Open Babel

Revision: 2915
          http://openbabel.svn.sourceforge.net/openbabel/?rev=2915&view=rev
Author:   dleidert
Date:     2009-03-02 17:48:23 +0000 (Mon, 02 Mar 2009)

Log Message:
-----------
Correct use of sprintf() depending on undefined behavior.
http://lists.debian.org/debian-devel/2008/12/msg01079.html

Modified Paths:
--------------
    openbabel/trunk/src/formats/smilesformat.cpp


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Revision: 3203
          http://openbabel.svn.sourceforge.net/openbabel/?rev=3203&view=rev
Author:   timvdm
Date:     2009-07-18 09:56:51 +0000 (Sat, 18 Jul 2009)

Log Message:
-----------
Merged revisions 3091-3094,3097-3100 via svnmerge from 
https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/branches/openbabel-2-2-x

........
  r3091 | ghutchis | 2009-06-22 00:24:46 +0200 (Mon, 22 Jun 2009) | 5 lines
  
          * src/chains.cpp (OpenBabel): Fix for PR#2691618. When writing
          hydrogen atoms without chain names, make sure there are never
          spaces.
........
  r3092 | ghutchis | 2009-06-22 15:24:47 +0200 (Mon, 22 Jun 2009) | 4 lines
  
          * src/generic.cpp: Fix unit cell when setting possibly zero
          translation vectors ( e.g. PR#1961604).
........
  r3093 | timvdm | 2009-06-22 22:54:24 +0200 (Mon, 22 Jun 2009) | 2 lines
  
  Fix phmodel.txt rules to match both free & polymerized amino acids.
........
  r3094 | ghutchis | 2009-06-24 00:06:49 +0200 (Wed, 24 Jun 2009) | 2 lines
  
  Updated from Tim's recent change.
........
  r3097 | ghutchis | 2009-06-24 21:26:55 +0200 (Wed, 24 Jun 2009) | 2 lines
  
  Added Craig's changes for randomized SMILES order.
........
  r3098 | ghutchis | 2009-06-25 05:36:47 +0200 (Thu, 25 Jun 2009) | 4 lines
  
          * src/generic.cpp (OBUnitCell): Make sure to set the space group
          to P1 by default and after FillUnitCell.
........
  r3099 | ghutchis | 2009-06-25 05:36:56 +0200 (Thu, 25 Jun 2009) | 6 lines
  
          * src/formats/mopacformat.cpp: Read and write translation vectors,
          if available.
  
          * src/formats/gaussformat.cpp: Ditto
........
  r3100 | ghutchis | 2009-06-25 20:14:18 +0200 (Thu, 25 Jun 2009) | 2 lines
  
  Fix PR#2784880 -- compiling with OPENBABEL_INSTALL set fails (e.g., on MacPorts).
........

Modified Paths:
--------------
    openbabel/trunk/src/formats/smilesformat.cpp


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Revision: 3228
          http://openbabel.svn.sourceforge.net/openbabel/?rev=3228&view=rev
Author:   timvdm
Date:     2009-07-18 22:21:18 +0000 (Sat, 18 Jul 2009)

Log Message:
-----------
Add some comments

Modified Paths:
--------------
    openbabel/trunk/src/formats/smilesformat.cpp


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Revision: 3232
          http://openbabel.svn.sourceforge.net/openbabel/?rev=3232&view=rev
Author:   timvdm
Date:     2009-07-18 22:22:28 +0000 (Sat, 18 Jul 2009)

Log Message:
-----------
Add RingClosureDigit struct for smiles parser and use it.

Modified Paths:
--------------
    openbabel/trunk/src/formats/smilesformat.cpp


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Revision: 3263
          http://openbabel.svn.sourceforge.net/openbabel/?rev=3263&view=rev
Author:   timvdm
Date:     2009-07-18 22:35:27 +0000 (Sat, 18 Jul 2009)

Log Message:
-----------
src/format/smilesformat.cpp: Add InsertStereoRef and use it.

