Commit Graph

Select branches

Hide Pull Requests

bfgs-optimization

confab

dependabot/github_actions/peter-evans/create-pull-request-7.0.7

experimental

fixfasta

maestro-extensions

master

ob-newf

openbabel-1-100

openbabel-1-100-x

openbabel-2-0-x

openbabel-2-1-x

openbabel-2-2-x

openbabel-2-3-x

openbabel-2-4-x

openbabel-3-0-x

openbabel-new-framework

openeye

revert-1870-FirstLast

revert-1952-updatestereo

#1

#1

#10

#10

#100

#101

#102

#103

#104

#105

#105

#106

#107

#107

#108

#109

#11

#11

#110

#111

#112

#113

#114

#115

#116

#117

#118

#119

#12

#12

#120

#120

#121

#122

#123

#124

#125

#126

#13

#13

#130

#132

#133

#136

#137

#137

#138

#139

#14

#14

#140

#141

#142

#144

#144

#146

#147

#148

#148

#149

#15

#15

#150

#153

#1544

#1545

#1546

#1547

#1549

#1550

#1553

#1553

#1554

#1556

#1558

#156

#156

#1560

#1560

#1562

#1562

#1563

#1563

#1564

#1565

#1567

#1568

#1572

#1575

#1576

#1578

#1579

#158

#1580

#1582

#1585

#1586

#1588

#1589

#159

#1592

#1593

#1594

#1596

#1597

#1597

#1598

#1599

#16

#16

#160

#1600

#1600

#1601

#1606

#1608

#1609

#161

#1610

#1613

#1614

#1614

#1617

#1619

#1622

#1623

#1626

#1627

#1629

#1630

#1631

#1632

#1634

#1637

#1638

#164

#1640

#1645

#1650

#1652

#1653

#1655

#1655

#1656

#1657

#1658

#166

#166

#1660

#1661

#1663

#1665

#1665

#1666

#1667

#1669

#1669

#167

#1670

#1671

#1673

#1674

#1675

#1677

#1678

#168

#168

#1686

#1687

#169

#169

#1696

#1697

#1698

#1699

#17

#1704

#1706

#1707

#1708

#1708

#171

#1710

#1710

#1712

#1714

#1715

#1716

#1718

#1719

#1720

#1721

#1723

#1724

#1725

#1727

#1728

#1729

#1733

#1734

#1736

#1737

#1738

#1739

#1739

#174

#1740

#1740

#1741

#1742

#1742

#1743

#1744

#1745

#1746

#1747

#1748

#1749

#175

#1750

#1751

#1752

#1753

#1754

#1755

#1757

#1759

#1762

#1765

#1770

#1771

#1772

#1773

#1775

#1776

#1777

#1779

#1784

#1787

#179

#179

#1790

#1792

#1793

#1795

#1796

#1797

#1798

#1799

#18

#18

#180

#1800

#1801

#1804

#1806

#1807

#181

#1811

#1813

#1814

#1814

#1815

#1818

#182

#1820

#1822

#1823

#1824

#1825

#1826

#1828

#1828

#1829

#183

#1831

#1832

#1833

#1834

#1835

#1836

#1839

#1839

#1845

#1846

#1847

#1848

#1849

#185

#1850

#1852

#1853

#1855

#1856

#1859

#1859

#186

#1862

#1862

#1864

#187

#1870

#1873

#1875

#1878

#188

#1880

#1882

#1885

#1887

#1888

#189

#1890

#1892

#1894

#1895

#1895

#1896

#19

#1902

#1904

#1904

#1908

#1909

#191

#1914

#1917

#1917

#1923

#1928

#1931

#1939

#1940

#1942

#1943

#1944

#1945

#1946

#1948

#1949

#1951

#1952

#1953

#1954

#1958

#1959

#1960

#1961

#1963

#1964

#1965

#1966

#1967

#1968

#1969

#197

#1970

#1971

#1972

#1973

#1974

#1975

#1976

#1977

#1977

#1978

#1979

#198

#198

#1980

#1981

#1985

#1988

#199

#1991

#1992

