                 specifies reporting on all selection pairs.
 
  threshold()       - threshold for clash determination
  setThreshold(val)
  int numRestraints() const { return -1; }
};
 
 
 
 
 
# This file was automatically generated by SWIG (http://www.swig.org).
# Version 4.0.2
#
# Do not make changes to this file unless you know what you are doing--modify
# the SWIG interface file instead.

 
Classes
       
builtins.object
CDSList_EEFxAtomEnergies
CDSList_SelectionPair
CDSList_VDW
EEFxAtomEnergies
EEFxPot
EEFxPot_LetterClass
EEFx_ElecPot
EEFx_ElecPot_LetterClass
EEFx_SolvPot
EEFx_SolvPot_LetterClass
EEFx_VDWPot
EEFx_VDWPot_LetterClass
Modified
ModifiedBase
Pair_AtomSel_AtomSel
VDWBump

 
class CDSList_EEFxAtomEnergies(builtins.object)
    CDSList_EEFxAtomEnergies(*args)
 

 
  Methods defined here:
__delitem__(self, *args, **kwargs) -> 'void'
__getitem__(self, *args) -> 'CDSList< EEFxAtomEnergies >'
__getslice__(self, *args, **kwargs) -> 'CDSList< EEFxAtomEnergies >'
__init__(self, *args)
Initialize self.  See help(type(self)) for accurate signature.
__len__(self, *args, **kwargs) -> 'int'
__repr__ = _swig_repr(self)
__setitem__(self, *args, **kwargs) -> 'void'
append(self, *args, **kwargs) -> 'void'
help(self, *args, **kwargs) -> 'String'
remove(self, *args, **kwargs) -> 'void'
removeAll(self, *args, **kwargs) -> 'void'

Static methods defined here:
__swig_destroy__ = delete_CDSList_EEFxAtomEnergies(...)

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

 
list of weak references to the object (if defined)
thisown

 
The membership flag

 
class CDSList_SelectionPair(builtins.object)
    CDSList_SelectionPair(*args)
 

 
  Methods defined here:
__delitem__(self, *args, **kwargs) -> 'void'
__getitem__(self, *args) -> 'CDSList< EEFxPot::SelectionPair >'
__getslice__(self, *args, **kwargs) -> 'CDSList< EEFxPot::SelectionPair >'
__init__(self, *args)
Initialize self.  See help(type(self)) for accurate signature.
__len__(self, *args, **kwargs) -> 'int'
__repr__ = _swig_repr(self)
__setitem__(self, *args, **kwargs) -> 'void'
append(self, *args, **kwargs) -> 'void'
help(self, *args, **kwargs) -> 'String'
remove(self, *args, **kwargs) -> 'void'
removeAll(self, *args, **kwargs) -> 'void'

Static methods defined here:
__swig_destroy__ = delete_CDSList_SelectionPair(...)

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

 
list of weak references to the object (if defined)
thisown

 
The membership flag

 
class CDSList_VDW(builtins.object)
    CDSList_VDW(*args)
 

 
  Methods defined here:
__delitem__(self, *args, **kwargs) -> 'void'
__getitem__(self, *args) -> 'CDSList< VDWBump >'
__getslice__(self, *args, **kwargs) -> 'CDSList< VDWBump >'
__init__(self, *args)
Initialize self.  See help(type(self)) for accurate signature.
__len__(self, *args, **kwargs) -> 'int'
__repr__ = _swig_repr(self)
__setitem__(self, *args, **kwargs) -> 'void'
append(self, *args, **kwargs) -> 'void'
help(self, *args, **kwargs) -> 'String'
remove(self, *args, **kwargs) -> 'void'
removeAll(self, *args, **kwargs) -> 'void'

Static methods defined here:
__swig_destroy__ = delete_CDSList_VDW(...)

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

 
list of weak references to the object (if defined)
thisown

 
The membership flag

 
class EEFxAtomEnergies(builtins.object)
    EEFxAtomEnergies(*args, **kwargs)
 

 
  Methods defined here:
__init__(self, *args, **kwargs)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)
clear(self, *args, **kwargs) -> 'void'

Static methods defined here:
__swig_destroy__ = delete_EEFxAtomEnergies(...)

