anandojha · lvotapka · Aug 4, 2023 · Aug 4, 2023 · Aug 4, 2023 · Aug 4, 2023
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1,3 +1,8 @@
 include CODE_OF_CONDUCT.md
+include LICENSE
+include MANIFEST.in
+include versioneer.py
 
+graft qmrebind
 global-exclude *.py[cod] __pycache__ *.so
+include qmrebind/_version.py
diff --git a/README.md b/README.md
@@ -5,8 +5,8 @@ qmrebind
 [![codecov](https://codecov.io/gh/anandojha/qmrebind/branch/main/graph/badge.svg)](https://codecov.io/gh/anandojha/qmrebind/branch/main)
 
 Quantum Mechanical - Molecular Mechanical reparameterization at the 
-receptor-ligand Binding site (qmrebind) implemented in Simulation Enabled Estimation of 
-Kinetic Rates (SEEKR) multiscale software package
+receptor-ligand Binding site (qmrebind) implemented in Simulation Enabled 
+Estimation of Kinetic Rates (SEEKR) multiscale software package
 
 Detailed installation and usage instructions can be found at 
 https://qmrebind.readthedocs.io/en/latest/index.html.
@@ -17,31 +17,31 @@ Make sure to install these packages before running qmrebind:
 * ORCA
 * SEEKR2 (optional)
 
-One is likely to want to create a unique conda environment for qmrebind
+One is likely to want to create a unique Mamba environment for qmrebind
 calculations:
 
 ```bash
-  conda create --name QMMM python=3.8
+  mamba create --name QMMM
 ```
 
-Section IA: Installing ORCA
+### Installing ORCA
 ********************** 
 Follow the instructions on this page: https://qmrebind.readthedocs.io/en/latest
 
 Alternatively, visit the official site for instructions to install ORCA: 
 https://www.orcasoftware.de/tutorials_orca/first_steps/install.html
 
-Section II: Installing SEEKR2 (optional)
+### Installing SEEKR2 (optional)
 **********************
 Use the instructions on this page to install SEEKR2, if desired:
 https://seekr2.readthedocs.io/en/latest/installation.html
 
 ## Installation and Setup Instructions :
 
-* Activate the previously created conda environment:
+* Activate the previously created Mamba environment:
 ```bash
-conda activate QMMM # activate the conda environment
-conda install -c conda-forge ambertools biopandas pandas matplotlib parmed regex openmm
+mamba activate QMMM # activate the mamba environment
+mamba install ambertools biopandas pandas matplotlib parmed regex openmm
 pip install PyPDF2
 ```
 * Clone the *qmrebind* repository :
@@ -54,8 +54,8 @@ Linux machine (Installation in the home directory is recommended) :
 
 ```bash
 cd qmrebind
-python setup.py install
-python setup.py test # optional
+python -m pip install .
+pytest # optional
 ```
 Detailed documentation can be found at 
 https://qmrebind.readthedocs.io/en/latest/installation.html.
@@ -66,9 +66,10 @@ Input PDB file Requirements.
 
 qmrebind accepts the PDB input file with the following requirements:
 
-* PDB file typically should have the box vector information.
+* PDB file typically should have the box vector information (In a CRYST1 line).
 
-* Ligand and the receptor must be assigned a residue name, with the ligand following the receptor. 
+* Ligand and the receptor must be assigned a residue name, with the ligand 
+  following the receptor. 
 
 ## Authors and Contributors
 The following people have contributed directly to the coding and validation 
@@ -85,11 +86,15 @@ this project by providing feedback, bug reports, or other comments.
 
 If you use qmrebind, please cite the following paper:
 
-* ADD PAPER HERE
+* Ojha AA, Votapka LW, Amaro RE. QMrebind: incorporating quantum mechanical 
+force field reparameterization at the ligand binding site for improved 
+drug-target kinetics through milestoning simulations. Chem Sci. 
+2023 Oct 24;14(45):13159-13175. doi: 10.1039/d3sc04195f. 
+PMID: 38023523; PMCID: PMC10664576.
 
