openbabel commits | Ecosyste.ms: OpenCollective

* include/openbabel/forcefield.h: Add virtual destructors to

OBFFCalculation2-4.

github.com/openbabel/openbabel - 60edac274540b25b05158d8dede1e0d92963f8c0 authored over 16 years ago

Fixed so that TIME_WITH_SYS_TIME is defined.

github.com/openbabel/openbabel - 48f100d57aad975edb7d415b9c315dbcd11ec19f authored over 16 years ago

* include/openbabel/forcefield.h, src/forcefields/forcefieldghemical.*,

src/forcefields/forcefielduff.*,src/forcefields/forcefieldmmff94.*:
OBFFCalculati...

github.com/openbabel/openbabel - 276083a6e108fd0f445cc7d60b47b4a3a5d690cd authored over 16 years ago

* scripts/openbabel-python.i: Add OBBitVec.

github.com/openbabel/openbabel - 844b134f09d437d7e0d45a307ddbe544c8a6a0ee authored over 16 years ago

Fixed include directory order.

github.com/openbabel/openbabel - e10829bc173892bd026a471f005d8694b85beb9a authored over 16 years ago

* data/atomtyp.*: Added amidine/guanidine IMPVAL rule (thanks to Steve

Constable for reporting & fixing the bug).

github.com/openbabel/openbabel - 3923701da64f104787e6adbc3dbdf8e6f887fa03 authored over 16 years ago

Updates in order to build after obmolecformat.cpp was moved.

github.com/openbabel/openbabel - ebaf052855d092f50f732a413bb7ec7e8d831d58 authored over 16 years ago

* autogen.sh, autoconf/: Add macros to work with new libtool 2.2.2.

* configure.in, configure, aclocal.m4: */Makefile.in: Use above.

github.com/openbabel/openbabel - 898b1b381ae4a94e91819765f037c721c69e2024 authored over 16 years ago

* autogen.sh, autoconf/: Add macros to work with new libtool 2.2.2.

* configure.in, configure, aclocal.m4: */Makefile.in: Use above.

github.com/openbabel/openbabel - 0e92a78f471a15569ba497c072ac585a6d2e3620 authored over 16 years ago

* src/obmolecformat.cpp: Move from src/formats to facilitate

external programs creating OBMolecFormat subclasses.

github.com/openbabel/openbabel - 5a1795b7814b571673d439a416f7c689165a3c02 authored over 16 years ago

* src/formats/opendxformat.cpp: New format for OpenDX grids from

APBS.

github.com/openbabel/openbabel - a01cbf111cb20c16e1f39df75ed7bcb6f3d260fd authored over 16 years ago

* include/openbabel/mol.h: Add units to documentation for

GetTorsion/SetTorsion.

* tools/obrotate.cpp: Total review of the code. Thanks to...

github.com/openbabel/openbabel - fdbc1b809792b7589d93a5eeab57d2d534384c09 authored over 16 years ago

Added autogen.sh to regenerate the automake/autoconf build system.

Should solve Noel's libtool problem.

github.com/openbabel/openbabel - a15c48542f318f0ef00e487752a6beff16f83f1d authored over 16 years ago

* src/mol.cpp: Added UnsetSSSRPerceived to all OBMol::Delete*()

functions. (not DeleteConformer(int i), doesn't change rings... )

github.com/openbabel/openbabel - 4423797b4d55ad3b54c560bc8ec714560b496068 authored over 16 years ago

* scripts/python/examples/*.py: Added some force field examples. More

will follow.

github.com/openbabel/openbabel - 206459784ebfa75282e1394131813e7f7a4c50b6 authored over 16 years ago

* include/openbabel/bond.h: Add some defensive checks to

OBBond::GetBeginAtomIdx, OBBond::GetEndAtomIdx and
OBBond::GetNbrAtomIdx. (close...

github.com/openbabel/openbabel - f4f9a4b6c2638fbd000bcffdb45abb80a33147f1 authored over 16 years ago

