From 70b83c5c8755b873f6c401bc3380af3462524ae5 Mon Sep 17 00:00:00 2001 From: diogom Date: Wed, 25 Sep 2024 06:48:20 -0700 Subject: [PATCH 01/61] initial readthedocs --- docs/Makefile | 20 +++++++++++++++++++ docs/make.bat | 35 ++++++++++++++++++++++++++++++++++ docs/source/conf.py | 37 ++++++++++++++++++++++++++++++++++++ docs/source/get_started.rst | 5 +++++ docs/source/index.rst | 37 ++++++++++++++++++++++++++++++++++++ docs/source/installation.rst | 21 ++++++++++++++++++++ 6 files changed, 155 insertions(+) create mode 100644 docs/Makefile create mode 100644 docs/make.bat create mode 100644 docs/source/conf.py create mode 100644 docs/source/get_started.rst create mode 100644 docs/source/index.rst create mode 100644 docs/source/installation.rst diff --git a/docs/Makefile b/docs/Makefile new file mode 100644 index 00000000..d0c3cbf1 --- /dev/null +++ b/docs/Makefile @@ -0,0 +1,20 @@ +# Minimal makefile for Sphinx documentation +# + +# You can set these variables from the command line, and also +# from the environment for the first two. +SPHINXOPTS ?= +SPHINXBUILD ?= sphinx-build +SOURCEDIR = source +BUILDDIR = build + +# Put it first so that "make" without argument is like "make help". +help: + @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) + +.PHONY: help Makefile + +# Catch-all target: route all unknown targets to Sphinx using the new +# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). +%: Makefile + @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) diff --git a/docs/make.bat b/docs/make.bat new file mode 100644 index 00000000..16d190d4 --- /dev/null +++ b/docs/make.bat @@ -0,0 +1,35 @@ +@ECHO OFF + +pushd %~dp0 + +REM Command file for Sphinx documentation + +if "%SPHINXBUILD%" == "" ( + set SPHINXBUILD=sphinx-build +) +set SOURCEDIR=source +set BUILDDIR=build + +%SPHINXBUILD% >NUL 2>NUL +if errorlevel 9009 ( + echo. + echo.The 'sphinx-build' command was not found. Make sure you have Sphinx + echo.installed, then set the SPHINXBUILD environment variable to point + echo.to the full path of the 'sphinx-build' executable. Alternatively you + echo.may add the Sphinx directory to PATH. + echo. + echo.If you don't have Sphinx installed, grab it from + echo.https://www.sphinx-doc.org/ + exit /b 1 +) + +if "%1" == "" goto help + +%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% +goto end + +:help +%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% + +:end +popd diff --git a/docs/source/conf.py b/docs/source/conf.py new file mode 100644 index 00000000..15a7a089 --- /dev/null +++ b/docs/source/conf.py @@ -0,0 +1,37 @@ +# Configuration file for the Sphinx documentation builder. +# +# For the full list of built-in configuration values, see the documentation: +# https://www.sphinx-doc.org/en/master/usage/configuration.html + +import os +import sys +sys.path.insert(0, os.path.abspath('../../meeko/')) +# -- Project information ----------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information + +project = 'meeko' +copyright = '2024, Forli lab' +author = 'Forli lab' +release = '0.6.0' + +# -- General configuration --------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration + +extensions = [ + 'sphinx.ext.autosectionlabel', + 'sphinx.ext.autodoc', + 'sphinx.ext.napoleon', + 'sphinx.ext.intersphinx', +] + +templates_path = ['_templates'] +exclude_patterns = [] + +pygments_style = 'sphinx' + + +# -- Options for HTML output ------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output + +html_theme = 'sphinx_book_theme' +html_static_path = [] diff --git a/docs/source/get_started.rst b/docs/source/get_started.rst new file mode 100644 index 00000000..b0ecfe18 --- /dev/null +++ b/docs/source/get_started.rst @@ -0,0 +1,5 @@ +.. _get_started: + Getting started with Meeko using the command line interface + +Command line scripts scripts ``mk_prepare_ligand.py`` and ``mk_prepare_receptor.py``. + diff --git a/docs/source/index.rst b/docs/source/index.rst new file mode 100644 index 00000000..d6c47fc3 --- /dev/null +++ b/docs/source/index.rst @@ -0,0 +1,37 @@ +Meeko +==================================== +*Interfacing RDKit and AutoDock* + +Both receptors and ligands. + +Full documentation +------------------------------ +* :ref:`Installation ` +* :ref:`Getting started ` + +.. toctree:: + :maxdepth: 2 + :caption: Get started + + about + installation + quick_ligand_cli + quick_ligand_py + quick_receptor_cli + quick_receptor_py + + +.. toctree:: + :maxdepth: 2 + :caption: Parameterization + + atom_types + charges + macrocycles + + +.. toctree:: + :maxdepth: 2 + :caption: Chorizos + + about_chorizos diff --git a/docs/source/installation.rst b/docs/source/installation.rst new file mode 100644 index 00000000..952dc1ba --- /dev/null +++ b/docs/source/installation.rst @@ -0,0 +1,21 @@ +.. _installation: + +Installing Meeko +================ + +Installation (from PyPI) +------------------------ +Please note that Meeko requires Python. + +.. code-block:: bash + + $ pip install meeko + +If using conda, ``pip`` installs the package in the active environment. + +Also note that if using MacOS, you may need to install Multiprocess separately: + +.. code-block:: bash + + $ pip install multiprocess + From 36a5d4a489b29481beeec60d34ddea6f46f0bf93 Mon Sep 17 00:00:00 2001 From: diogom Date: Wed, 25 Sep 2024 06:52:08 -0700 Subject: [PATCH 02/61] add .readthedocs.yaml --- .readthedocs.yaml | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 .readthedocs.yaml diff --git a/.readthedocs.yaml b/.readthedocs.yaml new file mode 100644 index 00000000..dd2aa46c --- /dev/null +++ b/.readthedocs.yaml @@ -0,0 +1,35 @@ +# Read the Docs configuration file for Sphinx projects +# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details + +# Required +version: 2 + +# Set the OS, Python version and other tools you might need +build: + os: ubuntu-22.04 + tools: + python: "3.12" + # You can also specify other tool versions: + # nodejs: "20" + # rust: "1.70" + # golang: "1.20" + +# Build documentation in the "docs/" directory with Sphinx +sphinx: + configuration: docs/conf.py + # You can configure Sphinx to use a different builder, for instance use the dirhtml builder for simpler URLs + # builder: "dirhtml" + # Fail on all warnings to avoid broken references + # fail_on_warning: true + +# Optionally build your docs in additional formats such as PDF and ePub +# formats: +# - pdf +# - epub + +# Optional but recommended, declare the Python requirements required +# to build your documentation +# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html +# python: +# install: +# - requirements: docs/requirements.txt From d4d16f4cc010ff1bb5bf1886700ec036d136a320 Mon Sep 17 00:00:00 2001 From: diogom Date: Wed, 25 Sep 2024 06:54:02 -0700 Subject: [PATCH 03/61] fix path to conf.py in .readthedocs.yaml --- .readthedocs.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.readthedocs.yaml b/.readthedocs.yaml index dd2aa46c..a83c2f35 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -16,7 +16,7 @@ build: # Build documentation in the "docs/" directory with Sphinx sphinx: - configuration: docs/conf.py + configuration: docs/source/conf.py # You can configure Sphinx to use a different builder, for instance use the dirhtml builder for simpler URLs # builder: "dirhtml" # Fail on all warnings to avoid broken references From b9dc9f02a330c8e2d7608b41fdc5da0433d632a6 Mon Sep 17 00:00:00 2001 From: diogom Date: Wed, 25 Sep 2024 07:00:36 -0700 Subject: [PATCH 04/61] add sphinx-book-theme to readthedocs requirements.txt --- .readthedocs.yaml | 6 +++--- docs/requirements.txt | 1 + 2 files changed, 4 insertions(+), 3 deletions(-) create mode 100644 docs/requirements.txt diff --git a/.readthedocs.yaml b/.readthedocs.yaml index a83c2f35..e952a46c 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -30,6 +30,6 @@ sphinx: # Optional but recommended, declare the Python requirements required # to build your documentation # See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html -# python: -# install: -# - requirements: docs/requirements.txt +python: + install: + - requirements: docs/requirements.txt diff --git a/docs/requirements.txt b/docs/requirements.txt new file mode 100644 index 00000000..31c781b4 --- /dev/null +++ b/docs/requirements.txt @@ -0,0 +1 @@ +sphinx-book-theme From 1e5d83c69fb655a3fb37e5fa531e0e585745fe2a Mon Sep 17 00:00:00 2001 From: diogom Date: Wed, 25 Sep 2024 08:28:55 -0700 Subject: [PATCH 05/61] add installation to readthedocs --- docs/source/get_started.rst | 5 ---- docs/source/index.rst | 55 ++++++++++++++++++++---------------- docs/source/installation.rst | 40 +++++++++++++++++++++----- 3 files changed, 63 insertions(+), 37 deletions(-) delete mode 100644 docs/source/get_started.rst diff --git a/docs/source/get_started.rst b/docs/source/get_started.rst deleted file mode 100644 index b0ecfe18..00000000 --- a/docs/source/get_started.rst +++ /dev/null @@ -1,5 +0,0 @@ -.. _get_started: - Getting started with Meeko using the command line interface - -Command line scripts scripts ``mk_prepare_ligand.py`` and ``mk_prepare_receptor.py``. - diff --git a/docs/source/index.rst b/docs/source/index.rst index d6c47fc3..50286b63 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -1,37 +1,42 @@ Meeko -==================================== -*Interfacing RDKit and AutoDock* +===== -Both receptors and ligands. +Preparation of molecules for AutoDock +------------------------------------- -Full documentation ------------------------------- -* :ref:`Installation ` -* :ref:`Getting started ` +Meeko assigns parameters to small organic molecules, to proteins, and to +nucleic acids. It prepares the input needed to run AutoDock from SD files +for small organic molecules, and from PDB or MMCIF files for proteins and +nucleic acids. It processes the output of AutoDock back into these formats. -.. toctree:: - :maxdepth: 2 - :caption: Get started +Meeko replaces MGLTools for preparing molecules. - about - installation - quick_ligand_cli - quick_ligand_py - quick_receptor_cli - quick_receptor_py +What Meeko does **not** do +-------------------------- -.. toctree:: - :maxdepth: 2 - :caption: Parameterization +Meeko doesn't calculate 3D positions or assign protonation states. + +Small organic molecules +----------------------- - atom_types - charges - macrocycles +Assign atom types, set rotatable bonds, assign partial charges, etc. +Proteins and nucleic acids +-------------------------- + +Protonation variants (e.g. HIE/HID) can be manually set. + +Interface with RDKit +-------------------- + +The Python API uses RDKit as input and output for small +organic molecules. This makes it easier to write custom programs +that integrate AutoDock with other software that also uses RDKit. .. toctree:: :maxdepth: 2 - :caption: Chorizos - - about_chorizos + :caption: MANUAL + + installation + diff --git a/docs/source/installation.rst b/docs/source/installation.rst index 952dc1ba..3178cc72 100644 --- a/docs/source/installation.rst +++ b/docs/source/installation.rst @@ -1,21 +1,47 @@ .. _installation: -Installing Meeko -================ +We recommend using micromamba to manage Python environments and install Meeko. +Other similar package managers also work, like mamba, conda, or miniconda. +We prefer micromamba because it uses conda-forge as its default channel. +If you use other package managers, please use the ``-c conda-forge`` option. -Installation (from PyPI) +To get micromamba, visit https://mamba.readthedocs.io/en/latest/ + + +From conda-forge +---------------- + +.. code-block:: bash + + $ micromamba install meeko + + +From PyPI ------------------------ -Please note that Meeko requires Python. .. code-block:: bash $ pip install meeko -If using conda, ``pip`` installs the package in the active environment. +If using micromamba or a similar package manager, ``pip`` installs the package +in the active environment. + + +From source +----------- -Also note that if using MacOS, you may need to install Multiprocess separately: +Here, we will checkout the ``develop`` branch, as it is likely more recent than the +default ``release`` branch. Accessing features that are not in a release yet is one +of the reasons to use the develop branch, which requires installing from source. .. code-block:: bash - $ pip install multiprocess + $ git clone https://github.com/forlilab/Meeko.git + $ cd Meeko + $ git checkout develop + $ pip install . +Alternatively, it is possible to install with ``pip install -e .``. Then, changes to +the source files take immediate effect without requiring further ``pip install .``. +This is useful for developers. Changes to the command line scripts may still require +a re-installation. From e71522314b1e1d0253a9f7baf89af36f9fbba747 Mon Sep 17 00:00:00 2001 From: diogom Date: Wed, 25 Sep 2024 09:40:31 -0700 Subject: [PATCH 06/61] move some stuff from README to docs --- README.md | 76 ------------------------------------ docs/source/conf.py | 6 +-- docs/source/index.rst | 24 +++++++++++- docs/source/installation.rst | 15 +++---- 4 files changed, 34 insertions(+), 87 deletions(-) diff --git a/README.md b/README.md index 83f6f30f..b990eb47 100644 --- a/README.md +++ b/README.md @@ -85,85 +85,9 @@ conda install -c conda-forge numpy scipy rdkit pip install prody # optional. pip recommended at http://prody.csb.pitt.edu/downloads/ ``` -## Installation (from PyPI) -```bash -$ pip install meeko -``` -If using conda, `pip` installs the package in the active environment. - -## Installation (from source) -You'll get the develop branch, which may be ahead of the latest release. -```bash -$ git clone https://github.com/forlilab/Meeko -$ cd Meeko -$ pip install . -``` - -Optionally include `--editable`. Changes in the original package location -take effect immediately without the need to run `pip install .` again. -```bash -$ pip install --editable . -``` - - -## Examples using the command line scripts - -#### 1. make PDBQT files -AutoDock-GPU and Vina read molecules in the PDBQT format. These can be prepared -by Meeko from SD files, or from Mol2 files, but SDF is strongly preferred. -```console -mk_prepare_ligand.py -i molecule.sdf -o molecule.pdbqt -mk_prepare_ligand.py -i multi_mol.sdf --multimol_outdir folder_for_pdbqt_files -``` - -#### 2. convert docking results to SDF -AutoDock-GPU and Vina write docking results in the PDBQT format. The DLG output -from AutoDock-GPU contains docked poses in PDBQT blocks. -Meeko generates RDKit molecules from PDBQT files (or strings) using the SMILES -string in the REMARK lines. The REMARK lines also have the mapping of atom indices -between SMILES and PDBQT. SD files with docked coordinates are written -from RDKit molecules. - -```console -mk_export.py molecule.pdbqt -o molecule.sdf -mk_export.py vina_results.pdbqt -o vina_results.sdf -mk_export.py autodock-gpu_results.dlg -o autodock-gpu_results.sdf -``` - -Making RDKit molecules from SMILES is safer than guessing bond orders -from the coordinates, specially because the PDBQT lacks hydrogens bonded -to carbon. As an example, consider the following conversion, in which -OpenBabel adds an extra double bond, not because it has a bad algorithm, -but because this is a nearly impossible task. -```console -$ obabel -:"C1C=CCO1" -o pdbqt --gen3d | obabel -i pdbqt -o smi -[C]1=[C][C]=[C]O1 -``` ## Python tutorial -#### 1. making PDBQT strings for Vina or for AutoDock-GPU - -```python -from meeko import MoleculePreparation -from meeko import PDBQTWriterLegacy -from rdkit import Chem - -input_molecule_file = "example/BACE_macrocycle/BACE_4.sdf" - -# there is one molecule in this SD file, this loop iterates just once -for mol in Chem.SDMolSupplier(input_molecule_file, removeHs=False): - preparator = MoleculePreparation() - mol_setups = preparator.prepare(mol) - for setup in mol_setups: - setup.show() # optional - pdbqt_string = PDBQTWriterLegacy.write_string(setup) -``` -At this point, `pdbqt_string` can be written to a file for -docking with AutoDock-GPU or Vina, or passed directly to Vina within Python -using `set_ligand_from_string(pdbqt_string)`. For context, see -[the docs on using Vina from Python](https://autodock-vina.readthedocs.io/en/latest/docking_python.html). - #### 2. RDKit molecule from docking results diff --git a/docs/source/conf.py b/docs/source/conf.py index 15a7a089..7d1c5ffa 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -10,9 +10,9 @@ # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information project = 'meeko' -copyright = '2024, Forli lab' -author = 'Forli lab' -release = '0.6.0' +copyright = '2024, Forli Lab at Scripps Research' +#author = 'Forli lab' +#release = '0.6.0' # -- General configuration --------------------------------------------------- # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration diff --git a/docs/source/index.rst b/docs/source/index.rst index 50286b63..9bcca86c 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -36,7 +36,29 @@ that integrate AutoDock with other software that also uses RDKit. .. toctree:: :maxdepth: 2 - :caption: MANUAL + :caption: Getting started installation +.. toctree:: + :maxdepth: 2 + :caption: Ligand preparation + + cli_lig_prep + In Python + +.. toctree:: + :maxdepth: 2 + :caption: Receptor preparation + + cli_rec_prep + +.. toctree:: + :maxdepth: 2 + :caption: Exporting results + + cli_export_result + In Python + + + diff --git a/docs/source/installation.rst b/docs/source/installation.rst index 3178cc72..d67e5b91 100644 --- a/docs/source/installation.rst +++ b/docs/source/installation.rst @@ -1,4 +1,5 @@ -.. _installation: +Installation +============ We recommend using micromamba to manage Python environments and install Meeko. Other similar package managers also work, like mamba, conda, or miniconda. @@ -13,7 +14,7 @@ From conda-forge .. code-block:: bash - $ micromamba install meeko + micromamba install meeko From PyPI @@ -21,7 +22,7 @@ From PyPI .. code-block:: bash - $ pip install meeko + pip install meeko If using micromamba or a similar package manager, ``pip`` installs the package in the active environment. @@ -36,10 +37,10 @@ of the reasons to use the develop branch, which requires installing from source. .. code-block:: bash - $ git clone https://github.com/forlilab/Meeko.git - $ cd Meeko - $ git checkout develop - $ pip install . + git clone https://github.com/forlilab/Meeko.git + cd Meeko + git checkout develop + pip install . Alternatively, it is possible to install with ``pip install -e .``. Then, changes to the source files take immediate effect without requiring further ``pip install .``. From 5a83ab3a48359f529d403d77de2bbbbd78f0a34c Mon Sep 17 00:00:00 2001 From: diogom Date: Wed, 25 Sep 2024 09:43:08 -0700 Subject: [PATCH 07/61] add files forgotten in previous commit --- docs/source/cli_export_result.rst | 33 +++++++++++++++++++++++++++ docs/source/cli_lig_prep.rst | 16 +++++++++++++ docs/source/cli_rec_prep.rst | 4 ++++ docs/source/py_export_result.rst | 38 +++++++++++++++++++++++++++++++ docs/source/py_lig_prep.rst | 33 +++++++++++++++++++++++++++ 5 files changed, 124 insertions(+) create mode 100644 docs/source/cli_export_result.rst create mode 100644 docs/source/cli_lig_prep.rst create mode 100644 docs/source/cli_rec_prep.rst create mode 100644 docs/source/py_export_result.rst create mode 100644 docs/source/py_lig_prep.rst diff --git a/docs/source/cli_export_result.rst b/docs/source/cli_export_result.rst new file mode 100644 index 00000000..b4f91db2 --- /dev/null +++ b/docs/source/cli_export_result.rst @@ -0,0 +1,33 @@ +mk_export.py +============ + +Convert docking results to SDF +------------------------------ + +AutoDock-GPU and Vina write docking results in the PDBQT format. The DLG output +from AutoDock-GPU contains docked poses in PDBQT blocks, plus additional information. +Meeko generates RDKit molecules from PDBQT using the SMILES +string in the REMARK lines. The REMARK lines also have the mapping of atom indices +between SMILES and PDBQT. SD files with docked coordinates are written +from RDKit molecules. + +.. code-block:: bash + + mk_export.py molecule.pdbqt -o molecule.sdf + mk_export.py vina_results.pdbqt -o vina_results.sdf + mk_export.py autodock-gpu_results.dlg -o autodock-gpu_results.sdf + +Why this matters +---------------- + +Making RDKit molecules from SMILES is safer than guessing bond orders +from the coordinates, specially because the PDBQT lacks hydrogens bonded +to carbon. As an example, consider the following conversion, in which +OpenBabel adds an extra double bond, not because it has a bad algorithm, +but because this is a nearly impossible task. + +.. code-block:: bash + + obabel -:"C1C=CCO1" -o pdbqt --gen3d | obabel -i pdbqt -o smi + [C]1=[C][C]=[C]O1 + diff --git a/docs/source/cli_lig_prep.rst b/docs/source/cli_lig_prep.rst new file mode 100644 index 00000000..91fe3224 --- /dev/null +++ b/docs/source/cli_lig_prep.rst @@ -0,0 +1,16 @@ +mk_prepare_ligand.py +==================== + +Command line tool to prepare small organic molecules. + +Write PDBQT files +----------------- + +AutoDock-GPU and Vina read molecules in the PDBQT format. These can be prepared +by Meeko from SD files, or from Mol2 files, but SDF is strongly preferred. + +.. code-block:: bash + + mk_prepare_ligand.py -i molecule.sdf -o molecule.pdbqt + mk_prepare_ligand.py -i multi_mol.sdf --multimol_outdir folder_for_pdbqt_files + diff --git a/docs/source/cli_rec_prep.rst b/docs/source/cli_rec_prep.rst new file mode 100644 index 00000000..6f0081b7 --- /dev/null +++ b/docs/source/cli_rec_prep.rst @@ -0,0 +1,4 @@ +mk_prepare_receptor.py +====================== + +These are the docs for receptor preparation with the command line script. diff --git a/docs/source/py_export_result.rst b/docs/source/py_export_result.rst new file mode 100644 index 00000000..91299426 --- /dev/null +++ b/docs/source/py_export_result.rst @@ -0,0 +1,38 @@ +Exporting docking results in Python +=================================== + +.. code-block:: python + + from meeko import PDBQTMolecule + from meeko import RDKitMolCreate + + fn = "autodock-gpu_results.dlg" + pdbqt_mol = PDBQTMolecule.from_file(fn, is_dlg=True, skip_typing=True) + rdkitmol_list = RDKitMolCreate.from_pdbqt_mol(pdbqt_mol) + +The length of ``rdkitmol_list`` is one if there are no sidechains and only one +ligand was docked. +If multiple ligands and/or sidechains are docked simultaneously, each will be +an individual RDKit molecule in ``rdkitmol_list``. +Sidechains are truncated at the C-alpha. +Note that docking multiple +ligands simultaneously is only available in Vina, and it differs from docking +multiple ligands one after the other. Each failed creation of an RDKit molecule +for a ligand or sidechain results in a ``None`` in ``rdkitmol_list``. + +For Vina's output PDBQT files, omit ``is_dlg=True``. + +.. code-block:: python + + pdbqt_mol = PDBQTMolecule.from_file("vina_results.pdbqt", skip_typing=True) + rdkitmol_list = RDKitMolCreate.from_pdbqt_mol(pdbqt_mol) + +When using Vina from Python, the output string can be passed directly. +See [the docs](https://autodock-vina.readthedocs.io/en/latest/docking_python.html) +for context on the `v` object. + +.. code-block:: python + + vina_output_string = v.poses() + pdbqt_mol = PDBQTMolecule(vina_output_string, is_dlg=True, skip_typing=True) + rdkitmol_list = RDKitMolCreate.from_pdbqt_mol(pdbqt_mol) diff --git a/docs/source/py_lig_prep.rst b/docs/source/py_lig_prep.rst new file mode 100644 index 00000000..279aee1b --- /dev/null +++ b/docs/source/py_lig_prep.rst @@ -0,0 +1,33 @@ +Ligand preparation in Python +============================ + + +Creating a PDBQT string from an RDKit molecule +---------------------------------------------- +.. code-block:: python + + from meeko import MoleculePreparation + from meeko import PDBQTWriterLegacy + from rdkit import Chem + + input_molecule_file = "example/BACE_macrocycle/BACE_4.sdf" + + # there is one molecule in this SD file, this loop iterates just once + for mol in Chem.SDMolSupplier(input_molecule_file, removeHs=False): + preparator = MoleculePreparation() + mol_setups = preparator.prepare(mol) + for setup in mol_setups: + setup.show() # optional + pdbqt_string = PDBQTWriterLegacy.write_string(setup) + +At this point, ``pdbqt_string`` can be written to a file for +docking with AutoDock-GPU or Vina, or passed directly to Vina within Python +using `set_ligand_from_string(pdbqt_string)`. For context, see +[the docs on using Vina from Python](https://autodock-vina.readthedocs.io/en/latest/docking_python.html). + +One advantage of this approach is that input PDBQT files are not written to the filesystem. +The PDBQT format is lossy, because it lacks bond orders and non-polar hydrogens, +making it a poor choice to store molecular information. + +Another advantage is to write custom workflows entirely from Python without external +calls to ``mk_prepare_ligand.py``. From c8a242156d1b68e0a86480231bd1aa1e5230ad02 Mon Sep 17 00:00:00 2001 From: diogom Date: Wed, 25 Sep 2024 10:41:45 -0700 Subject: [PATCH 08/61] add docs badge to README --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index b990eb47..2ace35dc 100644 --- a/README.md +++ b/README.md @@ -2,6 +2,7 @@ [![API stability](https://img.shields.io/badge/stable%20API-no-orange)](https://shields.io/) [![PyPI version fury.io](https://img.shields.io/badge/version-0.6.0--alpha.3-green.svg)](https://pypi.python.org/pypi/meeko/) +[![Documentation Status](https://readthedocs.org/projects/meeko/badge/?version=readthedocs)](https://meeko.readthedocs.io/en/readthedocs/?badge=readthedocs) Meeko reads an RDKit molecule object and writes a PDBQT string (or file) for [AutoDock-Vina](https://github.com/ccsb-scripps/AutoDock-Vina) From 4a12a40e28929ce6d7f9bda2cd74ca47e55fd023 Mon Sep 17 00:00:00 2001 From: diogom Date: Thu, 26 Sep 2024 11:41:08 -0700 Subject: [PATCH 09/61] improve home page of docs --- docs/source/about.rst | 8 +++++ docs/source/conf.py | 2 ++ docs/source/images/raccoon.png | Bin 0 -> 7534 bytes docs/source/index.rst | 52 +++++++++++++++++++-------------- docs/source/tutorials.rst | 5 ++++ 5 files changed, 45 insertions(+), 22 deletions(-) create mode 100644 docs/source/about.rst create mode 100644 docs/source/images/raccoon.png create mode 100644 docs/source/tutorials.rst diff --git a/docs/source/about.rst b/docs/source/about.rst new file mode 100644 index 00000000..33a6aa3d --- /dev/null +++ b/docs/source/about.rst @@ -0,0 +1,8 @@ +About +===== + + +This is to explain the philosofy and motivation behind meeko, implementation details, +comparison with MGLTools, possibly the engineering behind the Polymer, and stuff like +this. It may become relatively large and need to be broken down. It may be halfway between +technical documentation and an academic paper. diff --git a/docs/source/conf.py b/docs/source/conf.py index 7d1c5ffa..ce1776a5 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -24,6 +24,8 @@ 'sphinx.ext.intersphinx', ] +html_logo = "images/raccoon.png" + templates_path = ['_templates'] exclude_patterns = [] diff --git a/docs/source/images/raccoon.png b/docs/source/images/raccoon.png new file mode 100644 index 0000000000000000000000000000000000000000..8a6ffe62492574e7da996608f6139c806b4d81fc GIT binary patch literal 7534 zcmaKwWl$7u^zV1+E|G4K?vN6t8$@!6C8fK&LmH%0KvH&DSGomh>DWcOb7@3cuD_Z8 zow+aWz0b_^{myfq^Xi;8-}xlyXsZz7(cl39075lYMO^>@4FUiFBQVhaRRWq{)&c;e zMM3%?A6+YdCJ!%nJ4Y8=CZ9kLTPE88N4tM5i(UDSesq#VF;AD|-WdFV+^vYEVDD(j zzahiiBRRnh9eXLGx;gdr8Eho+ID&n*li%HMD4!IAh(6cNzjNL$A)sCenB79H1%y>| zPM+?SjOVS{e=j0_+;ZIoN#x99kDCv@FPe9^xS?Vl|GK9T9-eW3uY5|px;41TdVl}; z$R=50v6tEDE;@nIqVEcQgShRU4zjq>+<9aznGK?UI6d1@WK}n%uGtPz=RUt(u@K?> 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zgdsJrf>)xNi98MZ7IOfFb&d1PF!mfEiVA7bWd_D`ZZMu-wMZWx1cH`#Ic=m1F?}MTreq6@NR9_THQUG7N+wHfJKTzEa6TWLv7JR8bPG@+U*Gk&!WNc(ifP8(Mw^t-L9)3I zr6V5n!>wa>5ag|^e_dB8!cpzfSwr9Mj(eKidwk`fhV_}1C&U%y3;vX9^v&mth#ZbguLJHBcoRX&Z^Mq39TM@QsC&>9iM~jdHjiyk?x+Ez>Q&)B0vuX>-@)3WLx5TT5nfRi#9vtn2i`rTs5FN*Gcnd7ic@ERO zx}9TW7yH%x6G}saYm_GNu&H0DyRNzM{l%9P`kiSm&U{D;7l}C~1#n@mEWJXn5I&g0 zFW>Y!nlcDML9N9=pe9^rL&&pA3CFT4V@IgBDuZ82)+)Gnpt@Xw^s8;elxlX!ak#>! z=ay}|YxSR*p^H~dRTiWHYbJUQ_aMD2e1#$&~xvJ+bO)CX>^t!E~IH^pC(Dnn?}4; z_3a>qaU&HTY;Ot3YYKtcf3u2z)CP((y=^Xg68knEydf&FvMc*iYilJ)NWpTLL6u-{ zYaA&Ru_7wj2cn-|p42nvf>`n7@lHbuKbh2YKM`=wYC6=MMlsvt;(Wt|VZx#f$wq5Bk< ztGM$_XmdE;l;2Y+R)bx@nq_Dko~*Q-uQ)RfG7smMKZYM@Btp+_ Date: Mon, 30 Sep 2024 12:13:43 -0700 Subject: [PATCH 11/61] add github button --- docs/source/conf.py | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/docs/source/conf.py b/docs/source/conf.py index ce1776a5..af5c3d13 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -11,7 +11,7 @@ project = 'meeko' copyright = '2024, Forli Lab at Scripps Research' -#author = 'Forli lab' +author = 'The Meeko authors' #release = '0.6.0' # -- General configuration --------------------------------------------------- @@ -26,6 +26,7 @@ html_logo = "images/raccoon.png" + templates_path = ['_templates'] exclude_patterns = [] @@ -36,4 +37,10 @@ # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output html_theme = 'sphinx_book_theme' -html_static_path = [] + +html_theme_options = { + 'show_toc_level': 2, + 'repository_url': 'https://github.com/forlilab/meeko', + 'use_repository_button': True, # add a "link to repository" button + 'navigation_with_keys': False, +} From f6d23d15f43a904e6764426b1ea8723e40a72086 Mon Sep 17 00:00:00 2001 From: diogom Date: Thu, 10 Oct 2024 11:02:11 -0700 Subject: [PATCH 12/61] add Python 3.12 installation instructions --- docs/source/installation.rst | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/docs/source/installation.rst b/docs/source/installation.rst index d67e5b91..f80dbc32 100644 --- a/docs/source/installation.rst +++ b/docs/source/installation.rst @@ -46,3 +46,17 @@ Alternatively, it is possible to install with ``pip install -e .``. Then, change the source files take immediate effect without requiring further ``pip install .``. This is useful for developers. Changes to the command line scripts may still require a re-installation. + + +Support for Python 3.12 +----------------------- + +Meeko runs on Python 3.12 as long as Prody is not installed. To run on 3.12, +install all dependencies except Prody and install Meeko from source. + +Meeko uses Prody to parse PDB and mmCIF files. Without prody, PDB files +can be parsed with the command line option ``--read_pdb`` and with the Python +method ``LinkedRDKitChorizo.from_pdb_string()``. However, without ProDy it +won't be possible to read mmCIF files or use tethered docking. Prody developers +are working to support Python 3.12, so it is possible that Prody will work +on Python 3.12 soon. From 8d4b59f9fe73b7359cfcfe592bbba574937b65f5 Mon Sep 17 00:00:00 2001 From: diogom Date: Thu, 10 Oct 2024 11:22:35 -0700 Subject: [PATCH 13/61] docs for mk_prepare_receptor --write flags --- docs/source/cli_rec_prep.rst | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/docs/source/cli_rec_prep.rst b/docs/source/cli_rec_prep.rst index 6f0081b7..a69a199a 100644 --- a/docs/source/cli_rec_prep.rst +++ b/docs/source/cli_rec_prep.rst @@ -2,3 +2,30 @@ mk_prepare_receptor.py ====================== These are the docs for receptor preparation with the command line script. + + +Write flags +----------- + +The option flags starting with ``--write`` in ``mk_prepare_receptor`` can +be used both with an argument to specify the outpuf filename: +.. code-block:: bash + + --write_pdbqt myenzyme.pdbqt --write_json myenzyme.json + +and without the filename argument as long as a default basename is provided: + +.. code-block:: bash + + --output_basename myenzyme --write_pdbqt --write_json + +It is also possible to combine the two types of usage: + +.. code-block:: bash + + --output_basename myenzyme + --write_pdbqt + --write_json + --write_vina_box box_for_myenzyme.txt + +in which case the specified filenames have priority over the default basename. From 4b3a3a3e6df9e2d531d8ec97b60afcc74a69aa3a Mon Sep 17 00:00:00 2001 From: diogom Date: Fri, 11 Oct 2024 08:59:12 -0700 Subject: [PATCH 14/61] wip intro rec prep DOCS --- docs/source/cli_rec_prep.rst | 50 +++++++++++++++++++++++++++++++++--- 1 file changed, 47 insertions(+), 3 deletions(-) diff --git a/docs/source/cli_rec_prep.rst b/docs/source/cli_rec_prep.rst index a69a199a..7994b1a2 100644 --- a/docs/source/cli_rec_prep.rst +++ b/docs/source/cli_rec_prep.rst @@ -1,8 +1,52 @@ -mk_prepare_receptor.py -====================== -These are the docs for receptor preparation with the command line script. +The input structure is matched against templates to +guarantee chemical correctness and identify problems with the input structures. +This allows the user to identify and fix problems, resulting in a molecular +model that is correct with respect to heavy atoms, protonation state, +connectivity, bond orders, and formal charges. +The matching algorithm uses the connectivity and elements, but not bond orders +or atom names. Hydrogens are optional. This makes it compatible with input +files from various sources. + +Templates are matched on a per residue basis. Each residue is represented +as an instance of a PolymerResidue object, which contains: + - an RDKit molecule that represents the actual state + - a padded RDKit molecule containing a few atoms from the adjacent residues + - parameters such as partial charges + +The positions are set by the input, and the connectivity and formal charges +are defined by the templates. Heavy atoms must match exactly. If heavy atoms +are missing or in excess, the templates will fail to match. + +Missing hydrogens are added by RDKit, but are not subjected to minimization +with a force field. Thus, their bond lengths are not super accurate. + +Different states of the same residue are stored as different templates, +for example different protonation states of HIS, N-term, LYN/LYS, etc. +Residue name is primary key unless user overrides. + +Currently not supported: capped residues from charmm-gui. + +mk_prepare_receptor +=================== + +Basic usage +----------- + +.. code-block:: bash + + mk_prepare_receptor -i examples/system.pdb --write_pdbqt prepared.pdbqt + + + + +Protonation states +------------------ + + +Adding templates +---------------- Write flags ----------- From 18ed4cb3430638055068cc012bd820d0b7f2a084 Mon Sep 17 00:00:00 2001 From: Amy He Date: Fri, 11 Oct 2024 17:44:14 -0700 Subject: [PATCH 15/61] (WIP) add colab examples pages; update index doc; update gitignore --- .gitignore | 3 + docs/source/colab_examples.rst | 90 ++++++++++++++++++++++++ docs/source/images/docking_workflow.png | Bin 0 -> 628294 bytes docs/source/index.rst | 1 + 4 files changed, 94 insertions(+) create mode 100644 docs/source/colab_examples.rst create mode 100644 docs/source/images/docking_workflow.png diff --git a/.gitignore b/.gitignore index 04a43a26..75415f85 100644 --- a/.gitignore +++ b/.gitignore @@ -1,3 +1,6 @@ +# MacOS system files +*.DS_Store + # Byte-compiled / optimized / DLL files __pycache__/ *.py[cod] diff --git a/docs/source/colab_examples.rst b/docs/source/colab_examples.rst new file mode 100644 index 00000000..ceeffe1b --- /dev/null +++ b/docs/source/colab_examples.rst @@ -0,0 +1,90 @@ +.. _colab_examples: + +Colab Examples +============ + +`Google Colaboratory `_ (Colab) is a cloud-based platform that allows users to write and execute Python codes through a browser. Regardless of the user's operating system, Colab provides Linux computing backends and some free GPU access. + +The following Colab examples are created to provide **an install-free experience** & **some generalizable workflows** of AutoDock Vina via Google Colab notebooks, which work in a similar manner to `Jupyter Notebooks `_, in the pre-configured environment with `Meeko `_ for receptor and ligand preparation, and other modules - `RDKit `_, `Scrubber `_, `ProDy `_, `reduce2 `_ (formerly `reduce `_), and `py3Dmol `_ - for conformer generation, manipulation & pre-processing of protein structures and visualization. + +**Subscription is NOT required to run these Colab examples.** Additionally, the input files for the docking calculations are either directly pulled from open databases or generated from user inputs. With that, one can easily customize the notebooks and reuse the workflow for similar calculations on different biochemical systems. + +Overview +------------------------ + +**General Workflow of Docking Calculations in Examples** + +.. image:: images/docking_workflow.png + :alt: docking workflow + :width: 100% + :align: center + +*Major Python packages used* + +* **RDKit** `https://rdkit.org/ `_ +* **Scrubber** `https://github.com/forlilab/scrubber `_ +* **Meeko** `https://github.com/forlilab/Meeko `_ +* **ProDy** `http://www.bahargroup.org/prody/ `_ +* **cctbx-base** (for reduce2) `https://github.com/cctbx/cctbx_project `_ +* **py3Dmol** `https://3dmol.org/ `_ + +*Data* + +* **Phenix-project/geostd** (for reduce2) `https://github.com/phenix-project/geostd/ `_ + +[Scrubber -> Meeko -> Vina] Basic docking +------------------------ + +`Run on Colab! `_ + +The **basic docking example** is a rewrite based on the original basic docking example in the `Vina documentation `_. In this example, a small molecule ligand (Imatinib, PDB token `STI `_) is docked back to a hollow protein structure of mouse c-Abl (PDB token `1IEP `_) to reproduce the complex structure. A docked pose that closely resembles the original position of the ligand is expected among the top-ranked poses. + + +[Scrubber -> Meeko -> Vina] Flexible docking +------ + +`Run on Colab! `_ + +The **flexible docking example** is a rewrite based on the original flexible docking example in the `Vina documentation `_. In this example, a variant of Imatinib (PDB token `PRC `_) is docked back to a hollow protein structure of mouse c-Abl (PDB token `1FPU `_) to reproduce the complex structure. Additionally, Thr315 is set to be a flexible residue. A docked pose that closely resembles the original position of the ligand and **a flipped Thr315** are expected among the top-ranked poses. + + +[Scrubber -> Meeko -> Vina] Using AD4SF in Vina +--------------- + +`Run on Colab! `_ + +The **using AutoDock4 (AD4) scoring function (SF) example** is a rewrite based on the corresponding part of the original basic docking example in the `Vina documentation `_. This example conducts the same redocking experiment as in *Basic docking* with the AutoDock4 scoring function instead of Vina. To do this, Autogrid4 is used to compute the grid maps, as an additional step after receptor preparation. + + +[Scrubber -> Meeko -> Vina] Basic docking with an RNA receptor +--------------- + +`Run on Colab! `_ + +The basic docking example is developed after the **implementation of chemical templates for common nucleotides** in Meeko, which enables the preparation of RNA/DNA receptors. In this example, a small molecule inhibitor (Ribocil B, PDB token 51B) is docked back to a hollow protein structure of a bacteria FMN riboswitch (PDB token 5C45) to reproduce the complex structure. + + +[Scrubber -> Meeko -> Vina] Basic Docking with cofactors +--------------- + +`Run on Colab! `_ + +The basic docking example is developed to showcase the usage of **import additional chemical templates** into Meeko. In this example, a small molecule antibiotic (Kanamycin A, PDB token KAN) is docked back to a hollow protein structure of a bacteria aminoglycoside kinase APH(2)-Ia (PDB token 5IQB), together with two metal cofactor Magnesium (Mg2+) ions and the substrate phosphoaminophosphonic acid-guanylate ester (GMPPNP, PDB token GNP) to reproduce the complex structure. + + +[Scrubber -> Meeko -> AutoDock-GPU] Covalent Docking +--------------- + +`Run on Colab! `_ + +The covalent docking example is based on the ***two-point attractor and flexible side chain method***. In this example, a small molecule substrate (Adenosine monophosphate, PDB token AMP) is attached onto the catalytic histidine residue of a hollow protein structure of bacteria RNA 3' cyclase (PDB token 3KGD) to reproduce the covalent intermediate complex structure. A docked pose that closely resembles the original position of the ligand is expected among the top-ranked poses. + + +[Scrubber -> Meeko -> AutoDock-GPU] Reactive Docking +--------------- + +`Run on Colab! `_ + +The reactive docking example is based on reactive docking method that has been developed for high-throughput virtual screenings of reactive species. In this example, a small molecule substrate (Adenosine monophosphate, PDB token AMP) is targeting at the catalytic histidine residue of a hollow protein structure of bacteria RNA 3' cyclase (PDB token 3KGD) to generate the near-attack conformation for the formation of the phosphoamide bond. 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z(ySS4pTXfXXk-O-fe&!z6u4OG*v(L&Wd^=L%TjjS&p6-_+o;^^FyUb~|Ns3{r%v5F zU+Q{zDejwr=hIDmM1fN!~ltfMhpb?>2vlrtx7nGkK0plE{g#b4f#83rx1hpHNBCnc?!a>FoDBZ*TFmJ0cDF;E~!LnUl@RPUVRoTwL@u=A{hzqz5$(F4d#2k#SB2;>FVdQ&MBb@0J~=fod5s; literal 0 HcmV?d00001 diff --git a/docs/source/index.rst b/docs/source/index.rst index 60e89b8f..463f2433 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -42,6 +42,7 @@ Meeko superseeds the preparation scripts from MGLTools. List advantages here (** :caption: Getting started installation + colab_examples tutorials about From 2e920110cc701b3031e757928f0c7f5d7d66e1b5 Mon Sep 17 00:00:00 2001 From: Amy He Date: Fri, 11 Oct 2024 17:50:20 -0700 Subject: [PATCH 16/61] adjust subtitles and small fixes --- docs/source/colab_examples.rst | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/docs/source/colab_examples.rst b/docs/source/colab_examples.rst index ceeffe1b..9b00a4ef 100644 --- a/docs/source/colab_examples.rst +++ b/docs/source/colab_examples.rst @@ -32,7 +32,7 @@ Overview * **Phenix-project/geostd** (for reduce2) `https://github.com/phenix-project/geostd/ `_ -[Scrubber -> Meeko -> Vina] Basic docking +[Vina] Basic Docking ------------------------ `Run on Colab! `_ @@ -40,7 +40,7 @@ Overview The **basic docking example** is a rewrite based on the original basic docking example in the `Vina documentation `_. In this example, a small molecule ligand (Imatinib, PDB token `STI `_) is docked back to a hollow protein structure of mouse c-Abl (PDB token `1IEP `_) to reproduce the complex structure. A docked pose that closely resembles the original position of the ligand is expected among the top-ranked poses. -[Scrubber -> Meeko -> Vina] Flexible docking +[Vina] Flexible Docking ------ `Run on Colab! `_ @@ -48,7 +48,7 @@ The **basic docking example** is a rewrite based on the original basic docking e The **flexible docking example** is a rewrite based on the original flexible docking example in the `Vina documentation `_. In this example, a variant of Imatinib (PDB token `PRC `_) is docked back to a hollow protein structure of mouse c-Abl (PDB token `1FPU `_) to reproduce the complex structure. Additionally, Thr315 is set to be a flexible residue. A docked pose that closely resembles the original position of the ligand and **a flipped Thr315** are expected among the top-ranked poses. -[Scrubber -> Meeko -> Vina] Using AD4SF in Vina +[Vina] Using AD4SF in Vina --------------- `Run on Colab! `_ @@ -56,7 +56,7 @@ The **flexible docking example** is a rewrite based on the original flexible doc The **using AutoDock4 (AD4) scoring function (SF) example** is a rewrite based on the corresponding part of the original basic docking example in the `Vina documentation `_. This example conducts the same redocking experiment as in *Basic docking* with the AutoDock4 scoring function instead of Vina. To do this, Autogrid4 is used to compute the grid maps, as an additional step after receptor preparation. -[Scrubber -> Meeko -> Vina] Basic docking with an RNA receptor +[Vina] Basic Docking with an RNA Receptor --------------- `Run on Colab! `_ @@ -64,7 +64,7 @@ The **using AutoDock4 (AD4) scoring function (SF) example** is a rewrite based o The basic docking example is developed after the **implementation of chemical templates for common nucleotides** in Meeko, which enables the preparation of RNA/DNA receptors. In this example, a small molecule inhibitor (Ribocil B, PDB token 51B) is docked back to a hollow protein structure of a bacteria FMN riboswitch (PDB token 5C45) to reproduce the complex structure. -[Scrubber -> Meeko -> Vina] Basic Docking with cofactors +[Vina] Basic Docking with Cofactors --------------- `Run on Colab! `_ @@ -72,15 +72,15 @@ The basic docking example is developed after the **implementation of chemical te The basic docking example is developed to showcase the usage of **import additional chemical templates** into Meeko. In this example, a small molecule antibiotic (Kanamycin A, PDB token KAN) is docked back to a hollow protein structure of a bacteria aminoglycoside kinase APH(2)-Ia (PDB token 5IQB), together with two metal cofactor Magnesium (Mg2+) ions and the substrate phosphoaminophosphonic acid-guanylate ester (GMPPNP, PDB token GNP) to reproduce the complex structure. -[Scrubber -> Meeko -> AutoDock-GPU] Covalent Docking +[AutoDock-GPU] Covalent Docking --------------- `Run on Colab! `_ -The covalent docking example is based on the ***two-point attractor and flexible side chain method***. In this example, a small molecule substrate (Adenosine monophosphate, PDB token AMP) is attached onto the catalytic histidine residue of a hollow protein structure of bacteria RNA 3' cyclase (PDB token 3KGD) to reproduce the covalent intermediate complex structure. A docked pose that closely resembles the original position of the ligand is expected among the top-ranked poses. +The covalent docking example is based on the **two-point attractor and flexible side chain method**. In this example, a small molecule substrate (Adenosine monophosphate, PDB token AMP) is attached onto the catalytic histidine residue of a hollow protein structure of bacteria RNA 3' cyclase (PDB token 3KGD) to reproduce the covalent intermediate complex structure. A docked pose that closely resembles the original position of the ligand is expected among the top-ranked poses. -[Scrubber -> Meeko -> AutoDock-GPU] Reactive Docking +[AutoDock-GPU] Reactive Docking --------------- `Run on Colab! `_ From 6aa3bc169ccee7b6e123cfb60211c06827ccb17e Mon Sep 17 00:00:00 2001 From: Amy He Date: Fri, 11 Oct 2024 18:02:33 -0700 Subject: [PATCH 17/61] drop ad4sdf example --- docs/source/colab_examples.rst | 8 -------- 1 file changed, 8 deletions(-) diff --git a/docs/source/colab_examples.rst b/docs/source/colab_examples.rst index 9b00a4ef..ce42dca1 100644 --- a/docs/source/colab_examples.rst +++ b/docs/source/colab_examples.rst @@ -48,14 +48,6 @@ The **basic docking example** is a rewrite based on the original basic docking e The **flexible docking example** is a rewrite based on the original flexible docking example in the `Vina documentation `_. In this example, a variant of Imatinib (PDB token `PRC `_) is docked back to a hollow protein structure of mouse c-Abl (PDB token `1FPU `_) to reproduce the complex structure. Additionally, Thr315 is set to be a flexible residue. A docked pose that closely resembles the original position of the ligand and **a flipped Thr315** are expected among the top-ranked poses. -[Vina] Using AD4SF in Vina ---------------- - -`Run on Colab! `_ - -The **using AutoDock4 (AD4) scoring function (SF) example** is a rewrite based on the corresponding part of the original basic docking example in the `Vina documentation `_. This example conducts the same redocking experiment as in *Basic docking* with the AutoDock4 scoring function instead of Vina. To do this, Autogrid4 is used to compute the grid maps, as an additional step after receptor preparation. - - [Vina] Basic Docking with an RNA Receptor --------------- From 3f2f8060067d475570db807426d7d3f231a08520 Mon Sep 17 00:00:00 2001 From: diogom Date: Tue, 15 Oct 2024 19:13:15 -0700 Subject: [PATCH 18/61] docs note exported Hs positions set by RDKit --- docs/source/cli_export_result.rst | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/docs/source/cli_export_result.rst b/docs/source/cli_export_result.rst index b4f91db2..641fbd21 100644 --- a/docs/source/cli_export_result.rst +++ b/docs/source/cli_export_result.rst @@ -31,3 +31,13 @@ but because this is a nearly impossible task. obabel -:"C1C=CCO1" -o pdbqt --gen3d | obabel -i pdbqt -o smi [C]1=[C][C]=[C]O1 + +Caveats +------- + +If docking does not use explicit Hs, which it often does not, the +exported positions of hydrogens are calculated from RDKit. This can +be annoying if a careful forcefield minimization is employed before +docking, as probably rigorous Hs positions will be replaced by the +RDKit geometry rules, which are empirical and much simpler than most +force fields. From e288d4ddc58f1bad307ca54d319743f7d08d828c Mon Sep 17 00:00:00 2001 From: diogom Date: Thu, 17 Oct 2024 11:55:18 -0700 Subject: [PATCH 19/61] docs for polymer template smiles --- docs/source/cli_rec_prep.rst | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/docs/source/cli_rec_prep.rst b/docs/source/cli_rec_prep.rst index 7994b1a2..a38d36ba 100644 --- a/docs/source/cli_rec_prep.rst +++ b/docs/source/cli_rec_prep.rst @@ -73,3 +73,31 @@ It is also possible to combine the two types of usage: --write_vina_box box_for_myenzyme.txt in which case the specified filenames have priority over the default basename. + + +Templates +--------- + +The templates contain SMILES strings that are used to create the RDKit +molecules that constitute every residue in the processed model. In this way, +the chemistry of the processed model is fully defined by the templates, +and the only thing that is preserved from the input are the atom positions +and the connectivity between residues. + +The SMILES strings contain all atoms that exist in the final model, +and none that do not exist. This also applies to hydrogens, +meaning that the SMILES are expected to have real hydrogens. Note that +real hydrogens are different from explicit hydrogens. Real hydrogens will be +represented as an actual atom in an RDKit molecule, while explicit hydrogens +are a just property of heavy atoms. In the SMILES, real hydrogens are defined +with square brackets "[H]" and explicit hydrogens without, e.g. "[nH]" to set +the number of explicit hydrogens on an aromatic nitrogen to one. + +Residues that are part of a polymer, which is often all of them, will have +bonds to adjacent residues. The heavy atoms involved in the bonds will miss +a real hydrogen and have an implicit (or explicit) one instead. As an +example, consider modeling an alkyl chain as a polymer, in which the monomer +is a single carbon atom. Our template SMILES would be "[H]C[H]". The RDKit +molecule will have three atoms and the carbon will have two implicit hydrogens. +The implicit hydrogens correspond to bonds to adjacent residues in the +processed polymer. From b345820693eb4185c8e3a41e00b4dbb840834e33 Mon Sep 17 00:00:00 2001 From: Amy He Date: Tue, 29 Oct 2024 23:08:30 -0700 Subject: [PATCH 20/61] (WIP) add py_build_temp to doc --- docs/source/index.rst | 7 ++++ docs/source/py_build_temp.rst | 66 +++++++++++++++++++++++++++++++++++ 2 files changed, 73 insertions(+) create mode 100644 docs/source/py_build_temp.rst diff --git a/docs/source/index.rst b/docs/source/index.rst index 463f2433..5fee9d95 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -69,5 +69,12 @@ Meeko superseeds the preparation scripts from MGLTools. List advantages here (** cli_export_result In Python +.. toctree:: + :maxdepth: 2 + :hidden: + :caption: Building residue templates + + In Python + diff --git a/docs/source/py_build_temp.rst b/docs/source/py_build_temp.rst new file mode 100644 index 00000000..37208ff1 --- /dev/null +++ b/docs/source/py_build_temp.rst @@ -0,0 +1,66 @@ +Building residue templates in Python +=================================== + +.. code-block:: python + + from meeko.chemtempgen import * + from rdkit import Chem + from rdkit.Chem import Draw + from rdkit import RDLogger + from PIL import Image + import io + import copy + import logging + import sys + + rdkit_logger = RDLogger.logger() + rdkit_logger.setLevel(RDLogger.CRITICAL) + + # Create a chemical component from the definition CIF file + basename = "CRO" # must be a recognized name in CCD (chemical component library) + CRO_from_cif = ChemicalComponent.from_cif(fetch_from_pdb(basename), basename) # needs network connection to download the definition CIF file + + def draw_cc_mol(cc_mol: Chem.Mol): + # Label atoms by atom name + for atom in cc_mol.GetAtoms(): + atom.SetProp("atomNote", atom.GetProp("atom_id")) + + # Draw the molecule + drawer = Draw.MolDraw2DCairo(600, 600) + drawer.DrawMolecule(cc_mol) + drawer.FinishDrawing() + + # Get the image as PNG + png_data = drawer.GetDrawingText() + img = Image.open(io.BytesIO(png_data)) + img.show() + + draw_cc_mol(CRO_from_cif.rdkit_mol) + +.. code-block:: python + + cc = ( + cc + .make_pretty_smiles() + .make_link_labels_from_patterns(pattern_to_label_mapping = AA_recipe.pattern_to_label_mapping_standard) + ) + cc.ResidueTemplate_check() + export_chem_templates_to_json([cc]) + +.. code-block:: bash + + ******************** New Template Built ******************** + { + "ambiguous": { + "CRO": ["CRO"] + }, + "residue_templates": { + "CRO": { + "smiles": "[H]NC([H])(C1=NC(=C([H])C2=C([H])C([H])=C(O[H])C([H])=C2[H])C(=O)N1C([H])([H])C=O)C([H])(O[H])C([H])([H])[H]", + "atom_name": ["H", "N1", "CA1", "HA1", "C1", "N2", "CA2", "CB2", "HB2", "CG2", "CD1", "HD1", "CE1", "HE1", "CZ", "OH", "HOH", "CE2", "HE2", "CD2", "HD2", "C2", "O2", "N3", "CA3", "HA31", "HA32", "C3", "O3", "CB1", "HB1", "OG1", "HOG1", "CG1", "HG11", "HG12", "HG13"], + "link_labels": {"1": "N-term", "27": "C-term"} + } + } + } + ************************************************************ + From a50fad00ca35bcda22cc1a474999cbb2993e4a71 Mon Sep 17 00:00:00 2001 From: Amy He Date: Tue, 29 Oct 2024 23:44:23 -0700 Subject: [PATCH 21/61] (WIP) add introduction in py_build_temp --- docs/source/py_build_temp.rst | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/docs/source/py_build_temp.rst b/docs/source/py_build_temp.rst index 37208ff1..9cb92d58 100644 --- a/docs/source/py_build_temp.rst +++ b/docs/source/py_build_temp.rst @@ -1,6 +1,39 @@ Building residue templates in Python =================================== +The interpretation of the valence (bonds) and formal charge of atoms is an essential step when parsing a PDB/CIF file, and the accuracy of residue mapping is crucial to the creation of a macrobiomolecule system. In Meeko, the input residue names are used as keys and the chemical templates are retrieved accordingly based on :ref:`templates `. + +For the command line script for receptor preparatoin, ``mk_prepare_receptor.py``, there are three major ways of obtaining such templates: + +(1) Loading from the default JSON file: ``Meeko/meeko/data/residue_chem_templates.json`` +This is the default residue template set curated by us, including: +- the standard residues of proteins, RNAs and DNAs, +- the modified residues from the following Amber(24) OFF library files: + +.. code-block:: bash + lib + ├── amino19.lib + ├── amino19ipq_0.9.lib + ├── aminoct19ipq_0.9.lib + ├── aminont19ipq_0.9.lib + ├── phosaa19SB.lib + ├── mod_amino19.lib + ├── RNA.lib + ├── terminalphos.LJbb-RNA.lib + ├── DNA.OL15.lib + ├── parmBSC1.lib + └── all_modrna08.lib + +- residues or ligands in CCD (Chemical Component Dictionary) that have conflicting names with the above residues. + +(2) Loading by ``--add_template`` from an additional JSON file: (example) ``Meeko/meeko/data/NAKB_templates.json`` +This is an optional add-on template set generated by us, based on the curated set of modified nucleotides by Nucleic Acid Knowledgebase (NAKB). + +(3) Fetching by CCD name on the run +When an unknown residue is encountered, ``mk_prepare_receptor.py`` attempts to resolve its chemical identity by fetching a definition CIF file from PDB (Protein Data Bank) and generates chemical templates of all possible embedding forms of it when there are inter-residue bonds. Currently, this is an automated yet relatively simple process that only supports noncovalent ligands and residues with unmodified backbones. + +Here, we present a quick guide on how to build potentially complicated residue templates on your own. + .. code-block:: python from meeko.chemtempgen import * From 8754806aee317a073a106be018dc9809ba58bafc Mon Sep 17 00:00:00 2001 From: Amy He Date: Tue, 29 Oct 2024 23:57:14 -0700 Subject: [PATCH 22/61] add internal ref --- docs/source/cli_rec_prep.rst | 1 + docs/source/py_build_temp.rst | 8 ++++++-- 2 files changed, 7 insertions(+), 2 deletions(-) diff --git a/docs/source/cli_rec_prep.rst b/docs/source/cli_rec_prep.rst index a38d36ba..b7fabe73 100644 --- a/docs/source/cli_rec_prep.rst +++ b/docs/source/cli_rec_prep.rst @@ -1,3 +1,4 @@ +.. _cli_rec_prep: The input structure is matched against templates to guarantee chemical correctness and identify problems with the input structures. diff --git a/docs/source/py_build_temp.rst b/docs/source/py_build_temp.rst index 9cb92d58..c8404cb6 100644 --- a/docs/source/py_build_temp.rst +++ b/docs/source/py_build_temp.rst @@ -6,11 +6,13 @@ The interpretation of the valence (bonds) and formal charge of atoms is an essen For the command line script for receptor preparatoin, ``mk_prepare_receptor.py``, there are three major ways of obtaining such templates: (1) Loading from the default JSON file: ``Meeko/meeko/data/residue_chem_templates.json`` + This is the default residue template set curated by us, including: - the standard residues of proteins, RNAs and DNAs, -- the modified residues from the following Amber(24) OFF library files: +- the modified residues from the following Amber24 OFF library files: .. code-block:: bash + lib ├── amino19.lib ├── amino19ipq_0.9.lib @@ -27,12 +29,14 @@ This is the default residue template set curated by us, including: - residues or ligands in CCD (Chemical Component Dictionary) that have conflicting names with the above residues. (2) Loading by ``--add_template`` from an additional JSON file: (example) ``Meeko/meeko/data/NAKB_templates.json`` + This is an optional add-on template set generated by us, based on the curated set of modified nucleotides by Nucleic Acid Knowledgebase (NAKB). (3) Fetching by CCD name on the run + When an unknown residue is encountered, ``mk_prepare_receptor.py`` attempts to resolve its chemical identity by fetching a definition CIF file from PDB (Protein Data Bank) and generates chemical templates of all possible embedding forms of it when there are inter-residue bonds. Currently, this is an automated yet relatively simple process that only supports noncovalent ligands and residues with unmodified backbones. -Here, we present a quick guide on how to build potentially complicated residue templates on your own. +Here, we present a quick guide on how to build potentially complicated residue templates on your own. In this example, we will be working with residue ``CRO``, a naturally occuring fluorophore in green fluorescent proteins formed by condensation of three consecutive residues Ser-Tyr-Gly. .. code-block:: python From 31d5d5789df3e3778b6e570c931e2a9fd7ce3ac7 Mon Sep 17 00:00:00 2001 From: Amy He Date: Wed, 30 Oct 2024 00:03:17 -0700 Subject: [PATCH 23/61] fix ref tag? --- docs/source/cli_rec_prep.rst | 3 +-- docs/source/py_build_temp.rst | 23 ++++++++++++++--------- 2 files changed, 15 insertions(+), 11 deletions(-) diff --git a/docs/source/cli_rec_prep.rst b/docs/source/cli_rec_prep.rst index b7fabe73..6a699fdc 100644 --- a/docs/source/cli_rec_prep.rst +++ b/docs/source/cli_rec_prep.rst @@ -1,5 +1,3 @@ -.. _cli_rec_prep: - The input structure is matched against templates to guarantee chemical correctness and identify problems with the input structures. This allows the user to identify and fix problems, resulting in a molecular @@ -75,6 +73,7 @@ It is also possible to combine the two types of usage: in which case the specified filenames have priority over the default basename. +.. _templates: Templates --------- diff --git a/docs/source/py_build_temp.rst b/docs/source/py_build_temp.rst index c8404cb6..51e8c915 100644 --- a/docs/source/py_build_temp.rst +++ b/docs/source/py_build_temp.rst @@ -1,18 +1,20 @@ Building residue templates in Python =================================== -The interpretation of the valence (bonds) and formal charge of atoms is an essential step when parsing a PDB/CIF file, and the accuracy of residue mapping is crucial to the creation of a macrobiomolecule system. In Meeko, the input residue names are used as keys and the chemical templates are retrieved accordingly based on :ref:`templates `. +The interpretation of the valence (bonds) and formal charge of atoms is an essential step when parsing a PDB/CIF file, and the accuracy of residue mapping is crucial to the creation of a macrobiomolecule system. In Meeko, the input residue names are used as keys and the chemical templates are retrieved accordingly based on :ref:`templates `. For the command line script for receptor preparatoin, ``mk_prepare_receptor.py``, there are three major ways of obtaining such templates: -(1) Loading from the default JSON file: ``Meeko/meeko/data/residue_chem_templates.json`` +**(1) Loading from the default JSON file:** ``Meeko/meeko/data/residue_chem_templates.json`` This is the default residue template set curated by us, including: -- the standard residues of proteins, RNAs and DNAs, -- the modified residues from the following Amber24 OFF library files: + +(a) the standard residues of proteins, RNAs and DNAs, + +(b) the modified residues from the following Amber24 OFF library files: .. code-block:: bash - + lib ├── amino19.lib ├── amino19ipq_0.9.lib @@ -26,17 +28,20 @@ This is the default residue template set curated by us, including: ├── parmBSC1.lib └── all_modrna08.lib -- residues or ligands in CCD (Chemical Component Dictionary) that have conflicting names with the above residues. +(c) residues or ligands in CCD (Chemical Component Dictionary) that have conflicting names with the above residues. -(2) Loading by ``--add_template`` from an additional JSON file: (example) ``Meeko/meeko/data/NAKB_templates.json`` +**(2) Loading by ``--add_template`` from an additional JSON file:** (example) ``Meeko/meeko/data/NAKB_templates.json`` This is an optional add-on template set generated by us, based on the curated set of modified nucleotides by Nucleic Acid Knowledgebase (NAKB). -(3) Fetching by CCD name on the run +**(3) Fetching from PDB by CCD name on the run** When an unknown residue is encountered, ``mk_prepare_receptor.py`` attempts to resolve its chemical identity by fetching a definition CIF file from PDB (Protein Data Bank) and generates chemical templates of all possible embedding forms of it when there are inter-residue bonds. Currently, this is an automated yet relatively simple process that only supports noncovalent ligands and residues with unmodified backbones. -Here, we present a quick guide on how to build potentially complicated residue templates on your own. In this example, we will be working with residue ``CRO``, a naturally occuring fluorophore in green fluorescent proteins formed by condensation of three consecutive residues Ser-Tyr-Gly. +Example usage +------------- + +Here, we present a quick guide of building potentially complicated residue templates on your own using the ``meeko.chemtempgen`` submodule. 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Currently, this is an automated yet relatively simple process that only supports noncovalent ligands and residues with unmodified backbones. -Example usage +Here, we present a quick guide of building potentially complicated residue templates on your own using the ``meeko.chemtempgen`` submodule. In this example, we will be working with residue ``CRO``, a naturally occuring fluorophore in green fluorescent proteins formed by condensation of three consecutive residues Ser-Tyr-Gly. + +Basic usage ------------- -Here, we present a quick guide of building potentially complicated residue templates on your own using the ``meeko.chemtempgen`` submodule. In this example, we will be working with residue ``CRO``, a naturally occuring fluorophore in green fluorescent proteins formed by condensation of three consecutive residues Ser-Tyr-Gly. +Before we start, we will import the required modules and optionally, suppress excess rdkit loggings that may occur during the editing of molecular structures. Then we will create a ``ChemicalComponent`` from a definition CIF file, which will be obtained by ``fetch_from_pdb`` (Internet connection is required). .. code-block:: python @@ -59,8 +61,12 @@ Here, we present a quick guide of building potentially complicated residue templ rdkit_logger.setLevel(RDLogger.CRITICAL) # Create a chemical component from the definition CIF file - basename = "CRO" # must be a recognized name in CCD (chemical component library) - CRO_from_cif = ChemicalComponent.from_cif(fetch_from_pdb(basename), basename) # needs network connection to download the definition CIF file + basename = "CRO" + CRO_from_cif = ChemicalComponent.from_cif(fetch_from_pdb(basename), basename) + +The created ``ChemicalComponent`` object, ``CRO_from_cif``, has a corresponding RDKit molecule where the atom names from the definition CIF file are stored under the ``"atom_id"`` property per atom. For a quick check, you may draw the RDKit molecule with noted atom names: + +.. code-block:: python def draw_cc_mol(cc_mol: Chem.Mol): # Label atoms by atom name @@ -79,6 +85,11 @@ Here, we present a quick guide of building potentially complicated residue templ draw_cc_mol(CRO_from_cif.rdkit_mol) +.. image:: images/starting_CRO.png + :alt: starting CRO + :width: 100% + :align: center + .. code-block:: python cc = ( From d60a73662d606c4f6af158e699b0caa0902924be Mon Sep 17 00:00:00 2001 From: Amy He Date: Wed, 30 Oct 2024 00:31:45 -0700 Subject: [PATCH 25/61] fix pic name --- docs/source/py_build_temp.rst | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/docs/source/py_build_temp.rst b/docs/source/py_build_temp.rst index b8b68362..89f38e7b 100644 --- a/docs/source/py_build_temp.rst +++ b/docs/source/py_build_temp.rst @@ -90,6 +90,26 @@ The created ``ChemicalComponent`` object, ``CRO_from_cif``, has a corresponding :width: 100% :align: center +As we may see from the picture above, in order to forge ``CRO`` into a linking embedded fragment in a protein, some atoms need to be removed. In this example, we will simply do so by specifying the atom names. ``make_embedded`` calls function ``embed`` on the duplicated object ``cc``, which takes ``embed_allowed_smarts`` as the editable zone and removes atoms matching the names in ``leaving_names``. Here, the ``embed_allowed_smarts`` is chosen to be the SMARTS of altered backbone in residue ``CRO``. Note that by default, ``embed`` removes associated hydrogens for convenience. Therefore, in this case, ``leaving_names = {"H2", "OXT"}`` removes atoms ``H2``, ``OXT`` and the associated hydrogen, ``HXT``. The same task could be alternatively done by the equivalent SMARTS pattern. + +.. code-block:: python + # Dupicate CRO_from_cif for editing + cc = copy.deepcopy(CRO_from_cif) + + # Specify the editable zone + embed_allowed_smarts = "[NX2][CX4][CX3][NX3][CX4][CX3](=O)[OX2]" + # Remove atoms by names from the chemical component + cc = cc.make_embedded(allowed_smarts = embed_allowed_smarts, leaving_names = {"H2", "OXT"}) + + # Draw the edited molecule + draw_cc_mol(cc.rdkit_mol) + +.. image:: images/embedded_CRO.png + :alt: embedded CRO + :width: 100% + :align: center + + .. code-block:: python cc = ( From 1952a1b5bf29c93b443932cc420cea012577bbc2 Mon Sep 17 00:00:00 2001 From: Amy He Date: Wed, 30 Oct 2024 00:36:58 -0700 Subject: [PATCH 26/61] add ref tag for _py_build_temp --- docs/source/images/embedded_CRO.png | Bin 0 -> 34879 bytes docs/source/py_build_temp.rst | 3 +++ 2 files changed, 3 insertions(+) create mode 100644 docs/source/images/embedded_CRO.png diff --git 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b/docs/source/py_build_temp.rst @@ -87,12 +87,12 @@ The created ``ChemicalComponent`` object, ``CRO_from_cif``, has a corresponding draw_cc_mol(CRO_from_cif.rdkit_mol) -.. image:: images/starting_CRO.png +.. image:: images/embedded_CRO.png :alt: starting CRO - :width: 100% + :width: 60% :align: center -As we may see from the picture above, in order to forge ``CRO`` into a linking embedded fragment in a protein, some atoms need to be removed. In this example, we will simply do so by specifying the atom names. ``make_embedded`` calls function ``embed`` on the duplicated object ``cc``, which takes ``embed_allowed_smarts`` as the editable zone and removes atoms matching the names in ``leaving_names``. Here, the ``embed_allowed_smarts`` is chosen to be the SMARTS of altered backbone in residue ``CRO``. Note that by default, ``embed`` removes associated hydrogens for convenience. Therefore, in this case, ``leaving_names = {"H2", "OXT"}`` removes atoms ``H2``, ``OXT`` and the associated hydrogen, ``HXT``. The same task could be alternatively done by the equivalent SMARTS pattern. +As we may see from the picture above, in order to forge ``CRO`` into a linking embedded fragment in a protein, some atoms need to be removed. In this example, we will simply do so by specifying the atom names. ``make_embedded`` calls function ``embed`` on the duplicated object ``cc``, which takes ``embed_allowed_smarts`` as the editable zone and removes atoms matching the names in ``leaving_names``. Here, the ``embed_allowed_smarts`` is chosen to be the SMARTS of altered backbone in residue ``CRO``. Note that by default, ``embed`` removes associated hydrogens for convenience. Therefore, in this case, ``leaving_names = {"H2", "OXT"}`` removes atoms ``H2``, ``OXT`` as well as the bonded hydrogen, ``HXT``. The same task could be alternatively done by the equivalent SMARTS pattern. .. code-block:: python # Dupicate CRO_from_cif for editing @@ -108,7 +108,7 @@ As we may see from the picture above, in order to forge ``CRO`` into a linking e .. image:: images/embedded_CRO.png :alt: embedded CRO - :width: 100% + :width: 60% :align: center Looking at the structure of the edited picture. From 3da76a66d062b77c4a2558d873ed0dade5614115 Mon Sep 17 00:00:00 2001 From: Amy He Date: Wed, 30 Oct 2024 01:21:46 -0700 Subject: [PATCH 28/61] completed py_build_temp --- docs/source/py_build_temp.rst | 149 ++++++++++++++++++++++++++++++++-- 1 file changed, 143 insertions(+), 6 deletions(-) diff --git a/docs/source/py_build_temp.rst b/docs/source/py_build_temp.rst index ae4cc2ba..eaeb2837 100644 --- a/docs/source/py_build_temp.rst +++ b/docs/source/py_build_temp.rst @@ -87,7 +87,7 @@ The created ``ChemicalComponent`` object, ``CRO_from_cif``, has a corresponding draw_cc_mol(CRO_from_cif.rdkit_mol) -.. image:: images/embedded_CRO.png +.. image:: images/starting_CRO.png :alt: starting CRO :width: 60% :align: center @@ -95,15 +95,12 @@ The created ``ChemicalComponent`` object, ``CRO_from_cif``, has a corresponding As we may see from the picture above, in order to forge ``CRO`` into a linking embedded fragment in a protein, some atoms need to be removed. In this example, we will simply do so by specifying the atom names. ``make_embedded`` calls function ``embed`` on the duplicated object ``cc``, which takes ``embed_allowed_smarts`` as the editable zone and removes atoms matching the names in ``leaving_names``. Here, the ``embed_allowed_smarts`` is chosen to be the SMARTS of altered backbone in residue ``CRO``. Note that by default, ``embed`` removes associated hydrogens for convenience. Therefore, in this case, ``leaving_names = {"H2", "OXT"}`` removes atoms ``H2``, ``OXT`` as well as the bonded hydrogen, ``HXT``. The same task could be alternatively done by the equivalent SMARTS pattern. .. code-block:: python - # Dupicate CRO_from_cif for editing + cc = copy.deepcopy(CRO_from_cif) - # Specify the editable zone embed_allowed_smarts = "[NX2][CX4][CX3][NX3][CX4][CX3](=O)[OX2]" - # Remove atoms by names from the chemical component cc = cc.make_embedded(allowed_smarts = embed_allowed_smarts, leaving_names = {"H2", "OXT"}) - # Draw the edited molecule draw_cc_mol(cc.rdkit_mol) .. image:: images/embedded_CRO.png @@ -111,7 +108,7 @@ As we may see from the picture above, in order to forge ``CRO`` into a linking e :width: 60% :align: center -Looking at the structure of the edited picture. +Looking at the structure of the edited picture, we will see that the unneccessary atoms have gone and the hydrogens at the broken (blunt) ends become implict, which is exactly needed to generate the Smiles string for the chemical template. Function ``make_pretty_smiles`` makes the Smiles string with all Hs explicit for the template's RDKit molecule. Last but not least, we will determin the ``link_labels`` which specifies how ``CRO`` should be connected to other residues. Here, we will use the pattern from a built-in recipe, ``AA_recipe.pattern_to_label_mapping_standard``, which also applies to all other standard amino acid residues: ``{'[NX3h1]': 'N-term', '[CX3h1]': 'C-term'}``. Opionally, we can run a ``ResidueTemplate_check`` to see potential problems with the generated template. .. code-block:: python @@ -123,6 +120,8 @@ Looking at the structure of the edited picture. cc.ResidueTemplate_check() export_chem_templates_to_json([cc]) +``export_chem_templates_to_json`` returns a JSON string of the residue template, with the corresponding content printed to console: + .. code-block:: bash ******************** New Template Built ******************** @@ -140,3 +139,141 @@ Looking at the structure of the edited picture. } ************************************************************ +You may now wonder: What if the residue locates at the C- or N-terminal of the protein? Although this is not common for ``CRO``, we will go with it for demonstration purposes. + +To make the N-terminal embedding variant of ``CRO``: + +.. code-block:: python + + # Duplicate and start over from the original chemical component + cc_N = copy.deepcopy(CRO_from_cif) + + cc_N = ( + cc_N + # Remove atom OXT + .make_embedded(allowed_smarts = embed_allowed_smarts, leaving_names = {"OXT"}) + # Cap (protonate) atom N + .make_capped(allowed_smarts = embed_allowed_smarts, capping_names = {"N1"}, protonate = True) + # (Re)generate Smiles with all Hs explicit + .make_pretty_smiles() + # Find linker atoms + .make_link_labels_from_patterns(pattern_to_label_mapping = AA_recipe.pattern_to_label_mapping_standard) + ) + + cc_N.ResidueTemplate_check() + # In case there are already residue templates with the same parent (original) residue name + cc_N.resname += "_N" + export_chem_templates_to_json([cc_N]) + +In the chained procedure above, we have removed ``OXT`` and protonated ``N1``, which is done by ``make_capped`` that adds hydrogen(s) to matching atom(s) with specified ``capping_names`` within the region of ``allowed_smarts``. The expected outout from ``export_chem_templates_to_json`` is: + +.. code-block:: bash + + Atom # 0 (N1) in mol doesn't have implicit Hs -> continue with next atom... + Molecule doesn't contain wanted_smarts: [NX3h1] -> continue with next pattern... + Molecule doesn't contain pattern: [NX3h1] -> linker label for N-term will not be made. + ******************** New Template Built ******************** + { + "ambiguous": { + "CRO": ["CRO_N"] + }, + "residue_templates": { + "CRO": { + "smiles": "[H]OC1=C([H])C([H])=C(C([H])=C2N=C(C([H])(N([H])[H])C([H])(O[H])C([H])([H])[H])N(C([H])([H])C=O)C2=O)C([H])=C1[H]", + "atom_name": ["HOH", "OH", "CZ", "CE1", "HE1", "CD1", "HD1", "CG2", "CB2", "HB2", "CA2", "N2", "C1", "CA1", "HA1", "N1", "H", "H2", "CB1", "HB1", "OG1", "HOG1", "CG1", "HG11", "HG12", "HG13", "N3", "CA3", "HA31", "HA32", "C3", "O3", "C2", "O2", "CD2", "HD2", "CE2", "HE2"], + "link_labels": {"30": "C-term"} + } + } + } + ************************************************************ + +To make the C-terminal embedding variant of ``CRO``: + +.. code-block:: python + + # Duplicate and start over from the original chemical component + cc_C = copy.deepcopy(CRO_from_cif) + + cc_C = ( + cc_C + # Deprotonate the carboxylate group + .make_canonical(acidic_proton_loc = {'[H][O][C](=O)': 0}) + # Remove atom H2 + .make_embedded(allowed_smarts = embed_allowed_smarts, leaving_names = {"H2"}) + # (Re)generate Smiles with all Hs explicit + .make_pretty_smiles() + # Find linker atoms + .make_link_labels_from_patterns(pattern_to_label_mapping = AA_recipe.pattern_to_label_mapping_standard) + ) + + cc_C.ResidueTemplate_check() + # In case there are already residue templates with the same parent (original) residue name + cc_C.resname += "_C" + export_chem_templates_to_json([cc_C]) + +In the chained procedure above, we have deprotonated the carboxylate group(s) and removed ``H2``. The deprotonation is done by ``make_canonical`` that deprotonates all protons specified by ``acidic_proton_loc``, which includes a SMARTS pattern and the index of the proton. ``chemtempgen.py`` also includes a constant ``acidic_proton_loc_canonical``, which is potentially useful as a universal protocol to deprotonate the acidic protons to get the canonical protonation state at near physiological pH. + +.. code-block:: python + + # Constants for deprotonate + acidic_proton_loc_canonical = { + # any carboxylic acid, sulfuric/sulfonic acid/ester, phosphoric/phosphinic acid/ester + '[H][O]['+atom+'](=O)': 0 for atom in ('CX3', 'SX4', 'SX3', 'PX4', 'PX3') + } | { + # any thio carboxylic/sulfuric acid + '[H][O]['+atom+'](=S)': 0 for atom in ('CX3', 'SX4') + } | { + '[H][SX2][a]': 0, # thiophenol + } + +The expected output is: + +.. code-block:: bash + + ******************** New Template Built ******************** + { + "ambiguous": { + "CRO": ["CRO_C"] + }, + "residue_templates": { + "CRO_C": { + "smiles": "[H]NC([H])(C1=NC(=C([H])C2=C([H])C([H])=C(O[H])C([H])=C2[H])C(=O)N1C([H])([H])C(=O)[O-])C([H])(O[H])C([H])([H])[H]", + "atom_name": ["H", "N1", "CA1", "HA1", "C1", "N2", "CA2", "CB2", "HB2", "CG2", "CD1", "HD1", "CE1", "HE1", "CZ", "OH", "HOH", "CE2", "HE2", "CD2", "HD2", "C2", "O2", "N3", "CA3", "HA31", "HA32", "C3", "O3", "OXT", "CB1", "HB1", "OG1", "HOG1", "CG1", "HG11", "HG12", "HG13"], + "link_labels": {"1": "N-term"} + } + } + } + ************************************************************ + +If you have generated ``cc``, ``cc_N``, and ``cc_C``, you may write them all into one JSON file: + +.. code-block:: python + + export_chem_templates_to_json([cc, cc_N, cc_C], json_fname = "CRO_templates.json") + +And below is the content of ``CRO_templates.json``, which can be loaded by ``mk_prepare_receptor --add_templates CRO_templates.json`` during receptor preparation: + +.. code-block:: bash + + { + "ambiguous": { + "CRO": ["CRO", "CRO_N", "CRO_C"] + }, + "residue_templates": { + "CRO": { + "smiles": "[H]NC([H])(C1=NC(=C([H])C2=C([H])C([H])=C(O[H])C([H])=C2[H])C(=O)N1C([H])([H])C=O)C([H])(O[H])C([H])([H])[H]", + "atom_name": ["H", "N1", "CA1", "HA1", "C1", "N2", "CA2", "CB2", "HB2", "CG2", "CD1", "HD1", "CE1", "HE1", "CZ", "OH", "HOH", "CE2", "HE2", "CD2", "HD2", "C2", "O2", "N3", "CA3", "HA31", "HA32", "C3", "O3", "CB1", "HB1", "OG1", "HOG1", "CG1", "HG11", "HG12", "HG13"], + "link_labels": {"1": "N-term", "27": "C-term"} + }, + "CRO_N": { + "smiles": "[H]OC1=C([H])C([H])=C(C([H])=C2N=C(C([H])(N([H])[H])C([H])(O[H])C([H])([H])[H])N(C([H])([H])C=O)C2=O)C([H])=C1[H]", + "atom_name": ["HOH", "OH", "CZ", "CE1", "HE1", "CD1", "HD1", "CG2", "CB2", "HB2", "CA2", "N2", "C1", "CA1", "HA1", "N1", "H", "H2", "CB1", "HB1", "OG1", "HOG1", "CG1", "HG11", "HG12", "HG13", "N3", "CA3", "HA31", "HA32", "C3", "O3", "C2", "O2", "CD2", "HD2", "CE2", "HE2"], + "link_labels": {"30": "C-term"} + }, + "CRO_C": { + "smiles": "[H]NC([H])(C1=NC(=C([H])C2=C([H])C([H])=C(O[H])C([H])=C2[H])C(=O)N1C([H])([H])C(=O)[O-])C([H])(O[H])C([H])([H])[H]", + "atom_name": ["H", "N1", "CA1", "HA1", "C1", "N2", "CA2", "CB2", "HB2", "CG2", "CD1", "HD1", "CE1", "HE1", "CZ", "OH", "HOH", "CE2", "HE2", "CD2", "HD2", "C2", "O2", "N3", "CA3", "HA31", "HA32", "C3", "O3", "OXT", "CB1", "HB1", "OG1", "HOG1", "CG1", "HG11", "HG12", "HG13"], + "link_labels": {"1": "N-term"} + } + } + } \ No newline at end of file From fd78071b6cdd5cb159fafc3f36d3317574201878 Mon Sep 17 00:00:00 2001 From: Amy He Date: Wed, 30 Oct 2024 01:25:08 -0700 Subject: [PATCH 29/61] fix img --- docs/source/images/starting_CRO.PNG | Bin 36212 -> 0 bytes docs/source/images/starting_CRO.png | Bin 0 -> 37356 bytes 2 files changed, 0 insertions(+), 0 deletions(-) delete mode 100644 docs/source/images/starting_CRO.PNG create mode 100644 docs/source/images/starting_CRO.png diff --git a/docs/source/images/starting_CRO.PNG b/docs/source/images/starting_CRO.PNG deleted 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wanted_smarts: [CX3h1] -> continue with next pattern... + Molecule doesn't contain pattern: [CX3h1] -> linker label for C-term will not be made. ******************** New Template Built ******************** { "ambiguous": { From 64d3a496328b3c12d5ef4b5eb8f5b07b487fbc15 Mon Sep 17 00:00:00 2001 From: Amy He Date: Thu, 31 Oct 2024 12:10:22 -0700 Subject: [PATCH 31/61] remove covalent docking Colab example --- docs/source/colab_examples.rst | 8 -------- 1 file changed, 8 deletions(-) diff --git a/docs/source/colab_examples.rst b/docs/source/colab_examples.rst index ce42dca1..b92554da 100644 --- a/docs/source/colab_examples.rst +++ b/docs/source/colab_examples.rst @@ -64,14 +64,6 @@ The basic docking example is developed after the **implementation of chemical te The basic docking example is developed to showcase the usage of **import additional chemical templates** into Meeko. In this example, a small molecule antibiotic (Kanamycin A, PDB token KAN) is docked back to a hollow protein structure of a bacteria aminoglycoside kinase APH(2)-Ia (PDB token 5IQB), together with two metal cofactor Magnesium (Mg2+) ions and the substrate phosphoaminophosphonic acid-guanylate ester (GMPPNP, PDB token GNP) to reproduce the complex structure. -[AutoDock-GPU] Covalent Docking ---------------- - -`Run on Colab! `_ - -The covalent docking example is based on the **two-point attractor and flexible side chain method**. In this example, a small molecule substrate (Adenosine monophosphate, PDB token AMP) is attached onto the catalytic histidine residue of a hollow protein structure of bacteria RNA 3' cyclase (PDB token 3KGD) to reproduce the covalent intermediate complex structure. A docked pose that closely resembles the original position of the ligand is expected among the top-ranked poses. - - [AutoDock-GPU] Reactive Docking --------------- From 712f4782798c94122c091c7cfcd570f66783680d Mon Sep 17 00:00:00 2001 From: Amy He Date: Sat, 2 Nov 2024 17:22:02 -0700 Subject: [PATCH 32/61] (tutorial WIP) add toctree to tutorial.rst --- docs/source/{tutorials.rst => tutorial.rst} | 8 ++++++++ docs/source/tutorial1.rst | 4 ++++ docs/source/tutorial2.rst | 4 ++++ docs/source/tutorial3.rst | 4 ++++ 4 files changed, 20 insertions(+) rename docs/source/{tutorials.rst => tutorial.rst} (61%) create mode 100644 docs/source/tutorial1.rst create mode 100644 docs/source/tutorial2.rst create mode 100644 docs/source/tutorial3.rst diff --git a/docs/source/tutorials.rst b/docs/source/tutorial.rst similarity index 61% rename from docs/source/tutorials.rst rename to docs/source/tutorial.rst index af2014ec..4e55a0db 100644 --- a/docs/source/tutorials.rst +++ b/docs/source/tutorial.rst @@ -3,3 +3,11 @@ Tutorials These tutorials cover the use of meeko in integration with other packages, including vina, autodock-gpu, ringtail, and molscrub. + +.. toctree:: + :maxdepth: 2 + :caption: Tutorials + + tutorial1 + tutorial2 + tutorial3 diff --git a/docs/source/tutorial1.rst b/docs/source/tutorial1.rst new file mode 100644 index 00000000..cfdf655c --- /dev/null +++ b/docs/source/tutorial1.rst @@ -0,0 +1,4 @@ +.. _tutorial1: + +Basic Docking (Forlilab Tutorial) +------------------------------------- \ No newline at end of file diff --git a/docs/source/tutorial2.rst b/docs/source/tutorial2.rst new file mode 100644 index 00000000..db5d2a04 --- /dev/null +++ b/docs/source/tutorial2.rst @@ -0,0 +1,4 @@ +.. _tutorial2: + +Reactive Docking +------------------------------------- \ No newline at end of file diff --git a/docs/source/tutorial3.rst b/docs/source/tutorial3.rst new file mode 100644 index 00000000..eabf8c08 --- /dev/null +++ b/docs/source/tutorial3.rst @@ -0,0 +1,4 @@ +.. _tutorial3: + +Tethered Docking +------------------------------------- \ No newline at end of file From 00be71c6f6b4f0d004e4802d15dd45635b523aba Mon Sep 17 00:00:00 2001 From: Amy He Date: Sat, 2 Nov 2024 19:04:33 -0700 Subject: [PATCH 33/61] rename tutorial.rst to tutorials.rst --- docs/source/index.rst | 2 +- docs/source/tutorial1.rst | 4 +++- docs/source/{tutorial.rst => tutorials.rst} | 0 3 files changed, 4 insertions(+), 2 deletions(-) rename docs/source/{tutorial.rst => tutorials.rst} (100%) diff --git a/docs/source/index.rst b/docs/source/index.rst index 5fee9d95..3f73800c 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -43,7 +43,7 @@ Meeko superseeds the preparation scripts from MGLTools. List advantages here (** installation colab_examples - tutorials + tutorial about .. toctree:: diff --git a/docs/source/tutorial1.rst b/docs/source/tutorial1.rst index cfdf655c..af84640a 100644 --- a/docs/source/tutorial1.rst +++ b/docs/source/tutorial1.rst @@ -1,4 +1,6 @@ .. _tutorial1: Basic Docking (Forlilab Tutorial) -------------------------------------- \ No newline at end of file +------------------------------------- + +.. code-block:: python \ No newline at end of file diff --git a/docs/source/tutorial.rst b/docs/source/tutorials.rst similarity index 100% rename from docs/source/tutorial.rst rename to docs/source/tutorials.rst From c4dad7b9ff45f7c8071e84065e197d4761f45798 Mon Sep 17 00:00:00 2001 From: Amy He Date: Sat, 2 Nov 2024 19:12:00 -0700 Subject: [PATCH 34/61] change tutorials to tutorial in index.rst --- docs/source/index.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/index.rst b/docs/source/index.rst index 3f73800c..5fee9d95 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -43,7 +43,7 @@ Meeko superseeds the preparation scripts from MGLTools. List advantages here (** installation colab_examples - tutorial + tutorials about .. toctree:: From 5fc72cfa6e0db474b6f19033eecfe62a1d1c2c8f Mon Sep 17 00:00:00 2001 From: Amy He Date: Sat, 2 Nov 2024 19:19:46 -0700 Subject: [PATCH 35/61] change maxdepth to 3 for getting started --- docs/source/index.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/index.rst b/docs/source/index.rst index 5fee9d95..7803eb7a 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -37,7 +37,7 @@ Meeko superseeds the preparation scripts from MGLTools. List advantages here (** .. toctree:: - :maxdepth: 2 + :maxdepth: 3 :hidden: :caption: Getting started From 84f727f56c01f46088f41556599919024dc63bd6 Mon Sep 17 00:00:00 2001 From: Amy He Date: Sat, 2 Nov 2024 20:29:24 -0700 Subject: [PATCH 36/61] (WIP) TOC, introduction and prerequisites for tutorial2.rst --- docs/source/tutorial2.rst | 69 ++++++++++++++++++++++++++++++++++++++- 1 file changed, 68 insertions(+), 1 deletion(-) diff --git a/docs/source/tutorial2.rst b/docs/source/tutorial2.rst index db5d2a04..b4a25096 100644 --- a/docs/source/tutorial2.rst +++ b/docs/source/tutorial2.rst @@ -1,4 +1,71 @@ .. _tutorial2: +========================= Reactive Docking -------------------------------------- \ No newline at end of file +========================= + +This is a reactive docking example that uses the AutoDock-GPU executable to generate the near-attack conformation of a small molecule and a protein receptor. + +Follow the instructions to set up the environment and run this example on your own device (Linux, MacOS or WSL). To run this example in a Colab notebook, see :ref:`colab_examples`. + +.. contents:: + :local: + :depth: 2 + +Introduction +============ + +The reactive docking example is based on reactive docking method that has been developed for high-throughput virtual screenings of reactive species. This method is currently only implemented in AutoDock-GPU. In this example, a small molecule substrate (Adenosine monophosphate, PDB token AMP) is targeting at the catalytic histidine residue of a hollow protein structure of bacteria RNA 3' cyclase (PDB token 3KGD) to generate the near-attack conformation for the formation of the phosphoamide bond. A docked pose that closely resembles the original position of the ligand is expected among the top-ranked poses. + +This tutorial is intended to showcase the Meeko usage in the preparation of receptor and ligand for reactive docking. + +Prerequisites +============= + +1. **Create a new virtual environment (recommended)** + +.. code-block:: bash + + micromamba create -c conda-forge -n meeko_tutorial python=3.10 -y + micromamba activate meeko_tutorial + +In this tutorial, we will use `micromamba` as the example package manager. Visit `this official guide `_ for a quick install and setup of micromamba. There are many equivalent ways to manage Python packages, such as `conda` and `mamba`. You can easily adapt the commands to your preferred tool, as the syntax is largely compatible across these package managers. + +2. Install the required Python packages through `conda-forge` + +.. code-block:: bash + + micromamba install -c conda-forge cctbx-base numpy scipy rdkit gemmi -y + +3. Install the additional packages and data from GitHub repositories + +- (Python package) Meeko + +.. code-block:: bash + + git clone --single-branch --branch develop https://github.com/forlilab/Meeko.git + cd Meeko; pip install --use-pep517 -e .; cd .. + +- (Python package) scrubber + +.. code-block:: bash + + git clone --single-branch --branch develop https://github.com/forlilab/scrubber.git + cd scrubber; pip install --use-pep517 -e .; cd .. + +- (Python package) ProDy + +.. code-block:: bash + + pip install prody + +- (Required data package for reduce2) Phenix Project geostd (restraint) Library + +.. code-block:: bash + + goestd_repo = "https://github.com/phenix-project/geostd.git" + git clone {goestd_repo} + +Basic Usage +=========== + From 88d450f4b72542998902a9d68c25c665067c823a Mon Sep 17 00:00:00 2001 From: Amy He Date: Sat, 2 Nov 2024 21:05:15 -0700 Subject: [PATCH 37/61] (WIP) tutorial2 --- docs/source/py_build_temp.rst | 2 +- docs/source/tutorial2.rst | 33 +++++++++++++++++++++++++-------- 2 files changed, 26 insertions(+), 9 deletions(-) diff --git a/docs/source/py_build_temp.rst b/docs/source/py_build_temp.rst index 14460e6a..079151ee 100644 --- a/docs/source/py_build_temp.rst +++ b/docs/source/py_build_temp.rst @@ -42,7 +42,7 @@ When an unknown residue is encountered, ``mk_prepare_receptor.py`` attempts to r Here, we present a quick guide of building potentially complicated residue templates on your own using the ``meeko.chemtempgen`` submodule. In this example, we will be working with residue ``CRO``, a naturally occuring fluorophore in green fluorescent proteins formed by condensation of three consecutive residues Ser-Tyr-Gly. -Basic usage +Example usage ------------- Before we start, we will import the required modules and optionally, suppress excess rdkit loggings that may occur during the editing of molecular structures. Then we will create a ``ChemicalComponent`` from a definition CIF file, which will be obtained by ``fetch_from_pdb`` (Internet connection is required). diff --git a/docs/source/tutorial2.rst b/docs/source/tutorial2.rst index b4a25096..ce2b5f18 100644 --- a/docs/source/tutorial2.rst +++ b/docs/source/tutorial2.rst @@ -13,14 +13,14 @@ Follow the instructions to set up the environment and run this example on your o :depth: 2 Introduction -============ +------------ The reactive docking example is based on reactive docking method that has been developed for high-throughput virtual screenings of reactive species. This method is currently only implemented in AutoDock-GPU. In this example, a small molecule substrate (Adenosine monophosphate, PDB token AMP) is targeting at the catalytic histidine residue of a hollow protein structure of bacteria RNA 3' cyclase (PDB token 3KGD) to generate the near-attack conformation for the formation of the phosphoamide bond. A docked pose that closely resembles the original position of the ligand is expected among the top-ranked poses. This tutorial is intended to showcase the Meeko usage in the preparation of receptor and ligand for reactive docking. -Prerequisites -============= +Prerequisites and Environment Setup +----------------------------------- 1. **Create a new virtual environment (recommended)** @@ -29,7 +29,7 @@ Prerequisites micromamba create -c conda-forge -n meeko_tutorial python=3.10 -y micromamba activate meeko_tutorial -In this tutorial, we will use `micromamba` as the example package manager. Visit `this official guide `_ for a quick install and setup of micromamba. There are many equivalent ways to manage Python packages, such as `conda` and `mamba`. You can easily adapt the commands to your preferred tool, as the syntax is largely compatible across these package managers. +In this tutorial, we will use ``micromamba`` as the example package manager. Visit `this official guide `_ for a quick install and setup of micromamba. There are many equivalent ways to manage Python packages, such as ``conda`` and ``mamba``. You can easily adapt the commands to your preferred tool, as the syntax is largely compatible across these package managers. 