IMP
2.0.1
The Integrative Modeling Platform
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See IMP.display Overview for more information.
Classes | |
class | BildWriter |
Write a Bild file with the geometry. More... | |
class | BoundingBoxGeometry |
Display a bounding box. More... | |
class | ChimeraWriter |
Write geometry to a python file for Chimera to read. More... | |
class | CMMWriter |
Write a CMM file with the geometry. More... | |
class | Color |
Represent an RGB color. More... | |
class | Colored |
A particle with a color. More... | |
class | CylinderGeometry |
Display a cylinder. More... | |
class | EllipsoidGeometry |
Display a ellipsoid. More... | |
class | FilterGeometry |
Remove geometry which is not above a plane. More... | |
class | Geometry |
The base class for geometry. More... | |
class | GeometryProcessor |
Provide a standard geometry processing framework. More... | |
class | GeometrySet |
Group of set of geometric elements. More... | |
class | IsosurfaceGeometry |
Display an isosurface of a density map. More... | |
class | LabelGeometry |
A text label for a ball in space. More... | |
class | PairGeometry |
A base class for geometry contained in particles. More... | |
class | PairsGeometry |
A base class for geometry from a set of particles. More... | |
class | PivyWriter |
class | PlaneGeometry |
Display a plane as truncated to a bounding box. More... | |
class | PointGeometry |
Display a point. More... | |
class | PolygonGeometry |
class | PymolWriter |
Write a CGO file with the geometry. More... | |
class | ReferenceFrameGeometry |
Display a reference frame. More... | |
class | RestraintGeometry |
Try to draw some stuff for a generic restraint. More... | |
class | RestraintSetGeometry |
Geometry for a whole set of restraints. More... | |
class | SegmentGeometry |
Display a segment. More... | |
class | SingletonGeometry |
A base class for geometry contained in particles. More... | |
class | SingletonsGeometry |
A base class for geometry from a set of particles. More... | |
class | SkinSurfaceGeometry |
Display an isosurface of a density map. More... | |
class | SphereGeometry |
Display a sphere. More... | |
class | SurfaceMeshGeometry |
Display a surface mesh. More... | |
class | TextWriter |
class | TriangleGeometry |
Display a triangule. More... | |
class | WriteOptimizerState |
class | Writer |
Base class for writing geometry to a file. More... | |
class | WriterAdaptor |
Typedefs | |
typedef IMP::base::Vector< Color > | Colors |
typedef IMP::base::Vector < IMP::base::Pointer< Geometry > > | Geometries |
typedef IMP::base::Vector < IMP::base::Pointer < TextWriter > > | TextWriters |
typedef IMP::base::Vector < IMP::base::Pointer < WriteOptimizerState > > | WriteOptimizerStates |
typedef IMP::base::Vector < WriterAdaptor > | WriterAdaptors |
typedef IMP::base::Vector < IMP::base::Pointer< Writer > > | Writers |
Functions | |
SphereGeometry * | create_geometry (const algebra::Sphere3D &t, std::string name="algebra::Sphere3D"+"%1%") |
CylinderGeometry * | create_geometry (const algebra::Cylinder3D &t, std::string name="algebra::Cylinder3D"+"%1%") |
EllipsoidGeometry * | create_geometry (const algebra::Ellipsoid3D &t, std::string name="algebra::Ellipsoid3D"+"%1%") |
PointGeometry * | create_geometry (const algebra::Vector3D &t, std::string name="algebra::Vector3D"+"%1%") |
SegmentGeometry * | create_geometry (const algebra::Segment3D &t, std::string name="algebra::Segment3D"+"%1%") |
PolygonGeometry * | create_geometry (const algebra::Vector3Ds &t, std::string name="algebra::Vector3Ds"+"%1%") |
TriangleGeometry * | create_geometry (const algebra::Triangle3D &t, std::string name="algebra::Triangle3D"+"%1%") |
BoundingBoxGeometry * | create_geometry (const algebra::BoundingBoxD< 3 > &t, std::string name="algebra::BoundingBoxD<3>"+"%1%") |
ReferenceFrameGeometry * | create_geometry (const algebra::ReferenceFrame3D &t, std::string name="algebra::ReferenceFrame3D"+"%1%") |
Writer * | create_writer (std::string filename) |
std::string | get_data_path (std::string file_name) |
Return the full path to installed data. More... | |
Color | get_display_color (unsigned int i) |
std::string | get_example_path (std::string file_name) |
Return the path to installed example data for this module. More... | |
Color | get_interpolated_rgb (const Color &a, const Color &b, double f) |
Return a color interpolated between a and b in RGB space. More... | |
double | get_linear_color_map_value (double min, double max, double value) |
Colormaps | |
These functions map a number in the interval [0,1] to a color using some color map. | |
Color | get_jet_color (double f) |
Return the color for f from the jet color map. | |
Color | get_hot_color (double f) |
Return the color for f from the hot color map. | |
Color | get_rgb_color (double f) |
Return the color for f from the rgb color map. | |
Color | get_grey_color (double f) |
Return the a greyscale value for f. | |
Color | get_gnuplot_color (double f) |
Return colors using the gnuplot default color map. | |
typedef IMP::base::Vector< Color > IMP::display::Colors |
Store a set of objects.