Data descriptors defined here:
Eelec

 
Egc

 
Eslv

 
Evdw

 
Evolt

 
__dict__

 
dictionary for instance variables (if defined)
__weakref__

 
list of weak references to the object (if defined)
thisown

 
The membership flag

 
class EEFxPot_LetterClass(builtins.object)
    EEFxPot_LetterClass(*args, **kwargs)
 

 
  Methods defined here:
IMMx(self, *args, **kwargs) -> 'bool'
IMMx_GC(self, *args, **kwargs) -> 'bool'
IMMx_bicelle(self, *args, **kwargs) -> 'bool'
IMMx_micelle(self, *args, **kwargs) -> 'bool'
IMMx_pore(self, *args, **kwargs) -> 'bool'
IMMx_volt(self, *args, **kwargs) -> 'bool'
__init__(self, *args, **kwargs)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)
a(self, *args, **kwargs) -> 'float_type const'
addSelectionPair(self, *args, **kwargs) -> 'void'
atomEnergies(self, *args, **kwargs) -> 'CDSList< EEFxAtomEnergies > const &'
atomInfo(self, *args, **kwargs) -> 'String'
bicelleR(self, *args, **kwargs) -> 'float_type const'
calcEnergy(self, *args, **kwargs) -> 'float_type'
calcEnergyAndDerivs(self, *args, **kwargs) -> 'float_type'
collectAtomEnergies(self, *args, **kwargs) -> 'bool const'
cutoffDist(self, *args, **kwargs) -> 'float_type const'
defaultSelection(self, *args, **kwargs) -> 'AtomSel'
deleteSelectionPair(self, *args, **kwargs) -> 'void'
e14Factor(self, *args, **kwargs) -> 'float_type const'
elecPot_cxx(self, *args, **kwargs) -> 'rc_DerivedPot< EEFx_ElecPot >'
moveTol(self, *args, **kwargs) -> 'float_type const'
numRestraints(self, *args, **kwargs) -> 'int'
numSelectionPairs(self, *args, **kwargs) -> 'int'
poreR(self, *args, **kwargs) -> 'float_type const'
printTotalE(self, *args, **kwargs) -> 'void'
profileN(self, *args, **kwargs) -> 'int const'
pyXplorHelp(self, *args, **kwargs) -> 'String'
resetSelectionPairs(self, *args, **kwargs) -> 'void'
restraints(self, *args, **kwargs) -> 'CDSList< VDWBump >'
rms(self, *args, **kwargs) -> 'float_type'
selectionPairEnergy(self, *args, **kwargs) -> 'float_type'
selectionPairWeight(self, *args, **kwargs) -> 'float_type'
selectionPairs(self, *args, **kwargs) -> 'CDSList< EEFxPot::SelectionPair > const &'
setA(self, *args, **kwargs) -> 'void'
setCollectAtomEnergies(self, *args, **kwargs) -> 'void'
setCutoffDist(self, *args, **kwargs) -> 'void'
setE14Factor(self, *args, **kwargs) -> 'void'
setE14FullScale(self, *args, **kwargs) -> 'void'
setGCconc(self, *args, **kwargs) -> 'void'
setGCfraction(self, *args, **kwargs) -> 'void'
setGCoffset(self, *args, **kwargs) -> 'void'
setGCvalence(self, *args, **kwargs) -> 'void'
setGCvoltage(self, *args, **kwargs) -> 'void'
setIMMx(self, *args, **kwargs) -> 'void'
setIMMx_GC(self, *args, **kwargs) -> 'void'
setIMMx_bicelle(self, *args, **kwargs) -> 'void'
setIMMx_micelle(self, *args, **kwargs) -> 'void'
setIMMx_pore(self, *args, **kwargs) -> 'void'
setIMMx_volt(self, *args, **kwargs) -> 'void'
setMicelleX(self, *args, **kwargs) -> 'void'
setMicelleY(self, *args, **kwargs) -> 'void'
setMicelleZ(self, *args, **kwargs) -> 'void'
setMoveTol(self, *args, **kwargs) -> 'void'
setPoreR(self, *args, **kwargs) -> 'void'
setProfileN(self, *args, **kwargs) -> 'void'
setSelectionPairWeight(self, *args, **kwargs) -> 'void'
setTemperature(self, *args, **kwargs) -> 'void'
setThickness(self, *args, **kwargs) -> 'void'
setThreshold(self, *args, **kwargs) -> 'void'
setVerbose(self, *args, **kwargs) -> 'void'
setbicelleR(self, *args, **kwargs) -> 'void'
showParam(self, *args, **kwargs) -> 'String'
simulation(self, *args, **kwargs) -> 'Simulation *'
solvPot_cxx(self, *args, **kwargs) -> 'rc_DerivedPot< EEFx_SolvPot >'
testGroupCutoffDist(self, *args, **kwargs) -> 'bool'
thickness(self, *args, **kwargs) -> 'float_type const'
threshold(self, *args, **kwargs) -> 'float_type const'
updateValues(self, *args, **kwargs) -> 'void'
useCDIE(self, *args, **kwargs) -> 'void'
useGROUp(self, *args, **kwargs) -> 'void'
vdwPot_cxx(self, *args, **kwargs) -> 'rc_DerivedPot< EEFx_VDWPot >'
verbose(self, *args, **kwargs) -> 'bool const'
violations(self, *args, **kwargs) -> 'float_type'

