github.com/openbabel/openbabel commits | Ecosyste.ms: OpenCollective

Fix failing gziptest due to MOL2 file. MOL2 needs (a lot) more work but this is sufficient to keep the tests passing.

4f73b2b0cb2f323322ab82fc96aba5a552aed1c3 authored over 7 years ago

Fix test failure for GAFF forcefield

1. Gasteiger partial charges are no longer generated on molecule copy and so they need to be calc...

6b6d8696484fd3531cea6a0250754660745affbc authored over 7 years ago

Fix test failure for UFF forcefield by updating OBBond::IsAmide

94d9f7446a64f40af9b27c2bea4dd7bb19fb20e4 authored over 7 years ago

Make sure to trigger partial charge calculation. Previously it was "accidentally" and erroneously (I believe) triggered during OBAtom::Duplicate().

9f831905d4f262ca89d7fbcbcb019fbc2bfa65e3 authored over 7 years ago

Get smartstest to pass

1. Correctly handle [v]
2. Update test results due to explicit Hs no longer being created when re...

56661560acdcd6f109383012d04fec7be6b21dcb authored over 7 years ago

Get phmodel test to pass

1: Fix non-kekulizable SMILES for histidine in the test
2. Adjust implicit H count when changing ...

01fe44675595ea1f26676fc79ab5a6296814c0b3 authored over 7 years ago

Remove all of the original kekulization code. This includes helper/trigger functions such as OBBond::IsDouble().

5dbfff22a0d8d839d4f2898fa892076bf2df12b1 authored over 7 years ago

Update OBMol::PerceiveBondOrders to new kekulization

6164fffa69ed66cf20b4b46c8ab702fcd3e3baf6 authored over 7 years ago

Kekulize aromatic bonds if present in a MOL file

d5d0cbd9430667de5123e5eba0af94f6f1176140 authored over 7 years ago

Handle implicit and explicit hydrogens the same during canonicalisation

The current master gives different canon string for:
obabel -:"c1[14cH]cccc1" -ocan -d
versus
ob...

7d2ba1e1169cb5c9a066bad23a9079de74d2b8e0 authored over 7 years ago

Update test smiles

c8f16562878764d7d7367277f7d83adf7d0badea authored over 7 years ago

Remove (redundant) calls to OBMol::Kekulize in preparation for its removal.

35bc2465bf77f9b470ecb4f461979b09e2a1e9bf authored over 7 years ago

1. Tighten up the handling of when to write a bond symbol for BO of 1

2. Update the SMILES in canonstable.can to be consistent with (1) above
3. Don't set SpinMultipli...

d2720816e302edf0975f29e317da2622f3824e0c authored over 7 years ago

1. Minor speedup to FindPath

2. Add more comments on potential speedups/micro-opts

38839702405c70f1e5ab45673ec74a8caafc1e5e authored over 7 years ago

Tidy-up some comments

8ca21c2c769dd1bd64a248b49cfc69f8baf9154d authored over 7 years ago

More the backtracking efficient with visit flags

62300bd775db6f429adb5642a6c3ba9c864a91fa authored over 7 years ago

Add backtracking search if greedy search fails

0e8a5cf9da7a527976ba76b6a7260b90a912e1d5 authored over 7 years ago

Initial check in of new kekulization code

34bf271e7d668e5b6675b3e8fd7e9a366486dd75 authored over 7 years ago

Change function call to GetImplicitValence to use TotalNumberOfBonds instead.

1d5d816c44a4f1bf73446092fc4b394d6a536994 authored over 7 years ago

Update the canonfragment test as the atom numbers have changed.

618f8b4bc238978593d26f4f57075bab97efa1ab authored over 7 years ago

In the kekulization, change use of GetValence to TotalNumberOfBonds.

da8540b7d3648581b0bffdbd2e833367de6f1dcf authored over 7 years ago

Remove dubious test cases - these shouldn't kekulize in the first place.

4f4cb9b1c5606befb6d780a18f4c3622944e1b23 authored over 7 years ago

Correct the test case: The P is hypervalent (according to SMILES rules) and we write [P] for such cases (as discussed on the opensmiles list).

b6d4dab9c623a45b3992b3fe75b08ca5245ed277 authored over 7 years ago

1. Move implicit hydrogen adder to obfunctions.h

2. Use implicit hydrogen adder in PDB format
3. Note error in test case and update to match curre...

daaf2dacaf6c3f5a5f1049c42f520f6040759988 authored over 7 years ago

Minor fix for earlier commit. The vector was not being copied correctly. (??)