#1993

#1997

#1998

#2

#2

#20

#20

#200

#2001

#2002

#2003

#2005

#2008

#201

#2010

#2012

#2017

#2019

#2019

#202

#202

#2022

#2026

#2027

#2028

#2029

#2031

#2032

#2034

#2035

#2036

#2038

#2039

#204

#2040

#2042

#2043

#2044

#2045

#2047

#2049

#205

#2051

#2052

#2053

#2054

#2055

#2056

#2057

#2058

#2059

#2060

#2064

#207

#2072

#2073

#2074

#2075

#2075

#2076

#2079

#208

#2082

#2084

#2086

#209

#2091

#2091

#2093

#2094

#21

#21

#210

#2100

#2102

#2105

#2109

#211

#2110

#2114

#2115

#2119

#212

#2121

#2124

#213

#2132

#2136

#214

#214

#2145

#2149

#215

#2150

#2152

#2152

#2153

#2154

#2155

#2157

#2158

#2162

#2163

#2164

#2165

#2166

#2167

#2168

#2169

#217

#2170

#2171

#2172

#2173

#2175

#2176

#2177

#218

#2182

#2183

#2184

#2185

#2186

#2187

#2188

#2189

#2190

#2193

#2198

#2199

#22

#22

#220

#2200

#2203

#2204

#2205

#2208

#221

#2211

#2212

#2213

#2218

#2220

#2224

#2225

#2226

#2227

#2228

#2229

#223

#2230

#2232

#2233

#2235

#2239

#2240

#2241

#2241

#2242

#2243

#2248

#225

#2254

#226

#2273

#2273

#2283

#2285

#2287

#2289

#2292

#2293

#2295

#2296

#2297

#2299

#23

#2300

#2307

#231

#2315

#232

#2324

#2328

#233

#2337

#2338

#234

#2342

#2345

#2346

#235

#2354

#2355

#236

#237

#237

#2371

#2378

#2379

#2380

#2383

#2384

#2385

#2387

#2388

#2389

#239

#2395

#24

#24

#240

#2400

#2405

#241

#2410

#2421

#243

#2430

#244

#2449

#2456

#2460

#2463

#2464

#2465

#2466

#2468

#247

#2473

#2474

#2475

#2477

#248

#2480

#2486

#2487

#2489

#2490

#2491

#2492

#2493

#2499

#25

#25

#2500

#2501

#2504

#2504

#2507

#2509

#2510

#2511

#2515

#2516

#2518

#2519

#252

#252

#2520

#2521

#2527

#2527

#2529

#253

#2533

#2533

#2537

#2538

#2538

#2539

#2539

#254

#2540

#2540

#2546

#255

#2551

#2553

#2558

#2558

#256

#2563

#2565

#2569

#257

#2574

#2580

#2580

#2583

#2583

#2588

#259

#259

#2591

#2591

#2592

#2596

#2598

#26

#26

#260

#2601

#2608

#261

#2612

#2616

#2616

#262

#2629

#2634

#2635

#2637

#264

#2640

#2648

#2648

#2649

#265

#2653

#2654

#2661

#2661

#2663

#2664

#2664

#267

#2678

#2682

#2684

#269

#2693

#2693

#2694

#2694

#2695

#2697

#2698

#27

#27

#2702

#2705

#2706

#271

#2717

#2721

#273

#2734

#2735

#2735

#2737

#2738

#2738

#2739

#2740

#2741

#2742

#2743

#2744

#2745

#2746

#2746

#2747

#2748

#2748

#2749

#2749

#275

#2750

#2750

#2751

#2753

#2753

#2755

#2755

#2756

#2756

#2757

#2757

#276

#2760

#2762

#2769

#2769

#277

#2770

#2770

#2772

#2772

#2773

#2773

#2777

#2777

#278

#28

#28

#280

#281

#283

#284

#285

#287

#289

#29

#29

#290

#291

#292

#292

#295

#295

#296

#297

#299

#3

#3

#30

#302

#303

#304

#306

#307

#308

#309

#31

#311

#312

#313

#314

#315

#316

#317

#318

#319

#32

#32

#320

#320

#321

#323

#326

