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

Merge pull request #1779 from torcolvin/obabel_install

Install obabel target if using static build

00a8efa49aed0071f16c040e1a48f52d350bb383 authored almost 7 years ago

Merge pull request #1776 from mcs07/rapidjson

Switch to rapidjson library for JSON parsing/writing

e541a7daf09f612640f6cc15f1fdbd6aa02eb968 authored almost 7 years ago

Install obabel target if using static build

367fc47f2f52777d82c2c85355cd7c1d2d9997f3 authored almost 7 years ago

Merge pull request #1772 from boryszef/master

A small improvement of a bugfix solving segfault when reading GAMESS output with vibrations

e06b869512ccc218daa0cd12cf454d6126398b9b authored almost 7 years ago

Merge pull request #1770 from baoilleach/FuzzTest

Fix SMILES parsing fuzz test failures from AFL

d6ca0615cac1f55be5998d53a623e470d07bbefb authored almost 7 years ago

Merge pull request #1759 from baoilleach/asterisk

Fix regression. Ensure that asterisk is unbracketed when writing a SMILES string

df111a7e7e563595cbb21260ec8e8cb955b0020a authored almost 7 years ago

Merge pull request #1771 from baoilleach/FixWarningGenericH

Fix warning about size_t versus int cast

a4b53018e107da38eb0897aa02012317fe0b8781 authored almost 7 years ago

Merge pull request #1775 from baoilleach/DLOpenFlags

In the Python bindings, reset the DL open flags after importing _openbabel

615e5f515a2c0c171069a56a4e490683688c1389 authored almost 7 years ago

Add ChemDoodle JSON format tests to pybindtests

2c13bdae33f230799aecd15125ec17796226d9fe authored almost 7 years ago

Update PubChem JSON format for rapidjson

45cc3f04ad235f310f2f6a53bfc4d204624c0255 authored almost 7 years ago

Update ChemDoodle JSON format for rapidjson

2b1b06e5cddf6ad6208724fce86e02e849039112 authored almost 7 years ago

CMake use system rapidjson or download on demand

659cc92acf070adc56744b1af9b4a1f6228bdc90 authored almost 7 years ago

Remove bundled json-cpp

72dad03eb93f949482bbe2f79c9181fb3fbedbe3 authored almost 7 years ago

Add CMake module to check native optimizations

5a271fa552935202c0e355affaaca539bed85677 authored almost 7 years ago

Move the setting and resetting of the DL open flags to where 'import _openbabel' occurs in openbabel.py

3b86b037b46bfa052d6f463f120eacfca5892e31 authored almost 7 years ago

Reset the DL open flags after loading the plugins.

e287255158c2b220e169d8db4fcd4f85658a642d authored almost 7 years ago

Merge pull request #1773 from baoilleach/Fix1763

Change the behavior of OBMol.Separate so that it preserves atom order

ff0c41ffde35b92f702008e8d00278228f7cb57c authored almost 7 years ago

Change the behavior of OBMol.Separate so that it preserves atom order within each component. Previously it preserved the DFS order (which might be different).

106dfe58d42d1f38b11e3098265a2bae9d77d673 authored almost 7 years ago

This is a small improvement over a bugfix solving segfault when reading GAMESS output with vibrations

1cad46f7cfa3ea0fe5421b703174424f5bb4738f authored almost 7 years ago

Merge pull request #1765 from eloyfelix/make2d

add Molecule.make2D function

ab05cb6784c831082418a6bebbfc9a91b01a2414 authored almost 7 years ago

Merge pull request #1743 from ComPlat/cdx-object-header

Fix ChemDraw CDX incremental value

da2b3c35aae426a18efeccdd114d0f73701ec58d authored almost 7 years ago

removed OASA comment. OASA is not used anymore for 2D coordinates generation

336abe5694a8ef3a0d44d2c77778afb15308779b authored almost 7 years ago

Merge pull request #1762 from baoilleach/FixFFWarning

Fix MSVC warning about type conversion

a8f5fcb0c4b6a602bd26c760261445bcaa5f5bd0 authored almost 7 years ago

Fix warning about size_t versus int cast.

