Commit aefbf6cf authored by jdurrant's avatar jdurrant
Browse files

Final update to version 2.0.

parent 97895a28
......@@ -23,4 +23,7 @@ docs/docs
make.bat
docs
binana.zip
binana_web_app.zip
.vscode
make_zip_files_for_releases.sh
releases
......@@ -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{OpenFile}from"./binana._utils.shim.js";import*as shim from"./binana._utils.shim.js";import*as __module_binana__ from"./binana.js";__nest__(binana,"",__module_binana__);export{shim,OpenFile};var __name__="binana.fs";export var save_file=
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}from"./binana._utils.shim.js";import*as shim from"./binana._utils.shim.js";import*as __module_binana__ from"./binana.js";__nest__(binana,"",__module_binana__);export{OpenFile,shim};var __name__="binana.fs";export var save_file=
function(filename,text){var f=OpenFile(filename,"w");f.write(text);f.close()};export var ls=function(){print(binana._utils.shim.fake_fs.py_keys())};export var load_file=function(filename){var f=OpenFile(filename,"r");var txt=f.read();f.close();return txt};
//# sourceMappingURL=binana.fs.map
\ No newline at end of file
......@@ -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{_ligand_atom_types,ELECTROSTATIC_DIST_CUTOFF,_close,_set_default,SALT_BRIDGE_DIST_CUTOFF,_flexibility,HYDROGEN_BOND_ANGLE_CUTOFF,_hydrogen_bonds,_cat_pi,T_STACKING_ANGLE_TOLERANCE,_pi_pi,HYDROGEN_BOND_DIST_CUTOFF,CATION_PI_DIST_CUTOFF,HYDROPHOBIC_DIST_CUTOFF,_closest,PI_STACKING_ANGLE_TOLERANCE,default_params,CLOSE_CONTACTS_DIST1_CUTOFF,PI_PI_INTERACTING_DIST_CUTOFF,PI_PADDING_DIST,
_electrostatic_energies,T_STACKING_CLOSEST_DIST_CUTOFF,CLOSE_CONTACTS_DIST2_CUTOFF,_hydrophobics,ACTIVE_SITE_FLEXIBILITY_DIST_CUTOFF,_salt_bridges};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{_set_default,_ligand_atom_types,PI_PI_INTERACTING_DIST_CUTOFF,T_STACKING_ANGLE_TOLERANCE,SALT_BRIDGE_DIST_CUTOFF,HYDROPHOBIC_DIST_CUTOFF,_hydrophobics,_electrostatic_energies,_close,PI_STACKING_ANGLE_TOLERANCE,CLOSE_CONTACTS_DIST2_CUTOFF,ACTIVE_SITE_FLEXIBILITY_DIST_CUTOFF,_hydrogen_bonds,_cat_pi,ELECTROSTATIC_DIST_CUTOFF,_pi_pi,_flexibility,_closest,HYDROGEN_BOND_ANGLE_CUTOFF,
CATION_PI_DIST_CUTOFF,CLOSE_CONTACTS_DIST1_CUTOFF,PI_PADDING_DIST,default_params,HYDROGEN_BOND_DIST_CUTOFF,T_STACKING_CLOSEST_DIST_CUTOFF,_salt_bridges};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{load_ligand_receptor,interactions,_start,output,fs,_get_params};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,fs,interactions,_start,output,_get_params};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{_Point,_Mol,_math_functions};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{_Mol,_Point,_math_functions};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{dictionary,_openFile,_directory,_json,pdb_file,_log};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{_json,_log,dictionary,_openFile,_directory,pdb_file};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)};
......
# Script for testing binana from the Unix command line. Best to use `python
# run_binana.py -test true` instead.
python3 ../run_binana.py -receptor receptor.pdbqt -ligand ligand.pdbqt -output_file test.pdb
python3 ../run_binana.py -receptor receptor.pdbqt -ligand ligand.pdbqt -output_dir ./cli_example_output/
......@@ -2,8 +2,6 @@
// LICENSE.md or go to https://opensource.org/licenses/Apache-2.0 for full
// details. Copyright 2020 Jacob D. Durrant.
import { Any } from "@tensorflow/tfjs";
declare var Vue;
declare var jQuery;
......
