github.com/openbabel/openbabel commits | Ecosyste.ms: OpenCollective

PQR_WriteAtomRadius

ab8489fb52f33db18b813a903c4aab7110ad8093 authored over 9 years ago

Charge_Radius_Error

2e9eb2c33e7cb020577f0601c662d047853f3d26 authored over 9 years ago

Merge branch 'pluginfix'

a230e452845568b67e6a1a84d479129e7cfb80b7 authored over 9 years ago

fix for segfaulting similarity search with fastsearch index

option parameters were getting loaded after options were read, resulting in -s not initializing ...

493c7ce46f246a2876f35a3c2a5d6f2dd2bc2a80 authored over 9 years ago

Merge remote-tracking branch 'openbabel/master'

6fec4c4873aef8a17ed2695e6e8146c4c24994a8 authored over 9 years ago

cppcheck: fix reports "Prefer prefix ++/-- operators for non-primitive types"

aa1851bb6f43b7fcf80d6d321f812cf9057fba1b authored over 9 years ago

Fixed the cubic space groups 200-206 and 221-230 to treat 3-bar(-3) as 3

Assigned an equivalent space group for the above families.

445afcb1428c80d98fce5f03fb9a8ae763a170ff authored over 9 years ago

Merge pull request #231 from lenkd/master

small changes to compile on windows with msvc

2d45874928002488b3e9f72b0d489c3062add716 authored over 9 years ago

small changes to compile on windows with cairo and inchi

2c75a0947b355fd2fa2d569249e3a8a9137df504 authored over 9 years ago

small changes in orcaformat to compile with MSVC

f0a8dce3fd7750729a41262d7f3ccf4732769e0a authored over 9 years ago

Fix compiling errors under Windows & Cygwin

a05058b7058ae5c4a6dff1808abfa3755494c0f5 authored over 9 years ago

Mistake fix

c9b9b122ebecf48fcfa8bd52a023ace11318f135 authored over 9 years ago

Fixed compiller warning and some dirty code in multipole moment reader

cb89d92945448b96dd513023a9a538f037d02292 authored over 9 years ago

Merge branch 'master' of https://github.com/openbabel/openbabel.git

ce26e26f32fd536cbf9fa5026bdc95c7e852c6db authored over 9 years ago

Fixed NEB calculation reader

fd88aea33378924456c92d3124aa05fdd4a8618e authored over 9 years ago

Fix another bug in fingerprinting FP2, #224

When we reach an atom which is connected back the first atom in ring,
it was closing the ring us...

00266604639422e64377ef068c34c206cce208d3 authored over 9 years ago

Fix bug in the fingerprint algorithm.

If the atom currently being visited in a path through the atoms can
both close a ring back to th...

09d7f39f96ba9282c9f0625020d117eb89df45a1 authored over 9 years ago

Merge pull request #217 from mcs07/python

Fix swig include_dirs+library_dirs in setup.py

4f26f1bd78672961f612091baa33564786da9510 authored over 9 years ago

Merge pull request #221 from psavery/master

Added basic reading for siesta output (.out) files.

7ee6ef5fe6f8f8d1c3a8950489a3ba9d1ad9538b authored over 9 years ago

Merge pull request #218 from sroughley/master

Fixed bug in ob_make_rmat in /src/obutil.cpp

3fc99f8ca026e08b45849df6a3c69d65d1456b93 authored over 9 years ago

Merge pull request #220 from jnavila/fix_#219

Do not delete molecule in SVGFormat::WriteMolecule

39054b8236da2b757095230dcce5375280025874 authored over 9 years ago

Added basic reading for siesta output (.out) files. It searches for a .STRUCT_OUT file since the output coordinates are usually put there, but it can read the coordinates from a .out file if the coordinates are there as well. Also made a small change to vaspformat.cpp so that 'babel -iPOSCAR <filename> -o<whatever>' will work properly.

aec777dd8c66fc483de24ad2da81ad96ab23cb9d authored over 9 years ago

Do not delete molecule in SVGFormat::WriteMolecule

This patch hopefully fixes #219

2757f61f4349195887bbdc859672f7e498adbe77 authored over 9 years ago

Merge pull request #1 from sroughley/sroughley-patch-1

Update obutil.cpp

2c44a6f42e6113e222859800e9f6f653659fdb52 authored over 9 years ago

Update obutil.cpp

Corrected an error in the ob_make_rmat(double, double) function in which the normalisation of th...

