Re: [Open Babel] MSVCR80.dll error
Roe - there's something different about your setup compared to mine. Could you specify your OS, what exact version of MSVC++ you're using, whether you're building the trunk or the branch, and whether you're using Cmake or not. In general, these MS DLLs are available through VC++ redistributable packages (google "visual c++ redistributable 2005" etc). The OpenBabelGUI bundles this in with the installer. - Noel 2009/11/6 Rob Soe : > Hi all, > > I have been reading quite a lot for this MSVCR80.dll error and here is what > I found at: > > http://www.instant-registry-fixes.org/why-do-i-keep-receiving-msvcr80dll-missing-errors/ > > "If an application is unable to reach the dll in its side-by-side execution > folder, you may receive an error message similar to the one given below: > > This application has failed to start because MSVCR80.dll was not found. > Re-installing the application might fix the problem. > > This error occurs when an application that needs to use a DLL file from a > side-by-side assembly does not comprise an application manifest > file-application_name.exe.manifest or application_name.exe-in the WinSxS > folder specifying the assembly it uses. > > How do you resolve the missing MSVCR80.dll error? First check if the > manifest for the application is there in the WinSxS folder. If it is there, > then chances are that the manifest file is corrupt or damaged. You may try > to resolve the error by deleting this file and reinstalling your > application. > > However, if the file does not exist, then to permanently resolve the error > you may have to create a manifest for the application that is causing the > error and place it in the correct location. However, creating a manifest > requires you to have programming experience. If you do not have that, then > it is best that you report the error to the application manufacturer and ask > them to provide you with a solution." > > I don't know how to create a manifest file to resolve this error. Please > help. > > Thank you, > Rob > > On Thu, Nov 5, 2009 at 5:05 PM, Rob Soe wrote: >> >> Hi Noel, >> I just installed the OpenBabelGUI on my desktop and it runs fine. I >> converted a smile file to mol2 file and it worked. >> >> >> On Thu, Nov 5, 2009 at 4:38 AM, Noel O'Boyle wrote: >>> >>> If you install the OpenBabelGUI, does it work fine? >>> >>> 2009/11/5 Rob Soe : >>> > Hi all, >>> > >>> > I recently tried to run openbabel in my home pc. My lab pc has a >>> > working >>> > openbabel and I use it almost everyday. But it doesn't work at my home >>> > pc. I >>> > followed the instructions: >>> > http://openbabel.org/wiki/Install_%28MSVC%29. I >>> > built all the projects from OpenBabelOBF.sln except OBPythonOBF, >>> > OBJava, >>> > OBCSharp and OBGUI. >>> > >>> > When I tried to run the example1.vcproj, I got the following error: >>> > >>> > This application has failed to start because MSVCR80.dll was not found. >>> > Re-installing the application may fix this problem. >>> > >>> > May I know how to fix the error? >>> > >>> > >>> > Thanks a lot, >>> > Rob >>> > >>> > >>> > -- >>> > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 >>> > 30-Day >>> > trial. Simplify your report design, integration and deployment - and >>> > focus >>> > on >>> > what you do best, core application coding. Discover what's new with >>> > Crystal Reports now. http://p.sf.net/sfu/bobj-july >>> > ___ >>> > OpenBabel-discuss mailing list >>> > OpenBabel-discuss@lists.sourceforge.net >>> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >>> > >>> > >> > > > -- > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day > trial. Simplify your report design, integration and deployment - and focus > on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] installing open babel on cygwin failed
Hello Jana, I'm afraid that building OB on cygwin currently is broken (and has been for a long time). Some work was done on fixing it but problems remain. Is there some particular reason you require a cygwin build? - Noel 2009/11/6 Jana Kneslova : > Hello, > > I tried to install open babel version 2.2.0 on cygwin but wasn't successful. > The files configure.out and make.out are attached. > > Thanks, > > Jana > > -- > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day > trial. Simplify your report design, integration and deployment - and focus > on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
[Open Babel] Is RXN format is still supported
