Halogen bonds, updates to web-app UI, etc.

CHANGES.md

 Changes
 =======
 
+WIP
+---
+
+1. Can select multiple interactions at once.
+2. PNG file included in download from "Save" button. Also, log.txt file, for those not comfortable with JSON.
+3. Bonds now color coded.
+4. Certain interactions turned on by default.
+5. Clear button changed to "Reset" because resets to default value.
+6. No more coloring by molecule, interaction, etc. Too confusing.
+7. JSZip now dynamic import.
+8. zip download now includes vmd state directory.
+9. Vmd state file centers on ligand automatically.
+10. changed hydrogen_bond_dist_cutoff and hydrogen_bond_angle_cutoff parameter names to hydrogen_halogen_bond_dist_cutoff
+hydrogen_halogen_bond_angle_cutoff
+11. Removed ability to toggle on and off cylinder interactions, to simplify UI. Always on for those interaction where appropriate.
+12. Some interactions are shown as spheres, others as bonds. Keeps it simplier.
+
+Halogen bonds mention in all documentation?
+Halogen bonds counted twice? Good to check. In the chart in log file.
+
 2.0
 ---
 

COMMAND_LINE_USE.md

@@ -95,8 +95,8 @@ python3 run_binana.py -receptor /path/to/receptor.pdbqt -ligand /path/to/ligand.
 Though we recommend using program defaults, the following command-line tags can
 also be specified: `-close_contacts_dist1_cutoff` `-close_contacts_dist2_cutoff`
 `-electrostatic_dist_cutoff` `-active_site_flexibility_dist_cutoff`
-`-hydrophobic_dist_cutoff` `-hydrogen_bond_dist_cutoff`
-`-hydrogen_bond_angle_cutoff` `-pi_padding_dist`
+`-hydrophobic_dist_cutoff` `-hydrogen_halogen_bond_dist_cutoff`
+`-hydrogen_halogen_bond_angle_cutoff` `-pi_padding_dist`
 `-pi_pi_interacting_dist_cutoff` `-pi_stacking_angle_tolerance`
 `-T_stacking_angle_tolerance` `-T_stacking_closest_dist_cutoff`
 `-cation_pi_dist_cutoff` `-salt_bridge_dist_cutoff`
@@ -105,7 +105,7 @@ For example, if you want to tell BINANA to detect only hydrogen bonds where the
 donor and acceptor are less than 3.0 angstroms distant, run:
 
 ```bash
-python3 run_binana.py -receptor /path/to/receptor.pdbqt -ligand /path/to/ligand.pdbqt -hydrogen_bond_dist_cutoff 3.0
+python3 run_binana.py -receptor /path/to/receptor.pdbqt -ligand /path/to/ligand.pdbqt -hydrogen_halogen_bond_dist_cutoff 3.0
 ```
 
 What follows is a detailed description of the BINANA algorithm and a further
@@ -195,9 +195,9 @@ BINANA allows hydroxyl and amine groups to act as hydrogen-bond donors. Oxygen
 and nitrogen atoms can act as hydrogen-bond acceptors. Fairly liberal cutoffs
 are implemented in order to accommodate low-resolution crystal structures. A
 hydrogen bond is identified if the hydrogen-bond donor comes within
-`hydrogen_bond_dist_cutoff` angstroms of the hydrogen-bond acceptor, and the
+`hydrogen_halogen_bond_dist_cutoff` angstroms of the hydrogen-bond acceptor, and the
 angle formed between the donor, the hydrogen atom, and the acceptor is no
-greater than `hydrogen_bond_angle_cutoff` degrees. BINANA tallies the number of
+greater than `hydrogen_halogen_bond_angle_cutoff` degrees. BINANA tallies the number of
 hydrogen bonds according to the secondary structure of the receptor atom, the
 side-chain/backbone status of the receptor atom, and the location (ligand or
 receptor) of the hydrogen bond donor. Thus there are twelve possible

javascript/compile.sh

@@ -7,7 +7,7 @@ rm -rf ../python/__target__/ ./lib/
 # Compile the python file.
 cd ../python/
 # --nomin
-transcrypt --build --ecom --verbose binana.py
+transcrypt --build --nomin --ecom --verbose binana.py
 cd -
 
 # Move the javascript library to the lib directory.

javascript/lib/__future__.js

-'use strict';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";var __name__="__future__";export var all_feature_names=[];
+// Transcrypt'ed from Python, 2021-11-05 16:24:09
+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';
+var __name__ = '__future__';
+export var all_feature_names = [];
 
 //# sourceMappingURL=__future__.map
\ No newline at end of file

javascript/lib/binana._cli_params._get_params.js

@@ -2,14 +2,89 @@
 // LICENSE.md or go to https://opensource.org/licenses/Apache-2.0 for full
 // details. Copyright 2020 Jacob D. Durrant.
 