Conflicts:

	src/formats/smilesformat.cpp

Modified Paths:
--------------
    openbabel/trunk/src/formats/smilesformat.cpp


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Revision: 3276
          http://openbabel.svn.sourceforge.net/openbabel/?rev=3276&view=rev
Author:   timvdm
Date:     2009-07-18 22:38:44 +0000 (Sat, 18 Jul 2009)

Log Message:
-----------
smilesformat.cpp: Add some checking to make sure we don't overwrite
previous set reference ids.

Modified Paths:
--------------
    openbabel/trunk/src/formats/smilesformat.cpp


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Revision: 3285
          http://openbabel.svn.sourceforge.net/openbabel/?rev=3285&view=rev
Author:   timvdm
Date:     2009-07-18 22:41:01 +0000 (Sat, 18 Jul 2009)

Log Message:
-----------
src/formats/smilesformat.cpp: Take explicit hydrogens (i.e. [C@...]) into account when calculating the insertpos for
the stereo reference id.

Modified Paths:
--------------
    openbabel/trunk/src/formats/smilesformat.cpp


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Revision: 3286
          http://openbabel.svn.sourceforge.net/openbabel/?rev=3286&view=rev
Author:   timvdm
Date:     2009-07-18 22:41:16 +0000 (Sat, 18 Jul 2009)

Log Message:
-----------
src/formats/smilesformat.cpp: Some changes to the stereo ref handling for the smiles parser...

Modified Paths:
--------------
    openbabel/trunk/src/formats/smilesformat.cpp


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Revision: 3287
          http://openbabel.svn.sourceforge.net/openbabel/?rev=3287&view=rev
Author:   timvdm
Date:     2009-07-18 22:41:30 +0000 (Sat, 18 Jul 2009)

Log Message:
-----------
src/formats/smilesformat.cpp: found the difference between this branch and 2-2-x branch. All stereo references are
working now...

Modified Paths:
--------------
    openbabel/trunk/src/formats/smilesformat.cpp


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Revision: 3288
          http://openbabel.svn.sourceforge.net/openbabel/?rev=3288&view=rev
Author:   timvdm
Date:     2009-07-18 22:41:49 +0000 (Sat, 18 Jul 2009)

Log Message:
-----------
src/formats/smilesformat.cpp: Comment out debug output + remove obsolete code

Modified Paths:
--------------
    openbabel/trunk/src/formats/smilesformat.cpp


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Revision: 3311
          http://openbabel.svn.sourceforge.net/openbabel/?rev=3311&view=rev
Author:   timvdm
Date:     2009-07-18 22:47:44 +0000 (Sat, 18 Jul 2009)

Log Message:
-----------
For the moment, just clear any calculated symmetry in smiles format writer

Conflicts:

	src/formats/smilesformat.cpp

Modified Paths:
--------------
    openbabel/trunk/src/formats/smilesformat.cpp


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Revision: 3230
          http://openbabel.svn.sourceforge.net/openbabel/?rev=3230&view=rev
Author:   timvdm
Date:     2009-07-18 22:21:59 +0000 (Sat, 18 Jul 2009)

Log Message:
-----------
Add BondStruct to replace vector<vector<int> > _extbond with
vector<BondStruct> _extbond. Improves readability a bit.

Modified Paths:
--------------
    openbabel/trunk/src/formats/smilesformat.cpp


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Revision: 3258
          http://openbabel.svn.sourceforge.net/openbabel/?rev=3258&view=rev
Author:   timvdm
Date:     2009-07-18 22:34:10 +0000 (Sat, 18 Jul 2009)

Log Message:
-----------
Correct error in cerr statement

Modified Paths:
--------------
    openbabel/trunk/src/formats/smilesformat.cpp


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Revision: 3322
          http://openbabel.svn.sourceforge.net/openbabel/?rev=3322&view=rev
Author:   timvdm
Date:     2009-07-18 22:51:28 +0000 (Sat, 18 Jul 2009)

Log Message:
-----------
Final edits on 0D Cis/Trans. Need to look at tetrahedral now.

