Hi James, It turned out the problem is about how to include the library in LDFLAGS. I tried two waysand the second way worked in my cgi:
# http://openbabel.org/docs/current/UseTheLibrary/CppExamples.html, didn't work in cgi #LDFLAGS= -lopenbabel -L /mypath/openbabel-openbabel-3-1-1/lib #-lgsl -lgslcblas #https://www.chimie.ens.fr/cheron/tutorials/openbabel/, worked great! LDFLAGS =-rdynamic /mypath/openbabel-openbabel-3-1-1/lib/libopenbabel.so -Wl,-rpath,/mypath/openbabel-openbabel-3-1-1/lib Thanks! Jiyao From: Craig James <cja...@emolecules.com> Sent: Saturday, August 29, 2020 1:53 PM To: Wang, Jiyao (NIH/NLM/NCBI) [E] <wang...@ncbi.nlm.nih.gov> Cc: openbabel-discuss@lists.sourceforge.net Subject: Re: [Open Babel] How to disable output stream in openbabel library? You are welcome! I used OpenBabel extensively in CGIs and embedded in a database, and had no problems. You just have to specify the right logging level (off). Craig On Sat, Aug 29, 2020 at 10:16 AM Wang, Jiyao (NIH/NLM/NCBI) [E] <wang...@ncbi.nlm.nih.gov<mailto:wang...@ncbi.nlm.nih.gov>> wrote: Thanks a lot, Craig! I will tri it out. Before I included openbabel library in the makefile, my cgi works. Once I included openbabel in my makefile, the cgi has 500 error. I didn’t even add my program using openbabel yet. So I may need to modify the openbabel library. Thanks! Jiyao From: Craig James <cja...@emolecules.com<mailto:cja...@emolecules.com>> Sent: Saturday, August 29, 2020 1:01 PM To: Wang, Jiyao (NIH/NLM/NCBI) [E] <wang...@ncbi.nlm.nih.gov<mailto:wang...@ncbi.nlm.nih.gov>> Cc: openbabel-discuss@lists.sourceforge.net<mailto:openbabel-discuss@lists.sourceforge.net> Subject: Re: [Open Babel] How to disable output stream in openbabel library? Try: obErrorLog.StopLogging(); And/or you may need to use SetOutputLevel()<http://openbabel.org/dev-api/classOpenBabel_1_1OBMessageHandler.shtml#ae467fbd6fca625ae5ee0ea066810280f>. Craig On Sat, Aug 29, 2020 at 9:23 AM Wang, Jiyao (NIH/NLM/NCBI) [E] via OpenBabel-discuss <openbabel-discuss@lists.sourceforge.net<mailto:openbabel-discuss@lists.sourceforge.net>> wrote: Hi, I need to use openbabel to add hydrogens for ligands in PDB structures. The executable program works. But when I included the code as part of the C++ cgi, it has the error 500 because the output stream messed up with the output stream in cgi. I tried to comment out cout, printf, etc and it still didn’t work. Any suggestions? The compile alone caused the problem. I added the following to compile with openbabel library: ========= CPPFLAGS = … \ -I /mypath/openbabel-openbabel-3-1-1/include/openbabel3 LDFLAGS= -lopenbabel -L /mypath/delphi/openbabel-openbabel-3-1-1/lib ========= Here is my small program: ========= #include <iostream> #include <fstream> using namespace std; using namespace OpenBabel; string addHydrogen(string& pdbStr) { string pdbHStr = ""; cout.rdbuf(NULL); cerr.rdbuf(NULL); clog.rdbuf(NULL); OBConversion conv; conv.SetInFormat("pdb"); conv.SetOutFormat("pdb"); OBMol mol; //conv.ReadFile(&mol,filepath); conv.ReadString(&mol,pdbStr); mol.AddHydrogens(); //string filepath2 = "./test.pdbH"; //conv.WriteFile(&mol,filepath2.c_str()); bool trimWhitespace = true; pdbHStr = conv.WriteString(&mol, trimWhitespace); return pdbHStr; } ========= Thanks! Jiyao Wang _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net<mailto:OpenBabel-discuss@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss -- --------------------------------- Craig A. James Chief Technology Officer eMolecules, Inc. 3430 Carmel Mountain Road, Suite 250 San Diego, CA 92121 --------------------------------- -- --------------------------------- Craig A. James Chief Technology Officer eMolecules, Inc. 3430 Carmel Mountain Road, Suite 250 San Diego, CA 92121 ---------------------------------
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