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Commit 803a717f authored by Bienchen's avatar Bienchen
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Replaced string ProMod3 with the substitution tag

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......@@ -138,7 +138,7 @@ objects is performed in the
:class:`~promod3.core.pm3argparse.PM3ArgumentParser` class as described in
detail :meth:`here <promod3.core.pm3argparse.PM3ArgumentParser.AddFragments>`.
The default modelling pipeline in ProMod3 is optimized to generate a gap-free
The default modelling pipeline in |project| is optimized to generate a gap-free
model of the region in the target sequence(s) that is covered with template
information. Terminal extensions without template coverage are negelected.
You can enforce a model of the full target sequence(s) by adding ``-t``.
......
......@@ -14,7 +14,7 @@
.. limitations under the License.
:mod:`~promod3.core` - ProMod3 Core Functionality
:mod:`~promod3.core` - |project| Core Functionality
================================================================================
.. module:: promod3.core
......
......@@ -17,10 +17,10 @@
Docker
======
ProMod3's Own Docker Registry
-----------------------------
|project|'s Own Docker Registry
-------------------------------
For the current stable release of ProMod3, its
For the current stable release of |project|, its
`GitLab project <https://git.scicore.unibas.ch/schwede/ProMod3>`_ is equipped with its own
`registry for Docker images <https://git.scicore.unibas.ch/schwede/ProMod3/container_registry>`_. There you
can explore the current tag and simply pull a ready made built:
......
......@@ -14,11 +14,11 @@
.. limitations under the License.
ProMod3 and Containers
|project| and Containers
======================
ProMod3 offers build recipes for Docker and Singularity in
|project| offers build recipes for Docker and Singularity in
<PATH_TO_PROMOD3_CHECKOUT>/container. To avoid code duplication,
the Singularity container bootstraps from the Docker one and adds
some sugar on top.
......
......@@ -31,9 +31,9 @@ Available apps
This container includes the following apps:
* **OST** - OpenStructure executable
* **PM** - ProMod3 executable
* **IPython** - OST/ProMod3-powered iPython shell
* **Notebook** - A Jupyter notebook playground with OST, ProMod3 and nglview
* **PM** - |project| executable
* **IPython** - OST/|project|-powered iPython shell
* **Notebook** - A Jupyter notebook playground with OST, |project| and nglview
* **lDDT** - The Local Distance Difference Test
* **Molck** - Molecular checker
* **ChemdictTool** - Creating or update a compound library
......@@ -50,7 +50,7 @@ Eg.:
singularity run-help --app PM promod.img
To list all available ProMod3 modelling actions:
To list all available |project| modelling actions:
.. code-block:: bash
......
......@@ -17,7 +17,7 @@
ProMod3
=======
ProMod3 is a modelling engine based on the `OpenStructure <https://openstructure.org>`_ [biasini2013]_
|project| is a modelling engine based on the `OpenStructure <https://openstructure.org>`_ [biasini2013]_
computational structural biology framework that can perform all steps required
to generate a protein model by homology. Its modular design aims at
implementing flexible modelling pipelines and fast prototyping of novel
......
......@@ -16,11 +16,11 @@
Contributing
================================================================================
Please contact the ProMod3 developers if you implemented a modelling pipeline
Please contact the |project| developers if you implemented a modelling pipeline
that you believe is worth sharing with other users.
They can review the code and add it to the repository at:
https://git.scicore.unibas.ch/schwede/ProMod3. Consider
opening an account for the GitLab instance at sciCORE, University of Basel if
you directly want to contribute to ProMod3's core features. You can find more
you directly want to contribute to |project|'s core features. You can find more
information on that matter in the developer section of the documentation
(:ref:`how-to-contribute`).
......@@ -21,7 +21,7 @@ Structural Data
The :class:`StructureDB` serves as a container for structural backbone and
sequence data. Custom accessor objects can be implemented that relate
arbitrary features to structural data. Examples provided by ProMod3 include
arbitrary features to structural data. Examples provided by |project| include
accession using matching stem geometry (see: :class:`FragDB`) or sequence
features (see: :class:`Fragger`).
Besides backbone and sequence data, derived features can
......
......@@ -152,7 +152,7 @@ common rigid subsets of positions.
De Novo Modelling
--------------------------------------------------------------------------------
ProMod3 provides algorithms for sampling and fragment detection.
|project| provides algorithms for sampling and fragment detection.
Here we provide an object, that facilitates fragment detection and caching,
as well as a convenient function to combine the functionalities into an
example pipeline.
......@@ -168,7 +168,7 @@ Motif Finder
--------------------------------------------------------------------------------
Distinct spatial arrangements of atoms or functional groups are key for protein
function. For their detection, ProMod3 implements the MotifFinder algorithm
function. For their detection, |project| implements the MotifFinder algorithm
which is based on geometric hashing as described by Nussinov and Wolfson
[nussinov1991]_. The algorithm consists of a learning stage, a detection stage
and a refinement stage.
......
......@@ -22,7 +22,7 @@ Rotamer Graph
Once having a frame representing the rigid parts, the internal energies in
rotamer groups can be calculated. To come to a final solution of the sidechain
modelling problem, the pairwise energies also have to be evaluated and an
overall solution has to be found. ProMod3 implements a
overall solution has to be found. |project| implements a
:class:`promod3.core.GraphMinimizer` that allows to find solutions using
tree decomposition, A* and Monte Carlo algorithms.
......
......@@ -25,7 +25,7 @@
Tools and algorithms to model sidechains given backbone coordinates. The full
module is heavily based on SCWRL4 [krivov2009]_ . The according paper describes
the modelling of sidechains using two different rotamer models. A rigid model,
as well as a flexible model. Both models are implemented in ProMod3 and can be
as well as a flexible model. Both models are implemented in |project| and can be
applied in flexible ways.
The following code fragment shows an example of a basic sidechain reconstruction
......
......@@ -19,18 +19,18 @@ Loading Rotamer Libraries
.. currentmodule:: promod3.sidechain
There are several rotamer libraries that can be used in ProMod3. ProMod3
There are several rotamer libraries that can be used in |project| . |project|
is optimized for the use with backbone dependent rotamer libraries such
as the 2010 library provided by the Dunbrack lab [shapovalov2011]_.
You can request a licence `here <http://dunbrack.fccc.edu/bbdep2010/>`_
and generate such a library as described in
extras/data_generation/rotamer_library/README. Alternatively, ProMod3
extras/data_generation/rotamer_library/README. Alternatively, |project|
provides its own backbone dependent or backbone independent libraries
that can be loaded with :meth:`LoadBBDepLib` / :meth:`LoadLib`.
.. method:: LoadBBDepLib()
A backbone dependent rotamer library shipped with ProMod3. You can find
A backbone dependent rotamer library shipped with |project|. You can find
details on how it is created in extras/data_generation/rotamer_library/README.
All scripts to build it are in the same directory as the README file and
build the basis for custom versions.
......@@ -41,7 +41,7 @@ that can be loaded with :meth:`LoadBBDepLib` / :meth:`LoadLib`.
.. method:: LoadLib()
A backbone independent rotamer library shipped with ProMod3. You can find
A backbone independent rotamer library shipped with |project|. You can find
details on how it is created in extras/data_generation/rotamer_library/README.
All scripts to build it are in the same directory as the README file and
build the basis for custom versions.
......
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