53ac7972c896b9ec8655979b5653582f0816113f authored almost 7 years ago

Add test cases and get them to pass

a74ffe338869810f5ade10f50f7798c4e32bf5da authored almost 7 years ago

Tighten up the parsing of square planar stereo. Before it didn't check for the P in SP, nor that the value was one of 1/2/3. Fixes segfault with [H][S][S][S@S00]0[S][S@S00H](0[S@S00][S])0n

44d403555d707f2b9ccfc21c33174d8e15c765fc authored almost 7 years ago

Fix segfault from parsing c0C[C@H](B)00O0

b3d3cf30715fc7a52b6c803330d0845b961c3b3b authored almost 7 years ago

Reject SMILES that start with a bond, and self-bonding with ring closures.

e4e52f09f049b645dde78fa78c3da47692613a8a authored about 7 years ago

add Molecule.make2D function, fixed test

4baf8a674b859b904a0169e75196ed981d315307 authored about 7 years ago

add Molecule.make2D function

06e233e2ca0c6d9f86f74bafe74ffcb75e9d76cd authored about 7 years ago

Fix warning about type conversion

d73a3afbc3863ee2609c5c3f32c3d69a35b8db87 authored about 7 years ago

Fix regression. Ensure that when writing an asterisk in a SMILES string

that it is not bracketed unless neccessary. This involved adding asterisk
to the organic subset, ...

d0e1f0bbb5a50e7e503542fb7414a418526f5325 authored about 7 years ago

Merge pull request #1757 from mcs07/cmake-testdir-fix

Fix TESTDIR definition to allow space in path

28dbe451d73064332b1bee097bf1289bc8e91a53 authored about 7 years ago

Merge pull request #1755 from yishutu/master

Solving #1569

d5842841a00205da0524dfad51dc2ca4961f1fb1 authored about 7 years ago

Remove unneeded TESTDIR definition

5162f499367752e083267bf5ec7cf7287221d1a5 authored about 7 years ago

Fix TESTDIR definition to allow space in path

af9c5019cd03949d3a88e60a72b124a72146afd7 authored about 7 years ago

change EOF comparison when skipping tail blank lines.

daf4a0b5942cf8a2b917829109d3f6c06c3fba70 authored about 7 years ago

The codes removing tailing blank lines were rewritten to solve issue #1569.

3e2cd4e9c2c9d81b430bb1dbe44cd8b6b1a1ca74 authored about 7 years ago

dummy atomtyper copies to make swig work

a1c1a6eefbd20e6294780d3048d7abcdb05761f9 authored about 7 years ago

Merge pull request #1747 from baoilleach/FixWarnings

Fix GCC warnings

c094a424632990d784760e1bac8e0d491d2e728b authored about 7 years ago

Merge pull request #1749 from baoilleach/fastsearchbug

Fix warning in fastsearch substructure fingerprint screen

4736189bf621faedb979b8b5389d1c29bb17d42d authored about 7 years ago

Merge pull request #1751 from mmghahremanpour/gaussformat-ReadingExactPolarizability

Reading Exact Polairzability from Gaussian log file

5904179c839ebc3b4b1fac246d40a56eb7d3c127 authored about 7 years ago

Merge branch 'master' of github.com:dkoes/openbabel

bcf6f867853abe790142011d172327e4806760fc authored about 7 years ago

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

545c28192d0b97dc7cab73fe5a7704caced09d47 authored about 7 years ago

Use a portable way to mark variables as unused. Hopefully fix MSVC build.

a6c84d5a15fc5ece48309e0fcc8eefdb23c4c7a1 authored about 7 years ago

Rebase and fix error.

3934c5e356aaa6c48e38ce335e15a7076cd8c6d4 authored about 7 years ago

Add back the dtor I removed so that things compile.

1cfaebddce3b2df7d3f9e48d4161a24e47e27042 authored about 7 years ago

Get rid of warning about unused variable.

ba49902efdae365fcc38ffd07067edb2a7550d26 authored about 7 years ago

Fix reorder initialization warning

b6e1394f36a31bfe70d6b8a357df77e47d8de601 authored about 7 years ago

Fix signed/unsigned comp

a223ee2318616118749063d5a28c0c1162682946 authored about 7 years ago

Get rid of warning about unused static functions. Get rid of signed/unsigned warning.

b15bf4199d64ddbe375d7b4408ad6e634f229f1c authored about 7 years ago

Fix signed/unsigned. Also unused function parameter of OBBond* in OBRotor::SetRings() - fixed by removing it. I'm not sure that this function needs to be in the public API at all though.

