Commit 6c369628 authored by jdurrant's avatar jdurrant
Browse files

Minor updates.

parent eb406b72
......@@ -22,3 +22,4 @@ docs/docs
.ipynb_checkpoints
make.bat
docs
binana.zip
\ No newline at end of file
# BINANA 2.0
## Command-Line Use
See `./COMMAND-LINE-USE.md` for detailed instructions describing how to use BINANA
## Git Repository Contents
| Directory/File | Description
|-----------------------------------|------------------------------------------
| `./python/` | All Python code
| `./python/run_binana.py` | Script for command-line use
| `./python/binana/` | Python library (e.g., `import binana`)
| `./python/example/Examples.ipynb` | Jupyter notebook, Python-library demo
| `./javascript/lib/` | JavaScript library
| `./javascript/lib/Examples.ipynb` | Jupyter notebook, JavaScript-library demo
| `./javascript/lib/examples.html` | HTML file, JavaScript-library demo
| `./web_app/` | Web app
| `./web_app/src/` | Web-app source code
| `./web_app/binana.zip` | Compiled web-app
## Using BINANA
### Command-Line Use
See `./COMMAND_LINE_USE.md` for detailed instructions describing how to use BINANA
from the command line. Here is a simple example:
```bash
python3 run_binana.py -receptor /path/to/receptor.pdbqt -ligand /path/to/ligand.pdbqt -output_dir /path/to/output/directory/
```
## Python Library
### Python Library
The following files describe how to use BINANA as a Python library that can be
accessed from other Python scripts:
......@@ -19,11 +36,12 @@ accessed from other Python scripts:
don't use Jupyter.
- `./example/Examples.md`: A Markdown version of the notebook.
## JavaScript Library
### JavaScript Library
These files describe how to use BINANA as a JavaScript library that can be
accessed from the web browser (e.g., from web apps).
- `./javascript/lib/Examples.ipynb`: A Jupyter notebook demonstrating use.
- `./javascript/lib/Examples.ipynb.pdf`: A PDF version of the notebook, for
those who don't use Jupyter.
\ No newline at end of file
those who don't use Jupyter.
......@@ -2,16 +2,16 @@
# pip install transcrypt
# Clean previous version.
rm -rf ../__target__/ ./lib/
rm -rf ../python/__target__/ ./lib/
# Compile the python file.
cd ../
cd ../python/
# --nomin
transcrypt --build --ecom --verbose binana.py
cd -
# Move the javascript library to the lib directory.
mv ../__target__/ ./lib
mv ../python/__target__/ ./lib
# Copy aux files.
cp ./src_aux/* ./lib/
......
......@@ -10,10 +10,11 @@ parameters.params["receptor"]);var ligand=__left0__[0];var receptor=__left0__[1]
parameters.params["pi_pi_interacting_dist_cutoff"],parameters.params["pi_stacking_angle_tolerance"],parameters.params["T_stacking_angle_tolerance"],parameters.params["T_stacking_closest_dist_cutoff"],parameters.params["cation_pi_dist_cutoff"],parameters.params["salt_bridge_dist_cutoff"],pi_padding);for(var key of all_interacts["cat_pi"]["counts"].py_keys())all_interacts["pi_pi"]["counts"][key]=all_interacts["cat_pi"]["counts"][key];_write_main(parameters,ligand,receptor,all_interacts["closest"],all_interacts["close"],
all_interacts["hydrophobics"],all_interacts["hydrogen_bonds"],all_interacts["salt_bridges"],all_interacts["pi_pi"],all_interacts["cat_pi"],all_interacts["electrostatic_energies"],all_interacts["active_site_flexibility"],all_interacts["ligand_atom_types"])};export var _intro=function(){var version="1.2.1";var citation="BINANA: A Novel Algorithm for Ligand-Binding Characterization. Durrant JD, McCammon JA. J Mol Graph Model. 2011 Apr; 29(6): 888-893. doi: 10.1016/j.jmgm.2011.01.004";var lines=["","BINANA "+
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","python 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","python 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","python 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","python 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:",
"","```bash","python binana.py -receptor /path/to/receptor.pdbqt -ligand /path/to/ligand.pdbqt -output_dir /path/to/output/directory/ > errors.txt","```","","Though we recommend using program defaults, the following command-line tags can also be specified: `-close_contacts_dist1_cutoff` `-close_contacts_dist2_cutoff` `-electrostatic_dist_cutoff` `-active_site_flexibility_dist_cutoff` `-hydrophobic_dist_cutoff` `-hydrogen_bond_dist_cutoff` `-hydrogen_bond_angle_cutoff` `-pi_padding_dist` `-pi_pi_interacting_dist_cutoff` `-pi_stacking_angle_tolerance` `-T_stacking_angle_tolerance` `-T_stacking_closest_dist_cutoff` `-cation_pi_dist_cutoff` `-salt_bridge_dist_cutoff`",
