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:

• sele1 (EntityView) –

• sele2 (EntityView) –

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:

• sele1 (EntityView) –

• sele2 (EntityView) –

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:

• sele1 (EntityView) –

• sele2 (EntityView) –

Returns:

float