openbabel commits | Ecosyste.ms: OpenCollective

2010-03-11 Noel O'Boyle

* src/ops/unique.cpp: Enable compilation with the help of Boost on
GCC 3.4. Note to self, don'...

github.com/openbabel/openbabel - a420c076dc5f65f8fdaa891c825ec0259b25e706 authored almost 15 years ago

Fix for OBConversion crashes in multithreaded environments

github.com/openbabel/openbabel - 01d15903ceff86911ed4bfcec5a4ef90c8dae85a authored almost 15 years ago

Update cif format reader to fix Avogadro bug #2908845

github.com/openbabel/openbabel - 835557ab579136a299dfb7da48a5ced9f820ab21 authored almost 15 years ago

Fix minor kekule failure.

github.com/openbabel/openbabel - 3dc605f265616a377d511f5984b9969b99769636 authored almost 15 years ago

* src/alias.cpp: Downgrade errors over superatom.txt to warnings.

github.com/openbabel/openbabel - 8703d125900b65ee36d3a2731e90ed83e15331c6 authored almost 15 years ago

* src/formats/mdlformat.cpp: Check atom symbols for isotopes like

'D' or 'T'. Solves some inchiwrite failures.

github.com/openbabel/openbabel - aff00573fa783e93b2574fd62d8163b6289f4df2 authored almost 15 years ago

Added support for kekulization failing with a few remaining nitrogen atoms

(e.g., supplied as 'n' should be [nH].

github.com/openbabel/openbabel - 9744b5da38b67c04d9bc0e99badeded5b814910c authored almost 15 years ago

Fixed a few really invalid SMARTS in file.

github.com/openbabel/openbabel - d5f5a39a820cea716f5a0323178625921fef9f7b authored almost 15 years ago

Use tr1::unordered_map only with GCC >=4.1.x

github.com/openbabel/openbabel - fd48d50b588bd51cc03fb04dfbdcb982f846de17 authored almost 15 years ago

Use tr1::unordered_map instead of map when compiling with GCC 4.x

github.com/openbabel/openbabel - de4e8de8b8f10cedd6ac95c6a78abbcad48d473b authored almost 15 years ago

2010-03-06 Noel O'Boyle

* src/formats/inchiformat.cpp, mdlformat.cpp: Moved warning about 0D
from InChI to MDL where i...

github.com/openbabel/openbabel - d0aee09f3b777b0beaead4b9e0d32abbcb1c6a1d authored almost 15 years ago

Minor tidy up.

github.com/openbabel/openbabel - 0ae27ca6aa190bd675e23bc6e7a7ed4935f94ea1 authored almost 15 years ago

Fix small bug I introduced in my last commit. Fixes the failing graphsym test.

github.com/openbabel/openbabel - 3bafdea8da9fdae4cc25682f2594d54092d0bfd7 authored almost 15 years ago

* test/files/stereo/*: Add test structures from Razinger paper.

* include/openbabel/graphsym.h, src/graphsym.cpp: Add parameter for
NOT taking st...

github.com/openbabel/openbabel - 0b9e0b9d28021277a0db25b64248430b9cc6126b authored almost 15 years ago

* Add structure files from Razinger paper and use them for unit testing OBGraphSym.

* Add parameter to OBGraphSym::GetSymmetry for NOT taking stereochemistry into account.

github.com/openbabel/openbabel - 298c8d9b32fe9dc19f5b8b7f1b7fa148dda27bac authored almost 15 years ago

2010-03-05 Noel O'Boyle

* CMakeLists.txt: Require GCC >=4.2 for visibility support

github.com/openbabel/openbabel - 1a9cd31620929a440b56ad3fb730940dc7f2344b authored almost 15 years ago

Update changelog.

github.com/openbabel/openbabel - 2acbcf98c74ab0b0650db954c4117baeb5df637b authored almost 15 years ago

I had some local modifications to gen3d. Correcting the test.

github.com/openbabel/openbabel - b34308a9a5e09eff5614e67d8b41908db56ee3db authored almost 15 years ago

* test/files/testsym_2Dtests.sdf: Forgot to add test file

github.com/openbabel/openbabel - 59914d21f16021220e92b789b368c6514b13c0a8 authored almost 15 years ago

Some tests were skipped during development. 'Unskip' them.

github.com/openbabel/openbabel - c5ef44603bd85423aa8876cfb1949afdda960609 authored almost 15 years ago

2010-03-04 Noel O'Boyle

* src/stereo/perception.cpp: In TetrahedralFrom3D, if a bond to the
chiral center IsWedgeOrHas...