Hi, I have tested a few RXN files on Openbabel GUI on Windows but 0 result has been output. One of the RXN file is attached. I temporarily have to use Regexp to parse the RXN format to SDF as C# code as pasted below. It is even not trusted by myself. f = Regex.Replace(f, "\\$RXN(.*?)\\$MOL\\r?\\n", "", RegexOptions.Singleline); f = Regex.Replace(f, "\\$MOL", "", RegexOptions.Singleline); f = f + "\r\n"; Anyone knows what's the matter? Thanks, Charlie rxn-2.rxn Description: Binary data -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] MSVCR80.dll error
On Fri, Nov 6, 2009 at 11:43 PM, Rob Soe wrote: > Hi all, > > I have been reading quite a lot for this MSVCR80.dll error and here is what > I found at: > > http://www.instant-registry-fixes.org/why-do-i-keep-receiving-msvcr80dll-missing-errors/ > > "If an application is unable to reach the dll in its side-by-side execution > folder, you may receive an error message similar to the one given below: > > This application has failed to start because MSVCR80.dll was not found. > Re-installing the application might fix the problem. If you are using vista or windows 7, you can use sxstrace to find out what the exact problem is. See http://timvdm.blogspot.com/2009/04/sxstrace-making-manifest-hell-more.html for more info. Also, from http://avogadro.openmolecules.net/wiki/Compiling_on_Windows: NOTE: The redistributable manifest and the version Avogadro compile against do not match. This means that the redistributable's manifest must be altered in order to successfully use the redistributable DLLs. Go to "C:\Program Files\Microsoft Visual Studio 9.0\VC\redist\x86\Microsoft.VC90.CRT" and edit the file called "Microsoft.VC90.CRT.manifest". I used the version string, version="9.0.21022.8" After I changed that then the DLLs were successfully loaded and the mysterious error message stopped popping up. This was with the standard "free" version downloaded in January 2009. Cheers, Tim > This error occurs when an application that needs to use a DLL file from a > side-by-side assembly does not comprise an application manifest > file-application_name.exe.manifest or application_name.exe-in the WinSxS > folder specifying the assembly it uses. > > How do you resolve the missing MSVCR80.dll error? First check if the > manifest for the application is there in the WinSxS folder. If it is there, > then chances are that the manifest file is corrupt or damaged. You may try > to resolve the error by deleting this file and reinstalling your > application. > > However, if the file does not exist, then to permanently resolve the error > you may have to create a manifest for the application that is causing the > error and place it in the correct location. However, creating a manifest > requires you to have programming experience. If you do not have that, then > it is best that you report the error to the application manufacturer and ask > them to provide you with a solution." > > I don't know how to create a manifest file to resolve this error. Please > help. > > Thank you, > Rob > > On Thu, Nov 5, 2009 at 5:05 PM, Rob Soe wrote: >> >> Hi Noel, >> I just installed the OpenBabelGUI on my desktop and it runs fine. I >> converted a smile file to mol2 file and it worked. >> >> >> On Thu, Nov 5, 2009 at 4:38 AM, Noel O'Boyle wrote: >>> >>> If you install the OpenBabelGUI, does it work fine? >>> >>> 2009/11/5 Rob Soe : >>> > Hi all, >>> > >>> > I recently tried to run openbabel in my home pc. My lab pc has a >>> > working >>> > openbabel and I use it almost everyday. But it doesn't work at my home >>> > pc. I >>> > followed the instructions: >>> > http://openbabel.org/wiki/Install_%28MSVC%29. I >>> > built all the projects from OpenBabelOBF.sln except OBPythonOBF, >>> > OBJava, >>> > OBCSharp and OBGUI. >>> > >>> > When I tried to run the example1.vcproj, I got the following error: >>> > >>> > This application has failed to start because MSVCR80.dll was not found. >>> > Re-installing the application may fix this problem. >>> > >>> > May I know how to fix the error? >>> > >>> > >>> > Thanks a lot, >>> > Rob >>> > >>> > >>> > -- >>> > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 >>> > 30-Day >>> > trial. Simplify your report design, integration and deployment - and >>> > focus >>> > on >>> > what you do best, core application coding. Discover what's new with >>> > Crystal Reports now. http://p.sf.net/sfu/bobj-july >>> > ___ >>> > OpenBabel-discuss mailing list >>> > OpenBabel-discuss@lists.sourceforge.net >>> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >>> > >>> > >> > > > -- > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day > trial. Simplify your report design, integration and deployment - and focus > on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core app
Re: [Open Babel] MSVCR80.dll error
