version,"============","","BINANA is released under the GNU General Public License (see http://www.gnu.org/licenses/gpl.html). If you use BINANA in your work, please cite:","",citation,"","Introduction, Examples of Use","=============================","","BINANA (BINding ANAlyzer) is a python-implemented algorithm for analyzing ligand binding. The program identifies key binding characteristics like hydrogen bonds, salt bridges, and pi interactions. As input, BINANA accepts receptor and ligand files in the PDBQT format. PDBQT files can be generated from the more common PDB file format using the free converter provided with AutoDockTools, available at http://mgltools.scripps.edu/downloads",
"","As output, BINANA describes ligand binding. Here's a simple example of how to run the program:","","```bash","python3 run_binana.py -receptor /path/to/receptor.pdbqt -ligand /path/to/ligand.pdbqt","```","","To create a single PDB file showing the different binding characteristics with those characteristics described in the PDB header:","","```bash","python3 run_binana.py -receptor /path/to/receptor.pdbqt -ligand /path/to/ligand.pdbqt -output_file /path/to/output.pdb","```","","Note that in the above example, errors and warnings are not written to the output file. To save these to a file, try:",
"","```bash","python3 run_binana.py -receptor /path/to/receptor.pdbqt -ligand /path/to/ligand.pdbqt -output_file /path/to/output.pdb > errors.txt","```","","To additionally output a JSON file with all the characterized interactions between the protein and ligand:","","```bash","python3 run_binana.py -receptor /path/to/receptor.pdbqt -ligand /path/to/ligand.pdbqt -output_json /path/to/output.json","```","","You can also send the program output to a directory, which will be created if it does not already exist. If a directory is specified, the program automatically separates the output PDB file into separate files for each interaction analyzed, and a description of the interactions is written to a file called `log.txt`. Additionally, a VMD state file is created so the results can be easily visualized in VMD, a free program available for download at http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD Again, to save warnings and errors, append something like `> errors.txt` to the end of your command:",
import*asfsfrom"./binana.fs.js";import*as__module_binana__from"./binana.js";__nest__(binana,"",__module_binana__);export{load_ligand_receptor,_start,interactions,output,_get_params,fs};var__name__="__main__";exportvar_sys=binana.sys;exportvarrun=function(args){if(typeofargs=="undefined"||args!=null&&args.hasOwnProperty("__kwargtrans__"))varargs=null;console.warn("You probably don't want to call this using JavaScript (Python-only function).");if(args===null)varargs=_sys.argv.__getslice__(0,
import*asfsfrom"./binana.fs.js";import*as__module_binana__from"./binana.js";__nest__(binana,"",__module_binana__);export{interactions,_start,load_ligand_receptor,fs,_get_params,output};var__name__="__main__";exportvar_sys=binana.sys;exportvarrun=function(args){if(typeofargs=="undefined"||args!=null&&args.hasOwnProperty("__kwargtrans__"))varargs=null;console.warn("You probably don't want to call this using JavaScript (Python-only function).");if(args===null)varargs=_sys.argv.__getslice__(0,
null,1);elsefor(var[i,a]ofenumerate(args))args[i]=str(a);varcmd_params=_get_params.CommandLineParameters(args);if(cmd_params.params["test"])return;elseif(cmd_params.okay_to_proceed()==false){print("Error: You need to specify the ligand and receptor PDBQT files to analyze using\nthe -receptor and -ligand tags from the command line.\n");_sys.exit(0);return}if(cmd_params.error!=""){print("Warning: The following command-line parameters were not recognized:");print(""+cmd_params.error+"\n")}_start._get_all_interactions(cmd_params)};
version,"============","","BINANA is released under the GNU General Public License (see http://www.gnu.org/licenses/gpl.html). If you use BINANA in your work, please cite:","",citation,"","Introduction, Examples of Use","=============================","","BINANA (BINding ANAlyzer) is a python-implemented algorithm for analyzing ligand binding. The program identifies key binding characteristics like hydrogen bonds, salt bridges, and pi interactions. As input, BINANA accepts receptor and ligand files in the PDBQT format. PDBQT files can be generated from the more common PDB file format using the free converter provided with AutoDockTools, available at http://mgltools.scripps.edu/downloads",
"","As output, BINANA describes ligand binding. Here's a simple example of how to run the program:","","```bash","python3 run_binana.py -receptor /path/to/receptor.pdbqt -ligand /path/to/ligand.pdbqt","```","","To create a single PDB file showing the different binding characteristics with those characteristics described in the PDB header:","","```bash","python3 run_binana.py -receptor /path/to/receptor.pdbqt -ligand /path/to/ligand.pdbqt -output_file /path/to/output.pdb","```","","Note that in the above example, errors and warnings are not written to the output file. To save these to a file, try:",
"","```bash","python3 run_binana.py -receptor /path/to/receptor.pdbqt -ligand /path/to/ligand.pdbqt -output_file /path/to/output.pdb > errors.txt","```","","To additionally output a JSON file with all the characterized interactions between the protein and ligand:","","```bash","python3 run_binana.py -receptor /path/to/receptor.pdbqt -ligand /path/to/ligand.pdbqt -output_json /path/to/output.json","```","","You can also send the program output to a directory, which will be created if it does not already exist. If a directory is specified, the program automatically separates the output PDB file into separate files for each interaction analyzed, and a description of the interactions is written to a file called `log.txt`. Additionally, a VMD state file is created so the results can be easily visualized in VMD, a free program available for download at http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD Again, to save warnings and errors, append something like `> errors.txt` to the end of your command:",
import*asfsfrom"./binana.fs.js";import*as__module_binana__from"./binana.js";__nest__(binana,"",__module_binana__);export{load_ligand_receptor,_start,interactions,output,_get_params,fs};var__name__="__main__";exportvar_sys=binana.sys;exportvarrun=function(args){if(typeofargs=="undefined"||args!=null&&args.hasOwnProperty("__kwargtrans__"))varargs=null;console.warn("You probably don't want to call this using JavaScript (Python-only function).");if(args===null)varargs=_sys.argv.__getslice__(0,
import*asfsfrom"./binana.fs.js";import*as__module_binana__from"./binana.js";__nest__(binana,"",__module_binana__);export{interactions,_start,load_ligand_receptor,fs,_get_params,output};var__name__="__main__";exportvar_sys=binana.sys;exportvarrun=function(args){if(typeofargs=="undefined"||args!=null&&args.hasOwnProperty("__kwargtrans__"))varargs=null;console.warn("You probably don't want to call this using JavaScript (Python-only function).");if(args===null)varargs=_sys.argv.__getslice__(0,
null,1);elsefor(var[i,a]ofenumerate(args))args[i]=str(a);varcmd_params=_get_params.CommandLineParameters(args);if(cmd_params.params["test"])return;elseif(cmd_params.okay_to_proceed()==false){print("Error: You need to specify the ligand and receptor PDBQT files to analyze using\nthe -receptor and -ligand tags from the command line.\n");_sys.exit(0);return}if(cmd_params.error!=""){print("Warning: The following command-line parameters were not recognized:");print(""+cmd_params.error+"\n")}_start._get_all_interactions(cmd_params)};
