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        "author": "Matan Drory Retwitzer",
        "author_email": "matandro@post.bgu.ac.il",
        "bugtrack_url": null,
        "classifiers": [
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: MIT License",
            "Operating System :: OS Independent",
            "Programming Language :: Python :: 3",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
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        "description": "# RNAfbinv 2.0\n\nRNAfbinv is a fragment based RNA design tool. It uses a simulated annealing process to optimize a 2D RNA structure.<br/>\nThe similarity is based on fragment based design. A tree alignment is done based on nodes (structural motifs).<br/>\nNodes are comparable if they are both bounded motifs (stems) or unbounded motifs (multi loop, interior loops, bulges ect...).<br/>\nEach iteration the target motif tree will be aligned to the current candidate tree.<br/>\nThe best alignment with the addition of other valuable features will generate a design score.<br/>\nDesign score of 0 is exact fit but even higher scores can generate a good candidate.\n\n## Attaching Vienna RNA\n\n[Vienna RNA package](https://www.tbi.univie.ac.at/RNA/ \"Vienna RNA home\") is required for RNAfbinv to work. This must be installed separately.<br/>\nCurrent version was tested with Vienna 2.4 and above. RNAfbinv will identify Vienna package if it's bin directory is in PATH.<br/>\nIf you wish to link a specific installation of Vienna set the VIENNA_PATH environment variable to the correct bin directory.\n\nYou can set Vienna location in python\n```python\nimport os\nos.environ['VIENNA_PATH'] = \"VIENNA_BIN_DIR_PATH\"\n```\n\nor directly via the vienna script\n```python\nfrom rnafbinv import vienna\nvienna.set_vienna_path(\"VIENNA_BIN_DIR_PATH\")\n```\n\n## Usage\n\nThe design process can be ran using the following code:\n```python\nfrom rnafbinv import RNAfbinvCL\nRNAfbinvCL.main(command_line_arguments)\n```\n\nTo generate a tree for a specific sequence / structure:<br/>\nStructure is a dot bracket notation structure and sequence is an IUPAC string with the same length\n```python\nfrom rnafbinv import shapiro_tree_aligner\nshapiro_tree_aligner.get_tree(sructure, sequence)\n```\n\nTo compare two trees and score them:\nalignment_rules has a default value and is optional\n```python\nfrom rnafbinv import shapiro_tree_aligner\nshapiro_tree_aligner.align_trees(source_tree, tree_target, alignment_rules)\n```\n\n### Command line arguments:\n\n```\nUsage: python3 RNAsfbinvCL [Options]\n    -h : Shows usage text\n    -i <number of iterations> : sets the number of simulated annealing iterations (default is 100)\n    --seed <random number generator seed> : a long number that is used by the random number generator\n    -t <number of look ahead attempts> : number of look head mutation attempts for each iteration (default is 4)\n    -e : designs a circular RNA (default is False)\n    -m <motif[,...]> : comma separated list of motifs to preserve\n                       motif: <motif No>[M|H|E|I|S|B]<motif No of bases>\n                       Use ListMotifs.listMotif(structure) to retrieve a list of legal motifs for a given structure,  \n    -s <starting sequence> : the initial sequence for the simulated annealing process\n    -r : force starting simulated annealing with a random sequence\n    -p <MFE|centroid> : uses RNAfold centroid or MFE folding. (default is MFE)\n    --verbose : Additional info message on simulation process\n    --debug : Debug information\n    -l <log file path> : Logging information will be written to a given file path (rewrites file if exists)\n    --length <length diff> : The resulting sequence size is target structure length +- length diff (default it 0)\n\n    -f <input file path> : Path of ini file that includes mandatory information. Some options can also be set via file.\n                           command line options take precedence.\n    List of available configurations (* are mandetory and will be requested via command line if not inserted):\n    *TARGET_STRUCTURE=<target structure>\n    *TARGET_SEQUENCE=<target sequence>\n    TARGET_ENERGY=<target energy>\n    TARGET_MR=<target mutational robustness>\n    SEED=<random seed>\n    STARTING_SEQUENCE=<starting sequence>\n    ITERATION=<number of simulated annealing iterations>\n```\n\n### File input:\n\n```\n# mandatory\nTARGET_STRUCTURE=<target structure>\nTARGET_SEQUENCE=<target sequence>\n# optional\nTARGET_ENERGY=<target energy>\nTARGET_MR=<target mutational robustness>\nSEED=<random seed>\nSTARTING_SEQUENCE=<starting sequence>\nITERATION=<number of simulated annealing iterations>\n```\n\n## GUI / Command line\n\nYou can download the RNAfbinv wrapper from [RNAfbinv2.0 user application]()<br/>\nIt includes python code to run the GUI / command line and the [VARNA](http://varna.lri.fr/ \"VARNA rna homepage\") java package to generate 2D images.<br/>\nIf you remove the VARNA jar or do not have java installed, images will not be generated but the design process will proceed normally.<br/><br/>\n\nTo run command line just use the '-cl' flag for RNAfbinv.py. by default a GUI version will run.\n\nTo specify Vienna package location please update the 'VIENNA' parameter in config.ini (or set VIENNA_PATH environment variable)<br/>\nTo specify Java location please update the 'JAVA' parameter in config.ini (or set JAVA_PATH environment variable)<br/>\nIn both cases you need to specify the folder where the binary file sits. Only needed if not specified in PATH.\n\n## Webserver\n\nRNAfbinv2.0 can be found in a web server combined with incaRNAtion. The webserver generates starting seeds using incaRNAtion global sampling algorithm.<br/>\nTe seed sequences are then sent to RNAfbinv2.0 for design. [incaRNAfbinv web server](https://www.cs.bgu.ac.il/incaRNAfbinv/ \"incaRNAtion & RNAfbinv\")\n\n",
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