openbabel commits | Ecosyste.ms: OpenCollective

src/config.h.cmake: fix HAVE_TIME_WITH_SYS warning

github.com/openbabel/openbabel - dbc3b121ba1e79be066a473f99ba30adb414fb45 authored over 15 years ago by Tim Vandermeersch <[email protected]>

some GetIdx()-1 to GetIndex() changes

github.com/openbabel/openbabel - c848f0cbadb8caa0532966a84349ce0353e9ec67 authored over 15 years ago by Tim Vandermeersch <[email protected]>

remove some debug output

github.com/openbabel/openbabel - d68fab1f37422ae1bd9a79dfefb6790936653dcd authored over 15 years ago by Tim Vandermeersch <[email protected]>

src/mol.cpp: In OBMol::operator=(&OBMol), save the stereochemistry after translating the ids.

github.com/openbabel/openbabel - c1f3c197124d9f768ad7efff6a7edd9328a16658 authored over 15 years ago by Tim Vandermeersch <[email protected]>

src/stereo/perception.cpp: remove debug output

github.com/openbabel/openbabel - 00c55efd2b1920ae542986c0d8815c3806493cba authored over 15 years ago by Tim Vandermeersch <[email protected]>

src/stereo/tetrahedral.cpp: bugfix for code from 2 commits back

github.com/openbabel/openbabel - 954130afcce2e3ee9a830f1377b11a4e86d77558 authored over 15 years ago by Tim Vandermeersch <[email protected]>

src/graphsym.cpp: Fix a off-by-one bug + remove debug output

github.com/openbabel/openbabel - a66e030032f8f69f04f98d56f7a7f83694905fba authored over 15 years ago by Tim Vandermeersch <[email protected]>

merging

github.com/openbabel/openbabel - bc7f2baa04a91b897e3fb01cae87df806d9d1186 authored over 15 years ago by Tim Vandermeersch <[email protected]>

merging...

github.com/openbabel/openbabel - 17cc582ca264dc8f05074106a43f48b0a6f3c92c authored over 15 years ago by Tim Vandermeersch <[email protected]>

Merging... Commit 1

github.com/openbabel/openbabel - c5563adffb35a2375dcef64191b5e6b98f48f641 authored over 15 years ago by Tim Vandermeersch <[email protected]>

Some improvements to 2D stereochemistry perception + handle '@?' smiles input

github.com/openbabel/openbabel - 58029f036de6bb5e298acb8824c126b4561b449f authored over 15 years ago by Tim Vandermeersch <[email protected]>

src/formats/smilesformat.cpp: Comment out debug output + remove obsolete code

github.com/openbabel/openbabel - 9c61d50171bfe1d3f65c3bf55001d1b975c46520 authored over 15 years ago by Tim Vandermeersch <[email protected]>

src/formats/smilesformat.cpp: found the difference between this branch and 2-2-x branch. All stereo references are

working now...

github.com/openbabel/openbabel - 2a8a9f91ced73eab3aac4f6058527184cb44b8a6 authored over 15 years ago by Tim Vandermeersch <[email protected]>

src/formats/smilesformat.cpp: Some changes to the stereo ref handling for the smiles parser...

github.com/openbabel/openbabel - 57fbd5f80e0d63a5b59663ce91f3cca7b0557a3b authored over 15 years ago by Tim Vandermeersch <[email protected]>

src/formats/smilesformat.cpp: Take explicit hydrogens (i.e. [C@H]) into account when calculating the insertpos for

the stereo reference id.

github.com/openbabel/openbabel - 2c7cf55f9f462c3d933833cc53bd257b2bf5fc45 authored over 15 years ago by Tim Vandermeersch <[email protected]>

src/stereo/perception.cpp: Don't consider ring bonds to be CisTrans bonds...

github.com/openbabel/openbabel - c7110db73955cdd55e4fac8198f8dfd2841f3265 authored over 15 years ago by Tim Vandermeersch <[email protected]>

src/formats/smilesformat.cpp: set HasChiralityPerceived after adding hydrogens to chiral atoms, the previously

perceived stereochemistry is still valid.

github.com/openbabel/openbabel - 2ac340f3eec6a20ba09005165edff234f6be9e87 authored over 15 years ago by Tim Vandermeersch <[email protected]>

include/openbabel/graphsym.h, src/graphsym.cpp: Move constructor to cpp file + use new From0D functions.

