produce protein surface tesselation
 
Based on the SURF program by 
A. Varshney et al. IEEE Comput. Graphics Appl. 1994, 14, 19-25.
 
constructor: Surf(selection)
 
  selection is an atomSel.AtomSel object specifying the atoms to include
  when tesselating protein surface.
 
Accessors
 
  maxTessLen -  parameter controlling the number of triangles used in
                tessellation, the smaller the number, the more triangles, and
                thus, hogher fidelity. [6 Angstroms]
               
  probeRadius - radius of sphere rolled over the molecular surface. [1.4
                Angstroms] 
 
Methods
 
  update_radii
  (const CDSVector<float_type>& radii) - updates constants which 
                                         are as van der Waals radii of atoms.
 
  update_atoms()                       - updates atom positions from those 
                                         currently in the Simulation.
 
  updateRadii(vals)                    - set the atomic radii. The argument
                                         vals must be of size len(selection).
 
  tessellate()                         - tessellates protein surface. The
                                         method updateRadii must be called
                                         first.
 
  read_in
  (const char* filename, const double& Shell_radius) 
  - service routine which reads atoms from a PDB file and adds a constant 
    shell for all atoms' radii.
 
  atomPoints - a list of vertices for each atom in selection.
               each element has the following members:
                 grid  - a list of 3 times the number of triangles of
                         coord and normal, each of which is a vec3.Vec3
                         specifying a vertex position and normal vector
                 atom  - identifying atom.Atom
 
  surfOutput() - return a string with surface triangle information. The 
                 output format is:
                   index
                   V1x V1y V1z N1x N1y N1z
                   V2x V2y V2z N2x N2y N2z
                   V3x V3y V3z N3x N3y N3z
                 where index is the atom index and Via and Nia specify
                 the three triangle vertices and normals in the three
                 Cartesian dimensions. For each triangle of each atom,
                 the sequence above is repeated.
 
  asSTLstring(name='') - return the Surf object as a String in ASCII STL
                         format, used in 3D printing, and readable by VMD.
                         The optional name argument is an label.
 
The following static function:
  stlToString(triList, name="") - given a list of triangles, return an ASCII
                                  STL String. Currently, the triList cannot be
                                  generated in the Python interface.
 
SurfDiff:
 
Internal object which converts coordinates of tessellated surface into
a diffusion tensor and performs related operations.  
 
Used by diffPot.DiffPot and relaxRatioPot.RelaxRatioPot, and 
surfTessellation.SurfTessellation classes via methods associated
with surfTessellation class.
 
Based on ELM programm by Y. Ryabov et al. JACS 2006, 128 (48), pp 15432-15444.
 
constructor: No constructor available 
 
methods
 
  calcSA(sel) - return the solvent-accessible surface area of the atoms in
                sel, an atomSel.AtomSel, which defaults to all atoms.
                tessellate() must be called first.
 
  cvrm_W() - calculates weighted covariance matrix using partial linear and 
             bilinear sums ( Sum, Norm, and Sum2 ) calculates norm factors Norm_F.
 
  eig_calc( CovMat *c_vrm ) - calculates Eigen values and Eigen vectors for given 
                              covariance matrix CovMat *c_vrm.
 
  make_diffusion_tensor(eigS *eig, double TmP) - calculates diffusion tensor for 
      given set of Eigen values and Eigen vectors eigS *eig 
      and given value of temperature.
 
  ellipt_int_simp(const double& a_x_2, 
                          const double& a_y_2, 
                          const double& a_z_2, 
                          const double& dc ) - calculates elliptical integrals 
                                            using Simpson's quadratures. 
 
  calc_Tmp(double TmP) - calculates the factor taking into account the 
      temperature dependency of water viscosity for protein thumbing in water
      approximation from: 
      Weast, R.C. Handbook of Chemistry and Physics, 59th ed. 
      CRC press West Palm Beach, FL 1978
 
      dT=TmP-273;
 
      eta_t=(1e-3)*(1.7753-0.0565*(dT)+1.0751e-3*(dT*dT)-9.2222e-6*(dT*dT*dT));
 
  calc_sum(int a_, int b_, int k, 
           double a_m, double b_m ) - calculates a part of covariance matrix sum 
                                     which corresponds to a particular atom # k.
 
  calc_deriv_Per_x_Per_y_Per_z_on_Ax_Ay_Az(const double& Ax, 
                                         const double& Ay, 
                                         const double& Az, 
                                         const double& P, 
                                         const double& Q, 
                                         const double& R ) - 
      calculates partial derivatives of Per_x Per_y and Per_z with respect to 
      the values of ellipsoid semi-axes squares Ax, Ay, and Az.
 
