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# Use in the Wild
Examples of real-world use.
javascript/lib/binana.fs.js
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......@@ -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 _utils from"./binana._utils.js";import*as __module_binana__ from"./binana.js";__nest__(binana,"",__module_binana__);export{_utils,shim,
OpenFile};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(shim.fake_fs.py_keys())};export var load_file=function(filename){var f=OpenFile(filename,"r");var txt=f.read();f.close();return txt};
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 _utils from"./binana._utils.js";import*as __module_binana__ from"./binana.js";__nest__(binana,"",__module_binana__);export{OpenFile,_utils,
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(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
javascript/lib/binana.interactions.js
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......@@ -7,10 +7,10 @@ __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{METAL_COORDINATION_DIST_CUTOFF}from"./binana.interactions.default_params.js";import*as _metal_coordination from"./binana.interactions._metal_coordination.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_halogen_bonds from"./binana.interactions._hydrogen_halogen_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,HALOGEN_BOND_DIST_CUTOFF,HYDROGEN_BOND_DIST_CUTOFF,HYDROGEN_HALOGEN_BOND_ANGLE_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{_closest,_flexibility,METAL_COORDINATION_DIST_CUTOFF,_pi_pi,PI_PI_INTERACTING_DIST_CUTOFF,CLOSE_CONTACTS_DIST1_CUTOFF,_cat_pi,PI_PADDING_DIST,_set_default,
_close,_metal_coordination,_electrostatic_energies,HYDROPHOBIC_DIST_CUTOFF,_salt_bridges,_ligand_atom_types,default_params,HALOGEN_BOND_DIST_CUTOFF,CATION_PI_DIST_CUTOFF,PI_STACKING_ANGLE_TOLERANCE,HYDROGEN_HALOGEN_BOND_ANGLE_CUTOFF,T_STACKING_CLOSEST_DIST_CUTOFF,_hydrogen_halogen_bonds,ELECTROSTATIC_DIST_CUTOFF,ACTIVE_SITE_FLEXIBILITY_DIST_CUTOFF,HYDROGEN_BOND_DIST_CUTOFF,CLOSE_CONTACTS_DIST2_CUTOFF,SALT_BRIDGE_DIST_CUTOFF,_hydrophobics,T_STACKING_ANGLE_TOLERANCE};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=
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{T_STACKING_ANGLE_TOLERANCE,_close,_pi_pi,PI_STACKING_ANGLE_TOLERANCE,SALT_BRIDGE_DIST_CUTOFF,_hydrogen_halogen_bonds,PI_PADDING_DIST,ACTIVE_SITE_FLEXIBILITY_DIST_CUTOFF,
T_STACKING_CLOSEST_DIST_CUTOFF,_flexibility,default_params,_metal_coordination,HYDROGEN_HALOGEN_BOND_ANGLE_CUTOFF,_salt_bridges,CATION_PI_DIST_CUTOFF,_ligand_atom_types,CLOSE_CONTACTS_DIST2_CUTOFF,_set_default,_closest,_cat_pi,HYDROPHOBIC_DIST_CUTOFF,METAL_COORDINATION_DIST_CUTOFF,HYDROGEN_BOND_DIST_CUTOFF,_hydrophobics,ELECTROSTATIC_DIST_CUTOFF,PI_PI_INTERACTING_DIST_CUTOFF,_electrostatic_energies,CLOSE_CONTACTS_DIST1_CUTOFF,HALOGEN_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);var t_stacking_angle_tol=_set_default(t_stacking_angle_tol,T_STACKING_ANGLE_TOLERANCE);var t_stacking_closest_dist_cutoff=_set_default(t_stacking_closest_dist_cutoff,T_STACKING_CLOSEST_DIST_CUTOFF);
var pi_padding=_set_default(pi_padding,PI_PADDING_DIST);return _pi_pi.get_pi_pi(ligand,receptor,pi_pi_general_dist_cutoff,pi_stacking_angle_tol,t_stacking_angle_tol,t_stacking_closest_dist_cutoff,pi_padding)};export var get_ligand_atom_types=function(ligand){return _ligand_atom_types.get_ligand_atom_types(ligand)};export var get_hydrogen_bonds=function(ligand,receptor,dist_cutoff,angle_cutoff){if(typeof dist_cutoff=="undefined"||dist_cutoff!=null&&dist_cutoff.hasOwnProperty("__kwargtrans__"))var dist_cutoff=
......
