openbabel commits | Ecosyste.ms: OpenCollective

2009-09-25 Noel O'Boyle <[email protected]>

Fixed some errors when compiling the GUI on Mac.

github.com/openbabel/openbabel - 91a31bd6ca121e1556cd6ddf542199304fd68c65 authored over 15 years ago

2009-09-25 Noel O'Boyle <[email protected]>

Fixed some warnings when compiling with Intel Compiler.

github.com/openbabel/openbabel - 5ffaf2ecef316362b318dcc3a14c535be0b5fd0b authored over 15 years ago

2009-09-22 Noel O'Boyle <[email protected]>

* include/openbabel/format.h: Added include <typeinfo>. Now OB compiles
using Intel Compiler.

github.com/openbabel/openbabel - 4c58c2f33ad3a1ba64231a7da21d9ea14af6ab88 authored over 15 years ago

2009-09-22 Noel O'Boyle <[email protected]>

* src/GUI/babel.xpm: Applied patch from Riccardo Vianello (r_vianello
at SF) to avoid warnings...

github.com/openbabel/openbabel - e042341ac77fbfd1705c3faa17b55b79468f83f1 authored over 15 years ago

2009-09-21 Noel O'Boyle <[email protected]>

* scripts/*: Copied + pasted the scripts directory from 22x as a number
of commits were never ...

github.com/openbabel/openbabel - afb12d1eb750a0bdcde235fb35150ff5dbebe85e authored over 15 years ago

2009-09-20 Noel O'Boyle <[email protected]>

* scripts/CMakeLists.txt: Support for pybel. Revert regression that
prevented linked against P...

github.com/openbabel/openbabel - 36baf46d9e980501459ec525267915912041476a authored over 15 years ago

More miscellaneous static_casts added and unused variables removed to get rid of warnings under MSVC

github.com/openbabel/openbabel - ed656c6005dd580d0f4cb862f32eda18b1c73a1e authored over 15 years ago

2009-09-19 Noel O'Boyle <[email protected]>

Miscellaneous static_casts added and unused variables removed to get rid
of warnings under MSV

github.com/openbabel/openbabel - 96e03a3859080b160b3607b2eb6364c2c7c9bc72 authored over 15 years ago

2009-09-18 Noel O'Boyle <[email protected]>

* include/openbabel/generic.h: Remove unused declarations that caused
warnings under MSVC
* t...

github.com/openbabel/openbabel - 1e68f276e91d77c95f558a25d7d8429e62293ab5 authored over 15 years ago

2009-09-17 Noel O'Boyle <[email protected]>

* CMakeLists.txt, data/CMakeLists.txt: Tidy up the Windows build. The
goal is to...

github.com/openbabel/openbabel - c3fc0283d51921c94746016dd9b58631d3c1f3ea authored over 15 years ago

2009-09-17 Noel O'Boyle <[email protected]>

* include/stereo/stereo.h: Remove obsolete stereo functions and
associated documentation
* sc...

github.com/openbabel/openbabel - 7403d535cad3ea15e8d6757bc16b927d8e21a82e authored over 15 years ago

2009-09-17 Noel O'Boyle <[email protected]>

* src/parsmart.cpp: Handle ring-closure bonds involved in
stereochemistry.

github.com/openbabel/openbabel - 41e9b1fa0941165553cd3300c141bada586d49cb authored over 15 years ago

update ChangeLog

github.com/openbabel/openbabel - e943b3900c19d8140d215b6b37a12a09600da644 authored over 15 years ago

Implement Razinger paper rule 3 (unit test already added)

github.com/openbabel/openbabel - aa0b94aa6afda6a1cfeddf8ca7e5910d00415ef7 authored over 15 years ago

Implement Razinger paper rule 2a & 2b + unit tests for these rules

github.com/openbabel/openbabel - 1e2b592f6cbdfecbff19fe01bff5cb579ad6f29c authored over 15 years ago

Remove/Comment out debug output

github.com/openbabel/openbabel - 7676b1c2cdc3ed9f86f908f9a88eeacd660bf960 authored over 15 years ago

Remove obsolete code

github.com/openbabel/openbabel - 5adec1be2053e4bd0e74ece5679e7437afedc691 authored over 15 years ago

