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rwestrwest
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Merge branch 'rdkit' to switch from OpenBabel to RDKit
This closes #135 - Switch from OpenBabel to RDKit And also... closes #86 - Drawing of fused rings buggy closes #90 - molecule.fromSMILES(CC1=CC=CO1) gives "Unable to determine atom type for atom O." closes #121 - Furan inchi and SMILES cannot be resolved Should help with #106 in the future (I think RDKit has aromaticity detection). RDKit is now a requirement (but OpenBabel no longer is). Be sure to install RDKit with InChI Support, which at the moment requires building from source, I think. Note that anything being read in via InChI or SMILES will be Kekulized before making the RMG molecule. This means if you input benzene as SMILES="c1ccccc1" it will be equivalent to SMILES="C1=CC=CC=C1"
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‎Makefile

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@@ -29,6 +29,8 @@ bin/symmetry:
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QM: bin/symmetry
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echo "Checking you have rdkit..."
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python -c 'import rdkit; print rdkit.__file__'
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echo "Checking rdkit has InChI support..."
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python -c 'from rdkit import Chem; assert Chem.inchi.INCHI_AVAILABLE, "RDKit installed without InChI Support"'
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documentation:
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$(MAKE) -C documentation html

‎documentation/source/users/rmg/installation/index.rst

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@@ -13,8 +13,8 @@ Briefly, RMG depends on the following packages:
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* **NumPy:** fast matrix operations
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* **SciPy:** fast mathematical toolkit
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* **matplotlib:** generating plots
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* **rdkit:** open-source cheminformatics toolkit
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* **guppy:** memory profiling tools
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* **OpenBabel:** species format conversion
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* **Cython:** compiling Python modules to C
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* **quantities:** unit conversion
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* **nose:** advanced unit test controls

‎documentation/source/users/rmg/installation/linux.rst

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Linux Installation
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******************
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RMG-Py and all of its dependencies may be easily installed through a short series of Terminal commands. The instructions listed below have been confirmed on a fresh Ubuntu 12.04 installation and should generally apply to other distributions.
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RMG-Py and all of its dependencies may be easily installed through a short series of Terminal commands.
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The instructions listed below have been confirmed on a fresh Ubuntu 12.04 installation and should generally apply to other distributions.
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* Install compilers and libraries: ::
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cd PyDAS; make F77=gfortran; sudo make install
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cd ../PyDQED; make F77=gfortran; sudo make install
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* Install RDKit
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Full installation instructions: http://code.google.com/p/rdkit/wiki/GettingStarted
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Be sure to **build it with InChI support.** Here's a synopsis::
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cd ~
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sudo apt-get install flex bison build-essential python-numpy cmake python-dev sqlite3 libsqlite3-dev
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libboost-dev libboost-python-dev libboost-regex-dev
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git clone https://github.com/rdkit/rdkit.git
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cd rdkit
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export RDBASE=`pwd`
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export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$RDBASE/lib
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export PYTHONPATH=$PYTHONPATH:$RDBASE
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cd External/INCHI-API
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./download-inchi.sh
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cd ../../
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mkdir build
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cd build
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cmake .. -DRDK_BUILD_INCHI_SUPPORT=ON
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make
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make install
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You'll need various environment variables set (you may want to add these to your `.bash_profile` file), eg.::
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export RDBASE=$HOME/rdkit # CHECK THIS (maybe you put RDKit somewhere else)
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export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$RDBASE/lib
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export PYTHONPATH=$PYTHONPATH:$RDBASE # (or some other way to make sure it's on your Python path)
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* Install RMG-Py: ::
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cd ~
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git clone [email protected]:GreenGroup/RMG-database.git
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git clone [email protected]:GreenGroup/RMG-Py.git
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sudo pip install -r RMG-Py/requirements.txt
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cd RMG-Py; make
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* Run an example: ::
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python rmg.py examples/rmg/minimal/input.py
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Verify your installation by opening the resulting output.html file under the "examples/rmg/minimal" directory.
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You can also use the Makefile targets to test and run examples: ::
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make test
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make eg1
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make eg2