Static methods defined here:
__swig_destroy__ = delete_EEFxPot_LetterClass(...)

Readonly properties defined here:
elecPot_member

 
numAtoms

 
solvPot_member

 
vdwPot_member

 

Data descriptors defined here:
E14FullScale

 
IMMx_bicelle_

 
IMMx_micelle_

 
IMMx_pore_

 
__dict__

 
dictionary for instance variables (if defined)
__weakref__

 
list of weak references to the object (if defined)
elecEnergy

 
gcEnergy

 
selPairEnergies

 
selPairIncludeA

 
selPairIncludeB

 
selPairWeights

 
selPairs

 
solvEnergy

 
staleGradient

 
thisown

 
The membership flag
vdwEnergy

 
voltEnergy

 

 
class EEFx_ElecPot_LetterClass(builtins.object)
    EEFx_ElecPot_LetterClass(*args, **kwargs)
 

 
  Methods defined here:
__init__(self, *args, **kwargs)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)
calcEnergy(self, *args, **kwargs) -> 'float_type'
calcEnergyAndDerivs(self, *args, **kwargs) -> 'float_type'
numRestraints(self, *args, **kwargs) -> 'int'
pyXplorHelp(self, *args, **kwargs) -> 'String'
rms(self, *args, **kwargs) -> 'float_type'
violations(self, *args, **kwargs) -> 'float_type'

Static methods defined here:
__swig_destroy__ = delete_EEFx_ElecPot_LetterClass(...)

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

 
list of weak references to the object (if defined)
thisown

 
The membership flag

 
class EEFx_SolvPot_LetterClass(builtins.object)
    EEFx_SolvPot_LetterClass(*args, **kwargs)
 

 
  Methods defined here:
__init__(self, *args, **kwargs)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)
calcEnergy(self, *args, **kwargs) -> 'float_type'
calcEnergyAndDerivs(self, *args, **kwargs) -> 'float_type'
numRestraints(self, *args, **kwargs) -> 'int'
pyXplorHelp(self, *args, **kwargs) -> 'String'
rms(self, *args, **kwargs) -> 'float_type'
violations(self, *args, **kwargs) -> 'float_type'

Static methods defined here:
__swig_destroy__ = delete_EEFx_SolvPot_LetterClass(...)

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

 
list of weak references to the object (if defined)
thisown

 
The membership flag

 
class EEFx_VDWPot_LetterClass(builtins.object)
    EEFx_VDWPot_LetterClass(*args, **kwargs)
 

 
  Methods defined here:
__init__(self, *args, **kwargs)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)
bumps(self, *args, **kwargs) -> 'CDSList< VDWBump >'
calcEnergy(self, *args, **kwargs) -> 'float_type'
calcEnergyAndDerivs(self, *args, **kwargs) -> 'float_type'
findAtomBumps(self, *args, **kwargs) -> 'void'
numRestraints(self, *args, **kwargs) -> 'int'
pyXplorHelp(self, *args, **kwargs) -> 'String'
restraints(self, *args, **kwargs) -> 'CDSList< VDWBump >'
rms(self, *args, **kwargs) -> 'float_type'
violations(self, *args, **kwargs) -> 'float_type'

Static methods defined here:
__swig_destroy__ = delete_EEFx_VDWPot_LetterClass(...)