Add more unit tests + small fixes

github.com/openbabel/openbabel - beeac620106af83ef0c657d5af9c2df5fea372bf authored over 15 years ago

Remove obsolete code

github.com/openbabel/openbabel - 12d408f457fbdafab1f57ab8ba711a372b5fefbd authored over 15 years ago

Got all unit tests working + needed to fix one unit test (more failing unit tests will probably follow)

github.com/openbabel/openbabel - f2c26c279ba3b27cf7c7ab16278afa1239031308 authored over 15 years ago

Para-stereocenter detection working for tetrahedral and cistrans elements with assymetry on the non-ring atoms...

github.com/openbabel/openbabel - a1819335a9307a18a60c2c9bf576595d84e3834c authored over 15 years ago

Continue working on para-stereocenter support.

github.com/openbabel/openbabel - 3826be11746af7cdd770505b841900cc1f7c7d6b authored over 15 years ago

The molecule files for the para-stereocenter unit tests

github.com/openbabel/openbabel - fdd5ea5c0885aa789c98d54fa67379e6f28c46a8 authored over 15 years ago

Add unit tests for para-stereocenters

github.com/openbabel/openbabel - 5bf7eb2d50ea00e777a5987c5776e844a69f4fac authored over 15 years ago

OBStereoFacade: AddNumTetrahedralStereo & NumCisTransStereo

github.com/openbabel/openbabel - f14690baadd6d692611fc493f0caff0e022504ca authored over 15 years ago

ontest.h: Add OB_COMPARE

github.com/openbabel/openbabel - 2db5aa69a3054d3df6a6a0966fd81f37c71fd754 authored over 15 years ago

Make wxWidgets not REQUIRED, the if (wxWidget_FOUND) works fine without it...

github.com/openbabel/openbabel - 6eb26399d5c38d2f5fa576d7f2a2fe2895a14c65 authored over 15 years ago

Some improvemtents to para-stereocenter detection

github.com/openbabel/openbabel - eed72dbeca627570dcc5c8426883b6e9f4017831 authored over 15 years ago

Forgot to comment out MINIMAL_BUILD...

github.com/openbabel/openbabel - 06973145865ea493af0ba674ae46befcd47f86d3 authored over 15 years ago

2009-09-16 Noel O'Boyle <[email protected]>

* src/GUI/CMakeLists.txt: Add icon. Add comctl32.lib for Windows
build.
* windows-vc2008, win...

github.com/openbabel/openbabel - 0be4a5ec6086b7e7d449d9d1a6c382298596abe6 authored over 15 years ago

2009-09-16 Noel O'Boyle <[email protected]>

* src/GUI/optswx.cpp: Minor mods to compile on Linux.

github.com/openbabel/openbabel - fd652a30109854e65d8e47fc55a7d61b5d7060e9 authored over 15 years ago

GUI mods: file drag and drop update; options can now have parameters.

github.com/openbabel/openbabel - 9610f43381137082eeb3172eea15e90c7366e4c6 authored over 15 years ago

Some changes to low level stereo functions to make things like dimethylcyclohexane and many more work. See http://timvdm.blogspot.com/2009/09/as-promised-here-are-some-molecules.html.

github.com/openbabel/openbabel - 7c0f0ed88fce665c6de07f146d0f15fb5e09b22f authored over 15 years ago

* include/CMakeLists.txt: install stereo headers

github.com/openbabel/openbabel - d0ccfbdf2ee86bbaf784a2adf2659bc859d86140 authored over 15 years ago

Fix compile error (function I was about to add...)

github.com/openbabel/openbabel - fc090395a38c19be844ce4cdd86bb636367f7f96 authored over 15 years ago

Got some of the para-stereocenter cases working. However, to handle this correctly (and efficient), FindTetrahedralAtoms & FindCisTransBonds will need merging...

github.com/openbabel/openbabel - b6f5ada2e99acd93932e2f371f4a811f51c71913 authored over 15 years ago

2009-09-11 Noel O'Boyle <[email protected]>

* src/GUI/CMakeLists.txt: Added Win32 to ensure that on Windows
a command-line application was...

github.com/openbabel/openbabel - c18332d97c0940402b75d304b03fffa94c29c067 authored over 15 years ago

2009-09-11 Noel O'Boyle <[email protected]>

* src/GUI/*.h, *.cpp: Large number of minor mods for compatibility with unicode build of wxWidg...