-'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{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,LIGAND,OUTPUT_DIR,OUTPUT_FILE,OUTPUT_JSON,PI_PADDING_DIST,PI_PI_INTERACTING_DIST_CUTOFF,PI_STACKING_ANGLE_TOLERANCE,RECEPTOR,SALT_BRIDGE_DIST_CUTOFF,TEST,T_STACKING_ANGLE_TOLERANCE,T_STACKING_CLOSEST_DIST_CUTOFF}from"./binana.interactions.default_params.js";var __name__="binana._cli_params._get_params";export var os=binana.os;export var CommandLineParameters=__class__("CommandLineParameters",[object],{__module__:__name__,params:dict({}),get is_num(){return __get__(this,
-function(self,num){try{var t=float(num);return t}catch(__except0__){if(isinstance(__except0__,ValueError))return num;else throw __except0__;}})},get __init__(){return __get__(this,function(self,parameters){self.params["close_contacts_dist1_cutoff"]=CLOSE_CONTACTS_DIST1_CUTOFF;self.params["close_contacts_dist2_cutoff"]=CLOSE_CONTACTS_DIST2_CUTOFF;self.params["electrostatic_dist_cutoff"]=ELECTROSTATIC_DIST_CUTOFF;self.params["active_site_flexibility_dist_cutoff"]=ACTIVE_SITE_FLEXIBILITY_DIST_CUTOFF;
-self.params["hydrophobic_dist_cutoff"]=HYDROPHOBIC_DIST_CUTOFF;self.params["hydrogen_bond_dist_cutoff"]=HYDROGEN_BOND_DIST_CUTOFF;self.params["hydrogen_bond_angle_cutoff"]=HYDROGEN_BOND_ANGLE_CUTOFF;self.params["pi_padding_dist"]=PI_PADDING_DIST;self.params["pi_pi_interacting_dist_cutoff"]=PI_PI_INTERACTING_DIST_CUTOFF;self.params["pi_stacking_angle_tolerance"]=PI_STACKING_ANGLE_TOLERANCE;self.params["T_stacking_angle_tolerance"]=T_STACKING_ANGLE_TOLERANCE;self.params["T_stacking_closest_dist_cutoff"]=
-T_STACKING_CLOSEST_DIST_CUTOFF;self.params["cation_pi_dist_cutoff"]=CATION_PI_DIST_CUTOFF;self.params["salt_bridge_dist_cutoff"]=SALT_BRIDGE_DIST_CUTOFF;self.params["receptor"]=RECEPTOR;self.params["ligand"]=LIGAND;self.params["output_dir"]=OUTPUT_DIR;self.params["output_file"]=OUTPUT_FILE;self.params["output_json"]=OUTPUT_JSON;self.params["test"]=TEST;for(var index=0;index<len(parameters);index++){var item=parameters[index];if(len(item)>0&&item[0]=="-"){var key=item.py_replace("-","");var value=
-self.is_num(parameters[index+1]);if(__in__(key,list(self.params.py_keys()))){self.params[key]=value;parameters[index]="";parameters[index+1]=""}}}self.error="";for(var index=1;index<len(parameters);index++){var item=parameters[index];if(item!="")self.error=self.error+item+" "}if(self.params["output_dir"]!=""&&self.params["output_dir"].__getslice__(-1,null,1)!=os.sep)self.params["output_dir"]=self.params["output_dir"]+os.sep;var single_output_files=[tuple(["output_file","pdb"]),tuple(["output_json",
-"json"])];for(var [single_output_file,ext]of single_output_files)if(self.params["output_dir"]!=""&&self.params[single_output_file]=="")self.params[single_output_file]=self.params["output_dir"]+"output."+ext})},get okay_to_proceed(){return __get__(this,function(self){if(self.params["receptor"]!=""&&self.params["ligand"]!="")return true;else return false})}});
+// Transcrypt'ed from Python, 2021-11-05 16:24:08
+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 {ACTIVE_SITE_FLEXIBILITY_DIST_CUTOFF, CATION_PI_DIST_CUTOFF, CLOSE_CONTACTS_DIST1_CUTOFF, CLOSE_CONTACTS_DIST2_CUTOFF, ELECTROSTATIC_DIST_CUTOFF, HYDROGEN_HALOGEN_BOND_ANGLE_CUTOFF, HYDROGEN_HALOGEN_BOND_DIST_CUTOFF, HYDROPHOBIC_DIST_CUTOFF, LIGAND, OUTPUT_DIR, OUTPUT_FILE, OUTPUT_JSON, PI_PADDING_DIST, PI_PI_INTERACTING_DIST_CUTOFF, PI_STACKING_ANGLE_TOLERANCE, RECEPTOR, SALT_BRIDGE_DIST_CUTOFF, TEST, T_STACKING_ANGLE_TOLERANCE, T_STACKING_CLOSEST_DIST_CUTOFF} from './binana.interactions.default_params.js';
