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51 Commits
Author SHA1 Message Date
Geoff Hutchison a58af78056 Merge pull request #2909 from romanbsd/add-ket-format 
Add Ketcher KET (JSON) chemical structure format
 2026-05-22 23:32:04 -04:00
Geoff Hutchison 31c21cf4a8 Fix crashing test on Linux SWIG 
- Bind the molecule to a local so the OBAtom* doesn't dangle
- Also fix a few null de-reference defensive tests in alias code

Signed-off-by: Geoff Hutchison <geoff.hutchison@gmail.com>
 2026-05-22 19:01:35 -04:00
Eisuke Kawashima fb1ac6d366 style: comment out unused parameters 2026-05-08 14:52:25 +09:00
Eisuke Kawashima fbf096aeb3 Add override keyword 2022-07-28 12:29:24 +09:00
Eisuke Kawashima 305a6fd318 refactor: always use std::shared_ptr (#2501) 
* refactor(cmake): remove `SHARED_POINTER` variable
* refactor: remove `HAVE_SHARED_POINTER` macro
* refactor: replace `OB_SHARED_PTR_HEADER` with `<memory>`
* refactor: replace `OB_SHARED_PTR_IMPLEMENTATION` with `std::shared_ptr`
* refactor: replace `obsharedptr` with `std::shared_ptr`
* refactor: regenerate `scripts/R/examples/openbabelR/src/openbabel-R.cpp`
* refactor: remove `include/openbabel/shared_ptr.h`
 2022-07-26 22:16:44 -04:00
Eisuke Kawashima 074e260c0f Replace NULL with nullptr (C++11) 
`CMAKE_CXX_STANDARD` is set to 11
 2020-05-07 07:24:29 +09:00
Geoff Hutchison f758495218 Initial GitHub action - misspell-fixer 
Cleaned up a variety of typos and should prevent problems in PR
 2020-04-08 17:11:37 -04:00
Alex Ustinov a14c9d232b removed some code left after previous commit by mistake 2019-12-04 21:20:51 +03:00
Alex Ustinov 97f5bec788 Alias generation does not require copy construction of OBMol; added unit test for alias feature 2019-12-04 10:36:19 +03:00
Alex Ustinov ddfe87e97b Fix issue #2095, caused by incorrect application of protonated SMARTS from superatom.txt to non-protonated molecules 2019-11-30 00:13:12 +03:00
David Koes 24c926c918 Make bondtype more specific 
Fix problem with pdb_ligands_sdf/3dcv_55e.sdf (and many other structures
I've noticed)
 2019-07-21 22:40:25 -04:00
Noel O'Boyle e949134dc3 Rename or add Valence and Degree methods of OBAtom 2019-04-22 16:15:59 +01:00
Noel O'Boyle 63b166249f Add c standard libs required for g++ builds. 2019-04-06 16:40:50 +01:00
Noel O'Boyle 9c8579b638 Remove more includes in headers 2019-03-30 20:00:58 +00:00
Noel O'Boyle 6fedf40dd1 Initial attempt 2019-03-19 13:21:55 +00:00
Noel O'Boyle a6c84d5a15 Use a portable way to mark variables as unused. Hopefully fix MSVC build. 2018-01-11 08:03:25 +00:00
Noel O'Boyle 43dd0ac883 Get rid of warning about unused parameters for OpGenAlias. 2018-01-10 20:39:36 +00:00
Noel O'Boyle 1d9944fa0b Refactor handling of atom classes. Store them as "Atom Class" data on 
the atom, rather than in an OBAtomClassData object on the molecule.
 2017-12-28 21:02:27 +00:00
Noel O'Boyle a489bb8bbf Replace final uses of etab.GetAtomicNum with OBElements. 2017-07-03 21:24:11 +01:00
Noel O'Boyle 180e5ef56f Replace ref to shared_ptr to obsharedptr 2013-08-31 10:02:29 +01:00
Chris Morley 6675579799 Remove erroneous test for UNICODE character in alias.cpp, which may be responsible for some build problems. 
Improved error message in mdlformat.
Add DEPICTION2D flag to pngformat.
 2012-06-21 10:31:02 +00:00
Geoffrey Hutchison 42b423257d Merged patch ID: 3424383. Fix a bunch of compiler warnings. 
Contributed by My Th.
