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openbabel

We're on a mission to speak the many languages of chemical data
Collective - Host: opensource - https://opencollective.com/openbabel - Code: https://github.com/openbabel/openbabel

Bugfix for OBMol::DeleteResidue()

github.com/openbabel/openbabel - ea659d1ee3506ea8db9093c71e5be29e72883448 authored almost 17 years ago
Made pybel test suite compatible with Python 2.3

github.com/openbabel/openbabel - a093a951ce208ad4af627648bc3f5092f6e13a56 authored almost 17 years ago
Updated for local installation. Also it's no longer necessary for the user to run extconf.rb themselves (and in fact, would cause errors in many cases)

github.com/openbabel/openbabel - c16ef5b6460991cf12e10691866c1683119a2c2e authored almost 17 years ago
2008-01-30 Joshua Ballanco <[email protected]>

* scripts/ruby/extconf.rb: Reworked the mkmf fix to be more
generally applicable...

github.com/openbabel/openbabel - 7dace182102555cfd1903a21ba720028bbb0d5ab authored almost 17 years ago
Fixes contributed by Liu Zhiguo via e-mail.

* src/data.cpp (OBResidueData::AssignBonds): For pre-defined
residues, do not che...

github.com/openbabel/openbabel - fa5b76cc128e7bbed2fe799f2494c82a0d3c0e55 authored almost 17 years ago
Updating Java bindings to the same as Python...doesn't compile though.

github.com/openbabel/openbabel - 9363e2e8bcba7c3caacdd5a9c33c208da9d248dc authored almost 17 years ago
2008-01-29 Joshua Ballanco <[email protected]>

* scripts/ruby/extconf.rb: Fixed an error that had Ruby 1.8.6
using gcc to compile and link th...

github.com/openbabel/openbabel - 4fb392dc417673dceb28c7842bbe26bf0e40727a authored almost 17 years ago
Updating perl wrapper to the same as Python. Fixing setup.py for Python as wasn't finding openbabel.so on my system

github.com/openbabel/openbabel - 24ccf30c1bc7737a361faef58fc128e02965db51 authored almost 17 years ago
Remove #ifdef _WIN32 from InChIKey code

github.com/openbabel/openbabel - 03cf15414d0da5101ffa24ea243d65dc4a4bf3fa authored about 17 years ago
Applied Rich's fix to Ruby initialisation and updated the interface file for Ruby. Compiles fine now, but fingerprint.h is commented out.

github.com/openbabel/openbabel - 6cb96812df5243c7d9c09d1a084ca1d16e0f7066 authored about 17 years ago
* src/ops.cpp, src/pointgroup.cpp, src/kekulize.cpp, src/mol.cpp,

src/obutil.cpp, src/ring.cpp, src/atom.cpp,
src/forcefields/forcefielduff.cpp,
...

github.com/openbabel/openbabel - 0b37cb0bd627c7007e38fd7598c02a6025dd1091 authored about 17 years ago
* include/openbabel/ring.h (GetRootAtom): Return unsigned int for

comparison with atom indexes.

* include/openbabel/plugin.h: Remove unused parame...

github.com/openbabel/openbabel - e3b0147548dac1e5a4b05e98e051b2c075695c00 authored about 17 years ago
Correct MDL output for charged molecules

github.com/openbabel/openbabel - 530eb779321c61f732fa708c77dfa10ad932a673 authored about 17 years ago
2008-01-22 Jean Brefort <[email protected]>

* src/formats/yasaraformat.cpp: replaced const char* by string.

github.com/openbabel/openbabel - 69bd11beb73e3d404f502b212e2238e38f2acd69 authored about 17 years ago
Fixed bug with input and "variable" is not at the start of the line.

github.com/openbabel/openbabel - 17d65de187693240531aaf14e183f3b4885dc099 authored about 17 years ago
* src/formats/gausszmatformat.cpp: New format. Supports

reading/writing to Gaussian Z-matrix files. PR#1863673 and #1696776.

github.com/openbabel/openbabel - a41371a323eb205d61023ee8dd09537d061eccb8 authored about 17 years ago
* src/obconversion.cpp: When looking for .gz extensions, make sure

substrings go to the end of the string. This prevents problems on
extensions like...

github.com/openbabel/openbabel - a666a96e2d05b64525f205ae15e9b19ba167c5ed authored about 17 years ago
* include/openbabel/atom.h, src/atom.cpp: Handle SetType(string)

as const as well.