  calc_cov_dif(int C, int k, int A, int B, 
                             CovMat *c_vrm ) - calculates particular derivative with 
      respect to the C coordinate of atom # k for the components of covariance matrix 
      with indexes A and B.
 
 
  calculate_chi2( double TmpF, Mat3 target ) - calculates Chi2 for the energy of
                                               diffPot potential.
 
  calculate_energy_and_derivatives(double TmpF, 
                                       Mat3 target, 
                                       double sc_l, 
                                       DerivList& derivs, 
                                       const AtomSel& sel,
                                       double range_Tmp,
                                       double current_temperature,
                                       Atom Xa, Atom Ya, Atom Oa) - Calculates energy 
      and derivatives for diffPot potential.
 
  current_diffusion_tensor( double TmpF ) - calculates diffusion tensor for given TmpF.
 
  calculate_chi2_eigen_values( double TmpF, Mat3 target ) - calculates minimal Chi2 
      based on differences of eigen values only.
 
  dTmpF_dT( double TmP ) - calculates the partial difference of the temperature factor 
                           with respect to the temperature value
 
 
 
 
# 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 AtomPoints Big_Point CDSList_AtomPoints CDSList_Gp_Atom CDSList_SurfacePoint CovMat CovMat_Gradients Gp_Atom Surf SurfDiff SurfacePoint V_ector VertexType eigS   class AtomPoints(builtins.object)     AtomPoints(*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_AtomPoints(...) Data descriptors defined here: Norm   Sum   Sum2   __dict__   dictionary for instance variables (if defined) __weakref__   list of weak references to the object (if defined) atom   grid   thisown   The membership flag   class Big_Point(builtins.object)     Big_Point(*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_Big_Point(...) Data descriptors defined here: __dict__   dictionary for instance variables (if defined) __weakref__   list of weak references to the object (if defined) tes_dir   thisown   The membership flag vt     class CDSList_AtomPoints(builtins.object)     CDSList_AtomPoints(*args)       Methods defined here: __delitem__(self, *args, **kwargs) -> 'void' __getitem__(self, *args) -> 'CDSList< AtomPoints >' __getslice__(self, *args, **kwargs) -> 'CDSList< AtomPoints >' __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_AtomPoints(...) 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_Gp_Atom(builtins.object)     CDSList_Gp_Atom(*args)       Methods defined here: __delitem__(self, *args, **kwargs) -> 'void' __getitem__(self, *args) -> 'CDSList< Gp_Atom >' __getslice__(self, *args, **kwargs) -> 'CDSList< Gp_Atom >' __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_Gp_Atom(...) 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_SurfacePoint(builtins.object)     CDSList_SurfacePoint(*args)       Methods defined here: __delitem__(self, *args, **kwargs) -> 'void' __getitem__(self, *args) -> 'CDSList< SurfacePoint >' __getslice__(self, *args, **kwargs) -> 'CDSList< SurfacePoint >' __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_SurfacePoint(...) 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 CovMat(builtins.object)     CovMat(*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_CovMat(...) Data descriptors defined here: Cm   Norm_all   Sum_all   XX   XY   XZ   YY   YZ   ZZ   __dict__   dictionary for instance variables (if defined) __weakref__   list of weak references to the object (if defined) thisown   The membership flag   class CovMat_Gradients(builtins.object)     CovMat_Gradients(*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_CovMat_Gradients(...) Data descriptors defined here: __dict__   dictionary for instance variables (if defined) __weakref__   list of weak references to the object (if defined) dX_Diff   dX_Ecvrm   dX_mtrx   dX_mtrxV   dY_Diff   dY_Ecvrm   dY_mtrx   dY_mtrxV   dZ_Diff   dZ_Ecvrm   dZ_mtrx   dZ_mtrxV   thisown   The membership flag   class Gp_Atom(builtins.object)     Gp_Atom(*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_Gp_Atom(...) Data descriptors defined here: NmBr   __dict__   dictionary for instance variables (if defined) __weakref__   list of weak references to the object (if defined) boundary   center   num_cons   radius   tes_origin   thisown   The membership flag type     class Surf(builtins.object)     Surf(*args, **kwargs)       Methods defined here: __init__(self, *args, **kwargs) Initialize self.  