Skip to content

Commit

Permalink
Merge pull request #281 from openforcefield/charges-from-sdf
Browse files Browse the repository at this point in the history 
Implementing support for partial charge I/O in SDF
  • Loading branch information
@j-wags
j-wags authored Apr 11, 2020
2 parents 146c9c8 + 19f705c commit c1b13c2
Show file tree
Hide file tree
Showing 7 changed files with 720 additions and 113 deletions.
48 changes: 45 additions & 3 deletions docs/releasehistory.rst
View file
Original file line number Diff line number Diff line change
Expand Up @@ -7,8 +7,50 @@ Releases follow the ``major.minor.micro`` scheme recommended by `PEP440 <https:/
* ``minor`` increments add features but do not break API compatibility
* ``micro`` increments represent bugfix releases or improvements in documentation

0.6.1 - Bugfixes
----------------
0.7.0 - Current development
---------------------------

Behavior changed
""""""""""""""""
- `PR #508 <https://github.com/openforcefield/openforcefield/pull/508>`_:
In order to provide the same results for the same chemical species, regardless of input
conformation, fractional bond order calculation methods now default to ignore input conformers
and generate a new conformer of the molecule before running semiempirical calculations.
Users can override this behavior by specifying the keyword argument
``use_conformers=molecule.conformers``
- `PR #281 <https://github.com/openforcefield/openforcefield/pull/281>`_: Closes
`Issue #250 <https://github.com/openforcefield/openforcefield/issues/250>`_
by adding support for partial charge I/O in SDF. The partial charges are stored as a property in the
SDF molecule block under the tag ``<atom.dprop.PartialCharge>``.
- `PR #281 <https://github.com/openforcefield/openforcefield/pull/281>`_: If an OFFMol's
``partial_charges`` attribute is set to ``None`` (the default value), calling ``to_openeye`` will
now produce a OE molecule with partial charges set to ``nan``. This would previously produce an OE
molecule with partial charges of 0.0, which was a loss of information, since it wouldn't be clear
whether the original OFFMol's partial charges were REALLY all-zero as opposed to ``None``. OpenEye toolkit
wrapper methods such as ``from_smiles`` and ``from_file`` now produce OFFMols with
``partial_charges = None`` when appropriate (previously these would produce OFFMols with
all-zero charges, for the same reasoning as above).
- `PR #281 <https://github.com/openforcefield/openforcefield/pull/281>`_: ``Molecule.to_rdkit``
now sets partial charges on the RDAtom's ``PartialCharges`` property (this was previously set
on the ``partial_charges`` property). If the OFFMol's partial_charges attribute is None, this property
will not be defined on the RDAtoms.
- `PR #281 <https://github.com/openforcefield/openforcefield/pull/281>`_:
Enforce the behavior during SDF I/O that a SDF may contain multiple MOLECULES, but that the OFF Toolkit
DOES NOT assume that it contains multiple CONFORMERS of the same molecule. This is an
important distinction, since otherwise there is ambiguity around whether properties of one
entry in a SDF are shared among several molecule blocks or not, or how to resolve conflicts if properties
are defined differently for several "conformers" of chemically-identical species (More info
`here <https://docs.eyesopen.com/toolkits/python/oechemtk/oemol.html#dude-where-s-my-sd-data>`_.
If the user requests the OFF
Toolkit to write a multi-conformer ``Molecule`` to SDF, only the first conformer will be written.
For more fine-grained control of writing properties, conformers, and partial charges, consider
using ``Molecule.to_rdkit`` or ``Molecule.to_openeye`` and using the functionality offered by
those packages.
- `PR #281 <https://github.com/openforcefield/openforcefield/pull/281>`_: Due to different
constraints placed on the data types allowed by external toolkits, we make our best effort to
preserve ``offmol.properties`` when converting molecules to other packages, but users should be aware that
no guarantee of data integrity is made. The only data format for keys and values in the property dict that
we will try to support through a roundtrip to another toolkit's Molecule object is ``string``.

API-breaking changes
""""""""""""""""""""
Expand Down Expand Up @@ -202,7 +244,7 @@ Bugfixes
Example added
"""""""""""""
- `PR #472 <https://github.com/openforcefield/openforcefield/pull/472>`_: Adds an example notebook
`QCarchive_interface.ipynb <https://github.com/openforcefield/openforcefield/blob/master/examples/QCArchive_interface/QCarchive_interface.ipynb>`
`QCarchive_interface.ipynb <https://github.com/openforcefield/openforcefield/blob/master/examples/QCArchive_interface/QCarchive_interface.ipynb>`_
which shows users how to instance the :py:class:`Molecule <openforcefield.topology.Molecule>` from
a QCArchive entry level record and calculate the energy using RDKit through QCEngine.