github.com/openbabel/openbabel - 2c20b5e8a95d1bdafebf4b3d412e11fe5c12dbd9 authored almost 15 years ago

* include/openbabel/stereo/stereo.h, src/stereo/facade.cpp: Add support

for square-planar stereochemistry to OBStereoFacade.
* src/formats/smilesformat.c...

github.com/openbabel/openbabel - 7a1b6283a8584fd9144b93f4fb7d79b8d7969161 authored almost 15 years ago

Changes to UC to handle data more consistently. Note that this

depreciates the use of GetOrthoMatrix and GetFractionalMatrix for
conversions to/from fractional ...

github.com/openbabel/openbabel - e844407560fda06e7e26fbf0b794d33b89ec1fa2 authored almost 15 years ago

Removed invalid failing test

github.com/openbabel/openbabel - 0e78cbe06f12370522a0baefd462e42202657709 authored almost 15 years ago

* src/formats/mdlformat.cpp, src/stereo/perception.cpp,

include/openbabel/stereo/stereo.h, src/formats/inchiformat.cpp: More
work on 2D stereo. Tests t...

github.com/openbabel/openbabel - 992e89c2b100f19e0c338e87ee7a28e1f1ef46f7 authored almost 15 years ago

* include/openbabel/stereo/cistrans.h: Doc update.

* include/openbabel/stereo/squareplanar.h: Update OBSquarePlanarStereo
class to ...

github.com/openbabel/openbabel - a8a947fbe6874855eecdeab5b4874ff9aafd383b authored almost 15 years ago

Revive squareplanar test

github.com/openbabel/openbabel - 4cbfeeaa37c9ff101332ba5e65b82694c4ee2482 authored almost 15 years ago

Restored failing tests inchiwrite, graphsym, smartsparse

github.com/openbabel/openbabel - fa4c7b3ce04f0bc42f4aeed0e05662cacfac0dac authored almost 15 years ago

* test/CMakeLists.txt: Add back test for inchwrite and check

failures on Python tests better.

github.com/openbabel/openbabel - 0950fed332581f6f6b41cd0d310263b1b3c09d9e authored almost 15 years ago

* include/openbabel/stereo/tetrahedral.h, src/stereo/tetrahedral.cpp: When

comparing Config structs' stereochemistry, return true if either of the
Config st...

github.com/openbabel/openbabel - 5da6ad4bc503efab05af516bab19d6ece104e59f authored almost 15 years ago

Improvement of geometry steps reading from gamess

github.com/openbabel/openbabel - 138761ef920b1b2b38eace2549d85fbf03130d6b authored almost 15 years ago

Added test for kekule crash PR#2956135

github.com/openbabel/openbabel - 1e4145f6bd82bd06eb4676009b6331e64b676df9 authored almost 15 years ago

* src/kekulize.cpp (expand_kekulize): Fix crashing bug -- looking

for GetBond, not GetBondById -- the code iterates by bond indexes,
not unique ids...

github.com/openbabel/openbabel - c6ed81d7a8d179f57b256d8081beff93711d04a9 authored almost 15 years ago

* src/formats/mdlformat.cpp: Obey MDL stereo guidelines as described

by Greg Landrum on BO mailing list. Test cases to follow

github.com/openbabel/openbabel - b8127c0c4bd2eb38ecbefffd43d7c3e4f14a1f01 authored almost 15 years ago

* test/CMakeLists.txt: Added test smartsparse -- currently unused

(failing) to track SMARTS parsing on valid patterns.

github.com/openbabel/openbabel - 4223dcd4cae6a4a0fec71c7b9fa17328aac6c7a5 authored almost 15 years ago

* test/testkekule.py: Added test for PR#1842055 with

canonicalization and isotopes.

github.com/openbabel/openbabel - 656263e0c921b64bd7b6c20364d41a0930a03f80 authored almost 15 years ago

* test/inchiwrite.cpp: Fixed to compile. Probably needs a python

wrapper to call with appropriate arguments (e.g., inchi/Sample.sdf
inchi/Sample.t...

github.com/openbabel/openbabel - ae5f216103019df0352b7f12813b0ce61eebb4b1 authored almost 15 years ago

* tests/smilestest.cpp: Remove the 2 failing test cases for now. I

believe they were the result from parsing +100000 molecules. I've added
some more...

github.com/openbabel/openbabel - f7efafc3f983e9a0e9e4c9abf23fee0bf8988330 authored almost 15 years ago

* CMakeLists.txt, src/CMakeLists.txt, src/formats/CMakeLists.txt:

Updates to ensure ZLIB is not required PR#2947452.

github.com/openbabel/openbabel - 81d98c3aa2aefb6a91384f8e08567c6bf380660f authored almost 15 years ago

* test/testsym.py: Added test for PR#2101034

github.com/openbabel/openbabel - 37075460eaf02c02f77f8d2030bb7b4e94ef20cb authored almost 15 years ago

Attempt to decouple ZLIB from building PR#2947452

github.com/openbabel/openbabel - 88b63f9dea2a67d8da15587e3af2ce6ef2440ec0 authored almost 15 years ago

2010-03-02 Noel O'Boyle

* test/CMakeLists.txt: Set required environment variables for
"make test". Only works with CMa...

github.com/openbabel/openbabel - ee691e386d2ad79752ea42dc7749834ad553af31 authored almost 15 years ago

Added cast to enable compilation under GCC

github.com/openbabel/openbabel - ff5bbfb2d8663efc5b78ebd6ea1579f18ace10d0 authored almost 15 years ago

* src/formats/inchiformat.cpp: Add support for setting wedge/hash

bonds for 2D data

github.com/openbabel/openbabel - bb50e86e76c080f38c96c9cb4c5115e8ca1a0eb8 authored almost 15 years ago

* src/perception.cpp: Unified code for the wedge and

dash cases where there are two in-plane bonds.
* src/formats/mdlformat.cpp: Improve support for...

github.com/openbabel/openbabel - bf3eed158fac2462b9950e4371d846c26c2b223f authored almost 15 years ago

Forgot to add new Python test to CMakeLists.txt.

github.com/openbabel/openbabel - 34185c657aed97b6887baea8a7f9eb9f09d2e813 authored almost 15 years ago

* CMakeLists.txt: Don't use -fvisibility=hidden for

Mac/gcc-4.2. This feature appears buggy.

github.com/openbabel/openbabel - 4d562ac77f9d343fb393c4f5e5b6b7f7a8298b0b authored almost 15 years ago

* src/typer.cpp: Fix for PR#2889708 -- another patch from Fabian

to improve performance of SelectRootAtoms.

github.com/openbabel/openbabel - d20fd6a62ed5b50c6415e2b108b547b1d7c5ad79 authored almost 15 years ago

Add test for PR#2864334.

github.com/openbabel/openbabel - 4cb7270c89772656f0ad4e181c175c6aafa194fe authored almost 15 years ago

* src/stereo/perception.cpp: Add some more safety logic. (Fixes #2897750)

github.com/openbabel/openbabel - b520e85ae4ac1380887e3c6be6dfe48de6b95e46 authored almost 15 years ago

* src/formats/pdbformat.cpp: Fix for PR#2866659 from Fabian. Check

for chain numbers when assigning sequence numbers.

github.com/openbabel/openbabel - 2f9298a75396f292f640baf05d600ce136a72dca authored almost 15 years ago

* src/data.cpp: Fix for PR#2889763 from Fabian -- make

sure to check chain numbers as well -- or bond between chains!

github.com/openbabel/openbabel - 887f2369ebf15cb4ee88a018b8f6e5890b68f5a5 authored almost 15 years ago

* src/perception.cpp: Fixed error for perception of stereo from 2D for

3 in-plane bond + one wedge/dash. Also unified code for the wedge and
dash cases.
* src/format...

github.com/openbabel/openbabel - b4c61df523f6fb3d4323ed4392cba737eeb5ca06 authored almost 15 years ago

MacOSX was taking ten times longer than the others. After a quick google over to http://bugs.python.org/issue4194, it seemed like it would be a good idea to enable buffering.

github.com/openbabel/openbabel - 299a81b2e0dfd07db3a47b5c2f6969d1dc2844bd authored almost 15 years ago

Adding ignore for OpenBabel::FptIndex; as it was breaking the linking step. Not sure why.

github.com/openbabel/openbabel - c5621afbb4a9b14f26339da107e8978b0950cafb authored almost 15 years ago

Update PWscf format reader to handle fixed-cell calculation outputs.

github.com/openbabel/openbabel - 83375c79736e4176fe28912babd93da3e362cc2b authored almost 15 years ago

Clean up, no difference to output or algorithm.

github.com/openbabel/openbabel - a8e9d324580b29d3b37d3c181f724275df727b51 authored almost 15 years ago

Added PWscf output format reader.

github.com/openbabel/openbabel - fb67c85a89a623d23743eee473c4c89b0e00dbdd authored almost 15 years ago