github.com/openbabel/openbabel - 21782bc3e2b67d33287e2dd655c2dcb2227c9d31 authored over 15 years ago

Simple typo fix.

github.com/openbabel/openbabel - 37c86cf0e213c4365f96c48761db58b98cc57628 authored over 15 years ago

Fix buffer overflow in Random & Systematic Rotor Search.

github.com/openbabel/openbabel - 99389ebe7f541a8946e3bed27114539209124eba authored over 15 years ago

Bugfix for: echo "CC(O)C(N)C(=O)O" | obgrep "C[C@@H](O)C(N)C(=O)O"

github.com/openbabel/openbabel - d6a2ee11f575e72625d145b10862c25664da9000 authored over 15 years ago

Some bug fixes to stereochemical SMARTS

github.com/openbabel/openbabel - dffad87ee3c55fdad1fe856e7b0ee22244b549e7 authored over 15 years ago

First attempt to make SMARTS work with new stereo classes. Should be working for tetrahedral stereochemistry. Still have to do cis/trans I think.

github.com/openbabel/openbabel - 54244e966454b7c2c4c715173d3f29ab854eb8bc authored over 15 years ago

* src/formats/xml/cmlformat.cpp: Make sure to read in all wedge/hash bonds

github.com/openbabel/openbabel - 6fcd076265dc7c4ef9f1cf2f6b1c2345a3fcd82e authored over 15 years ago

* src/fingerprint.cpp, include/openbabel/fingerprint.h,

src/formats/fastsearchformat.cpp: Patches from Izhar Wallach for a
similarity sea...

github.com/openbabel/openbabel - 92558886fd9efe604adb84694aba34ad73c5de51 authored over 15 years ago

src/formats/mdlformat.cpp: minor change to slightly improve performance

reading CTAB in MOL and SDF.

github.com/openbabel/openbabel - 976dcb003c718da0d208ddc2d18829a4fb8a427f authored over 15 years ago

See the ChangeLog. Fixed a number of bugs and core dumps in mdlformat.cpp,

obiter.cpp, a couple bugs in smilesformat.cpp, and added "ignore"
instructions so that Subversion...

github.com/openbabel/openbabel - 0c883332dbfeb3191e71bf3ad7268027b8c212f9 authored over 15 years ago

Fix crash in gamess input reader.

github.com/openbabel/openbabel - 2485c1c71ab6d01714d9a417483fed7d18e9f9ee authored over 15 years ago

Rename excited states generic data to OBElectronicTransitionData.

github.com/openbabel/openbabel - deca1894ea7eca775d84a4e68c93696cd7513d52 authored over 15 years ago

Added excited states support for gaussian.

github.com/openbabel/openbabel - 4a53eaecbf73f57bda1d49a67a217c5d76b9cd90 authored over 15 years ago

Added an excited states generic type to hold extracted data about electronic excitations.

github.com/openbabel/openbabel - bc8e9c9cdc9eeaa4c5a9cc8fa4bfe1a9000b6111 authored over 15 years ago

* src/obiter.cpp: Add _ptr checks for Atom and Bonds BFS iterators. (as suggested by Craig A. James)

github.com/openbabel/openbabel - d93a17ff99f07d00a6ddd60547b31ccaab6cb3e5 authored over 15 years ago

Add changes from 2.2.x: r3359 forcefield initialization fix

github.com/openbabel/openbabel - fabc6f45b5c3ddb4071c3da5d062dc472d1e6a00 authored over 15 years ago

Initialized merge tracking via "svnmerge" with revisions "1-2697" from

https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/branches/openbabel-2-2-x

github.com/openbabel/openbabel - c4dc2fdd2c179315da7ed973c2c648b3f5a11d02 authored over 15 years ago

Add changes from 2.2.x: r3349 GAMESS energy

github.com/openbabel/openbabel - 4502e52e690a5ce31cbf0e51100d081706c1a7df authored over 15 years ago

Reorder DOS SetData arguments to be a bit more intuitive.

github.com/openbabel/openbabel - fe8b7ad14d9f9938432f6dbd01776dc3bf695a27 authored over 15 years ago

Indentation/whitespace cleanup.

github.com/openbabel/openbabel - 4a816b63a168318d733eed03e6d3e8629756007f authored over 15 years ago

