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Gabriel Studer's avatar
make removing atoms fast again
Studer Gabriel authored 
Removing atoms from huge structures was observed to be super slow.
Reason was the removal from the spatial organizer which helps to find atoms
based on spatial proximity. The organizer is organized in buckets which
occupy a certain volume in space. Removing an element meant to iterate over
all buckets and all their items until the atom is found. However, we know
the position of the atom and thus can pinpoint the bucket in which its
expected to be. The SpatialOrganizer::Remove was therefore overloaded with
a version that accepts a position as hint in which bucket to look.
If the atom is there, delete and return. If not, call Remove without position
hint.
f04f0859
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Gabriel Studer's avatar f04f0859
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Name Last commit Last update
..
base
bindings
config
conop
db
doc
geom
gfx
gui
img
info
io
mol
seq
CMakeLists.txt
index.rst
index.rst

OpenStructure documentation

For Starters

Installation: :doc:`install from source <install>`

Tutorial Style: :doc:`introduction <intro>` | :doc:`molecules intro <intro-01>` | :doc:`images intro <intro-02>` | :doc:`graphics intro <intro-03>`

Molecules

Overview: :doc:`molecules intro <intro-01>` | :doc:`mol overview <mol/base/mol>` | :doc:`graphical entity<gfx/entity>` | :doc:`entity <mol/base/entity>` | :doc:`queries <mol/base/query>` | :doc:`algorithms <mol/alg/molalg>` | :doc:`mm <mol/mm/molmm>`

Trajectories: :doc:`basics <mol/base/traj>` | :ref:`analysis <traj-analysis>`

Input/Output: :ref:`loading and saving molecules <mol-io>`

Connectivity: :doc:`the conop module <conop/conop>` | :doc:`compound library <conop/compoundlib>`

Density Maps and Images

Overview: :doc:`images intro <intro-02>` | :doc:`img module <img/base/img>` | :doc:`img.alg module <img/alg/alg>`

Input/Output: :ref:`loading and saving density maps <img-io>`

Sequences and Alignments

Overview: :doc:`sequence module <seq/base/seq>` | :doc:`sequence algorithms <seq/alg/seqalg>`

Input/Output: :ref:`loading and saving sequences <seq-io>`

Graphics

Overview: :doc:`graphics intro <intro-03>`

Main Classes: :doc:`the scene <gfx/scene>` | :doc:`graphical entity <gfx/entity>`

Graphical User Interface

Overview: :doc:`module overview <gui/gui>` | :doc:`organization <gui/layout>` :doc:`tools <gui/tools>`

Widgets: :doc:`python shell <gui/python_shell>` | :doc:`sequence viewer <gui/sequence_viewer>`

Varia

Datasets: :doc:`tabular data <table>`

Supported File Formats: :doc:`structure formats<io/structure_formats>` | :doc:`sequence formats <io/sequence_formats>` | :doc:`sequence profile formats <io/sequence_profile_formats>` | :doc:`image formats <io/image_formats>`

Users: :doc:`Reporting a problem <users>`

lDDT: :doc:`lDDT command line executable and Python API<mol/alg/lddt>`

Molck: :doc:`Molecular Checker<mol/alg/molck>`

Actions: :doc:`OST Actions<actions>`

Database: :doc:`Efficiently store structural data<db/db>`

Extending OpenStructure

External Tools: :doc:`bindings <bindings/bindings>`

Howto: :doc:`write new modules <newmodule>` | :doc:`integrate third-party tools <external>` | :doc:`logging <base/logging>` | :doc:`instructions for developers <contributing>`