github.com/openbabel/openbabel - 934342992b6566b523769d926c664096c5d22e3f authored over 15 years ago by Tim Vandermeersch <[email protected]>

include/openbabel/stereo/stereo.h, src/stereo/perception.cpp: Add StereoFrom0D, TetrahedralFrom0D and CisTransFrom0D

github.com/openbabel/openbabel - 3dd40f377bd13701f1e3d661dd7d6e28aab9c6f8 authored over 15 years ago by Tim Vandermeersch <[email protected]>

src/stereo/facade.cpp: minor performance improvement

github.com/openbabel/openbabel - 3ba190f4c84919b12ceb85da4efe3fcf60af74f6 authored over 15 years ago by Tim Vandermeersch <[email protected]>

src/atom.cpp: Reimplement OBAtom::IsChiral

github.com/openbabel/openbabel - 2f521b2d47d0203c3f39f86030dded90ba925b5d authored over 15 years ago by Tim Vandermeersch <[email protected]>

Replace explicit H's symmetry class with OBStereo::ImplicitId for the

canonical ordered refConfig.

github.com/openbabel/openbabel - 35e8cf682d55cb14c8691bcc0b2113431bb9b3e5 authored over 15 years ago by Tim Vandermeersch <[email protected]>

graphsym.cpp: Some corrections to the way BreakChiralTies is used.

github.com/openbabel/openbabel - b1eac5be8439a5b86cf291bef0ce4fa02f787334 authored over 15 years ago by Tim Vandermeersch <[email protected]>

smilesformat.cpp: Add some checking to make sure we don't overwrite

previous set reference ids.

github.com/openbabel/openbabel - 5798b4e9ca6821c0381f9f8b68400c342f5554ea authored over 15 years ago by Tim Vandermeersch <[email protected]>

Fix handling of allenes (not CisTransStereo), and possibly speed up mayHaveCisTransBond

github.com/openbabel/openbabel - 7ddf40f71fbd820d04eaf4bc7c7f3487ee1f25cb authored over 15 years ago by Tim Vandermeersch <[email protected]>

Reverting Tim's commit

github.com/openbabel/openbabel - d1221297959d0d0dae364f3cb630500d89028da7 authored over 15 years ago by Tim Vandermeersch <[email protected]>

Reverted Tim's commit

github.com/openbabel/openbabel - 7be83d493b1d51c24dd566eb97e267fb759c179d authored over 15 years ago by Tim Vandermeersch <[email protected]>

Add some debug messages to src/graphsym.cpp

github.com/openbabel/openbabel - 2377b99072e8c713486865614c62db7f5c1fd215 authored over 15 years ago by Tim Vandermeersch <[email protected]>

src/graphsym.cpp: remove the break chiral ties from CanonicalLabels,

this is already done in the symmetry analysis.

github.com/openbabel/openbabel - ac13f4ede6d98cc93e44b2d96ff867a2594549ad authored over 15 years ago by Tim Vandermeersch <[email protected]>

src/formats/smilesformat.cpp: delete objects in _tetrahedralMap after

parsing smiles. Correct an of-by-one error. Will add more checks to see
if we are "overwriting" a...

github.com/openbabel/openbabel - e16c40eefdef235623716d731bfeeb481e8d6345 authored over 15 years ago by Tim Vandermeersch <[email protected]>

src/stereo/perception.cpp: minor improvements, error messages

github.com/openbabel/openbabel - ebf45b365727038a5df500fd719e50f9387feef2 authored over 15 years ago by Tim Vandermeersch <[email protected]>

Updated smiles format to use OBGraphSym

Conflicts:

src/formats/smilesformat.cpp

github.com/openbabel/openbabel - 67625fa3d6a69d434b08bf41afe470c38e2285b1 authored over 15 years ago by Tim Vandermeersch <[email protected]>

Add canonical labels to OBGraphSym

github.com/openbabel/openbabel - 81c7b79a4885cc12cdef880498b6008c1fd86e94 authored over 15 years ago by Tim Vandermeersch <[email protected]>

src/mol.cpp: minor improvements to 2D hydrogen addition.