8fd7fa0feb2d0ebc6f860bcb940ba24a87b8f95a authored about 7 years ago

Update PDB-based file formats for change to AssignBonds() function

3d8301d8bc86355c0717c8b9c1a2c77b9236b8c9 authored about 7 years ago

Fix signed/unsigned. Also initialization reorder.

0300b927417725621789712b754f1b850f6b29ba authored about 7 years ago

Fix signed/unsigned by changing the parameter type for StripSalts and GetConformer. Fix warning about type qualifiers being ignored for 'internal' function DeleteStereoOnAtom by changing 'const' to 'static' (presumably a mistype (pun alert))

c6625285e5bb29aae3da06ecbcb23e49a418d8a4 authored about 7 years ago

Change API for OBVirtualBond to use unsigned ints for bgn,end,order. I'm not sure that we really need this class in the first place, but if we do, it should use unsigned ints. This fixes a signed/unsigned comparison warning in mol.cpp.

f3d4c755e402e6f937ea68ba4517b027e6e8b9f8 authored about 7 years ago

An API change to two OBStereo functions to avoid signed/unsigned comparison. Why allow signed integers as a parameter if negative values are not allowed?

38f2b416c92fce711dc6e2b424791e0cba78a17f authored about 7 years ago

Fix signed/unsigned comps.

51d81cc89c66840fe6608df2053cba7f46f4bcf1 authored about 7 years ago

Fix warnings. Signed/unsigned. Parameter init order. Suggested parentheses in expression.

8df5c9e0d60876f8697d22d2709b8e89f49f963f authored about 7 years ago

Fix signed/unsigned comp.

24915b6107de59d4742a28b338c7fe5ad0cb167f authored about 7 years ago

Get rid of warning about signed/unsigned comparison.

51cebb6962e5f60b994fd494cdcd3ccee2b0d2f8 authored about 7 years ago

Get rid of warning about unused parameter by removing it. It is part of the API but is already marked as deprecated in the doxygen description.

c84e1b5d504d536d5363c140515c2394baf8f6c9 authored about 7 years ago

Get rid of warnings about uninitialized variables.

80d2c3f055d9b787b0a5f42ec0f7a25ff6eaefc2 authored about 7 years ago

Get rid of warning about initialization order (by reordering the parameter list). Get rid of warning about unused parameter by removing the parameter.

633bafe6c64aa4c73c07b132145799663994e51b authored about 7 years ago

Get rid of warnings about multiline comments (comments that end with a backslash). Get rid of warning about possibly uninitialized value.

d28a2c4ce9560ce4af4ec47f710f0c86b5f48130 authored about 7 years ago

Fix a warning about an unused param by trimming down a bunch of no-longer used methods in OBAromaticTyper. To begin with, this no longer needed to inherit from OBGlobalDatabase, and so I removed that, and the associated private variables and public methods. In the end, it's essentially a single function and could be turned into that, but I've left it as it is.

1cf13c017e9c908263585bf1766de81fe2b51367 authored about 7 years ago

Compiling the Python bindings (at least) failed as OBBitVec was not yet defined. I've moved it before the mol.h include.

65074163eed4cdb92539b3f97ee0b8b4412474ca authored about 7 years ago

Get rid of warning about signed/unsigned comparison in that key convenience function, OBAtom::HighestBondOrder()

766e3d9787d84f6bb825a809546ee1d568a2bdb2 authored about 7 years ago

Get rid of warning about unused parameters for OpGenAlias.

43dd0ac883958defef2c892703a89a26f0346a04 authored about 7 years ago

Fix signed/unsigned comparison warning. There was a mismatch between the type of stored value of the HOMO and the type of the parameter in some of the functions.

dd3306cedc90b6776480fcdb33627391350f377c authored about 7 years ago

Fix warning about signed/unsigned comparison

e33e14a97259f882d4f49002d9c9b2015ee8e86f authored about 7 years ago

Merge pull request #1750 from Acpharis/numCompare

Fix #1684

4b684c64e9dbe5e451d7fbcbbc178ef3b8911ea4 authored about 7 years ago

Reading Exact Polairzability from Gaussian log file

7d74d738b759ca8caa058915dcd9e1162db5f490 authored about 7 years ago

Fix #1684

When figuring out if a filter value is numeric by casting to double, Mac and Linux
set the failb...

58774501ed6cb3f3699d707a49879b161d3b34e3 authored about 7 years ago

Fix warning about evaluation order being undefined due to use of ppat and ppat++ in the same statement. Made slightly faster, I think too, but this is not the slow part of substructure searching.