#327

#328

#329

#33

#330

#330

#331

#332

#333

#336

#337

#337

#339

#34

#343

#344

#348

#35

#350

#352

#355

#355

#357

#359

#36

#360

#361

#364

#364

#367

#369

#37

#370

#371

#372

#376

#376

#377

#377

#378

#378

#38

#38

#380

#380

#381

#383

#386

#39

#4

#4

#40

#41

#42

#43

#44

#45

#46

#47

#48

#48

#49

#5

#5

#50

#51

#52

#53

#54

#55

#56

#57

#58

#59

#6

#6

#60

#61

#62

#63

#64

#65

#66

#67

#68

#69

#69

#7

#7

#70

#71

#72

#73

#74

#74

#75

#76

#77

#78

#79

#8

#8

#80

#80

#81

#81

#82

#83

#84

#85

#86

#87

#88

#89

#9

#9

#90

#91

#91

#92

#93

#94

#95

#96

#97

#98

#98

#99

initial

openbabel-1-100-0

openbabel-1-100-1

openbabel-1-100-2

openbabel-1-99

openbabel-2-0-0

openbabel-2-0-1

openbabel-2-0-2

openbabel-2-1-0

openbabel-2-1-1

openbabel-2-2-0

openbabel-2-2-1

openbabel-2-2-2

openbabel-2-2-3

openbabel-2-3-0

openbabel-2-3-1

openbabel-2-3-2

openbabel-2-4-0

openbabel-2-4-1

openbabel-3-0-0

openbabel-3-0-0a1

openbabel-3-0-0a2

openbabel-3-1-0

openbabel-3-1-1

Mono Color

• 47c51264b3 Bump peter-evans/create-pull-request from 7.0.5 to 7.0.7 dependabot/github_actions/peter-evans/create-pull-request-7.0.7 dependabot[bot] 2025-02-24 22:54:17 +00:00
• 889c350feb Merge pull request #2747 from romanbsd/inchi-crash-fix master Geoff Hutchison 2024-12-20 19:24:53 -05:00
• 134f91711e Merge pull request #2751 from e-kwsm/2715 Geoff Hutchison 2024-12-20 19:24:09 -05:00
• 5d453a0c9a build(intel): use CMake IPO and strip at linkage for Release build Eisuke Kawashima 2024-08-07 12:41:28 +09:00
• 289a9ab9a4 Fix crash when converting some bad CML to inchi Roman Shterenzon 2024-12-08 11:24:22 +02:00
• 10da8d7b89 Merge pull request #2574 from correaa/patch-1 Geoff Hutchison 2024-12-07 13:26:09 -05:00
• 44eab115b1 Merge pull request #2684 from fredrikw/gh_1996 Geoff Hutchison 2024-12-07 13:15:20 -05:00
• c6a4cfd7ef Merge pull request #2744 from openbabel/dependabot/github_actions/actions/setup-python-5 Geoff Hutchison 2024-12-07 11:22:43 -05:00
• 1c0a2bb22a Merge branch 'master' into dependabot/github_actions/actions/setup-python-5 Geoff Hutchison 2024-12-07 11:22:33 -05:00
• a852c5b85c Merge pull request #2743 from openbabel/dependabot/github_actions/peter-evans/create-pull-request-7.0.5 Geoff Hutchison 2024-12-07 11:21:42 -05:00
• e83eb008ec Merge pull request #2742 from openbabel/dependabot/github_actions/github/codeql-action-3 Geoff Hutchison 2024-12-07 11:21:26 -05:00
• d4468054f4 Merge pull request #2741 from openbabel/dependabot/github_actions/actions/checkout-4 Geoff Hutchison 2024-12-07 11:20:55 -05:00
• f81ffb6610 Merge pull request #2740 from openbabel/dependabot/github_actions/actions/upload-artifact-4 Geoff Hutchison 2024-12-07 11:20:40 -05:00
• 86a53e5878 Bump actions/setup-python from 4 to 5 dependabot[bot] 2024-12-07 16:19:12 +00:00