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

 
list of weak references to the object (if defined)
thisown

 
The membership flag

 
class Modified(builtins.object)
    Modified(*args, **kwargs)
 

 
  Methods defined here:
__call__(self, *args, **kwargs) -> 'int'
Call self as a function.
__init__(self, *args, **kwargs)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)
clear(self, *args, **kwargs) -> 'void'
set(self, *args, **kwargs) -> 'void'
update(self, *args, **kwargs) -> 'void'
value(self, *args, **kwargs) -> 'int'

Static methods defined here:
__swig_destroy__ = delete_Modified(...)

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

 
list of weak references to the object (if defined)
thisown

 
The membership flag

Data and other attributes defined here:
MOD_SELF = 1
MOD_SIMULATION = 2

 
class ModifiedBase(builtins.object)
    ModifiedBase(*args, **kwargs)
 

 
  Methods defined here:
__init__(self, *args, **kwargs)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)
registerTo(self, *args, **kwargs) -> 'void'
unRegister(self, *args, **kwargs) -> 'void'
updateValues(self, *args, **kwargs) -> 'void'

Static methods defined here:
__swig_destroy__ = delete_ModifiedBase(...)

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

 
list of weak references to the object (if defined)
modified

 
registeredSimulations

 
thisown

 
The membership flag

 
class Pair_AtomSel_AtomSel(builtins.object)
    Pair_AtomSel_AtomSel(*args)
 

 
  Methods defined here:
__eq__(self, *args, **kwargs) -> 'bool'
Return self==value.
__init__(self, *args)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)

Static methods defined here:
__swig_destroy__ = delete_Pair_AtomSel_AtomSel(...)

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

 
list of weak references to the object (if defined)
a

 
b

 
thisown

 
The membership flag

Data and other attributes defined here:
__hash__ = None

 
class VDWBump(builtins.object)
    VDWBump(*args)
 

 
  Methods defined here:
__init__(self, *args)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)
diff(self, *args, **kwargs) -> 'float_type'
name(self, *args, **kwargs) -> 'String'
violated(self, *args, **kwargs) -> 'bool'

Static methods defined here:
__swig_destroy__ = delete_VDWBump(...)

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

 
list of weak references to the object (if defined)
atomi

 
atomj

 
dist

 
dist0

 
energy

 
thisown

 
The membership flag

 
realEEFxPot = class EEFxPot(builtins.object)
    realEEFxPot(*args)
 