"","For example, if you want to tell BINANA to detect only hydrogen bonds where the donor and acceptor are less than 3.0 angstroms distant, run:","","```bash","python binana.py -receptor /path/to/receptor.pdbqt -ligand /path/to/ligand.pdbqt -hydrogen_bond_dist_cutoff 3.0","```","","What follows is a detailed description of the BINANA algorithm and a further explaination of the optional parameters described above. Parameter names are enclosed in braces.","","Close Contacts","==============","","BINANA begins by identifying all ligand and protein atoms that come within `close_contacts_dist1_cutoff` angstroms of each other. These close-contact atoms are then characterized according to their respective AutoDock atom types, without regard for the receptor or ligand. The number of each pair of close-contact atoms of given AutoDock atom types is then tallied. For example, the program counts the number of times a hydrogen-bond accepting oxygen atom (atom type OA), either on the ligand or the receptor, comes within `close_contacts_dist1_cutoff` angstroms of a polar hydrogen atom (atom type HD) on the corresponding binding partner, be it the receptor or the ligand. A similar list of atom-type pairs is tallied for all ligand and receptor atoms that come within `close_contacts_dist2_cutoff` angstroms of each other, where `close_contacts_dist2_cutoff` > `close_contacts_dist1_cutoff`.",
"","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:",
"","```bash","python3 run_binana.py -receptor /path/to/receptor.pdbqt -ligand /path/to/ligand.pdbqt -output_dir /path/to/output/directory/ > errors.txt","```","","Though we recommend using program defaults, the following command-line tags can also be specified: `-close_contacts_dist1_cutoff` `-close_contacts_dist2_cutoff` `-electrostatic_dist_cutoff` `-active_site_flexibility_dist_cutoff` `-hydrophobic_dist_cutoff` `-hydrogen_bond_dist_cutoff` `-hydrogen_bond_angle_cutoff` `-pi_padding_dist` `-pi_pi_interacting_dist_cutoff` `-pi_stacking_angle_tolerance` `-T_stacking_angle_tolerance` `-T_stacking_closest_dist_cutoff` `-cation_pi_dist_cutoff` `-salt_bridge_dist_cutoff`",
"","For example, if you want to tell BINANA to detect only hydrogen bonds where the donor and acceptor are less than 3.0 angstroms distant, run:","","```bash","python3 run_binana.py -receptor /path/to/receptor.pdbqt -ligand /path/to/ligand.pdbqt -hydrogen_bond_dist_cutoff 3.0","```","","What follows is a detailed description of the BINANA algorithm and a further explaination of the optional parameters described above. Parameter names are enclosed in braces.","","Close Contacts","==============","",
"BINANA begins by identifying all ligand and protein atoms that come within `close_contacts_dist1_cutoff` angstroms of each other. These close-contact atoms are then characterized according to their respective AutoDock atom types, without regard for the receptor or ligand. The number of each pair of close-contact atoms of given AutoDock atom types is then tallied. For example, the program counts the number of times a hydrogen-bond accepting oxygen atom (atom type OA), either on the ligand or the receptor, comes within `close_contacts_dist1_cutoff` angstroms of a polar hydrogen atom (atom type HD) on the corresponding binding partner, be it the receptor or the ligand. A similar list of atom-type pairs is tallied for all ligand and receptor atoms that come within `close_contacts_dist2_cutoff` angstroms of each other, where `close_contacts_dist2_cutoff` > `close_contacts_dist1_cutoff`.",
"","Electrostatic Interactions","==========================","","For each atom-type pair of atoms that come within `electrostatic_dist_cutoff` angstroms of each other, as described above, a summed electrostatic energy is calculated using the Gasteiger partial charges assigned by AutoDockTools.","","Binding-Pocket Flexibility","==========================","","BINANA also provides useful information about the flexibility of a binding pocket. Each receptor atom that comes with `active_site_flexibility_dist_cutoff` angstroms of any ligand atom is characterized according to whether or not it belongs to a protein side chain or backbone. Additionally, the secondary structure of the corresponding protein residue of each atom, be it alpha helix, beta sheet, or other, is also determined. Thus, there are six possible characterizations for each atom: alpha-sidechain, alpha-backbone, beta-sidechain, beta-backbone, other-sidechain, other-backbone. The number of close-contact receptor atoms falling into each of these six categories is tallied as a metric of binding-site flexibility.",