Added DOS reading to VASP format reader.

github.com/openbabel/openbabel - 6a6984218371771bf5470fc82395a3b052ededf9 authored over 15 years ago

Added a DOSData data type for density of states information.

github.com/openbabel/openbabel - 444d8d7a7d66507790c9a483f07e15d93b41eb98 authored over 15 years ago

Changes to maintain compatibility with CMake 2.4.8.

github.com/openbabel/openbabel - 19c2ca1a7853a20b4b19c43c85bb4fbada248870 authored over 15 years ago

Made the building of unit tests optional.

github.com/openbabel/openbabel - 3f0f02f8a5fef35b9db87e196c54d0dc1f976055 authored over 15 years ago

* CMakeLists.txt: Only add the scripts directory if ENABLE_PYTHON is set.

github.com/openbabel/openbabel - 14310476f727ab93848feeba8e1fd074ed091c6f authored over 15 years ago

2009-08-03 Jean Brefort <[email protected]>

* include/openbabel/math/transform3d.h: add missing const to operator*.
* src/math/transform3d...

github.com/openbabel/openbabel - 4d5f4378ae23c4f397e92d357852fa31be60b771 authored over 15 years ago

2009-08-02 Jean Brefort <[email protected]>

* data/space-groups.txt: updated after group 229 fix.

github.com/openbabel/openbabel - bb16d989259c56a88d199c14544bb9e062631589 authored over 15 years ago

* doc/babel.1, doc/obchiral.1: Fixed "mdoc warning: Extraneous .Re".

github.com/openbabel/openbabel - f993a659bfb413bf694e8f1f16638996d7986b2d authored over 15 years ago

Ensure orderedConfig is canonical in BreakChiralTies (graphsym.cpp)

github.com/openbabel/openbabel - 002a16932c0c5b6ac450cc1b1538056075ebb3a1 authored over 15 years ago

Improve TetrahedralFrom3D to interpret 3 in-plane bonds + 1 hash or wedge

github.com/openbabel/openbabel - 1e4def70dcb873143fa44b1b6355bffbeeccd956 authored over 15 years ago

More stereochemistry documentation

github.com/openbabel/openbabel - 1fdd47a3e08a84fa280d58664ab6f957584b1e80 authored over 15 years ago

More stereochemistry documentation updates

github.com/openbabel/openbabel - 58284bcd319912184e4bba7b8021a3dda739031b authored over 15 years ago

Documentation updates + Add typedef for Ref (unsigned long), change NoId & ImplicitId to NoRef & ImplicitRef

Conflicts:

include/openbabel/stereo/stereo.h

github.com/openbabel/openbabel - ad53314142cf8b262b49b65be5d4f66449170580 authored over 15 years ago

New test file to exercise the SMILES canonicalizer.

github.com/openbabel/openbabel - e6337d0549cd720f2be6b84c224e75a707ee4554 authored over 15 years ago

Added "-xC" option ("anti-canonical") to produce randomly-ordered SMILES

for testing purposes.

Conflicts:

src/formats/smilesformat.cpp

github.com/openbabel/openbabel - bda1f0b4582bfea878ccfa5cbe782b70d8ffabfc authored over 15 years ago

Minor mods to enable 's' option

github.com/openbabel/openbabel - b3b46c4ca7b0063fd9477761cc5b29cf447662ee authored over 15 years ago

Added option to MDLFormat to allow 2D tet stereo perception from 0D data

github.com/openbabel/openbabel - 47ff6e3cb4f824e7c42c6ac8aa773f0215d14e30 authored over 15 years ago

Spurious Tetrahedral centers now removed.

github.com/openbabel/openbabel - 6de004742eb3045bb312d3db714f7275aded4797 authored over 15 years ago

Can read 0D MDL now. Next to update TetFrom0D to delete spurious TetStereos.

github.com/openbabel/openbabel - 291b17faf1f0210d95e5283ce6957794210db718 authored over 15 years ago

Can write out MDL format with tetrahedral stereo

github.com/openbabel/openbabel - 1ec9701c05b36920b56a9f310179522103c7d030 authored over 15 years ago

Final edits on 0D Cis/Trans. Need to look at tetrahedral now.

