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github.com/openbabel/openbabel

Open Babel is a chemical toolbox designed to speak the many languages of chemical data.
https://github.com/openbabel/openbabel

Add HM short name to space groups

This helps match some files which do not provide full HM notation
or fall back to symmetry match...

c7c20b0025375696194a6ddb26b627708fb360af authored about 10 years ago
Merge pull request #114 from dkoes/upstream

Enable static building with eigen3

dca2d6e7169d05f5fa3b7130f6a2c9ff5aca42eb authored about 10 years ago
Merge pull request #115 from mohebifar/patch-1

Fix typo in mol.h

5f297f0c04ee2408c83ac4a7bf6a4c5488902921 authored about 10 years ago
Update mol.h

bb83d8f08ed8f34faa90aa709deb58fe970bb17c authored about 10 years ago
partially undo commit that broke bound order detection

also, reduce warnings for static builds

d1b539dc388ce41de6730b03f7952c21a08aadc9 authored about 10 years ago
Enable static building with eigen3

bccf9bd9ec577857f86d0bcdfde99dce62dcc569 authored about 10 years ago
Enable static building with eigen3

154496be5bbbc5ebe708590275c8d717e6c68eb6 authored about 10 years ago
Merge remote-tracking branch 'upstream/master'

80f1ab01ebccdbee9e58f00291e659a677e164ac authored about 10 years ago
Merge branch 'master' of github.com:dkoes/openbabel

ee075fb60a41cfbcec71303768505a52a1380ef1 authored about 10 years ago
aoforce format

aoforce files are generated from vibrational analyses with TurboMole.

8229715380f4593c5785a53af02dc4b890df8b60 authored about 10 years ago
Merge pull request #108 from orex/changecell_commit

Add new ops plug-in changecell: add/change cell during conversion

437feceb9788f3b58b73866938d71ed97418dd4b authored about 10 years ago
Merge pull request #110 from orex/bugfix_dlp

DL_POLY format plugin will read cell information now.

83448f2efb6cb50b37396b8976a842d712ad7bb5 authored about 10 years ago
Merge pull request #109 from orex/mdff_pullreq

Support for MDFF format added: http://code.google.com/p/mdff/

6405f36c1be34f55a85564bdf2e7d279d4d52de4 authored about 10 years ago
Merge pull request #111 from Synss/fix-molden

Fix normal mode parsing in molden format

ed54c714cc46b103df7a049896fb6ab7955a660d authored about 10 years ago
Fix normal mode parsing in molden format

This fixes a bug in the parsing of the normal modes in the Molden format
where the parser would ...

3fa6c7d6c1cb81f7c922820b03ad3e2228636d03 authored about 10 years ago
DL_POLY format plugin will read cell information now.

6ecf044095a1746eaf155cdf33db9ef0cdf8ea93 authored about 10 years ago
Support for MDFF format added: http://code.google.com/p/mdff/

2ed0aded3528a181011a3fb8427ba8437ec1191e authored about 10 years ago
Changecell separated to commit branch.

29a67f54ab15e50c18e6a61b07c0ff0c7997a073 authored about 10 years ago
Merge pull request #104 from Synss/vasp-intensities

Compute vibration intensities for VASP format

7d2386013cfa0f788b9c521e9ea0bfb5c669e962 authored over 10 years ago
remove asserts

54ee261a2d1ab9f6ed0ed13a4143a082dd5da544 authored over 10 years ago
Merge pull request #99 from patrickfuller/pip

setup.py now 2/3 compatible

301267f07a0c2e041b0e636bcf42535d77ab2cf0 authored over 10 years ago
Merge pull request #84 from ghutchis/ENH-builder-covalent-bo-radii

Use averaged bond order corrections from Pyykko and Atsumi 2009.

c494feea451836f5366aaa6f47123b0aa7079f92 authored over 10 years ago
Merge pull request #94 from leeping/master

Add a threshold to single fragment scaling

39e7a77ec48c7e5693243c525c9403cd057d0c68 authored over 10 years ago
Merge pull request #97 from mwojcikowski/master

Parse HND1 etc atoms in DUD-E

603596fccc8966e10b925d7be88859c8f7557105 authored over 10 years ago
Merge pull request #106 from dkoes/upstream

Fix a performance problem with parsing PDB files that have overlapping

7122a0e8a93eefc5f0ddfb7e9f4e1eacd503be8b authored over 10 years ago
Fix a performance problem with parsing PDB files that have overlapping

fragments in them. Since the fragments overlap, ConnectTheDots adds a
ton of bonds, most of whic...