"",'All protein atoms with the atom names "CA," "C," "O," or "N" are assumed to belong to the backbone. All other receptor atoms are assigned side-chain status. Determining the secondary structure of the corresponding residue of each close-contact receptor atom is more difficult. First, preliminary secondary-structure assignments are made based on the phi and psi angles of each residue. If phi in (-145, -35) and psi in (-70, 50), the residue is assumed to be in the alpha-helix conformation. If phi in [-180, -40) and psi in (90,180], or phi in [-180,-70) and psi in [-180, -165], the residue is assumed to be in the beta-sheet conformation. Otherwise, the secondary structure of the residue is labeled "other."',
"",'Inspection of actual alpha-helix structures revealed that the alpha carbon of an alpha-helix residue i is generally within 6.0 angstroms of the alpha carbon of an alpha-helix residue three residues away (i + 3 or i - 3). Any residue that has been preliminarily labeled "alpha helix" that fails to meet this criteria is instead labeled "other." Additionally, the residues of any alpha helix comprised of fewer than four consecutive residues are also labeled "other," as these tended belong to be small loops rather than genuine helices.',
......@@ -30,7 +31,7 @@ version,"============","","BINANA is released under the GNU General Public Licen
"","To detect T-stacking or edge-face interactions, every aromatic ring of the ligand is again compared to every aromatic ring of the receptor. If the centers of two rings are within `pi_pi_interacting_dist_cutoff` angstroms of each other, the angle between the two vectors normal to the planes of each ring is again calculated. If this angle shows that the two planes are within `T_stacking_angle_tolerance` degrees of being perpendicular, a second distance check is performed to verify that the two rings come within `T_stacking_closest_dist_cutoff` angstroms at their nearest point. If so, each of the coordinates of the ring center points is projected onto the plane of the opposite ring by identifying the nearest point on the respective plane. If either of the projected center points falls within the ring disk of the opposite ring, the two aromatic rings are said to participate in a T-stacking interaction.",
"","Finally, BINANA also detects cation-pi interactions between the ligand and the receptor. Each of the representative coordinates identifying charged functional groups is compared to each of the center points of the identified aromatic rings. If the distance between any of these pairs is less than `cation_pi_dist_cutoff` angstroms, the coordinate identifying the charged functional group is projected onto the plane of the aromatic ring by identifying the nearest point on that plane. If the projected coordinate falls within the ring disk of the aromatic ring, a cation-pi interaction is identified. ",
"","pi-pi stacking, T-stacking, and cation-pi interactions are tallied according to the secondary structure of the receptor residue containing the associated aromatic ring or charged functional group: alpha helix, beta sheet, or other.","","Ligand Atom Types and Rotatable Bonds","=====================================",""," BINANA also tallies the number of atoms of each AutoDock type present in the ligand as well as the number of ligand rotatable bonds identified by the AutoDockTools scripts used to generate the input PDBQT files.",
""," [- END INTRO -]",""];var wrapped=[];for(var line of lines)if(line=="")wrapped.append("");else if(__in__("python binana.py",line))wrapped.append(line);else wrapped.extend(textwrap.wrap(line,80));print("");print(" |[]{};");print(" .|[]{}");print(" .| {}");print(" | }");
""," [- END INTRO -]",""];var wrapped=[];for(var line of lines)if(line=="")wrapped.append("");else if(__in__("python3 run_binana.py",line))wrapped.append(line);else wrapped.extend(textwrap.wrap(line,80));print("");print(" |[]{};");print(" .|[]{}");print(" .| {}");print(" | }");
print(" | }");print(" | }");print(" .| };");print(" .| :'\"");print(' +. "');print(' =+ "/');print(' _= "/');
print(' -_ "/');print(' ,- "/');print(' <> "/');print(' |\\ "');print(" :'\"/ '\"");print(" .|[]{}; :'");print(" ,-_=+.|[]{};:'\"/|\\<>,-_=+ :'");
print(" |\\<> ;:");print(" /| {};");print(" /| ]{}");print(" /| []");print(" |\\ .|[");print(" \\< =+.");print(" >, -_=");
......