Modified Paths:
--------------
    openbabel/trunk/src/formats/smilesformat.cpp


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Revision: 3268
          http://openbabel.svn.sourceforge.net/openbabel/?rev=3268&view=rev
Author:   timvdm
Date:     2009-07-18 22:36:42 +0000 (Sat, 18 Jul 2009)

Log Message:
-----------
Updated smiles format to use OBGraphSym

Conflicts:

	src/formats/smilesformat.cpp

Modified Paths:
--------------
    openbabel/trunk/src/formats/smilesformat.cpp


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Revision: 3321
          http://openbabel.svn.sourceforge.net/openbabel/?rev=3321&view=rev
Author:   timvdm
Date:     2009-07-18 22:51:11 +0000 (Sat, 18 Jul 2009)

Log Message:
-----------
Reverting some

Modified Paths:
--------------
    openbabel/trunk/src/formats/smilesformat.cpp


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Revision: 3231
          http://openbabel.svn.sourceforge.net/openbabel/?rev=3231&view=rev
Author:   timvdm
Date:     2009-07-18 22:22:14 +0000 (Sat, 18 Jul 2009)

Log Message:
-----------
Make sure it compiles

Modified Paths:
--------------
    openbabel/trunk/src/formats/smilesformat.cpp


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Revision: 3283
          http://openbabel.svn.sourceforge.net/openbabel/?rev=3283&view=rev
Author:   timvdm
Date:     2009-07-18 22:40:35 +0000 (Sat, 18 Jul 2009)

Log Message:
-----------
src/formats/smilesformat.cpp: set HasChiralityPerceived after adding hydrogens to chiral atoms, the previously
perceived stereochemistry is still valid.

Modified Paths:
--------------
    openbabel/trunk/src/formats/smilesformat.cpp


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Revision: 4041
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4041&view=rev
Author:   ghutchis
Date:     2010-09-14 14:33:31 +0000 (Tue, 14 Sep 2010)

Log Message:
-----------
Make sure to always bracket elements when required, e.g. [H][H] or [W].
Fixes some roundtrip errors reported by Tim.

Modified Paths:
--------------
    openbabel/trunk/src/formats/smilesformat.cpp


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Revision: 4042
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4042&view=rev
Author:   ghutchis
Date:     2010-09-14 14:42:52 +0000 (Tue, 14 Sep 2010)

Log Message:
-----------
Eliminate another case of broken roundtrip errors n vs. [n] when no "H" is required.

Modified Paths:
--------------
    openbabel/trunk/src/formats/smilesformat.cpp


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Revision: 4048
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4048&view=rev
Author:   ghutchis
Date:     2010-09-16 00:44:54 +0000 (Thu, 16 Sep 2010)

Log Message:
-----------
Handle [s] vs. s, or other aromatic atoms which don't need brackets.

Modified Paths:
--------------
    openbabel/trunk/src/formats/smilesformat.cpp


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Revision: 4062
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4062&view=rev
Author:   timvdm
Date:     2010-09-20 03:28:58 +0000 (Mon, 20 Sep 2010)

Log Message:
-----------
src/formats/smilesformat.cpp: Use lazy evaluation for regular smiles.

Modified Paths:
--------------
    openbabel/trunk/src/formats/smilesformat.cpp


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Revision: 4072
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4072&view=rev
Author:   timvdm
Date:     2010-09-22 03:41:32 +0000 (Wed, 22 Sep 2010)

Log Message:
-----------
src/formats/smilesformat.cpp: Call StereoFrom0D after reading again.

Modified Paths:
--------------
    openbabel/trunk/src/formats/smilesformat.cpp


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Revision: 4093
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4093&view=rev
Author:   timvdm
Date:     2010-09-24 01:52:23 +0000 (Fri, 24 Sep 2010)

Log Message:
-----------
src/formats/smilesformat.cpp: Prevent crash when reading TB smiles.