9029d7b86da77c188cd7688f6ac940addaea63a9 authored over 10 years ago
Fix a performance problem with parsing PDB files that have overlapping

fragments in them. Since the fragments overlap, ConnectTheDots adds a
ton of bonds, most of whic...

3a07c2b37261acdb529783306724a60a37e14580 authored over 10 years ago
Parse HND1 etc atoms in DUD-E

Dock 3.7 receptor files contain HND1 etc atoms, parse them correctly.

4e69f6d27b1453324cff4096e310ad5c0bcd6032 authored over 10 years ago
Compute vibration intensities for VASP format

The vibration intensities are not explicitely present in VASP output but
can be computed from th...

4a1a8e34eef1a2fe652c4d11eb501605fc0e7c4c authored over 10 years ago
Merge pull request #102 from Synss/vector3-iterators

STL-like iterator protocol for vector3

4fb2f98cc0c50d03d5a9e188edd46207e0d64f74 authored over 10 years ago
Merge pull request #103 from cowsandmilk/CO2H

Add CO2H to superatom.txt

7e7397f5a0642be228d5b199bd99f31c7974ad16 authored over 10 years ago
Add CO2H to superatom.txt

I note that CO2H is in osra, just in spelling.txt instead of superatom

2b7f5c0c0d93d9c42da36e7ef4742bf7f797e7ec authored over 10 years ago
STL-like iterator protocol for vector3

Providing iterator and const_iterator typedefs as well as begin() and
end() methods allow using ...

3d948082ec87215aa3659feb4050605e057ccc9b authored over 10 years ago
Merge pull request #100 from Synss/gauss

Fix normal mode parsing in Gaussian format

c4a00bd46e4776f5c7cc0c0bdf5e7304e4d4fbc8 authored over 10 years ago
Merge pull request #101 from Synss/vasp

Identify frequencies with header

8d62b1c5941e0c4d0e9a77b1faa7240fcd865172 authored over 10 years ago
Identify frequencies with header

In the VASP format, frequency parsing was done until tokenization
returned less than two element...

dd27be434d336c516b21242401c7e42a5ee75204 authored over 10 years ago
Fix normal mode parsing in Gaussian format

This fixes a bug in the parsing of normal modes in the Gaussian format
where values in a single ...

9298daf7cc2915d43ab6d3cae557d65a485d0e07 authored over 10 years ago
setup.py now 2/3 compatible

4a7966cc85419a4a88f703afba69e923ab75f8ac authored over 10 years ago
obrms improvements

2103c1458df48c2bf95e697b33b822d924598971 authored over 10 years ago
Merge remote-tracking branch 'upstream/master'

c2accb0ee8a547fbc95be427d00ce271a4d6c08c authored over 10 years ago
Merge pull request #96 from mwojcikowski/patch-1

Define bit 44 in MACCS.txt

da8f2d6db1ae55fa5eaecb0a87409728721462d7 authored over 10 years ago
Define bit 44 in MACCS.txt

As suggested by Andrew Dalke [http://www.dalkescientific.com/writings/diary/archive/2014/10/17/m...

de0d2921119af2ec6528c383cdd0efa4581c322a authored over 10 years ago
Merge pull request #95 from patrickfuller/cif-mmcif

CIFFormat::ReadMolecule now defaults to mmCIFFormat::ReadMolecule

3d8a39b9e5e818b52de304c64fce61538567ba53 authored over 10 years ago
CIFFormat::ReadMolecule now defaults to mmCIFFormat::ReadMolecule

1014d1858d3c0ef820b7afaf50595dd2202b03fb authored over 10 years ago
Updated abs() -> fabs()

b59917385a8655b68a01201ae7858f1788d402fd authored over 10 years ago
Update comment

2fbcb7c32cdabd673f2960bb5566096090b2a0f1 authored over 10 years ago
Merge branch 'master' of github.com:openbabel/openbabel

3cb4126637abddbb0712195dfe7fabd1909d672f authored over 10 years ago
Add a threshold to single fragment scaling

cefe0d3b513c41b2e468ea565c65be34767cc8b6 authored over 10 years ago
Merge pull request #90 from patrickfuller/ipython