javascript/lib/binana.js
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'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{_get_params,_start,interactions,load_ligand_receptor,fs,output};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{interactions,output,_start,load_ligand_receptor,_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
javascript/lib/binana.load_ligand_receptor.js
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'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 _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{pi,sqrt}from"./math.js";import*as __module_binana__ from"./binana.js";
__nest__(binana,"",__module_binana__);export{pi,_Mol,_math_functions,sqrt,_Point};var __name__="binana.load_ligand_receptor";export var _ligand_receptor_dists_cache=dict({});export var _ligand_receptor_aromatic_dists=null;export var from_texts=function(ligand_text,receptor_text,max_cutoff){if(typeof max_cutoff=="undefined"||max_cutoff!=null&&max_cutoff.hasOwnProperty("__kwargtrans__"))var max_cutoff=null;var ligand=_Mol();ligand.load_pdb_from_text(ligand_text);var receptor=_Mol();if(max_cutoff===
__nest__(binana,"",__module_binana__);export{sqrt,pi,_Point,_math_functions,_Mol};var __name__="binana.load_ligand_receptor";export var _ligand_receptor_dists_cache=dict({});export var _ligand_receptor_aromatic_dists=null;export var from_texts=function(ligand_text,receptor_text,max_cutoff){if(typeof max_cutoff=="undefined"||max_cutoff!=null&&max_cutoff.hasOwnProperty("__kwargtrans__"))var max_cutoff=null;var ligand=_Mol();ligand.load_pdb_from_text(ligand_text);var receptor=_Mol();if(max_cutoff===
null)receptor.load_pdb_from_text(receptor_text);else receptor.load_pdb_from_text(receptor_text,null,ligand.min_x-max_cutoff,ligand.max_x+max_cutoff,ligand.min_y-max_cutoff,ligand.max_y+max_cutoff,ligand.min_z-max_cutoff,ligand.max_z+max_cutoff);receptor.assign_secondary_structure();_clear_cache();return tuple([ligand,receptor])};export var from_files=function(ligand_filename,receptor_filename,max_cutoff){if(typeof max_cutoff=="undefined"||max_cutoff!=null&&max_cutoff.hasOwnProperty("__kwargtrans__"))var max_cutoff=
null;var ligand=_Mol();ligand.load_pdb_file(ligand_filename);var receptor=_Mol();if(max_cutoff===null)receptor.load_pdb_file(receptor_filename);else receptor.load_pdb_file(receptor_filename,ligand.min_x-max_cutoff,ligand.max_x+max_cutoff,ligand.min_y-max_cutoff,ligand.max_y+max_cutoff,ligand.min_z-max_cutoff,ligand.max_z+max_cutoff);receptor.assign_secondary_structure();_clear_cache();return tuple([ligand,receptor])};export var _clear_cache=function(){_ligand_receptor_dists_cache=dict({});_ligand_receptor_aromatic_dists=
null};export var _get_coor_mol_dists=function(atom,coor,mol_all_atoms,max_dist_sqr,dist_inf_list){for(var mol_atom of mol_all_atoms){var mol_coor=mol_atom.coordinates;var delta_x=mol_coor.x-coor.x;var summed=delta_x*delta_x;if(summed>max_dist_sqr)continue;var delta_y=mol_coor.y-coor.y;summed+=delta_y*delta_y;if(summed>max_dist_sqr)continue;var delta_z=mol_coor.z-coor.z;summed+=delta_z*delta_z;if(summed>max_dist_sqr)continue;var dist=sqrt(summed);var val=tuple([atom,mol_atom,dist]);dist_inf_list.append(val)}};
......