github.com/openbabel/openbabel - a6de43f612ec7cf192fc8091732dec40bbc7e704 authored over 15 years ago by Tim Vandermeersch <[email protected]>

replace if (Has3D()) StereoFrom3D ... with generic PerceiveStereo call

github.com/openbabel/openbabel - d59e5caa8d5681b78d2d8f043c54165275e08e8b authored over 15 years ago by Tim Vandermeersch <[email protected]>

Update all functions to use _pmol and _fragatoms

github.com/openbabel/openbabel - d3c12343b9f81e65a55ac9228ae12ab12bc57a89 authored over 15 years ago by Tim Vandermeersch <[email protected]>

src/format/smilesformat.cpp: Add InsertStereoRef and use it.

Conflicts:

src/formats/smilesformat.cpp

github.com/openbabel/openbabel - 6eaba07b8dead607354494bee539211112b1ae42 authored over 15 years ago by Tim Vandermeersch <[email protected]>

don't assign OBTetrahedralStereo objects to N, P and S

github.com/openbabel/openbabel - c451b884da7a2cb8145f97401e1f8a625167840a authored over 15 years ago by Tim Vandermeersch <[email protected]>

Add in the new python files (already available on 22x

github.com/openbabel/openbabel - 8940190757f77ca998453674e25d21661d6d59fc authored over 15 years ago by Tim Vandermeersch <[email protected]>

Removed pybel.py which has already been replaced

github.com/openbabel/openbabel - f30e3c476ae91db2b3cb892955bec92bbae75f49 authored over 15 years ago by Tim Vandermeersch <[email protected]>

Remove unneeded include

github.com/openbabel/openbabel - a3100e9a3a80755d516ca2c9ae594dc9b857a05a authored over 15 years ago by Tim Vandermeersch <[email protected]>

Correct error in cerr statement

github.com/openbabel/openbabel - d0f099b0042550d49051452cd1e8a146fc08ab49 authored over 15 years ago by Tim Vandermeersch <[email protected]>

Update headers to enable python bindings to work.

github.com/openbabel/openbabel - ba44a484d68bb9aa509b9170158842427f64f911 authored over 15 years ago by Tim Vandermeersch <[email protected]>

smilesformat: insertPos -1 = config.from

github.com/openbabel/openbabel - 48c5f5d52e253d680da7da4391586d2392cf70c4 authored over 15 years ago by Tim Vandermeersch <[email protected]>

src/stereo/perception.cpp: Don't consider aromatic bonds to be

cis/trans!

github.com/openbabel/openbabel - fc26deaec22c1846095a2d63b85e2215937ac960 authored over 15 years ago by Tim Vandermeersch <[email protected]>

forgot builder.h

github.com/openbabel/openbabel - 38d1ae542a72acd0c1a5785d5acde73becf0e54f authored over 15 years ago by Tim Vandermeersch <[email protected]>

src/builder.cpp: some changes from 2-2-x branch (correct bond length)

Conflicts:

src/builder.cpp

github.com/openbabel/openbabel - a2dffb36ee0e6e7addae39cb13649424c9499f9c authored over 15 years ago by Tim Vandermeersch <[email protected]>

Same for OBMol::AddHydrogens(OBAtom*)

Conflicts:

src/mol.cpp

github.com/openbabel/openbabel - 4da05b053a93480654ef21129d636e129ef1aedb authored over 15 years ago by Tim Vandermeersch <[email protected]>

src/builder.cpp: OBBuilder::GetNewBondVec(), compute 2D coordinates for

molecules where OBMol::GetDimensions() == 2. Also, check for
stereochemistry, if we find a hash o...

github.com/openbabel/openbabel - 3e8de62c6dbc09941c48b5576977f40bdb60458d authored over 15 years ago by Tim Vandermeersch <[email protected]>

src/stereo/perception.cpp: remove debug output.

github.com/openbabel/openbabel - bd411fd68803746f725292e39b15b0af7dcfa1f2 authored over 15 years ago by Tim Vandermeersch <[email protected]>

Small bugfix for CisTransFrom3D, wasen't returning anything at the end

while is should always return a std::vector<unsigned long>, even if it
is empty...

github.com/openbabel/openbabel - 22ec966332c25b3b9dee40df453fbb8905f303db authored over 15 years ago by Tim Vandermeersch <[email protected]>

