Python: module surfD

surfD

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