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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

extra string temp variable so that it will compile on gcc

github.com/openbabel/openbabel - 59c7274683655c84689e2bcfb6b0fad2b7781687 authored about 17 years ago by Chris Morley <[email protected]>
Fix for Request ID 1834344 - Allowing multiple MODEL records

in pdb files.

github.com/openbabel/openbabel - 55fadfe9bf0d8299d8fa95fb262e13e9a57c3ed1 authored about 17 years ago by Kevin Shepherd <[email protected]>
New alias class and use in mdlformat

github.com/openbabel/openbabel - 9d18721ac9967aa242eac676c977dffefd6b577b authored about 17 years ago by Chris Morley <[email protected]>
added OBRingTyper

github.com/openbabel/openbabel - e5c8ac08388cc556b9d87c8e007cb084ed479b2c authored about 17 years ago by Tim Vandermeersch <[email protected]>
2007-11-16 Michael Banck <[email protected]>

Make libinchi.la a convenience library.

* src/formats/inchi/Makefile.am (lib_LT...

github.com/openbabel/openbabel - d25a59229027d21c65bd71cc121c533d94556abd authored about 17 years ago by Michael Banck <[email protected]>
2007-11-16 Michael Banck <[email protected]>

* src/formats/xml/Makefile.am (INCLUDES): Added
-I$(top_builddir)/include.
...

github.com/openbabel/openbabel - 47f5284a383843da8efacf01f635b7a682373b6f authored about 17 years ago by Michael Banck <[email protected]>
Update Windows build files

github.com/openbabel/openbabel - 589a0c846e1ed23e3f2fe70ab74e414b3dc1b2a4 authored about 17 years ago by Chris Morley <[email protected]>
* src/griddata.cpp, src/grid.cpp: Change to new SetLimits method

for assigning axes, origin -- everything required by OBFloatGrid.

* src/formats/...

github.com/openbabel/openbabel - b19cd19d9f39a180b3bd66f171e9ec1696735b0b authored about 17 years ago by Geoffrey Hutchison <[email protected]>
* include/openbabel/Makefile.am: Make sure to install new headers

griddata.h, op.h.

github.com/openbabel/openbabel - d88b9b0f8331bd3aa421d5838f84d85e48b96045 authored about 17 years ago by Geoffrey Hutchison <[email protected]>
* src/Makefile.am: Add "ops" code introduced by Chris, including

gen3d coordinate generation.

github.com/openbabel/openbabel - 5904d85a0d8b7aa6f737baaed197be71c8e31c1d authored about 17 years ago by Geoffrey Hutchison <[email protected]>
Remove Java interface from SVN control, to match Python, Perl, and Ruby practice.

github.com/openbabel/openbabel - deb1c82abd6e32675941f22561cd7f1465628268 authored about 17 years ago by Geoffrey Hutchison <[email protected]>
pngformat.cpp: Remove class name in declaration

github.com/openbabel/openbabel - 59561b34f4257e7fc3c427a2572812bc6ff7d0fd authored about 17 years ago by Chris Morley <[email protected]>
* src/formats/chemkinformat.cpp

(ChemKinFormat::ParseReactionLine): Added some compilation fixes
for GCC.

github.com/openbabel/openbabel - c0e950445faf6e632b34fa8fc2bf5f4900fac1d0 authored about 17 years ago by Geoffrey Hutchison <[email protected]>
Added gen3D.cpp, a wrapper for OBBuilder to make plugin option.

github.com/openbabel/openbabel - 0e372e49df80ea8e4b5cae30cc548004a3eea31f authored about 17 years ago by Chris Morley <[email protected]>
Chemical kinetic formats revised.

github.com/openbabel/openbabel - 4b741429360399788a4afb85b7a22968bf7408f6 authored about 17 years ago by Chris Morley <[email protected]>
* src/formats/inchi/*.c, include/inchi/*.h: Import InChI v1.02b

distribution code.

github.com/openbabel/openbabel - 90f678e7f0e2ca0fe9c447a3bdfe825e5e331858 authored about 17 years ago by Geoffrey Hutchison <[email protected]>
merged my old svn version with current (mmff94 force field code)

github.com/openbabel/openbabel - 22b76f8e59f7ea29d780b4bcd819bd756fa322e5 authored about 17 years ago by Tim Vandermeersch <[email protected]>
another update for the fragment library + reader function

github.com/openbabel/openbabel - 09b21c0bc6694bd86d4df192a98ce036af098755 authored about 17 years ago by Tim Vandermeersch <[email protected]>
* src/Makefile.*: Updated for new files.