53008496353fb1d74386232c37c8758a57d90e61 authored over 7 years ago

More on MDL Implicit Valence:

1. Move the expansion of aliases to *after* the application of implicit valence (as those atoms a...

d57436ef314d684f8999718f13b36b9a3e86895c authored over 7 years ago

1. Avoid function calls when copying OBAtom

2. Rewrite KBOSum to use GetImplicitHydrogen()

cfbe143fa30bace5669f53a1b3e78bd1a06da645 authored over 7 years ago

Simplification of test runner code. Needs to avoid running tests in the base class.

1552d263e88703508dca85e360c57d1d9bcfe6c4 authored over 7 years ago

Remove 'h' as an option as it's now obligatory

c351cd68666c41d1372a1b6489e1205cd94e1a23 authored over 7 years ago

Change handling of implicit H in CML - always write out the hydrogenCount attribute and only fall back to guessing the number of hydrogens if it is not specified.

5fd3c6aa4cb24de4bd205414d3c65d0ffbb78a6d authored over 7 years ago

Convert AssignSpinMultiplicity to a no-op for the moment

e9918150297040ece1a7998f5e3ac18c6ef2b859 authored over 7 years ago

Correct "mol" test. You now need to set the number of implicit hydrogens.

e06f5fb721ccb292ea47e9d2beb24fb9c368d43b authored over 7 years ago

No more assignspinmultiplicity until we sort it out

4a8d6aa9340fd567fa5546145e7491b7250f5b4a authored over 7 years ago

When reading MOL, set the count of implicit hydrogens

fb28628ac124f47cd76ed64402bf008acc7ae1ad authored over 7 years ago

Convert formula generators to use the new implicit h count.

4226c12ccc553678ccbaa39fa8206227872e72a7 authored over 7 years ago

Search and replace of ImplicitHydrogenCount() with GetImplicitHydrogen()

2bf42fa3d76057bec416c2c3e26701a2e53c4a0b authored over 7 years ago

Use GetValence() instead of EndBonds()-BeginBonds().

0d3d41cb6b19e686148689f9a5fc97fbe81fc77b authored over 7 years ago

When reading/writing InChI, set the implicit hydrogen count.

bff0819b2aaf41f32600d3edaf55ef4d930e078b authored over 7 years ago

Correct the number of implicit hydrogens when calling DeleteHydrogens().

28c163b9c9b21d5840db5c32ffd177dd58d75526 authored over 7 years ago

1. Write square brackets for hypervalent organic subset atoms in SMILES

2. Combine three different "if" statements for using brackets

82d20c434f01f46cac26d606eb13e58e8dc99afe authored over 7 years ago

Replace usage of GetImplicitValence() with equivalent function.

bec423046bf459211e4af19be3f92341c0be04e1 authored over 7 years ago

Get implicit hydrogen tests working using the new _imph.

73e8333b19acc0ed6272c4b70010bfddf8a08253 authored over 7 years ago

Add initial support for _imph field

7fbd06ee08f82d054d24e26eea4152d73cb0c362 authored over 7 years ago

Boron is element 5, idiot.

bd791a38e45fdf968ddddd812cc95303ccf6a241 authored over 7 years ago

Update ringresults test case: atom and bond indices are now different when parsing SMILES

f6ec80f45e84812607b4223a20a2c4d00bb4e333 authored over 7 years ago

Make sure that implicit valence is handled correctly when calling AddHydrogens() or using the 3D builder

1. Set the implicit valence on newly added hydrogens
2. Make sure that implicit valence is copied...

74c79ef81434ebf07ed95ce103b12e18a9471468 authored over 7 years ago

Correctly handle aromatic atoms on writing

b3377b016e690b3590a3fa2be1034817fedf4e96 authored over 7 years ago

Correctly handle aromatic atoms on parsing

0fa0ceb04656d571e25876a0493055563f1c9ece authored over 7 years ago

Add code to correctly handle "s" (write as SMARTS) option and associated testcases

d1739f913fc90dc6c25dacd9933fd9b2a4e8d83b authored over 7 years ago

Latest changes

e64456bb9051df2292b8b03ad4aa97f5b5b21d20 authored over 7 years ago

Add SMILES valence model header file. Still needs to be integrated into smilesformat.cpp though.

