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namespace ost { namespace gfx {
/*!
\page gfx_ent Graphical Entity
\section gfx_ent_intro Introduction
The main bunch of functionality to render molecular entities is provided by the
Entity class. The rendering is very flexible: The coloring and render style of
every atom and bond can be configured independently.
\section gfx_color Coloring
The graphical entity has a sophisticated interface to modify the color of an
entity. A very common use-case is to color an entity based on the atom
elements with Entity::ColorByElement(). Entity::SetColor() is used to set the
color of one or more atoms to a uniform color. To set the full entity to a nice
red color, use
\code
gfx::Entity gfx_ent=...;
gfx_ent->SetColor(gfx::RED)
\endcode
It is also possible to only change the color of certain parts:
\code
gfx::Entity gfx_ent=...;
gfx_ent->SetColor(gfx::RED, "rname=ARG");
\endcode
One of the most powerful features is the functionality offered by
Entity::ColorBy(). These functions allow you to map numeric properties to
colors. For example, to color an entity from N- to C-terminus in a gradient
from RED to BLUE, use the following code:
\code
gfx::Entity gfx_ent=...;
gfx_ent->ColorBy('rnum', gfx::RED, gfx::BLUE);
\endcode
Here, rnum refers to residue number. All numeric properties that are undestood
by the query language can be used as an argument to ColorBy. In addition,
ColorBy can also use generic properties.
The color operations are remembered, even after changing the render mode. If
you plan to change the color of an entity repeatedly it is of importance to
reset the color state of the entity to remove unneccessary color operations by
calling Entity::CleanColorOps().
\subsection gfx_detail_color Fine-tuning the coloring
The \ref RenderMode::HSC "cartoon" render mode uses two colors to color the
secondary structure elements. The main color affects the top and bottom of
extended and the outside of helical elements. The %detail color is used for
the inner side of helices and the rim of extended elements. This color is
changed with Entity::SetDetailColor().
\section gfx_rm Render Modes
Render modes broadly fall into categories: Render modes at full connectivity level such as the \ref RenderMode::SIMPLE "simple", \ref RenderMode::CPK "spheres" and \ref RenderMode::CUSTOM "balls & sticks" render modes and render modes that simplify the geometry of molecular entities. The latter class is represented by the \ref RenderMode::LINE_TRACE "trace", \ref RenderMode::SLINE "smooth line", \ref RenderMode::TUBE "tube" and \ref RenderMode::HSC "cartoon" render modes. Each of the entities can have more than one render mode at the same time, for example rendering one part at full connectivity level and one part at reduced %detail level. The following Python code snippet shows how to display an entity with a smooth backbone and showing sidechains that are close to the bound HEM at full connectivity. This example makes heavy use of the query language, for reference \ref query "see here".
\code
myo_go.SetRenderMode(gfx.SLINE)
near_hem=myo_go.view.Select('5.0 <> [rname=HEM]', mol.MATCH_RESIDUES)
ss_near_hem=near_hem.Select('aname!=CA,C,N,O', mol.EXCLUSIVE_BONDS)
myo_go.SetRenderMode(gfx.SIMPLE, ss_near_hem)
\endcode
\section gfx_sel Selection
Graphical entities have a selection. By default, the selection is rendered using a green halo. The view that describes the selection can be obtained with gfx::Entity::GetSelection() and changed with gfx::Entity::SetSelection().
*/
}}
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