Prevent segfault in cistrans.cpp (case where the refs don't share a

single id). Conformers_00000001_00025000.sdf now parses again.

github.com/openbabel/openbabel - d0e34eb3ae13931b48aed4750a24b5405bfdc0d2 authored over 15 years ago by Tim Vandermeersch <[email protected]>

Translate OBCisTransStereo::Config ids too in OBMol::operator=()

github.com/openbabel/openbabel - 0e7919b67b11951db78fbdf82660496f06fd7f31 authored over 15 years ago by Tim Vandermeersch <[email protected]>

Some stereo bug fixes, reading/writing smiles with tetrahedral atoms is

possible again. (OBMol::operator= didn't copy the HasChiralityPerceived
flag which resulted in lo...

github.com/openbabel/openbabel - 03ffe78da75b82664565b898cf66d55f102a2aeb authored over 15 years ago by Tim Vandermeersch <[email protected]>

remove debug messages + add some test molecules

github.com/openbabel/openbabel - dabed39f38a5db09a6ea384901db9323232a8957 authored over 15 years ago by Tim Vandermeersch <[email protected]>

* Continue integrating OBGraphSym with the new stereo code, molecules like

C/C=C/[C@H](/C=C\C)C(C)(C)C are now working!! (see test/files/complex2D_2.mol)
The basis for ...

github.com/openbabel/openbabel - 9b1c2fe6cff73f0b5a1fc82fd58aa115320b5894 authored over 15 years ago by Tim Vandermeersch <[email protected]>

Various Stereochemistry related changes

1) Start removing obsolete methods from OBAtom/OBBond
2) Use new stereo code for MDL format (mol,...

github.com/openbabel/openbabel - ebd15e34bcb8802e40d3db17093c531cef7babd7 authored over 15 years ago by Tim Vandermeersch <[email protected]>

Update MSVC++ build files

github.com/openbabel/openbabel - fa110d6e384e13d3cf47bf14063874379fede425 authored over 15 years ago by Tim Vandermeersch <[email protected]>

Added OBAPI magic to Tetrahedral::Config to avoid linking error with smilesformat.cpp under MSVC++ 2005

github.com/openbabel/openbabel - ca160dc8dcb00b83226a313bb9bf60bed12cfc8a authored over 15 years ago by Tim Vandermeersch <[email protected]>

Continue working on stereochemistry

Conflicts:

test/CMakeLists.txt

github.com/openbabel/openbabel - 78dfc7a4bfb62e7628c1a15046f7652ada9ec1b9 authored over 15 years ago by Tim Vandermeersch <[email protected]>

Add initial code for 3D -> Stereo conversion

github.com/openbabel/openbabel - 2073d51e00557f41d192a0d7371e74f64d697160 authored over 15 years ago by Tim Vandermeersch <[email protected]>

unit test for bond ids

github.com/openbabel/openbabel - 54d40ec10cb9802b5af439db7125635bf531880f authored over 15 years ago by Tim Vandermeersch <[email protected]>

Add unique ids for bonds.

github.com/openbabel/openbabel - e19738642d2ca4da321582d19659bbbd97ebb9e9 authored over 15 years ago by Tim Vandermeersch <[email protected]>

Updated Python build to that of 22x branch

Conflicts:

scripts/openbabel-python.i

github.com/openbabel/openbabel - e4fa3d172dad5c90727ea418280eaffd40644b37 authored over 15 years ago by Tim Vandermeersch <[email protected]>

Get rid of private data

github.com/openbabel/openbabel - 284221cdbdad59ebf3c0c007da575cc68d7391bd authored over 15 years ago by Tim Vandermeersch <[email protected]>

First steps into turning canon.cpp into a class

github.com/openbabel/openbabel - 59a5873f6d0059401bc59e8e05e5b129232db846 authored over 15 years ago by Tim Vandermeersch <[email protected]>

Basic cis/trans working again, still some calls to IsUp etc for ring

closures and external bonds

github.com/openbabel/openbabel - dec00919e4d63974eb538f93e29a729389b6eb64 authored over 15 years ago by Tim Vandermeersch <[email protected]>

Add RingClosureDigit struct for smiles parser and use it.