On Tue, Nov 10, 2009 at 4:21 PM, Tim Vandermeersch wrote: > On Fri, Nov 6, 2009 at 11:43 PM, Rob Soe wrote: >> Hi all, >> >> I have been reading quite a lot for this MSVCR80.dll error and here is what >> I found at: >> >> http://www.instant-registry-fixes.org/why-do-i-keep-receiving-msvcr80dll-missing-errors/ >> >> "If an application is unable to reach the dll in its side-by-side execution >> folder, you may receive an error message similar to the one given below: >> >> This application has failed to start because MSVCR80.dll was not found. >> Re-installing the application might fix the problem. > > If you are using vista or windows 7, you can use sxstrace to find out > what the exact problem is. See > http://timvdm.blogspot.com/2009/04/sxstrace-making-manifest-hell-more.html > for more info. > > Also, from http://avogadro.openmolecules.net/wiki/Compiling_on_Windows: > > NOTE: The redistributable manifest and the version Avogadro compile > against do not match. This means that the redistributable's manifest > must be altered in order to successfully use the redistributable DLLs. > Go to "C:\Program Files\Microsoft Visual Studio > 9.0\VC\redist\x86\Microsoft.VC90.CRT" and edit the file called > "Microsoft.VC90.CRT.manifest". I used the version string, > > version="9.0.21022.8" There are also programs to view, edit or remove manifests: ResourceTuner (commercial) & ResourceHacker (free) > After I changed that then the DLLs were successfully loaded and the > mysterious error message stopped popping up. This was with the > standard "free" version downloaded in January 2009. > > Cheers, > Tim > >> This error occurs when an application that needs to use a DLL file from a >> side-by-side assembly does not comprise an application manifest >> file-application_name.exe.manifest or application_name.exe-in the WinSxS >> folder specifying the assembly it uses. >> >> How do you resolve the missing MSVCR80.dll error? First check if the >> manifest for the application is there in the WinSxS folder. If it is there, >> then chances are that the manifest file is corrupt or damaged. You may try >> to resolve the error by deleting this file and reinstalling your >> application. >> >> However, if the file does not exist, then to permanently resolve the error >> you may have to create a manifest for the application that is causing the >> error and place it in the correct location. However, creating a manifest >> requires you to have programming experience. If you do not have that, then >> it is best that you report the error to the application manufacturer and ask >> them to provide you with a solution." >> >> I don't know how to create a manifest file to resolve this error. Please >> help. >> >> Thank you, >> Rob >> >> On Thu, Nov 5, 2009 at 5:05 PM, Rob Soe wrote: >>> >>> Hi Noel, >>> I just installed the OpenBabelGUI on my desktop and it runs fine. I >>> converted a smile file to mol2 file and it worked. >>> >>> >>> On Thu, Nov 5, 2009 at 4:38 AM, Noel O'Boyle wrote: If you install the OpenBabelGUI, does it work fine? 2009/11/5 Rob Soe : > Hi all, > > I recently tried to run openbabel in my home pc. My lab pc has a > working > openbabel and I use it almost everyday. But it doesn't work at my home > pc. I > followed the instructions: > http://openbabel.org/wiki/Install_%28MSVC%29. I > built all the projects from OpenBabelOBF.sln except OBPythonOBF, > OBJava, > OBCSharp and OBGUI. > > When I tried to run the example1.vcproj, I got the following error: > > This application has failed to start because MSVCR80.dll was not found. > Re-installing the application may fix this problem. > > May I know how to fix the error? > > > Thanks a lot, > Rob > > > -- > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 > 30-Day > trial. Simplify your report design, integration and deployment - and > focus > on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july > ___ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > >>> >> >> >> -- >> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day >> trial. Simplify your report design, integration and deployment - and focus >> on >> what you do best, core application coding. Discover what's new with >> Crystal Reports now. http://p.sf.net/sfu/bobj-july >> ___ >> OpenBabel-discuss mailing list >> OpenBabel-discuss@lists.sourceforge.net >> https://lists.sour
[Open Babel] SMARTS to SMILES
Hi Can anyone help to know, how to convert from SMARTS to SMILES. Thanks With Warm Regards Vinay __ Ask a question on any topic and get answers from real people. Go to Yahoo! Answers and share what you know at http://ca.answers.yahoo.com-- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] SMARTS to SMILES