Modified Paths:
--------------
    openbabel/trunk/src/formats/smilesformat.cpp


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Revision: 4095
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4095&view=rev
Author:   ghutchis
Date:     2010-09-24 04:03:40 +0000 (Fri, 24 Sep 2010)

Log Message:
-----------


Modified Paths:
--------------
    openbabel/trunk/src/formats/smilesformat.cpp


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Revision: 4101
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4101&view=rev
Author:   ghutchis
Date:     2010-09-24 19:08:16 +0000 (Fri, 24 Sep 2010)

Log Message:
-----------
Carefully count explicit hydrogens. Subtract those which would be written separately (e.g., charged, bridging, etc.)

Modified Paths:
--------------
    openbabel/trunk/src/formats/smilesformat.cpp


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Revision: 4161
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4161&view=rev
Author:   ghutchis
Date:     2010-10-09 14:39:31 +0000 (Sat, 09 Oct 2010)

Log Message:
-----------
Don't write '=' between two aromatic atoms -- not useful information.

Modified Paths:
--------------
    openbabel/trunk/src/formats/smilesformat.cpp


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Revision: 4188
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4188&view=rev
Author:   ghutchis
Date:     2010-10-13 18:56:48 +0000 (Wed, 13 Oct 2010)

Log Message:
-----------
Add support for charges bigger than one digit, e.g., [Li+251] -- this is an absurd ion, but should be legal SMILES.

Modified Paths:
--------------
    openbabel/trunk/src/formats/smilesformat.cpp


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Revision: 4190
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4190&view=rev
Author:   timvdm
Date:     2010-10-13 22:51:52 +0000 (Wed, 13 Oct 2010)

Log Message:
-----------
src/formats/smilesformat.cpp: Fix bug in last commit.

Modified Paths:
--------------
    openbabel/trunk/src/formats/smilesformat.cpp


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Revision: 4199
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4199&view=rev
Author:   ghutchis
Date:     2010-10-15 03:14:13 +0000 (Fri, 15 Oct 2010)

Log Message:
-----------
Warn about large charges on atoms.

Modified Paths:
--------------
    openbabel/trunk/src/formats/smilesformat.cpp


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Revision: 4252
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4252&view=rev
Author:   timvdm
Date:     2010-10-23 11:10:39 +0000 (Sat, 23 Oct 2010)

Log Message:
-----------
src/format/smilesformat.cpp: Fix segfault in 5 million molecule shuffle test.

Modified Paths:
--------------
    openbabel/trunk/src/formats/smilesformat.cpp


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Revision: 4306
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4306&view=rev
Author:   baoilleach
Date:     2010-11-16 17:03:11 +0000 (Tue, 16 Nov 2010)

Log Message:
-----------
Final part of chirality bug fix. The shuffle test now passes. The problem is that EndModify wipes all flags, so it's necessary to keep restoring the chirality flag or all the carefully conserved stereo data will be lost.

Modified Paths:
--------------
    openbabel/trunk/src/formats/smilesformat.cpp


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Revision: 4522
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4522&view=rev
Author:   baoilleach
Date:     2011-07-06 19:11:22 +0000 (Wed, 06 Jul 2011)

Log Message:
-----------
smilesformat.cpp: Add output option "l <atomno>" to enable the user to specify the 'last atom'; really it's the atom to which any additional SMILES atoms should attach. I just need to implement "f" for first atom (by analogy with the -f and -l global options), which is much easier, and it will be good to go. "-xl" tested on all available connection points in the first 1000 members of PubChem... 100% success.

Modified Paths:
--------------
    openbabel/trunk/src/formats/smilesformat.cpp


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Revision: 4525
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4525&view=rev
Author:   baoilleach
Date:     2011-07-07 19:01:12 +0000 (Thu, 07 Jul 2011)

Log Message:
-----------
smilesformat.cpp: Add output option "f <atomno>" to enable the user to specify the 'first atom' of the SMILES string. Note to self: one corner case to handle for "l" option still.