• 3fab3acfe0 Bump peter-evans/create-pull-request from 3.8.0 to 7.0.5 dependabot[bot] 2024-12-07 16:19:09 +00:00
• f7c15dc6bc Bump github/codeql-action from 2 to 3 dependabot[bot] 2024-12-07 16:19:07 +00:00
• 3464963e84 Bump actions/checkout from 2 to 4 dependabot[bot] 2024-12-07 16:19:06 +00:00
• b3edf3ad6e Bump actions/upload-artifact from 1 to 4 dependabot[bot] 2024-12-07 16:19:01 +00:00
• ed52008b48 Merge pull request #2739 from ghutchis/add-dependabot Geoff Hutchison 2024-12-07 11:18:11 -05:00
• 25fb5bb3ef Add GitHub dependabot scanning for GitHub actions Geoff Hutchison 2024-12-07 11:16:49 -05:00
• e2135c8c8f Merge pull request #2551 from DavidKorczynski/cifuzz Geoff Hutchison 2024-12-07 11:14:37 -05:00
• 60c2ca1f77 Merge pull request #2546 from lgtm-migrator/codeql Geoff Hutchison 2024-12-07 11:12:29 -05:00
• 03dfbd1ffa Merge pull request #2698 from romanbsd/uninitialized Geoff Hutchison 2024-12-07 11:06:54 -05:00
• 060334f5ba Merge pull request #2695 from romanbsd/int-overflow Geoff Hutchison 2024-12-07 11:06:28 -05:00
• 3c3702e0c1 Merge pull request #2705 from romanbsd/cml-parsing-crash Geoff Hutchison 2024-12-07 11:05:56 -05:00
• abbbcb4dcb Merge pull request #2717 from romanbsd/inchi-crash Geoff Hutchison 2024-12-07 11:05:25 -05:00
• 81b2e6c4d1 Merge pull request #2737 from tyler92/fuzz_convert Geoff Hutchison 2024-12-07 10:52:00 -05:00
• 378e91983e Merge pull request #2721 from matterhorn103/master Geoff Hutchison 2024-12-07 10:48:48 -05:00
• c82abd1796 Merge pull request #2678 from fredrikw/gh_2677 Geoff Hutchison 2024-12-07 10:48:01 -05:00
• 7e6dedd942 Merge pull request #2734 from ghutchis/set-residues-fasta Geoff Hutchison 2024-12-07 10:46:15 -05:00
• 291f165b51 Implement fuzz_convert fuzzer Mikhail Khachayants 2024-12-03 00:13:46 +02:00
• 3a60721a49 Ensure chains and residues are retained in FASTA generation Geoff Hutchison 2024-12-01 10:20:29 -05:00
• 00d3595fd3 Merge pull request #2706 from romanbsd/inchi-memory-leak Geoff Hutchison 2024-12-01 10:19:42 -05:00
• 693d3db568 Use current rapidjson commit hash rather than master Matt Milner 2024-09-16 23:52:54 +02:00
• cc447423b0 Use 'master' as version number Matthew J. Milner 2024-09-16 09:35:45 +02:00
• 4beabdafd0 Fetch current rapidjson codebase rather than last release Matthew J. Milner 2024-09-16 09:11:57 +02:00
• 9c1cea7c27 Don't crash on an invalid InChI Roman Shterenzon 2024-08-16 10:41:28 +03:00
• 450ebfc21f Fix memory leak in InChi handling Roman Shterenzon 2024-07-10 13:08:59 +03:00
• 1d6b6fe820 Fix crash on specific CML format Roman Shterenzon 2024-07-07 17:21:24 +03:00
• 7acf50c9d7 Merge pull request #2702 from merkys/libxml2-2.12.7 Geoff Hutchison 2024-06-21 08:37:08 -04:00
• 3601e081f9 Restore compatibility with libxml2 2.12.7. Andrius Merkys 2024-06-21 14:23:31 +03:00
• e13da94e54 ReadyToInput member wasn't initialized Roman Shterenzon 2024-05-23 12:28:55 +03:00
• 756ebaaa2f Merge pull request #2697 from fredrikw/gh2696 Geoff Hutchison 2024-05-22 10:27:43 -04:00