+var __name__ = 'binana._cli_params._get_params';
+export var sep = '/';
+export var CommandLineParameters =  __class__ ('CommandLineParameters', [object], {
+	__module__: __name__,
+	params: dict ({}),
+	get is_num () {return __get__ (this, function (self, num) {
+		try {
+			var t = float (num);
+			return t;
+		}
+		catch (__except0__) {
+			if (isinstance (__except0__, ValueError)) {
+				return num;
+			}
+			else {
+				throw __except0__;
+			}
+		}
+	});},
+	get __init__ () {return __get__ (this, function (self, parameters) {
+		self.params ['close_contacts_dist1_cutoff'] = CLOSE_CONTACTS_DIST1_CUTOFF;
+		self.params ['close_contacts_dist2_cutoff'] = CLOSE_CONTACTS_DIST2_CUTOFF;
+		self.params ['electrostatic_dist_cutoff'] = ELECTROSTATIC_DIST_CUTOFF;
+		self.params ['active_site_flexibility_dist_cutoff'] = ACTIVE_SITE_FLEXIBILITY_DIST_CUTOFF;
+		self.params ['hydrophobic_dist_cutoff'] = HYDROPHOBIC_DIST_CUTOFF;
+		self.params ['hydrogen_halogen_bond_dist_cutoff'] = HYDROGEN_HALOGEN_BOND_DIST_CUTOFF;
+		self.params ['hydrogen_halogen_bond_angle_cutoff'] = HYDROGEN_HALOGEN_BOND_ANGLE_CUTOFF;
+		self.params ['pi_padding_dist'] = PI_PADDING_DIST;
+		self.params ['pi_pi_interacting_dist_cutoff'] = PI_PI_INTERACTING_DIST_CUTOFF;
+		self.params ['pi_stacking_angle_tolerance'] = PI_STACKING_ANGLE_TOLERANCE;
+		self.params ['T_stacking_angle_tolerance'] = T_STACKING_ANGLE_TOLERANCE;
+		self.params ['T_stacking_closest_dist_cutoff'] = T_STACKING_CLOSEST_DIST_CUTOFF;
+		self.params ['cation_pi_dist_cutoff'] = CATION_PI_DIST_CUTOFF;
+		self.params ['salt_bridge_dist_cutoff'] = SALT_BRIDGE_DIST_CUTOFF;
+		self.params ['receptor'] = RECEPTOR;
+		self.params ['ligand'] = LIGAND;
+		self.params ['output_dir'] = OUTPUT_DIR;
+		self.params ['output_file'] = OUTPUT_FILE;
+		self.params ['output_json'] = OUTPUT_JSON;
+		self.params ['test'] = TEST;
+		for (var index = 0; index < len (parameters); index++) {
+			var item = parameters [index];
+			if (len (item) > 0 && item [0] == '-') {
+				var key = item.py_replace ('-', '');
+				var value = self.is_num (parameters [index + 1]);
+				if (__in__ (key, list (self.params.py_keys ()))) {
+					self.params [key] = value;
+					parameters [index] = '';
+					parameters [index + 1] = '';
+				}
+			}
+		}
+		self.error = '';
+		for (var index = 1; index < len (parameters); index++) {
+			var item = parameters [index];
+			if (item != '') {
+				self.error = (self.error + item) + ' ';
+			}
+		}
+		if (self.params ['output_dir'] != '' && self.params ['output_dir'].__getslice__ (-(1), null, 1) != sep) {
+			self.params ['output_dir'] = self.params ['output_dir'] + sep;
+		}
+		var single_output_files = [tuple (['output_file', 'pdb']), tuple (['output_json', 'json'])];
+		for (var [single_output_file, ext] of single_output_files) {
+			if (self.params ['output_dir'] != '' && self.params [single_output_file] == '') {
+				self.params [single_output_file] = (self.params ['output_dir'] + 'output.') + ext;
+			}
+		}
+	});},
+	get okay_to_proceed () {return __get__ (this, function (self) {
+		if (self.params ['receptor'] != '' && self.params ['ligand'] != '') {
+			return true;
+		}
+		else {
+			return false;
+		}
+	});}
+});
 
