Activity for Igor
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Igor committed [r1101] on Code
Optimizations and bug fixes
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Fixed a bug with MOL file output
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Moved superatom/spelling map loading out of image processing loop
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Added option to process multiple input files or give a folder as an input.
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configure: error: GOCR API check failed; make sure you have installed libgocr-dev package or check config.log
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Lyubomir, When you were building gocr did you run: make libs make all install The header should not be installed in src folder, and there certainly needs to be a library built.
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Lyobomir, Please download and build patched versions of gocr and openbabel available from osra.sf.net: https://sourceforge.net/projects/osra/files/gocr-patched/ https://sourceforge.net/projects/osra/files/openbabel-patched/ If osra configure script does not detect GOCR or OpenBabel headers you can use command-line options to point to the installation folders, for example: --with-gocr-include=/usr/local/include/gocr/ --with-openbabel-include=/usr/local/include/openbabel3/ Hope this helps, Igor
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Updated spelling and superatom dictionaries
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Fixed gocr call
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Implemented rotation detection 0,90,180,270 degrees
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Do not ping image type for ps and pdf files
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Updated configure.ac and configure for osx
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get_points did not actually return found points
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Improved bracket recognition
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Fix for extend terminal bonds to labels
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Improved arrow bond recognition and connection
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Added detection of arrow bonds
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Reverted previous commit
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Pick up best resolution per structure, not per page
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Improved recognition of horizontally fused characters
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Improved label assembly
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Improved superatom coordinate calculation
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Comment out debug output
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Improved dash bond recognition and aromatic ring perception
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Improved detection of old style aromatic rings
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Added check for in_ring when detected bracket atoms.
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Improved charge recognition close to hash bond and fixed total mol charge assignment
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Improvements for bracket recognition
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Improvements for remove_bracket_atoms() and remove_vertical_bonds_close_to_brackets()
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Added find_ions/add_ions functions
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Detect total charge on the top right corner of the bracket.
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Fix for find_wavy_bonds. Added Osmium to spelling dict.
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Andrius, I tested this on a couple of systems I use for development - centos 7 and fedora 35. The former is very old, the latter is the most recent I currently run (I know that fedora 36 is already out). Both have autoconf 2.69 which parses configure.ac without any problems. Given a choice I would prefer to target the oldest system available because my goal is to compile OSRA with static linking, then it can be run pretty much everywhere. If I do a static build on a more recent system there is a...
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Autoconf directives need updating
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I would say the solution then is to avoid Debian package builder, at least as far as OSRA is concerned.
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Andrius, Have you tried running the original OSRA configure without running autoconf? Igor
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Version bump to 2.1.4
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Fixed handling of reversables reaction arrows
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Installation problem on macOS - osra configure
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Great, glad to hear it resolves the problem!
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Guy, I see the following errors in the config.log where it's checking for openbabel: clang: error: no such file or directory: '/libxml2.a' clang: error: no such file or directory: '/libiconv.a' clang: error: no such file or directory: '/libz.a' Try installing libxml2, libiconv, and libz first? Statically linked. I also believe there is a brew version of OSRA floating around, though I neither created nor maintain it. Regards, Igor
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Jordi, There is no demo version I am afraid. Once you have purchased the binary code there are no other fees, renewal or otherwise. However, the purchase does not give you access to the newer binary versions of the software. The source code is always freely available of course, under the GNU GPL terms. Igor
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osra 2.1.3 release
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Fixed coordinate box calculation after rotation
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problems to install
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that's the header file, I am talking about the library. Either libocrad.a or libocrad.so.
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Jordi, Where was libocrad installed? You may have to specify the location with a command line option for configure.
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Jordi, There are options for configure script which allow to specify the location of the headers and such, not to mention standard environment variables like CPPFLAGS and LDFLAGS. The error you mention seems to come from the OpenMP library, I think you can include openmp support by using -fopenmp flag to either CPPFLAGS or LDFLAGS before running configure for OSRA.
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Jordi, OCRAD and GOCR are two separate libraries. Installing gocr has nothing to do with ocrad. You might want to examine config.log to see what exactly is happening that OSRA configure is unable to locate OCRAD installation.