 2012-05-13 19:30:48 +00:00
Noel O'Boyle 3eeb15e955 alias.cpp, formats/mdlformat.cpp: Fix PR#3481603 - alias on stereo bond loses tet stereo when reading MOL file. 2012-03-15 18:55:41 +00:00
Chris Morley 12522eedb4 Fix alias bugs #3505116 and #3505126 
Make --highlight and png2format work with GUI
 2012-03-15 14:00:24 +00:00
Chris Morley a3593f925c Correct erroneous charge on an alias atom made from nitro or isocyanide group, visible in mol or svg. 2011-11-17 13:29:31 +00:00
Geoffrey Hutchison 89beb7a57e First set of warnings from clang static analyzer -- possible unitialized variables. 2011-10-27 21:05:11 +00:00
Chris Morley 74e9d82c79 Support for R' aliases. Should have been in previous commit. 2011-03-05 15:57:02 +00:00
Chris Morley e82280949f Make mdlformat and OBDepict read and write * atoms with atomclass as an RGroup. These are already read and written in SMILES as, e.g. [*:2] . See 
http://blueobelisk.shapado.com/questions/how-r-group-atoms-should-be-represented-in-smiles
 2010-12-22 15:22:15 +00:00
Chris Morley 8f76e79511 Fix #3117349 - crash when unattached alias expanded. 2010-11-25 13:57:30 +00:00
Geoffrey Hutchison a73515dfb9 Fix minor warnings indicated by Clang-2.8. 2010-10-07 19:58:06 +00:00
Chris Morley 3c6e0fa74c In AliasData::FromNameLookup allow multiply bonded placeholder atoms, which disappeared when FormulaParse was deleted. Should fix fail in inchitest. 2010-10-06 15:34:21 +00:00
Chris Morley cc916ea4a9 Delete implementation of AliasData::FormulaParse and replace it by entries in superatom.txt. 
In pngformat.cpp correct the memory leak when the decompression fails.
In fastsearchformat.cpp initialize a variable.
 2010-10-05 12:20:42 +00:00
Chris Morley 4ffe1646e0 In OBMol::operator+= remove atom and bond IDs of molecule being added to ensure their uniqueness in the combined molecule. 2010-10-01 08:47:12 +00:00
Chris Morley e791f45e5a Fix alias expansion in 2D molecules. 2010-09-30 20:55:14 +00:00
Geoffrey Hutchison 8816a75fed Remove trailing whitespace. (Used python script). 2010-09-07 17:26:18 +00:00
Chris Morley 1780f87478 Misc bugs gaussformat, alias etc 2010-08-24 10:25:14 +00:00
Geoffrey Hutchison aa2470da63 Removed debugging information inadvertently committed. 2010-04-12 11:09:33 +00:00
Geoffrey Hutchison 20f53c5e5b * data/element.h, data/atomtyp.h: Regenerate. Need to add CMake 
targets for these.
 2010-04-12 11:07:52 +00:00
Chris Morley 766e8888a2 Segregate failures in inchiwrite test 2010-03-23 12:28:33 +00:00
Geoffrey Hutchison 8703d12590 * src/alias.cpp: Downgrade errors over superatom.txt to warnings. 2010-03-09 02:54:19 +00:00
Chris Morley bcac0b14d4 Mods to OBOp to allow a wide range of operations. 2010-02-19 17:59:04 +00:00
Chris Morley 54e831f0e9 Add coordinates when expanding aliases. mdlformat writes alias form. 2009-11-21 09:02:26 +00:00
Noel O'Boyle 8075ee6878 Correct error. Wrong method name. 2009-11-17 16:46:59 +00:00
Chris Morley b2ea180f78 Add warning that AliasData::Expand() currently does not add atom coordinates. 2009-10-25 11:39:00 +00:00
Chris Morley ac41e164bb Improved support for aliases (superatoms) 2009-10-24 22:09:39 +00:00
Chris Morley b2fa6b917f Correct small memory leak 2009-10-19 09:45:18 +00:00
Chris Morley d6dabfa95c Added code to handle isotopic atoms to fix 2777494. 2009-04-21 15:18:14 +00:00
Geoffrey Hutchison 1c87f2e042 Doxygen updates. 2008-06-09 03:10:40 +00:00
Marcus D. Hanwell e74150f019 Added newlines to the end of these files - fix compiler warnings. 2008-04-14 01:05:13 +00:00
Geoffrey Hutchison aecb5a192b * src/ops.cpp, src/forcefield.cpp, src/ops/loader.cpp, 
src/ops/optransform.cpp, src/descriptors/cmpdfilter.cpp,
        src/descriptors/smartsdescriptors.cpp,
        src/descriptors/groupcontrib.cpp, src/format.cpp, src/alias.cpp,
        src/forcefields/forcefieldmmff94.cpp, src/formats/MCDLformat.cpp, 
        Change to UNIX line-endings for consistency. (Some files also had
        multiple line formats.)
 2008-03-16 03:03:37 +00:00