* include/openbabel/base.h: New data type for grid data.

* include/openbabel/gr...

github.com/openbabel/openbabel - d6d9b6051d87d43271e1e3e5bf093e87eae09230 authored about 17 years ago by Geoffrey Hutchison <[email protected]>
* src/formats/gromos96format.cpp: Fix typo caused by residue

numbers as strings.

github.com/openbabel/openbabel - 7b0c8b30a0e8f49763482156478c6e25d03d1737 authored about 17 years ago by Geoffrey Hutchison <[email protected]>
first coordinate for fragment is now the correct one instead of atoi("C")

github.com/openbabel/openbabel - fb2e27a5ef832cb71f2045e66a594c7f283ffba8 authored about 17 years ago by Tim Vandermeersch <[email protected]>
new fragment library and read function for OBBuilder

github.com/openbabel/openbabel - c849bdf1b8a704e34711ac6e3028bcf6fadca25b authored about 17 years ago by Tim Vandermeersch <[email protected]>
updated fragment library + fix to make sure last fragment is included

github.com/openbabel/openbabel - 9cecf811cb8b3c2077b4b784d62478005763ef41 authored about 17 years ago by Tim Vandermeersch <[email protected]>
OBBuilder: rotation works!

github.com/openbabel/openbabel - 0a795a7d3bfcfd92578e9ebec18a35b32b713c7c authored about 17 years ago by Tim Vandermeersch <[email protected]>
update for rotations

github.com/openbabel/openbabel - 60edb5e427ccba87ee6e710ceac5ee7c54e3cabe authored about 17 years ago by Tim Vandermeersch <[email protected]>
* src/*.cpp, include/*.h: Change to UNIX line endings for

consistency.

github.com/openbabel/openbabel - 5170306e386e0ba505c538fa50a0b6eb570a4f50 authored about 17 years ago by Geoffrey Hutchison <[email protected]>
fragment translation for OBBuilder

github.com/openbabel/openbabel - 4226e345bd70914db061760cfe133baafde14d2a authored about 17 years ago by Tim Vandermeersch <[email protected]>
Fixed compile error in last commit.

github.com/openbabel/openbabel - 933a511f219a9d710d4114bc77e26c69f28e8021 authored about 17 years ago by Geoffrey Hutchison <[email protected]>
Added OBBuilder class

github.com/openbabel/openbabel - 24ec4118de5506da36b5eeae743c522c7db75737 authored about 17 years ago by Tim Vandermeersch <[email protected]>
* src/forcefields/forcefielduff.cpp: Fix VDW gradients.

github.com/openbabel/openbabel - a4798c34b7f74cc5ba93042929bb084f9bda844f authored about 17 years ago by Geoffrey Hutchison <[email protected]>
* src/forcefield.cpp (WeightedRotorSearch): Improved conformer

searching. Still needs geometry optimization for each
rotamer. (That seems to unc...

github.com/openbabel/openbabel - 0ec9ee7926883086d744e874fee4b55faf0c6475 authored about 17 years ago by Geoffrey Hutchison <[email protected]>
* data/UFF.prm: Improved typing.

github.com/openbabel/openbabel - 8ed348e96ef7ff98af859cdc27682456d6623dbd authored about 17 years ago by Geoffrey Hutchison <[email protected]>
ChangeLog for r2096.

github.com/openbabel/openbabel - 1bf27e6672bf4f9fa6f66c1641bcc79a507dc4ce authored about 17 years ago by Geoffrey Hutchison <[email protected]>
* src/forcefields/*: Add delayed initialization. Only parse the

parameter file when the force field is called by Setup on a
particular molecule.
...