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Alternatively you can uninstall wxWidgets prior to building OpenBabel.
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Jordi, It looks like your OpenBabel install finds pre-installed wxWidgets headers which do not quite match the version it expects. OSRA compilation does not require wxWidgets so you might want to look for a way to disable OpenBabel GUI build. I am using the following flags to build OpenBabel: cmake3 -DBUILD_SHARED=FALSE -DWITH_STATIC_INCHI=ON .. I think setting BUILD_SHARED=FALSE will disable building the GUI part of Openbabel.
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Alan, This exception is due to GraphicsMagick trying to process the PDF file through using Ghostscript instead of leaving it up to libpoppler. There are some config files you can edit to remove gs invocation from GraphicsMagick but I would have to google them myself at this point.
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Alan, I don't think OSRA parameters have anything to do with this error. This is specific to libpoppler processing of PDF files. The unpaper default value is 0, the recognized characters value is this string: oOcCnNHFsSBuUgMeEXYZRPp23456789AmThDGQ
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Alan, I haven't seen this error myself, but googling it comes up with this: https://bugs.launchpad.net/ubuntu/+source/xpdf/+bug/943195 Is it failing for every pdf file or just some of them? Perhaps updating/patching libpoppler might help.
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Remove auto-generated shell scripts
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Version bump to 2.1.2
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Package version specified once only in configure.ac and populated from templates.
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Fixed aromatic bond creation for OB 3.0.0
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Alan, the compiled version of OSRA comes with a statically linked binary it does not contain libosra, nor libosra_java. Just so you know before making a purchase. The executable does have the capability to process PDF files.
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Alan, Even if the shared libraries are visible for the command line tool they might not be accessible to the java code. Regarding your second question - recent versions of OSRA are using poppler library to process PDF files, it looks like you compiled OSRA without poppler - see the README file for required dependencies.
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Alan, libosra and libosra_java haven't been supported in a while unfortunately. If you got it to compile - great! Looking at the error message perhaps it is unable to find some dependent libraries during the java call - e.g. libpng?
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Correct.
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No, I meant installing MinGW on a Windows PC and compiling there. It might be possible to cross-compile on Linux, but I've never tried it.
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Yes, it is possible to build OSRA for Windows using MinGW compiler. You can also consider purchasing a pre-build binary version. There is an older plugin for OSRA and ChemDraw, it might be possible to update it to work with a more recent version of ChemDraw but I no longer maintain this plugin so it is entirely up to the user. The old plugin can be found here: https://sourceforge.net/projects/osra/files/plugins/chemoffice/
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Home
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Reverted to the old segmentation method
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Reverted to the old segmentation method
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Fixing the segment mask size calculation
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Fixed -k option single image processing
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Replaced segmentation routine
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Thank you for the quick response. I suspected that the problem is on my side!
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rieman and ricci tensors for schwarzschild metric
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Fixed total confidence computation bug
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About the terms of use for the binary version
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The binary version of OSRA is the same version that a user gets when getting the source code. It is governed by the same license - GNU GPL. If you are planning to include OSRA within your product that means that GNU GPL will apply to the whole package and the source code of your product will have to be made available to the end users under the GNU GPL terms.
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PDF file cannot be processed
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lopenbabel dependency fail
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Glad to hear it is working now!
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You need to add the location of your poppler libs (e.g /usr/local/lib) to ld.so.conf or LD_LIBRARY_PATH. You can check what libraries OSRA is linked against by running: ldd /path/to/osra/binary
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It looks like your installed version of poppler is not 0.73.0 but much older and does not have set_image_format function available. Either upgrade your installed version of poppler or remove that version and try to proceed with the one you build from source.
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Shiyi, Yes, two different installations of poppler could be a problem. Perhaps try removing one or the other? I would probably start by removing the static version. Igor
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Shiyi, I am not quite sure what your question has to do with the openbabel dependency, which is the topic of this ticket. OSRA can be compiled with poppler 0.73.0. The new release - OSRA 2.1.1 has been build with this version of poppler. The error message seems to indicate that configure cannot find libpng16.so. You can try to make sure it is installed and that it's included either in ld.so.conf or LD_LIBRRARY_PATH prior to running configure. Igor
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