......@@ -7,8 +7,8 @@ __ipow__,__irshift__,__isub__,__ixor__,__jsUsePyNext__,__jsmod__,__k__,__kwargtr
filter,float,getattr,hasattr,input,int,isinstance,issubclass,len,list,map,max,min,object,ord,pow,print,property,py_TypeError,py_iter,py_metatype,py_next,py_reversed,py_typeof,range,repr,round,set,setattr,sorted,str,sum,tuple,zip}from"./org.transcrypt.__runtime__.js";import*as _closest from"./binana.interactions._closest.js";import*as _close from"./binana.interactions._close.js";import*as _electrostatic_energies from"./binana.interactions._electrostatic_energies.js";import*as _flexibility from"./binana.interactions._flexibility.js";
import*as _hydrophobics from"./binana.interactions._hydrophobics.js";import*as _hydrogen_bonds from"./binana.interactions._hydrogen_bonds.js";import*as _ligand_atom_types from"./binana.interactions._ligand_atom_types.js";import*as _pi_pi from"./binana.interactions._pi_pi.js";import*as _salt_bridges from"./binana.interactions._salt_bridges.js";import*as _cat_pi from"./binana.interactions._cat_pi.js";import*as __module_binana_interactions__ from"./binana.interactions.js";__nest__(binana,"interactions",
__module_binana_interactions__);import*as __module_binana__ from"./binana.js";__nest__(binana,"",__module_binana__);import{ACTIVE_SITE_FLEXIBILITY_DIST_CUTOFF,CATION_PI_DIST_CUTOFF,CLOSE_CONTACTS_DIST1_CUTOFF,CLOSE_CONTACTS_DIST2_CUTOFF,ELECTROSTATIC_DIST_CUTOFF,HYDROGEN_BOND_ANGLE_CUTOFF,HYDROGEN_BOND_DIST_CUTOFF,HYDROPHOBIC_DIST_CUTOFF,PI_PADDING_DIST,PI_PI_INTERACTING_DIST_CUTOFF,PI_STACKING_ANGLE_TOLERANCE,SALT_BRIDGE_DIST_CUTOFF,T_STACKING_ANGLE_TOLERANCE,T_STACKING_CLOSEST_DIST_CUTOFF}from"./binana.interactions.default_params.js";
import{_set_default}from"./binana._utils.shim.js";import*as default_params from"./binana.interactions.default_params.js";export{_electrostatic_energies,_hydrogen_bonds,HYDROGEN_BOND_ANGLE_CUTOFF,CLOSE_CONTACTS_DIST2_CUTOFF,_cat_pi,_closest,ACTIVE_SITE_FLEXIBILITY_DIST_CUTOFF,_ligand_atom_types,_salt_bridges,SALT_BRIDGE_DIST_CUTOFF,_set_default,_hydrophobics,_pi_pi,HYDROPHOBIC_DIST_CUTOFF,_flexibility,T_STACKING_ANGLE_TOLERANCE,default_params,PI_PI_INTERACTING_DIST_CUTOFF,PI_STACKING_ANGLE_TOLERANCE,
PI_PADDING_DIST,HYDROGEN_BOND_DIST_CUTOFF,CATION_PI_DIST_CUTOFF,CLOSE_CONTACTS_DIST1_CUTOFF,_close,T_STACKING_CLOSEST_DIST_CUTOFF,ELECTROSTATIC_DIST_CUTOFF};var __name__="binana.interactions";export var get_cation_pi=function(ligand,receptor,cutoff,pi_padding){if(typeof cutoff=="undefined"||cutoff!=null&&cutoff.hasOwnProperty("__kwargtrans__"))var cutoff=null;if(typeof pi_padding=="undefined"||pi_padding!=null&&pi_padding.hasOwnProperty("__kwargtrans__"))var pi_padding=null;var cutoff=_set_default(cutoff,
import{_set_default}from"./binana._utils.shim.js";import*as default_params from"./binana.interactions.default_params.js";export{PI_PI_INTERACTING_DIST_CUTOFF,_set_default,ACTIVE_SITE_FLEXIBILITY_DIST_CUTOFF,_closest,_hydrogen_bonds,_electrostatic_energies,PI_PADDING_DIST,_flexibility,T_STACKING_ANGLE_TOLERANCE,_ligand_atom_types,CATION_PI_DIST_CUTOFF,PI_STACKING_ANGLE_TOLERANCE,ELECTROSTATIC_DIST_CUTOFF,_salt_bridges,CLOSE_CONTACTS_DIST1_CUTOFF,default_params,_pi_pi,_hydrophobics,HYDROGEN_BOND_ANGLE_CUTOFF,
T_STACKING_CLOSEST_DIST_CUTOFF,_cat_pi,CLOSE_CONTACTS_DIST2_CUTOFF,SALT_BRIDGE_DIST_CUTOFF,_close,HYDROPHOBIC_DIST_CUTOFF,HYDROGEN_BOND_DIST_CUTOFF};var __name__="binana.interactions";export var get_cation_pi=function(ligand,receptor,cutoff,pi_padding){if(typeof cutoff=="undefined"||cutoff!=null&&cutoff.hasOwnProperty("__kwargtrans__"))var cutoff=null;if(typeof pi_padding=="undefined"||pi_padding!=null&&pi_padding.hasOwnProperty("__kwargtrans__"))var pi_padding=null;var cutoff=_set_default(cutoff,
CATION_PI_DIST_CUTOFF);var pi_padding=_set_default(pi_padding,PI_PADDING_DIST);return _cat_pi.get_cation_pi(ligand,receptor,cutoff,pi_padding)};export var get_salt_bridges=function(ligand,receptor,cutoff){if(typeof cutoff=="undefined"||cutoff!=null&&cutoff.hasOwnProperty("__kwargtrans__"))var cutoff=null;var cutoff=_set_default(cutoff,SALT_BRIDGE_DIST_CUTOFF);return _salt_bridges.get_salt_bridges(ligand,receptor,cutoff)};export var get_pi_pi=function(ligand,receptor,pi_pi_general_dist_cutoff,pi_stacking_angle_tol,