......@@ -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{OpenFile}from"./binana._utils.shim.js";import*as shim from"./binana._utils.shim.js";import*as __module_binana__ from"./binana.js";__nest__(binana,"",__module_binana__);export{shim,OpenFile};var __name__="binana.fs";export var save_file=
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}from"./binana._utils.shim.js";import*as shim from"./binana._utils.shim.js";import*as __module_binana__ from"./binana.js";__nest__(binana,"",__module_binana__);export{OpenFile,shim};var __name__="binana.fs";export var save_file=
function(filename,text){var f=OpenFile(filename,"w");f.write(text);f.close()};export var ls=function(){print(binana._utils.shim.fake_fs.py_keys())};export var load_file=function(filename){var f=OpenFile(filename,"r");var txt=f.read();f.close();return txt};
//# sourceMappingURL=binana.fs.map
\ No newline at end of file
......@@ -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{_ligand_atom_types,ELECTROSTATIC_DIST_CUTOFF,_close,_set_default,SALT_BRIDGE_DIST_CUTOFF,_flexibility,HYDROGEN_BOND_ANGLE_CUTOFF,_hydrogen_bonds,_cat_pi,T_STACKING_ANGLE_TOLERANCE,_pi_pi,HYDROGEN_BOND_DIST_CUTOFF,CATION_PI_DIST_CUTOFF,HYDROPHOBIC_DIST_CUTOFF,_closest,PI_STACKING_ANGLE_TOLERANCE,default_params,CLOSE_CONTACTS_DIST1_CUTOFF,PI_PI_INTERACTING_DIST_CUTOFF,PI_PADDING_DIST,
_electrostatic_energies,T_STACKING_CLOSEST_DIST_CUTOFF,CLOSE_CONTACTS_DIST2_CUTOFF,_hydrophobics,ACTIVE_SITE_FLEXIBILITY_DIST_CUTOFF,_salt_bridges};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{_set_default,_ligand_atom_types,PI_PI_INTERACTING_DIST_CUTOFF,T_STACKING_ANGLE_TOLERANCE,SALT_BRIDGE_DIST_CUTOFF,HYDROPHOBIC_DIST_CUTOFF,_hydrophobics,_electrostatic_energies,_close,PI_STACKING_ANGLE_TOLERANCE,CLOSE_CONTACTS_DIST2_CUTOFF,ACTIVE_SITE_FLEXIBILITY_DIST_CUTOFF,_hydrogen_bonds,_cat_pi,ELECTROSTATIC_DIST_CUTOFF,_pi_pi,_flexibility,_closest,HYDROGEN_BOND_ANGLE_CUTOFF,
CATION_PI_DIST_CUTOFF,CLOSE_CONTACTS_DIST1_CUTOFF,PI_PADDING_DIST,default_params,HYDROGEN_BOND_DIST_CUTOFF,T_STACKING_CLOSEST_DIST_CUTOFF,_salt_bridges};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{load_ligand_receptor,interactions,_start,output,fs,_get_params};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,fs,interactions,_start,output,_get_params};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{_Point,_Mol,_math_functions};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{_Mol,_Point,_math_functions};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{dictionary,_openFile,_directory,_json,pdb_file,_log};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{_json,_log,dictionary,_openFile,_directory,pdb_file};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)};
......
......@@ -16,7 +16,7 @@ cd -
# compatibility.
echo "Check for errors above. Enter to start compiling vendor js and other js files..."
cd dist
ls app*js vendors*js runtime*js styles*js | awk '{print "echo Compiling " $1 ";node ../node_modules/google-closure-compiler/cli.js " $1 " > t; mv t " $1}' | bash
ls app*js vendors*js runtime*js styles*js *Worker.js | awk '{print "echo Compiling " $1 ";node ../node_modules/google-closure-compiler/cli.js " $1 " > t; mv t " $1}' | bash
cd -
# If there is a .min.js file, delete any associated .js file.
......@@ -26,7 +26,7 @@ find dist/ -name "*.min.js" | sed "s/\.min\././g" | awk '{print "rm -rf " $0}' |
# closure compiler didn't put it right at the top.
cd dist
echo "/**
* BINANA Copyright 2019 Jacob Durrant
* BINANA Copyright 2021 Jacob Durrant
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
......@@ -40,15 +40,15 @@ echo "/**
* See the License for the specific language governing permissions and
* limitations under the License.
*/" > t
ls app.*js | awk '{print "cat t > " $1 ".tmp; cat " $1 " >> " $1 ".tmp; mv " $1 ".tmp " $1}' | bash
ls app.*js *Worker.js | awk '{print "cat t > " $1 ".tmp; cat " $1 " >> " $1 ".tmp; mv " $1 ".tmp " $1}' | bash
rm t
cd -
# Also create a ZIP file of the dist directory, for convenient distribution.
mv dist binana
rm binana.zip
zip -r binana.zip binana
mv binana dist
mv dist binana_web_app
rm binana_web_app.zip
zip -r binana_web_app.zip binana_web_app
mv binana_web_app dist
# Let the user know that compilation is finished. Works only on macOS.
say "Beep"
......@@ -65,8 +65,8 @@ module.exports = merge(common, {
},
{
from: 'src/binana',
to: 'binana'
from: 'src/binanajs',
to: 'binanajs'
},
// {
// from: 'src/styles/favicon.ico',
......@@ -92,10 +92,10 @@ module.exports = merge(common, {
// from: 'src/Webina/dist',
// to: 'Webina'
// },
{
from: 'src/minimal_example.html',
to: 'minimal_example.html'
},
// {
// from: 'src/minimal_example.html',
// to: 'minimal_example.html'
// },
// {
// from: 'src/babel_convert.html',
// to: 'babel_convert.html'
......
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