 ### Copyright
 
-Copyright (c) 2022, Anupam Anand Ojha
+Copyright (c) 2023, Anupam Anand Ojha
 
 
 #### Acknowledgements

diff --git a/docs/conf.py b/docs/conf.py
@@ -28,9 +28,9 @@
 author = 'Anupam Anand Ojha'
 
 # The short X.Y version
-version = ''
+version = '0.4.0'
 # The full version, including alpha/beta/rc tags
-release = ''
+release = '0.4.0'
 
 
 # -- General configuration ---------------------------------------------------
@@ -50,6 +50,7 @@
     'sphinx.ext.napoleon',
     'sphinx.ext.intersphinx',
     'sphinx.ext.extlinks',
+    'sphinx_rtd_theme',
 ]
 
 autosummary_generate = True

diff --git a/docs/index.rst b/docs/index.rst
@@ -31,7 +31,8 @@ Cite QMrebind
 
 If you wish to cite QMrebind, please cite the following paper:
 
-* Citation not yet available
+* Ojha AA, Votapka LW, Amaro RE. QMrebind: incorporating quantum mechanical force field reparameterization at the ligand binding site for improved drug-target kinetics through milestoning simulations. Chem Sci. 2023 Oct 24;14(45):13159-13175. doi: 10.1039/d3sc04195f. PMID: 38023523; PMCID: PMC10664576.
+
 
 Getting Involved
 ================

diff --git a/docs/installation.rst b/docs/installation.rst
@@ -70,23 +70,37 @@ These are separate downloaded tar files.
 5. Extract all three parts and copy all the contents into the folder named 
 "orca".
 
-6. Move the entire content to the home folder.
+.. code-block:: bash
+
+    tar -xf orca_5_0_3_linux_x86-64_openmpi411_part1.tar.xz
+    tar -xf orca_5_0_3_linux_x86-64_openmpi411_part2.tar.xz
+    tar -xf orca_5_0_3_linux_x86-64_openmpi411_part3.tar.xz
+    mv orca_5_0_3_linux_x86-64_openmpi411_part1/* .
+    mv orca_5_0_3_linux_x86-64_openmpi411_part2/* .
+    mv orca_5_0_3_linux_x86-64_openmpi411_part3/* .
+
 
-7. To assign the path variable and source it, open the bashrc file 
+6. To assign the path variable and source it, open the bashrc file 
 (vi ~/.bashrc) and add the following lines:
 
 .. code-block:: bash
 
     export PATH="$HOME/orca:$PATH"
     export LD_LIBRARY_PATH="$HOME/orca:$LD_LIBRARY_PATH"
 
-8. Source the bashrc file:
+7. Source the bashrc file:
 
 .. code-block:: bash
 
   source ~/.bashrc
+
+The correct environment probably deactivated:
+
+.. code-block:: bash
 
-9. Run ORCA using the following command by typing "orca" in the terminal. 
+  conda activate QMMM
+
+8. Run ORCA using the following command by typing "orca" in the terminal. 
 The expected outcome for a successful installation will be similar to the 
 following:
 
@@ -105,10 +119,15 @@ Install OpenMPI
 https://download.open-mpi.org/release/open-mpi/v4.1/openmpi-4.1.1.tar.bz2 
 (It *must* be this version)
 
-3. Extract the file and rename the folder as "openmpi". Move this folder to 
-the home directory. 
+3. Extract the file and rename the folder as "openmpi". Enter this directory.
+
+.. code-block::
+
+  tar -xzf openmpi-4.1.1.tar.gz
+  mv openmpi-4.1.1 $HOME/openmpi
+  cd $HOME/openmpi
 
-4. Go to the openmpi folder in the home directory. Open the terminal and 
+4. Go into to the openmpi folder. Open the terminal and 
 execute the following command in the terminal:
 
 .. code-block::
@@ -130,6 +149,12 @@ execute the following command in the terminal:
 
   source ~/.bashrc
 
+The correct environment probably deactivated:
+
+.. code-block:: bash
+
+  conda activate QMMM
+
 Install XTB
 -----------
 
@@ -141,10 +166,16 @@ https://github.com/grimme-lab/xtb/releases/tag/v6.5.1
 3. Download the xtb tar file, xtb-6.5.1-linux-x86_64.tar.xz, and extract the 
 file.
 
