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


Sparta class:
 
[FIX: needs much work]
 
  enum ShiftTerms { TERM_RING  =1,
                    TERM_EFIELD=2,
                    TERM_ORDER =4,
                    TERM_HBOND =8,
                    TERM_PHIM  =16,
                    TERM_PHI   =32,
                    TERM_PHIP  =64,
                    TERM_PSIM  =128,
                    TERM_PSI   =256,
                    TERM_PSIP  =512,
                    TERM_CHI1M =1024,
                    TERM_CHI1  =2048,
                    TERM_CHI1P =4096,
                    TERM_CHI2M =8192,
                    TERM_CHI2  =16384,
                    TERM_CHI2P =32768 };
 
  int indexBlosumM  ; //indices into ANN input vector
  int indexPhiM     ;
  int indexPsiM     ;
  int indexChi1M    ;
  int indexChi2M    ;
  int indexBlosum   ;
  int indexPhi      ;
  int indexPsi      ;
  int indexChi1     ;
  int indexChi2     ;
  int indexBlosumP  ;
  int indexPhiP     ;
  int indexPsiP     ;
  int indexChi1P    ;
  int indexChi2P    ;
  int indexHbondOM  ;
  int indexHbondHN  ;
  int indexHbondHA  ;
  int indexHbondO   ;
  int indexHbondHNP ;
  int indexOrder    ;
  
  enum ANNSet { ANNSET_20110211, ANNSET_20110225, ANNSET_20110324 };
 
  MODACCESSOR(termsUsed,TermsUsed,int);
  ANNSet annSet;
  void setAnnSet( ANNSet );
 
  GDB RC_Tab; // random coil chemical shift table
 
  // for each OMP thread
  // for each atom index
  // a list of DerivData contributions
  CDSList<DerivData> derivAccumList;
 
  SPARTA(const AtomSel& sel);
 
  bool addAtomType(const Atom&); // returns false if atomtype isn't supported
 
  void printSyntax();
 
  void init();
 
  SPARTA_PDB inPDB;
  const AtomSel& selection() const { return sel; }
 
  AtomSel chemShiftAtomSel;
 
  ACCESSOR(annInputDim,AnnInputDim,int); // dimension of ANN input vector
  ACCESSOR(annHiddenDim,AnnHiddenDim,int); // dimension of ANN hidden layer
  
  ACCESSOR(matchCount,MatchCount,int); //Max Match Count per query triplet
  ACCESSOR(excluded,Excluded,String); //Max Match Count per query triplet
  //  ACCESSOR(inName,InName,String); // input PDB coordinates file name
  ACCESSOR(tripFileName,TripFileName,String); // triplet filename
  ACCESSOR(weightFileName,WeightFileName,String); //weight table of score funct
  ACCESSOR(homoFileName,HomoFileName,String); // sequence homology table
  ACCESSOR(fitFileName,FitFileName,String); // table of "fitting parameters"
  ACCESSOR(refCSFileName,RefCSFileName,String);
  ACCESSOR(rcFileName,RCFileName,String); // random coil chemical shift table
  ACCESSOR(adjFileName,AdjFileName,String); // adjustment of RC CS table
  ACCESSOR(prevFileName,PrevFileName,String); // RC Adj for Prev Residue Type
  ACCESSOR(nextFileName,NextFileName,String); // RC Adj for Next Residue Type
  ACCESSOR(B62FileName,B62FileName,String);       // BLOSUM62 table 
  ACCESSOR(annLevel1Pattern,ANNLevel1Pattern,String); //pattern for ANN db files
  ACCESSOR(surfPattern,SurfPattern,String); 
 
  ACCESSOR(dynamicSSBonds,DynamicSSBonds,bool);
  ACCESSOR(verbose,Verbose,bool);
 
  //Get the list of useful shifts from a given residue. 
  //   get 2nd chemical shift and apply correction
  void getResInfo(CDSList<DerivData>*); 
        
  // Initiate an ANN prediction for a single protein
  void runANN_Prediction(); 
  // 
  run_A_ANN_Prediction(calcDerivs=False) - Run ANN prediction, and optionally
                                           compute gradient with respect to
                                           atomic coordinates.
        
