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From: <ghu...@us...> - 2006-05-03 21:27:50
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Revision: 1351 Author: ghutchis Date: 2006-05-03 14:27:45 -0700 (Wed, 03 May 2006) ViewCVS: http://svn.sourceforge.net/openbabel/?rev=1351&view=rev Log Message: ----------- * src/chains.h, src/chains.cpp: Initial work on documenting, indentation, and general cleanup of chains.cpp. (ConstrainBackbone): Check for valence of backbone atoms should actually be for HvyValence() since all hydrogens are ignored. Fixes PR#1442779. Modified Paths: -------------- openbabel/trunk/ChangeLog openbabel/trunk/src/chains.cpp openbabel/trunk/src/chains.h This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
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From: <ghu...@us...> - 2006-05-03 17:42:14
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Revision: 1350 Author: ghutchis Date: 2006-05-03 10:42:01 -0700 (Wed, 03 May 2006) ViewCVS: http://svn.sourceforge.net/openbabel/?rev=1350&view=rev Log Message: ----------- Fixed typo with WriteFile. Modified Paths: -------------- openbabel/branches/openbabel-2-0-x/src/obconversion.cpp This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
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From: <ghu...@us...> - 2006-05-03 15:52:43
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Revision: 1349 Author: ghutchis Date: 2006-05-03 08:52:36 -0700 (Wed, 03 May 2006) ViewCVS: http://svn.sourceforge.net/openbabel/?rev=1349&view=rev Log Message: ----------- Minor updates to test set. Modified Paths: -------------- test-set/trunk/test.sh Added Paths: ----------- test-set/trunk/original/drexler-axel.xyz test-set/trunk/others/MiscStructures.mol test-set/trunk/others/MiscStructuresCD.cml This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
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From: Geoff H. <ghu...@us...> - 2006-04-27 17:27:46
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openbabel/src generic.h Update of /cvsroot/openbabel/openbabel/src In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv9505/src Modified Files: generic.h Log Message: * Doxyfile: Add map of included files in headers to documentation. Need to work on removing un-necessary #includes in headers. * src/math/*: Minimize #include headers. * src/generic.h: Include obutil.h for triple class -- was included indirectly by way of vector3.h. |
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From: Geoff H. <ghu...@us...> - 2006-04-27 17:27:46
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openbabel/src/math matrix3x3.cpp matrix3x3.h vector3.cpp vector3.h Update of /cvsroot/openbabel/openbabel/src/math In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv9505/src/math Modified Files: matrix3x3.cpp matrix3x3.h vector3.cpp vector3.h Log Message: * Doxyfile: Add map of included files in headers to documentation. Need to work on removing un-necessary #includes in headers. * src/math/*: Minimize #include headers. * src/generic.h: Include obutil.h for triple class -- was included indirectly by way of vector3.h. |
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From: Geoff H. <ghu...@us...> - 2006-04-27 17:27:45
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openbabel ChangeLog Doxyfile Update of /cvsroot/openbabel/openbabel In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv9505 Modified Files: ChangeLog Doxyfile Log Message: * Doxyfile: Add map of included files in headers to documentation. Need to work on removing un-necessary #includes in headers. * src/math/*: Minimize #include headers. * src/generic.h: Include obutil.h for triple class -- was included indirectly by way of vector3.h. |
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From: Geoff H. <ghu...@us...> - 2006-04-27 17:25:58
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openbabel/test smartsresults.txt smartstest.cpp smartstest.txt Update of /cvsroot/openbabel/openbabel/test In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv7371/test Modified Files: smartsresults.txt smartstest.cpp smartstest.txt Log Message: * test/smartstest.cpp: Changed the way tests are counted -- per molecule instead of per pattern AND per molecule (cuts drastically down on the test overhead). Remove endl and sync with stio to improve buffering. * test/smartstest.txt, test/smartsresults.txt: Add additional SMARTS pattern tests and results. |
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From: Chris M. <chr...@us...> - 2006-04-24 16:07:34
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openbabel ChangeLog Update of /cvsroot/openbabel/openbabel In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv15439 Modified Files: ChangeLog Log Message: Changes to cmlformat.cpp, etc |
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From: Chris M. <chr...@us...> - 2006-04-24 16:06:16
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openbabel/src/formats smilesformat.cpp Update of /cvsroot/openbabel/openbabel/src/formats In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv14398/src/formats Modified Files: smilesformat.cpp Log Message: Repair after change to ImplictHydrogenCount() |
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From: Chris M. <chr...@us...> - 2006-04-24 16:06:16
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openbabel/src mol.cpp Update of /cvsroot/openbabel/openbabel/src In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv14398/src Modified Files: mol.cpp Log Message: Repair after change to ImplictHydrogenCount() |
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From: Chris M. <chr...@us...> - 2006-04-24 16:04:07
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openbabel/src/GUI OBGUI.cpp Update of /cvsroot/openbabel/openbabel/src/GUI In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv12818/src/GUI Modified Files: OBGUI.cpp Log Message: uncommented standard stream redirection. |
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From: Chris M. <chr...@us...> - 2006-04-24 16:03:16