github.com/openbabel/openbabel - 26f6f6b4de2105bfefc054eafbb4038e3207f078 authored about 17 years ago
2008-01-21 Jean Brefort <[email protected]>

* src/math/spacegroup.cpp: fixed all g++ warnings.

github.com/openbabel/openbabel - 6d7a2b5e972459487e3cfb7ec364a5441cbf8a94 authored about 17 years ago
Merged changes to the Python SWIG interface to the other scripting languages. Haven't yet been able to test (am trying to set up a VM with a decent amount of RAM...)

github.com/openbabel/openbabel - 72b9f5011daa49f7b7f2d9e9362f9ced4e77b8f4 authored about 17 years ago
2008-01-20 Jean Brefort <[email protected]>

* include/openbabel/atom.h: replace char* by const char* where
appropriate to get rid of the d...

github.com/openbabel/openbabel - 505fd0c5efe1649d6e32791af4fcba8e049ac9ba authored about 17 years ago
2008-01-20 Jean Brefort <[email protected]>

* src/formats/cifformat.cpp: don't try to find he group when there
is no symmetry related data...

github.com/openbabel/openbabel - 896d249c7a10c3084a682bf79bbb55725f5bd538 authored about 17 years ago
Added headers found missing in 2.2.0b2 snapshot by Rathann.

github.com/openbabel/openbabel - 4767234f071f069192ef122395e0a5d055738235 authored about 17 years ago
Update svn ignore for .libs directory.

github.com/openbabel/openbabel - 18158e7360daacc5256b997ce5012a95990c7839 authored about 17 years ago
Small revision of python bindings

github.com/openbabel/openbabel - c6b8d931dfffee745030c4c8c9aa442934b3a60f authored about 17 years ago
2008-01-19 Jean Brefort <[email protected]>

* src/math/spacegroup.cpp: accept white spaces in transforms
descriptions in cif files. Fixes ...

github.com/openbabel/openbabel - 4113370b28a162231656884f39e0d8c4f3902fb8 authored about 17 years ago
Remove dock.h, dock.cpp until these are complete.

github.com/openbabel/openbabel - b16a2b868449ca54848e94bea1e3f04c489cf2e9 authored about 17 years ago
Fix minor documentation issue with Allred-Rochow electronegativity.

github.com/openbabel/openbabel - ee9692fb1b91dd23e1315f71d915234ae3c57786 authored about 17 years ago
* scripts/python/pybel.py, scripts/python/examples/testpybel.py:

Updated to use plugin descriptors. Changed to create a single instance
of plugin descriptors an...

github.com/openbabel/openbabel - 37588a1d49481dca362a0142c03adb2f71c314f8 authored about 17 years ago
Minor speedup with minimization -- set the forcefield only once, not once per

molecule in a multi-molecule file.

github.com/openbabel/openbabel - 5979664d02f81c17ccbda96a4f0fe0543aff1f9c authored about 17 years ago
Get SWIG for Python to compile

github.com/openbabel/openbabel - eb0050dbfe44f112d340ba6380e8dd7fcbf6ce35 authored about 17 years ago
2008-01-16 Noel O'Boyle <[email protected]>

* include/openbabel/forcefield.h, plugin.h: Documentation fixes
* src/bitvec.cpp: Documentatio...

github.com/openbabel/openbabel - f0e30f8cb42c674405d8e4d51f3d8a0874dd5558 authored about 17 years ago
Corrected data in Changelog

github.com/openbabel/openbabel - 91d7c394c5976a45dbbcd210d8f25bb5adc3731e authored about 17 years ago
Updated openbabel-python.i to allow compilation.

github.com/openbabel/openbabel - 0a34b924d042095496a627718b69cace850425fa authored about 17 years ago
Update SVN ignore for .deps Makefile, etc.

github.com/openbabel/openbabel - 69b555fdfbabd5b9062218445cc87404519307a5 authored about 17 years ago
* src/base.cpp: Fix API documentation for return(1), as mentioned

by Andrew Dalke. PR#1827795.

