IMP Reference Guide
2.21.0
The Integrative Modeling Platform
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Output IMP model data in various file formats. More...
Output IMP model data in various file formats.
The IMP::display::Writer class provides the base class for objects which write to specific file formats and the IMP::display::Geometry class provides a means of describing geometry. Currently it supports output to
And display of boxes, points, spheres, segments, ellipsoids are supported.
You should probably check out IMP::rmf for a more general file format and one that is read natively by both IMP and Chimera.
Author(s): Daniel Russel
Maintainer: benmwebb
License: LGPL This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.
Publications:
Classes | |
class | BoundingBoxGeometry |
Display a bounding box. 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 triangle. More... | |
class | WriteOptimizerState |
class | Writer |
Base class for writing geometry to a file. More... | |
class | WriterAdaptor |
Typedefs | |
typedef IMP::Vector< Colored > | Coloreds |
typedef IMP::Vector< Color > | Colors |
typedef IMP::Vector < IMP::Pointer< Geometry > > | Geometries |
typedef IMP::Vector < IMP::WeakPointer< Geometry > > | GeometriesTemp |
typedef IMP::Vector < IMP::Pointer< TextWriter > > | TextWriters |
typedef IMP::Vector < IMP::WeakPointer< TextWriter > > | TextWritersTemp |
typedef IMP::Vector < WriterAdaptor > | WriterAdaptors |
typedef IMP::Vector < IMP::Pointer< Writer > > | Writers |
typedef IMP::Vector < IMP::WeakPointer< Writer > > | WritersTemp |
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) |
Color | get_display_color (unsigned int i) |
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. More... | |
Color | get_hot_color (double f) |
Return the color for f from the hot color map. More... | |
Color | get_rgb_color (double f) |
Return the color for f from the RGB color map. More... | |
Color | get_gray_color (double f) |
Return the a grayscale value for f. More... | |
Color | get_gnuplot_color (double f) |
Return colors using the gnuplot default color map. More... | |
Standard module functions | |
All | |
std::string | get_module_version () |
Return the version of this module, as a string. More... | |
std::string | get_module_name () |
std::string | get_data_path (std::string file_name) |
Return the full path to one of this module's data files. More... | |
std::string | get_example_path (std::string file_name) |
Return the full path to one of this module's example files. More... | |
typedef IMP::Vector< Color > IMP::display::Colors |
typedef IMP::Vector<IMP::Pointer< Geometry > > IMP::display::Geometries |
A vector of reference-counting object pointers.
Definition at line 18 of file declare_Geometry.h.
typedef IMP::Vector<IMP::WeakPointer< Geometry > > IMP::display::GeometriesTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 19 of file declare_Geometry.h.
typedef IMP::Vector<IMP::Pointer< TextWriter > > IMP::display::TextWriters |
A vector of weak (non reference-counting) pointers to specified objects.
typedef IMP::Vector< WriterAdaptor > IMP::display::WriterAdaptors |
Pass or store a set of WriterAdaptor .
typedef IMP::Vector<IMP::Pointer< Writer > > IMP::display::Writers |
typedef IMP::Vector<IMP::WeakPointer< Writer > > IMP::display::WritersTemp |
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 | ) |
Return the full path to one of this module's data files.
To read the data file "data_library" that was placed in the data
directory of this module, do something like
This will ensure that the code works both when IMP is installed or if used via the setup_environment.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 | ) |
Return the full path to one of this module's example files.
To read the example file "example_protein.pdb" that was placed in the examples
directory of this module, do something like
This will ensure that the code works both when IMP is installed or if used via the setup_environment.sh
script.
Color IMP::display::get_gnuplot_color | ( | double | f | ) |
Return colors using the gnuplot default color map.
Color IMP::display::get_hot_color | ( | double | f | ) |
Return the color for f from the hot color map.
Color IMP::display::get_interpolated_rgb | ( | const Color & | a, |
const Color & | b, | ||
double | f | ||
) |
Color IMP::display::get_jet_color | ( | double | f | ) |
Return the color for f from the jet color map.
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).
std::string IMP::display::get_module_version | ( | ) |
Return the version of this module, as a string.
Definition at line 5 of file EMageFit/__init__.py.