 
  Methods defined here:
IMMx(self, *args, **kwargs) -> 'bool'
IMMx_GC(self, *args, **kwargs) -> 'bool'
IMMx_bicelle(self, *args, **kwargs) -> 'bool'
IMMx_micelle(self, *args, **kwargs) -> 'bool'
IMMx_pore(self, *args, **kwargs) -> 'bool'
IMMx_volt(self, *args, **kwargs) -> 'bool'
__deref__(self, *args, **kwargs) -> 'EEFxPot *'
__init__(self, *args)
__oldinit__ = __init__(self, *args, **kwargs)
__ref__(self, *args, **kwargs) -> 'EEFxPot &'
__repr__ = _swig_repr(self)
a(self, *args, **kwargs) -> 'float_type const'
addSelectionPair(self, *args, **kwargs) -> 'void'
atomEnergies(self, *args, **kwargs) -> 'CDSList< EEFxAtomEnergies > const &'
atomInfo(self, *args, **kwargs) -> 'String'
bicelleR(self, *args, **kwargs) -> 'float_type const'
calcEnergy(self, *args, **kwargs) -> 'float_type'
calcEnergyAndDerivs(self, *args, **kwargs) -> 'float_type'
collectAtomEnergies(self, *args, **kwargs) -> 'bool const'
cutoffDist(self, *args, **kwargs) -> 'float_type const'
decrRefCnt(self, *args, **kwargs) -> 'void'
defaultSelection(self, *args, **kwargs) -> 'AtomSel'
deleteSelectionPair(self, *args, **kwargs) -> 'void'
e14Factor(self, *args, **kwargs) -> 'float_type const'
elecPot(self)
elecPot_cxx(self, *args, **kwargs) -> 'rc_DerivedPot< EEFx_ElecPot >'
incrRefCnt(self, *args, **kwargs) -> 'void'
instanceData(self, *args, **kwargs) -> 'PyObject *'
instanceName(self, *args, **kwargs) -> 'char const *'
moveTol(self, *args, **kwargs) -> 'float_type const'
numRestraints(self, *args, **kwargs) -> 'int'
numSelectionPairs(self, *args, **kwargs) -> 'int'
poreR(self, *args, **kwargs) -> 'float_type const'
potName(self, *args, **kwargs) -> 'char const *'
printTotalE(self, *args, **kwargs) -> 'void'
profileN(self, *args, **kwargs) -> 'int const'
pyXplorHelp(self, *args, **kwargs) -> 'String'
refCnt(self, *args, **kwargs) -> 'int'
registerInstanceData(self, *args, **kwargs) -> 'void'
registerTo(self, *args, **kwargs) -> 'void'
resetInstanceName(self, *args, **kwargs) -> 'void'
resetPotName(self, *args, **kwargs) -> 'void'
resetSelectionPairs(self, *args, **kwargs) -> 'void'
restraints(self, *args, **kwargs) -> 'CDSList< VDWBump >'
rms(self, *args, **kwargs) -> 'float_type'
scale(self, *args, **kwargs) -> 'float_type const'
selectionPairEnergy(self, *args, **kwargs) -> 'float_type'
selectionPairWeight(self, *args, **kwargs) -> 'float_type'
selectionPairs(self, *args, **kwargs) -> 'CDSList< EEFxPot::SelectionPair > const &'
setA(self, *args, **kwargs) -> 'void'
setCollectAtomEnergies(self, *args, **kwargs) -> 'void'
setCutoffDist(self, *args, **kwargs) -> 'void'
setE14Factor(self, *args, **kwargs) -> 'void'
setE14FullScale(self, *args, **kwargs) -> 'void'
setGCconc(self, *args, **kwargs) -> 'void'
setGCfraction(self, *args, **kwargs) -> 'void'
setGCoffset(self, *args, **kwargs) -> 'void'
setGCvalence(self, *args, **kwargs) -> 'void'
setGCvoltage(self, *args, **kwargs) -> 'void'
setIMMx(self, *args, **kwargs) -> 'void'
setIMMx_GC(self, *args, **kwargs) -> 'void'
setIMMx_bicelle(self, *args, **kwargs) -> 'void'
setIMMx_micelle(self, *args, **kwargs) -> 'void'
setIMMx_pore(self, *args, **kwargs) -> 'void'
setIMMx_volt(self, *args, **kwargs) -> 'void'
setMicelleX(self, *args, **kwargs) -> 'void'
setMicelleY(self, *args, **kwargs) -> 'void'
setMicelleZ(self, *args, **kwargs) -> 'void'
setMoveTol(self, *args, **kwargs) -> 'void'
setPoreR(self, *args, **kwargs) -> 'void'
setProfileN(self, *args, **kwargs) -> 'void'
setScale(self, *args, **kwargs) -> 'void'
setSelectionPairWeight(self, *args, **kwargs) -> 'void'
setTemperature(self, *args, **kwargs) -> 'void'
setThickness(self, *args, **kwargs) -> 'void'
setThreshold(self, *args, **kwargs) -> 'void'
setVerbose(self, *args, **kwargs) -> 'void'
setbicelleR(self, *args, **kwargs) -> 'void'
showParam(self, *args, **kwargs) -> 'String'
simulation(self, *args, **kwargs) -> 'Simulation *'
solvPot(self)
solvPot_cxx(self, *args, **kwargs) -> 'rc_DerivedPot< EEFx_SolvPot >'
testGroupCutoffDist(self, *args, **kwargs) -> 'bool'
thickness(self, *args, **kwargs) -> 'float_type const'
threshold(self, *args, **kwargs) -> 'float_type const'
unRegister(self, *args, **kwargs) -> 'void'
updateDelta(self, *args, **kwargs) -> 'void'
updateValues(self, *args, **kwargs) -> 'void'
useCDIE(self, *args, **kwargs) -> 'void'
useGROUp(self, *args, **kwargs) -> 'void'
vdwPot(self)
vdwPot_cxx(self, *args, **kwargs) -> 'rc_DerivedPot< EEFx_VDWPot >'
verbose(self, *args, **kwargs) -> 'bool const'
violations(self, *args, **kwargs) -> 'float_type'

