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

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. 
 
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
redge
rface
rvertex
tedge
tface
tvertex

 
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)
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(...)

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

 
class redge(builtins.object)
    redge(*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_redge(...)

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

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

 
end_pts

 
int_pts

 
thisown

 
The membership flag

 
class rface(builtins.object)
    rface(*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_rface(...)

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

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

 
id

 
num_verts

 
thisown

 
The membership flag
vert

 

 
class rvertex(builtins.object)
    rvertex(*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_rvertex(...)

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

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

 
in_edges

 
sq_dist

 
thisown

 
The membership flag
v

 

 
class tedge(builtins.object)
    tedge(*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_tedge(...)

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

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

 
deleted

 
ednum

 
endpts

 
next

 
prev

 
thisown

 
The membership flag

 
class tface(builtins.object)
    tface(*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_tface(...)

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

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

 
fnum

 
next

 
p

 
prev

 
sq_dist

 
thisown

 
The membership flag
vert

 
visible

 

 
class tvertex(builtins.object)
    tvertex(*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_tvertex(...)

Data descriptors defined here:
__dict__

 
dictionary for instance variables (if defined)
__weakref__

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

 
data_ptr

 
duplicate

 
mark

 
next

 
prev

 
thisown

 
The membership flag
v

 
vnum

 

 
Functions
       
pyXplorHelp(*args) -> 'String'

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