2c30924a4afdd7b47e0f903840deca61293fc830 authored over 9 years ago

Fix swig include_dirs+library_dirs in setup.py

distutils/setuptools now appear to add some default SWIG `include_dirs` and `library_dirs`, so w...

41337524ba2138169edcd50ea6e76e7d71c7336d authored over 9 years ago

Ensure tautomertest is exercised.

Should fix #216

7be9ee2fb614bfc5a2c0ffa97a14f94815ea5382 authored over 9 years ago

Reworked Dipole moment handler to universal multipole handler

Multipole handler parses both charge, dipole and quadrupole moments

77d5f0b3163016375edf4c5dc2e452a6504baf30 authored over 9 years ago

Merge pull request #215 from psavery/master

Added a needed Bohr-to-Angstrom conversion in pwscfformat.cpp

5943f3a38e9c9e567209e0975d0a1db230510a59 authored over 9 years ago

Added a needed Bohr-to-Angstrom conversion in pwscfformat.cpp

7ce66bce042b82f2fcb7474c49e09aac6da36491 authored over 9 years ago

NEB calculation handler implementation. (not tested)

ecc11e2816732d50e60a50008088efe1e5395353 authored over 9 years ago

MEP (IRC) calculation handler implementation

a51a3f907bcb3d4b86a4ee40648d1522ee9cf7de authored over 9 years ago

Merge pull request #213 from xomachine/master

NWChem format parser improvements

89f95f1223dc0a93bb8fa523fa7669fcfeb42f99 authored over 9 years ago

Fix build warning

(warning C4146: unary minus operator applied to unsigned type, result still unsigned)

68f2a29e0ff4b5a9af7f2ce67cd56ab26b22b9c3 authored over 9 years ago

Merge branch 'HEAD' of https://github.com/xomachine/openbabel.git

c55e37df5b500dc82d5292dfa6574f991db62484 authored over 9 years ago

Corrected EndOfFile checks.

7edbb76d91da4950c72b1693a01f6f9f0cdd829f authored over 9 years ago

Corrected EndOfFile checks.

73a66acbfc54477097011283fbc9b628996794c0 authored over 9 years ago

Merge branch 'master' of https://github.com/openbabel/openbabel.git

07bd278fef22246b158e971aff0a8ac77c11e90c authored over 9 years ago

Dipole moment reader implementation.

961ca38ada5b9191b0fa4a66d3366407d370e3c4 authored over 9 years ago

UV Spectra TD-DFT Calculation recognition implemented.

3b7d4bc8a97adb609b7b1f4dd5c01adffed49722 authored over 9 years ago

Orbitals detection reworked.

92168a4b0776288941bd26d30640fe9dd90992c8 authored over 9 years ago

Dead code elimination

4a58f472ccec6e052db23cc07025e326344225d8 authored over 9 years ago

Frequency calculation handler reworked.

Charges and orbital data recognition added.

dddcbb8ec05ee5004fa32035b33ea247c32724ae authored over 9 years ago

Added patterns for esp and python calculations

939f57d7e2b902c791bef53a5af2d4f9978715f6 authored over 9 years ago

ZTS calculation handler implementation.

85b8ca491ceaed658f24e5e832f2bd0ffee0ebae authored over 9 years ago

More correct input coordinates recognition (to avoid failure in zts and other calculations)

43442539c75183cc0a21a8690ad34056cc61a705 authored over 9 years ago

Geometry read method reworked.

9d701413e2069f3c06971746fa3c081926670466 authored over 9 years ago

Partial charges handler reworked. Some minor improovements.

Minor improovements include:
Additional NULL-checks in functions
Uniform style of pointers declar...

686285fc26f4257975611bed25dcf39804ef2ecc authored over 9 years ago

Documentation fix

84878a8b3058e1b716ed9bb3735c7a13d25f494c authored over 9 years ago

Geometry optimization handler reworked

8f3bd0c8079eaa34f9b9b5a4a70e6be4bfe68693 authored over 9 years ago

Deleted some unused variables

a5fee88686274661f785df96de954f964bab796b authored over 9 years ago

Added Partial Charges recognition if they're avalible.