github.com/openbabel/openbabel - daa8e6b353c09bc72985ea7893c4d468b61bc070 authored about 17 years ago by Geoffrey Hutchison <[email protected]>
Fix for Request ID 1825751. Ignore extra data columns to allow

more xyz file varients to be correctly read.

github.com/openbabel/openbabel - fe8b588b0ed38fae90e31d6c4c9a03ddd1470ce3 authored about 17 years ago by Kevin Shepherd <[email protected]>
* CMakeLists.txt */CMakeLists.txt: CMake build files contributed

via Saro Engels and Christian Ehrlicher and the KDE-Win project.

github.com/openbabel/openbabel - 03883bed928e06405792af5b91973f81cf783a57 authored about 17 years ago by Geoffrey Hutchison <[email protected]>
Move OBGenericData declaration to reduce dependencies.

Corrrect bug in forcefieldghemical.cpp

github.com/openbabel/openbabel - 9bff43221df7eff293b4814bcc7a04eedcb465b2 authored about 17 years ago by Chris Morley <[email protected]>
Added mmCIF format conversion module, as Request ID 573869

Handles read, write and skip. Includes atoms, residues,
space groups and unit cells. Please se...

github.com/openbabel/openbabel - fa434507bf870503cb38c934cde5ead75e01f08f authored about 17 years ago by Kevin Shepherd <[email protected]>
This fixes Request ID 1825346, where some elments were mis-parsed.

Please see the test repository for PTABLE.mol2 which illustrates
this.

github.com/openbabel/openbabel - 52df7fec0065d6fe62dd3b2d95dbc8475936727f authored about 17 years ago by Kevin Shepherd <[email protected]>
* src/forcefields/forcefielduff.*: Calculates UFF energies, but

still missing analytical derivatives.

* data/UFF.prm: Better atom typing rules.

github.com/openbabel/openbabel - c6587f419d466f633e7320b00930c0605387a3fd authored about 17 years ago by Geoffrey Hutchison <[email protected]>
2007-11-02 Michael Banck <[email protected]>

* src/formats/inchi/inchi.sym: New file.
* src/formats/inchi/Makefile.am (libinc...

github.com/openbabel/openbabel - fe4d4541fa654bfc2872c155bb9ec0f637cb5c38 authored about 17 years ago by Michael Banck <[email protected]>
Further to 1821894 this patch implements vincefn's suggestion

i.e. "whenever reading a data name (tag),replace all '.' by '_'"
and rolls back the previous changes

github.com/openbabel/openbabel - 1f6396703b83ca4379620b0170cb97bf309f30bb authored about 17 years ago by Kevin Shepherd <[email protected]>
Fixed a few typos.

github.com/openbabel/openbabel - ef2780bcdd353a0efb34fc3d9d8cdab6bf3eb781 authored about 17 years ago by Geoffrey Hutchison <[email protected]>
* configure, Makefile.in, */Makefile.in: Rebuild with current

autoconf, libtool, etc.

github.com/openbabel/openbabel - 3203da465829206e6a6426066efa6fb5638d8355 authored about 17 years ago by Geoffrey Hutchison <[email protected]>
* src/forcefields/forcefielduff.*: First pass at a UFF

implementation. It compiles, but that's about it for now.

* data/UFF.prm: Initia...

github.com/openbabel/openbabel - efd2c66b51b598183d749a3d59d3dafe6ef0c0fd authored about 17 years ago by Geoffrey Hutchison <[email protected]>
* include/openbabel/rotamer.h, src/rotamer.cpp

(SetCurrentCoordinates): New method to set the current coordinate
set, rather tha...

github.com/openbabel/openbabel - cd613e2b4609920bff7f1e21bbd5409817f5e595 authored about 17 years ago by Geoffrey Hutchison <[email protected]>
* include/openbabel/residue.h, src/residue.cpp: Switch residue

numbers to be strings internally. Added GetNumString() to return
the number as a ...

github.com/openbabel/openbabel - 566e4ba093b1930bc8bd5af3f989388b02bdf946 authored about 17 years ago by Geoffrey Hutchison <[email protected]>
Fix for Request ID 1821894. This change allows more CIF files

to be understood, allowing the _atom_site.XXXX varient of the naming

github.com/openbabel/openbabel - dfb93952bdf3c90fd720a7d0d67959442afdecd2 authored about 17 years ago by Kevin Shepherd <[email protected]>
Altered the ReadMolecule function to be more flexible

in handling comments and whitespace.
This fixes Request ID 1821003,
and can be tested with Te...