* src/formats/cacheformat.cpp: Fix incorrect chemic...

github.com/openbabel/openbabel - 6d3438426a0e23b1886e4d2c01aa961951964fb7 authored about 17 years ago
Add tokenst.h to Makefile.*

github.com/openbabel/openbabel - bde24200756dcb9dec83dd47a9831d69b7f4ea27 authored about 17 years ago
* src/Makefile.am (SUBDIRS): Added descriptors and ops.

(libopenbabel_la_SOURCES): Removed filters.cpp, gen3d.cpp,
smartsdescriptors.cpp ...

github.com/openbabel/openbabel - b7191943106f00add58e7ef6b30cc0b374a924bd authored about 17 years ago
* include/openbabel/tokenst.h: Add newline at end of file.

github.com/openbabel/openbabel - b24ed46d926fb365fcd470af40273d15a712a018 authored about 17 years ago
Correct commit of Windows OBF build again

github.com/openbabel/openbabel - 26f76053b751ba6a5456227df5d309c6096a78ee authored about 17 years ago
Correct commit of Windows build files

github.com/openbabel/openbabel - ccf91ae83140d18bdd62f825947393d2df8dd35c authored about 17 years ago
New features: compound descriptor, chemical transforms, plugins from textfiles. New ops directory.

github.com/openbabel/openbabel - b928784265162df244db16a250770e9a289a0ff5 authored about 17 years ago
removed debug output

github.com/openbabel/openbabel - bd2aaa4a90a169ed1633b2eae8a8c80d40359f29 authored about 17 years ago
Added OBRotorKeys

github.com/openbabel/openbabel - e98740557faa5e9174c96fc8c6d0e47ef98e0b76 authored about 17 years ago
remove _fix.Clear() from OBRotorList::Clear()

github.com/openbabel/openbabel - 5fbe44634e683cc1c844d3ffe45d0e5a3a7805bc authored about 17 years ago
* test/cml.sh: Use /bin/bash to run, not /bin/sh as "source" is a

bashism.

github.com/openbabel/openbabel - 70b9f2f4079adaa39e696fb7ec4d8aba22afcb63 authored about 17 years ago
* src/formats/xyzformat.cpp: Accept non-standard XYZ files with an

atom number rather than an element symbol in the first column.

github.com/openbabel/openbabel - adfb881e490790895fdd44368ebef42a2bf0f017 authored about 17 years ago
2007-12-20 Jean Brefort <[email protected]>

* src/formats/pdbformat.cpp: fix crash [#1846728].
* src/math/spacegroup.cpp: add missing header.

github.com/openbabel/openbabel - a2ac61d85262cd85d3469bf5671eacd901ba49c3 authored about 17 years ago
* include/openbabel/forcefield.h (HasAnalyticalGradients): New

method to define if full analytical gradients are implemented for
a force field. ...

github.com/openbabel/openbabel - 3a344dab4d50cca43e8deaef28976f382cd1b57d authored about 17 years ago
Ignore obsym executable if srcdir==builddir

github.com/openbabel/openbabel - e2d4d652d126aebc4230a789b6117fbab5b785e4 authored about 17 years ago
Code cleanup, documentation, molecular dynamics

github.com/openbabel/openbabel - e03459646d1c11fead65cad3de83628a4258a438 authored about 17 years ago
Miscellaneous minor bug fixes and mods.

github.com/openbabel/openbabel - 646a7dec4775f554ab1b4fa4854b7b79be98bbcf authored about 17 years ago
MMFF analytical gradients for all terms except OOP

github.com/openbabel/openbabel - 06b0b975161063346a7dbd87a96188b203bf3755 authored about 17 years ago
* src/forcefields/forcefieldmmff94.[h,cpp]: Solved problem with VDW

interactions. H-Bond donor/acceptor reactions were not handled
correctly.

github.com/openbabel/openbabel - 15c7c86960e55674f9f825e07a12df7a25344380 authored about 17 years ago
* srd/mol.cpp: Bugfix for FindTorsion. Now checkes to make sure the

wing atoms are not the same atom. This occurs in 3-membered rings.