  // get the prediction error from error surface
  float_type getANN_PredError(const float_type& phi, 
                              const float_type& psi, 
                              const char        aa,
                              const String&     aName);
        void init_PredErrorSurface();
        
        void Compile();
        void Compile(const String &name);
 
        // get random coil chemical shift for atom 'aName' of residue 'resName'
  float_type getRC(const char resName, const String& aName);
  float_type getRCadj(const char resName, const String& aName);
  float_type getPrevRCadj(const String& prev_rName, const String& aName);
  float_type getNextRCadj(const String& next_rName, const String& aName);
 
  float_type getPred2ndShift(const Atom&               atom,
                             const int                 resIndex,
                                   CDSList<DerivData>* derivData=0);            
 
  String summarizeInput();
  String summary();
  String comparisonOutput();
  String refCSOutput();
 
        
        char * ftoa( float_type n, char *buff, char f='g', int prec=6 );
        char * itoa( int n, char *buff, int base=10 );
 
  CDSVector<float_type> predictedShifts;
  CDSVector<float_type> randomCoilShifts;
  CDSVector<float_type> predictedSigma;
 
  float_type getShift(const Atom&);
 
  getDerivs(atom) - return the gradient information for the chemical shift
                    of the specified atom. The returned object is a list of
                    DerivDataElement, which has members
                       index - index into simulation, specifying an atom
                       val   - a vec3.Vec3 specifying gradient value.
 
 
  float_type getRCShift(const Atom&);
  float_type getSigma(const Atom&);
 
  void calcDerivsOn();
  // update all values in an instance. This is only required if
  // coordinates or some other parameter has changed.
  virtual void updateValues();  
};
 
namespace EnumNamespace {
  extern EnumNameMap ANNSet[];
};
 
 
 
GDB class:
 
  Read/Write access to text database files used by Talos+ and Sparta+.
 
  These files consist of XPLOR-like REMARK comments, a DATA section which
  contains key-value string pairs, and more general entries with field names 
  and type specified.
 
methods:
 
   data() - return the DATA entries as a map
 
   getVars() - return field names
 
   getEntry(name,
            value,
            index=1) - return the entry in the database for which the field 
                       specified by name matches value. There may be multiple 
                       such matches. The index argument specified which is
                       returned, by one-offset order in the database file.
 
   getValues(name) - given a field name, return all possible values for the
                     field. The order of the returned keys may differ from
                     that in the database.
 
   getEntries(name) - return all entries which match the specified field name.
 
   entry(index)     - return entry by offset 1 index
 
   numEntries()     - return the number of entries.
 
//FIX: complete this: CDS 2013/09/09
 
public:
 
        String GDBfileName;
 
        String FORMAT_str, VARS_str;
 
        GDB_Entry EMPTY;
 
 
        GDB();
        GDB(const String& fileName);
 
  
 
  StringList remarks() const { return REMARKS; }
 
        void loadGDB(const String &fileName);
        void saveGDB(const String &fileName);
        void saveGDB(ostream&);
 
        //add one VAR with given FORMAT
        void addVAR(const String &VAR_Name, const String &FORMAT_Name);
        //re-set one VAR with given FORMAT
        void setVAR(int index, const String &VAR_Name, const String &FORMAT_Name);
 
  //return field names
  CDSList<String> getVars() const { return VARS; }
 
        //set the DATA with 'DataVal'
        void setData(const String &DataName, const String &DataVal);
        //get the DATA value with 'DataName'
        String getData(const String &DataName);
 
  //return DATA field as a map
  CDSMap<String,String> data() const;
 
 
        const GDB_Entry& getEntry(int number);
        const GDB_Entry& getEntry(const String &VName, 
                                  const String &VVal, 
                                        int index=1);
  const GDB_Entry& getEntry(const String &VName1, 
                            const String &VVal1, 
                            const String &VName2, 
                            const String &VVal2, 
                                  int index);
 
  //given a field name, return a unique list of all possible values of that
  // field. The order of the keys in this list is random, and will not 
  // correspond to that in the database table.
  CDSList<String> getValues(const String &VName) const;
  
  // return all entries for which field VName is VVal
  CDSList<GDB_Entry> getEntries(const String &VName, 
                                const String &VVal);
  
        //re-set the 'index'-th data entry with new 'VarVal' for given 
        // 'VarName'
        void setEntry(int index, const String &VarName, const String &VarVal);
        //add one data entry to the end of current Entries
        void addEntry(const String &VarName, const String &VarVal);
 
 
        void addRemark(const String &str); // add one REMARK
 
        void presetClass(const String &ClassName); // pre-set the VARS and FORMAT
 
        bool checkFormat(const String& f); // check if f is a valid FORMAT
 
        bool isVarFloat(int index);
        bool isVarInt(int index);
        bool isVarString(int index);
 
        bool isVarFloat(const String &VarName);
        bool isVarInt(const String &VarName);
        bool isVarString(const String &VarName);
 
        void VARS_str_parser(const String &str);
        void FORMAT_str_parser(const String &str);
 
        void set_plaintext();
 
 
//      //Strings functions
//      static int contains( const String &str, const String &c );
//      static int contains( const String &str, const char &c );
        //
        
        static bool isDigit( const char &c );
        static bool isSpace( const char &c );
        