9a9f734ebf542ce522bcb47cb246a8375eccdbac authored over 7 years ago

cppcheck: Condition '1==0' is always false

[src/math/spacegroup.cpp:434]: (style) Condition '1==0' is always false
commit 6d448d8a6967b5edc...

0c3c210b955566fb1cfaa58bd2e6a799e740c8a1 authored over 7 years ago

Merge pull request #1565 from bbucior/formula

Fix segfault in OBMol::GetSpacedFormula

36112dec7f1048b1b1d13575d277d8be57096960 authored over 7 years ago

Merge pull request #1564 from nsoranzo/fix_linchi_cmakelists

Link libinchi with math library

59504a3050710544913e7a53d8d7fa66fa773557 authored over 7 years ago

Merge pull request #1567 from serval2412/master

Fix regression + minor cppcheck report

92eb50fb1926db73971e64fe65ab469757b7c303 authored over 7 years ago

Merge pull request #1568 from adamjstewart/fixes/tabs-vs-spaces

Convert tabs to spaces in testpdbformat.py

07ada4ea32730a3b16e991fc3210e6ff56cfea71 authored over 7 years ago

Convert tabs to spaces in testpdbformat.py

08cd38485d4cf1df8802da540f3018921dbc735e authored over 7 years ago

Fix regression + minor cppcheck report

regression from 624abd353f8ea2c889edb663adf84e50ee81e8d2 (2008-03-06)
- if (atoi(nbr->GetType())...

8284e83d6281875a06984cffd64d21ef4080b77c authored over 7 years ago

Update element list in OBMol::GetSpacedFormula

Running GetFormula on molecules containing the heaviest elements
(atomic number > 110) could cau...

f9df8694c51b9255c181a12e985d8a3160743b89 authored over 7 years ago

Link libinchi with math library

When trying to build openbabel in a Conda environment for [Bioconda](https://bioconda.github.io/...

ff483611e45fe927ff8fe0cb4ba0631806d744a8 authored over 7 years ago

Remove spaces in too long space group names

PDB format allows 11 characters in the space group name. Added test.

2e8e0822aca2f72e31680750cecd9f8b88940a6a authored over 7 years ago

Enable fixRhombohedralSpaceGroupWriter (removed by mistake)

Added test

3ac2d1a48e9b3ff226ecd06ae81c9af9f612b32c authored almost 8 years ago

Add test CIF file

a63a7751000c7c01d0023c2916a4ae319b83c54c authored almost 8 years ago

Improved SpaceGroup::Find to return correct group

Added tests.

907fb709ad8dfc959521fc088ad0aa00c0f526ba authored almost 8 years ago

Correctly deal with alternate origin, added tests

9ab6191e0ca640709e22ff7f00526be7f5966421 authored almost 8 years ago

Merge pull request #1556 from djhogan/master

Remove delete statement.

2fbda4ca984c593d3c380386f6d3a76bda313dd2 authored almost 8 years ago

Update CMakeLists.txt

06c4d18e2dad65f85bbd63f9863c2af7b19e8953 authored almost 8 years ago

Update cifspacegrouptest.cpp

d44631b220cb06af4d08b14d6282045b4da4858c authored almost 8 years ago

Update pdbformat.cpp

4280d029d5a0311d4ffb089a5d0bb24a33ac6f82 authored almost 8 years ago

Update CMakeLists.txt

702ce526fe6e4084fc30469488e15294a7e54f75 authored almost 8 years ago

Update cifspacegrouptest.cpp

ec6a70107e22a9814a1e59ba33555d202bbb38f5 authored almost 8 years ago

Add files via upload

14c53c89dc0b75ecbf9a2b91d9ff3a36fca15358 authored almost 8 years ago

Update cifspacegrouptest.cpp

116c2f09adedadde53307692e42ca1933d59c244 authored almost 8 years ago

Update spacegroup.h

877086b1ecc64ac0757093590f671d74a886262e authored almost 8 years ago

Always parse space group origin

This is fixed by removed overloaded version of SpaceGroup::SetHMName.
Unrelated, removed simila...

a2bed8a8499b1e51420e26cc8c6497a76ec6d480 authored almost 8 years ago

Remove delete statement.