* src/formats/CMakeLists.txt: Fix to allow compile of InChI with

ops/unique.cpp correctly.

github.com/openbabel/openbabel - bb5bbdb2d229367a246c9acb1efcf9410217aa54 authored almost 15 years ago

* src/formats/gaussformat.cpp: Fix crash with reading Gaussian

files with only one geometry.

github.com/openbabel/openbabel - ee00695246dbd31307f72bad106281c76b46fce3 authored almost 15 years ago

Missing 'self' in last commit

github.com/openbabel/openbabel - 66b8c953eae75bb25eb1680b7b2340f766e574b6 authored almost 15 years ago

* test/testunique.py: Implement Chris' tests for --unique

* test/files/dupset.smi: Remove file as these test cases are included
in the Python script

github.com/openbabel/openbabel - 63b8919195ce7f23a4242793b03cbf43726bf184 authored almost 15 years ago

Avoid error when running SWIG.

github.com/openbabel/openbabel - 9658f5afb9b963c3b1a6b10bffd04be2ac024fce authored almost 15 years ago

Make header file for unordered_map conditional

github.com/openbabel/openbabel - 741a682189cf0691925087f7f9bd1f808ab0c304 authored almost 15 years ago

Revert 3566, 3567

github.com/openbabel/openbabel - e7f6e820edd5cdc64c06022b04dc5450bdbaa30b authored almost 15 years ago

Gamess optimization read (fix in EFP)

github.com/openbabel/openbabel - 78bdb198c35b4ac9b9c8e92e4703ac79671627e5 authored almost 15 years ago

Removed unique from formats

github.com/openbabel/openbabel - a331e17e4ced139b2fc44deef5d4ed75ddf1013e authored almost 15 years ago

Adding the unique ops

github.com/openbabel/openbabel - f9377ec3b7c872c495822e896ff943748cf18d15 authored almost 15 years ago

2010-02-27 Noel O'Boyle

* test/CMakelists.txt, test/testfastsearch.py, test/testbabel.py:
Added a new test for fastsea...

github.com/openbabel/openbabel - 813e5e9d12e23289ef34c2876f12358eb0c22f8b authored almost 15 years ago

use unordered_map without c++0x

github.com/openbabel/openbabel - 60f87bdb349eeb025b8ccf84f9ff666bf1c841d5 authored almost 15 years ago

Fixed compilation with wxWidgets

github.com/openbabel/openbabel - 7383bb4e06a57e3dff44cbe4f93712b8aca6364e authored almost 15 years ago

New ops --sort and --unique and associated changes

github.com/openbabel/openbabel - d00f35bb8b865b9ce869a919b4986e470409633d authored almost 15 years ago

Initial support for parsing of geometry optimization from GAMESS

github.com/openbabel/openbabel - 244d82b860b23f0a60150e426617b6ccf07eb985 authored almost 15 years ago

fingerprint.h missed at last commit.

github.com/openbabel/openbabel - 21e846c724d464a352d947e882dafa2b406b9103 authored almost 15 years ago

* src/chains.cpp: Apply patch from Juergen Wieferink: PR#2948548.

github.com/openbabel/openbabel - 8a66eafa6f6f6cfac6b4939bc84d627e36f6bf1b authored almost 15 years ago

* CMakeLists.txt: Add option for disabling boost detection -- can

cause problems compiling.

github.com/openbabel/openbabel - a0292cfab5e7d9e9a125dab796cbc3febcebc1ba authored almost 15 years ago

2010-02-26 Noel O'Boyle

* src/formats/xml/cmlformat.cpp: Add support for 0D cistrans symmetry
* test/testsym.py: Add t...

github.com/openbabel/openbabel - 23fe0592361d05afbf771a757435d8d08d757367 authored almost 15 years ago

Mods for reading UNIX files on Windows and fastsearch files.

github.com/openbabel/openbabel - 4cbbe5435829f392ff5c8dffb0933657f42f8976 authored almost 15 years ago

2010-02-26 Noel O'Boyle

* src/stereo/cistrans.cpp, include/openbabel/stereo/cistrans.h: Fix
bug in GetCisRef, and unif...

github.com/openbabel/openbabel - 6c92560131206bb0a6912dd45b1ff46d3a13dd5f authored almost 15 years ago

Forgot to add the assert...

github.com/openbabel/openbabel - 34818fad8b5927a73d864225c1e53280ed7c0125 authored almost 15 years ago