//      static StringList split( const char &sep, const String &str );
//      static StringList split( const String &sep, const String &str );
//      //splits the String str into Strings wherever a separator 'sep' occurs, and returns the list of those Strings.
//      static StringList split_WhiteSpace(const String &str);
        
        //returns a section of the String, each section is defined by char 'sep', numbers of start and end are the index number (begin with 0)
        static char* section( const String &str, const char &seq, char *buff, int start, int end= 0xffffffff );
 
        //Returns a String that has whitespace removed from the start and the end, 
        //and which has each sequence of internal whitespace replaced with a single space.
        static String simplifyWhiteSpace( const String &str );
};
 
 
 
 
 
# 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_DerivDataElement
DerivDataElement
GDB
SPARTA
SPARTA_ANN
SPARTA_Dihedral
SPARTA_HydrogenBond
SPARTA_PDB
SPARTA_ResidueEntry
SPARTA_RingData
rc_ptr_SPARTA

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

 
  Methods defined here:
__delitem__(self, *args, **kwargs) -> 'void'
__getitem__(self, *args) -> 'CDSList< DerivDataElement >'
__getslice__(self, *args, **kwargs) -> 'CDSList< DerivDataElement >'
__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_DerivDataElement(...)

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 DerivDataElement(builtins.object)
    DerivDataElement(*args)
 

 
  Methods defined here:
__init__(self, *args)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)

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

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

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

 
thisown

 
The membership flag
val

 

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

 
  Methods defined here:
FORMAT_str_parser(self, *args, **kwargs) -> 'void'
VARS_str_parser(self, *args, **kwargs) -> 'void'
__init__(self, *args)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)
addEntry(self, *args, **kwargs) -> 'void'
addRemark(self, *args, **kwargs) -> 'void'
addVAR(self, *args, **kwargs) -> 'void'
checkFormat(self, *args, **kwargs) -> 'bool'
data(self, *args, **kwargs) -> 'CDSMap< String,String >'
entry(self, *args, **kwargs) -> 'GDB_Entry const &'
getData(self, *args, **kwargs) -> 'String'
getEntries(self, *args, **kwargs) -> 'CDSList< GDB_Entry >'
getEntry(self, *args) -> 'GDB_Entry const &'
getValues(self, *args, **kwargs) -> 'CDSList< String >'
getVars(self, *args, **kwargs) -> 'CDSList< String >'
isVarFloat(self, *args) -> 'bool'
isVarInt(self, *args) -> 'bool'
isVarString(self, *args) -> 'bool'
loadGDB(self, *args, **kwargs) -> 'void'
numEntries(self, *args, **kwargs) -> 'int'
presetClass(self, *args, **kwargs) -> 'void'
remarks(self, *args, **kwargs) -> 'StringList'
saveGDB(self, *args) -> 'void'
setData(self, *args, **kwargs) -> 'void'
setEntry(self, *args, **kwargs) -> 'void'
setVAR(self, *args, **kwargs) -> 'void'
set_plaintext(self, *args, **kwargs) -> 'void'

Static methods defined here:
__swig_destroy__ = delete_GDB(...)
isDigit(*args, **kwargs) -> 'bool'
isSpace(*args, **kwargs) -> 'bool'
section(*args, **kwargs) -> 'char *'
simplifyWhiteSpace(*args, **kwargs) -> 'String'