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openbabel/src/formats/xml cmlformat.cpp Update of /cvsroot/openbabel/openbabel/src/formats/xml In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv12415/src/formats/xml Modified Files: cmlformat.cpp Log Message: Accept coordinate2 and coordinate3 elements for CML1. Laxer acceptance of atomRef?? which is sometimes misused - but added warning. Converted cerr calls to obError. Added option to read 2D rather than 3D coordinates. Output formula only when no bonds AND no coordinates. Ensured atoms from formula marked as having no H. GetMolID() gets name or number for error messages. |
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From: Chris M. <chr...@us...> - 2006-04-24 16:01:54
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openbabel/src/formats/xml xml.cpp Update of /cvsroot/openbabel/openbabel/src/formats/xml In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv11312/src/formats/xml Modified Files: xml.cpp Log Message: (gettomatch): rewrite to allow stream to be discarded up to next match. |
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From: Noel O'B. <bao...@us...> - 2006-04-24 11:04:25
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openbabel/scripts/python pyopenbabel.py Update of /cvsroot/openbabel/openbabel/scripts/python In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv18578 Modified Files: pyopenbabel.py Log Message: Added a class to allow molecules to be written to a multiple molecule file. |
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From: Geoff H. <ghu...@us...> - 2006-04-21 21:26:30
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openbabel/src obconversion.cpp Update of /cvsroot/openbabel/openbabel/src In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv3104/src Modified Files: obconversion.cpp Log Message: * src/obconversion.cpp: Fix broken gzip-decoding of input (PR#1473243) introduced by 2006-04-11 change. Fix bug when writing multi-molecule files using WriteFile() (PR#1474265). |
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From: Geoff H. <ghu...@us...> - 2006-04-21 21:26:29
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openbabel ChangeLog Update of /cvsroot/openbabel/openbabel In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv3104 Modified Files: ChangeLog Log Message: * src/obconversion.cpp: Fix broken gzip-decoding of input (PR#1473243) introduced by 2006-04-11 change. Fix bug when writing multi-molecule files using WriteFile() (PR#1474265). |
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From: Geoff H. <ghu...@us...> - 2006-04-21 21:26:06
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openbabel/src atom.cpp residue.cpp Update of /cvsroot/openbabel/openbabel/src In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv2707/src Modified Files: atom.cpp residue.cpp Log Message: * src/atom.cpp, src/residue.cpp: Remove inadvertant debug messages. |
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From: Geoff H. <ghu...@us...> - 2006-04-21 20:21:02
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openbabel/src obconversion.cpp Update of /cvsroot/openbabel/openbabel/src In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv30709/src Modified Files: Tag: openbabel-2-0-x obconversion.cpp Log Message: * src/obconversion.cpp: Fix broken gzip-decoding of input (PR#1473243) introduced by 2006-04-11 change. Fix bug when writing multi-molecule files using WriteFile() (PR#1474265). |
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From: Geoff H. <ghu...@us...> - 2006-04-21 20:20:58
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openbabel ChangeLog Update of /cvsroot/openbabel/openbabel In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv30709 Modified Files: Tag: openbabel-2-0-x ChangeLog Log Message: * src/obconversion.cpp: Fix broken gzip-decoding of input (PR#1473243) introduced by 2006-04-11 change. Fix bug when writing multi-molecule files using WriteFile() (PR#1474265). |
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From: Chris M. <chr...@us...> - 2006-04-20 09:01:24
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openbabel ChangeLog Update of /cvsroot/openbabel/openbabel In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv12156 Modified Files: ChangeLog Log Message: added OBCOMMON macro to aid DLL build, Prevent formats with WRITEONEONLY from writing more than once. |
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From: Chris M. <chr...@us...> - 2006-04-20 08:59:30
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openbabel/windows-vc2005 babelconfig.h Update of /cvsroot/openbabel/openbabel/windows-vc2005 In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv10579/windows-vc2005 Modified Files: babelconfig.h Log Message: added OBCOMMON macro to aid DLL build |
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From: Chris M. <chr...@us...> - 2006-04-20 08:59:27
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openbabel/src/formats/xml xml.h Update of /cvsroot/openbabel/openbabel/src/formats/xml In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv10579/src/formats/xml Modified Files: xml.h Log Message: added OBCOMMON macro to aid DLL build |
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From: Chris M. <chr...@us...> - 2006-04-20 08:59:21
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openbabel/src/formats obmolecformat.h Update of /cvsroot/openbabel/openbabel/src/formats In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv10579/src/formats Modified Files: obmolecformat.h Log Message: added OBCOMMON macro to aid DLL build |
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From: Chris M. <chr...@us...> - 2006-04-20 08:57:28
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openbabel/src obconversion.cpp Update of /cvsroot/openbabel/openbabel/src In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv8974/src Modified Files: obconversion.cpp Log Message: Prevent formats with WRITEONEONLY writing more than one object |
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From: Noel O'B. <bao...@us...> - 2006-04-20 08:07:57
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openbabel/scripts/python pyopenbabel.py Update of /cvsroot/openbabel/openbabel/scripts/python In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv31934a Modified Files: pyopenbabel.py Log Message: Adding the ability to iterate over molecules in multiple-molecule input files. Note to self: Need to look at how single-molecule files are handled. |