t_stacking_angle_tol,t_stacking_closest_dist_cutoff,pi_padding){if(typeof pi_pi_general_dist_cutoff=="undefined"||pi_pi_general_dist_cutoff!=null&&pi_pi_general_dist_cutoff.hasOwnProperty("__kwargtrans__"))var pi_pi_general_dist_cutoff=null;if(typeof pi_stacking_angle_tol=="undefined"||pi_stacking_angle_tol!=null&&pi_stacking_angle_tol.hasOwnProperty("__kwargtrans__"))var pi_stacking_angle_tol=null;if(typeof t_stacking_angle_tol=="undefined"||t_stacking_angle_tol!=null&&t_stacking_angle_tol.hasOwnProperty("__kwargtrans__"))var t_stacking_angle_tol=
null;if(typeof t_stacking_closest_dist_cutoff=="undefined"||t_stacking_closest_dist_cutoff!=null&&t_stacking_closest_dist_cutoff.hasOwnProperty("__kwargtrans__"))var t_stacking_closest_dist_cutoff=null;if(typeof pi_padding=="undefined"||pi_padding!=null&&pi_padding.hasOwnProperty("__kwargtrans__"))var pi_padding=null;var pi_pi_general_dist_cutoff=_set_default(pi_pi_general_dist_cutoff,PI_PI_INTERACTING_DIST_CUTOFF);var pi_stacking_angle_tol=_set_default(pi_stacking_angle_tol,PI_STACKING_ANGLE_TOLERANCE);
......
......@@ -5,7 +5,7 @@
'use strict';var binana={};import{AssertionError,AttributeError,BaseException,DeprecationWarning,Exception,IndexError,IterableError,KeyError,NotImplementedError,RuntimeWarning,StopIteration,UserWarning,ValueError,Warning,__JsIterator__,__PyIterator__,__Terminal__,__add__,__and__,__call__,__class__,__envir__,__eq__,__floordiv__,__ge__,__get__,__getcm__,__getitem__,__getslice__,__getsm__,__gt__,__i__,__iadd__,__iand__,__idiv__,__ijsmod__,__ilshift__,__imatmul__,__imod__,__imul__,__in__,__init__,__ior__,
__ipow__,__irshift__,__isub__,__ixor__,__jsUsePyNext__,__jsmod__,__k__,__kwargtrans__,__le__,__lshift__,__lt__,__matmul__,__mergefields__,__mergekwargtrans__,__mod__,__mul__,__ne__,__neg__,__nest__,__or__,__pow__,__pragma__,__proxy__,__pyUseJsNext__,__rshift__,__setitem__,__setproperty__,__setslice__,__sort__,__specialattrib__,__sub__,__super__,__t__,__terminal__,__truediv__,__withblock__,__xor__,abs,all,any,assert,bool,bytearray,bytes,callable,chr,copy,deepcopy,delattr,dict,dir,divmod,enumerate,
filter,float,getattr,hasattr,input,int,isinstance,issubclass,len,list,map,max,min,object,ord,pow,print,property,py_TypeError,py_iter,py_metatype,py_next,py_reversed,py_typeof,range,repr,round,set,setattr,sorted,str,sum,tuple,zip}from"./org.transcrypt.__runtime__.js";import*as _get_params from"./binana._cli_params._get_params.js";import*as _start from"./binana._start.js";import*as output from"./binana.output.js";import*as interactions from"./binana.interactions.js";import*as load_ligand_receptor from"./binana.load_ligand_receptor.js";
import*as fs from"./binana.fs.js";import*as __module_binana__ from"./binana.js";__nest__(binana,"",__module_binana__);export{interactions,fs,_start,output,_get_params,load_ligand_receptor};var __name__="__main__";export var _sys=binana.sys;export var run=function(args){if(typeof args=="undefined"||args!=null&&args.hasOwnProperty("__kwargtrans__"))var args=null;console.warn("You probably don't want to call this using JavaScript (Python-only function).");if(args===null)var args=_sys.argv.__getslice__(0,
import*as fs from"./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__";export var _sys=binana.sys;export var run=function(args){if(typeof args=="undefined"||args!=null&&args.hasOwnProperty("__kwargtrans__"))var args=null;console.warn("You probably don't want to call this using JavaScript (Python-only function).");if(args===null)var args=_sys.argv.__getslice__(0,
null,1);else for(var [i,a]of enumerate(args))args[i]=str(a);var cmd_params=_get_params.CommandLineParameters(args);if(cmd_params.params["test"])return;else if(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)};
//# sourceMappingURL=binana.map
\ No newline at end of file
......@@ -5,7 +5,7 @@