* scripts/openbabel-python.i: Added OBForceField::SetLogToStdOut() and

OBForceField::SetLogToStdErr() to replace SetLogFile(std::ostream
*pos) in python.

github.com/openbabel/openbabel - 596d57d9b4db966bc8da106a5e3a44afb3bf1ef2 authored over 16 years ago

Moved the obmolecformat.cpp linkage back to where it was - this works on

both Windows and Linux and so seems the better solution.

github.com/openbabel/openbabel - adb18f616627bfedca2a3c55ba4b502d32af377d authored over 16 years ago

* src/forcefield.cpp: Torsion constraints are working now.

github.com/openbabel/openbabel - e40a5b88bd3185a8c1f278e94a7aba35430b7ec5 authored over 16 years ago

Removed trailing white space.

github.com/openbabel/openbabel - cae963806b3bacae3d3c38152085775fcb6f7583 authored over 16 years ago

* src/forcefields/forcefielduff.cpp: Added groups and Ignore.

* src/forcefields/forcefieldghemical.cpp: Added groups and Ignore.

* src/forcef...

github.com/openbabel/openbabel - 5048db2e457a12a2a63362e55d25d54b16e17334 authored over 16 years ago

Prevent molecules from computational chemistry formats being given implicit hydrogen

github.com/openbabel/openbabel - c97b7ef7affc0e095274e21dac890b051b985b0e authored over 16 years ago

Updated a parameter value in mr.txt.

github.com/openbabel/openbabel - 9814cdb6301b07516194e656fff2e68f8f992a49 authored almost 17 years ago

Add hydrogens before calculating logP etc.

github.com/openbabel/openbabel - da7864a5db44d126e1eb75669d8fff709a33cbba authored almost 17 years ago

* src/formats/xml/cmlformat.cpp: change line 1810 from

s = pUnitCell.GetSpaceGroupName(); to
s = pUnitCell->GetSpaceGroupName();

github.com/openbabel/openbabel - 1a21e4888ef2fa76baa9ceb578bb67206f6125ce authored almost 17 years ago

2008-04-22 Jean Brefort <[email protected]>

* src/formats/xml/cmlformat.cpp: import/export crystal symmetry.
* src/math/spacegroup.cpp: fi...

github.com/openbabel/openbabel - 652dffdaebd0a5774b59889700b329e9c490600f authored almost 17 years ago

* include/openbabel/forcefield.h: Documentation update.

* src/forcefield.cpp: Fixed (X, Y, Z, XYZ) atoms are now checked in
SteepestDesc...

github.com/openbabel/openbabel - a6608dfb7a08238735ed9009084ad8eadd3c7e3b authored almost 17 years ago

Moved the Formatpos typedef outside of the class in order to preserve the old

API call.

github.com/openbabel/openbabel - 6fb09669387b3db413bf4796e5dcb6da580d53da authored almost 17 years ago

Reinstate OBConversion::GetNextFormat

github.com/openbabel/openbabel - 27ca38e6db4ac48e7d84aaf58d6ea64a1809c309 authored almost 17 years ago

Now using std::vector to store data internally. Made safer where possible.

github.com/openbabel/openbabel - 784f391b0ba781e753f7f8cca09701f81a1d3dc5 authored almost 17 years ago

Worked on improvements to the cube writing function. It now staggers cubes in

the z correctly and I think I got the rest of it lining up correctly now.

github.com/openbabel/openbabel - e8eea87487b312f3a2090ccaefe3bbbc1b135f47 authored almost 17 years ago

Cleaned up support for large cube files. Large cubes can now be read in, were

causing a segfault previously due to assumption all cube numbers were on one
line. Also actually ...

github.com/openbabel/openbabel - 951d191d2e679722d1c2c089a633e3335d26c5f8 authored almost 17 years ago

* include/openbabel/forcefield.h, src/forcefield.cpp: Added

SetupPointer. Added Framework for specifying groups using OBBitVec for
now until ...