github.com/openbabel/openbabel - 81173b69d66ffdc45682939cf1fac3cdd8486d42 authored about 17 years ago by Kevin Shepherd <[email protected]>
* src/formats/pdbformat.cpp: Fix some issues with multiple-chain

proteins. This is likely a minor fix until David Ogusthorpe
contributes his changes.

github.com/openbabel/openbabel - 07ff0e4acd194b5ef194e61f963216fbc3ace057 authored about 17 years ago by Geoffrey Hutchison <[email protected]>
* data/torlib.[h,txt]: New torsional library data, improving conformer searching.

* tools/obconformer.cpp: New tool to do real conformer searching,
using new rand...

github.com/openbabel/openbabel - 838175924a2fc3d258926e064448628f4b7ce7fc authored about 17 years ago by Geoffrey Hutchison <[email protected]>
Implement exact fastsearch option

github.com/openbabel/openbabel - 56c92b2ebe699e74b01140af01ea3a21ec89246f authored about 17 years ago by Chris Morley <[email protected]>
scripts/Makefile.am: The dl Python module is not present on (many?)

64-bit systems, so it falls back to the DLFCN module which hopefully
*is* present. I would apprec...

github.com/openbabel/openbabel - 5303ff9b9128d1f4d4c7166b0f10c0acec5ac047 authored about 17 years ago by Noel O'Boyle <[email protected]>
Fixed minor bug in previous change to ConjugateGradients -- now properly

implements nonlinear-cg steps.
(Bug: previously did not save the length of moves along the direc...

github.com/openbabel/openbabel - 7cc692f60e14c85038a0c402dcba6a3195b8ba85 authored about 17 years ago by Geoffrey Hutchison <[email protected]>
* include/openbabel/forcefield.h: New LineSearch() method to

update a step over the entire molecule's coordinates at once. Much
faster, since ...

github.com/openbabel/openbabel - 0282737a5728b35f8a8ff80aa60fc5d701764af1 authored about 17 years ago by Geoffrey Hutchison <[email protected]>
Mods to -H option of babel and nbabel

github.com/openbabel/openbabel - 75fdfb29d978e575534f477f29ebffd80e482544 authored about 17 years ago by Chris Morley <[email protected]>
Proper exit when trying to write to readonly format

github.com/openbabel/openbabel - 64de9c75d83b5684868f5d7eb38322497916e4f1 authored about 17 years ago by Chris Morley <[email protected]>
Format change with Fingerprintformat functional-group output

github.com/openbabel/openbabel - 081dd1ffed18d2d91a5a777fd961463e8b974d32 authored about 17 years ago by Chris Morley <[email protected]>
* src/forcefield.cpp, src/forcefields/forcefieldghemical.cpp:

Defensive programming patch contributed by Ross
Braithwaite. Prevents divide by z...

github.com/openbabel/openbabel - b5b16af1ee3af2460ceea531a27667f111db940c authored about 17 years ago by Geoffrey Hutchison <[email protected]>
MDLformats remove erroneous warning and ignore empty alias blocks. Small changes in text formating in fptformat

github.com/openbabel/openbabel - ed8626ded48e1ad8890114da7d665f823ac53ff8 authored about 17 years ago by Chris Morley <[email protected]>
Fix bug in cmlformat

github.com/openbabel/openbabel - d17a4eb5734cb3e69e780a1d4103e7025b5fa03e authored over 17 years ago by Chris Morley <[email protected]>
Merged force field fix from r2066 on 2.1 branch.

github.com/openbabel/openbabel - 206171cf62fc5fa10b385b115d32e9419c637cb9 authored over 17 years ago by Geoffrey Hutchison <[email protected]>
Add M CHG statement to MDL format

github.com/openbabel/openbabel - 002f1e550e1a4320ffae0c4603149239b15c775b authored over 17 years ago by Chris Morley <[email protected]>
Smiles parser bug, extend getinchi

github.com/openbabel/openbabel - b5876ace20a8a022a288fe96fa74e8a2cb611e6d authored over 17 years ago by Chris Morley <[email protected]>
2007-10-03 Jean Brefort <[email protected]>