‎documentation/source/users/rmg/installation/macos.rst

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@@ -17,12 +17,6 @@ but other methods like the `Scipy Superpack <http://fonnesbeck.github.com/ScipyS
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brew update
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brew install git
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* Install `Open Babel <http://openbabel.org/>`_ and its Python bindings. For now, the easiest way to get version 2.3.1 and the Python bindings is::
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brew install https://raw.github.com/rwest/homebrew/open-babel-new/Library/Formula/eigen2.rb
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brew install https://raw.github.com/rwest/homebrew/open-babel-new/Library/Formula/open-babel.rb
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* Make a directory to put everything in::
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mkdir ~/Code
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cd ~/Code
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git clone [email protected]:GreenGroup/RMG-database.git
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git clone [email protected]:GreenGroup/RMG-Py.git
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* Install the Python dependencies listed in the :file:`RMG-Py/requirements.txt` file using `pip` (do ``easy_install pip`` if you don't already have it)::
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cd RMG-Py
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make
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* Install RDKit, *if* (and only if) you want to use the new 3D geometry branch::
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* Install RDKit::
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brew uninstall boost
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brew install boost --build-from-source
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brew tap rwest/homebrew-rdkit
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brew tap edc/homebrew-rdkit
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brew install rdkit --with-inchi
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You'll need various environment variables set, eg.::
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export RDBASE=$HOME/rdkit # CHECK THIS (maybe you put RDKit somewhere else)
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export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$RDBASE/lib
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export PYTHONPATH=$PYTHONPATH:$RDBASE
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* Run an example: ::
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cd ~/Code/RMG-Py/
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python rmg.py examples/rmg/minimal/input.py
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Verify your installation by opening the resulting output.html file under the "examples/rmg/minimal" directory.
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You can also use the Makefile targets to test and run examples: ::
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make test
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make eg1
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make eg2

‎documentation/source/users/rmg/installation/windows.rst

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.. _remainingdependencies:
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RDKit
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================
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Project home on GitHub: https://github.com/rdkit/rdkit
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Installation instructions: http://code.google.com/p/rdkit/wiki/GettingStarted
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Build it with InChI support.
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Required environment variables:
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* RDBASE pointing to the root of the distribution
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* PYTHONPATH: should include $RDBASE
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* PATH: should include $RDBASE/lib
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Remaining Dependencies
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======================
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Install the remaining six python dependencies using 'pip': ::
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curl https://raw.github.com/pypa/pip/master/contrib/get-pip.py | python
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easy_install pip
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pip install nose quantities sphinx pydot psutil xlwt cython==0.16
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pip install nose quantities sphinx pydot psutil xlwt cython
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.. _rmgsources:
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‎examples/rmg/1,3-hexadiene/input.py

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species(
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label='HXD13',
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reactive=True,
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structure=CML(
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"""
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<molecule>
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<atomArray>
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<atom id="a1" elementType="C" />
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<atom id="a2" elementType="C" />
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<atom id="a3" elementType="C" />
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<atom id="a4" elementType="C" />
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<atom id="a5" elementType="C" />
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<atom id="a6" elementType="C" />
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</atomArray>
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<bondArray>
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<bond atomRefs2="a1 a2" order="D" />
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<bond atomRefs2="a2 a3" order="S" />
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<bond atomRefs2="a3 a4" order="D" />
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<bond atomRefs2="a4 a5" order="S" />
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<bond atomRefs2="a5 a6" order="S" />
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</bondArray>
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</molecule>
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"""),
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structure=SMILES("C=CC=CCC"),
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)
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species(
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label='CH4',

‎rmgpy/data/base.py

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provide these.
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"""
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# Collision efficiencies are in SMILES format, so we'll need OpenBabel
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# Collision efficiencies are in SMILES format, so we'll need RDKit
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# to convert them to Molecule objects
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# Do the import here to ensure it is imported from a pure Python
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# environment (as opposed to a Cythonized environment, which is not
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# allowed during an exec() call)
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import pybel
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from rdkit import Chem
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# Clear any previously-loaded data
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self.entries = {}

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