github.com/openbabel/openbabel - 1154eaf6fb0618ec017906ffb50443f87513ba4a authored almost 17 years ago

Updates to the auto* build tools, added HAVE_GCC_VISIBILITY logic and the

defines to use it.

github.com/openbabel/openbabel - f7d83b86d3032864499be9bc9268ce3dcaf04d37 authored almost 17 years ago

For Windows Python build, moving OBPython to OBPythonOBF.

github.com/openbabel/openbabel - ad126f5350c868ff61fd3172547b79d7a315984f authored almost 17 years ago

Build files for tools programs for Windows installer

github.com/openbabel/openbabel - 5a536a831a453ee9cc2b3812931d8320396951f0 authored almost 17 years ago

* ltmain.sh, configure.in, configure, */Makefile.*: Upgrade to

libtool 2.2.x, which offers improved build speed and bug fixes.

github.com/openbabel/openbabel - 2620acb74ce809ea5e311d8d9ae48f33a0dc858f authored almost 17 years ago

* src/formats/gamessukformat.cpp: New format contributed by Jens

Thomas to support the GAMESS-UK variant.

github.com/openbabel/openbabel - 45ad3f95a3d2a5863df76a2807c9101796ed208a authored almost 17 years ago

* src/formats/moldenformat.cpp, src/formats/msmsformat.cpp: Ensure

namespace is properly included.

github.com/openbabel/openbabel - 23111fa2432451f9752b9a87a179e0940dca2069 authored almost 17 years ago

* src/formats/atomrecord.cpp: Fix from Louis Ricard to handle PDB

files from platon. An example has been added to the test
repository.

github.com/openbabel/openbabel - 26d9b4c939812637966642c73e01717acdba7c4f authored almost 17 years ago

Added newlines to the end of these files - fix compiler warnings.

github.com/openbabel/openbabel - e74150f0194cf54e839e41ce789b12c1a8afafd6 authored almost 17 years ago

Added visibility support when using a recent GCC compiler. Various related

fixes to ensure everything compiles and links correctly.

github.com/openbabel/openbabel - 3d8a7123baecf4bed1dc90af669d50899f8d8e84 authored almost 17 years ago

Removed extra qualifier.

github.com/openbabel/openbabel - 239ff33c9bc05d43c29fea1b5755fc6c9cabc208 authored almost 17 years ago

IMPVAL revision for sulphur to fix bug #1938652

github.com/openbabel/openbabel - 18be3dc43f194be8cb5c8cc6a4bbc597cdf015a8 authored almost 17 years ago

* src/forcefields/forcefielduff.cpp: Fix issue with C atoms not

being set for OOP terms. Thanks to Bob Hanson for spotting this.

github.com/openbabel/openbabel - 59a80a98f70ffa636a470438f5cea4671773e44f authored almost 17 years ago

* src/forcefield.cpp: Remove inline declaration on constraints --

prevents Python script bindings from compiling.

github.com/openbabel/openbabel - 9c5a66077bfc18f525f3c48553f1206d8cab84ad authored almost 17 years ago

* src/formats/hinformat.cpp: Read in partial charges. Fixes

PR#1931260.

github.com/openbabel/openbabel - 29ef0b499bd13a9cce9ec3b5c1ae685bdbe240fd authored almost 17 years ago

Update Windows build files

github.com/openbabel/openbabel - b6d0daa7c6518ad8ddfe6e43c5c42c5c9f3ace80 authored almost 17 years ago

Error in my previous commit.

github.com/openbabel/openbabel - 78915a732b2094e1f48cd9afe2bef045c9e87064 authored almost 17 years ago

Minor dependency mod in Windows OBF build.

github.com/openbabel/openbabel - b447f12d05aacfdbaba534264a2152ae5915b3cb authored almost 17 years ago

* include/openbabel/forcefield.h, src/forcefield.cpp: Fix conjugate

gradients. (my previous commit had a bug..)

github.com/openbabel/openbabel - 48833957f97e827f3a80a182367b954d53e83b03 authored almost 17 years ago