* include/openbabel/groupcontrib.h: removed undefined OBDESC.
* include/openbabel/op.h: remove...

github.com/openbabel/openbabel - 255aaadaffb08eb4bfa30059ccf901bbcddd15c5 authored over 17 years ago by Jean Brefort <[email protected]>
2007-10-03 Jean Brefort <[email protected]>

* include/openbabel/forcefield.h: fixed typos.

github.com/openbabel/openbabel - 1d7fd957d1737827989eedf49d2fdd9fd45a0d89 authored over 17 years ago by Jean Brefort <[email protected]>
Add build for Windows multiple DLLs. Corrected InChIKey code.

github.com/openbabel/openbabel - 8d630cd833f09a94683b2a216ae3ae9f3d02396e authored over 17 years ago by Chris Morley <[email protected]>
2007-09-02 Jean Brefort <[email protected]>

* src/formats/chemdrawcdx.cpp: fixed bond order for triple and
aromatic bonds.

github.com/openbabel/openbabel - ab15bbbd7e5933e1dd2a73d285f1143ffc4de6da authored over 17 years ago by Jean Brefort <[email protected]>
Fix OBMol::GetTotalSpinMultiplicity bug

github.com/openbabel/openbabel - d77ececaaa50b1c9c836b6f31bcc2fe1221c279c authored over 17 years ago by Chris Morley <[email protected]>
* src/mol.cpp (Separate): More defensive programming to prevent

crashing with incomplete OBChiralData.

* src/formats/cansmilesformat.cpp: Add support for ne...

github.com/openbabel/openbabel - be8a570e1a0f3c5825638e2fcc31a2e5922d6f54 authored over 17 years ago by Geoffrey Hutchison <[email protected]>
Branch revison r2049.

github.com/openbabel/openbabel - e8f271229fe36faf79e35a36f551dff403529ff0 authored over 17 years ago by Geoffrey Hutchison <[email protected]>
Branch revision 2048.

github.com/openbabel/openbabel - 89f11e892db1b2ada38cc01b0b70a3538d475431 authored over 17 years ago by Geoffrey Hutchison <[email protected]>
Trunk version of r2046 -- small force field improvements.

github.com/openbabel/openbabel - d292474c34636e07d409706e45d0eb48d6deac81 authored over 17 years ago by Geoffrey Hutchison <[email protected]>
InChI 1.02 beta Windows files and InChIKey added

github.com/openbabel/openbabel - ee7233528f6b3d7889f28175f23c1b9bbef21164 authored over 17 years ago by Chris Morley <[email protected]>
Update Windows build files

github.com/openbabel/openbabel - e59d8e56c36e22a3cab166fe6e49f3ae1b3c24ae authored over 17 years ago by Chris Morley <[email protected]>
Correct bug in rxnformat.cpp and add write capability to PNGFormat

github.com/openbabel/openbabel - 0c5313450ab49f2d07e248ac2ca18b9bdb0d6fc6 authored over 17 years ago by Chris Morley <[email protected]>
* Merged in changes from 2.1.x branch.

github.com/openbabel/openbabel - 858f8a39f9ec6b9a71ba0e4edc36b9f38a386949 authored over 17 years ago by Geoffrey Hutchison <[email protected]>
Fix bugs in freefracformat OBMol::Separate and Chemkinformat

github.com/openbabel/openbabel - 3cc4e8cee5613d8cc3a0e6673910dd217eb5a241 authored over 17 years ago by Chris Morley <[email protected]>
2007-09-02 Jean Brefort <[email protected]>

* src/fingerprints/finger3.cpp: fixed compilation with g++.

github.com/openbabel/openbabel - 9b841203ace24fef7a896ce852bbe7a4a5a228e9 authored over 17 years ago by Jean Brefort <[email protected]>
forgot to commit this one...