Also started restructurization.

9626a48e00cab68b442efbf9b46ebb9dc4653d40 authored over 9 years ago

AddNonExistentData documentation fix

3bc306ddc9a65ac1ffa7dd025b33c05eb40c13fa authored over 9 years ago

Changed molecule merging scheme, now only nessesary data will be merged

5453de5ad856dc4e8763dcd3faf482a46261fceb authored over 9 years ago

Merge pull request #212 from psavery/master

For pwscfformat.cpp, fixed a few reading problems caused by newer ver…

dfc951050dfaa8cbb2003e023142df0b0c6ed5a9 authored over 9 years ago

For pwscfformat.cpp, fixed a few reading problems caused by newer versions of quantum espresso. The 'alat' term can now be read correctly, and it doesn't crash anymore from the extra 'CELL_PARAMETER' use at the beginning of the output.

a0968e0f72f99cee993c6a0f487e7f9103685ca5 authored over 9 years ago

Merge pull request #211 from ghutchis/z-sort-depictions

Make sure to z-sort atoms for depictions.

96e339a62f916f649aeb5d50a479b1359cf70d15 authored over 9 years ago

Use atomic number directly instead of symbol of atom when reading geometry

9265732f95cca59560b7ee84b3a9900fcf51de3a authored over 9 years ago

Make sure to z-sort atoms for depictions.

Adds a very small amount of time, but greatly improves the look
of the ball-and-stick depictions...

c177464c08485fa19c609f81ec2b8f664911b66c authored over 9 years ago

Merge remote-tracking branch 'upstream/master'

eca7747ae4b8c878a282f751d90bf0663eb8b22c authored over 9 years ago

NWChem format: All raw strings in orbital parser replaced by them mnemonic names

9758eda5fc6fb954d981024578681b84ef55386b authored over 9 years ago

NWChem format: added orbital occupation reading in single-point calculations

194e4ee70e2189f9b5e3628afb755a1a977ad519 authored over 9 years ago

NWChem format: Added orbital data reading method (not tested yet)

1146a3d2033c594e01654ca60e701ceb60a34882 authored over 9 years ago

Merge pull request #210 from cstein/feature-svg_options

Adds documentation to ball and stick depicition of SVG format.

f01ee95ca3075ce935c98a91b5191fddb57adc08 authored over 9 years ago

NWChem format: fix for MCSCF single point energy calculation and other possible *SCF and *DFT single point calculations

da615af6e44d5e69cea21f2f5c94ed22a8487d84 authored over 9 years ago

Adds documentation to ball and stick depicition of svg molecules.

83b2514184533a96180b51ab0cc24837d5ff3ee2 authored over 9 years ago

Merge pull request #209 from ghutchis/readcharges_fromfile

Read partial charges from file

fd5699bf4a56893dafe6281455450a3d99d08c64 authored over 9 years ago

Merge branch 'master' of github.com:openbabel/openbabel

254671525e65b2415e2f06b113c393dc11d35bea authored over 9 years ago

float->double to stop MSVC carping

78ab1c15658eb13dbbc79d80ce6fb2a690ae5a09 authored over 9 years ago

Merge pull request #208 from ghutchis/svg-bs-perspective-opacity

Add support for opacity (not yet used) and perspective.

4f638021cd412b546cc8a6bbcd04e2f78f233b34 authored over 9 years ago

fix ComputeCharges - failing tests

31e70224facef2bd82f115206f27d9bb85f82767 authored over 9 years ago

partialcharge fromfile

ec7794d9006c936dc438b73c1f0f99e47e754dd3 authored over 9 years ago

Add support for opacity (not yet used) and perspective.

Particularly improves the pseudo-3D SVG ball-and-stick depiction.