• 2724e31813 Clear ImplicitHydrogens on multi-fragment cdxml documents. Fixes segfault when converting particular CDXML file #2696 Fredrik Wallner 2024-05-22 15:48:28 +02:00
• 6841d54e65 Fix ASAN reported integer overflow Roman Shterenzon 2024-05-07 15:49:20 +03:00
• 765078d657 Change check for rpc/xdr.h fredrikw 2024-03-22 09:45:51 +01:00
• fffa4afe95 Merge pull request #2682 from fredrikw/fix_test_obconvwriter_pcjson Geoff Hutchison 2024-03-11 12:23:18 -04:00
• 5a0d001685 Fix failing test in testobconv_writers fredrikw 2024-03-11 16:33:07 +01:00
• 1e20208972 Make CorrectForPH respect perceived chains. Fredrik Wallner 2024-03-05 09:37:48 +01:00
• 32cf131444 Merge pull request #2654 from ghutchis/more-cjson Geoff Hutchison 2023-12-06 09:59:04 -05:00
• f67d6bc3e4 Merge pull request #2653 from ghutchis/fix-xtb-gaussian-vibrations Geoff Hutchison 2023-12-06 00:08:04 -05:00
• 283cc846ac Merge pull request #2637 from dkoes/segnames Geoff Hutchison 2023-12-06 00:07:37 -05:00
• 182c80f003 Merge pull request #2649 from fredrikw/gh_2646 Geoff Hutchison 2023-12-06 00:05:20 -05:00
• c39cf723c7 Add more cjson features, including conformer energies Geoff Hutchison 2023-12-05 23:39:55 -05:00
• 0ad3717f23 Fixup new bug with xtb Gaussian vibration output (Raman = 0.0) Geoff Hutchison 2023-12-01 07:31:25 -05:00
• 824587a1a1 Fix parsing "Gaussian" vibration output from xtb program Geoff Hutchison 2023-11-30 22:23:51 -05:00
• 5def2f7555 Added aromtic handling as in mdlformat Fredrik Wallner 2023-11-23 08:38:40 +01:00
• e53604f427 Add test Fredrik Wallner 2023-11-23 08:21:54 +01:00
• 754dad6efa Fix bugs with segnames David Koes 2023-11-07 10:15:47 -05:00
• bcb790049b Merge pull request #2640 from ghutchis/add-cjson-spacegroup Geoff Hutchison 2023-11-05 13:41:56 -05:00
• 730a57de82 Make sure to add cell vectors & space group info to CJSON Geoff Hutchison 2023-11-04 09:50:53 -04:00
• d62e51262c Merge pull request #2635 from timvdm/modern-cpp-iterators Geoff Hutchison 2023-10-26 17:09:46 -04:00
• b334832efe segname test case David Koes 2023-10-24 08:41:41 -04:00
• 5119d178e9 Parse and handle segment name in pdb file. David Koes 2023-10-24 07:56:19 -04:00
• 2e11d9b57d Merge pull request #2598 from DStarEpoch/bugfix/residue_obj_bug_on_reading_gro_file Geoff Hutchison 2023-10-23 21:21:11 -04:00
• 8fa5c367f9 Add support for C++11 (was using C++20) Tim Vandermeersch 2023-10-21 00:34:58 +02:00
• 6c5599008b Add OBAtom::GetNbrs() Tim Vandermeersch 2023-10-21 00:28:37 +02:00
• a0ec8c9655 Add support for range-based for loops Tim Vandermeersch 2023-10-20 23:56:53 +02:00
• f9efcc9ea4 Merge pull request #2608 from dkoes/obrmsfix Geoff Hutchison 2023-10-20 17:10:54 -04:00
• 7d6fd4cd49 Merge pull request #2634 from timvdm/bugfixes Geoff Hutchison 2023-10-20 17:09:08 -04:00
• 3c0d24c775 Merge branch 'master' of https://github.com/openbabel/openbabel Tim Vandermeersch 2023-10-20 21:41:56 +02:00