2010-02-26 Noel O'Boyle

* test/testsym.py: Add a test for 0D tetrahedral symmetry across SMI,
InChI, SDF and XML

github.com/openbabel/openbabel - 555a96783f8e3fd234a1a6b4b4dd8416c4bafbf8 authored almost 15 years ago

2010-02-25 Noel O'Boyle

* src/xml/cmlformat.cpp: Add support for 0D tetrahedral stereochem

github.com/openbabel/openbabel - ed09462c802caa9fdd3bbfa9709c43dad9816e65 authored almost 15 years ago

Fix some minor bugs with conformer support -- reading geometry optimizations.

github.com/openbabel/openbabel - 5b72295f4604314701a839ba4d29b755fbd807b3 authored almost 15 years ago

2010-02-23 Noel O'Boyle

* src/builder.cpp: Fix bug where a sp2-hybridised atom could be added
at 180 deg instead of 12...

github.com/openbabel/openbabel - 2a28557ccb437ac2f7e7ef2bc6818fabb7c801e5 authored almost 15 years ago

* src/formats/gaussformat.cpp: Add support for reading multiple

conformers (e.g., geometry optimization) including energy for each step.

github.com/openbabel/openbabel - 48c0bd04a94392446d7c3beb7c8b89278bc6c358 authored almost 15 years ago

Fix minor 32-bit conversion warnings with GCC (mostly truncated float/double).

github.com/openbabel/openbabel - bb9eb694e0a315870ddc59243afad39673404540 authored almost 15 years ago

Updated test results. MW for failing test is now correct.

github.com/openbabel/openbabel - 81b728c744ca5dfbc31188831d4fc030890b4f38 authored almost 15 years ago

2010-02-22 Noel O'Boyle

Enable testing of OpenBabel executables from Python
* test/testbabel.py: Initial checkin of te...

github.com/openbabel/openbabel - 37f083556e59fc6fd0356f71d1ebb85f7832be63 authored almost 15 years ago

Fixed bug in GetAtomicNum

github.com/openbabel/openbabel - 0f73d518eeb9fc95f0bd4fab1a7ae2c7b90afbfb authored almost 15 years ago

Return intensities in km/mol from Gamess outs

github.com/openbabel/openbabel - 1777da1e6896a6809e2cc729739df32c8d1795e8 authored almost 15 years ago

2010-02-21 Tim Vandermeersch

* src/stereo/perception.cpp: Allow S, P and bridgehead N atoms to be
chiral. The...

github.com/openbabel/openbabel - de0279a50a2a909142b43f3b06285e291198849e authored almost 15 years ago

* src/formats/gausscubeformat.cpp: Revert of change made in r3534. It

just changed the warning to a different warning.

github.com/openbabel/openbabel - 9e43a0443356cbcb5f9136b09e62c5f3d2d0a378 authored almost 15 years ago

2010-02-21 Noel O'Boyle

* src/CMakeLists.txt: Add LIBXML2 as a dependency of the XML formats

github.com/openbabel/openbabel - 77aeed9b98ecdead7cb8e2c751b65c5f197aff43 authored almost 15 years ago

2010-02-20 Noel O'Boyle

* src/CMakeLists.txt: Remove LIBXML2 as a dependency of the openbabel
DLL

github.com/openbabel/openbabel - 27adb790fc323c1f6fc8077e7b389beb516500af authored almost 15 years ago

Updated -- [*] now functions correctly.

github.com/openbabel/openbabel - 99bbf0b8f857076703dc8e322a8f66988b428429 authored almost 15 years ago

Update Ghemical test results -- adjusted for previous bugfix

github.com/openbabel/openbabel - c8ee41a8582c46a99fa7fbdf3616624421f1fd72 authored almost 15 years ago

2010-02-20 Noel O'Boyle

* include/openbabel/obmolecformat.h: Error compiling on some platforms
due to extra qualificat...

github.com/openbabel/openbabel - 0bd8e287808f4e7bd4fcc95a49c29973f9f79ffa authored almost 15 years ago

Mods to OBOp to allow a wide range of operations.

github.com/openbabel/openbabel - bcac0b14d463dcbb26e079473c925ee472fa6f23 authored almost 15 years ago

MSVC CMake build re shared pointer

github.com/openbabel/openbabel - 60aa91e465612f5bc95127c873fe7b5853190656 authored almost 15 years ago

* src/formats/gausscubeformat.cpp: Add cast to a long to enable size_t

value to be printed out (gets rid of warning on Mac + Intel Compiler)
* src/descriptor.cpp: Usi...

github.com/openbabel/openbabel - 385f48fcab682f782994836f40953a59fa62cf1c authored almost 15 years ago