github.com/openbabel/openbabel - c53409a85aa6d6647721ab8c2d55c0a7a123484c authored over 15 years ago

Reverting some

github.com/openbabel/openbabel - 56c26864364e663adaff54defd9acd5adceb7a60 authored over 15 years ago

0D now working for inchi, smiles and mdl.

github.com/openbabel/openbabel - a57fdb1980767f204f64572f9112e5bc46e5cef8 authored over 15 years ago

CisTransFrom0D now should work as intended. Need to test.

github.com/openbabel/openbabel - a99da868662d9363f5ed1a7954dbbe86b400ec1c authored over 15 years ago

Now it compiles.

github.com/openbabel/openbabel - a6f85eb397eb46559c2ef353c3387db8e0b06011 authored over 15 years ago

Stash

github.com/openbabel/openbabel - a9cf8a8cf91ffaad811689621e872bf956f4efef authored over 15 years ago

Adding CisTransFromUpDown

github.com/openbabel/openbabel - 76f37feb38607b6daf146b06834d92949be9ff74 authored over 15 years ago

Stash

github.com/openbabel/openbabel - a5ce7a78d71179569e135dcc2bf8774ad3983044 authored over 15 years ago

Add new bfs iterator over bonds

Conflicts:

include/openbabel/obiter.h

github.com/openbabel/openbabel - 0c2a24b92a0518d9fefdb1e83c2740f5f6f31072 authored over 15 years ago

Fix bug when creating C=N, N=N stereo bonds. Also, for the moment don't create stereo objects where the cis/trans stereo is unspecified

github.com/openbabel/openbabel - a55b81759093374fe5547db2176142719f908dba authored over 15 years ago

Make OBGraphSym::CalculateSymmetry private, replace calls to it with OBGraphSym::GetSymmetry

github.com/openbabel/openbabel - d0b9124db546c6efe0cdadb0c0fe9ac21676c56f authored over 15 years ago

For the moment, just clear any calculated symmetry in smiles format writer

Conflicts:

src/formats/smilesformat.cpp

github.com/openbabel/openbabel - 59cee8769dc90b1d2c1696970a70ea0508927f25 authored over 15 years ago

commit Noel: Simplify logic for perception of cis/trans with valence 2

github.com/openbabel/openbabel - 6268db1d677936fe49e6f5605ff46232db408e4a authored over 15 years ago

commit Noel: Simplify constructor

github.com/openbabel/openbabel - 152ea12802ba064c55ac4e4333601b4b60624ff0 authored over 15 years ago

InChI now seems to be working. Need to run a big test though.

github.com/openbabel/openbabel - 15d58f957a695fc51c68dc7dd650b7d5aefaa2c1 authored over 15 years ago

Writing InChI cis/trans stereo added. Well, it compiles anyway.

github.com/openbabel/openbabel - 8c1bad168b87fd0d778bab404213203e1168ce3e authored over 15 years ago

InChI can now handle tetrahedral unspecified

github.com/openbabel/openbabel - ef6db809d37d16a422f3a26f28b5ce6c7391a598 authored over 15 years ago

Added tetrahedral stereo handling for inchi

github.com/openbabel/openbabel - 6593a8e9ede07395b6052e1c35c665a0483b986b authored over 15 years ago

commit Noel: Add public method OBGraphSym::ClearSymmetry

github.com/openbabel/openbabel - 3c43fbb2e594e8679276a3154e43d4391314419b authored over 15 years ago

commit from Noel: "Now parses cached value. Need to test properly."

github.com/openbabel/openbabel - 06e35caa129339e1ca5c5eb4af66d4057c4a2628 authored over 15 years ago

Changes from Noel's "More of the same" commit.

github.com/openbabel/openbabel - c780a0b4876ccccd86e6ebc63c2ec5eaf105b738 authored over 15 years ago

Clean up (remove obsolete code, unused variables, ..)

github.com/openbabel/openbabel - 13e4a426222db8f6e684cdc9b8f9566b869b5b5a authored over 15 years ago

Finally found the problem with Canonical smiles. In CanonicalLabels, after converting

the result from CalculateSymmetry(vector<uint>) to a vector<pair<OBAtom*, uint>>, we
need to sort...

github.com/openbabel/openbabel - 4b769812824ddc4be8c2a31a1d3c2fce0df1b555 authored over 15 years ago