github.com/openbabel/openbabel - cf8a13308e97486404edd91abc88da27e936ccce authored over 15 years ago by Tim Vandermeersch <[email protected]>

Make sure it compiles

github.com/openbabel/openbabel - 14951f124b0829caeb10162769eb2594e06d254d authored over 15 years ago by Tim Vandermeersch <[email protected]>

Add BondStruct to replace vector<vector<int> > _extbond with

vector<BondStruct> _extbond. Improves readability a bit.

github.com/openbabel/openbabel - 44b134ff344341ee7bbe1850063cd29e47a109c6 authored over 15 years ago by Tim Vandermeersch <[email protected]>

smilesformat.cpp: Start removing OBBond::IsUp OBBond::IsDown

bond.h: correct definition for '/' and '\', obsolete but still needed
untill I finish...

github.com/openbabel/openbabel - 59eaa7301919d346514c24db2215ae804f0a23b2 authored over 15 years ago by Tim Vandermeersch <[email protected]>

Add some comments

github.com/openbabel/openbabel - 018d9f930908d43f164a76d09473931dd680a5f6 authored over 15 years ago by Tim Vandermeersch <[email protected]>

Various updates to stereochemistry

* Use Config structs for Tetrahedral and CisTrans
* Merge Changes from Noel

Conflicts:

scripts...

github.com/openbabel/openbabel - 06ac95285dc09cfdd07eaadeb2d2ea8a2372184f authored over 15 years ago by Tim Vandermeersch <[email protected]>

Use chiral_neighbors paramter in smiles writing...

github.com/openbabel/openbabel - 6156d63291d624551b5139e9daad2fc10f984d76 authored over 15 years ago by Tim Vandermeersch <[email protected]>

First attempt to use new stereo classes in smiles format (Fix: 2581919)

Conflicts:

src/formats/smilesformat.cpp

github.com/openbabel/openbabel - a89af44140c2aa42d7f63e45735395586b148946 authored over 15 years ago by Tim Vandermeersch <[email protected]>

src/formats/pqrformat.cpp: Add write support (copied from pdbformat) and

add atom radii.

github.com/openbabel/openbabel - bd11b1fb6c17fef20d7adfc69d72a74f970b0740 authored over 15 years ago by Tim Vandermeersch <[email protected]>

Removed merge tracking for "svnmerge" for

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

github.com/openbabel/openbabel - e332e2159466b3d09fefae20a8f48df99361e300 authored over 15 years ago by Tim Vandermeersch <[email protected]>

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r3195 | chrismorl | 2009-07-18 10:56:24 +0200 (Sat, 18 Jul 2009) | 1 line

Update...

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r3148 | dleidert | 2009-07-15 01:14:49 +0200 (Wed, 15 Jul 2009) | 3 lines

* conf...

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r3132 | timvdm | 2009-07-08 08:46:45 +0200 (Wed, 08 Jul 2009) | 5 lines

* src/fo...

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r3127 | ghutchis | 2009-07-06 18:02:03 +0200 (Mon, 06 Jul 2009) | 2 lines

Only b...

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r3120 | ghutchis | 2009-07-02 01:33:32 +0200 (Thu, 02 Jul 2009) | 2 lines

Bump f...

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r3111 | ghutchis | 2009-06-27 13:01:48 +0200 (Sat, 27 Jun 2009) | 2 lines

Fix co...

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r3101 | ghutchis | 2009-06-25 20:58:09 +0200 (Thu, 25 Jun 2009) | 2 lines

Final ...

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r3095 | ghutchis | 2009-06-24 00:07:15 +0200 (Wed, 24 Jun 2009) | 2 lines

Hopefu...

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github.com/openbabel/openbabel - 5ee5500e102730523b8ed6d84cbdeccf3388ce0a authored over 15 years ago by Tim Vandermeersch <[email protected]>

Merged revisions 3081-3085 via svnmerge from

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

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github.com/openbabel/openbabel - ad46d171211654d3ed8f183876b27d482e941b93 authored over 15 years ago by Tim Vandermeersch <[email protected]>

Merged revisions 3071,3073-3080 via svnmerge from

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

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github.com/openbabel/openbabel - 967ec607306448e9c2fdd9b168fec33c6b4d3ffd authored over 15 years ago by Tim Vandermeersch <[email protected]>