• e17312ab43 Fix bug in distance geometry code Tim Vandermeersch 2023-10-20 21:34:40 +02:00
• e7aa0942f6 Merge pull request #2629 from ghutchis/dont-wrap-cif-coordinates Geoff Hutchison 2023-09-20 15:47:37 -04:00
• b0dae464af By default do not wrap atomic coordinates to the unit cell Geoff Hutchison 2023-09-13 18:50:41 -04:00
• 60461a525a More python2 test changes for macos David Koes 2023-07-24 11:57:00 -04:00
• e6680c7949 Old style formatting David Koes 2023-07-24 10:36:36 -04:00
• 48ddc9b333 Use old style string formating for MacOS David Koes 2023-07-24 09:27:57 -04:00
• f495cc6bae Merge pull request #2601 from flatstik/flatstik-patch-1 Geoff Hutchison 2023-07-14 16:48:06 -04:00
• ef2b499d17 Merge pull request #2563 from e-kwsm/vaspformat Geoff Hutchison 2023-07-14 15:32:33 -04:00
• f827a725df Merge pull request #2569 from e-kwsm/bind2nd Geoff Hutchison 2023-07-14 15:31:23 -04:00
• 6275946964 Fix potential crash reading and writing CJSON files (#2612) Geoff Hutchison 2023-07-14 15:29:57 -04:00
• fa222a36a9 updated runner python setup (#2592) Michael Blakey 2023-07-14 20:16:49 +01:00
• cb5287570f Write x and y, not x and x (#2596) magnusrahm 2023-07-14 21:16:14 +02:00
• 253271442a obrms improvements David Koes 2023-07-01 15:02:06 -04:00
• 3048639f31 Fixed alignment of partial charges for PDBQT-files Ville Takio 2023-06-18 20:52:11 +03:00
• e9f4c82264 fix bug when read gro file as first residue idx is 0 * when the first resid is 0, it will trigger object res without initialization * fix with check whether object res is nullptr yeqing 2023-06-15 18:40:42 +08:00
• 55b8af1eef OpenBabel3Config.cmake to keep include information Alfredo Correa 2023-02-22 22:36:42 -08:00
• f334129373 refactor: remove deprecated std::bind2nd Eisuke Kawashima 2023-01-30 07:40:37 +09:00
• d6fbb2f74b fix: vaspformat Eisuke Kawashima 2023-01-30 07:25:35 +09:00
• 2b211d6acf Assign implicit hydrogens when reading pdbqt (#2553) fredrikw 2022-12-07 04:12:56 +01:00
• 0d4f56e58d ci: add CIFuzz Github Action David Korczynski 2022-11-23 06:51:03 -08:00
• 55d7e332e0 Add CodeQL workflow for GitHub code scanning LGTM Migrator 2022-11-11 14:36:25 +00:00
• 530dbfa333 Fix 338 (#2537) fredrikw 2022-09-22 20:34:59 +02:00
• 7702b2bc44 update interface pybel.py (#2509) Xiang Zhong 2022-08-04 22:23:50 +08:00
• 90df8ddbd6 Remove deprecated std::bind1st and std::binder1st (#2001) Eisuke Kawashima 2022-08-03 23:10:11 +09:00
• b59ba6dd04 Remove std::binary_function, which is removed in C++17 (#2464) Eisuke Kawashima 2022-08-03 23:01:58 +09:00
• e44c677810 WLN Reader Additions (#2510) Michael Blakey 2022-08-03 14:19:34 +01:00
• a25d9c4918 Update obminimize help message & docs (#2519) Daniel Sabo 2022-08-03 06:14:17 -07:00
• 0e922d075b Merge pull request #2521 from ghutchis/orca5-vibrations Geoff Hutchison 2022-08-03 09:10:39 -04:00
• d3e5311c8e Tweak vibration reading for Orca 5, which adds header lines Geoff Hutchison 2022-08-02 20:46:54 -04:00