3ae13b8959054b9ab683bc8b49433ebf34a6e629 authored over 9 years ago

Merge pull request #207 from jnavila/ballandstick_depict

SVG Ball-and-stick depiction

50526e562180169cdfaa5110732cab7f450ec3a4 authored over 9 years ago

Add aromatic ring rendering to depictor

6a8c04db047debc42623decee6de86c32f8dfae8 authored over 9 years ago

Add dashed lines capability to painters

b278e52b152fa5959b546be334e7b909e2317a0d authored over 9 years ago

Add svg balls and sticks output

12e49bd65a7abf0177c3c79bd3935531634dd331 authored over 9 years ago

Merge pull request #205 from dkoes/addH_multiconformer_fix

do not reset conformer in addH

9dd91b10cbcaefb2f7b49e39e7d765204d0be136 authored over 9 years ago

Merge pull request #204 from jnavila/speedup_travis

speed up travis builds

933696e98901683d5e40abc7af027e85b9e7b6b9 authored over 9 years ago

NWChem format: All molecules data transfer routines moved into one separated method

1b2f197f154b7e5480d2c67ed8e32289be3f5a62 authored over 9 years ago

Merge pull request #200 from dspoel/master

New obthermo tool with corresponding data

c564a644e6bf37bc2798fc579f0ee1867d39459d authored over 9 years ago

NWChem format: Method names unification

52b1d69dd08b093e22fc1fe0eec674c66c6a92cf authored over 9 years ago

Merge pull request #1 from baoilleach/my_obthermo

Tweaks to obthermo code

aa5edd7315234c10ee69a1b08377fe1a8e952bfc authored over 9 years ago

Forgot to remove the now unused convenience function

a0d5b47a71ba38b4cef35a44f0d98ea28f59e729 authored over 9 years ago

Replace unit conversion utility function with constants. Still need it though for initialising heat of formation table, but replaced it with more efficient lookup. Add extract_thermochemistry to the public DLL API and namespace it in Open Babel.

a2207464f165ffff8faaec3d6b2769d6dcb0c973 authored over 9 years ago

NWChem format: Replaced all raw string patterns to its mnemonic names.

88407d47ca6e1475ab21e8774365c04cc0d8e6fc authored over 9 years ago

NWChem format: Added single point calculation handler.

Some cleanups and documentation improovements also made.

bf373eb02bcf4fc2f169f7b3c6d27febba82764b authored over 9 years ago

NWChem format: Deleted unnessesary code and fixed conformers detection broken in previous commit

01d7fd17daf36802ced1b56a60823c45c22f496b authored over 9 years ago

NWChemformat: Multi-molucules calculations supported

fb99c67256250ea5b6061a5344bd16700310ccd9 authored over 9 years ago

Major restructurization of nwchem format reading.

New structure allows recognition of sequential calculations
like "optimize->freq->property".
Opti...

4a7ae31ed9247c60a2ed8edb6181e9776c0b4bdb authored over 9 years ago

do not reset conformer in addH

previously all but the currently set conformer were blown away; now that they are kept around, S...

1721d4f82748a49df3d75832679bffdfbd901baa authored over 9 years ago

don't reset conformer in addh

dec5a580bf3189ff0aeb83c5c3c617ff1626deb1 authored over 9 years ago

Reading vibration data is separated to new method.

(Required for futher modifications)

638f4329395f08473155d13372f851eeb65b04be authored over 9 years ago

nwchemformat: Moved coordinates reading to separated method to make it reusable.

(Required for futher modifications)

6ec9062e110bd5cf626c780255274de95c58f0be authored over 9 years ago

Implemented calculation type detection (required for futher changes)

bc926336804ed86e913cd020ab225d08871ec2cf authored over 9 years ago

Added energy extraction from NWChem output

281a96ac1cf38b77cf77b50efd0b8d35beed3307 authored over 9 years ago

Do the same for tests

16614af34d97ac92636dd16a32180ec6710afdda authored over 9 years ago

speed up travis builds

Travis uses 1.5 core per build machine. Most of the time, the build is
slowed by disk access, so...

d202c5100f07da475d9b7ecceb7779e551d0294d authored over 9 years ago

Fixed detection of imaginary frequencies

e482e0803f1b128299614a20d0601c892bcfd0f6 authored over 9 years ago

Corrected atoms recognition in an output file when geometry in input file supplied in zmatrix format

2c3954c5d6c77ec0b4b3b94a9a4d565acb010d28 authored over 9 years ago