javascript/lib/binana.output._directory.js
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'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 shim from"./binana._utils.shim.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,shim,pdbs};var __name__="binana.output._directory";export var os=shim;export var make_directory_output=function(parameters,closest,close,active_site_flexibility,hydrophobics,hydrogen_bonds,halogen_bonds,pi_pi,cat_pi,salt_bridges,metal_coordinations,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"],
export{pdbs,vmd_state,shim};var __name__="binana.output._directory";export var os=shim;export var make_directory_output=function(parameters,closest,close,active_site_flexibility,hydrophobics,hydrogen_bonds,halogen_bonds,pi_pi,cat_pi,salt_bridges,metal_coordinations,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"],halogen_bonds["mol"],pi_pi["mols"]["pi_stacking"],pi_pi["mols"]["T_stacking"],cat_pi["mol"],salt_bridges["mol"],metal_coordinations["mol"],ligand,receptor);binana.output._directory.vmd_state.vmd_state_file(parameters)};
//# sourceMappingURL=binana.output._directory.map
\ No newline at end of file
javascript/lib/binana.output.js
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......@@ -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 csv from"./binana.output.csv.js";import*as dictionary from"./binana.output.dictionary.js";import*as _directory from"./binana.output._directory.js";export{_json,_directory,_log,csv,_openFile,pdb_file,dictionary};var __name__="binana.output";export var _write_main=function(parameters,ligand,receptor,closest,close,hydrophobics,hydrogen_bonds,halogen_bonds,salt_bridges,metal_coordinations,pi_pi,cat_pi,electrostatic_energies,active_site_flexibility,
import*as _log from"./binana.output._log.js";import*as csv from"./binana.output.csv.js";import*as dictionary from"./binana.output.dictionary.js";import*as _directory from"./binana.output._directory.js";export{_json,_log,pdb_file,_openFile,dictionary,_directory,csv};var __name__="binana.output";export var _write_main=function(parameters,ligand,receptor,closest,close,hydrophobics,hydrogen_bonds,halogen_bonds,salt_bridges,metal_coordinations,pi_pi,cat_pi,electrostatic_energies,active_site_flexibility,
ligand_atom_types){var json_output=binana.output.dictionary.collect(closest,close,hydrophobics,hydrogen_bonds,halogen_bonds,salt_bridges,metal_coordinations,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,halogen_bonds,salt_bridges,metal_coordinations,pi_pi,cat_pi,electrostatic_energies,active_site_flexibility,
ligand_atom_types,json_output);if(parameters.params["output_csv"]!=""){var csv_txt=csv.collect(json_output);var f=_openFile(parameters.params["output_csv"],"w");f.write(csv_txt);f.close()}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,halogen_bonds,salt_bridges,metal_coordinations,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,halogen_bonds,pi_pi,cat_pi,salt_bridges,metal_coordinations,ligand,receptor)};
......
web_app/src/binanajs/binana.fs.js
View file @ 1ff8d3dd
......@@ -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 _utils from"./binana._utils.js";import*as __module_binana__ from"./binana.js";__nest__(binana,"",__module_binana__);export{_utils,shim,
OpenFile};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(shim.fake_fs.py_keys())};export var load_file=function(filename){var f=OpenFile(filename,"r");var txt=f.read();f.close();return txt};
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 _utils from"./binana._utils.js";import*as __module_binana__ from"./binana.js";__nest__(binana,"",__module_binana__);export{OpenFile,_utils,
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(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
web_app/src/binanajs/binana.interactions.js
View file @ 1ff8d3dd
......@@ -7,10 +7,10 @@ __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{METAL_COORDINATION_DIST_CUTOFF}from"./binana.interactions.default_params.js";import*as _metal_coordination from"./binana.interactions._metal_coordination.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_halogen_bonds from"./binana.interactions._hydrogen_halogen_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,HALOGEN_BOND_DIST_CUTOFF,HYDROGEN_BOND_DIST_CUTOFF,HYDROGEN_HALOGEN_BOND_ANGLE_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{_closest,_flexibility,METAL_COORDINATION_DIST_CUTOFF,_pi_pi,PI_PI_INTERACTING_DIST_CUTOFF,CLOSE_CONTACTS_DIST1_CUTOFF,_cat_pi,PI_PADDING_DIST,_set_default,