2. Install the required Python packages through `conda-forge` @@ -37,6 +37,8 @@ In this tutorial, we will use `micromamba` as the example package manager. Visit micromamba install -c conda-forge cctbx-base numpy scipy rdkit gemmi -y +Expose ``reduce2.py`` to system ``PATH`` + 3. Install the additional packages and data from GitHub repositories - (Python package) Meeko @@ -63,9 +65,24 @@ In this tutorial, we will use `micromamba` as the example package manager. Visit .. code-block:: bash - goestd_repo = "https://github.com/phenix-project/geostd.git" - git clone {goestd_repo} + git clone https://github.com/phenix-project/geostd.git + + +Ligand Peparation +----------------- + + +Receptor Peparation +----------------- -Basic Usage -=========== +.. code-block:: bash + + pdb_token="3kgd" + curl "http://files.rcsb.org/view/$pdb_token.pdb" -o "$pdb_token.pdb" + +.. code-block:: bash + reduce2="$(python -c "import site; print(site.getsitepackages()[0])")/mmtbx/command_line/reduce2.py" + chmod +x $reduce2 + geostd="$(realpath geostd)" + export MMTBX_CCP4_MONOMER_LIB=$geostd \ No newline at end of file From 672dafa8202f4a396e3eccccd3010e13b427e220 Mon Sep 17 00:00:00 2001 From: Amy He Date: Sat, 2 Nov 2024 21:52:26 -0700 Subject: [PATCH 38/61] (WIP) tutorial2, code block --- docs/source/tutorial2.rst | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/docs/source/tutorial2.rst b/docs/source/tutorial2.rst index ce2b5f18..f23aa32d 100644 --- a/docs/source/tutorial2.rst +++ b/docs/source/tutorial2.rst @@ -71,6 +71,16 @@ Expose ``reduce2.py`` to system ``PATH`` Ligand Peparation ----------------- +.. code-block:: bash + ligand_smiles="c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)([O-])[O-])O)O)N" + scrub.py $ligand_smiles -o AMP.sdf --ph 6.5 --skip_tautomer --skip_acidbase + +.. code-block:: bash + reactive_smarts="COP(=O)([O-])[O-]" + reactive_smarts_idx=3 + mk_prepare_ligand.py -i AMP.sdf -o AMP.pdbqt \ + --reactive_smarts $reactive_smarts \ + --reactive_smarts_idx $reactive_smarts_idx Receptor Peparation ----------------- From 4567b86149a84fe3e31d33b14b2e68b068c4404b Mon Sep 17 00:00:00 2001 From: Amy He Date: Sat, 2 Nov 2024 22:04:09 -0700 Subject: [PATCH 39/61] format code blocks that are multiple lines --- docs/source/tutorial2.rst | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/docs/source/tutorial2.rst b/docs/source/tutorial2.rst index f23aa32d..d8081c97 100644 --- a/docs/source/tutorial2.rst +++ b/docs/source/tutorial2.rst @@ -72,10 +72,12 @@ Ligand Peparation ----------------- .. code-block:: bash + ligand_smiles="c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)([O-])[O-])O)O)N" scrub.py $ligand_smiles -o AMP.sdf --ph 6.5 --skip_tautomer --skip_acidbase .. code-block:: bash + reactive_smarts="COP(=O)([O-])[O-]" reactive_smarts_idx=3 mk_prepare_ligand.py -i AMP.sdf -o AMP.pdbqt \ @@ -90,6 +92,19 @@ Receptor Peparation pdb_token="3kgd" curl "http://files.rcsb.org/view/$pdb_token.pdb" -o "$pdb_token.pdb" +.. code-block:: bash + + python - < Date: Sat, 2 Nov 2024 22:36:18 -0700 Subject: [PATCH 40/61] add code blocks in tutorial2 --- docs/source/tutorial2.rst | 48 +++++++++++++++++++++++++++++++++++++-- 1 file changed, 46 insertions(+), 2 deletions(-) diff --git a/docs/source/tutorial2.rst b/docs/source/tutorial2.rst index d8081c97..fa478165 100644 --- a/docs/source/tutorial2.rst +++ b/docs/source/tutorial2.rst @@ -90,7 +90,7 @@ Receptor Peparation .. code-block:: bash pdb_token="3kgd" - curl "http://files.rcsb.org/view/$pdb_token.pdb" -o "$pdb_token.pdb" + curl "http://files.rcsb.org/view/${pdb_token}.pdb" -o "${pdb_token}.pdb" .. code-block:: bash @@ -105,9 +105,53 @@ Receptor Peparation writePDB(prody_receptorPDB, receptor_atoms) EOF + # Add CRYST1 card (temporarily required for reduce2) + cat <(grep "CRYST1" "${pdb_token}.pdb") "${pdb_token}_receptor_atoms.pdb" > "${pdb_token}_receptor.pdb" + .. code-block:: bash reduce2="$(python -c "import site; print(site.getsitepackages()[0])")/mmtbx/command_line/reduce2.py" chmod +x $reduce2 geostd="$(realpath geostd)" - export MMTBX_CCP4_MONOMER_LIB=$geostd \ No newline at end of file + export MMTBX_CCP4_MONOMER_LIB=$geostd + reduce_opts="approach=add add_flip_movers=True" + python $reduce2 "${pdb_token}_receptor.pdb" $reduce_opts + +.. code-block:: bash + + python - < 2510 atoms and 1 coordinate set(s) were parsed in 0.01s. + + Flexible residues: + chain resnum is_reactive reactive_atom + A 309 True NE2 + reactive_flexres={'A:309'} + + For reactive docking, pass the configuration file to AutoDock-GPU: + autodock_gpu -C 1 --import_dpf 3kgd_receptorH.reactive_config --flexres 3kgd_receptorH_flex.pdbqt -L + + + Files written: + 3kgd_receptorH_flex.pdbqt <-- flexible receptor input file + 3kgd_receptorH_rigid.pdbqt <-- static (i.e., rigid) receptor input file + boron-silicon-atom_par.dat <-- atomic parameters for B and Si (for autogrid) + 3kgd_receptorH_rigid.gpf <-- autogrid input file + 3kgd_receptorH.box.pdb <-- PDB file to visualize the grid box + 3kgd_receptorH.reactive_config <-- reactive parameters for AutoDock-GPU \ No newline at end of file From 5928ae87df22ae1d8b2b3b1936c82880405ceee8 Mon Sep 17 00:00:00 2001 From: Amy He Date: Sat, 2 Nov 2024 22:38:20 -0700 Subject: [PATCH 41/61] use python highlitighting for heredoc --- docs/source/tutorial2.rst | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/docs/source/tutorial2.rst b/docs/source/tutorial2.rst index fa478165..dd78e236 100644 --- a/docs/source/tutorial2.rst +++ b/docs/source/tutorial2.rst @@ -92,7 +92,7 @@ Receptor Peparation pdb_token="3kgd" curl "http://files.rcsb.org/view/${pdb_token}.pdb" -o "${pdb_token}.pdb" -.. code-block:: bash +.. code-block:: python python - < "${pdb_token}_receptor.pdb" @@ -117,7 +119,7 @@ Receptor Peparation reduce_opts="approach=add add_flip_movers=True" python $reduce2 "${pdb_token}_receptor.pdb" $reduce_opts -.. code-block:: bash +.. code-block:: python python - < Date: Sat, 2 Nov 2024 22:49:49 -0700 Subject: [PATCH 42/61] add level4 heading for 1.2.3. in Prerequisites --- docs/source/tutorial2.rst | 3 +++ 1 file changed, 3 insertions(+) diff --git a/docs/source/tutorial2.rst b/docs/source/tutorial2.rst index dd78e236..eea17607 100644 --- a/docs/source/tutorial2.rst +++ b/docs/source/tutorial2.rst @@ -23,6 +23,7 @@ Prerequisites and Environment Setup ----------------------------------- 1. **Create a new virtual environment (recommended)** +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. code-block:: bash @@ -32,6 +33,7 @@ Prerequisites and Environment Setup In this tutorial, we will use ``micromamba`` as the example package manager. Visit `this official guide `_ for a quick install and setup of micromamba. There are many equivalent ways to manage Python packages, such as ``conda`` and ``mamba``. You can easily adapt the commands to your preferred tool, as the syntax is largely compatible across these package managers. 2. Install the required Python packages through `conda-forge` +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. code-block:: bash @@ -40,6 +42,7 @@ In this tutorial, we will use ``micromamba`` as the example package manager. Vis Expose ``reduce2.py`` to system ``PATH`` 3. Install the additional packages and data from GitHub repositories +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - (Python package) Meeko From c8a5ba3d05700758a57adf1a7d6d5a8882db5f6c Mon Sep 17 00:00:00 2001 From: Amy He Date: Sat, 2 Nov 2024 22:50:05 -0700 Subject: [PATCH 43/61] add level4 heading for 1.2.3. in Prerequisites 2 --- docs/source/tutorial2.rst | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/docs/source/tutorial2.rst b/docs/source/tutorial2.rst index eea17607..d19d5fa5 100644 --- a/docs/source/tutorial2.rst +++ b/docs/source/tutorial2.rst @@ -13,14 +13,14 @@ Follow the instructions to set up the environment and run this example on your o :depth: 2 Introduction ------------- +============ The reactive docking example is based on reactive docking method that has been developed for high-throughput virtual screenings of reactive species. This method is currently only implemented in AutoDock-GPU. In this example, a small molecule substrate (Adenosine monophosphate, PDB token AMP) is targeting at the catalytic histidine residue of a hollow protein structure of bacteria RNA 3' cyclase (PDB token 3KGD) to generate the near-attack conformation for the formation of the phosphoamide bond. A docked pose that closely resembles the original position of the ligand is expected among the top-ranked poses. This tutorial is intended to showcase the Meeko usage in the preparation of receptor and ligand for reactive docking. Prerequisites and Environment Setup ------------------------------------ +=================================== 1. **Create a new virtual environment (recommended)** ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -72,7 +72,9 @@ Expose ``reduce2.py`` to system ``PATH`` Ligand Peparation ------------------ +================= + +In this step, the ligand molecule is prepared from a Smiles string. A protonated 3D conformer of ligand is generated by ``scrub.py``, and the conversion to a tangible ligand PDBQT file is done by ``mk_prepare_ligand.py``. .. code-block:: bash @@ -88,7 +90,7 @@ Ligand Peparation --reactive_smarts_idx $reactive_smarts_idx Receptor Peparation ------------------ +=================== .. code-block:: bash From 3b4f3c99afc22bcdb62178db520b680f50e7e85b Mon Sep 17 00:00:00 2001 From: Amy He Date: Sun, 3 Nov 2024 11:32:24 -0800 Subject: [PATCH 44/61] (WIP) insert pic to tutorial2 --- docs/source/images/highlighted_AMP.png | Bin 0 -> 33520 bytes docs/source/tutorial2.rst | 27 ++++++++++++++++--------- 2 files changed, 18 insertions(+), 9 deletions(-) create mode 100644 docs/source/images/highlighted_AMP.png diff --git a/docs/source/images/highlighted_AMP.png b/docs/source/images/highlighted_AMP.png new file mode 100644 index 0000000000000000000000000000000000000000..b9a3622142003db94807d79f49b932afbc07468d GIT binary patch literal 33520 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zI-XzcztI_jh1DOTBMx~71^pRzQ*%ESJWKj!3m)il1_~$pa9HZ#_J@9vHuS4r zN1JBnv)7f&9S$7EkWBWybl1&;83n#Q#vTq1#;yUtaZ-8CrM8Rs)d1u1tEutO0JW>ezBbYa!n%HV7643{F!O= zEsFPkz175TM)3pfkF{54Hn+>{XHPc~N%Y-P4{BOby$U!AB*TOWb=?!b?A(VjbdyLs zX4l;mDX*_xyX9A=NWif|LMQeIjuolsdWy;48#qIfll83_9p#MLKBR z4}78hZAD2GG08-;iJ@ct$3%1mAB-xEKf4W89I6oPg|nT>Bgcmb=Yol6qN1IK^MNym zJ{$oNIK$|m*+g0MwZcbpE5)Vc`(}lfZNCUF1s`Le2c|*;2O5-z!g!834G(M*C9Cx%lh=89ulVn; z{J#(ao8I|NL;JJ-Z-@UI!~dN&|GQHD3vUjKH~K5@-o2ZUl@wF`FS<9r!634;i=wgf S9s^(Qovf6CWSO|0|NjBU2F&UJ literal 0 HcmV?d00001 diff --git a/docs/source/tutorial2.rst b/docs/source/tutorial2.rst index d19d5fa5..7fa8b03d 100644 --- a/docs/source/tutorial2.rst +++ b/docs/source/tutorial2.rst @@ -22,8 +22,8 @@ This tutorial is intended to showcase the Meeko usage in the preparation of rece Prerequisites and Environment Setup =================================== -1. **Create a new virtual environment (recommended)** -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +Create a new virtual environment (recommended) +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. code-block:: bash @@ -32,17 +32,15 @@ Prerequisites and Environment Setup In this tutorial, we will use ``micromamba`` as the example package manager. Visit `this official guide `_ for a quick install and setup of micromamba. There are many equivalent ways to manage Python packages, such as ``conda`` and ``mamba``. You can easily adapt the commands to your preferred tool, as the syntax is largely compatible across these package managers. -2. Install the required Python packages through `conda-forge` -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +Install the required Python packages through ``conda-forge`` +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. code-block:: bash micromamba install -c conda-forge cctbx-base numpy scipy rdkit gemmi -y -Expose ``reduce2.py`` to system ``PATH`` - -3. Install the additional packages and data from GitHub repositories -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +Install the additional packages and data from GitHub repositories +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - (Python package) Meeko @@ -76,10 +74,19 @@ Ligand Peparation In this step, the ligand molecule is prepared from a Smiles string. A protonated 3D conformer of ligand is generated by ``scrub.py``, and the conversion to a tangible ligand PDBQT file is done by ``mk_prepare_ligand.py``. +.. image:: images/highlighted_AMP.png + :alt: highlighted AMP + :width: 60% + :align: center + +The ligand of this example is AMP (adenosine monophosphate). We will use its isomeric Smiles string as the input, and manually write the phosphate group in the -2 charge state. ``scrub.py`` will generate an SDF file, ``AMP.sdf``, containing a 3D conformer of AMP (2-) with all explicit hydrogens. + .. code-block:: bash ligand_smiles="c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)([O-])[O-])O)O)N" - scrub.py $ligand_smiles -o AMP.sdf --ph 6.5 --skip_tautomer --skip_acidbase + scrub.py $ligand_smiles -o AMP.sdf --skip_tautomer --skip_acidbase + +To prepare AMP (2-) as an reactive ligand, we specify the reactive phosphoryl atom by Smarts string ``COP(=O)([O-])[O-]`` and the index number ``3``. With ``AMP.sdf`` as the input file, the command-line script ``mk_prepare_ligand.py`` looks for matches of the Smarts string ``reactive_smarts`` in the input molecule structure, making the ith atom in the match a reactive atom based on the 1-based index number ``reactive_smarts_idx``. .. code-block:: bash @@ -89,6 +96,8 @@ In this step, the ligand molecule is prepared from a Smiles string. A protonated --reactive_smarts $reactive_smarts \ --reactive_smarts_idx $reactive_smarts_idx +The expected output + Receptor Peparation =================== From 5b8dcec66b74163998ee89f7c606b2e92eec2949 Mon Sep 17 00:00:00 2001 From: Amy He Date: Sun, 3 Nov 2024 11:57:53 -0800 Subject: [PATCH 45/61] (WIP) done ligand preparation --- docs/source/tutorial2.rst | 60 +++++++++++++++++++++++++++++++++++++-- 1 file changed, 58 insertions(+), 2 deletions(-) diff --git a/docs/source/tutorial2.rst b/docs/source/tutorial2.rst index 7fa8b03d..1d65afd6 100644 --- a/docs/source/tutorial2.rst +++ b/docs/source/tutorial2.rst @@ -6,7 +6,7 @@ Reactive Docking This is a reactive docking example that uses the AutoDock-GPU executable to generate the near-attack conformation of a small molecule and a protein receptor. -Follow the instructions to set up the environment and run this example on your own device (Linux, MacOS or WSL). To run this example in a Colab notebook, see :ref:`colab_examples`. +Follow the instructions to set up the environment and run this command-line example on your own device (Linux, MacOS or WSL). To run this example in a Colab notebook, see :ref:`colab_examples`. .. contents:: :local: @@ -96,11 +96,67 @@ To prepare AMP (2-) as an reactive ligand, we specify the reactive phosphoryl at --reactive_smarts $reactive_smarts \ --reactive_smarts_idx $reactive_smarts_idx -The expected output +The generated ligand PDBQT file, ``AMP.pdbqt``, will contain special AutoDock atom types for the reactive docking. The reactive atom types encode the atom type as well as the adjacency to the reactive atom. In this example: ``P1`` denotes the reactive phosphorus atom (with order number = 1). ``O5`` denotes the neighbor ``OA`` atoms (with order number = 2). Because the original atom type (``OA``) contains 2 letters, an additional increment of +3 is applied to the number suffix. And finally ``C3`` denotes the further ``C`` type atom (aliphatic carbon, with order number = 3). + +.. code-block:: bash + REMARK SMILES Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)([O-])[O-])[C@@H](O)[C@H]1O + REMARK SMILES IDX 11 1 22 2 20 3 13 4 12 5 10 6 4 7 3 8 5 9 2 10 6 11 7 12 + REMARK SMILES IDX 8 13 9 14 1 15 23 18 21 20 14 22 15 23 16 24 17 25 18 26 + REMARK SMILES IDX 19 27 + REMARK H PARENT 1 16 1 17 23 19 21 21 + ROOT + ATOM 1 C UNL 1 0.091 -0.756 0.545 1.00 0.00 0.253 C + ATOM 2 C UNL 1 0.369 -1.495 -0.773 1.00 0.00 0.195 C + ATOM 3 C UNL 1 1.476 -0.670 -1.387 1.00 0.00 0.179 C + ATOM 4 C UNL 1 2.147 -0.047 -0.164 1.00 0.00 0.178 C + ATOM 5 O UNL 1 1.163 0.124 0.832 1.00 0.00 -0.347 OA + ENDROOT + BRANCH 1 6 + ATOM 6 N UNL 1 -1.156 0.007 0.449 1.00 0.00 -0.285 N + ATOM 7 C UNL 1 -4.095 -1.786 1.544 1.00 0.00 0.226 A + ATOM 8 N UNL 1 -5.018 -0.824 1.216 1.00 0.00 -0.217 NA + ATOM 9 N UNL 1 -2.764 -1.577 1.316 1.00 0.00 -0.216 NA + ATOM 10 C UNL 1 -4.639 0.363 0.654 1.00 0.00 0.155 A + ATOM 11 C UNL 1 -2.392 -0.395 0.766 1.00 0.00 0.167 A + ATOM 12 C UNL 1 -3.282 0.566 0.430 1.00 0.00 0.150 A + ATOM 13 N UNL 1 -2.654 1.617 -0.131 1.00 0.00 -0.231 NA + ATOM 14 C UNL 1 -1.348 1.232 -0.108 1.00 0.00 0.204 A + BRANCH 10 15 + ATOM 15 N UNL 1 -5.614 1.348 0.310 1.00 0.00 -0.382 N + ATOM 16 H UNL 1 -5.332 2.257 -0.120 1.00 0.00 0.158 HD + ATOM 17 H UNL 1 -6.627 1.168 0.488 1.00 0.00 0.158 HD + ENDBRANCH 10 15 + ENDBRANCH 1 6 + BRANCH 2 18 + ATOM 18 O UNL 1 0.753 -2.832 -0.545 1.00 0.00 -0.386 OA + ATOM 19 H UNL 1 1.495 -2.835 0.115 1.00 0.00 0.211 HD + ENDBRANCH 2 18 + BRANCH 3 20 + ATOM 20 O UNL 1 2.354 -1.419 -2.197 1.00 0.00 -0.387 OA + ATOM 21 H UNL 1 2.901 -2.009 -1.617 1.00 0.00 0.211 HD + ENDBRANCH 3 20 + BRANCH 4 22 + ATOM 22 C UNL 1 2.798 1.302 -0.496 1.00 0.00 0.201 C3 + BRANCH 22 23 + ATOM 23 O UNL 1 3.411 1.842 0.657 1.00 0.00 -0.348 O5 + BRANCH 23 24 + ATOM 24 P UNL 1 5.100 1.600 0.586 1.00 0.00 0.060 P1 + ATOM 25 O UNL 1 5.699 2.493 -0.477 1.00 0.00 -0.326 O5 + ATOM 26 O UNL 1 5.775 1.996 2.085 1.00 0.00 -0.790 O5 + ATOM 27 O UNL 1 5.459 -0.015 0.231 1.00 0.00 -0.790 O5 + ENDBRANCH 23 24 + ENDBRANCH 22 23 + ENDBRANCH 4 22 + TORSDOF 7 + Receptor Peparation =================== +The preparation of a rigid receptor consists of two steps. The receptor structure is first sourced from a PDB file and sent to ``reduce2.py`` for hydrogen addition and optimization, and then, the conversion to a tangible receptor PDBQT file is done by ``mk_prepare_receptor.py``. + +In this example, we will retrieve the PDB structure by token ``3kgd`` from + .. code-block:: bash pdb_token="3kgd" From 9d5a1ac076bb67b2f50f89eef7abdaea8271e2d0 Mon Sep 17 00:00:00 2001 From: Amy He Date: Sun, 3 Nov 2024 13:22:32 -0800 Subject: [PATCH 46/61] (WIP) done receptor preparation --- docs/source/tutorial2.rst | 29 ++++++++++++++++++++++++----- 1 file changed, 24 insertions(+), 5 deletions(-) diff --git a/docs/source/tutorial2.rst b/docs/source/tutorial2.rst index 1d65afd6..0e15d6af 100644 --- a/docs/source/tutorial2.rst +++ b/docs/source/tutorial2.rst @@ -69,7 +69,7 @@ Install the additional packages and data from GitHub repositories git clone https://github.com/phenix-project/geostd.git -Ligand Peparation +Ligand Preparation ================= In this step, the ligand molecule is prepared from a Smiles string. A protonated 3D conformer of ligand is generated by ``scrub.py``, and the conversion to a tangible ligand PDBQT file is done by ``mk_prepare_ligand.py``. @@ -150,18 +150,20 @@ The generated ligand PDBQT file, ``AMP.pdbqt``, will contain special AutoDock at TORSDOF 7 -Receptor Peparation +Receptor Preparation =================== The preparation of a rigid receptor consists of two steps. The receptor structure is first sourced from a PDB file and sent to ``reduce2.py`` for hydrogen addition and optimization, and then, the conversion to a tangible receptor PDBQT file is done by ``mk_prepare_receptor.py``. -In this example, we will retrieve the PDB structure by token ``3kgd`` from +In this example, we begin from retrieving the PDB structure by token ``3kgd`` from RCSB PDB. .. code-block:: bash pdb_token="3kgd" curl "http://files.rcsb.org/view/${pdb_token}.pdb" -o "${pdb_token}.pdb" +Next, we will run a Python script to write ProDy selection ``chain A and not water and not hetero and not resname AMP`` to a PDB file ``3kgd_receptor_atoms.pdb``. + .. code-block:: python python - < "${pdb_token}_receptor.pdb" +In this example, we use ``reduce2.py`` to add hydrogen atoms to the receptor structure and optimize the positions. There are various other tools (``H++``, ``APBS``, etc.) of choices for this task. It should also be noted that ``mk_prepare_receptor.py`` does not neccessarily need the presence of all hydrogens in the input receptor structure – The missing hydrogens will be added through RDKit functions during the receptor preparation with ProDy selection ``chain A and not water and not hetero and not resname AMP`` to a PDB file ``3kgd_receptor_atoms.pdb``. + .. code-block:: bash + # setting up reduce2 for the first time in the environment reduce2="$(python -c "import site; print(site.getsitepackages()[0])")/mmtbx/command_line/reduce2.py" chmod +x $reduce2 geostd="$(realpath geostd)" export MMTBX_CCP4_MONOMER_LIB=$geostd + + # running reduce2 on the example receptor PDB reduce_opts="approach=add add_flip_movers=True" python $reduce2 "${pdb_token}_receptor.pdb" $reduce_opts +After running the last command above, ``reduce2.py`` will conclude a normal execution with a log file ``3kgd_receptorH.txt`` and a protonated receptor structure file ``3kgd_receptorH.pdb`` – The PDB file can then be fed to ``mk_prepare_receptor.py`` to generate the receptor PDBQT file. But before that, we could (optionally) save the original position of residue AMP and use it to define the grid box for docking. To do this, we will use ProDy selection ``chain A and resname AMP`` to write a PDB file ``LIG.pdb`` + .. code-block:: python python - < 2510 atoms and 1 coordinate set(s) were parsed in 0.01s. @@ -228,4 +244,7 @@ In this example, we will retrieve the PDB structure by token ``3kgd`` from boron-silicon-atom_par.dat <-- atomic parameters for B and Si (for autogrid) 3kgd_receptorH_rigid.gpf <-- autogrid input file 3kgd_receptorH.box.pdb <-- PDB file to visualize the grid box - 3kgd_receptorH.reactive_config <-- reactive parameters for AutoDock-GPU \ No newline at end of file + 3kgd_receptorH.reactive_config <-- reactive parameters for AutoDock-GPU + +Docking Calculation +================= \ No newline at end of file From e9df2a8934124a6fe4a4820c249a7c1c93328bde Mon Sep 17 00:00:00 2001 From: Amy He Date: Sun, 3 Nov 2024 14:24:51 -0800 Subject: [PATCH 47/61] finish editing tutorial2 --- docs/source/tutorial2.rst | 59 +++++++++++++++++++++++++++++++++++++-- 1 file changed, 57 insertions(+), 2 deletions(-) diff --git a/docs/source/tutorial2.rst b/docs/source/tutorial2.rst index 0e15d6af..2455732b 100644 --- a/docs/source/tutorial2.rst +++ b/docs/source/tutorial2.rst @@ -99,6 +99,7 @@ To prepare AMP (2-) as an reactive ligand, we specify the reactive phosphoryl at The generated ligand PDBQT file, ``AMP.pdbqt``, will contain special AutoDock atom types for the reactive docking. The reactive atom types encode the atom type as well as the adjacency to the reactive atom. In this example: ``P1`` denotes the reactive phosphorus atom (with order number = 1). ``O5`` denotes the neighbor ``OA`` atoms (with order number = 2). Because the original atom type (``OA``) contains 2 letters, an additional increment of +3 is applied to the number suffix. And finally ``C3`` denotes the further ``C`` type atom (aliphatic carbon, with order number = 3). .. code-block:: bash + REMARK SMILES Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)([O-])[O-])[C@@H](O)[C@H]1O REMARK SMILES IDX 11 1 22 2 20 3 13 4 12 5 10 6 4 7 3 8 5 9 2 10 6 11 7 12 REMARK SMILES IDX 8 13 9 14 1 15 23 18 21 20 14 22 15 23 16 24 17 25 18 26 @@ -149,7 +150,6 @@ The generated ligand PDBQT file, ``AMP.pdbqt``, will contain special AutoDock at ENDBRANCH 4 22 TORSDOF 7 - Receptor Preparation =================== @@ -246,5 +246,60 @@ For output control: We are expecting at least two types of files, the receptor P 3kgd_receptorH.box.pdb <-- PDB file to visualize the grid box 3kgd_receptorH.reactive_config <-- reactive parameters for AutoDock-GPU +The expected ``3kgd_receptorH_flex.pdbqt`` contains the reactive flexible residue, His309. Note that for the receptor residues, the reactive atom types may include a number prefix as an identifier to distinguish among possible multiple reactive residues. + +.. code-block:: bash + + BEGIN_RES HIS A 309 + REMARK INDEX MAP 3 1 15 2 18 3 19 4 20 5 21 6 22 7 25 8 + ROOT + ATOM 1 CA HIS A 309 -1.221 -40.602 -5.650 1.00 0.00 0.177 C + ENDROOT + BRANCH 1 2 + ATOM 2 CB HIS A 309 -2.472 -39.882 -5.156 1.00 0.00 0.093 C + BRANCH 2 3 + ATOM 3 CG HIS A 309 -3.505 -40.770 -4.538 1.00 0.00 0.061 1A3 + ATOM 4 ND1 HIS A 309 -3.678 -42.083 -4.910 1.00 0.00 -0.242 1N6 + ATOM 5 CD2 HIS A 309 -4.442 -40.512 -3.593 1.00 0.00 0.107 1A2 + ATOM 6 CE1 HIS A 309 -4.660 -42.611 -4.192 1.00 0.00 0.196 1A2 + ATOM 7 NE2 HIS A 309 -5.152 -41.670 -3.401 1.00 0.00 -0.350 1N1 + ATOM 8 HE2 HIS A 309 -5.940 -41.788 -2.748 1.00 0.00 0.167 1H5 + ENDBRANCH 2 3 + ENDBRANCH 1 2 + END_RES HIS A 309 + Docking Calculation -================= \ No newline at end of file +=================== + +The reactive docking method is only implemented in AutoDock-GPU, which also requires grid map computation with AutoGrid4 before the docking calculation. + +The previously generated GPF file (``3kgd_receptorH_rigid.gpf``), together with the PDBQT file of the rigid part of the receptor (``3kgd_receptorH_rigid.pdbqt``), will be used to compute the grid maps: + +.. code-block:: bash + + ./autogrid4 -p 3kgd_receptorH_rigid.gpf + +And to run the docking calculation, the ligand PDBQT file (``AMP.pdbqt``), the flexible residue PDBQT file (``3kgd_receptorH_flex.pdbqt``), the special docking parameter file (DPF) for reactive docking (``3kgd_receptorH.reactive_config``), and the map files will be needed. With the following command for docking calculation, the output file will have basename ``AMP``. + +.. code-block:: bash + + ./adgpu --lfile AMP.pdbqt --flexres 3kgd_receptorH_flex.pdbqt --ffile 3kgd_receptorH_rigid.maps.fld --import_dpf 3kgd_receptorH.reactive_config --resnam AMP + + +If you're running these calculations on Google T4 backends, here are the pre-compiled executables of autogrid4 and adgpu specifically for T4: + +- autodock-gpu v1.5.3 +`autodock_gpu_128wi `_ +`adgpu_analysis `_ + +- autogrid v4.2.6 +`autogrid4 `_ + +Export the Docking Poses +======================== + +``mk_export.py`` is a command-line script in Meeko to export docking poses from PDBQT or DLG formats. For this example, if we want to export the ligand docking poses to a (possibly multi-model) SDF file with fully explicit hydrogens: + +.. code-block:: bash + + mk_export.py AMP.dlg -s 3kgd_AMP_adgpu_out.sdf From 69712ed3a87e61f0bf44fe7ddcb0fc12274ddf08 Mon Sep 17 00:00:00 2001 From: Amy He Date: Mon, 4 Nov 2024 11:06:07 -0800 Subject: [PATCH 48/61] (WIP) tutorial3 --- docs/source/tutorial2.rst | 2 ++ docs/source/tutorial3.rst | 31 ++++++++++++++++++++++++++++++- 2 files changed, 32 insertions(+), 1 deletion(-) diff --git a/docs/source/tutorial2.rst b/docs/source/tutorial2.rst index 2455732b..677932ed 100644 --- a/docs/source/tutorial2.rst +++ b/docs/source/tutorial2.rst @@ -19,6 +19,8 @@ The reactive docking example is based on reactive docking method that has been d This tutorial is intended to showcase the Meeko usage in the preparation of receptor and ligand for reactive docking. +.. _env_setup_like_colab: + Prerequisites and Environment Setup =================================== diff --git a/docs/source/tutorial3.rst b/docs/source/tutorial3.rst index eabf8c08..00211ac6 100644 --- a/docs/source/tutorial3.rst +++ b/docs/source/tutorial3.rst @@ -1,4 +1,33 @@ .. _tutorial3: +========================= Tethered Docking -------------------------------------- \ No newline at end of file +========================= + +This is a tethered (two-point attached covalent) docking example that uses the AutoDock-GPU executable to reproduce a covalent complex of a small molecule and a protein receptor. + +Follow the instructions to set up the environment and run this command-line example on your own device (Linux, MacOS or WSL). To run this example in a Colab notebook, see :ref:`colab_examples`. + +.. contents:: + :local: + :depth: 2 + +Introduction +============ + +The covalent docking example is based on the two-point attractor and flexible sidechain method. In this example, a small molecule substrate (Adenosine monophosphate, PDB token AMP) is attached onto the catalytic histidine residue of a hollow protein structure of bacteria RNA 3' cyclase (PDB token 3KGD) to reproduce the covalent intermediate complex structure. A docked pose that closely resembles the original position of the ligand is expected among the top-ranked poses. + +This tutorial is intended to showcase the Meeko usage in the preparation of receptor and ligand for tethered docking. + +Prerequisites and Environment Setup +=================================== + +Follow the instructions to set up the environment: :ref:`env_setup_like_colab:`. + +Ligand Preparation +================= + +In this step, the ligand molecule is prepared from a Smiles string. A protonated 3D conformer of ligand is generated by ``scrub.py``, and the conversion to a tangible ligand PDBQT file is done by ``mk_prepare_ligand.py``. + + +The ligand of this example will be the covalent conjugate ``AMP-HIE``, where AMP is attached to the Nε atom of a histidine residue via forms a phosphoamide bond. We will use its isomeric Smiles string as the input, and manually write the phosphoester group in the -1 charge state. ``scrub.py`` will generate an SDF file, ``AMP.sdf``, containing a 3D conformer of AMP-HIE (1-) with all explicit hydrogens. \ No newline at end of file From d2b6b0f9b415d295a96c5bf69028682698a071dc Mon Sep 17 00:00:00 2001 From: Amy He Date: Mon, 4 Nov 2024 13:23:36 -0800 Subject: [PATCH 49/61] complete tutorial3 --- docs/source/images/annotated_HIE_AMP.png | Bin 0 -> 41692 bytes docs/source/tutorial2.rst | 9 +- docs/source/tutorial3.rst | 179 ++++++++++++++++++++++- test/BANANACUUBER.json | 1 + 4 files changed, 181 insertions(+), 8 deletions(-) create mode 100644 docs/source/images/annotated_HIE_AMP.png create mode 100644 test/BANANACUUBER.json diff --git a/docs/source/images/annotated_HIE_AMP.png b/docs/source/images/annotated_HIE_AMP.png new file mode 100644 index 0000000000000000000000000000000000000000..c72183801aa93d1f4796c27e9d68db7f80e0754c GIT binary patch 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in each dimension. The box definition will be written to the GPF. -For output control: We are expecting at least two types of files, the receptor PDBQT file (in response to ``-p``) and an Autogrid4 GPF (in response to ``-g``). Specifically for reactive docking, there will be a few more input files generated by ``mk_prepare_receptor.py`` – They are listed at the end of the standard output after running the ``mk_prepare_receptor.py`` command. +For output control: We are expecting at least two types of files, the receptor PDBQT files (in response to ``-p``) and an Autogrid4 GPF (in response to ``-g``). Specifically for reactive docking, there will be a few more input files generated by ``mk_prepare_receptor.py`` – They are listed at the end of the standard output after running the ``mk_prepare_receptor.py`` command. .. code-block:: bash @@ -284,9 +284,12 @@ The previously generated GPF file (``3kgd_receptorH_rigid.gpf``), together with And to run the docking calculation, the ligand PDBQT file (``AMP.pdbqt``), the flexible residue PDBQT file (``3kgd_receptorH_flex.pdbqt``), the special docking parameter file (DPF) for reactive docking (``3kgd_receptorH.reactive_config``), and the map files will be needed. With the following command for docking calculation, the output file will have basename ``AMP``. .. code-block:: bash + + ./adgpu --lfile AMP.pdbqt --flexres 3kgd_receptorH_flex.pdbqt \ + --ffile 3kgd_receptorH_rigid.maps.fld --import_dpf 3kgd_receptorH.reactive_config \ + --resnam AMP - ./adgpu --lfile AMP.pdbqt --flexres 3kgd_receptorH_flex.pdbqt --ffile 3kgd_receptorH_rigid.maps.fld --import_dpf 3kgd_receptorH.reactive_config --resnam AMP - +.. _T4_executables: If you're running these calculations on Google T4 backends, here are the pre-compiled executables of autogrid4 and adgpu specifically for T4: diff --git a/docs/source/tutorial3.rst b/docs/source/tutorial3.rst index 00211ac6..38f4e5a4 100644 --- a/docs/source/tutorial3.rst +++ b/docs/source/tutorial3.rst @@ -22,12 +22,181 @@ This tutorial is intended to showcase the Meeko usage in the preparation of rece Prerequisites and Environment Setup =================================== -Follow the instructions to set up the environment: :ref:`env_setup_like_colab:`. +Follow the instructions in the previous tutorial for environment setup: :ref:`env_setup_like_colab:`. -Ligand Preparation -================= +Ligand Conformer Generation +=========================== -In this step, the ligand molecule is prepared from a Smiles string. A protonated 3D conformer of ligand is generated by ``scrub.py``, and the conversion to a tangible ligand PDBQT file is done by ``mk_prepare_ligand.py``. +In this step, the ligand molecule is prepared from a Smiles string. A protonated 3D conformer of the covalent residue-ligand conjugate will be generated by ``scrub.py``. +For tethered docking, the ligand needs to a covalent conjugate of ligand and a residue that include the following components: -The ligand of this example will be the covalent conjugate ``AMP-HIE``, where AMP is attached to the Nε atom of a histidine residue via forms a phosphoamide bond. We will use its isomeric Smiles string as the input, and manually write the phosphoester group in the -1 charge state. ``scrub.py`` will generate an SDF file, ``AMP.sdf``, containing a 3D conformer of AMP-HIE (1-) with all explicit hydrogens. \ No newline at end of file +- the part of ligand present in the covalent conjuage, flexible in docking. +- the part of residue sidechain present in the covalent conjugate, flexible in docking. +- the residue's C-alpha and C-beta, which work as the two-point attractors and their positions remain unchanged in docking. The other backbone atoms are not required. + +.. image:: images/annotated_HIE_AMP.png + :alt: highlighted AMP + :width: 60% + :align: center + +The ligand of this example will be the covalent conjugate ``HIE_AMP``, where AMP is attached to the Nε atom of a histidine residue via forms a phosphoamide bond. We will use its isomeric Smiles string as the input, and manually write the phosphoester group in the -1 charge state. ``scrub.py`` will generate an SDF file, ``HIE_AMP.sdf``, containing a 3D conformer of HIE-AMP (1-) with all explicit hydrogens. + +.. code-block:: bash + + ligand_smiles="c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)([O-])N1C=C(CC)N=C1)O)O)N" + scrub.py $ligand_smiles -o HIE_AMP.sdf --skip_tautomer --skip_acidbase + +To prepare HIE-AMP (1-) as an covalent flexible residue, we will hold this SDF file for further mapping with the specific catalytic residue in receptor structure. In fact, the SDF file can be re-used for different Histidine residues in different receptor structures. + +Receptor Preparation +=================== + +The preparation of a rigid receptor consists of two steps. The receptor structure is first sourced from a PDB file and sent to ``reduce2.py`` for hydrogen addition and optimization, and then, the conversion to a tangible receptor PDBQT file is done by ``mk_prepare_receptor.py``. + +The first step (hydrogen addition and optimization) of this example will be the same as the reactive docking tutorial :ref:`tutorial2`. You may skip to the second step from here :ref:`covalent_receptor_prep` if you already have ``3kgd_receptorH.pdb`` or an equivalent (a protonated receptor PDB file). If not, we will begin from retrieving the PDB structure by token ``3kgd`` from RCSB PDB. + +.. code-block:: bash + + pdb_token="3kgd" + curl "http://files.rcsb.org/view/${pdb_token}.pdb" -o "${pdb_token}.pdb" + +Next, we will run a Python script to write ProDy selection ``chain A and not water and not hetero and not resname AMP`` to a PDB file ``3kgd_receptor_atoms.pdb``. + +.. code-block:: python + + python - < "${pdb_token}_receptor.pdb" + +In this example, we use ``reduce2.py`` to add hydrogen atoms to the receptor structure and optimize the positions. There are various other tools (``H++``, ``APBS``, etc.) of choices for this task. It should also be noted that ``mk_prepare_receptor.py`` does not neccessarily need the presence of all hydrogens in the input receptor structure – The missing hydrogens will be added through RDKit functions during the receptor preparation with ProDy selection ``chain A and not water and not hetero and not resname AMP`` to a PDB file ``3kgd_receptor_atoms.pdb``. + +.. code-block:: bash + + # setting up reduce2 for the first time in the environment + reduce2="$(python -c "import site; print(site.getsitepackages()[0])")/mmtbx/command_line/reduce2.py" + chmod +x $reduce2 + geostd="$(realpath geostd)" + export MMTBX_CCP4_MONOMER_LIB=$geostd + + # running reduce2 on the example receptor PDB + reduce_opts="approach=add add_flip_movers=True" + python $reduce2 "${pdb_token}_receptor.pdb" $reduce_opts + +After running the last command above, ``reduce2.py`` will conclude a normal execution with a log file ``3kgd_receptorH.txt`` and a protonated receptor structure file ``3kgd_receptorH.pdb`` – The PDB file can then be fed to ``mk_prepare_receptor.py`` to generate the receptor PDBQT file. But before that, we could (optionally) save the original position of residue AMP and use it to define the grid box for docking. To do this, we will use ProDy selection ``chain A and resname AMP`` to write a PDB file ``LIG.pdb`` + +.. code-block:: python + + python - < PDB file is found in working directory (3kgd.pdb). + @> 11804 atoms and 1 coordinate set(s) were parsed in 0.14s. + @> 5062 atoms and 1 coordinate set(s) were parsed in 0.05s. + + Flexible residues: + chain resnum is_reactive reactive_atom + A 309 False + reactive_flexres=set() + + Files written: + 3kgd_receptorH_flex.pdbqt <-- flexible receptor input file + 3kgd_receptorH_rigid.pdbqt <-- static (i.e., rigid) receptor input file + boron-silicon-atom_par.dat <-- atomic parameters for B and Si (for autogrid) + 3kgd_receptorH_rigid.gpf <-- autogrid input file + 3kgd_receptorH.box.pdb <-- PDB file to visualize the grid box + +Covalent Ligand Preparation +======================== + +In this step, we will use mk_prepare_ligand.py to generate the PDBQT file for the covalent ligand. Along with the previously generated 3D conformer of the covalent ligand (``HIE_AMP.sdf``), which may be at an arbitrary position, here a reference protein PDB file (``3kgd_receptor.pdb``) will be used to source the positions of the attractor atoms, Cα and Cβ, to keep them unchanged in docking. The reference PDB file does not have to be the full receptor, but it must contain the target residue that matches exactly with ``rec_residue``. Additionally, a SMARTS pattern ``tether_smarts`` is required. Together with the 1-based ``tether_smarts_indices``, they are used to locate the attractor atoms that correspond to Cα and Cβ of a hisitidine (His) residue: + +.. code-block:: bash + + rec_residue="A:HIS:309" + tether_smarts="n1cc(CC)nc1" + tether_smarts_indices="5 4" + mk_prepare_ligand.py -i HIE_AMP.sdf --receptor 3kgd_receptor.pdb --rec_residue $rec_residue \ + --tether_smarts "${tether_smarts}" --tether_smarts_indices $tether_smarts_indices \ + -o HIE_AMP.pdbqt + +Docking Calculation +=================== + +The tethered docking method needs an empty ligand file, which is allowed in AutoDock-GPU that requires grid map computation with AutoGrid4 before the docking calculation. + +The previously generated GPF file (``3kgd_receptorH_rigid.gpf``), together with the PDBQT file of the rigid part of the receptor (``3kgd_receptorH_rigid.pdbqt``), will be used to compute the grid maps: + +.. code-block:: bash + + ./autogrid4 -p 3kgd_receptorH_rigid.gpf + +And to run the docking calculation, the ligand PDBQT file (``HIE_AMP.pdbqt``) and the map files will be needed. Please note that althogh the commands and the filenames look the same, the GPF from the reactive docking tutorial :ref:`tutorial2` has additional parameters for reactive docking, and therefore the maps cannot be reused in this example. Also, we will be passing ``HIE_AMP.pdbqt`` as a flexible residue file instead of a ligand file to AD-GPU. In this docking calculation, the ligand will be ``empty`` which is indeed an empty file. With the following command for docking calculation, the output file will have basename ``HIE_AMP``. + +.. code-block:: bash + + touch empty + ./adgpu --lfile empty --flexres HIE_AMP.pdbqt \ + --ffile 3kgd_receptorH_rigid.maps.fld\ + --resnam HIE_AMP + +If you're running these calculations on Google T4 backends, here are the pre-compiled executables of autogrid4 and adgpu specifically for T4: :ref:`T4_executables` + +Export the Docking Poses +======================== + +``mk_export.py`` is a command-line script in Meeko to export docking poses from PDBQT or DLG formats. For this example, if we want to export the docking poses to a (possibly multi-model) SDF file with fully explicit hydrogens, we can use the ``-k`` option to keep the covalent ligand which is treated as a flexible residue: + +.. code-block:: bash + + mk_export.py HIE_AMP.dlg -s 3kgd_HIE_AMP_adgpu_out.sdf -k + +It is also possible to export the docking poses to a multi-model PDB file with updated conformatons of His309 and the covalently bonded AMP. To do this, we need a receptor JSON file that could be generated with ``mk_prepare_receptor.py`` option ``-j`` during the receptor preparation. + +.. code-block:: bash + + # rerun as needed to generate the receptor json file + flexres="A:309" + mk_prepare_receptor.py -i "${pdb_token}_receptorH.pdb" -o "${pdb_token}_receptorH" -j \ + --default_altloc A -f $flexres \ + --box_enveloping "LIG.pdb" --padding 8.0 + + mk_export.py HIE_AMP.dlg -s 3kgd_HIE_AMP_adgpu_out.sdf -k 3kgd_receptorH.json -p 3kgd_HIE_AMP_adgpu_out.pdb \ No newline at end of file diff --git a/test/BANANACUUBER.json b/test/BANANACUUBER.json new file mode 100644 index 00000000..5d5ce2ca --- /dev/null +++ b/test/BANANACUUBER.json @@ -0,0 +1 @@ +{"residue_chem_templates": {"residue_templates": {"NME": {"mol": 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"modified_atom_positions": [], "dihedral_interactions": [], "dihedral_partaking_atoms": {}, "dihedral_labels": {}, "atom_to_ring_id": {}, "ring_corners": {}, "rmsd_symmetry_indices": [[0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 17]]}, "is_flexres_atom": [false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false], "is_movable": false, "molsetup_mapidx": {"0": 0, "1": 1, "2": 2, "3": 4, "13": 3, "14": 6, "15": 7, "16": 8, "17": 9, "18": 5}}}, "log": {"chosen_by_fewest_missing_H": {}, "chosen_by_default": {}, "no_match": [], "no_mol": [], "msg": ""}} \ No newline at end of file From aa9192804303fcee966ce3f94e5dfec30493e135 Mon Sep 17 00:00:00 2001 From: Amy He Date: Mon, 4 Nov 2024 18:48:23 -0800 Subject: [PATCH 51/61] fix ref tags in tutorial2 and 3 --- docs/source/tutorial3.rst | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/docs/source/tutorial3.rst b/docs/source/tutorial3.rst index 38f4e5a4..58dea718 100644 --- a/docs/source/tutorial3.rst +++ b/docs/source/tutorial3.rst @@ -22,7 +22,7 @@ This tutorial is intended to showcase the Meeko usage in the preparation of rece Prerequisites and Environment Setup =================================== -Follow the instructions in the previous tutorial for environment setup: :ref:`env_setup_like_colab:`. +Follow the instructions in the previous tutorial for environment setup: :ref:`env_setup_like_colab`. Ligand Conformer Generation =========================== @@ -54,7 +54,7 @@ Receptor Preparation The preparation of a rigid receptor consists of two steps. The receptor structure is first sourced from a PDB file and sent to ``reduce2.py`` for hydrogen addition and optimization, and then, the conversion to a tangible receptor PDBQT file is done by ``mk_prepare_receptor.py``. -The first step (hydrogen addition and optimization) of this example will be the same as the reactive docking tutorial :ref:`tutorial2`. You may skip to the second step from here :ref:`covalent_receptor_prep` if you already have ``3kgd_receptorH.pdb`` or an equivalent (a protonated receptor PDB file). If not, we will begin from retrieving the PDB structure by token ``3kgd`` from RCSB PDB. +The first step (hydrogen addition and optimization) of this example will be the same as the reactive docking tutorial :ref:`tutorial2`. You may skip the steps and proceed to the next ``mk_prepare_receptor.py`` code block if you already have ``3kgd_receptorH.pdb`` or an equivalent (a protonated receptor PDB file). If not, we will begin from retrieving the PDB structure by token ``3kgd`` from RCSB PDB. .. code-block:: bash @@ -111,8 +111,6 @@ After running the last command above, ``reduce2.py`` will conclude a normal exec writePDB(prody_ligandPDB, ligand_atoms) EOF -.. _covalent_receptor_prep: - Now we're ready with the H-optimized receptor structure ``3kgd_receptorH.pdb`` and the position of the original ligand PDB file ``LIG.pdb``, we will proceed to receptor preparation. Here, we will specify that the flexible residue in the receptor is His309 in PDB structure ``3kgd``, a bacteria RNA 3’ cyclase – The full argument will be ``-f "A:309"``. Additionally, we will let the default AltLoc ID to be ``A`` for any residues with alternate locations. .. code-block:: bash From 35cceff2678a72c905f9563db53a778519b191a9 Mon Sep 17 00:00:00 2001 From: Amy He Date: Tue, 5 Nov 2024 12:24:49 -0800 Subject: [PATCH 52/61] (WIP) make TOC and ref tags in tutorial1 --- docs/source/tutorial1.rst | 102 +++++++++++++++++++++++++++++++++++++- docs/source/tutorial3.rst | 2 +- 2 files changed, 101 insertions(+), 3 deletions(-) diff --git a/docs/source/tutorial1.rst b/docs/source/tutorial1.rst index af84640a..188821b2 100644 --- a/docs/source/tutorial1.rst +++ b/docs/source/tutorial1.rst @@ -1,6 +1,104 @@ .. _tutorial1: -Basic Docking (Forlilab Tutorial) +Basic Docking ------------------------------------- -.. code-block:: python \ No newline at end of file +This tutorial provides a step-by-step guide for the five basic procedures with Meeko for molecular docking and virtual screening with `AutoDock Vina `_ and `AutoDock-GPU `_: + +- Ligand Preparation +- Receptor Preparation +- Molecular Docking (Single Ligand) and Analysis +- Virtual Screening (Batch Docking) and Analysis + +It is based on, but not a full version of the tutorial materials in `Forlilab tutorials `_. + +.. contents:: + :local: + :depth: 2 + +Prerequisites and Environment Setup +=================================== + +Create a new virtual environment (recommended) +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +.. code-block:: bash + + micromamba create -c conda-forge -n meeko_tutorial_py39 python=3.9 -y + micromamba activate meeko_tutorial_py39 + +In this tutorial, we will use ``micromamba`` as the example package manager. Visit `this official guide `_ for a quick install and setup of micromamba. There are many equivalent ways to manage Python packages, such as ``conda`` and ``mamba``. You can easily adapt the commands to your preferred tool, as the syntax is largely compatible across these package managers. + +Install the required Python packages through ``conda-forge`` +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +.. code-block:: bash + + micromamba install -c conda-forge numpy scipy rdkit gemmi vina -y + +Install the additional packages and data from GitHub repositories +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +- (Python package) Meeko + +.. code-block:: bash + + git clone --single-branch --branch develop https://github.com/forlilab/Meeko.git + cd Meeko; pip install --use-pep517 -e .; cd .. + +- (Python package) scrubber + +.. code-block:: bash + + git clone --single-branch --branch develop https://github.com/forlilab/scrubber.git + cd scrubber; pip install --use-pep517 -e .; cd .. + +- (Python package) Ringtail + +.. code-block:: bash + + git clone --single-branch --branch develop https://github.com/forlilab/Ringtail.git + cd