From 803a717fc608ec0f525b3e6b0702a5b7b36cf8a4 Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Wed, 11 Mar 2020 02:58:45 +0100
Subject: [PATCH] Replaced string ProMod3 with the substitution tag
---
actions/doc/index.rst | 2 +-
core/doc/index.rst | 2 +-
doc/container/docker.rst | 6 +++---
doc/container/index.rst | 4 ++--
doc/container/singularity.rst | 8 ++++----
doc/index.rst | 2 +-
doc/user_contributions.rst | 4 ++--
loop/doc/structure_db.rst | 2 +-
modelling/doc/algorithms.rst | 4 ++--
sidechain/doc/graph.rst | 2 +-
sidechain/doc/index.rst | 2 +-
sidechain/doc/loading.rst | 8 ++++----
12 files changed, 23 insertions(+), 23 deletions(-)
diff --git a/actions/doc/index.rst b/actions/doc/index.rst
index e13e33b5..a456b7ef 100644
--- a/actions/doc/index.rst
+++ b/actions/doc/index.rst
@@ -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``.
diff --git a/core/doc/index.rst b/core/doc/index.rst
index 6d0e8f25..22caa264 100644
--- a/core/doc/index.rst
+++ b/core/doc/index.rst
@@ -14,7 +14,7 @@
.. limitations under the License.
-:mod:`~promod3.core` - ProMod3 Core Functionality
+:mod:`~promod3.core` - |project| Core Functionality
================================================================================
.. module:: promod3.core
diff --git a/doc/container/docker.rst b/doc/container/docker.rst
index 808ed9c1..9ac5eb13 100644
--- a/doc/container/docker.rst
+++ b/doc/container/docker.rst
@@ -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:
diff --git a/doc/container/index.rst b/doc/container/index.rst
index 7733b34e..352f285c 100644
--- a/doc/container/index.rst
+++ b/doc/container/index.rst
@@ -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.
diff --git a/doc/container/singularity.rst b/doc/container/singularity.rst
index 8999dcc4..30d7e853 100644
--- a/doc/container/singularity.rst
+++ b/doc/container/singularity.rst
@@ -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
diff --git a/doc/index.rst b/doc/index.rst
index ae8ba3bd..cb7b8e6c 100644
--- a/doc/index.rst
+++ b/doc/index.rst
@@ -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
diff --git a/doc/user_contributions.rst b/doc/user_contributions.rst
index ed8b5909..cbd88335 100644
--- a/doc/user_contributions.rst
+++ b/doc/user_contributions.rst
@@ -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`).
diff --git a/loop/doc/structure_db.rst b/loop/doc/structure_db.rst
index 152ef605..edb31a87 100644
--- a/loop/doc/structure_db.rst
+++ b/loop/doc/structure_db.rst
@@ -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
diff --git a/modelling/doc/algorithms.rst b/modelling/doc/algorithms.rst
index 347634f1..b36bf5bb 100644
--- a/modelling/doc/algorithms.rst
+++ b/modelling/doc/algorithms.rst
@@ -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.
diff --git a/sidechain/doc/graph.rst b/sidechain/doc/graph.rst
index a5efe680..5ac809fb 100644
--- a/sidechain/doc/graph.rst
+++ b/sidechain/doc/graph.rst
@@ -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.
diff --git a/sidechain/doc/index.rst b/sidechain/doc/index.rst
index ffa2e04e..cb13f38a 100644
--- a/sidechain/doc/index.rst
+++ b/sidechain/doc/index.rst
@@ -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
diff --git a/sidechain/doc/loading.rst b/sidechain/doc/loading.rst
index 1e18fcdf..e6f48243 100644
--- a/sidechain/doc/loading.rst
+++ b/sidechain/doc/loading.rst
@@ -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.
--
GitLab