See help(type(self)) for accurate signature. __repr__ = _swig_repr(self) asSTLstring(self, *args, **kwargs) -> 'String' atomSel(self, *args, **kwargs) -> 'AtomSel const &' calcSA(self, *args, **kwargs) -> 'float_type' calc_sums_out_dat(self, *args, **kwargs) -> 'void' check_duplicates(self, *args, **kwargs) -> 'void' compute_bounding_tetra(self, *args, **kwargs) -> 'void' compute_components(self, *args, **kwargs) -> 'bool' compute_extents(self, *args, **kwargs) -> 'void' dump_out_dat(self, *args, **kwargs) -> 'void' init_and_compute(self, *args, **kwargs) -> 'void' int_out_dat(self, *args, **kwargs) -> 'void' mark_duplicates(self, *args, **kwargs) -> 'void' maxTessLen(self, *args, **kwargs) -> 'float_type const' probeRadius(self, *args, **kwargs) -> 'float_type const' pyXplorHelp(self, *args, **kwargs) -> 'String' remove_duplicates(self, *args, **kwargs) -> 'void' setMaxTessLen(self, *args, **kwargs) -> 'void' setProbeRadius(self, *args, **kwargs) -> 'void' surfOutput(self, *args, **kwargs) -> 'String' tessellate(self, *args, **kwargs) -> 'void' updateAtomPos(self, *args, **kwargs) -> 'void' updateGridDelta(self, *args, **kwargs) -> 'void' update_radii(self, *args, **kwargs) -> 'void' Static methods defined here: __swig_destroy__ = delete_Surf(...) stlToString(*args, **kwargs) -> 'String' Readonly properties defined here: atomSel_   Data descriptors defined here: Bounding_Tetra   Checks_On   Extents   Max_Radius   Num_Voxels   Num_p   Num_polys   Voxel_Side   __dict__   dictionary for instance variables (if defined) __weakref__   list of weak references to the object (if defined) atomPoints   atoms   max_cons   thisown   The membership flag tot_cons     class SurfDiff(builtins.object)     SurfDiff(*args, **kwargs)       Methods defined here: __init__(self, *args, **kwargs) Initialize self.  See help(type(self)) for accurate signature. __repr__ = _swig_repr(self) bra_Mat_ket(self, *args, **kwargs) -> 'double' calc_Tmp(self, *args, **kwargs) -> 'double' calc_cov_dif(self, *args, **kwargs) -> 'double' calc_deriv_Per_x_Per_y_Per_z_on_Ax_Ay_Az(self, *args, **kwargs) -> 'Mat3' calc_sum(self, *args, **kwargs) -> 'double' calculate_chi2(self, *args, **kwargs) -> 'double' calculate_chi2_eigen_values(self, *args, **kwargs) -> 'double' calculate_derivatives(self, *args, **kwargs) -> 'void' calculate_energy_and_derivatives(self, *args, **kwargs) -> 'double' current_diffusion_tensor(self, *args, **kwargs) -> 'Mat3' cvrm_W(self, *args, **kwargs) -> 'CovMat *' dTmpF_dT(self, *args, **kwargs) -> 'double' eig_calc(self, *args, **kwargs) -> 'eigS *' element_prod(self, *args, **kwargs) -> 'Mat3' ellipt_int_simp(self, *args, **kwargs) -> 'double' make_diffusion_tensor(self, *args, **kwargs) -> 'Mat3' num_calc_deriv_P_Q_R_on_Ax_Ay_Az(self, *args, **kwargs) -> 'void' num_calc_deriv_Per_XYZ_on_Ax_Ay_Az(self, *args, **kwargs) -> 'void' pyXplorHelp(self, *args, **kwargs) -> 'String' Static methods defined here: __swig_destroy__ = delete_SurfDiff(...) 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 SurfacePoint(builtins.object)     SurfacePoint(*args, **kwargs)       Methods defined here: __init__(self, *args, **kwargs) Initialize self.  See help(type(self)) for accurate signature. __repr__ = _swig_repr(self) dCoord(self, *args, **kwargs) -> 'Vec3' Static methods defined here: __swig_destroy__ = delete_SurfacePoint(...) Data descriptors defined here: __dict__   dictionary for instance variables (if defined) __weakref__   list of weak references to the object (if defined) atom   coord   delta   normal   thisown   The membership flag triType   weight     class V_ector(builtins.object)     V_ector(*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_V_ector(...) Data descriptors defined here: __dict__   dictionary for instance variables (if defined) __weakref__   list of weak references to the object (if defined) atom_id   coeff   thisown   The membership flag   class VertexType(builtins.object)     VertexType(*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_VertexType(...) Data descriptors defined here: Coord   Normal   __dict__   dictionary for instance variables (if defined) __weakref__   list of weak references to the object (if defined) thisown   The membership flag   class eigS(builtins.object)     eigS(*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_eigS(...) Data descriptors defined here: Ex   Ey   Ez   Vx   Vy   Vz   __dict__   dictionary for instance variables (if defined) __weakref__   list of weak references to the object (if defined) thisown   The membership flag

Functions
		Surf_stlToString(*args, **kwargs) -> 'String' pyXplorHelp(*args) -> 'String'

Data
		TRI_CONCAVE = 1 TRI_CONVEX = 0 TRI_DUAL = 3 TRI_TORUS = 2