Fix for MacOSX to allow compilation of Python bindings against local build tree.

github.com/openbabel/openbabel - e160ab259a8f8c35eae37d9930020ccfc38da24e authored almost 17 years ago

GUI: Click on menu item copies plugin id to clipboard

github.com/openbabel/openbabel - 62de2201ae95fadb3c8857926092bc4626081f29 authored almost 17 years ago

Fixed a typo reported by Patrick Spendrin

github.com/openbabel/openbabel - 66078bdcd17d44dda42a1acf5df8d4910e558e79 authored almost 17 years ago

* src/forcefields/forcefieldghemical.cpp,

src/forcefields/forcefielduff.cpp,
src/forcefields/forcefieldmmff94.cpp: Don't us...

github.com/openbabel/openbabel - 766c85bfa61861f8c78f0152885b883cbf24e2e3 authored almost 17 years ago

* include/openbabel/forcefield.h, src/forcefield.cpp: Implement

methods to handle cut-offs. Added SetLineSearchType().

* src/forcefields/forcefi...

github.com/openbabel/openbabel - 6dda162b6026a1c859735fb91c559df5c2f37221 authored almost 17 years ago

* src/formats/inchiformat.cpp: Add output options

"include fixed hydrogen layer" and "include bonds to metal"
as shortcuts to NIST's InChI functi...

github.com/openbabel/openbabel - 7731ba3ef86cb3d84f84d4de1cb15472e15251b6 authored almost 17 years ago

* data/UFF.prm: Improved N sp, sp2 atom typing, suggested by Bob Hanson.

* src/forcefields/forcefielduff.*: Many bug fixes for angle and
torsion terms, s...

github.com/openbabel/openbabel - d8c212fc3b2345f3375179115a50432817b025b1 authored almost 17 years ago

* configure, configure.in, */Makefile.in: Bump to 2.2.0b5 and

update build files.

github.com/openbabel/openbabel - f7b3f75362f7c467992310acdfe2fe3074f2aa25 authored almost 17 years ago

* test/files/uffresults.txt: Update UFF results for recent bug fixes.

github.com/openbabel/openbabel - 5a012984969dc0f429618c0d0e20037882c049a9 authored almost 17 years ago

* src/forcefield.cpp: Always call SetCoordinates in Setup.

github.com/openbabel/openbabel - 1129b53b5bcec779aced6543cb8fd6060788ddd6 authored almost 17 years ago

* include/openbabel/forcefield.h, src/forcefield.cpp: Working

Newton2NumLineSearch. Used only for SteepestDescent at the moment.

github.com/openbabel/openbabel - ec6f72e61facbbb4eede56a03a435b065ebaa8fe authored almost 17 years ago

Fix bug #1906462. SMARTS pattern containing [H]

github.com/openbabel/openbabel - 0ad8754f25ec5a396ef2bf5a048106f0d1103612 authored almost 17 years ago

* src/forcefields/forcefielduff.cpp: changed anglecalc.zi = ..[0] to

... [5]. This bug was reported by Bob Hanson in mail.

github.com/openbabel/openbabel - aa9b8430cb4d745d5ef5db5ea42650c472525418 authored almost 17 years ago

* src/forcefield.cpp: Fix LineSearch(*,*) to respect fixed atoms.

Don't calculate gradient in NumericalDerivative.

github.com/openbabel/openbabel - a38300df710eed0d4a52edef09cee4cd8b625c74 authored almost 17 years ago

* src/formats/gaussformat.cpp: Fix bug #1924342 by looking for "Multiplicity" as suggested by Richard West

github.com/openbabel/openbabel - 72876328e991d6da7adcce234399f945ed8f46f0 authored almost 17 years ago

2008-03-24 Noel O'Boyle <[email protected]>

* windows-vc2005/OBPython/openbabel.py: Removed from SVN (it is
created using SWIG as part of...