_close,_metal_coordination,_electrostatic_energies,HYDROPHOBIC_DIST_CUTOFF,_salt_bridges,_ligand_atom_types,default_params,HALOGEN_BOND_DIST_CUTOFF,CATION_PI_DIST_CUTOFF,PI_STACKING_ANGLE_TOLERANCE,HYDROGEN_HALOGEN_BOND_ANGLE_CUTOFF,T_STACKING_CLOSEST_DIST_CUTOFF,_hydrogen_halogen_bonds,ELECTROSTATIC_DIST_CUTOFF,ACTIVE_SITE_FLEXIBILITY_DIST_CUTOFF,HYDROGEN_BOND_DIST_CUTOFF,CLOSE_CONTACTS_DIST2_CUTOFF,SALT_BRIDGE_DIST_CUTOFF,_hydrophobics,T_STACKING_ANGLE_TOLERANCE};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=
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{T_STACKING_ANGLE_TOLERANCE,_close,_pi_pi,PI_STACKING_ANGLE_TOLERANCE,SALT_BRIDGE_DIST_CUTOFF,_hydrogen_halogen_bonds,PI_PADDING_DIST,ACTIVE_SITE_FLEXIBILITY_DIST_CUTOFF,
T_STACKING_CLOSEST_DIST_CUTOFF,_flexibility,default_params,_metal_coordination,HYDROGEN_HALOGEN_BOND_ANGLE_CUTOFF,_salt_bridges,CATION_PI_DIST_CUTOFF,_ligand_atom_types,CLOSE_CONTACTS_DIST2_CUTOFF,_set_default,_closest,_cat_pi,HYDROPHOBIC_DIST_CUTOFF,METAL_COORDINATION_DIST_CUTOFF,HYDROGEN_BOND_DIST_CUTOFF,_hydrophobics,ELECTROSTATIC_DIST_CUTOFF,PI_PI_INTERACTING_DIST_CUTOFF,_electrostatic_energies,CLOSE_CONTACTS_DIST1_CUTOFF,HALOGEN_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);var t_stacking_angle_tol=_set_default(t_stacking_angle_tol,T_STACKING_ANGLE_TOLERANCE);var t_stacking_closest_dist_cutoff=_set_default(t_stacking_closest_dist_cutoff,T_STACKING_CLOSEST_DIST_CUTOFF);
var pi_padding=_set_default(pi_padding,PI_PADDING_DIST);return _pi_pi.get_pi_pi(ligand,receptor,pi_pi_general_dist_cutoff,pi_stacking_angle_tol,t_stacking_angle_tol,t_stacking_closest_dist_cutoff,pi_padding)};export var get_ligand_atom_types=function(ligand){return _ligand_atom_types.get_ligand_atom_types(ligand)};export var get_hydrogen_bonds=function(ligand,receptor,dist_cutoff,angle_cutoff){if(typeof dist_cutoff=="undefined"||dist_cutoff!=null&&dist_cutoff.hasOwnProperty("__kwargtrans__"))var dist_cutoff=
......
web_app/src/binanajs/binana.js
View file @ 1ff8d3dd
......@@ -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{_get_params,_start,interactions,load_ligand_receptor,fs,output};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{interactions,output,_start,load_ligand_receptor,_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
web_app/src/binanajs/binana.load_ligand_receptor.js
View file @ 1ff8d3dd
......@@ -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 _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{pi,sqrt}from"./math.js";import*as __module_binana__ from"./binana.js";
__nest__(binana,"",__module_binana__);export{pi,_Mol,_math_functions,sqrt,_Point};var __name__="binana.load_ligand_receptor";export var _ligand_receptor_dists_cache=dict({});export var _ligand_receptor_aromatic_dists=null;export var from_texts=function(ligand_text,receptor_text,max_cutoff){if(typeof max_cutoff=="undefined"||max_cutoff!=null&&max_cutoff.hasOwnProperty("__kwargtrans__"))var max_cutoff=null;var ligand=_Mol();ligand.load_pdb_from_text(ligand_text);var receptor=_Mol();if(max_cutoff===
__nest__(binana,"",__module_binana__);export{sqrt,pi,_Point,_math_functions,_Mol};var __name__="binana.load_ligand_receptor";export var _ligand_receptor_dists_cache=dict({});export var _ligand_receptor_aromatic_dists=null;export var from_texts=function(ligand_text,receptor_text,max_cutoff){if(typeof max_cutoff=="undefined"||max_cutoff!=null&&max_cutoff.hasOwnProperty("__kwargtrans__"))var max_cutoff=null;var ligand=_Mol();ligand.load_pdb_from_text(ligand_text);var receptor=_Mol();if(max_cutoff===
null)receptor.load_pdb_from_text(receptor_text);else receptor.load_pdb_from_text(receptor_text,null,ligand.min_x-max_cutoff,ligand.max_x+max_cutoff,ligand.min_y-max_cutoff,ligand.max_y+max_cutoff,ligand.min_z-max_cutoff,ligand.max_z+max_cutoff);receptor.assign_secondary_structure();_clear_cache();return tuple([ligand,receptor])};export var from_files=function(ligand_filename,receptor_filename,max_cutoff){if(typeof max_cutoff=="undefined"||max_cutoff!=null&&max_cutoff.hasOwnProperty("__kwargtrans__"))var max_cutoff=
