Ecosyste.ms: OpenCollective
An open API service for software projects hosted on Open Collective.
github.com/openbabel/openbabel
Open Babel is a chemical toolbox designed to speak the many languages of chemical data.
https://github.com/openbabel/openbabel
This helps match some files which do not provide full HM notation
or fall back to symmetry match...
Enable static building with eigen3
dca2d6e7169d05f5fa3b7130f6a2c9ff5aca42eb authored about 10 years agoFix typo in mol.h
5f297f0c04ee2408c83ac4a7bf6a4c5488902921 authored about 10 years agobb83d8f08ed8f34faa90aa709deb58fe970bb17c authored about 10 years ago
also, reduce warnings for static builds
d1b539dc388ce41de6730b03f7952c21a08aadc9 authored about 10 years agobccf9bd9ec577857f86d0bcdfde99dce62dcc569 authored about 10 years ago
154496be5bbbc5ebe708590275c8d717e6c68eb6 authored about 10 years ago
80f1ab01ebccdbee9e58f00291e659a677e164ac authored about 10 years ago
ee075fb60a41cfbcec71303768505a52a1380ef1 authored about 10 years ago
aoforce files are generated from vibrational analyses with TurboMole.
8229715380f4593c5785a53af02dc4b890df8b60 authored about 10 years agoAdd new ops plug-in changecell: add/change cell during conversion
437feceb9788f3b58b73866938d71ed97418dd4b authored about 10 years agoDL_POLY format plugin will read cell information now.
83448f2efb6cb50b37396b8976a842d712ad7bb5 authored about 10 years agoSupport for MDFF format added: http://code.google.com/p/mdff/
6405f36c1be34f55a85564bdf2e7d279d4d52de4 authored about 10 years agoFix normal mode parsing in molden format
ed54c714cc46b103df7a049896fb6ab7955a660d authored about 10 years ago
This fixes a bug in the parsing of the normal modes in the Molden format
where the parser would ...
6ecf044095a1746eaf155cdf33db9ef0cdf8ea93 authored about 10 years ago
2ed0aded3528a181011a3fb8427ba8437ec1191e authored about 10 years ago
29a67f54ab15e50c18e6a61b07c0ff0c7997a073 authored about 10 years ago
Compute vibration intensities for VASP format
7d2386013cfa0f788b9c521e9ea0bfb5c669e962 authored over 10 years ago54ee261a2d1ab9f6ed0ed13a4143a082dd5da544 authored over 10 years ago
setup.py now 2/3 compatible
301267f07a0c2e041b0e636bcf42535d77ab2cf0 authored over 10 years agoUse averaged bond order corrections from Pyykko and Atsumi 2009.
c494feea451836f5366aaa6f47123b0aa7079f92 authored over 10 years agoAdd a threshold to single fragment scaling
39e7a77ec48c7e5693243c525c9403cd057d0c68 authored over 10 years agoParse HND1 etc atoms in DUD-E
603596fccc8966e10b925d7be88859c8f7557105 authored over 10 years agoFix a performance problem with parsing PDB files that have overlapping
7122a0e8a93eefc5f0ddfb7e9f4e1eacd503be8b authored over 10 years agofragments in them. Since the fragments overlap, ConnectTheDots adds a
ton of bonds, most of whic...
fragments in them. Since the fragments overlap, ConnectTheDots adds a
ton of bonds, most of whic...
Dock 3.7 receptor files contain HND1 etc atoms, parse them correctly.
4e69f6d27b1453324cff4096e310ad5c0bcd6032 authored over 10 years ago
The vibration intensities are not explicitely present in VASP output but
can be computed from th...
STL-like iterator protocol for vector3
4fb2f98cc0c50d03d5a9e188edd46207e0d64f74 authored over 10 years agoAdd CO2H to superatom.txt
7e7397f5a0642be228d5b199bd99f31c7974ad16 authored over 10 years agoI note that CO2H is in osra, just in spelling.txt instead of superatom
2b7f5c0c0d93d9c42da36e7ef4742bf7f797e7ec authored over 10 years ago
Providing iterator and const_iterator typedefs as well as begin() and
end() methods allow using ...
Fix normal mode parsing in Gaussian format
c4a00bd46e4776f5c7cc0c0bdf5e7304e4d4fbc8 authored over 10 years agoIdentify frequencies with header
8d62b1c5941e0c4d0e9a77b1faa7240fcd865172 authored over 10 years ago
In the VASP format, frequency parsing was done until tokenization
returned less than two element...
This fixes a bug in the parsing of normal modes in the Gaussian format
where values in a single ...
4a7966cc85419a4a88f703afba69e923ab75f8ac authored over 10 years ago
2103c1458df48c2bf95e697b33b822d924598971 authored over 10 years ago
c2accb0ee8a547fbc95be427d00ce271a4d6c08c authored over 10 years ago
Define bit 44 in MACCS.txt
da8f2d6db1ae55fa5eaecb0a87409728721462d7 authored over 10 years agoAs suggested by Andrew Dalke [http://www.dalkescientific.com/writings/diary/archive/2014/10/17/m...