Data descriptors defined here:
EMPTY

 
FORMAT_str

 
GDBfileName

 
VARS_str

 
__dict__

 
dictionary for instance variables (if defined)
__weakref__

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

 
The membership flag

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

 
  Methods defined here:
B62FileName(self, *args, **kwargs) -> 'String const'
Compile(self, *args) -> 'void'
__init__(self, *args, **kwargs)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)
addAtomType(self, *args, **kwargs) -> 'bool'
adjFileName(self, *args, **kwargs) -> 'String const'
annHiddenDim(self, *args, **kwargs) -> 'int const'
annInputDim(self, *args, **kwargs) -> 'int const'
annLevel1Pattern(self, *args, **kwargs) -> 'String const'
calcDerivsOn(self, *args, **kwargs) -> 'void'
comparisonOutput(self, *args, **kwargs) -> 'String'
dynamicSSBonds(self, *args, **kwargs) -> 'bool const'
excluded(self, *args, **kwargs) -> 'String const'
fitFileName(self, *args, **kwargs) -> 'String const'
ftoa(self, *args, **kwargs) -> 'char *'
getANN_PredError(self, *args, **kwargs) -> 'float_type'
getDerivs(self, *args, **kwargs) -> 'CDSList< DerivDataElement > const'
getNextRCadj(self, *args, **kwargs) -> 'float_type'
getPred2ndShift(self, *args, **kwargs) -> 'float_type'
getPrevRCadj(self, *args, **kwargs) -> 'float_type'
getRC(self, *args, **kwargs) -> 'float_type'
getRCShift(self, *args, **kwargs) -> 'float_type'
getRCadj(self, *args, **kwargs) -> 'float_type'
getResInfo(self, *args, **kwargs) -> 'void'
getShift(self, *args, **kwargs) -> 'float_type'
getSigma(self, *args, **kwargs) -> 'float_type'
homoFileName(self, *args, **kwargs) -> 'String const'
init(self, *args, **kwargs) -> 'void'
init_PredErrorSurface(self, *args, **kwargs) -> 'void'
itoa(self, *args, **kwargs) -> 'char *'
matchCount(self, *args, **kwargs) -> 'int const'
nextFileName(self, *args, **kwargs) -> 'String const'
prevFileName(self, *args, **kwargs) -> 'String const'
printSyntax(self, *args, **kwargs) -> 'void'
rcFileName(self, *args, **kwargs) -> 'String const'
refCSFileName(self, *args, **kwargs) -> 'String const'
refCSOutput(self, *args, **kwargs) -> 'String'
runANN_Prediction(self, *args, **kwargs) -> 'void'
run_A_ANN_Prediction(self, *args, **kwargs) -> 'void'
selection(self, *args, **kwargs) -> 'AtomSel const &'
setANNLevel1Pattern(self, *args, **kwargs) -> 'void'
setAdjFileName(self, *args, **kwargs) -> 'void'
setAnnHiddenDim(self, *args, **kwargs) -> 'void'
setAnnInputDim(self, *args, **kwargs) -> 'void'
setAnnSet(self, *args, **kwargs) -> 'void'
setB62FileName(self, *args, **kwargs) -> 'void'
setDynamicSSBonds(self, *args, **kwargs) -> 'void'
setExcluded(self, *args, **kwargs) -> 'void'
setFitFileName(self, *args, **kwargs) -> 'void'
setHomoFileName(self, *args, **kwargs) -> 'void'
setMatchCount(self, *args, **kwargs) -> 'void'
setNextFileName(self, *args, **kwargs) -> 'void'
setPrevFileName(self, *args, **kwargs) -> 'void'
setRCFileName(self, *args, **kwargs) -> 'void'
setRefCSFileName(self, *args, **kwargs) -> 'void'
setSurfPattern(self, *args, **kwargs) -> 'void'
setTermsUsed(self, *args, **kwargs) -> 'void'
setTripFileName(self, *args, **kwargs) -> 'void'
setVerbose(self, *args, **kwargs) -> 'void'
setWeightFileName(self, *args, **kwargs) -> 'void'
summarizeInput(self, *args, **kwargs) -> 'String'
summary(self, *args, **kwargs) -> 'String'
surfPattern(self, *args, **kwargs) -> 'String const'
termsUsed(self, *args, **kwargs) -> 'int const'
tripFileName(self, *args, **kwargs) -> 'String const'
updateValues(self, *args, **kwargs) -> 'void'
verbose(self, *args, **kwargs) -> 'bool const'
weightFileName(self, *args, **kwargs) -> 'String const'

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

Data descriptors defined here:
RC_Tab

 
__dict__

 
dictionary for instance variables (if defined)
__weakref__

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

 
chemShiftAtomSel

 
derivAccumList

 
inPDB

 
indexBlosum

 
indexBlosumM

 
indexBlosumP

 
indexChi1

 
indexChi1M

 
indexChi1P

 
indexChi2

 
indexChi2M

 
indexChi2P

 
indexHbondHA

 
indexHbondHN

 
indexHbondHNP

 
indexHbondO

 
indexHbondOM

 
indexOrder

 
indexPhi

 
indexPhiM

 
indexPhiP

 
indexPsi

 
indexPsiM

 
indexPsiP

 
predictedShifts

 
predictedSigma

 
randomCoilShifts

 
thisown

 
The membership flag

Data and other attributes defined here:
ANNSET_20110211 = 0
ANNSET_20110225 = 1
ANNSET_20110324 = 2
TERM_ALL = 65535
TERM_CHI1 = 2048
TERM_CHI1M = 1024
TERM_CHI1P = 4096
TERM_CHI2 = 16384
TERM_CHI2M = 8192
TERM_CHI2P = 32768
TERM_DIHEDRAL = 65520
TERM_EFIELD = 2
TERM_HBOND = 8
TERM_ORDER = 4
TERM_PHI = 32
TERM_PHIM = 16
TERM_PHIP = 64
TERM_PSI = 256
TERM_PSIM = 128
TERM_PSIP = 512
TERM_RING = 1