Static methods defined here:
__swig_destroy__ = delete_EEFxPot(...)

Readonly properties defined here:
elecPot_member

 
numAtoms

 
solvPot_member

 
vdwPot_member

 

Data descriptors defined here:
E14FullScale

 
IMMx_bicelle_

 
IMMx_micelle_

 
IMMx_pore_

 
__dict__

 
dictionary for instance variables (if defined)
__weakref__

 
list of weak references to the object (if defined)
elecEnergy

 
gcEnergy

 
instanceDataCleanup

 
instanceDataCreate

 
instanceData_

 
modified

 
registeredSimulations

 
selPairEnergies

 
selPairIncludeA

 
selPairIncludeB

 
selPairWeights

 
selPairs

 
solvEnergy

 
staleGradient

 
thisown

 
The membership flag
vdwEnergy

 
voltEnergy

 

 
realEEFx_ElecPot = class EEFx_ElecPot(builtins.object)
    realEEFx_ElecPot(*args)
 

 
  Methods defined here:
__deref__(self, *args, **kwargs) -> 'EEFx_ElecPot *'
__init__(self, *args)
__oldinit__ = __init__(self, *args, **kwargs)
__ref__(self, *args, **kwargs) -> 'EEFx_ElecPot &'
__repr__ = _swig_repr(self)
calcEnergy(self, *args, **kwargs) -> 'float_type'
calcEnergyAndDerivs(self, *args, **kwargs) -> 'float_type'
decrRefCnt(self, *args, **kwargs) -> 'void'
incrRefCnt(self, *args, **kwargs) -> 'void'
instanceData(self, *args, **kwargs) -> 'PyObject *'
instanceName(self, *args, **kwargs) -> 'char const *'
numRestraints(self, *args, **kwargs) -> 'int'
potName(self, *args, **kwargs) -> 'char const *'
pyXplorHelp(self, *args, **kwargs) -> 'String'
refCnt(self, *args, **kwargs) -> 'int'
registerInstanceData(self, *args, **kwargs) -> 'void'
registerTo(self, *args, **kwargs) -> 'void'
resetInstanceName(self, *args, **kwargs) -> 'void'
resetPotName(self, *args, **kwargs) -> 'void'
rms(self, *args, **kwargs) -> 'float_type'
scale(self, *args, **kwargs) -> 'float_type const'
setScale(self, *args, **kwargs) -> 'void'
setThreshold(self, *args, **kwargs) -> 'void'
threshold(self, *args, **kwargs) -> 'float_type const'
unRegister(self, *args, **kwargs) -> 'void'
updateDelta(self, *args, **kwargs) -> 'void'
updateValues(self, *args, **kwargs) -> 'void'
violations(self, *args, **kwargs) -> 'float_type'

Static methods defined here:
__swig_destroy__ = delete_EEFx_ElecPot(...)

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

 
list of weak references to the object (if defined)
instanceDataCleanup

 
instanceDataCreate

 
instanceData_

 
modified

 
registeredSimulations

 
thisown

 
The membership flag

 
realEEFx_SolvPot = class EEFx_SolvPot(builtins.object)
    realEEFx_SolvPot(*args)
 

