biomacromolecules (bio)
=======================
.. automodule:: jscatter.bio
MDA universe
------------
`MDAnalysis `_ scatteringUniverse contains all atoms of a PDB structure or a simulation box
with methods for adding hydrogens, repair structures, volume determination
and merging of biological assemblies.
See the `MDAnalysis User Guideās `_ for non scattering topics.
.. currentmodule:: jscatter.bio.mda
.. autosummary::
~scatteringUniverse
scatteringUniverse.setSolvent
scatteringUniverse.view
scatteringUniverse.guess_bonds
~getSurfaceVolumePoints
~pdb2pqr
~fastpdb2pqr
~addH_Pymol
~getNativeContacts
~copyUnivProp
~mergePDBModel
Formfactors
-----------
Formfactors of universes containing a protein or DNA.
Explicit hydration layer might be included allowing simultaneous SAXS/SANS fitting.
.. currentmodule:: jscatter.bio.scatter
.. autosummary::
~scatIntUniv
~xscatIntUniv
~nscatIntUniv
~scatIntUnivYlm
Effective diffusion of rigid structures
---------------------------------------
Effective diffusion D(Q) for scalar trans/rot or tensor diffusion coefficients.
.. currentmodule:: jscatter.bio.scatter
.. autosummary::
~diffusionTRUnivTensor
~diffusionTRUnivYlm
.. currentmodule:: jscatter.libs.HullRad
.. autosummary::
~hullRad
.. currentmodule:: jscatter.bio.utilities
.. autosummary::
~runHydropro
Intermediate scattering functions (ISF)
---------------------------------------
The time dependent intermediate scattering function I(Q,t) describes changes in scattering intensity
due to dynamic processes of an atomic structure.
.. currentmodule:: jscatter.bio.scatter
.. autosummary::
~intScatFuncYlm
~intScatFuncPMode
~intScatFuncOU
Normal modes
------------
.. currentmodule:: jscatter.bio.nma
.. image:: ../../examples/images/arg61_animation.gif
:align: right
:width: 30 %
:alt: arg61_animation
Normal modes of atomic structures using the Anisotropic Network Model (ANMA)
implementing mass or friction weighted mode analysis.
- See example in :func:`~ANMA` for usage and how to deform structures.
- See different NM for specific methods as :func:`~NM.raw`,
:func:`~NM.rmsd`, :func:`~NM.animate`, :func:`~NM.allatommode`, :func:`~ANMA.forceConstant`,
:func:`~ANMA.frequency`, :func:`~vibNM.effectiveMass`,
:func:`~brownianNMdiag.effectiveFriction`, :func:`~brownianNMdiag.invRelaxTime`,
.. autosummary::
~NM
.. autosummary::
~ANMA
~vibNM
~brownianNMdiag
~explicitNM
~Mode
======
.. automodule:: jscatter.bio.mda
:members:
.. automodule:: jscatter.bio.scatter
:members:
.. autoclass:: jscatter.bio.nma.NM
:members:
.. autoclass:: jscatter.bio.nma.ANMA
:members:
.. autoclass:: jscatter.bio.nma.brownianNMdiag
:members:
.. autoclass:: jscatter.bio.nma.vibNM
:members:
.. autoclass:: jscatter.bio.nma.explicitNM
:members:
.. autoclass:: jscatter.bio.nma.Mode
:members:
:special-members: eigenvalue
.. autofunction:: jscatter.libs.HullRad.hullRad
.. autofunction:: jscatter.bio.utilities.runHydropro
.. autofunction:: jscatter.bio.utilities.readHydroproResult