'use strict';var binana={};var math={};import{AssertionError,AttributeError,BaseException,DeprecationWarning,Exception,IndexError,IterableError,KeyError,NotImplementedError,RuntimeWarning,StopIteration,UserWarning,ValueError,Warning,__JsIterator__,__PyIterator__,__Terminal__,__add__,__and__,__call__,__class__,__envir__,__eq__,__floordiv__,__ge__,__get__,__getcm__,__getitem__,__getslice__,__getsm__,__gt__,__i__,__iadd__,__iand__,__idiv__,__ijsmod__,__ilshift__,__imatmul__,__imod__,__imul__,__in__,
__init__,__ior__,__ipow__,__irshift__,__isub__,__ixor__,__jsUsePyNext__,__jsmod__,__k__,__kwargtrans__,__le__,__lshift__,__lt__,__matmul__,__mergefields__,__mergekwargtrans__,__mod__,__mul__,__ne__,__neg__,__nest__,__or__,__pow__,__pragma__,__proxy__,__pyUseJsNext__,__rshift__,__setitem__,__setproperty__,__setslice__,__sort__,__specialattrib__,__sub__,__super__,__t__,__terminal__,__truediv__,__withblock__,__xor__,abs,all,any,assert,bool,bytearray,bytes,callable,chr,copy,deepcopy,delattr,dict,dir,
divmod,enumerate,filter,float,getattr,hasattr,input,int,isinstance,issubclass,len,list,map,max,min,object,ord,pow,print,property,py_TypeError,py_iter,py_metatype,py_next,py_reversed,py_typeof,range,repr,round,set,setattr,sorted,str,sum,tuple,zip}from"./org.transcrypt.__runtime__.js";import*as _math_functions from"./binana._utils._math_functions.js";import{Mol as _Mol}from"./binana._structure.mol.js";import{Point as _Point}from"./binana._structure.point.js";import*as __module_math__ from"./math.js";
__nest__(math,"",__module_math__);import*as __module_binana__ from"./binana.js";__nest__(binana,"",__module_binana__);export{_math_functions,_Point,_Mol};var __name__="binana.load_ligand_receptor";export var _ligand_receptor_dists=null;export var _ligand_receptor_aromatic_dists=null;export var from_texts=function(ligand_text,receptor_text){var ligand=_Mol();ligand.load_pdb_from_text(ligand_text);var receptor=_Mol();receptor.load_pdb_from_text(receptor_text);receptor.assign_secondary_structure();_clear_cache();
__nest__(math,"",__module_math__);import*as __module_binana__ from"./binana.js";__nest__(binana,"",__module_binana__);export{_Point,_math_functions,_Mol};var __name__="binana.load_ligand_receptor";export var _ligand_receptor_dists=null;export var _ligand_receptor_aromatic_dists=null;export var from_texts=function(ligand_text,receptor_text){var ligand=_Mol();ligand.load_pdb_from_text(ligand_text);var receptor=_Mol();receptor.load_pdb_from_text(receptor_text);receptor.assign_secondary_structure();_clear_cache();
return tuple([ligand,receptor])};export var from_files=function(ligand_filename,receptor_filename){var ligand=_Mol();ligand.load_pdb_file(ligand_filename);var receptor=_Mol();receptor.load_pdb_file(receptor_filename);receptor.assign_secondary_structure();_clear_cache();return tuple([ligand,receptor])};export var _clear_cache=function(){_ligand_receptor_dists=null;_ligand_receptor_aromatic_dists=null};export var _get_ligand_receptor_dists=function(ligand,receptor){if(_ligand_receptor_dists!==null)return _ligand_receptor_dists;
_ligand_receptor_dists=[];for(var ligand_atom_index of ligand.all_atoms.py_keys())for(var receptor_atom_index of receptor.all_atoms.py_keys()){var ligand_atom=ligand.all_atoms[ligand_atom_index];var receptor_atom=receptor.all_atoms[receptor_atom_index];var dist=ligand_atom.coordinates.dist_to(receptor_atom.coordinates);_ligand_receptor_dists.append(tuple([ligand_atom,receptor_atom,dist]))}return _ligand_receptor_dists};export var _get_ligand_receptor_aromatic_dists=function(ligand,receptor,pi_pi_general_dist_cutoff){if(_ligand_receptor_aromatic_dists!==
null)return _ligand_receptor_aromatic_dists;_ligand_receptor_aromatic_dists=[];for(var ligand_aromatic of ligand.aromatic_rings)for(var receptor_aromatic of receptor.aromatic_rings){var dist=ligand_aromatic.center.dist_to(receptor_aromatic.center);if(dist<pi_pi_general_dist_cutoff){var ligand_aromatic_norm_vector=_Point(ligand_aromatic.plane_coeff[0],ligand_aromatic.plane_coeff[1],ligand_aromatic.plane_coeff[2]);var receptor_aromatic_norm_vector=_Point(receptor_aromatic.plane_coeff[0],receptor_aromatic.plane_coeff[1],
......