Modified Paths:
--------------
    openbabel/trunk/src/formats/smilesformat.cpp


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Revision: 4528
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4528&view=rev
Author:   baoilleach
Date:     2011-07-09 12:22:00 +0000 (Sat, 09 Jul 2011)

Log Message:
-----------
smilesformat.cpp: Finish off "f" and "l" options: (1) Add docs, (2) Handle corner cases of "l" specified for [nH] and [C@...], (3) Avoid rearranging the canonical tree after we've already dealt with _endatom as there's no need at that point.

Modified Paths:
--------------
    openbabel/trunk/src/formats/smilesformat.cpp


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Revision: 4529
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4529&view=rev
Author:   baoilleach
Date:     2011-07-12 18:08:08 +0000 (Tue, 12 Jul 2011)

Log Message:
-----------
smilesformat.cpp: Finish off "f" options: Handle corner cases of "f" specified for [nH] and [C@...]

Modified Paths:
--------------
    openbabel/trunk/src/formats/smilesformat.cpp


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Revision: 4554
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4554&view=rev
Author:   baoilleach
Date:     2011-09-04 12:32:32 +0000 (Sun, 04 Sep 2011)
Log Message:
-----------
NEW_ENUM_VALUE: Partial revert of smilesformat.cpp (r4552) where I accidentally committed some local changes.

Revision Links:
--------------
    http://openbabel.svn.sourceforge.net/openbabel/?rev=4552&view=rev

Modified Paths:
--------------
    openbabel/trunk/src/formats/smilesformat.cpp

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Revision: 4558
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4558&view=rev
Author:   baoilleach
Date:     2011-09-05 20:35:16 +0000 (Mon, 05 Sep 2011)
Log Message:
-----------
src/formats/smilesformat.cpp: Add option "I" to smiles output to allow specifying order of atoms in the output. Need to test it.

Modified Paths:
--------------
    openbabel/trunk/src/formats/smilesformat.cpp

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Revision: 4559
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4559&view=rev
Author:   baoilleach
Date:     2011-09-06 08:20:48 +0000 (Tue, 06 Sep 2011)
Log Message:
-----------
Revert r4558.

Revision Links:
--------------
    http://openbabel.svn.sourceforge.net/openbabel/?rev=4558&view=rev

Modified Paths:
--------------
    openbabel/trunk/src/formats/smilesformat.cpp

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Revision: 4666
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4666&view=rev
Author:   baoilleach
Date:     2011-11-11 12:34:57 +0000 (Fri, 11 Nov 2011)
Log Message:
-----------
smilesformat.cpp: Fix PR#3428432. Memory leak from evil SMILES from the mind of Andrew Dalke.

Modified Paths:
--------------
    openbabel/trunk/src/formats/smilesformat.cpp

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Revision: 4736
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4736&view=rev
Author:   chrismorl
Date:     2012-04-03 09:49:36 +0000 (Tue, 03 Apr 2012)
Log Message:
-----------
Fix bug #3514243 raised by Samuele Sommariva, in which SMILES output of aromatic radicals was wrong.

Modified Paths:
--------------
    openbabel/trunk/src/formats/smilesformat.cpp

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Revision: 4763
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4763&view=rev
Author:   cjames53
Date:     2012-05-24 15:07:27 +0000 (Thu, 24 May 2012)
Log Message:
-----------
Removed a full-molecule-copy operation that was (apparently) added by
accident.  It caused the molecule to be copied, and forced aromaticity to
be recomputed, each time a SMILES was created.

Modified Paths:
--------------
    openbabel/trunk/src/formats/smilesformat.cpp

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Revision: 4764
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4764&view=rev
Author:   cjames53
Date:     2012-05-24 18:57:08 +0000 (Thu, 24 May 2012)
Log Message:
-----------
Fixed a bug: smilesformat.cpp silently truncated strings at 32767
characters with no warning.  Now it issues an error message and doesn't try
to parse the truncated SMILES.