Ringtail; pip install --use-pep517 -e .; cd .. + +Ligand Preparation +================== + +Ligand Preparation is + + +Receptor Preparation +==================== + +Receptor Preparation is + + + +Molecular Docking (Single Ligand) +================================= + +Docking with AutoDock-Vina +~~~~~~~~~~~~~~~~~~~~~~~~~~ + +Docking with AutoDock-GPU +~~~~~~~~~~~~~~~~~~~~~~~~~ + +Processing the Docking Results +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +Virtual Screening (Batch Docking) +================================= + +Batch Docking with AutoDock-Vina +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +Batch Docking with AutoDock-GPU +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +Processing the Screening Results +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + + +What's Next? +------------ + +Now that you've completed this tutorial, you're ready to move on to :ref:`tutorial2` and :ref:`tutorial3` where we dive deeper into more advanced docking methods: reactive docking and tethered docking. diff --git a/docs/source/tutorial3.rst b/docs/source/tutorial3.rst index 58dea718..ce4c602e 100644 --- a/docs/source/tutorial3.rst +++ b/docs/source/tutorial3.rst @@ -173,7 +173,7 @@ And to run the docking calculation, the ligand PDBQT file (``HIE_AMP.pdbqt``) an touch empty ./adgpu --lfile empty --flexres HIE_AMP.pdbqt \ - --ffile 3kgd_receptorH_rigid.maps.fld\ + --ffile 3kgd_receptorH_rigid.maps.fld \ --resnam HIE_AMP If you're running these calculations on Google T4 backends, here are the pre-compiled executables of autogrid4 and adgpu specifically for T4: :ref:`T4_executables` From eca8f696c27707373d45ca3bcfb64cd01ddbcf65 Mon Sep 17 00:00:00 2001 From: Amy He Date: Tue, 5 Nov 2024 15:27:57 -0800 Subject: [PATCH 53/61] (WIP) Ligand Preparation in tutorial1 --- docs/source/tutorial1.rst | 47 ++++++++++++++++++++++++++++++++++----- 1 file changed, 41 insertions(+), 6 deletions(-) diff --git a/docs/source/tutorial1.rst b/docs/source/tutorial1.rst index 188821b2..e9a9cb21 100644 --- a/docs/source/tutorial1.rst +++ b/docs/source/tutorial1.rst @@ -3,12 +3,12 @@ Basic Docking ------------------------------------- -This tutorial provides a step-by-step guide for the five basic procedures with Meeko for molecular docking and virtual screening with `AutoDock Vina `_ and `AutoDock-GPU `_: +This tutorial provides practice examples and a step-by-step guide for the four basic procedures with Meeko for molecular docking and virtual screening with `AutoDock Vina `_ and `AutoDock-GPU `_: -- Ligand Preparation -- Receptor Preparation -- Molecular Docking (Single Ligand) and Analysis -- Virtual Screening (Batch Docking) and Analysis +- Ligand Preparation +- Receptor Preparation +- Molecular Docking (Single Ligand) +- Virtual Screening (Batch Docking) It is based on, but not a full version of the tutorial materials in `Forlilab tutorials `_. @@ -60,10 +60,45 @@ Install the additional packages and data from GitHub repositories git clone --single-branch --branch develop https://github.com/forlilab/Ringtail.git cd Ringtail; pip install --use-pep517 -e .; cd .. +- (Example files for this tutorial) Forlilab Tutorials + +.. code-block:: bash + + git clone https://github.com/forlilab/tutorials.git + Ligand Preparation ================== -Ligand Preparation is +Ligand Preparation is the process that generates ligand input files for docking calculation and virtual screening. At present, AutoDock Vina and AutoDock-GPU need the ligand input files in the PDBQT format. In this example, we will use ``mk_prepare_ligand.py``, a command-line script in Meeko, to prepare such ligand PDBQT files. + +Prepare a Single Ligand from a Smiles string +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +`Imatinib _` is a small-molecule drug. You can find the SMILES string for Imatinib from various reliable chemical databases and resources, including but not limited to `PubChem _` and `DrugBank `_. + +``scrub.py`` is a command-line script in Scrubber that generates 3D conformers of protomers and tautomers for given small molecules at a specified (range of) pH. Given a pH range of 5 to 9, the output protomers will include those which make up no less than 1% of the total population at pH = 7. Based on the reference pKa values, the amine nitrogens and the pyridine nitrogen will be considered for acid/base enumeration. With the ``meeko_tutorial_py39`` micromamba environment active, run ``scrub.py`` to generate 3D conformers of Imatinib from the SMILES string. + +.. code-block:: bash + + smiles_string="CC1=C(C=C(C=C1)NC(=O)C2=CC=C(C=C2)CN3CCN(CC3)C)NC4=NC=CC(=N4)C5=CN=CC=C5" + scrub.py $smiles_string -o imatinib.sdf --skip_tautomers --ph_low 5 --ph_high 9 + +The output file ``imatinib.sdf`` will contain two protomers of Imatinib, one with a neutral pyridine group and the other with a (+1) pyridinium group. All of the aliphatic amininium nitrogens will be protonated. + +.. code-block:: bash + + Scrub completed. + Summary of what happened: + Input molecules supplied: 1 + mols processed: 1, skipped by rdkit: 0, failed: 0 + nr isomers (tautomers and acid/base conjugates): 2 (avg. 2.000 per mol) + nr conformers: 2 (avg. 1.000 per isomer, 2.000 per mol) + +In case there are multiple molecules in the SDF file, ``mk_prepare_ligand.py`` needs to know the prefix of filenames (by ``--multimol_prefix``) or alternatively where to output (by ``--multimol_outdir``) the multiple PDBQT files. Here, we will give the PDBQT files a prefix ``imatinib_protomer`` in the names. The output PDBQT files will be ``imatinib_protomer-1.pdbqt`` and ``imatinib_protomer-2.pdbqt``. + +.. code-block:: bash + + mk_prepare_ligand.py -i imatinib.sdf --multimol_prefix imatinib_protomer Receptor Preparation From 819c2d03f24faf1a80540ae5521e0a20d3f2d1b4 Mon Sep 17 00:00:00 2001 From: diogom Date: Tue, 5 Nov 2024 19:06:00 -0800 Subject: [PATCH 54/61] minor edits to docs --- docs/source/about.rst | 8 ------- docs/source/index.rst | 41 +++++++++++++++++------------------- docs/source/installation.rst | 2 +- 3 files changed, 20 insertions(+), 31 deletions(-) delete mode 100644 docs/source/about.rst diff --git a/docs/source/about.rst b/docs/source/about.rst deleted file mode 100644 index 33a6aa3d..00000000 --- a/docs/source/about.rst +++ /dev/null @@ -1,8 +0,0 @@ -About -===== - - -This is to explain the philosofy and motivation behind meeko, implementation details, -comparison with MGLTools, possibly the engineering behind the Polymer, and stuff like -this. It may become relatively large and need to be broken down. It may be halfway between -technical documentation and an academic paper. diff --git a/docs/source/index.rst b/docs/source/index.rst index 7803eb7a..dce4fe98 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -1,39 +1,37 @@ Meeko ===== -Preparation of molecules for AutoDock -------------------------------------- +Parameterization of molecules for AutoDock +------------------------------------------ -Meeko assigns parameters to small organic molecules (a.k.a. ligands), and to -biological polymers (proteins and nucleic acids). +Meeko assigns parameters to small organic molecules, often called ligands, +and to proteins and to nucleic acids, often called receptors. This includes assigning atom types, partial charges, setting bonds as rotatable or fixed, and making receptor sidechains flexible. -It does not calculate 3D positions or assign protonation states of ligands -but for receptors it allows the user to manually choose the protonation -variant of tritable amino acids. -Meeko write the input PDBQT files for AutoDock-Vina and AutoDock-GPU, and it -It also converts the output files from docking, which are PDBQT for Vina and -DLG for AutoDock-GPU, into useful file formats that other software besides -AutoDock can read: SDF for ligands and PDB for receptor. +Write input and process output +------------------------------ + +Meeko writes the input PDBQT files for AutoDock-Vina and AutoDock-GPU, and it +also converts the output files from docking, which are PDBQT for Vina and +DLG for AutoDock-GPU, into SDF for ligands and PDB for receptor. + +Python API +---------- + +Meeko is written in Python and exposes functions and classes that operate on +RDKit molecules for the ligands, leveraging RDKit's popularity to facilitate +integration with external software. Command line scripts are also available. AutoDock ecosystem ------------------ -Meeko by itself it's not very useful. It is part of a larger collection of -tools to computationally dock ligands onto receptors. +To run a docking, more packages are required besides Meeko: - * interface with RDKit by desing, for Python scripting * AutoDock-Vina - * AutoDOck-GPU + * AutoDock-GPU * Ringtail - * Molscrub - * RSD3 website - -Comparison to MGLTools ----------------------- -Meeko superseeds the preparation scripts from MGLTools. List advantages here (**TODO**). .. toctree:: @@ -44,7 +42,6 @@ Meeko superseeds the preparation scripts from MGLTools. List advantages here (** installation colab_examples tutorials - about .. toctree:: :maxdepth: 2 diff --git a/docs/source/installation.rst b/docs/source/installation.rst index f80dbc32..28e44151 100644 --- a/docs/source/installation.rst +++ b/docs/source/installation.rst @@ -56,7 +56,7 @@ install all dependencies except Prody and install Meeko from source. Meeko uses Prody to parse PDB and mmCIF files. Without prody, PDB files can be parsed with the command line option ``--read_pdb`` and with the Python -method ``LinkedRDKitChorizo.from_pdb_string()``. However, without ProDy it +method ``Polymer.from_pdb_string()``. However, without ProDy it won't be possible to read mmCIF files or use tethered docking. Prody developers are working to support Python 3.12, so it is possible that Prody will work on Python 3.12 soon. From 0a389ae6095e5c4ad5545613e85a2caf1e9b9584 Mon Sep 17 00:00:00 2001 From: Amy He Date: Tue, 5 Nov 2024 19:35:29 -0800 Subject: [PATCH 55/61] (WIP) receptor preparation in tutorial1 --- docs/source/tutorial1.rst | 121 +++++++++++++++++++++++++++++++++++++- 1 file changed, 118 insertions(+), 3 deletions(-) diff --git a/docs/source/tutorial1.rst b/docs/source/tutorial1.rst index e9a9cb21..bf9a67c6 100644 --- a/docs/source/tutorial1.rst +++ b/docs/source/tutorial1.rst @@ -71,10 +71,10 @@ Ligand Preparation Ligand Preparation is the process that generates ligand input files for docking calculation and virtual screening. At present, AutoDock Vina and AutoDock-GPU need the ligand input files in the PDBQT format. In this example, we will use ``mk_prepare_ligand.py``, a command-line script in Meeko, to prepare such ligand PDBQT files. -Prepare a Single Ligand from a Smiles string +Prepare a Single Ligand from a Smiles String ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -`Imatinib _` is a small-molecule drug. You can find the SMILES string for Imatinib from various reliable chemical databases and resources, including but not limited to `PubChem _` and `DrugBank `_. +`Imatinib `_ is a small-molecule drug. You can find the SMILES string for Imatinib from various reliable chemical databases and resources, including but not limited to `PubChem `_ and `DrugBank `_. ``scrub.py`` is a command-line script in Scrubber that generates 3D conformers of protomers and tautomers for given small molecules at a specified (range of) pH. Given a pH range of 5 to 9, the output protomers will include those which make up no less than 1% of the total population at pH = 7. Based on the reference pKa values, the amine nitrogens and the pyridine nitrogen will be considered for acid/base enumeration. With the ``meeko_tutorial_py39`` micromamba environment active, run ``scrub.py`` to generate 3D conformers of Imatinib from the SMILES string. @@ -101,12 +101,127 @@ In case there are multiple molecules in the SDF file, ``mk_prepare_ligand.py`` n mk_prepare_ligand.py -i imatinib.sdf --multimol_prefix imatinib_protomer +Prepare Ligands in Batch from a ``.smi`` File +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +In preparation for virtual screening, it is possible to prepare ligands in batch from a ``.smi`` File. There is one such example file at ``tutorials/imatinib/step-4/mols.smi`` from `Forlilab tutorials `_. Follow the example commands to process ``mols.smi``: + +.. code-block:: bash + + smi_file="tutorials/imatinib/step-4/mols.smi" + scrub.py $smi_file -o mols.sdf + +At the end of the execution, the expected standard output will tell you the total number of isomers written to the multi-molecule SDF file ``mols.sdf``. This will help you estimate the expected file size and system requirements beforehand. + +.. code-block:: bash + + Scrub completed. + Summary of what happened: + Input molecules supplied: 491 + mols processed: 491, skipped by rdkit: 0, failed: 0 + nr isomers (tautomers and acid/base conjugates): 741 (avg. 1.509 per mol) + nr conformers: 741 (avg. 1.000 per isomer, 1.509 per mol) + +For ``mols.sdf``, we will run ``mk_prepare_ligand.py`` with ``--multimol_prefix mols_pdbqt``, a directory to be created to hold the ligand PDBQT files. If you expect a large number of isomers (potentially millions), consider writing to a temporary directory or scratch space to manage storage efficiently. + +.. code-block:: bash + + mk_prepare_ligand.py -i mols.sdf --multimol_outdir mols_pdbqt + Receptor Preparation ==================== -Receptor Preparation is +Receptor Preparation is the process that generates receptor input files for docking calculation and virtual screening. It typically begins with a PDB file of a biomacromolecule system, with or without coordinates of explicit hydrogens. At present, AutoDock Vina and AutoDock-GPU may require different types of files as receptor inputs. ``mk_prepare_receptor.py`` is the command-line script in Meeko that is designed to handle the different situations. + +For AutoDock-Vina +~~~~~~~~~~~~~~~~~ + +Docking with AutoDock-Vina requires the following receptor input files: +- Receptor PDBQT file +- (Optional) a TXT file that contains the box specifications, which can be re-used as the config file for Vina + +Starting from a provided PDB file at ``tutorials/imatinib/step-3/2hzn_protein.pdb`` from `Forlilab tutorials `_, the generation of a Receptor PDBQT file is very straightforward: + +.. code-block:: bash + + pdb_file="tutorials/imatinib/step-3/2hzn_protein.pdb" + mk_prepare_receptor.py --read_pdb $pdb_file -o rec_2hzn -p --allow_bad_res + +Here, we use ``-o`` to set the basename of the output files to ``rec_2hzn`` with request ``-p``. The execution will generate only the receptor PDBQT file, ``rec_2hzn.pdbqt``. In addition, option ``--allow_bad_res`` is used to ignore residues with missing heavy atoms in the input PDB files. + +Note that ``--read_pdb``, which uses the PDB parser in RDKit, is not the only way for ``mk_prepare_receptor.py`` to parse a receptor PDB file. The alternate is ``-i`` (short for ``--read_with_prody``) and it requires ProDy as an additional dependency. If you wish to use the ProDy parser, run ``pip install prody`` to install ProDy. + +To generate the TXT file that has the box dimension, we must find a way to define the wanted docking box. In this example, we will use a provided PDB file of ligand Imatinib at ``tutorials/imatinib/step-3/xray-imatinib.pdb`` that has been aligned to the expected binding site of the provided receptor PDB file. + +.. code-block:: bash + + pdb_file="tutorials/imatinib/step-3/2hzn_protein.pdb" + lig_file="tutorials/imatinib/step-3/xray-imatinib.pdb" + mk_prepare_receptor.py --read_pdb $pdb_file -o rec_2hzn -p -v --allow_bad_res \ + --box_enveloping $lig_file --padding 5 + +Here, we add the ``-v`` to request the Vina-style box files to be generated along with the receptor PDBQT files. To define the box, we are using the combination of ``--box_enveloping`` and ``--padding``, which is to sete the center of the box by the given object, and the size of the box by a constant padding in each dimension around the given object. Note that this is not the only way to define the box. Read the help message printed from ``mk_prepare_receptor.py -h`` to learn about other combinations. + +At the end of the execution with ``-p -v``, the expected standard output will be: + +.. code-block:: bash + + Files written: + rec_2hzn.pdbqt <-- static (i.e., rigid) receptor input file + rec_2hzn.box.txt <-- Vina-style box dimension file + rec_2hzn.box.pdb <-- PDB file to visualize the grid box + +.. _receptor_preparation_for_vina_with_adf4sf: + +For AutoDock-Vina (and with AutoDock4 Scoring Function) +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +To use the AutoDock4 Scoring Function in AutoDock-Vina, an additional step needs to be taken to compute the grid maps prior to the docking calculation. At present, this is only possible with AutoGrid, and therefore needs a (GPF) Grid Parameter File for it. Using ``mk_prepare_receptor.py`` option ``-g``, such GPF file can be generated in the same step as the receptor PDBQT file as well as the box dimension files. Here's an example: + +.. code-block:: bash + + pdb_file="tutorials/imatinib/step-3/2hzn_protein.pdb" + lig_file="tutorials/imatinib/step-3/xray-imatinib.pdb" + mk_prepare_receptor.py --read_pdb $pdb_file -o rec_2hzn -p -v -g --allow_bad_res \ + --box_enveloping $lig_file --padding 5 + +At the end of the execution with ``-p -v -g``, the expected standard output is now: + +.. code-block:: bash + + Files written: + rec_2hzn.pdbqt <-- static (i.e., rigid) receptor input file + boron-silicon-atom_par.dat <-- atomic parameters for B and Si (for autogrid) + rec_2hzn.gpf <-- autogrid input file + rec_2hzn.box.txt <-- Vina-style box dimension file + rec_2hzn.box.pdb <-- PDB file to visualize the grid box + +To compute the grid maps, the GPF file (``rec_2hzn.gpf``) will be the input command file for AutoGrid. The receptor PDBQT file (``rec_2hzn.pdbqt``) and the additional parameter file (``boron-silicon-atom_par.dat``) need to be in the same directory from which AutoGrid is run. + +For AutoDock-GPU +~~~~~~~~~~~~~~~~ + +At present, AutoDock-GPU also needs the pre-computed grid maps from AutoGrid. Therefore, Receptor Preparation for docking calculations with AutoDock-GPU is similar to preparation in the previous section :ref:`receptor_preparation_for_vina_with_adf4sf`. But in this case, we can drop the ``-v`` option as the Vina-style box definition TXT file is no longer needed for AutoGrid-GPU. + +Below is the sample command: + +.. code-block:: bash + + pdb_file="tutorials/imatinib/step-3/2hzn_protein.pdb" + lig_file="tutorials/imatinib/step-3/xray-imatinib.pdb" + mk_prepare_receptor.py --read_pdb $pdb_file -o rec_2hzn -p -g --allow_bad_res \ + --box_enveloping $lig_file --padding 5 + +And the expected standard output will be: + +.. code-block:: bash + Files written: + rec_2hzn.pdbqt <-- static (i.e., rigid) receptor input file + boron-silicon-atom_par.dat <-- atomic parameters for B and Si (for autogrid) + rec_2hzn.gpf <-- autogrid input file + rec_2hzn.box.pdb <-- PDB file to visualize the grid box Molecular Docking (Single Ligand) ================================= From 47e45ec2df67b1b115ff94dace71b736619fb229 Mon Sep 17 00:00:00 2001 From: Amy He Date: Tue, 5 Nov 2024 21:10:02 -0800 Subject: [PATCH 56/61] (WIP) Export Poses in tutorial1 --- docs/source/tutorial1.rst | 150 ++++++++++++++++++++++++++++++-------- 1 file changed, 121 insertions(+), 29 deletions(-) diff --git a/docs/source/tutorial1.rst b/docs/source/tutorial1.rst index bf9a67c6..2acd42ea 100644 --- a/docs/source/tutorial1.rst +++ b/docs/source/tutorial1.rst @@ -141,14 +141,14 @@ Docking with AutoDock-Vina requires the following receptor input files: - Receptor PDBQT file - (Optional) a TXT file that contains the box specifications, which can be re-used as the config file for Vina -Starting from a provided PDB file at ``tutorials/imatinib/step-3/2hzn_protein.pdb`` from `Forlilab tutorials `_, the generation of a Receptor PDBQT file is very straightforward: +Starting from a provided PDB file at ``tutorials/imatinib/step-3/1iep_protein.pdb`` from `Forlilab tutorials `_, the generation of a Receptor PDBQT file is very straightforward: .. code-block:: bash - pdb_file="tutorials/imatinib/step-3/2hzn_protein.pdb" - mk_prepare_receptor.py --read_pdb $pdb_file -o rec_2hzn -p --allow_bad_res + pdb_file="tutorials/imatinib/step-3/1iep_protein.pdb" + mk_prepare_receptor.py --read_pdb $pdb_file -o rec_1iep -p -Here, we use ``-o`` to set the basename of the output files to ``rec_2hzn`` with request ``-p``. The execution will generate only the receptor PDBQT file, ``rec_2hzn.pdbqt``. In addition, option ``--allow_bad_res`` is used to ignore residues with missing heavy atoms in the input PDB files. +Here, we use ``-o`` to set the basename of the output files to ``rec_1iep`` with request ``-p``. The execution will generate only the receptor PDBQT file, ``rec_1iep.pdbqt``. Note that ``--read_pdb``, which uses the PDB parser in RDKit, is not the only way for ``mk_prepare_receptor.py`` to parse a receptor PDB file. The alternate is ``-i`` (short for ``--read_with_prody``) and it requires ProDy as an additional dependency. If you wish to use the ProDy parser, run ``pip install prody`` to install ProDy. @@ -156,9 +156,9 @@ To generate the TXT file that has the box dimension, we must find a way to defin .. code-block:: bash - pdb_file="tutorials/imatinib/step-3/2hzn_protein.pdb" + pdb_file="tutorials/imatinib/step-3/1iep_protein.pdb" lig_file="tutorials/imatinib/step-3/xray-imatinib.pdb" - mk_prepare_receptor.py --read_pdb $pdb_file -o rec_2hzn -p -v --allow_bad_res \ + mk_prepare_receptor.py --read_pdb $pdb_file -o rec_1iep -p -v \ --box_enveloping $lig_file --padding 5 Here, we add the ``-v`` to request the Vina-style box files to be generated along with the receptor PDBQT files. To define the box, we are using the combination of ``--box_enveloping`` and ``--padding``, which is to sete the center of the box by the given object, and the size of the box by a constant padding in each dimension around the given object. Note that this is not the only way to define the box. Read the help message printed from ``mk_prepare_receptor.py -h`` to learn about other combinations. @@ -168,22 +168,22 @@ At the end of the execution with ``-p -v``, the expected standard output will be .. code-block:: bash Files written: - rec_2hzn.pdbqt <-- static (i.e., rigid) receptor input file - rec_2hzn.box.txt <-- Vina-style box dimension file - rec_2hzn.box.pdb <-- PDB file to visualize the grid box + rec_1iep.pdbqt <-- static (i.e., rigid) receptor input file + rec_1iep.box.txt <-- Vina-style box dimension file + rec_1iep.box.pdb <-- PDB file to visualize the grid box .. _receptor_preparation_for_vina_with_adf4sf: For AutoDock-Vina (and with AutoDock4 Scoring Function) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -To use the AutoDock4 Scoring Function in AutoDock-Vina, an additional step needs to be taken to compute the grid maps prior to the docking calculation. At present, this is only possible with AutoGrid, and therefore needs a (GPF) Grid Parameter File for it. Using ``mk_prepare_receptor.py`` option ``-g``, such GPF file can be generated in the same step as the receptor PDBQT file as well as the box dimension files. Here's an example: +To use the AutoDock4 Scoring Function in AutoDock-Vina, an additional step needs to be taken to compute the grid maps prior to the docking calculation. At present, this is only possible with AutoGrid, and therefore needs a Grid Parameter File (GPF) for it. Using ``mk_prepare_receptor.py`` option ``-g``, such GPF file can be generated in the same step as the receptor PDBQT file as well