github.com/openbabel/openbabel - ad6a165f0889e8518b4ccc3538afdbf4a958d138 authored almost 17 years ago

2008-03-24 Noel O'Boyle <[email protected]>

* scripts/openbabel-python.i: Added griddata.h

github.com/openbabel/openbabel - b7eeaf4666773afbf3e2ef7f6d5c5d236afeafe5 authored almost 17 years ago

* scripts/python/pybel.py: First attempts at incorporating the recent work by Tim, Geoff and others on geometry optimisation and 3D coordinate generation.

github.com/openbabel/openbabel - 33495778f2304bff5cef68a33e13abe17468af68 authored almost 17 years ago

Revert to version with last test commented out (Changed by mistake)

github.com/openbabel/openbabel - a8b8dbe5464e922d93bc289225724de4874740a1 authored almost 17 years ago

scripts/openbabel-python.i: Fix for bug reported by Florian Nigsch. The Python iterators didn't correctly handle the case where there was nothing to iterate over.

github.com/openbabel/openbabel - 6b982f897384b08e2a8687c9ad8b995e9e1a0bcd authored almost 17 years ago

* include/openbabel/forcefield.h, src/forcefield.cpp: Move GetGrid to OBForceField to implement it for all force fields at once.

* src/forcefields/forcefieldmmff94.*: Remove GetGrid.

* tools/obprobe.cpp: Impl...

github.com/openbabel/openbabel - 74ee5dac2e2995222afc8a8009d326e9dbe747a3 authored almost 17 years ago

Tidy some newer formats; Python Windows OBF build

github.com/openbabel/openbabel - 78b4ca98b3eedf685455a40d0614256020caede3 authored almost 17 years ago

* ChangeLog: update for last commits

github.com/openbabel/openbabel - e1c356ee6f13c1a487a331e312b3c509861a150d authored almost 17 years ago

* src/formats/atomrecord.cpp: Added using namespace std.

github.com/openbabel/openbabel - 359e4e3dfcc34556e47ebdc085cf786e5bef2f2a authored almost 17 years ago

Changes as discused in mails with Bob Hansen

github.com/openbabel/openbabel - 09d65e8fb5ffda0e6c41d0e30a42cd6f0371ffd2 authored almost 17 years ago

Add obprobe tool.

github.com/openbabel/openbabel - d381ef6ce66170312455cbf77df3b9a00aeadffb authored almost 17 years ago

Add GetGrid probe method.

github.com/openbabel/openbabel - 0dc80b7edcf1033a04658fceef67b012adc3980f authored almost 17 years ago

2008-03-22 Noel O'Boyle <[email protected]>

* src/formats/xml/Makefile.am: CML format can now be built without
shared_ptr, so I removed t...

github.com/openbabel/openbabel - 674bd0a1c6f02eb6b23214c888d2f22e91e97c4d authored almost 17 years ago

* src/formats/gausscubeformat.cpp: Applied patch from Louis Ricard and

make it work. Read function is done, write still needs to be done.

github.com/openbabel/openbabel - 6df90534b4b8d85faec947a80c53e0fecb1cddca authored almost 17 years ago

Parse fragments.txt in OBBuilder only once

github.com/openbabel/openbabel - 6c8b48d5b71fa4a995bfac58be2c2dfc13fe589e authored almost 17 years ago

* src/formats/atomrecord.cpp: New file to handle PDB-style atom

records -- shared between PDB and PQR formats.

* src/formats/pdbformat.cpp: Use ...

github.com/openbabel/openbabel - ebea7a153d5d71729483785c39abe78d724ec8c9 authored almost 17 years ago

* src/formats/cansmilesformat.cpp: Fix for bug exposed by Avogadro

-- sometimes we only have one atom (and no canonical order data).

github.com/openbabel/openbabel - 61a46f05435d03af3833368b8b8f5c73962fe38d authored almost 17 years ago

* tools/obfragment.cpp: Update to generate new OBBuilder database.

github.com/openbabel/openbabel - 799a9fad12984f7520ba504b3a051c4f4ed76dcd authored almost 17 years ago

* src/formats/smilesformat.cpp: Fixes from Craig James. Allow ring closure

bonds in SMILES to be aromatic. Also check for ring closures in
ParseComplex.