 
  Methods defined here:
__deref__(self, *args, **kwargs) -> 'EEFx_SolvPot *'
__init__(self, *args)
__oldinit__ = __init__(self, *args, **kwargs)
__ref__(self, *args, **kwargs) -> 'EEFx_SolvPot &'
__repr__ = _swig_repr(self)
calcEnergy(self, *args, **kwargs) -> 'float_type'
calcEnergyAndDerivs(self, *args, **kwargs) -> 'float_type'
decrRefCnt(self, *args, **kwargs) -> 'void'
incrRefCnt(self, *args, **kwargs) -> 'void'
instanceData(self, *args, **kwargs) -> 'PyObject *'
instanceName(self, *args, **kwargs) -> 'char const *'
numRestraints(self, *args, **kwargs) -> 'int'
potName(self, *args, **kwargs) -> 'char const *'
pyXplorHelp(self, *args, **kwargs) -> 'String'
refCnt(self, *args, **kwargs) -> 'int'
registerInstanceData(self, *args, **kwargs) -> 'void'
registerTo(self, *args, **kwargs) -> 'void'
resetInstanceName(self, *args, **kwargs) -> 'void'
resetPotName(self, *args, **kwargs) -> 'void'
rms(self, *args, **kwargs) -> 'float_type'
scale(self, *args, **kwargs) -> 'float_type const'
setScale(self, *args, **kwargs) -> 'void'
setThreshold(self, *args, **kwargs) -> 'void'
threshold(self, *args, **kwargs) -> 'float_type const'
unRegister(self, *args, **kwargs) -> 'void'
updateDelta(self, *args, **kwargs) -> 'void'
updateValues(self, *args, **kwargs) -> 'void'
violations(self, *args, **kwargs) -> 'float_type'

Static methods defined here:
__swig_destroy__ = delete_EEFx_SolvPot(...)

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

 
list of weak references to the object (if defined)
instanceDataCleanup

 
instanceDataCreate

 
instanceData_

 
modified

 
registeredSimulations

 
thisown

 
The membership flag

 
realEEFx_VDWPot = class EEFx_VDWPot(builtins.object)
    realEEFx_VDWPot(*args)
 

 
  Methods defined here:
__deref__(self, *args, **kwargs) -> 'EEFx_VDWPot *'
__init__(self, *args)
__oldinit__ = __init__(self, *args, **kwargs)
__ref__(self, *args, **kwargs) -> 'EEFx_VDWPot &'
__repr__ = _swig_repr(self)
bumps(self, *args, **kwargs) -> 'CDSList< VDWBump >'
calcEnergy(self, *args, **kwargs) -> 'float_type'
calcEnergyAndDerivs(self, *args, **kwargs) -> 'float_type'
decrRefCnt(self, *args, **kwargs) -> 'void'
findAtomBumps(self, *args, **kwargs) -> 'void'
incrRefCnt(self, *args, **kwargs) -> 'void'
instanceData(self, *args, **kwargs) -> 'PyObject *'
instanceName(self, *args, **kwargs) -> 'char const *'
numRestraints(self, *args, **kwargs) -> 'int'
potName(self, *args, **kwargs) -> 'char const *'
pyXplorHelp(self, *args, **kwargs) -> 'String'
refCnt(self, *args, **kwargs) -> 'int'
registerInstanceData(self, *args, **kwargs) -> 'void'
registerTo(self, *args, **kwargs) -> 'void'
resetInstanceName(self, *args, **kwargs) -> 'void'
resetPotName(self, *args, **kwargs) -> 'void'
restraints(self, *args, **kwargs) -> 'CDSList< VDWBump >'
rms(self, *args, **kwargs) -> 'float_type'
scale(self, *args, **kwargs) -> 'float_type const'
setScale(self, *args, **kwargs) -> 'void'
setThreshold(self, *args, **kwargs) -> 'void'
threshold(self, *args, **kwargs) -> 'float_type const'
unRegister(self, *args, **kwargs) -> 'void'
updateDelta(self, *args, **kwargs) -> 'void'
updateValues(self, *args, **kwargs) -> 'void'
violations(self, *args, **kwargs) -> 'float_type'

Static methods defined here:
__swig_destroy__ = delete_EEFx_VDWPot(...)

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

 
list of weak references to the object (if defined)
instanceDataCleanup

 
instanceDataCreate

 
instanceData_

 
modified

 
registeredSimulations

 
thisown

 
The membership flag

 
Functions
       
EEFxPot(*args)
EEFx_ElecPot(*args)
EEFx_SolvPot(*args)
EEFx_VDWPot(*args)
pyXplorHelp(*args) -> 'String'