as the box dimension files. Here's an example: .. code-block:: bash - pdb_file="tutorials/imatinib/step-3/2hzn_protein.pdb" + pdb_file="tutorials/imatinib/step-3/1iep_protein.pdb" lig_file="tutorials/imatinib/step-3/xray-imatinib.pdb" - mk_prepare_receptor.py --read_pdb $pdb_file -o rec_2hzn -p -v -g --allow_bad_res \ + mk_prepare_receptor.py --read_pdb $pdb_file -o rec_1iep -p -v -g \ --box_enveloping $lig_file --padding 5 At the end of the execution with ``-p -v -g``, the expected standard output is now: @@ -191,13 +191,13 @@ At the end of the execution with ``-p -v -g``, the expected standard output is n .. code-block:: bash Files written: - rec_2hzn.pdbqt <-- static (i.e., rigid) receptor input file + rec_1iep.pdbqt <-- static (i.e., rigid) receptor input file boron-silicon-atom_par.dat <-- atomic parameters for B and Si (for autogrid) - rec_2hzn.gpf <-- autogrid input file - rec_2hzn.box.txt <-- Vina-style box dimension file - rec_2hzn.box.pdb <-- PDB file to visualize the grid box + rec_1iep.gpf <-- autogrid input file + rec_1iep.box.txt <-- Vina-style box dimension file + rec_1iep.box.pdb <-- PDB file to visualize the grid box -To compute the grid maps, the GPF file (``rec_2hzn.gpf``) will be the input command file for AutoGrid. The receptor PDBQT file (``rec_2hzn.pdbqt``) and the additional parameter file (``boron-silicon-atom_par.dat``) need to be in the same directory from which AutoGrid is run. +To compute the grid maps, the GPF file (``rec_1iep.gpf``) will be the input command file for AutoGrid. The receptor PDBQT file (``rec_1iep.pdbqt``) and the additional parameter file (``boron-silicon-atom_par.dat``) need to be in the same directory from which AutoGrid is run. For AutoDock-GPU ~~~~~~~~~~~~~~~~ @@ -208,9 +208,9 @@ Below is the sample command: .. code-block:: bash - pdb_file="tutorials/imatinib/step-3/2hzn_protein.pdb" + pdb_file="tutorials/imatinib/step-3/1iep_protein.pdb" lig_file="tutorials/imatinib/step-3/xray-imatinib.pdb" - mk_prepare_receptor.py --read_pdb $pdb_file -o rec_2hzn -p -g --allow_bad_res \ + mk_prepare_receptor.py --read_pdb $pdb_file -o rec_1iep -p -g \ --box_enveloping $lig_file --padding 5 And the expected standard output will be: @@ -218,23 +218,115 @@ And the expected standard output will be: .. code-block:: bash Files written: - rec_2hzn.pdbqt <-- static (i.e., rigid) receptor input file + rec_1iep.pdbqt <-- static (i.e., rigid) receptor input file + boron-silicon-atom_par.dat <-- atomic parameters for B and Si (for autogrid) + rec_1iep.gpf <-- autogrid input file + rec_1iep.box.pdb <-- PDB file to visualize the grid box + +Saving a Receptor JSON File for Docking with Flexible and/or Reactive Residues +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +Docking with flexible and/or reactive residues may require more files than basic docking, and ``mk_prepare_receptor.py`` is able to prepare those simultaneously when creating the receptor PDBQT file. The detailed procedure for Reactive Docking can be found in :ref:`tutorial2`. Here, we will use a different PDB file at ``tutorials/imatinib/step-3/2hzn_protein.pdb`` to showcase a simple docking preparation with flexible sidechains: + +.. code-block:: bash + + pdb_file="tutorials/imatinib/step-3/2hzn_protein.pdb" + lig_file="tutorials/imatinib/step-3/xray-imatinib.pdb" + mk_prepare_receptor.py --read_pdb $pdb_file -o rec_2hzn -p -v -g -j \ + --box_enveloping $lig_file --padding 5 \ + -f A:286,359 --allow_bad_res + +Note that several additional arguments are introduced for this particular receptor structure and for flexible docking. First and for most, ``-f A:286,359`` specifies that we are making two residues flexible, which are Glu286 and Phe359 in chain A of the receptor PDB file ``2hzn_protein.pdb``. Moreover, we add the ``--allow_bad_res`` so that partially resolved residues in the input PDB file can be ignored. Finally, we make the request ``-j`` to not only write the typical input files for docking calculations, but also a receptor JSON file. This receptor JSON file may be used in future steps in order to export the full receptor structure with updated sidechain conformations from the docking output. + +With that, the standard output and the list of generated files from ``mk_prepare_receptor.py`` will be: + +.. code-block:: bash + + - Template matching failed for: ['A:238', 'A:262', 'A:263', 'A:264', 'A:281', 'A:356', 'A:462', 'A:466', 'A:502'] Ignored due to allow_bad_res. + + Flexible residues: + chain resnum is_reactive reactive_atom + A 359 False + A 286 False + reactive_flexres=set() + + Files written: + rec_2hzn.json <-- parameterized receptor + rec_2hzn_flex.pdbqt <-- flexible receptor input file + rec_2hzn_rigid.pdbqt <-- static (i.e., rigid) receptor input file boron-silicon-atom_par.dat <-- atomic parameters for B and Si (for autogrid) - rec_2hzn.gpf <-- autogrid input file + rec_2hzn_rigid.gpf <-- autogrid input file + rec_2hzn.box.txt <-- Vina-style box dimension file rec_2hzn.box.pdb <-- PDB file to visualize the grid box -Molecular Docking (Single Ligand) -================================= +Export Poses from Molecular Docking (Single Ligand) +=================================================== + +From AutoDock-Vina +~~~~~~~~~~~~~~~~~~ -Docking with AutoDock-Vina -~~~~~~~~~~~~~~~~~~~~~~~~~~ +With AutoDock-Vina, The required files (generated from the previous steps) and the command to run a basic docking calculation of a single ligand is as follows: -Docking with AutoDock-GPU -~~~~~~~~~~~~~~~~~~~~~~~~~ +.. code-block:: bash -Processing the Docking Results + lig_pdbqt="imatinib_protomer-1.pdbqt" + rec_pdbqt="rec_1iep.pdbqt" + config_txt="rec_1iep.box.txt" + ./vina --ligand $lig_pdbqt --receptor $rec_pdbqt --config $config_txt + +Without giving Vina a custom output name, the default output PDBQT file will be named ``imatinib_protomer-1_out.pdbqt``. Using the Smiles and mapping information stored in the REMARKS section of the PDBQT file, ``mk_export.py`` is able to reconstruct the all-atom structures of the docked ligand and export the poses to a SDF file, ``imatinib_protomer-1_vina_out.sdf``, which includes the reconstructed coordinates of all hydrogen atoms: + +.. code-block:: bash + + docked_pdbqt="imatinib_protomer-1_out.pdbqt" + mk_export.py $docked_pdbqt -s imatinib_protomer-1_vina_out.sdf + +From AutoDock-GPU +~~~~~~~~~~~~~~~~~ + +With AutoDock-GPU, the required files (generated from the previous steps) and the command to run a basic docking calculation of a single ligand is as follows: + +.. code-block:: bash + + lig_name="imatinib_protomer-1" + lig_pdbqt="${lig_name}.pdbqt" + rec_prefix="rec_1iep" + rec_map_fld="${rec_prefix}.maps.fld" + ./adgpu --lfile $lig_pdbqt --ffile $rec_map_fld --resnam $lig_name + +With that, the output DLG file will be named ``imatinib_protomer-1.dlg``. Similarly, ``mk_export.py`` is able to reconstruct the atomistic structures of the docked ligand and export the poses to a SDF file as follows: + +.. code-block:: bash + + docked_dlg="imatinib_protomer-1.dlg" + mk_export.py $docked_dlg -s imatinib_protomer-1_adgpu_out.sdf + +Note that by default, only the cluster leads will be exported to the SDF file. To export all generated poses in the DLG file, add the ``--all_dlg_poses`` option when exporting the poses. + +From Flexible Receptor Docking ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +Here we will use AutoDock-GPU as the docking engine to demonstrate result processing from flexible receptor docking. A flexible docking example with Vina can be found `here in the Vina documentation `_. With AutoDock-GPU, the required files (generated from the previous steps) and the command to run a flexible docking calculation of a single ligand is as follows: + +.. code-block:: bash + + lig_name="imatinib_protomer-1" + lig_pdbqt="${lig_resnam}.pdbqt" + rec_prefix="rec_2hzn" + flexres_pdbqt="${rec_prefix}_flex.pdbqt" + rec_map_fld="${rec_prefix}_rigid.maps.fld" + ./adgpu --lfile $lig_pdbqt --flexres $flexres_pdbqt --ffile $rec_map_fld --resnam ${lig_name}_flexres + +With that, the output DLG file will be named ``imatinib_protomer-1_flexres.dlg``. If given the receptor JSON file (``rec_2hzn.json``) generated when the other receptor files were created, ``mk_export.py`` is able to reconstruct the atomistic structures of the full receptor and export the updated models to a PDB file as follows: + +.. code-block:: bash + + rec_json="rec_2hzn.json" + docked_dlg="imatinib_protomer-1_flexres.dlg" + mk_export.py $docked_dlg -j $rec_json -p imatinib_protomer-1_flexres_adgpu_out.pdb + +At present, all docking poses will be exported, whether they are cluster leads or not. + Virtual Screening (Batch Docking) ================================= @@ -249,6 +341,6 @@ Processing the Screening Results What's Next? ------------- +^^^^^^^^^^^^ Now that you've completed this tutorial, you're ready to move on to :ref:`tutorial2` and :ref:`tutorial3` where we dive deeper into more advanced docking methods: reactive docking and tethered docking. From aee75a3f5de9b82be7defb37e7f6b48d04cbad05 Mon Sep 17 00:00:00 2001 From: Amy He Date: Tue, 5 Nov 2024 21:16:47 -0800 Subject: [PATCH 57/61] remove headings for virtual screening data management is not in the scope of Meeko doc --- docs/source/tutorial1.rst | 24 ++---------------------- 1 file changed, 2 insertions(+), 22 deletions(-) diff --git a/docs/source/tutorial1.rst b/docs/source/tutorial1.rst index 2acd42ea..620b7fb3 100644 --- a/docs/source/tutorial1.rst +++ b/docs/source/tutorial1.rst @@ -3,14 +3,7 @@ Basic Docking ------------------------------------- -This tutorial provides practice examples and a step-by-step guide for the four basic procedures with Meeko for molecular docking and virtual screening with `AutoDock Vina `_ and `AutoDock-GPU `_: - -- Ligand Preparation -- Receptor Preparation -- Molecular Docking (Single Ligand) -- Virtual Screening (Batch Docking) - -It is based on, but not a full version of the tutorial materials in `Forlilab tutorials `_. +This tutorial provides practice examples and a step-by-step guide for the two basic procedures, Ligand Preparation and Receptor Preparation, with Meeko for molecular docking and virtual screening with `AutoDock Vina `_ and `AutoDock-GPU `_. It is based on, but not a full version of the tutorial materials in `Forlilab tutorials `_. .. contents:: :local: @@ -223,7 +216,7 @@ And the expected standard output will be: rec_1iep.gpf <-- autogrid input file rec_1iep.box.pdb <-- PDB file to visualize the grid box -Saving a Receptor JSON File for Docking with Flexible and/or Reactive Residues +Save a Receptor JSON File for Docking with Flexible and/or Reactive Residues ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Docking with flexible and/or reactive residues may require more files than basic docking, and ``mk_prepare_receptor.py`` is able to prepare those simultaneously when creating the receptor PDBQT file. The detailed procedure for Reactive Docking can be found in :ref:`tutorial2`. Here, we will use a different PDB file at ``tutorials/imatinib/step-3/2hzn_protein.pdb`` to showcase a simple docking preparation with flexible sidechains: @@ -327,19 +320,6 @@ With that, the output DLG file will be named ``imatinib_protomer-1_flexres.dlg`` At present, all docking poses will be exported, whether they are cluster leads or not. -Virtual Screening (Batch Docking) -================================= - -Batch Docking with AutoDock-Vina -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - -Batch Docking with AutoDock-GPU -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - -Processing the Screening Results -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - - What's Next? ^^^^^^^^^^^^ From f253af00d1df12c3e8df557b65e3596e8191a32f Mon Sep 17 00:00:00 2001 From: Amy He Date: Tue, 5 Nov 2024 21:22:56 -0800 Subject: [PATCH 58/61] mention Ringtail at the end of tutorial1 for processing screening (batch docking) results --- docs/source/tutorial1.rst | 16 +++++++--------- 1 file changed, 7 insertions(+), 9 deletions(-) diff --git a/docs/source/tutorial1.rst b/docs/source/tutorial1.rst index 620b7fb3..a4f5cf4c 100644 --- a/docs/source/tutorial1.rst +++ b/docs/source/tutorial1.rst @@ -46,13 +46,6 @@ Install the additional packages and data from GitHub repositories git clone --single-branch --branch develop https://github.com/forlilab/scrubber.git cd scrubber; pip install --use-pep517 -e .; cd .. -- (Python package) Ringtail - -.. code-block:: bash - - git clone --single-branch --branch develop https://github.com/forlilab/Ringtail.git - cd Ringtail; pip install --use-pep517 -e .; cd .. - - (Example files for this tutorial) Forlilab Tutorials .. code-block:: bash @@ -252,8 +245,8 @@ With that, the standard output and the list of generated files from ``mk_prepare rec_2hzn.box.txt <-- Vina-style box dimension file rec_2hzn.box.pdb <-- PDB file to visualize the grid box -Export Poses from Molecular Docking (Single Ligand) -=================================================== +Export Poses from Docking +========================= From AutoDock-Vina ~~~~~~~~~~~~~~~~~~ @@ -320,6 +313,11 @@ With that, the output DLG file will be named ``imatinib_protomer-1_flexres.dlg`` At present, all docking poses will be exported, whether they are cluster leads or not. +Processing the Screening (Batch Docking) Results +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +To process results from Screening (Batch Docking), please use the `Ringtail `_ package for SQL-based data management, streamlined analysis and filtering. The documentation of Ringtail can be found `here `_. + What's Next? ^^^^^^^^^^^^ From fd28a7fbf13da613b8a1d3bf989eb2a04e2b90a7 Mon Sep 17 00:00:00 2001 From: Amy He Date: Tue, 5 Nov 2024 21:31:39 -0800 Subject: [PATCH 59/61] small fixes and formatting --- docs/source/cli_rec_prep.rst | 3 ++- docs/source/py_export_result.rst | 3 +-- docs/source/py_lig_prep.rst | 3 +-- docs/source/tutorial1.rst | 2 +- 4 files changed, 5 insertions(+), 6 deletions(-) diff --git a/docs/source/cli_rec_prep.rst b/docs/source/cli_rec_prep.rst index 6a699fdc..2fadd173 100644 --- a/docs/source/cli_rec_prep.rst +++ b/docs/source/cli_rec_prep.rst @@ -51,7 +51,8 @@ Write flags ----------- The option flags starting with ``--write`` in ``mk_prepare_receptor`` can -be used both with an argument to specify the outpuf filename: +be used both with an argument to specify the outpuf filename: + .. code-block:: bash --write_pdbqt myenzyme.pdbqt --write_json myenzyme.json diff --git a/docs/source/py_export_result.rst b/docs/source/py_export_result.rst index 91299426..f6e55da4 100644 --- a/docs/source/py_export_result.rst +++ b/docs/source/py_export_result.rst @@ -28,8 +28,7 @@ For Vina's output PDBQT files, omit ``is_dlg=True``. rdkitmol_list = RDKitMolCreate.from_pdbqt_mol(pdbqt_mol) When using Vina from Python, the output string can be passed directly. -See [the docs](https://autodock-vina.readthedocs.io/en/latest/docking_python.html) -for context on the `v` object. +See `the docs `_ for context on the ``Vina`` object. .. code-block:: python diff --git a/docs/source/py_lig_prep.rst b/docs/source/py_lig_prep.rst index 279aee1b..16c3c367 100644 --- a/docs/source/py_lig_prep.rst +++ b/docs/source/py_lig_prep.rst @@ -22,8 +22,7 @@ Creating a PDBQT string from an RDKit molecule At this point, ``pdbqt_string`` can be written to a file for docking with AutoDock-GPU or Vina, or passed directly to Vina within Python -using `set_ligand_from_string(pdbqt_string)`. For context, see -[the docs on using Vina from Python](https://autodock-vina.readthedocs.io/en/latest/docking_python.html). +using ``set_ligand_from_string (pdbqt_string)``. For context, see `the docs on using Vina from Python `_. One advantage of this approach is that input PDBQT files are not written to the filesystem. The PDBQT format is lossy, because it lacks bond orders and non-polar hydrogens, diff --git a/docs/source/tutorial1.rst b/docs/source/tutorial1.rst index a4f5cf4c..1a433ed7 100644 --- a/docs/source/tutorial1.rst +++ b/docs/source/tutorial1.rst @@ -3,7 +3,7 @@ Basic Docking ------------------------------------- -This tutorial provides practice examples and a step-by-step guide for the two basic procedures, Ligand Preparation and Receptor Preparation, with Meeko for molecular docking and virtual screening with `AutoDock Vina `_ and `AutoDock-GPU `_. It is based on, but not a full version of the tutorial materials in `Forlilab tutorials `_. +This tutorial provides practice examples and a step-by-step guide for the two basic procedures, **Ligand Preparation** and **Receptor Preparation**, with Meeko for molecular docking and virtual screening with `AutoDock Vina `_ and `AutoDock-GPU `_. It is based on, but not a full version of the tutorial materials in `Forlilab tutorials `_. .. contents:: :local: From 97aaea0b956cedcf5c8150e770182a61c02abda7 Mon Sep 17 00:00:00 2001 From: Amy He Date: Tue, 5 Nov 2024 22:34:12 -0800 Subject: [PATCH 60/61] add export from flexible docking with Vina example --- docs/source/tutorial1.rst | 33 ++++++++++++++++++++++++++++----- 1 file changed, 28 insertions(+), 5 deletions(-) diff --git a/docs/source/tutorial1.rst b/docs/source/tutorial1.rst index 1a433ed7..50acc810 100644 --- a/docs/source/tutorial1.rst +++ b/docs/source/tutorial1.rst @@ -289,21 +289,44 @@ With that, the output DLG file will be named ``imatinib_protomer-1.dlg``. Simila Note that by default, only the cluster leads will be exported to the SDF file. To export all generated poses in the DLG file, add the ``--all_dlg_poses`` option when exporting the poses. -From Flexible Receptor Docking -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +From Flexible Receptor Docking (with AutoDock-Vina) +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -Here we will use AutoDock-GPU as the docking engine to demonstrate result processing from flexible receptor docking. A flexible docking example with Vina can be found `here in the Vina documentation `_. With AutoDock-GPU, the required files (generated from the previous steps) and the command to run a flexible docking calculation of a single ligand is as follows: +With AutoDock-Vina, the required files (generated from the previous steps) and the command to run a flexible docking calculation of a single ligand is as follows: .. code-block:: bash lig_name="imatinib_protomer-1" - lig_pdbqt="${lig_resnam}.pdbqt" + lig_pdbqt="${lig_name}.pdbqt" + rec_prefix="rec_2hzn" + flexres_pdbqt="${rec_prefix}_flex.pdbqt" + rec_pdbqt="${rec_prefix}_rigid.pdbqt" + config_txt="${rec_prefix}.box.txt" + ./vina --ligand $lig_pdbqt --flex $flexres_pdbqt --receptor $rec_pdbqt --config $config_txt --out ${lig_name}_flexres.pdbqt + +With that, the output PDBQT file will be named ``imatinib_protomer-1_flexres.pdbqt``. If given the receptor JSON file (``rec_2hzn.json``) generated when the other receptor files were created, ``mk_export.py`` is able to reconstruct the atomistic structures of the full receptor and export the updated models to a multi-model PDB file (``imatinib_protomer-1_flexres_vina_out.pdb``) with the following command: + +.. code-block:: bash + + rec_json="rec_2hzn.json" + docked_pdbqt="imatinib_protomer-1_flexres.pdbqt" + mk_export.py $docked_pdbqt -j $rec_json -p imatinib_protomer-1_flexres_vina_out.pdb + +From Flexible Receptor Docking (with AD-GPU) +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +With AutoDock-GPU, the required files (generated from the previous steps) and the command to run a flexible docking calculation of a single ligand is as follows: + +.. code-block:: bash + + lig_name="imatinib_protomer-1" + lig_pdbqt="${lig_name}.pdbqt" rec_prefix="rec_2hzn" flexres_pdbqt="${rec_prefix}_flex.pdbqt" rec_map_fld="${rec_prefix}_rigid.maps.fld" ./adgpu --lfile $lig_pdbqt --flexres $flexres_pdbqt --ffile $rec_map_fld --resnam ${lig_name}_flexres -With that, the output DLG file will be named ``imatinib_protomer-1_flexres.dlg``. If given the receptor JSON file (``rec_2hzn.json``) generated when the other receptor files were created, ``mk_export.py`` is able to reconstruct the atomistic structures of the full receptor and export the updated models to a PDB file as follows: +With that, the output DLG file will be named ``imatinib_protomer-1_flexres.dlg``. Again, if given the receptor JSON file (``rec_2hzn.json``) generated when the other receptor files were created, ``mk_export.py`` is able to export the updated models to a PDB file (``imatinib_protomer-1_flexres_adgpu_out.pdb``): .. code-block:: bash From 258977af41bb92315e4324d257abebba9e622bad Mon Sep 17 00:00:00 2001 From: diogom Date: Wed, 6 Nov 2024 13:07:35 -0800 Subject: [PATCH 61/61] add docs ligand prep overview --- docs/source/index.rst | 27 ++++++++++++++------------- docs/source/lig_overview.rst | 17 +++++++++++++++++ 2 files changed, 31 insertions(+), 13 deletions(-) create mode 100644 docs/source/lig_overview.rst diff --git a/docs/source/index.rst b/docs/source/index.rst index dce4fe98..2027b60f 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -1,20 +1,20 @@ -Meeko -===== +Meeko: interface for AutoDock +============================= -Parameterization of molecules for AutoDock ------------------------------------------- +Parameterization of molecules +----------------------------- -Meeko assigns parameters to small organic molecules, often called ligands, -and to proteins and to nucleic acids, often called receptors. -This includes assigning atom types, partial charges, setting -bonds as rotatable or fixed, and making receptor sidechains flexible. +Meeko assigns parameters to small organic molecules, referred to as ligands, +and to proteins and nucleic acids, referred to as receptors. +Parameterization includes assigning atom types, partial charges, setting +bonds as rotatable, and making receptor sidechains flexible. -Write input and process output ------------------------------- +Prepare input and convert output +-------------------------------- -Meeko writes the input PDBQT files for AutoDock-Vina and AutoDock-GPU, and it -also converts the output files from docking, which are PDBQT for Vina and -DLG for AutoDock-GPU, into SDF for ligands and PDB for receptor. +Meeko writes the input PDBQT files (or strings in Python) for AutoDock-Vina +and AutoDock-GPU, and exports docking results in SDF format for ligands and +in PDB format for receptor. Python API ---------- @@ -48,6 +48,7 @@ To run a docking, more packages are required besides Meeko: :hidden: :caption: Ligand preparation + Overview cli_lig_prep In Python diff --git a/docs/source/lig_overview.rst b/docs/source/lig_overview.rst new file mode 100644 index 00000000..1fbd47ad --- /dev/null +++ b/docs/source/lig_overview.rst @@ -0,0 +1,17 @@ +Overview of ligand preparation +============================== + +Meeko takes as input an RDKit molecule that has 3D positions and +all hydrogens as real atoms, and creates an object called MoleculeSetup +that stores all the parameters, such as atom types, partial charges, or +rotatable bonds. Adding hydrogens and 3D positions is not performed by Meeko. + +The MoleculePreparation class stores all the configuration required to +parameterize a ligand, and containes the methods that take an RDKit molecule +as input, and return a parameterized MoleculeSetup. The MoleculePreparation +offers several option to control how molecules are parameterized, and many of +which are exposed as command line options in ``mk_prepare_ligand.py``. + +PDBQT files, or strings in Python, are produced using a parameterized instance +of MoleculeSetup. The methods for that live in the PDBQTWriterLegacy class. +PDBQT strings can be passed directly to Vina using its Python API.