de0d2921119af2ec6528c383cdd0efa4581c322a authored over 10 years agoCIFFormat::ReadMolecule now defaults to mmCIFFormat::ReadMolecule
3d8a39b9e5e818b52de304c64fce61538567ba53 authored over 10 years ago1014d1858d3c0ef820b7afaf50595dd2202b03fb authored over 10 years ago
b59917385a8655b68a01201ae7858f1788d402fd authored over 10 years ago
2fbcb7c32cdabd673f2960bb5566096090b2a0f1 authored over 10 years ago
3cb4126637abddbb0712195dfe7fabd1909d672f authored over 10 years ago
cefe0d3b513c41b2e468ea565c65be34767cc8b6 authored over 10 years ago
Round 2: Updated IPython rendering
461e493f573123c9e619109c3584275da45efece authored over 10 years agommCIF reading now saves atom labels (like CIF reading)
f3e250ecf2e4d416fb3447e54af4369accf82ba8 authored over 10 years agoorcaformat reads now also the UVvis and CD spectra
25f4d4955e5585193d804692a9079a45626f4d28 authored over 10 years agoAdded SVG output option for all atoms explicitly declared
d0e4f20dccbf473c615100261be30662b757de49 authored over 10 years agoba397aa5a01cd3753072fadf9535d0092dfcf784 authored over 10 years ago
22b46776ba0228020abf8d988846f3f5b2082240 authored over 10 years ago
a8ff003d8ccf581050efc87a8307aef37c3ee0f3 authored over 10 years ago
XTCFormat::ReadMolecule() used to pass a pointer to the storage of a local
std::vector to OBMol:...
7fa5c42e31904858d5dab696b4cc47f7015ea046 authored over 10 years ago
b83813a9087c360be26585a41c85b0bff25ab81a authored over 10 years ago
Improved mmCIF reading
b20567f740d50ee46f29e290f983d885886b3af6 authored over 10 years agoe04b26e381072e2346264695f49713870ab958f6 authored over 10 years ago
d15e5572d1db1e28f4f17dc736d9e60609f6929d authored over 10 years ago
ac023d0a1d95e3bae291c7bef1e3590bd4f3d5fd authored over 10 years ago
Improve compilation on Visual Studio 2013
92ab8c8a656f39b0f525bc3a54f4aed4da1ee540 authored over 10 years agocf73bf3dacdd5727f67ad18bdf02561795d8c938 authored over 10 years ago
469041139f402fb70bba38a4d817c46549051696 authored over 10 years ago
Change cout to obErrorLog in cifformat
15f5eb8277f22a58138d422bc666560a81dbdbf1 authored over 10 years agoInstead of a specific `v` option for the CIF format to show verbose debug messages, instead use ...
afbc98b17bdf3d8bc8c9662d70721c7e0a5d7766 authored over 10 years agoSet cmake policy CMP0042 to continue old behaviour
9be3d6e7f2c291b574e29707b8aa37359296c676 authored over 10 years agoc792443f1d2cafae7f6d9c8e071e0d5bbaa5df7a authored over 10 years ago
f614f35f34f452800cc069dcc63fabd5ba3dca42 authored over 10 years ago
Slight modifications from previous versions, but likely better
overall, since they're systematic...
Only allow single bonds to ring sulfurs, e.g., methylene-dithioles.
Aromaticity detection will a...
Maximum gradient for convergenece is 0.1. No interface for changing (yet).
Also switch conformer...
Different atoms could be transformed to the same symmetry spot.
The simplest solution seemed to ...
Also add a DABCO template.
060a65d486655af18a1bc238becc5d4a549b7347 authored over 10 years ago
Conformer searches that perform a geometry optimization before
calculating the energy or RMSD to...
e313363614f5a90e6a5a760d021abf773ff799b4 authored over 10 years ago
Allow disordered options for obgen
ad71e96f105be9d8dd5eea7377e8aac7507f9c6d authored over 10 years agoAdded explicit spaces in output lines of MOL2 to avoid field overflowing...
323f78bb764eb360c278fa622e7a442cc5245cf0 authored over 10 years ago4cada8f8c852fc27a17740a866fb6fcfbccdb4c5 authored over 10 years ago
a730ad7d5ab745ed2e413a43a0308e905e1ed356 authored over 10 years ago
ff131bd4efbb7cec20b2ba3f3721584b32db356f authored over 10 years ago
c7bcb870dc09b3b50388153d76b8fd1579abc3f4 authored over 10 years ago
4544600a459748202606d3467f557ab63c156330 authored over 10 years ago
inside an aromatic ring.
06dedd06f64fbb6d50c02581d72f9b3b3935cf3f authored over 10 years ago
Make MMFF94 the default force field for everything (about time)
A variety of other minor fixes.
d43bf9af5c19f0f1798eed72b3be46524f265be1 authored almost 11 years ago
Deal properly with multiple molecules with multi-line properties.
4c69150d5b8aa03c89bb6cbecad34adbd610af87 authored almost 11 years ago
per discussion on the list under "obabel: Converting sdf with multi-line properties" and
suggest...
Suppress cout in CIF format unless verbose option set
d8ec59313e5910a6c49312215ccb11d5dfb2d6c6 authored almost 11 years agoBigfix: Do not include header for DiverseConfGen if Eigen isn't present....
8ee1c2a17a86219b91737f72689fc20add8dc855 authored almost 11 years ago7214568c3eb9a1968a34451899393011e43df4e6 authored almost 11 years ago
Fix use of & instead of && in "if" statement.
b78ff1a9a893ad6e87fd289e0136dfd3f2849048 authored almost 11 years agoe35cba23777e0ec0b22ff08eb4a1bbf149f090c9 authored almost 11 years ago
4a4d219783db6af217761e35b84f5e21bace11e5 authored almost 11 years ago
9493cd49f95d904275030944ee7ec6b099225d88 authored almost 11 years ago
319663e95b9e8cd4fd9e3e4aa7e3f6741d8560ac authored almost 11 years ago
new formats - orca output files and extended xyz files
3f0e45f6b0014db928ac354a95d19ca053b4233b authored almost 11 years agoFirst import of exyz file format (extended xyz format)
a9c186e8b180effc4f785b2d0e8067e6a564c53f authored almost 11 years ago5f083787cfc36a4f208f376693232fc6d6e33ef7 authored almost 11 years ago