......@@ -4,7 +4,7 @@
'use strict';var binana={};import{AssertionError,AttributeError,BaseException,DeprecationWarning,Exception,IndexError,IterableError,KeyError,NotImplementedError,RuntimeWarning,StopIteration,UserWarning,ValueError,Warning,__JsIterator__,__PyIterator__,__Terminal__,__add__,__and__,__call__,__class__,__envir__,__eq__,__floordiv__,__ge__,__get__,__getcm__,__getitem__,__getslice__,__getsm__,__gt__,__i__,__iadd__,__iand__,__idiv__,__ijsmod__,__ilshift__,__imatmul__,__imod__,__imul__,__in__,__init__,__ior__,
__ipow__,__irshift__,__isub__,__ixor__,__jsUsePyNext__,__jsmod__,__k__,__kwargtrans__,__le__,__lshift__,__lt__,__matmul__,__mergefields__,__mergekwargtrans__,__mod__,__mul__,__ne__,__neg__,__nest__,__or__,__pow__,__pragma__,__proxy__,__pyUseJsNext__,__rshift__,__setitem__,__setproperty__,__setslice__,__sort__,__specialattrib__,__sub__,__super__,__t__,__terminal__,__truediv__,__withblock__,__xor__,abs,all,any,assert,bool,bytearray,bytes,callable,chr,copy,deepcopy,delattr,dict,dir,divmod,enumerate,
filter,float,getattr,hasattr,input,int,isinstance,issubclass,len,list,map,max,min,object,ord,pow,print,property,py_TypeError,py_iter,py_metatype,py_next,py_reversed,py_typeof,range,repr,round,set,setattr,sorted,str,sum,tuple,zip}from"./org.transcrypt.__runtime__.js";import*as __module_binana__ from"./binana.js";__nest__(binana,"",__module_binana__);import*as vmd_state from"./binana.output._directory.vmd_state.js";import*as pdbs from"./binana.output._directory.pdbs.js";export{vmd_state,pdbs};var __name__=
filter,float,getattr,hasattr,input,int,isinstance,issubclass,len,list,map,max,min,object,ord,pow,print,property,py_TypeError,py_iter,py_metatype,py_next,py_reversed,py_typeof,range,repr,round,set,setattr,sorted,str,sum,tuple,zip}from"./org.transcrypt.__runtime__.js";import*as __module_binana__ from"./binana.js";__nest__(binana,"",__module_binana__);import*as vmd_state from"./binana.output._directory.vmd_state.js";import*as pdbs from"./binana.output._directory.pdbs.js";export{pdbs,vmd_state};var __name__=
"binana.output._directory";export var os=binana.os;export var make_directory_output=function(parameters,closest,close,active_site_flexibility,hydrophobics,hydrogen_bonds,pi_pi,cat_pi,salt_bridges,ligand,receptor){if(!os.path.exists(parameters.params["output_dir"]))os.mkdir(parameters.params["output_dir"]);binana.output._directory.pdbs.output_dir_pdbs(closest["mol"],parameters,close["mol"],active_site_flexibility["mols"]["alpha_helix"],active_site_flexibility["mols"]["beta_sheet"],active_site_flexibility["mols"]["other_2nd_structure"],
active_site_flexibility["mols"]["back_bone"],active_site_flexibility["mols"]["side_chain"],hydrophobics["mol"],hydrogen_bonds["mol"],pi_pi["mols"]["pi_stacking"],pi_pi["mols"]["T_stacking"],cat_pi["mol"],salt_bridges["mol"],ligand,receptor);binana.output._directory.vmd_state.vmd_state_file(parameters)};
......