Round 2: Updated IPython rendering

461e493f573123c9e619109c3584275da45efece authored over 10 years ago
Merge pull request #89 from patrickfuller/mmcif

mmCIF reading now saves atom labels (like CIF reading)

f3e250ecf2e4d416fb3447e54af4369accf82ba8 authored over 10 years ago
Merge pull request #92 from lenkd/devOpenbabel

orcaformat reads now also the UVvis and CD spectra

25f4d4955e5585193d804692a9079a45626f4d28 authored over 10 years ago
Merge pull request #93 from leeping/master

Added SVG output option for all atoms explicitly declared

d0e4f20dccbf473c615100261be30662b757de49 authored over 10 years ago
Added SVG output option for all atoms explicitly declared

ba397aa5a01cd3753072fadf9535d0092dfcf784 authored over 10 years ago
orcaformat reads now also the UVvis and CD spectra

22b46776ba0228020abf8d988846f3f5b2082240 authored over 10 years ago
IPython 3D view now has a draggable resizer

a8ff003d8ccf581050efc87a8307aef37c3ee0f3 authored over 10 years ago
Fix use-after-free in xtcformat from Tomas Trnka

XTCFormat::ReadMolecule() used to pass a pointer to the storage of a local
std::vector to OBMol:...

f4ff1db06b38fb36b284cf688b22113c41952651 authored over 10 years ago
Updated IPython rendering to use v2.0 style, now works on nbviewer and on local machines

7fa5c42e31904858d5dab696b4cc47f7015ea046 authored over 10 years ago
mmCIF reading now saves atom labels (like cif reading)

b83813a9087c360be26585a41c85b0bff25ab81a authored over 10 years ago
Merge pull request #88 from patrickfuller/mmcif

Improved mmCIF reading

b20567f740d50ee46f29e290f983d885886b3af6 authored over 10 years ago
Fractional coordinate now wraps

e04b26e381072e2346264695f49713870ab958f6 authored over 10 years ago
mmCIF symbol inference from label now ignores label digits

d15e5572d1db1e28f4f17dc736d9e60609f6929d authored over 10 years ago
Improved mmCIF fractional coordinate reading

ac023d0a1d95e3bae291c7bef1e3590bd4f3d5fd authored over 10 years ago
Merge pull request #87 from zmbq/master

Improve compilation on Visual Studio 2013

92ab8c8a656f39b0f525bc3a54f4aed4da1ee540 authored over 10 years ago
Fix for minimal Visual C++ 2013 compilation.

cf73bf3dacdd5727f67ad18bdf02561795d8c938 authored over 10 years ago
Compile with Visual Studio 2013

469041139f402fb70bba38a4d817c46549051696 authored over 10 years ago
Merge pull request #86 from mcs07/cifformat

Change cout to obErrorLog in cifformat

15f5eb8277f22a58138d422bc666560a81dbdbf1 authored over 10 years ago
Change cout to obErrorLog in cifformat

Instead of a specific `v` option for the CIF format to show verbose debug messages, instead use ...

afbc98b17bdf3d8bc8c9662d70721c7e0a5d7766 authored over 10 years ago
Merge pull request #85 from mcs07/CMP0042

Set cmake policy CMP0042 to continue old behaviour

9be3d6e7f2c291b574e29707b8aa37359296c676 authored over 10 years ago
Fix compatibility for old cmake before CMP0042

c792443f1d2cafae7f6d9c8e071e0d5bbaa5df7a authored over 10 years ago
Set cmake policy CMP0042 to continue old behaviour

f614f35f34f452800cc069dcc63fabd5ba3dca42 authored over 10 years ago
Use averaged bond order corrections from Pyykko and Atsumi 2009.

Slight modifications from previous versions, but likely better
overall, since they're systematic...

1c43adb1c12f8a975613b6f52d4c8208209caa08 authored over 10 years ago
Fix bond typing for conjugated sulufurs in rings.

Only allow single bonds to ring sulfurs, e.g., methylene-dithioles.
Aromaticity detection will a...

59d683cd268134830b5d0f1126f5cb62a1bc9167 authored over 10 years ago
Better ensure forcefield convergence by checking maximum gradient.

Maximum gradient for convergenece is 0.1. No interface for changing (yet).
Also switch conformer...

ca45cc9a8db35b10459e138750326d0b25a9c79b authored over 10 years ago
Fix --fillUC wrapping with duplicated atoms.

Different atoms could be transformed to the same symmetry spot.
The simplest solution seemed to ...

809952cd3caa8b5c87fa4b4d925dcbcf59f86d35 authored over 10 years ago
Make sure all SDF templates are installed for use with 2D layout.

Also add a DABCO template.

060a65d486655af18a1bc238becc5d4a549b7347 authored over 10 years ago
Patch from Torsten Sachse to re-enable minimizing rmsd and minenergy.

