Replaced string ProMod3 with the substitution tag

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``. 

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

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:

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.

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
 

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 

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`).

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  

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.

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.
 

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

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.