structure_analysis – Functions to Analyze Structures

Some functions for analyzing structures

Author: Niklaus Johner (Niklaus.Johner@unibas.ch)

CalculateBestFitLine(sele1)

This function calculates the best fit line to the atoms in sele1.

Parameters:

sele1 (EntityView) –

Returns:

Line3

CalculateBestFitPlane(sele1)

This function calculates the best fit plane to the atoms in sele1.

Parameters:

sele1 (EntityView) –

Returns:

Plane

CalculateDistanceDifferenceMatrix(sele1, sele2)

This function calculates the pairwise distance differences between two selections (EntityView). The two selections should have the same number of atoms It returns an NxN DistanceDifferenceMatrix M (where N is the number of atoms in sele1) where M[i,j]=||(sele2.atoms[i].pos-sele2.atoms[j].pos)||-||(sele1.atoms[i].pos-sele1.atoms[j].pos)||

Parameters:
Returns:

NxN numpy matrix

CalculateHelixAxis(sele1)

This function calculates the best fit cylinder to the CA atoms in sele1, and returns its axis. Residues should be ordered correctly in sele1.

Parameters:

sele1 (EntityView) –

Returns:

Line3

GetAlphaHelixContent(sele1)

This function calculates the content of alpha helix in a view. All residues in the view have to ordered and adjacent (no gaps allowed)

Parameters:

sele1 (EntityView) –

Returns:

float

GetDistanceBetwCenterOfMass(sele1, sele2)

This function calculates the distance between the centers of mass of sele1 and sele2, two selections from the same Entity.

Parameters:
Returns:

float

GetFrameFromEntity(eh)

This function returns a CoordFrame from an EntityHandle

Parameters:

eh (EntityHandle) –

Returns:

ost.mol.CoordFrame

GetMinDistBetwCenterOfMassAndView(sele1, sele2)

This function calculates the minimal distance between sele2 and the center of mass of sele1, two selections from the same Entity.

Parameters:
  • sele1 (EntityView) – The selection from which the center of mass is taken

  • sele2 (EntityView) –

Returns:

distance (float)

GetMinDistanceBetweenViews(sele1, sele2)

This function calculates the minimal distance between sele1 and sele2, two selections from the same Entity.

Parameters:
Returns:

float

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Contents

Documentation is available for the following OpenStructure versions:

(Currently viewing dev) / 2.8 / 2.7 / 2.6 / 2.5 / 2.4 / 2.3.1 / 2.3 / 2.2 / 2.1 / 2.0 / 1.9 / 1.8 / 1.7.1 / 1.7 / 1.6 / 1.5 / 1.4 / 1.3 / 1.2 / 1.11 / 1.10 / 1.1

This documentation is still under heavy development!
If something is missing or if you need the C++ API description in doxygen style, check our old documentation for further information.