8fd19840c65e5c92c70495c4eef1c9fb0566b6fc authored about 7 years ago

Merge pull request #1746 from baoilleach/Fix1731New

Fix for 1731. Store atom classes in CML atomids by appending _ATOMCLASS.

eb408c7e655fc295d5cdc6708438baac96539cdf authored about 7 years ago

Gaussformat reading electrostatic potentials (#1748)

* Reading Electrostatic Potentials from Gaussian log files

2be791c805c3524214c15c050b7fb3e37da214bf authored about 7 years ago

Fix for #1731. Changes how atom class information is used in CML. If we must hack it into the atomid, let's do it in a very simple way by appending _ATOMCLASS to the end of the atomid.

a7aaeb9bf6ec3a32fec8f08ad171b7e2ff65f44c authored about 7 years ago

Merge pull request #1745 from baoilleach/Fix1676

Fix error in VASPformat found by static code analysis

771b917388b9fa282af1494ddf6434b8e584c2c9 authored about 7 years ago

Merge pull request #1744 from baoilleach/FixUnsignedChar

Ensure portability to ARM platforms

ee11c98a655296550710db1207b294f00e168216 authored about 7 years ago

Fix ChemDraw CDX incremental value

ee6cd1855f3b208cf5e513449908a2b1063ea72e authored about 7 years ago

Fix error in code. Should have been using (*it) in loop, not atom.

48fe969e51188da53d20b1bed8b1394a43c4bfb1 authored about 7 years ago

Fix yasara compile

8d707b8ebbe1742b0f626032cd6227eeb62393ac authored about 7 years ago

Fix #1689 by using positive values and explicitly stating unsigned char

e26491017efefdc6aaf73d4d49f284f4e9436244 authored about 7 years ago

Merge pull request #1741 from baoilleach/MoveAtomClass

Refactor atom class to being data on an atom rather than on a molecule

731713770db45432778421600e9786e1e04c196c authored about 7 years ago

Add missing include to fix Linux build

02e94141ceb5a60f1a05c10fa1cddac6b8a1b934 authored about 7 years ago

Port TinkerXYZ to using the new atom class. Get rid of warnings about

unused variables. Minor update to Description string.
Add test for TinkerXYZ, and also for Delete...

6f0a0ff18ba2fd186d9e7fa179dc9d304c858640 authored about 7 years ago

Merge pull request #1727 from baoilleach/SwitchStatement

Moved more inside the switch statement for SMILES parsing

52c739431e5607ab3da1c535bc4932d500c319e7 authored about 7 years ago

Update bindings

bb4bc5f521a0f03898a530796e7b5400a939a88d authored about 7 years ago

Avoid string copy with GetData(const char*)

77c722b4560a51a6b42157ee86ef1e3287f73b6b authored about 7 years ago

Refactor handling of atom classes. Store them as "Atom Class" data on

the atom, rather than in an OBAtomClassData object on the molecule.

1d9944fa0b71ca2e6930f395b502a172255bcd3a authored about 7 years ago

Merge pull request #1720 from ComPlat/cdx-reaction-map

Read reaction map from ChemDraw CDX files

152c0246c2e600b876a38f8e3a2a5394441816b4 authored about 7 years ago

A test was failing due to Windows line-endings. Added code to explicitly handle the \r.

30aba1e3ce9febdd93bae1f7cbdb0704f87a3a68 authored about 7 years ago

Use a switch statement for the entire body of the parsing loop, instead of some 'if's and a switch.

8a966e5c7b5472c7c0ce71a3d717e44887200ff9 authored about 7 years ago

Merge pull request #1592 from nakatamaho/master

Fix wrong spin multiplicity assignment

7972033d68a7604280cc9f4a643ee6a6ef85d5bc authored about 7 years ago

Obthermo update patch (#1598)

* updates for obthermo

c11d051e2c343e1f1592d999cdc33a9be701467a authored about 7 years ago

Fix Python3 compatibility (#1737)

Fix Python3 compatibility by using items() instead of itertools

41c83677fd5925275bbfde1bff7299480cd2820b authored about 7 years ago

More changes.

1589942bfbcf7c4e9817b198541669510beaade6 authored about 7 years ago

Updated, working version

c11a198d45ca91d2aee241390614776a7b1a9e28 authored about 7 years ago

Fix unit test to actually fail with incorrect stereo

936db37a51e79a05ddda7fa8350f4c86eb48cabf authored about 7 years ago