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mbanck committed revision 3456 to the Open Babel SVN repository, changing 2 files.
2009-11-10 10:51:44 UTC by mbanck
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Here are lot of input formats. Complete description is here: http://quantum-espresso.org/wiki/index.php/Input_Data_Description
But all of them contain strings marked as * here:
...
&system
ibrav=4, *
celldm(1)=4.6189, *
celldm(3)=12.681, *
nat=4, *
ntyp=1, *
ecutwfc=18.0,
nbnd=16
/
...
ATOMIC_SPECIES
C 12.0 C.pz-vbc.UPF...
2009-11-10 05:21:40 UTC by vitruss
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Coordinates in Molpro output often contain numbering. This patch makes possible correct reading of atomic symbols for such cases:
Atomic Coordinates
Nr Atom Charge X Y Z
1 H1 1.00 0.000000000 0.000000000 -3.145729574
2 C1 6.00 0.000000000 0.000000000 -1.140724726
3 C2 6.00 0.000000000 0.000000000...
2009-11-06 18:42:41 UTC by annulen
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ghutchis committed revision 3455 to the Open Babel SVN repository, changing 2 files.
2009-11-06 15:16:23 UTC by ghutchis
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ghutchis committed revision 3454 to the Open Babel SVN repository, changing 1 files.
2009-11-06 15:08:25 UTC by ghutchis
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echo 'CC[C@H](C)[C@@H](C)CC' | babel -ismi -osdf | babel -isdf -osmi
produces CCC(C)C(C)CC and not CC[C@H](C)[C@@H](C)CC what it should do.
so seen in the lates 2.2.3.
2009-11-04 15:54:38 UTC by nobody
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Minor bug in data.cpp : OBResidueData::AssignBonds(...)
the function connects atoms of a residue according to atom names defined in "resdata.txt" by stepping
through the atom list _vatoms and breaks when the residue information of the atoms under investigation
are different. Residues are only compared according to the residue name and the residue number, which
is a problem when subsequen.
2009-10-30 23:00:40 UTC by fab5
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Hi,
Not really a bug, but here it goes anyway:
I'm using babel (parts of the source code) to process protein structures from the PDB and
realized that for a couple of (admittedly very) large protein structures such as the ribosome,
babel takes quite some time ( up to one hour) to prepare a file with the "-p7" option.
Profiling revealed that a considerable amount of time is spent in...
2009-10-30 21:30:26 UTC by fab5
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Thanks a lot for your patch.
As a general guideline, it is best to send patches in unidiff format using the -u option and reverse the files, so that the original version is the first argument and the modified version is the second argument as in
diff -u outformat.cpp.old outformat.cpp
No need to resubmit your patch, it is perfectly readable as is and I have committed it on trunk as...
2009-10-29 12:02:15 UTC by mbanck
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I have applied the Patch from #2888693 on trunk which should address this. Please let us know if further changes are needed.
2009-10-29 12:01:21 UTC by mbanck