github.com/openbabel/openbabel - 52f46bfb549154169d7cee0b1473509ae46dad13 authored over 17 years ago by Jean Brefort <[email protected]>
2007-09-02 Jean Brefort <[email protected]>

* configure.in: applied patch from Klaus Heinz fixes #1786288.

github.com/openbabel/openbabel - a5ed44ba7f44950eed71ffd2d86d1873d87fa531 authored over 17 years ago by Jean Brefort <[email protected]>
Add description of functional groups to fingerprintformat and tidy up fingerprints FP3 and FP4

github.com/openbabel/openbabel - ed0bee278b7f8ac3d12e984f16890ac575ef14c6 authored over 17 years ago by Chris Morley <[email protected]>
2007-08-27 Jean Brefort <jean@acer>

* include/openbabel/generic.h: make OBUnitCell use SpaceGroup.
* include/openbabel/math/Makefi...

github.com/openbabel/openbabel - b072abea4fda3d3c05496f5dcdfb47bfc2635c1e authored over 17 years ago by Jean Brefort <[email protected]>
2007-08-20 Jean Brefort <[email protected]>

* src/formats/xml/Makefile.am: removed obsolete cmlreactlformat stuff.
* src/obconversion.cpp:...

github.com/openbabel/openbabel - ff6611c21841623a3055ff50508fbd0eb8531547 authored over 17 years ago by Jean Brefort <[email protected]>
Add chemical kinetics formats

github.com/openbabel/openbabel - 2a4ce5bc510a2d41b369e58c64fcc43e62dfde13 authored over 17 years ago by Chris Morley <[email protected]>
Format for chemical data embedded in PNG files

github.com/openbabel/openbabel - 4ca6cdfec8b77c9eb32b56ad73bb4b761ca53fbb authored over 17 years ago by Chris Morley <[email protected]>
Format for chemical data embedded in PNG files

github.com/openbabel/openbabel - 6c58547dac3e0c0b48733dc3d4ff640a0ee08ab7 authored over 17 years ago by Chris Morley <[email protected]>
Rationalize Windows build macros, etc

github.com/openbabel/openbabel - 8967f4507bc3295efd5d76d988e55cc47f35893f authored over 17 years ago by Chris Morley <[email protected]>
2007-08-18 Jean Brefort <[email protected]>

* data/Makefile.am: add space groups descriptions.
* data/space-groups.txt: ditto.
* data/spa...

github.com/openbabel/openbabel - 0e41aa0d9ed4985eeffb596af7a0097ce6792236 authored over 17 years ago by Jean Brefort <[email protected]>
2007-08-13 Jean Brefort <[email protected]>

* include/openbabel/obconversion.h:b removed extra
OBConversion:: which made compilation fail.

github.com/openbabel/openbabel - 83d4a5e13c44c960e50a896a1ecf00ad96bcdaa4 authored over 17 years ago by Jean Brefort <[email protected]>
Additional functions for OBConversion

github.com/openbabel/openbabel - 2fb44d2985156e25a2bcf6ec3f1d729730f41b98 authored over 17 years ago by Chris Morley <[email protected]>
COLLECTION block in V3000 now benignly ignored with warning.

github.com/openbabel/openbabel - 2a352a8ec7b588f9bf6e285438ef7fda9402feb8 authored over 17 years ago by Chris Morley <[email protected]>
Added interface with Boost Graph Library from Gerde Menche

github.com/openbabel/openbabel - 04e3ccc5705d0556de3f7689d2c2cf2d016c41a2 authored over 17 years ago by Chris Morley <[email protected]>
2007-08-03 Jean Brefort <[email protected]>

* include/openbabel/format.h: Format::FormatsMIMEMap() must
return a reference, otherwise, a n...

github.com/openbabel/openbabel - 05667ea5958cd07fc73409bb4adb64e75ec285b6 authored over 17 years ago by Jean Brefort <[email protected]>
Added more tests to prevent ill-formed lines in M RAD, CHG and ISO lines from causing a crash. Deficiency pointed out by Andrew Dalke.

github.com/openbabel/openbabel - a5784601abf0766d2be8ec0e3a610cf084cdb57b authored over 17 years ago by Chris Morley <[email protected]>