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

 
  Methods defined here:
__init__(self, *args)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)
calcLevel1(self, *args, **kwargs) -> 'void'
getConfidence(self, *args, **kwargs) -> 'ANN_Float'
getNumberMissCS(self, *args, **kwargs) -> 'int'
init(self, *args, **kwargs) -> 'void'
loadWeightBias3(self, *args, **kwargs) -> 'void'
loadWeights(self, *args, **kwargs) -> 'void'
runANN(self, *args, **kwargs) -> 'void'
runSpartaANN(self, *args, **kwargs) -> 'void'
set_input_code(self, *args, **kwargs) -> 'void'

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

Data descriptors defined here:
ANN_IN_MTX_LEVEL1

 
ANN_IN_MTX_LEVEL2

 
ANN_OUT_MTX_LEVEL1

 
ANN_OUT_MTX_LEVEL2

 
__dict__

 
dictionary for instance variables (if defined)
__weakref__

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

 
thisown

 
The membership flag

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

 
  Methods defined here:
__init__(self, *args)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)
atom0(self, *args, **kwargs) -> 'Atom const &'
atom1(self, *args, **kwargs) -> 'Atom const &'
atom2(self, *args, **kwargs) -> 'Atom const &'
atom3(self, *args, **kwargs) -> 'Atom const &'
derivs(self, *args, **kwargs) -> 'void'
value(self, *args, **kwargs) -> 'float_type'

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

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

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

 
switchSign

 
thisown

 
The membership flag
valid

 

Data and other attributes defined here:
MAXNUM = <Swig Object of type 'float_type *'>

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

 
  Methods defined here:
__init__(self, *args)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)
cosDHO(self, *args, **kwargs) -> 'float_type'
cosHOA(self, *args, **kwargs) -> 'float_type'
factor(self, *args, **kwargs) -> 'float_type'
valid(self, *args, **kwargs) -> 'bool'

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

Data descriptors defined here:
E

 
HB_prefactor

 
__dict__

 
dictionary for instance variables (if defined)
__weakref__

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

 
aB

 
asympDist

 
d

 
dB

 
dist

 
pdb

 
thisown

 
The membership flag

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

 
  Methods defined here:
__init__(self, *args, **kwargs)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)
calcHBonds(self, *args, **kwargs) -> 'void'
collect_HN_S2_and_EF(self, *args, **kwargs) -> 'void'
efieldOff(self, *args, **kwargs) -> 'float_type const'
efieldOn(self, *args, **kwargs) -> 'float_type const'
getBondAngle(self, *args) -> 'float_type'
getChi1(self, *args, **kwargs) -> 'float_type'
getChi2(self, *args, **kwargs) -> 'float_type'
getOmega(self, *args, **kwargs) -> 'float_type'
getOrbitalShifts(self, *args, **kwargs) -> 'CDSVector< float_type >'
getPhi(self, *args, **kwargs) -> 'float_type'
getPsi(self, *args, **kwargs) -> 'float_type'
hbCutoff(self, *args, **kwargs) -> 'float_type const'
hbondOff(self, *args, **kwargs) -> 'float_type const'
hbondOn(self, *args, **kwargs) -> 'float_type const'
initEField(self, *args, **kwargs) -> 'void'
initHBond(self, *args, **kwargs) -> 'void'
initOrbitalShift(self, *args, **kwargs) -> 'void'
isAcceptor(self, *args, **kwargs) -> 'Atom'
isDonor(self, *args, **kwargs) -> 'Atom'
isSSBonded(self, *args, **kwargs) -> 'bool'
loadPDB(self, *args, **kwargs) -> 'void'
moveTol(self, *args, **kwargs) -> 'float_type const'
ringOff(self, *args, **kwargs) -> 'float_type const'
ringOn(self, *args, **kwargs) -> 'float_type const'
setEfieldOff(self, *args, **kwargs) -> 'void'
setEfieldOn(self, *args, **kwargs) -> 'void'
setHBCutoff(self, *args, **kwargs) -> 'void'
setHbondOff(self, *args, **kwargs) -> 'void'
setHbondOn(self, *args, **kwargs) -> 'void'
setMoveTol(self, *args, **kwargs) -> 'void'
setRingOff(self, *args, **kwargs) -> 'void'
setRingOn(self, *args, **kwargs) -> 'void'

Static methods defined here:
__swig_destroy__ = delete_SPARTA_PDB(...)
getOneAAName(*args, **kwargs) -> 'char'
getThreeAAName(*args, **kwargs) -> 'String'
switchFunc(*args, **kwargs) -> 'float_type'
switchFuncDeriv(*args, **kwargs) -> 'float_type'

