ost::mol::alg::structure_analysis Namespace Reference
Detailed Description
Some functions for analyzing structures
Author: Niklaus Johner (Niklaus.Johner@unibas.ch)
Function Documentation
def ost::mol::alg::structure_analysis::CalculateBestFitLine |
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sele1 |
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This function calculates the best fit line to the atoms in **sele1**.
:param sele1:
:type sele1: :class:`~ost.mol.EntityView`
:return: :class:`~ost.geom.Line3`
Definition at line 105 of file structure_analysis.py.
def ost::mol::alg::structure_analysis::CalculateBestFitPlane |
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sele1 |
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This function calculates the best fit plane to the atoms in **sele1**.
:param sele1:
:type sele1: :class:`~ost.mol.EntityView`
:return: :class:`~ost.geom.Plane`
Definition at line 121 of file structure_analysis.py.
def ost::mol::alg::structure_analysis::CalculateDistanceDifferenceMatrix |
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sele1, |
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sele2 | |
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This function calculates the pairwise distance differences between two selections (\ :class:`~ost.mol.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)||
:param sele1:
:param sele2:
:type sele1: :class:`~ost.mol.EntityView`
:type sele2: :class:`~ost.mol.EntityView`
:return: NxN numpy matrix
Definition at line 156 of file structure_analysis.py.
def ost::mol::alg::structure_analysis::CalculateHelixAxis |
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sele1 |
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This function calculates the best fit cylinder to the CA atoms in **sele1**,
and returns its axis. Residues should be ordered correctly
in **sele1**.
:param sele1:
:type sele1: :class:`~ost.mol.EntityView`
:return: :class:`~ost.geom.Line3`
Definition at line 137 of file structure_analysis.py.
def ost::mol::alg::structure_analysis::GetAlphaHelixContent |
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sele1 |
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This function calculates the content of alpha helix in a view.
All residues in the view have to ordered and adjacent (no gaps allowed)
:param sele1:
:type sele1: :class:`~ost.mol.EntityView`
:return: :class:`float`
Definition at line 87 of file structure_analysis.py.
def ost::mol::alg::structure_analysis::GetDistanceBetwCenterOfMass |
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sele1, |
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sele2 | |
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This function calculates the distance between the centers of mass
of **sele1** and **sele2**, two selections from the same Entity.
:param sele1:
:param sele2:
:type sele1: :class:`~ost.mol.EntityView`
:type sele2: :class:`~ost.mol.EntityView`
:return: :class:`float`
Definition at line 20 of file structure_analysis.py.
def ost::mol::alg::structure_analysis::GetFrameFromEntity |
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eh |
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This function returns a CoordFrame from an EntityHandle
:param eh:
:type eh: :class:`~ost.mol.EntityHandle`
:return: :class:`ost.mol.CoordFrame`
Definition at line 9 of file structure_analysis.py.
def ost::mol::alg::structure_analysis::GetMinDistanceBetweenViews |
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sele1, |
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sele2 | |
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This function calculates the minimal distance between
**sele1** and **sele2**, two selections from the same Entity.
:param sele1:
:param sele2:
:type sele1: :class:`~ost.mol.EntityView`
:type sele2: :class:`~ost.mol.EntityView`
:return: :class:`float`
Definition at line 42 of file structure_analysis.py.
def ost::mol::alg::structure_analysis::GetMinDistBetwCenterOfMassAndView |
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sele1, |
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sele2 | |
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This function calculates the minimal distance between **sele2** and
the center of mass of **sele1**, two selections from the same Entity.
:param sele1: The selection from which the center of mass is taken
:param sele2:
:type sele1: :class:`~ost.mol.EntityView`
:type sele2: :class:`~ost.mol.EntityView`
:return: distance (\ :class:`float`\ )
Definition at line 64 of file structure_analysis.py.