Expand Down
26 changes: 26 additions & 0 deletions openforcefield/data/molecules/ethanol_partial_charges.sdf
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,26 @@
*****
OpenBabel02041915453D

9 8 0 0 0 0 0 0 0 0999 V2000
1.0616 -0.2681 -0.0006 C 0 0 0 0 0 0 0 0 0 0 0 0
1.9101 0.9126 -0.4220 C 0 0 0 0 0 0 0 0 0 0 0 0
1.5170 1.3236 -1.7228 O 0 0 0 0 0 0 0 0 0 0 0 0
2.0787 2.0794 -1.9612 H 0 0 0 0 0 0 0 0 0 0 0 0
1.3393 -0.6108 1.0001 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.0000 -0.0002 -0.0006 H 0 0 0 0 0 0 0 0 0 0 0 0
1.1801 -1.0990 -0.7040 H 0 0 0 0 0 0 0 0 0 0 0 0
2.9684 0.6361 -0.4446 H 0 0 0 0 0 0 0 0 0 0 0 0
1.7730 1.7499 0.2687 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 5 1 0 0 0 0
1 6 1 0 0 0 0
1 7 1 0 0 0 0
2 3 1 0 0 0 0
2 8 1 0 0 0 0
2 9 1 0 0 0 0
3 4 1 0 0 0 0
M END
> <atom.dprop.PartialCharge> (1)
-0.40000000000000002 -0.29999999999999999 -0.20000000000000001 -0.10000000000000001 0.01 0.10000000000000001 0.20000000000000001 0.29999999999999999 0.40000000000000002

$$$$
32 changes: 32 additions & 0 deletions openforcefield/data/molecules/methane_multiconformer.sdf
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,32 @@

-OEChem-02042019153D

5 4 0 0 0 0 0 0 0999 V2000
0.9999 1.0000 1.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.9433 2.0874 0.9141 H 0 0 0 0 0 0 0 0 0 0 0 0
1.6195 0.6029 0.1928 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.0043 0.5764 0.9304 H 0 0 0 0 0 0 0 0 0 0 0 0
1.4416 0.7334 1.9627 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 3 1 0 0 0 0
1 4 1 0 0 0 0
1 5 1 0 0 0 0
M END

$$$$

-OEChem-02042019153D

5 4 0 0 0 0 0 0 0999 V2000
2.2299 2.2300 2.2300 C 0 0 0 0 0 0 0 0 0 0 0 0
2.1733 3.3174 2.1441 H 0 0 0 0 0 0 0 0 0 0 0 0
2.8495 1.8329 1.4228 H 0 0 0 0 0 0 0 0 0 0 0 0
1.2257 1.8064 2.1604 H 0 0 0 0 0 0 0 0 0 0 0 0
2.6716 1.9634 3.1927 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 3 1 0 0 0 0
1 4 1 0 0 0 0
1 5 1 0 0 0 0
M END

$$$$
45 changes: 45 additions & 0 deletions openforcefield/data/molecules/methane_multiconformer_properties.sdf
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,45 @@

-OEChem-02042019153D

5 4 0 0 0 0 0 0 0999 V2000
0.9999 1.0000 1.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.9433 2.0874 0.9141 H 0 0 0 0 0 0 0 0 0 0 0 0
1.6195 0.6029 0.1928 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.0043 0.5764 0.9304 H 0 0 0 0 0 0 0 0 0 0 0 0
1.4416 0.7334 1.9627 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 3 1 0 0 0 0
1 4 1 0 0 0 0
1 5 1 0 0 0 0
M END
> <test_property_key>
test_property_value

> <atom.dprop.PartialCharge>
-0.108680 0.027170 0.027170 0.027170 0.027170

$$$$

-OEChem-02042019153D

5 4 0 0 0 0 0 0 0999 V2000
2.2299 2.2300 2.2300 C 0 0 0 0 0 0 0 0 0 0 0 0
2.1733 3.3174 2.1441 H 0 0 0 0 0 0 0 0 0 0 0 0
2.8495 1.8329 1.4228 H 0 0 0 0 0 0 0 0 0 0 0 0
1.2257 1.8064 2.1604 H 0 0 0 0 0 0 0 0 0 0 0 0
2.6716 1.9634 3.1927 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 3 1 0 0 0 0
1 4 1 0 0 0 0
1 5 1 0 0 0 0
M END
> <test_property_key>
test_property_value2

> <another_test_property_key>
another_test_property_value

> <atom.dprop.PartialCharge>
0.027170 0.027170 0.027170 0.027170 -0.108680

$$$$
Loading

0 comments on commit c1b13c2

Please sign in to comment.