* src/forcefi...

github.com/openbabel/openbabel - 01ac5a46e8f8e23195a55e9a52a02c7da283d124 authored about 17 years ago
make sure we have valid atom pointers when GetDistance is called. This makes it possible to add bond constraints while Avogadro's AutoOpt is running.

github.com/openbabel/openbabel - a22e178f867eeba05f01392866f8b5ff673bfdce authored about 17 years ago
Small changes to OBForceField::Setup(), see Changelog

github.com/openbabel/openbabel - bff46509419e621d30c76a6f65cdd66991344470 authored about 17 years ago
2007-12-10 Jean Brefort <[email protected]>

* include/openbabel/base.h: add missing headers, see debian bug #455170.
* include/openbabel/d...

github.com/openbabel/openbabel - b1698b4873e258cc4ffda7c94a81db9537cf1048 authored about 17 years ago
Added OBDock class

github.com/openbabel/openbabel - 098ca68a627477407253d74e48ac0215c14b2d31 authored about 17 years ago
Added functions to get energy for conformers

github.com/openbabel/openbabel - 1b690b79cf8f3c0ccf89aa712750cde4ef3edfcc authored about 17 years ago
* src/formats/xyzformat.cpp: Fix bogus warning about titles when

reading past the end of the file.

github.com/openbabel/openbabel - 1af78f3fce997a201b3f7f258c44b9cbf5139d7d authored about 17 years ago
* data/element.*: Fix atom colors to match Jmol standard. (Changes

in Fe, Co, Ni, Cu only.)

github.com/openbabel/openbabel - 31df1667ed64bb77cbbeea06dd8f2921e009f665 authored about 17 years ago
removed OBForceField::GenereteCoordinates call

github.com/openbabel/openbabel - 2c3602ae65b1042ed8dd4ae786e3348765ba8b66 authored about 17 years ago
Bond constraints

github.com/openbabel/openbabel - f2b609d0f69e3f8b630cd55b1fee1b0dfb66b656 authored about 17 years ago
OBFFConstraints added

github.com/openbabel/openbabel - 106363bb43023306ec336e3029bf5326bda696f1 authored about 17 years ago
* src/CMakeLists.txt, src/forcefields/Makefile.*: Update to remove

MM2 forcefield from building.

github.com/openbabel/openbabel - 659c4da08c660b4a43ae7b7015ac2e1893f1af5a authored about 17 years ago
* tools/Makefile.am, tools/obsym.cpp: New tool to detect point

group symmetry and eventually write newly "symmetrized" coordinates.

github.com/openbabel/openbabel - 87651e8caebed4d42818024dd66e4922eaea07bf authored about 17 years ago
* include/openbabel/pointgroup.h, src/pointgroup.cpp: New class to

wrap S. Patchkovskii's brute-force 3D point group symmetry
code. Still needs som...

github.com/openbabel/openbabel - ee9e40c9ac0476b0b0f8385a62851c90920e32ed authored about 17 years ago
Small bugfix to Chris' commit

github.com/openbabel/openbabel - 6e7bd2459648c72c9ad904c8de1ea605ef2c5a2e authored about 17 years ago
Added IsSetupNeeded()

github.com/openbabel/openbabel - c006a206844e205fba3d52b02913d2cd2137bcfa authored about 17 years ago
Give forcefield classes a MakeNewInstance function.

github.com/openbabel/openbabel - 43ddc1b9a261108e148e61633f2687847c0273dd authored about 17 years ago
Request ID 1840682 this revision speeds up, corrects and fully

documents bit vectors.

github.com/openbabel/openbabel - 73c84180f2f98bf6a4200500af6c93e94639efc0 authored about 17 years ago
Added ignore and fix atom support

github.com/openbabel/openbabel - c05bfcdd5cffab215bbfa82e51093f75de470607 authored about 17 years ago
idem for RandomRotorSearch

github.com/openbabel/openbabel - caa84a4e4249c99b0948c4e7d632fccdf1217894 authored about 17 years ago
split SystematicRotorSearch

github.com/openbabel/openbabel - be731218854d537974c35bf8f13e5f7f4467fe58 authored about 17 years ago
analytical gradients for angles in Ghemical force field weren't correct anymore. * DEG_TO_RAD was added to dE since the 2.1 release. This is not

needed, so I removed it again. While debugging this I maded some changed to tor = 0.0, this is ch...

github.com/openbabel/openbabel - 47c849e9efc70c34074de826a5909b8a93971e11 authored about 17 years ago
* include/openbabel/atom.h, src/atom.cpp: New method GetResidue()

to optionally request no chain perception. Useful in
builders/editors (e.g., Avog...

github.com/openbabel/openbabel - 835e740e4e7d39afdc6826671ab84b64bcf44503 authored about 17 years ago
* src/chains.cpp: Improve speed when clearing residue info in

molecules with no residues.