......@@ -5,7 +5,7 @@
'use strict';var binana={};import{AssertionError,AttributeError,BaseException,DeprecationWarning,Exception,IndexError,IterableError,KeyError,NotImplementedError,RuntimeWarning,StopIteration,UserWarning,ValueError,Warning,__JsIterator__,__PyIterator__,__Terminal__,__add__,__and__,__call__,__class__,__envir__,__eq__,__floordiv__,__ge__,__get__,__getcm__,__getitem__,__getslice__,__getsm__,__gt__,__i__,__iadd__,__iand__,__idiv__,__ijsmod__,__ilshift__,__imatmul__,__imod__,__imul__,__in__,__init__,__ior__,
__ipow__,__irshift__,__isub__,__ixor__,__jsUsePyNext__,__jsmod__,__k__,__kwargtrans__,__le__,__lshift__,__lt__,__matmul__,__mergefields__,__mergekwargtrans__,__mod__,__mul__,__ne__,__neg__,__nest__,__or__,__pow__,__pragma__,__proxy__,__pyUseJsNext__,__rshift__,__setitem__,__setproperty__,__setslice__,__sort__,__specialattrib__,__sub__,__super__,__t__,__terminal__,__truediv__,__withblock__,__xor__,abs,all,any,assert,bool,bytearray,bytes,callable,chr,copy,deepcopy,delattr,dict,dir,divmod,enumerate,
filter,float,getattr,hasattr,input,int,isinstance,issubclass,len,list,map,max,min,object,ord,pow,print,property,py_TypeError,py_iter,py_metatype,py_next,py_reversed,py_typeof,range,repr,round,set,setattr,sorted,str,sum,tuple,zip}from"./org.transcrypt.__runtime__.js";import{OpenFile as _openFile}from"./binana._utils.shim.js";import*as _json from"./binana._utils.shim.js";import*as __module_binana__ from"./binana.js";__nest__(binana,"",__module_binana__);import*as pdb_file from"./binana.output.pdb_file.js";
import*as _log from"./binana.output._log.js";import*as dictionary from"./binana.output.dictionary.js";import*as _directory from"./binana.output._directory.js";export{pdb_file,_log,dictionary,_directory,_json,_openFile};var __name__="binana.output";export var _write_main=function(parameters,ligand,receptor,closest,close,hydrophobics,hydrogen_bonds,salt_bridges,pi_pi,cat_pi,electrostatic_energies,active_site_flexibility,ligand_atom_types){var json_output=binana.output.dictionary.collect(closest,close,
import*as _log from"./binana.output._log.js";import*as dictionary from"./binana.output.dictionary.js";import*as _directory from"./binana.output._directory.js";export{pdb_file,_directory,_log,_json,_openFile,dictionary};var __name__="binana.output";export var _write_main=function(parameters,ligand,receptor,closest,close,hydrophobics,hydrogen_bonds,salt_bridges,pi_pi,cat_pi,electrostatic_energies,active_site_flexibility,ligand_atom_types){var json_output=binana.output.dictionary.collect(closest,close,
hydrophobics,hydrogen_bonds,salt_bridges,pi_pi,cat_pi,electrostatic_energies,active_site_flexibility,ligand_atom_types,__kwargtrans__({ligand_rotatable_bonds:ligand.rotatable_bonds_count}));var log_output=binana.output._log.collect(parameters,ligand,closest,close,hydrophobics,hydrogen_bonds,salt_bridges,pi_pi,cat_pi,electrostatic_energies,active_site_flexibility,ligand_atom_types,json_output);if(parameters.params["output_json"]!=""){var f=_openFile(parameters.params["output_json"],"w");f.write(_json.dumps(json_output,
__kwargtrans__({indent:2,sort_keys:true,separators:tuple([",",": "])})));f.close()}if(parameters.params["output_file"]!="")binana.output.pdb_file.write(ligand,receptor,closest,close,hydrophobics,hydrogen_bonds,salt_bridges,pi_pi,cat_pi,active_site_flexibility,log_output,false,parameters.params["output_file"]);if(parameters.params["output_dir"]!="")_directory.make_directory_output(parameters,closest,close,active_site_flexibility,hydrophobics,hydrogen_bonds,pi_pi,cat_pi,salt_bridges,ligand,receptor)};
......
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\ No newline at end of file
......@@ -94,7 +94,7 @@ def _get_all_interactions(parameters):
def _intro():
# TODO: If you ever change below, be sure to update COMMAND-LINE-USE.md with
# TODO: If you ever change below, be sure to update COMMAND_LINE_USE.md with
# this file too!
version = "1.2.1"
......
......@@ -6,12 +6,12 @@ To run the BINANA command-line example, type the following into the Unix command
line, from the current directory:
```
python ../run_binana.py -receptor ./receptor.pdbqt -ligand ./ligand.pdbqt -output_dir ./cli_example_output/ > output.txt
python3 ../run_binana.py -receptor ./receptor.pdbqt -ligand ./ligand.pdbqt -output_dir ./cli_example_output/ > output.txt
```
A similar command should work from the Windows command line.
See `../README.md` for more details.
See `../COMMAND_LINE_USE.md` for more details.
## Jupyter Notebook
......
......@@ -2,12 +2,9 @@
// LICENSE.md or go to https://opensource.org/licenses/Apache-2.0 for full
// details. Copyright 2020 Jacob D. Durrant.
import * as binana from "./binana/binana";
import * as binana from "./binanajs/binana";
self.onmessage = function(e) {
// import * as binana from './binana/binana.js';
let pdbtxt = e.data[0];
let ligtxt = e.data[1];
let binanaParams = e.data[2];
......
......@@ -5,6 +5,7 @@
import { Any } from "@tensorflow/tfjs";
declare var Vue;
declare var jQuery;
/** An object containing the vue-component computed functions. */
let computedFunctions = {
......
......@@ -15,6 +15,7 @@ import ExampleLigandPDBQT from "../example/ATP.pdbqt";
import ExampleOutputPDBQT from "../example/binana_out.pdbqt";
declare var Vuex;
declare var jQuery;
interface IVueXStoreSetVar {
name: string;
......
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\ No newline at end of file
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