Definition at line 18 of file declare_Geometry.h.
typedef IMP::base::Vector<IMP::base::Pointer< WriteOptimizerState > > IMP::display::WriteOptimizerStates |
Store a set of objects.
Definition at line 43 of file LogOptimizerState.h.
Pass or store a set of WriterAdaptor .
typedef IMP::base::Vector<IMP::base::Pointer< Writer > > IMP::display::Writers |
SphereGeometry* IMP::display::create_geometry | ( | const algebra::Sphere3D & | t, |
std::string | name = "algebra::Sphere3D"+"%1%" |
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) |
Create a Geometry with the passed primitive.
CylinderGeometry* IMP::display::create_geometry | ( | const algebra::Cylinder3D & | t, |
std::string | name = "algebra::Cylinder3D"+"%1%" |
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) |
Create a Geometry with the passed primitive.
EllipsoidGeometry* IMP::display::create_geometry | ( | const algebra::Ellipsoid3D & | t, |
std::string | name = "algebra::Ellipsoid3D"+"%1%" |
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) |
Create a Geometry with the passed primitive.
PointGeometry* IMP::display::create_geometry | ( | const algebra::Vector3D & | t, |
std::string | name = "algebra::Vector3D"+"%1%" |
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) |
Create a Geometry with the passed primitive.
SegmentGeometry* IMP::display::create_geometry | ( | const algebra::Segment3D & | t, |
std::string | name = "algebra::Segment3D"+"%1%" |
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) |
Create a Geometry with the passed primitive.
PolygonGeometry* IMP::display::create_geometry | ( | const algebra::Vector3Ds & | t, |
std::string | name = "algebra::Vector3Ds"+"%1%" |
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) |
Create a Geometry with the passed primitive.
TriangleGeometry* IMP::display::create_geometry | ( | const algebra::Triangle3D & | t, |
std::string | name = "algebra::Triangle3D"+"%1%" |
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) |
Create a Geometry with the passed primitive.
BoundingBoxGeometry* IMP::display::create_geometry | ( | const algebra::BoundingBoxD< 3 > & | t, |
std::string | name = "algebra::BoundingBoxD<3>"+"%1%" |
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) |
Create a Geometry with the passed primitive.
ReferenceFrameGeometry* IMP::display::create_geometry | ( | const algebra::ReferenceFrame3D & | t, |
std::string | name = "algebra::ReferenceFrame3D"+"%1%" |
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) |
Create a Geometry with the passed primitive.
Writer* IMP::display::create_writer | ( | std::string | filename | ) |
Create an appropriate writer based on the file suffix.
std::string IMP::display::get_data_path | ( | std::string | file_name | ) |
Each module has its own data directory, so be sure to use the version of this function in the correct module. To read the data file "data_library" that was placed in the data
directory of module "mymodule", do something like
This will ensure that the code works when IMP
is installed or used via the tools/imppy.sh
script.
Color IMP::display::get_display_color | ( | unsigned int | i | ) |
Produce a color that is attempted to be contrasting with the i-1 previous colors. Currently, they recycle after 11, but they can be darkened instead. Just ask.
std::string IMP::display::get_example_path | ( | std::string | file_name | ) |
Each module has its own example directory, so be sure to use the version of this function in the correct module. For example to read the file example_protein.pdb
located in the examples
directory of the IMP::atom module, do
This will ensure that the code works when IMP
is installed or used via the tools/imppy.sh
script.
Color get_interpolated_rgb | ( | const Color & | a, |
const Color & | b, | ||
double | f | ||
) |
double IMP::display::get_linear_color_map_value | ( | double | min, |
double | max, | ||
double | value | ||
) |
Return a number suitable for being passed to a color map that is gotten by linearly scaling between the passed min and max (and truncating values that are out of range).