Data descriptors defined here:
ElectricField

 
HN_S2

 
Rings

 
SpherePointNo

 
SpherePoints

 
SurfPrec

 
__dict__

 
dictionary for instance variables (if defined)
__weakref__

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

 
charges

 
chi1

 
chi2

 
donorList

 
ef_savePos

 
hbList

 
hb_savePos

 
heavyAtoms

 
lsel

 
omega

 
phi

 
protonList

 
psi

 
rc_savePos

 
residueList

 
sel

 
thisown

 
The membership flag

Data and other attributes defined here:
CTERMINAL = 2
INTERNAL = 0
NTERMINAL = 1

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

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

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

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

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

 
resid

 
resnameOne

 
segid

 
terminal

 
thisown

 
The membership flag

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

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

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

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

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

 
atoms

 
resName

 
residueIndex

 
ringFact

 
thisown

 
The membership flag

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

 
  Methods defined here:
B62FileName(self, *args, **kwargs) -> 'String const'
Compile(self, *args) -> 'void'
__deref__(self, *args, **kwargs) -> 'SPARTA *'
__init__(self, *args)
Initialize self.  See help(type(self)) for accurate signature.
__ref__(self, *args, **kwargs) -> 'SPARTA &'
__repr__ = _swig_repr(self)
addAtomType(self, *args, **kwargs) -> 'bool'
adjFileName(self, *args, **kwargs) -> 'String const'
annHiddenDim(self, *args, **kwargs) -> 'int const'
annInputDim(self, *args, **kwargs) -> 'int const'
annLevel1Pattern(self, *args, **kwargs) -> 'String const'
calcDerivsOn(self, *args, **kwargs) -> 'void'
comparisonOutput(self, *args, **kwargs) -> 'String'
count(self, *args, **kwargs) -> 'int'
decr(self, *args, **kwargs) -> 'void'
dynamicSSBonds(self, *args, **kwargs) -> 'bool const'
excluded(self, *args, **kwargs) -> 'String const'
fitFileName(self, *args, **kwargs) -> 'String const'
forceDelete(self, *args, **kwargs) -> 'void'
ftoa(self, *args, **kwargs) -> 'char *'
getANN_PredError(self, *args, **kwargs) -> 'float_type'
getDerivs(self, *args, **kwargs) -> 'CDSList< DerivDataElement > const'
getNextRCadj(self, *args, **kwargs) -> 'float_type'
getPred2ndShift(self, *args, **kwargs) -> 'float_type'
getPrevRCadj(self, *args, **kwargs) -> 'float_type'
getRC(self, *args, **kwargs) -> 'float_type'
getRCShift(self, *args, **kwargs) -> 'float_type'
getRCadj(self, *args, **kwargs) -> 'float_type'
getResInfo(self, *args, **kwargs) -> 'void'
getShift(self, *args, **kwargs) -> 'float_type'
getSigma(self, *args, **kwargs) -> 'float_type'
homoFileName(self, *args, **kwargs) -> 'String const'
incr(self, *args, **kwargs) -> 'void'
init(self, *args, **kwargs) -> 'void'
init_PredErrorSurface(self, *args, **kwargs) -> 'void'
itoa(self, *args, **kwargs) -> 'char *'
matchCount(self, *args, **kwargs) -> 'int const'
nextFileName(self, *args, **kwargs) -> 'String const'
prevFileName(self, *args, **kwargs) -> 'String const'
printSyntax(self, *args, **kwargs) -> 'void'
ptr(self, *args, **kwargs) -> 'SPARTA *'
rcFileName(self, *args, **kwargs) -> 'String const'
refCSFileName(self, *args, **kwargs) -> 'String const'
refCSOutput(self, *args, **kwargs) -> 'String'
release(self, *args, **kwargs) -> 'SPARTA *'
reset(self, *args, **kwargs) -> 'void'
runANN_Prediction(self, *args, **kwargs) -> 'void'
run_A_ANN_Prediction(self, *args, **kwargs) -> 'void'
selection(self, *args, **kwargs) -> 'AtomSel const &'
setANNLevel1Pattern(self, *args, **kwargs) -> 'void'
setAdjFileName(self, *args, **kwargs) -> 'void'
setAnnHiddenDim(self, *args, **kwargs) -> 'void'
setAnnInputDim(self, *args, **kwargs) -> 'void'
setAnnSet(self, *args, **kwargs) -> 'void'
setB62FileName(self, *args, **kwargs) -> 'void'
setDynamicSSBonds(self, *args, **kwargs) -> 'void'
setExcluded(self, *args, **kwargs) -> 'void'
setFitFileName(self, *args, **kwargs) -> 'void'
setHomoFileName(self, *args, **kwargs) -> 'void'
setMatchCount(self, *args, **kwargs) -> 'void'
setNextFileName(self, *args, **kwargs) -> 'void'
setPrevFileName(self, *args, **kwargs) -> 'void'
setRCFileName(self, *args, **kwargs) -> 'void'
setRefCSFileName(self, *args, **kwargs) -> 'void'
setSurfPattern(self, *args, **kwargs) -> 'void'
setTermsUsed(self, *args, **kwargs) -> 'void'
setTripFileName(self, *args, **kwargs) -> 'void'
setVerbose(self, *args, **kwargs) -> 'void'
setWeightFileName(self, *args, **kwargs) -> 'void'
summarizeInput(self, *args, **kwargs) -> 'String'
summary(self, *args, **kwargs) -> 'String'
surfPattern(self, *args, **kwargs) -> 'String const'
termsUsed(self, *args, **kwargs) -> 'int const'
tripFileName(self, *args, **kwargs) -> 'String const'
updateValues(self, *args, **kwargs) -> 'void'
verbose(self, *args, **kwargs) -> 'bool const'
weightFileName(self, *args, **kwargs) -> 'String const'