-4. After extracting, the folder is named xtb-6.5.1-linux-x86_64.
+.. code-block:: bash
+
+    tar -xf xtb-6.5.1-linux-x86_64.tar.xz
+
+4. Copy the xtb executable to the 
+orca folder in HOME, and rename it as otool_xtb.
+
+.. code-block:: bash
 
-5. Go to the folder, get into xtb-6.5.1/bin, copy the xtb executable to the 
-orca folder in the home, and rename it as otool_xtb.
+    cp xtb-6.5.1/bin/xtb ~/orca/otool_xtb
 
 Install QMrebind
 ----------------
@@ -153,7 +184,8 @@ Install QMrebind
 .. code-block:: bash
 
   conda activate QMMM # activate the conda environment
-  conda install -c conda-forge ambertools biopandas pandas matplotlib parmed regex openmm
+  conda install -c conda-forge ambertools 
+  conda install -c conda-forge openmm
   pip install PyPDF2
 
 2. Clone the *qmrebind* repository :
@@ -168,6 +200,6 @@ Linux machine (Installation in the home directory is recommended) :
 .. code-block:: bash
 
   cd qmrebind
-  python setup.py install
-  python setup.py test # optional
+  python -m pip install .
+  pytest # optional
 
diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -0,0 +1 @@
+sphinx-rtd-theme
diff --git a/docs/requirements.yaml b/docs/requirements.yaml
@@ -1,17 +1,13 @@
 name: docs
 channels:
-  - conda-forge
   - defaults
 dependencies:
-  - python=3.8
-  - ambertools
-  - biopandas
-  - pandas
-  - matplotlib
-  - parmed
-  - regex
+    # Base depends
+  - python=3.12
+  - pip
+  - cython
   - pip
 
   - pip:
     - sphinx-autoapi
-    - PyPDF2
+    - versioneer
diff --git a/docs/tutorial1_hsp90.rst b/docs/tutorial1_hsp90.rst
@@ -166,11 +166,12 @@ inhibitor itself has the resname BSM, so enter the following command:
 
 .. code-block:: bash
 
-  python ~/qmrebind/qmrebind/run_qmrebind_amber.py hsp90_compound3.pdb hsp90_compound3.parm7 -L BSM -Q -1
+  python ~/qmrebind/qmrebind/run_qmrebind_amber.py hsp90_compound3.pdb hsp90_compound3.parm7 -L BSM -c 5.0 -m MP2 -b "cc-pVTZ" -n 4
 
-Notice that we had to specify that the QM2 region has a charge of -1 using the
-'-Q' argument. This is because of a deprotonated aspartate close to the 
-inhibitor in the crystal structure.
+This specifies a QM2 region cutoff of 5.0 Angstroms (any residue with any atoms 
+within 5 Angstroms of any ligand atom will be added to the QM2 region). It also
+specifies that the MP2 method will be used, and the cc-pVTZ basis set, and
+4 CPU cores will be used to accelerate the calculation.
 
 References
 ----------

diff --git a/pyproject.toml b/pyproject.toml
@@ -20,20 +20,22 @@ classifiers = [
 ]
 requires-python = ">=3.8"
 # Declare any run-time dependencies that should be installed with the package.
-#dependencies = [
-#    "importlib-resources;python_version<'3.10'",
-#]
+dependencies = [
+    "pytest",
+    "numpy",
+    "scipy",
+    "matplotlib",
+    "parmed",
+    "nptyping",
+    "regex",
+    "pandas",
+    "biopandas",
+]
 
 # Update the urls once the hosting is set up.
-#[project.urls]
-#"Source" = "https://github.com/<username>/qmrebind/"
-#"Documentation" = "https://qmrebind.readthedocs.io/"
-
-[project.optional-dependencies]
-test = [
-  "pytest>=6.1.2",
-  "pytest-runner"
-]
+[project.urls]
+"Source" = "https://github.com/seekrcentral/qmrebind"
+"Documentation" = "https://qmrebind.readthedocs.io"
 
 [tool.setuptools]
 # This subkey is a beta stage development and keys may change in the future, see https://setuptools.pypa.io/en/latest/userguide/pyproject_config.html for more details
@@ -63,11 +65,12 @@ where = ["."]
 # Ref https://setuptools.pypa.io/en/latest/userguide/datafiles.html#package-data
 [tool.setuptools.package-data]
 qmrebind = [
-    "py.typed"
+    "py.typed",
+    "*.dat"
 ]
 
 [tool.versioningit]
-default-version = "1+unknown"
+default-version = "1.0.0"
 
 [tool.versioningit.format]
 distance = "{base_version}+{distance}.{vcs}{rev}"

diff --git a/qmrebind/__init__.py b/qmrebind/__init__.py
@@ -2,4 +2,6 @@
 Quantum Mechanical - Molecular Mechanical Re-parameterization of the 
 Receptor-Ligand Binding site implemented in Simulation Enabled Estimation of 
 Kinetic Rates (SEEKR)
-"""
+"""
+
+__version__ = "{version}"