[Open Babel] chemdraw bond lenghts
seems that files converted from the cdx or cdxml have wrong bond lenght (I've the feeling that is related to the document properties in chemoffice); benzene bond lenght --> 70Angstrom anyone has already find a solution? I'm thinking to something like a "feed2babel" style, or something similar. thanks anyone -- View this message in context: http://forums.openbabel.org/chemdraw-bond-lenghts-tp4449415p4449415.html Sent from the General discussion mailing list archive at Nabble.com. -- Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] chemdraw bond lenghts
Yes, this is a serious problem in Chemdraw. I found that using OpenBabel to convert to 3D then back to 2D adjusted the bonds to the correct dimensions. Quoting cadeddu on Tue, 6 Mar 2012 03:06:02 -0800 (PST): > seems that files converted from the cdx or cdxml have wrong bond lenght (I've > the feeling that is related to the document properties in chemoffice); > benzene bond lenght --> 70Angstrom > anyone has already find a solution? I'm thinking to something like a > "feed2babel" style, or something similar. > thanks anyone > > > > -- > View this message in context: > http://forums.openbabel.org/chemdraw-bond-lenghts-tp4449415p4449415.html > Sent from the General discussion mailing list archive at Nabble.com. > > -- > Keep Your Developer Skills Current with LearnDevNow! > The most comprehensive online learning library for Microsoft developers > is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, > Metro Style Apps, more. Free future releases when you subscribe now! > http://p.sf.net/sfu/learndevnow-d2d > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > _ Dr. Douglas R. Houston Lecturer Room 3.23 Institute of Structural and Molecular Biology Michael Swann Building King's Buildings University of Edinburgh Edinburgh, EH9 3JR, UK Tel. 0131 650 7358 -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] chemdraw bond lenghts
can you specify which 3D format? I've tested this series babel -h -i cdxml benzeneACS.cdxml -o c3d1 benzeneACSvi.c3d babel -h -i c3d1 benzeneACSvi.c3d -o pdb benzeneACSviac3d.pdb and I still have 14.9 angstrom for a benzene double bond. Did someone has already produced a stylefile (.chm?), and want to share it? that will be of tremendous help, and eventually be a fast patch On 6/3/12 12:52 PM, Douglas Houston wrote: > Yes, this is a serious problem in Chemdraw. I found that using > OpenBabel to convert to 3D then back to 2D adjusted the bonds to the > correct dimensions. > > > Quoting cadeddu on Tue, 6 Mar 2012 03:06:02 -0800 (PST): > >> seems that files converted from the cdx or cdxml have wrong bond lenght (I've >> the feeling that is related to the document properties in chemoffice); >> benzene bond lenght --> 70Angstrom >> anyone has already find a solution? I'm thinking to something like a >> "feed2babel" style, or something similar. >> thanks anyone >> >> >> >> -- >> View this message in context: >> http://forums.openbabel.org/chemdraw-bond-lenghts-tp4449415p4449415.html >> Sent from the General discussion mailing list archive at Nabble.com. >> >> -- >> Keep Your Developer Skills Current with LearnDevNow! >> The most comprehensive online learning library for Microsoft developers >> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, >> Metro Style Apps, more. Free future releases when you subscribe now! >> http://p.sf.net/sfu/learndevnow-d2d >> ___ >> OpenBabel-discuss mailing list >> OpenBabel-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >> >> > > > > > _ > Dr. Douglas R. Houston > Lecturer > Room 3.23 > Institute of Structural and Molecular Biology > Michael Swann Building > King's Buildings > University of Edinburgh > Edinburgh, EH9 3JR, UK > Tel. 0131 650 7358 > -- Andrea Cadeddu -- Nanochemistry Laboratory Institut de Science et d'Ingénierie Supramoléculaires (I.S.I.S.) Université de Strasbourg 8, allée Gaspard Monge F-67000 Strasbourg (France) Tel: +33-(0)3-68855185 Fax: +33-(0)3-68855161 cade...@unistra.fr -- Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] chemdraw bond lenghts
Hi, I used the --gen3D option, so something like babel -isdf chemdraw.sdf -osdf chemdraw3d.sdf --gen3D babel -isdf chemdraw3D.sdf -osdf chemdraw.sdf --gen2D cheers, Doug Quoting cadeddu on Tue, 06 Mar 2012 13:39:28 +0100: > can you specify which 3D format? I've tested this series > > babel -h -i cdxml benzeneACS.cdxml -o c3d1 benzeneACSvi.c3d > babel -h -i c3d1 benzeneACSvi.c3d -o pdb benzeneACSviac3d.pdb > > and I still have 14.9 angstrom for a benzene double bond. > > Did someone has already produced a stylefile (.chm?), and want to share > it? that will be of tremendous help, and eventually be a fast patch > > > On 6/3/12 12:52 PM, Douglas Houston wrote: >> Yes, this is a serious problem in Chemdraw. I found that using >> OpenBabel to convert to 3D then back to 2D adjusted the bonds to the >> correct dimensions. >> >> >> Quoting cadeddu on Tue, 6 Mar 2012 03:06:02 >> -0800 (PST): >> >>> seems that files converted from the cdx or cdxml have wrong bond >>> lenght (I've >>> the feeling that is related to the document properties in chemoffice); >>> benzene bond lenght --> 70Angstrom >>> anyone has already find a solution? I'm thinking to something like a >>> "feed2babel" style, or something similar. >>> thanks anyone >>> >>> >>> >>> -- >>> View this message in context: >>> http://forums.openbabel.org/chemdraw-bond-lenghts-tp4449415p4449415.html >>> Sent from the General discussion mailing list archive at Nabble.com. >>> >>> -- >>> Keep Your Developer Skills Current with LearnDevNow! >>> The most comprehensive online learning library for Microsoft developers >>> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, >>> Metro Style Apps, more. Free future releases when you subscribe now! >>> http://p.sf.net/sfu/learndevnow-d2d >>> ___ >>> OpenBabel-discuss mailing list >>> OpenBabel-discuss@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >>> >>> >> >> >> >> >> _ >> Dr. Douglas R. Houston >> Lecturer >> Room 3.23 >> Institute of Structural and Molecular Biology >> Michael Swann Building >> King's Buildings >> University of Edinburgh >> Edinburgh, EH9 3JR, UK >> Tel. 0131 650 7358 >> > > > -- > Andrea Cadeddu > > -- > Nanochemistry Laboratory > Institut de Science et d'Ingénierie Supramoléculaires (I.S.I.S.) > Université de Strasbourg > 8, allée Gaspard Monge > F-67000 Strasbourg (France) > Tel: +33-(0)3-68855185 > Fax: +33-(0)3-68855161 > cade...@unistra.fr > > -- > Keep Your Developer Skills Current with LearnDevNow! > The most comprehensive online learning library for Microsoft developers > is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, > Metro Style Apps, more. Free future releases when you subscribe now! > http://p.sf.net/sfu/learndevnow-d2d > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > _ Dr. Douglas R. Houston Lecturer Room 3.23 Institute of Structural and Molecular Biology Michael Swann Building King's Buildings University of Edinburgh Edinburgh, EH9 3JR, UK Tel. 0131 650 7358 -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Chembl fs file
Hello, this sounds great. But i NEED Open Babel. This is not my decision. Any other ideas why this not work? With best Jochen Schreiber On Mar 5, 2012, at 3:22 AM, Jochen Schreiber wrote: > i have download the chembl_sdf archive and unpack it. > > The resulting sd file from that archive has 2.5 GB. > > Now i want to create the fs index datei from that sd file with: > > babel -isdf chemble_13.sdf -ofs chembl_13.fs > > This command works but if i want to search with an sd file against the fs > file it doesn't work. Perhaps chemfp ( http://code.google.com/p/chem-fingerprints/ )might be useful for this case, instead of using OpenBabel directly. I did the following with ChEBI 87, which I downloaded a few hours ago: % ob2fps --id-tag "ChEBI ID" ~/databases/ChEBI_complete.sdf.gz -o chebi.fps.gz == *** Open Babel Warning in Translate Cannot perform atom type translation: table cannot find requested types. == *** Open Babel Warning in Translate Cannot perform atom type translation: table cannot find requested types. % gzcat chebi.fps.gz | head -8 #FPS1 #num_bits=1021 #type=OpenBabel-FP2/1 #software=OpenBabel/2.2.3 #source=/Users/dalke/databases/ChEBI_complete.sdf.gz #date=2012-03-05T23:47:50 0201100201220884001000410100 CHEBI:165 00040200020002010200120001801000404100020008000101020220400200020002080008002000a0002a8400d0004010084008080801020240080201000201002008630100 CHEBI:776 # Get the first SD record and use that as the query % gzcat ~/databases/ChEBI_complete.sdf.gz | head -85 | ob2fps --in sdf --id-tag "ChEBI ID" | simsearch --threshold 0.9 chebi.fps #Simsearch/1 #num_bits=1021 #type=Tanimoto k=all threshold=0.9 #software=chemfp/1.1b3 #targets=chebi.fps #target_sources=ChEBI_lite.sdf.gz 25 CHEBI:165 CHEBI:15396 1.0 CHEBI:15397 1.0 CHEBI:15410 0.92857 CHEBI:15994 1.0 CHEBI:16074 1.0 CHEBI:16985 1.0 CHEBI:17762 1.0 CHEBI:179341.0 CHEBI:28952 1.0 CHEBI:30154 1.0 CHEBI:36492 0.92857 CHEBI:36742 0.92857 CHEBI:40611 0.92857 CHEBI:310.92857 CHEBI:165 1.0 CHEBI:4999 1.0 CHEBI:9577 0.9 CHEBI:18533 1.0 CHEBI:36496 0.92857 CHEBI:36612 1.0 CHEBI:36773 1.0 CHEBI:50040 0.9 CHEBI:50043 0.9 CHEBI:50045 0.9 CHEBI:50046 0.9 This says that there are 25 matches to CHEBI:165, which are CHEBI:15396, CHEBI:15397, CHEBI:15410, and more at 1.0 similarity down to CHEBI:50046 at 0.9 similarity. -- Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Chembl fs file
Hi Jochen, On Mar 6, 2012, at 10:45 AM, Jochen Schreiber wrote: > this sounds great. But i NEED Open Babel. This is not my decision. What does it mean to "NEED Open Babel"? Chemfp's 'ob2fps' command-line tool uses the Open Babel Python API for the fingerprint generation. Andrew da...@dalkescientific.com -- Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
[Open Babel] show structures as a picture
Hi all, after getting "OpenBabel" running for the first time (generation of exact masses from smiles and sdf) I wonder if there is any chance to convert smiles to a picture. Why this? I want to add the smiles into a SQLExpress database and it would be fine to get the structure as a picture when displaying in the GUI. This would be funny and would help me. Best regards Andreas -- Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] chemdraw bond lenghts
I can confirm that Doug's solution works. the series: babel -icdxml benzene.cdxml -osdf benzene3d.sdf --gen3D babel -isdf benzene3d.sdf -opdb benzeneViaSdfgen.pdb --gen2D works fine. thank you! ps: maybe we should add this /escamotage/ to the wiki? -- View this message in context: http://forums.openbabel.org/chemdraw-bond-lenghts-tp4449415p4452433.html Sent from the General discussion mailing list archive at Nabble.com. -- Virtualization & Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/ ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