Modified Paths:
--------------
    openbabel/trunk/src/formats/smilesformat.cpp

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Revision: 4803
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4803&view=rev
Author:   th9
Date:     2012-05-29 20:35:03 +0000 (Tue, 29 May 2012)
Log Message:
-----------
formats/smilesformat.cpp: Fix comparison between signed and unsigned int

Modified Paths:
--------------
    openbabel/trunk/src/formats/smilesformat.cpp

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Revision: 4843
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4843&view=rev
Author:   baoilleach
Date:     2012-05-31 14:27:16 +0000 (Thu, 31 May 2012)
Log Message:
-----------
formats/smilesformat.cpp: Add output option "R" which prevents reuse of bond-closure symbols on writing. The default has not been changed (to reuse symbols).

Modified Paths:
--------------
    openbabel/trunk/src/formats/smilesformat.cpp

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Revision: 4844
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4844&view=rev
Author:   baoilleach
Date:     2012-05-31 15:13:59 +0000 (Thu, 31 May 2012)
Log Message:
-----------
formats/smilesformat.cpp: Add SMILES output option -xo <ordering> which allows the user to specify the canonical labels for the atoms. If these labels form a depth-first tree, then it is equivalent to specifying an ordering of the atoms in the output SMILES.

Modified Paths:
--------------
    openbabel/trunk/src/formats/smilesformat.cpp

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Revision: 4847
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4847&view=rev
Author:   baoilleach
Date:     2012-06-01 13:38:25 +0000 (Fri, 01 Jun 2012)
Log Message:
-----------
src/formats/smilesformat.cpp: Initial merge of code for Inchified and Universal SMILES. I've checked that it doesn't alter regular can smiles. I need to do some more testing on it just to doublecheck I've merged it accurately.

Modified Paths:
--------------
    openbabel/trunk/src/formats/smilesformat.cpp

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Revision: 4858
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4858&view=rev
Author:   baoilleach
Date:     2012-06-05 15:11:27 +0000 (Tue, 05 Jun 2012)
Log Message:
-----------
smilesformat.cpp: Replace OBConversion::SetOptions by AddOption. Thanks Chris.

Modified Paths:
--------------
    openbabel/trunk/src/formats/smilesformat.cpp

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Revision: 4999
          http://openbabel.svn.sourceforge.net/openbabel/?rev=4999&view=rev
Author:   baoilleach
Date:     2012-09-03 15:07:57 +0000 (Mon, 03 Sep 2012)
Log Message:
-----------
smilesformat.cpp: Patch by Andrew Dalke for buffer overflow (PR#3165083)

Modified Paths:
--------------
    openbabel/trunk/src/formats/smilesformat.cpp

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Revision: 5005
          http://openbabel.svn.sourceforge.net/openbabel/?rev=5005&view=rev
Author:   baoilleach
Date:     2012-09-05 18:51:02 +0000 (Wed, 05 Sep 2012)
Log Message:
-----------
formats/smilesformat.cpp: Patch from Andrew Dalke, PR#3426020, to ensure that Unicode characters raise an error message instead of being ignored.

Modified Paths:
--------------
    openbabel/trunk/src/formats/smilesformat.cpp

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Revision: 5006
          http://openbabel.svn.sourceforge.net/openbabel/?rev=5006&view=rev
Author:   baoilleach
Date:     2012-09-06 09:07:27 +0000 (Thu, 06 Sep 2012)
Log Message:
-----------
formats/smilesformat.cpp: Revert r5005. Causes inchiSteffen_PubChem.smi_Test to fail on Linux platforms (but not under MSVC). Don't have time now to sort it out, so just reverting.

Revision Links:
--------------
    http://openbabel.svn.sourceforge.net/openbabel/?rev=5005&view=rev

Modified Paths:
--------------
    openbabel/trunk/src/formats/smilesformat.cpp

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