github.com/openbabel/openbabel - 1977287d21e5086ad163f760b8779ad5e90daa10 authored about 17 years ago
Fix warning with initialization of OBElement.

github.com/openbabel/openbabel - fceea1e50f016aa5a379dba67ac6edeac9b00f53 authored about 17 years ago
* test/iterators.cpp: Fix #include for OBRing. Now compiles cleanly.

github.com/openbabel/openbabel - f3275949e484fd14be7a6fbfec38bb495150e699 authored about 17 years ago
MMFF94 always uses OBFFLog() now (instead of * logos << ..)

github.com/openbabel/openbabel - f8215a0240ef4e359416bc9b62a095e21f3795ba authored about 17 years ago
* scripts/Makefile.am, tools/Makefile.am: Fixes for building

outside of the source tree.

github.com/openbabel/openbabel - 9a5b3c2436bc8817a4b67a2dda193950ffc9a275 authored about 17 years ago
added builder.h to Makefile.in and Makefile.am

github.com/openbabel/openbabel - dbdb52bed4015f2644c5cd31466eda1fa4bf77c2 authored about 17 years ago
Allred-Rochow electronegativities

github.com/openbabel/openbabel - 68c9e83e3a75a989a8cbba6a756291fa6b6a61ad authored about 17 years ago
Torsion changed back to 0.0 for UFF and Ghemical...

github.com/openbabel/openbabel - 8d01869b8475373441a8781e127a65d24ef88713 authored about 17 years ago
Fix SMILES parser bug #1839589

github.com/openbabel/openbabel - 0b563cc91b68892af72120e1520d9ec457d75bc4 authored about 17 years ago
more changes to MMFF

github.com/openbabel/openbabel - cdc0d092d570a51375ddce6856f10ee55b0b3f19 authored about 17 years ago
MMFF94 partial charges now assigned correctly

github.com/openbabel/openbabel - dc6f23a64a6bd4d8864a6d927d15950f7c12fc6b authored about 17 years ago
Small change in SMILES file reading; Add Reaction SMILES format.

github.com/openbabel/openbabel - 1b2ed36a68c4c3464995328ec4ed64284ea7a497 authored about 17 years ago
* tools/obminimize.cpp: Fix a bug to use conjugate gradients when

-cg is specified. (Explosions seem to occur more often with CG for me.)

github.com/openbabel/openbabel - 37dc30a503ad9109fd8c6feca1e5c7cc769bd897 authored about 17 years ago
* src/forcefield.cpp (VectorOOPDerivative): Calculate forces, as

per Tim's reference.

* src/forcefields/forcefielduff.cpp: Use it.

github.com/openbabel/openbabel - 9980eec85425844afe1b5d4c92af330e66768fc6 authored about 17 years ago
MMFF94 Formal charges assigned correctly.

github.com/openbabel/openbabel - cdc925751fddddbca1fdc39b3cbec6760368f5a9 authored about 17 years ago
some more improvements of cmake build system, mostly on win32

github.com/openbabel/openbabel - 4733f3a959d4e090607daa2fe2c4d2788c366e2c authored about 17 years ago
Move some #includes to maintain code segregation

github.com/openbabel/openbabel - 470d47ca460785f03f5cb8acd6b93e0b1185e98d authored about 17 years ago
some changes for building on win32 with cmake - both mingw and msvc

github.com/openbabel/openbabel - 974d95f4deb81151135d40db0b4368a42e44e827 authored about 17 years ago
update MMFF94 code

github.com/openbabel/openbabel - 7c8cdba60b12330d32f4abe45d61372a06a4942f authored about 17 years ago
MMFF atom typing works, fixes for OBRingTyper, DetectExplosion, ..

github.com/openbabel/openbabel - 9617e46d9ffa89c7f02f2e39fba17dbff6fa6a02 authored about 17 years ago
As requested by Jean, CMLFormat now handles OBReaction as well as OBMol objects.

github.com/openbabel/openbabel - 6bf58c3f233e66c02a373c8a334761ef8c851958 authored about 17 years ago
those changes make OB2 compiling under mingw with cmake.

babel -Hall doesn't work though - there are no formats recognized.

github.com/openbabel/openbabel - 229c5324b40900846db5a9b9a4313d1ea549084a authored about 17 years ago