Conformer searches that perform a geometry optimization before
calculating the energy or RMSD to...

1a8dc0a32f7ed470699084ab858b15c35f5cf7f6 authored over 10 years ago
Merge branch 'master' of github.com:openbabel/openbabel

e313363614f5a90e6a5a760d021abf773ff799b4 authored over 10 years ago
Merge pull request #82 from ktns/obgenoption

Allow disordered options for obgen

ad71e96f105be9d8dd5eea7377e8aac7507f9c6d authored over 10 years ago
Merge pull request #83 from yishutu/master

Added explicit spaces in output lines of MOL2 to avoid field overflowing...

323f78bb764eb360c278fa622e7a442cc5245cf0 authored over 10 years ago
Added explicit spaces in output lines of MOL2 to avoid field overflowing problem.

4cada8f8c852fc27a17740a866fb6fcfbccdb4c5 authored over 10 years ago
don't create a new obrandom everytime a random vector is desired

a730ad7d5ab745ed2e413a43a0308e905e1ed356 authored over 10 years ago
Allow disordered options for obgen

ff131bd4efbb7cec20b2ba3f3721584b32db356f authored over 10 years ago
Merge branch 'master' of github.com:openbabel/openbabel

c7bcb870dc09b3b50388153d76b8fd1579abc3f4 authored over 10 years ago
Darken Pt color for depiction, as suggested by PR#924.

4544600a459748202606d3467f557ab63c156330 authored over 10 years ago
OBDepict: Draw aromatic rings first to ensure all double bonds are

inside an aromatic ring.

06dedd06f64fbb6d50c02581d72f9b3b3935cf3f authored over 10 years ago
Force field updates.

Make MMFF94 the default force field for everything (about time)
A variety of other minor fixes.

521514ae362b12b4899c22dd3f79957efc6a35be authored over 10 years ago
Add template for RN-CN2 guanidine bond typing.

d43bf9af5c19f0f1798eed72b3be46524f265be1 authored almost 11 years ago
Merge pull request #79 from jeffjanes/multiline

Deal properly with multiple molecules with multi-line properties.

4c69150d5b8aa03c89bb6cbecad34adbd610af87 authored almost 11 years ago
Deal properly with multiple molecules with multi-line properties.

per discussion on the list under "obabel: Converting sdf with multi-line properties" and
suggest...

ea7464984067b4c0346b10536425136d1671b0d7 authored almost 11 years ago
Merge pull request #76 from mcs07/cif

Suppress cout in CIF format unless verbose option set

d8ec59313e5910a6c49312215ccb11d5dfb2d6c6 authored almost 11 years ago
Merge pull request #78 from nextmovesoftware/BugFix_EigenDiverseConfGen

Bigfix: Do not include header for DiverseConfGen if Eigen isn't present....

8ee1c2a17a86219b91737f72689fc20add8dc855 authored almost 11 years ago
Bigfix: Do not include header for DiverseConfGen if Eigen isn't present. (As there is no definition present, and this will cause linker errors when linking bindings against the library.)

7214568c3eb9a1968a34451899393011e43df4e6 authored almost 11 years ago
Merge pull request #77 from nextmovesoftware/Bugfix_WrongAND

Fix use of & instead of && in "if" statement.

b78ff1a9a893ad6e87fd289e0136dfd3f2849048 authored almost 11 years ago
Fix use of & instead of && in "if" statement.

e35cba23777e0ec0b22ff08eb4a1bbf149f090c9 authored almost 11 years ago
Suppress cout unless verbose option set

4a4d219783db6af217761e35b84f5e21bace11e5 authored almost 11 years ago
Merge branch 'master' of github.com:openbabel/openbabel

9493cd49f95d904275030944ee7ec6b099225d88 authored almost 11 years ago
Set default force fields to MMFF94.

319663e95b9e8cd4fd9e3e4aa7e3f6741d8560ac authored almost 11 years ago
Merge pull request #75 from lenkd/devOpenbabel

new formats - orca output files and extended xyz files

3f0e45f6b0014db928ac354a95d19ca053b4233b authored almost 11 years ago
First import of orca input/output format files

First import of exyz file format (extended xyz format)

a9c186e8b180effc4f785b2d0e8067e6a564c53f authored almost 11 years ago
Fix pybel test failure by renaming expected output to UNL from LIG

5f083787cfc36a4f208f376693232fc6d6e33ef7 authored almost 11 years ago