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Gabriel Studer's avatar
resolve deprecation warning in base.table
Studer Gabriel authored 
Use np.isnan instead of scipy.isnan. Starting from scipy 1.12
(or earlier), scipy.isnan was definitely deprecated. This made the
SpearmanCorrel function silently return None which triggered a failing
unit test that was reported by Andrius Merkys.
15a49948
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Gabriel Studer's avatar 15a49948
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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>`