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

Data descriptors defined here:
RC_Tab

 
__dict__

 
dictionary for instance variables (if defined)
__weakref__

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

 
chemShiftAtomSel

 
derivAccumList

 
inPDB

 
indexBlosum

 
indexBlosumM

 
indexBlosumP

 
indexChi1

 
indexChi1M

 
indexChi1P

 
indexChi2

 
indexChi2M

 
indexChi2P

 
indexHbondHA

 
indexHbondHN

 
indexHbondHNP

 
indexHbondO

 
indexHbondOM

 
indexOrder

 
indexPhi

 
indexPhiM

 
indexPhiP

 
indexPsi

 
indexPsiM

 
indexPsiP

 
predictedShifts

 
predictedSigma

 
randomCoilShifts

 
thisown

 
The membership flag

Data and other attributes defined here:
TERM_ALL = 65535
TERM_CHI1 = 2048
TERM_CHI1M = 1024
TERM_CHI1P = 4096
TERM_CHI2 = 16384
TERM_CHI2M = 8192
TERM_CHI2P = 32768
TERM_DIHEDRAL = 65520
TERM_EFIELD = 2
TERM_HBOND = 8
TERM_ORDER = 4
TERM_PHI = 32
TERM_PHIM = 16
TERM_PHIP = 64
TERM_PSI = 256
TERM_PSIM = 128
TERM_PSIP = 512
TERM_RING = 1

 
s = class SPARTA(builtins.object)
    s(*args, **kwargs)
 