When from_scratch is true, coordinates is not allocated. A separate if
statement was added to ha...

52cea818bf68f8a2d3c48d55d00c2f8b7da25e4c authored almost 8 years ago

Merge pull request #1554 from djhogan/master

Ignore some non-functioning python SWIG bindings.

452bcdce384ce6aca77055af827bdba7879d50eb authored almost 8 years ago

Add comment.

bf840d512cb4c58af3cbe91b51d02da710af5040 authored almost 8 years ago

Fix ignore statement for FindChildren (correct function signature).

9070b4def79be9b5b9cf5a6e1c4c9d16d8478e60 authored almost 8 years ago

Add semicolons.

e16cd513aba2aa9184d43c11654a3bf2bec560cb authored almost 8 years ago

Ignore unusable C++ functions in SWIG python bindings.

6a64952476b55d817f12fadde340e09360bba8e1 authored almost 8 years ago

Update README.md

Fix typos in Markdown syntax

261293d162a7882aea65c6d4f46b998c0dbedb46 authored almost 8 years ago

Merge pull request #372 from hseara/master

Fix bug #368: Python3.6 openbabel: No module named 'DLFCN'

906fadc489666158497197ec766abdfa07bd2056 authored almost 8 years ago

Merge pull request #1550 from ghutchis/FIX_gaussian-bonding

Set default coordinates before doing bond perception.

ba7c5d77e7e17e16b2a37b3ae48cd13bf6e048be authored almost 8 years ago

Set default coordinates before doing bond perception.

4b09e2c54968fb10831f5a0ab5eb7d5534059efc authored almost 8 years ago

Merge pull request #1549 from ghutchis/read-gaussian-conformers

Make sure to add conformers *after* performing bond perception.

f9e999d2c5c3b6b8bfa26fd2806ee73e644b17b0 authored almost 8 years ago

Make sure to add conformers *after* performing bond perception.

OBMol::ConnectTheDots() kills conformer data.
Hat tip to Adrian Roitberg for reporting the bug v...

eccdfdef186868f674e967e1e3f4896498bc517c authored almost 8 years ago

Merge pull request #1547 from baoilleach/fix_data_install

Don't try to install aromatic.txt as it is no longer present

d1c1a6a0181687ea842d2f28859b983ab1332257 authored almost 8 years ago

Don't try to install aromatic.txt as it has been deleted

5e65e21c398775bbed051dee898c65af810e7c01 authored almost 8 years ago

Merge pull request #1545 from baoilleach/aromaticswitch

Change the OBAromTyper from using SMARTS patterns to a switch statement (rebased)

a34d0cf803192a69cd29f14c6c94917364886150 authored almost 8 years ago

Merge pull request #1546 from dkoes/fastsearch_64_fix

Fastsearch 64 fix

84f4480903b55bee49fd45af533a4dd87323044b authored almost 8 years ago

Remove unneccessary check of boolean

a87e1537f4855f5392ca78da9449ea3a76f5392f authored almost 8 years ago

Change AromaticTyper to use switch statement instead of SMARTS lookup

c19681355db2d25f786c9fefad8104324ee70da8 authored almost 8 years ago

Merge branch 'master' of https://github.com/openbabel/openbabel into fastsearch_64_fix

af4ef10b6f0f49386ac02b8b387ffb9edfbd2a42 authored almost 8 years ago

store seek positions in fastsearch index as 64bit numbers so we can

search large files

8359042765237d6dab9afcb2e67e9674748c6560 authored almost 8 years ago

store seek positions in fastsearch index as 64bit numbers so we can

search large files

4c9add3240b8bf655d23b3aac4254ca7d16cf17f authored almost 8 years ago

Merge pull request #386 from timvdm/master

Add an option to the canonical SMILES format to specify the timeout.

b525f4cd16f96e5d2f1b586affaeb7cd574473c0 authored almost 8 years ago

enable larger fastsearch indices if on a 64bit system

ac83d005d0f47b4849c7c0f06ef570b258a8bb7f authored almost 8 years ago

enable larger fastsearch indices if on a 64bit system

8d57a4bd3f86e50f07071cadc0766828041ca996 authored almost 8 years ago

Merge pull request #381 from baoilleach/fixglobalstate

Improve thread safety for global objects.

80b4e28be59e599ffdb56d8cf00ce2f11d550cb1 authored almost 8 years ago