null;var ligand=_Mol();ligand.load_pdb_file(ligand_filename);var receptor=_Mol();if(max_cutoff===null)receptor.load_pdb_file(receptor_filename);else receptor.load_pdb_file(receptor_filename,ligand.min_x-max_cutoff,ligand.max_x+max_cutoff,ligand.min_y-max_cutoff,ligand.max_y+max_cutoff,ligand.min_z-max_cutoff,ligand.max_z+max_cutoff);receptor.assign_secondary_structure();_clear_cache();return tuple([ligand,receptor])};export var _clear_cache=function(){_ligand_receptor_dists_cache=dict({});_ligand_receptor_aromatic_dists=
null};export var _get_coor_mol_dists=function(atom,coor,mol_all_atoms,max_dist_sqr,dist_inf_list){for(var mol_atom of mol_all_atoms){var mol_coor=mol_atom.coordinates;var delta_x=mol_coor.x-coor.x;var summed=delta_x*delta_x;if(summed>max_dist_sqr)continue;var delta_y=mol_coor.y-coor.y;summed+=delta_y*delta_y;if(summed>max_dist_sqr)continue;var delta_z=mol_coor.z-coor.z;summed+=delta_z*delta_z;if(summed>max_dist_sqr)continue;var dist=sqrt(summed);var val=tuple([atom,mol_atom,dist]);dist_inf_list.append(val)}};
......
web_app/src/binanajs/binana.output._directory.js
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......@@ -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 shim from"./binana._utils.shim.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,shim,pdbs};var __name__="binana.output._directory";export var os=shim;export var make_directory_output=function(parameters,closest,close,active_site_flexibility,hydrophobics,hydrogen_bonds,halogen_bonds,pi_pi,cat_pi,salt_bridges,metal_coordinations,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"],
export{pdbs,vmd_state,shim};var __name__="binana.output._directory";export var os=shim;export var make_directory_output=function(parameters,closest,close,active_site_flexibility,hydrophobics,hydrogen_bonds,halogen_bonds,pi_pi,cat_pi,salt_bridges,metal_coordinations,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"],halogen_bonds["mol"],pi_pi["mols"]["pi_stacking"],pi_pi["mols"]["T_stacking"],cat_pi["mol"],salt_bridges["mol"],metal_coordinations["mol"],ligand,receptor);binana.output._directory.vmd_state.vmd_state_file(parameters)};
//# sourceMappingURL=binana.output._directory.map
\ No newline at end of file
web_app/src/binanajs/binana.output.js
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'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 csv from"./binana.output.csv.js";import*as dictionary from"./binana.output.dictionary.js";import*as _directory from"./binana.output._directory.js";export{_json,_directory,_log,csv,_openFile,pdb_file,dictionary};var __name__="binana.output";export var _write_main=function(parameters,ligand,receptor,closest,close,hydrophobics,hydrogen_bonds,halogen_bonds,salt_bridges,metal_coordinations,pi_pi,cat_pi,electrostatic_energies,active_site_flexibility,
import*as _log from"./binana.output._log.js";import*as csv from"./binana.output.csv.js";import*as dictionary from"./binana.output.dictionary.js";import*as _directory from"./binana.output._directory.js";export{_json,_log,pdb_file,_openFile,dictionary,_directory,csv};var __name__="binana.output";export var _write_main=function(parameters,ligand,receptor,closest,close,hydrophobics,hydrogen_bonds,halogen_bonds,salt_bridges,metal_coordinations,pi_pi,cat_pi,electrostatic_energies,active_site_flexibility,
ligand_atom_types){var json_output=binana.output.dictionary.collect(closest,close,hydrophobics,hydrogen_bonds,halogen_bonds,salt_bridges,metal_coordinations,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,halogen_bonds,salt_bridges,metal_coordinations,pi_pi,cat_pi,electrostatic_energies,active_site_flexibility,
ligand_atom_types,json_output);if(parameters.params["output_csv"]!=""){var csv_txt=csv.collect(json_output);var f=_openFile(parameters.params["output_csv"],"w");f.write(csv_txt);f.close()}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,halogen_bonds,salt_bridges,metal_coordinations,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,halogen_bonds,pi_pi,cat_pi,salt_bridges,metal_coordinations,ligand,receptor)};
......
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