Vinay M wrote: > Can anyone help to know, how to convert from SMARTS to SMILES. You can't. SMARTS is a superset of SMILES, and most SMARTS are not valid SMILES. Perhaps if you explain why you need to do this, we might be able to suggest a solution. Craig -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] SMARTS to SMILES
> Thanks for your reply, i was using smiles to view the > structure, so few are in smarts. I just wanted to convert smiles to smarts > and smarts to smiles. SMILES is a subset of SMARTS, so any SMILES string can be used as a SMARTS. The reverse is not true. I can design many SMARTS, which are not valid SMILES. For example [*] matches any atom. So no, as Craig said, you cannot interconvert them. -Geoff -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] SMARTS to SMILES
Hi Thanks a lot for your reply. I then use smiles for SMARTS. Vinay --- On Tue, 11/10/09, Geoffrey Hutchison wrote: From: Geoffrey Hutchison Subject: Re: [Open Babel] SMARTS to SMILES To: "Vinay M" Cc: "babel" Received: Tuesday, November 10, 2009, 8:55 PM > Thanks for your reply, i was using smiles to view the >structure, so few are in smarts. I just wanted to convert smiles to smarts and >smarts to smiles. SMILES is a subset of SMARTS, so any SMILES string can be used as a SMARTS. The reverse is not true. I can design many SMARTS, which are not valid SMILES. For example [*] matches any atom. So no, as Craig said, you cannot interconvert them. -Geoff __ Yahoo! Canada Toolbar: Search from anywhere on the web, and bookmark your favourite sites. Download it now http://ca.toolbar.yahoo.com.-- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
[Open Babel] SMARTS to SMILES
Hi Craig, Thanks for your reply, i was using smiles to view the structure, so few are in smarts. I just wanted to convert smiles to smarts and smarts to smiles. Thanks Kindly help With Warm regards Vinay --- On Tue, 11/10/09, Craig A. James wrote: From: Craig A. James Subject: Re: [Open Babel] SMARTS to SMILES To: "Vinay M" , openbabel-discuss@lists.sourceforge.net Received: Tuesday, November 10, 2009, 7:29 PM Vinay M wrote: > Can anyone help to know, how to convert from SMARTS to SMILES. You can't. SMARTS is a superset of SMILES, and most SMARTS are not valid SMILES. Perhaps if you explain why you need to do this, we might be able to suggest a solution. Craig __ Get a sneak peak at messages with a handy reading pane with All new Yahoo! Mail: http://ca.promos.yahoo.com/newmail/overview2/-- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] SMARTS to SMILES
Vinay, Thanks for your reply, i was using smiles to view the structure, so few are in smarts. I just wanted to convert smiles to smarts and smarts to smiles. Ok, now that I know what you're doing, I can suggest a possible way to do it, but it's not easy. Attached is a little Perl program that might work for 95% of the SMARTS you will encounter. With a bit of work, you might be able to improve it even more. (If you need this in C or C++, it's a lot harder.) You should be able to modify this example to suit your needs. This will parse a SMARTS, and also knows what symbols are valid for SMILES atoms and bonds. Any time it encounters a SMARTS atom that's not a valid SMILES atom, it is replaced it with '*'. C1[C,N]1 ==> C1*1 CC-=CC ==> CC-CC It's made more difficult by aromatic structures, for example, c1[n,c]1 becomes c1*1, which in theory is a valid aromatic SMILES, but in practice some interpreters don't consider it aromatic. It doesn't try to deal with bonds, and there are probably SMARTS that it doesn't get right, I just spent a few minutes on it. Craig smarts2smiles.pl Description: Perl program -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
[Open Babel] SMARTS to SMILES
Hi Craig, Thanks a lot, could you please send me the C or C++ code, since it deal with it a lot. I will follow those in perl and try. Thanks a lot. __ Looking for the perfect gift? Give the gift of Flickr! http://www.flickr.com/gift/-- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] SMARTS to SMILES
Vinay, > Thanks a lot, could you please send me the C or C++ code, > since it deal with it a lot. I will follow those in perl and try. Thanks > a lot. You're welcome, but I can't do it in C or C++. It would take days to do the same thing. Perl has very powerful string-handling functions, which is the only reason I could write the program so quickly. That's why we use Perl so much. You should try to find a way to incorporate a Perl program into your system. If you rewrite this in C or C++, it will be very difficult. Craig -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
