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Surfaces
================================================================================
.. currentmodule:: ost.mol
.. class:: SurfaceHandle
TODO
.. method:: Attach(entity, cutoff)
Attach an :class:`EntityHandle` or :class:`EntityView` to a molecular
surface. For each vertex of the surface, the atom which is closest to this
vertex and within the cutoff distance is attached. Like this, the atom and
its properties can be retrieved efficiently, which is e.g. used for coloring
a surface according to the underlying entity (see
:meth:`gfx.Surface.ColorBy`).
Be aware that increasing the cutoff distance will significantly increase the
time needed to attach an entity to the surface.
:param entity: entity to be attached to the surface
:type entity: :class:`EntityHandle`, :class:`EntityView`
:param cutoff: distance cutoff
:type cutoff: float
:rtype: None
.. method:: FindWithin(position, cutoff)
Returns all :class:`surface vertices<SurfaceVertex>` within a certain cutoff
distance of a specified position.
:param position: position
:type position: :class:`~ost.geom.Vec3`
:param cutoff: distance cutoff
:type cutoff: float
:rtype: :class:`SurfaceVertexList`
.. method:: GetTriIDList()
Returns a list containing all IDs of all triangles of a surface.
:rtype: list of ints
.. method:: GetVertex(id)
Returns a :class:`SurfaceVertex` with the specified ID.
:param id: vertex id
:type id: int
:rtype: :class:`SurfaceVertex`
.. method:: GetVertexIDList()
Returns a list containing all IDs of all vertices of a surface.
:rtype: list of ints
.. method:: Invert()
Does an in place inversion of all vertex normal vectors.
:rtype: None
.. class:: SurfaceVertex
TODO
.. method:: SurfaceVertex()
SurfaceVertex(pos, norm, type, atom)
Creates a new SurfaceVertex.
:param pos: vertex position
:type pos: :class:`geom.Vec3`
:param norm: vertex normal vector
:type norm: :class:`geom.Vec3`
:param type: vertex type
:type type: int
:param atom: attached atom
:type atom: :class:`AtomHandle`
.. attribute:: Atom
:class:`AtomHandle` attached to the surface vertex.
The AtomHandle is invalid, if no :class:`~ost.mol.EntityHandle` has been
attached or if no atom was found within the cutoff distance.
See :meth:`SurfaceHandle.Attach` for further details.
:type: :class:`AtomHandle`
.. attribute:: Normal
Normal vector of the surface vertex.
:type: :class:`~ost.geom.Vec3`
.. attribute:: Position
Spatial position of the surface vertex.
:type: :class:`~ost.geom.Vec3`
.. class:: SurfaceVertexList
.. method:: append(vertex)
Add a single surface vertex.
:param vertex: surface vertex
:type vertex: :class:`SurfaceVertex`
:rtype: None
.. method:: extend(list)
Add a list of surface vertices.
:param list: list of surface vertices
:type list: :class:`SurfaceVertexList`
:rtype: None
.. class:: SurfaceTriIDList
.. method:: append(id)
Add a single triangle ID.
:param id: trinangle vertex id
:type id: int
:rtype: None
.. method:: extend(list)
Add a list of triangle IDs.
:param list: list of triangle vertex ids
:type list: list of ints
:rtype: None
|