 
  Methods defined here:
B62FileName(self, *args, **kwargs) -> 'String const'
Compile(self, *args) -> 'void'
__init__(self, *args, **kwargs)
Initialize self.  See help(type(self)) for accurate signature.
__repr__ = _swig_repr(self)
addAtomType(self, *args, **kwargs) -> 'bool'
adjFileName(self, *args, **kwargs) -> 'String const'
annHiddenDim(self, *args, **kwargs) -> 'int const'
annInputDim(self, *args, **kwargs) -> 'int const'
annLevel1Pattern(self, *args, **kwargs) -> 'String const'
calcDerivsOn(self, *args, **kwargs) -> 'void'
comparisonOutput(self, *args, **kwargs) -> 'String'
dynamicSSBonds(self, *args, **kwargs) -> 'bool const'
excluded(self, *args, **kwargs) -> 'String const'
fitFileName(self, *args, **kwargs) -> 'String const'
ftoa(self, *args, **kwargs) -> 'char *'
getANN_PredError(self, *args, **kwargs) -> 'float_type'
getDerivs(self, *args, **kwargs) -> 'CDSList< DerivDataElement > const'
getNextRCadj(self, *args, **kwargs) -> 'float_type'
getPred2ndShift(self, *args, **kwargs) -> 'float_type'
getPrevRCadj(self, *args, **kwargs) -> 'float_type'
getRC(self, *args, **kwargs) -> 'float_type'
getRCShift(self, *args, **kwargs) -> 'float_type'
getRCadj(self, *args, **kwargs) -> 'float_type'
getResInfo(self, *args, **kwargs) -> 'void'
getShift(self, *args, **kwargs) -> 'float_type'
getSigma(self, *args, **kwargs) -> 'float_type'
homoFileName(self, *args, **kwargs) -> 'String const'
init(self, *args, **kwargs) -> 'void'
init_PredErrorSurface(self, *args, **kwargs) -> 'void'
itoa(self, *args, **kwargs) -> 'char *'
matchCount(self, *args, **kwargs) -> 'int const'
nextFileName(self, *args, **kwargs) -> 'String const'
prevFileName(self, *args, **kwargs) -> 'String const'
printSyntax(self, *args, **kwargs) -> 'void'
rcFileName(self, *args, **kwargs) -> 'String const'
refCSFileName(self, *args, **kwargs) -> 'String const'
refCSOutput(self, *args, **kwargs) -> 'String'
runANN_Prediction(self, *args, **kwargs) -> 'void'
run_A_ANN_Prediction(self, *args, **kwargs) -> 'void'
selection(self, *args, **kwargs) -> 'AtomSel const &'
setANNLevel1Pattern(self, *args, **kwargs) -> 'void'
setAdjFileName(self, *args, **kwargs) -> 'void'
setAnnHiddenDim(self, *args, **kwargs) -> 'void'
setAnnInputDim(self, *args, **kwargs) -> 'void'
setAnnSet(self, *args, **kwargs) -> 'void'
setB62FileName(self, *args, **kwargs) -> 'void'
setDynamicSSBonds(self, *args, **kwargs) -> 'void'
setExcluded(self, *args, **kwargs) -> 'void'
setFitFileName(self, *args, **kwargs) -> 'void'
setHomoFileName(self, *args, **kwargs) -> 'void'
setMatchCount(self, *args, **kwargs) -> 'void'
setNextFileName(self, *args, **kwargs) -> 'void'
setPrevFileName(self, *args, **kwargs) -> 'void'
setRCFileName(self, *args, **kwargs) -> 'void'
setRefCSFileName(self, *args, **kwargs) -> 'void'
setSurfPattern(self, *args, **kwargs) -> 'void'
setTermsUsed(self, *args, **kwargs) -> 'void'
setTripFileName(self, *args, **kwargs) -> 'void'
setVerbose(self, *args, **kwargs) -> 'void'
setWeightFileName(self, *args, **kwargs) -> 'void'
summarizeInput(self, *args, **kwargs) -> 'String'
summary(self, *args, **kwargs) -> 'String'
surfPattern(self, *args, **kwargs) -> 'String const'
termsUsed(self, *args, **kwargs) -> 'int const'
tripFileName(self, *args, **kwargs) -> 'String const'
updateValues(self, *args, **kwargs) -> 'void'
verbose(self, *args, **kwargs) -> 'bool const'
weightFileName(self, *args, **kwargs) -> 'String const'

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

Data descriptors defined here:
RC_Tab

 
__dict__

 
dictionary for instance variables (if defined)
__weakref__

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

 
chemShiftAtomSel

 
derivAccumList

 
inPDB

 
indexBlosum

 
indexBlosumM

 
indexBlosumP

 
indexChi1

 
indexChi1M

 
indexChi1P

 
indexChi2

 
indexChi2M

 
indexChi2P

 
indexHbondHA

 
indexHbondHN

 
indexHbondHNP

 
indexHbondO

 
indexHbondOM

 
indexOrder

 
indexPhi

 
indexPhiM

 
indexPhiP

 
indexPsi

 
indexPsiM

 
indexPsiP

 
predictedShifts

 
predictedSigma

 
randomCoilShifts

 
thisown

 
The membership flag

Data and other attributes defined here:
ANNSET_20110211 = 0
ANNSET_20110225 = 1
ANNSET_20110324 = 2
TERM_ALL = 65535
TERM_CHI1 = 2048
TERM_CHI1M = 1024
TERM_CHI1P = 4096
TERM_CHI2 = 16384
TERM_CHI2M = 8192
TERM_CHI2P = 32768
TERM_DIHEDRAL = 65520
TERM_EFIELD = 2
TERM_HBOND = 8
TERM_ORDER = 4
TERM_PHI = 32
TERM_PHIM = 16
TERM_PHIP = 64
TERM_PSI = 256
TERM_PSIM = 128
TERM_PSIP = 512
TERM_RING = 1

 
Functions
       
GDB_isDigit(*args, **kwargs) -> 'bool'
GDB_isSpace(*args, **kwargs) -> 'bool'
GDB_section(*args, **kwargs) -> 'char *'
GDB_simplifyWhiteSpace(*args, **kwargs) -> 'String'
SPARTA_PDB_getOneAAName(*args, **kwargs) -> 'char'
SPARTA_PDB_getThreeAAName(*args, **kwargs) -> 'String'
SPARTA_PDB_switchFunc(*args, **kwargs) -> 'float_type'
SPARTA_PDB_switchFuncDeriv(*args, **kwargs) -> 'float_type'
cdsMapConvertToInt(*args, **kwargs) -> 'int'
pyXplorHelp(*args) -> 'String'

 
Data
        MAX_NUM = 9999.0
cvar = <Swig global variables>
name = 'ORDER'