...

github.com/openbabel/openbabel - b7facef1858d4464a7b752ead35dda622af36585 authored almost 17 years ago

Require CMake 2.4.5, adding the line which tells CMake our .txt files are in cmake/modules. As we don't have those files yet I added a comment.

github.com/openbabel/openbabel - e02f14743b944ec622874422c4764d69dbfb90a8 authored almost 17 years ago

38 typo fixes

github.com/openbabel/openbabel - be7eb73da6770dd29954edb1ffd182464874306e authored almost 17 years ago

These two lines are definetly wrong. Fixed (Typo and missing $)

github.com/openbabel/openbabel - 79cb47cca3d535da0d9d66b12b40f728cfa82ef7 authored almost 17 years ago

Setting SVN property svn:eol to native for all .cpp and .h files

github.com/openbabel/openbabel - 9b2759f744cd9d7742f69961faa2c40c7d71f05c authored almost 17 years ago

ChangeLog with recent changes.

github.com/openbabel/openbabel - ad86c0adba866506d8579c68feb620ac83c28930 authored almost 17 years ago

* src/ops.cpp, src/forcefield.cpp, src/ops/loader.cpp,

src/ops/optransform.cpp, src/descriptors/cmpdfilter.cpp,
src/descriptors/smartsde...

github.com/openbabel/openbabel - aecb5a192bce2ddfefd72121585544f478d84109 authored almost 17 years ago

* src/CMakeLists.txt: Add ops and descriptors subdirectories.

github.com/openbabel/openbabel - 946df0c35cc5660c4a36681c3c55d2f52c1859e2 authored almost 17 years ago

* include/openbabel/math/matrix3x3.h,

include/openbabel/forcefield.h: Move to loop form. Compiler
loop unrolling is eff...

github.com/openbabel/openbabel - 7a488137ffc36622269ab5d5c3205724345f4067 authored almost 17 years ago

* include/openbabel/builder.h, src/builder.cpp: More robust way to

determine OBBitVec fragment masks. This is now handled internally and
actually c...

github.com/openbabel/openbabel - 7f6ade1ae0070493848531cd7f0889492f4402c5 authored almost 17 years ago

* src/CMakeLists.txt: Remove groupcontrib.cpp, added some new files.

Not sure if the ops/ dir is included.

* data/CMakeLists.txt: Update data files t...

github.com/openbabel/openbabel - 581d17af0e2da8ee3c8a3bb82b40dfefc9a34a82 authored almost 17 years ago

* include/openbabel/builder.h, src/builder.cpp: Moved some

functionality from Build to Connect(). OBBuilder now constructs
molecules with a ...

github.com/openbabel/openbabel - 3b61304b7aafcbc03df9b9fa7cd64057d1b5865e authored almost 17 years ago

Replacement for strcasestr, allow cmlformat to be compiled without shared_ptr, etc

github.com/openbabel/openbabel - d75ea041e1a07e7b79480373e9a76c8823a6ef58 authored almost 17 years ago

* tools/obgen.cpp: Update to add hydrogens, cleanup geometry,

perform weighted rotor search, etc. Should produce decent 3D
structures with MMFF94.

github.com/openbabel/openbabel - c0126d8c6421133f1c960ca4f077d7814346ded3 authored almost 17 years ago

Fix bug introduced in last commit and potential crash with NULL SMARTS patterns.

(Defensive programming.)

github.com/openbabel/openbabel - bf5ed08393c64f98afecccf3d2de5517422ab23b authored almost 17 years ago

* src/builder.cpp: Support new fragment.txt format with comments,

etc.

github.com/openbabel/openbabel - fb82ed3fc6eafc9084a8e75eb56fb748a0a527d1 authored almost 17 years ago