 //# sourceMappingURL=binana._cli_params._get_params.map
\ No newline at end of file

javascript/lib/binana._structure.atom.js

@@ -2,17 +2,169 @@
 // LICENSE.md or go to https://opensource.org/licenses/Apache-2.0 for full
 // details. Copyright 2020 Jacob D. Durrant.
 
-'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{r_just,round_to_thousandths_to_str}from"./binana._utils.shim.js";import{Point}from"./binana._structure.point.js";import*as __module_binana__ from"./binana.js";__nest__(binana,"",__module_binana__);var __name__="binana._structure.atom";
-export var Atom=__class__("Atom",[object],{__module__:__name__,get __init__(){return __get__(this,function(self){self.atom_name="";self.residue="";self.coordinates=Point(99999,99999,99999);self.element="";self.pdb_index="";self.line="";self.atom_type="";self.indecies_of_atoms_connecting=[];self.charge=0;self.resid=0;self.chain="";self.structure="";self.comment=""})},get copy_of(){return __get__(this,function(self){var theatom=Atom();theatom.atom_name=self.atom_name;theatom.residue=self.residue;theatom.coordinates=
-self.coordinates.copy_of();theatom.element=self.element;theatom.pdb_index=self.pdb_index;theatom.line=self.line;theatom.atom_type=self.atom_type;theatom.indecies_of_atoms_connecting=self.indecies_of_atoms_connecting.__getslice__(0,null,1);theatom.charge=self.charge;theatom.resid=self.resid;theatom.chain=self.chain;theatom.structure=self.structure;theatom.comment=self.comment;return theatom})},get string_id(){return __get__(this,function(self){var to_return="";if(self.chain.strip()!="")var to_return=
-to_return+self.chain.strip()+":";var to_return=to_return+self.residue.strip()+"("+str(self.resid)+"):"+self.atom_name.strip()+"("+str(self.pdb_index)+")";return to_return})},get create_pdb_line(){return __get__(this,function(self,index){var output="ATOM ";var output=output+r_just(str(index),6)+r_just(self.atom_name,5)+r_just(self.residue,4);var output=output+r_just(round_to_thousandths_to_str(self.coordinates.x),18);var output=output+r_just(round_to_thousandths_to_str(self.coordinates.y),8);var output=
-output+r_just(round_to_thousandths_to_str(self.coordinates.z),8);var output=output+r_just(self.element,24);return output})},get number_of_neighbors(){return __get__(this,function(self){return len(self.indecies_of_atoms_connecting)})},get add_neighbor_atom_index(){return __get__(this,function(self,index){if(!__in__(index,self.indecies_of_atoms_connecting))self.indecies_of_atoms_connecting.append(index)})},get side_chain_or_backbone(){return __get__(this,function(self){if(self.atom_name.strip()=="CA"||
-self.atom_name.strip()=="C"||self.atom_name.strip()=="O"||self.atom_name.strip()=="N")return"BACKBONE";else return"SIDECHAIN"})},get read_pdb_line(){return __get__(this,function(self,line){self.line=line;self.atom_name=line.__getslice__(11,16,1).strip();if(len(self.atom_name)==1)self.atom_name=self.atom_name+"  ";else if(len(self.atom_name)==2)self.atom_name=self.atom_name+" ";else if(len(self.atom_name)==3)self.atom_name=self.atom_name+" ";self.coordinates=Point(float(line.__getslice__(30,38,1)),
-float(line.__getslice__(38,46,1)),float(line.__getslice__(46,54,1)));self.atom_type=line.__getslice__(77,79,1).strip().upper();if(line.__getslice__(69,76,1).strip()!="")self.charge=float(line.__getslice__(69,76,1));else self.charge=0;if(self.element==""){var two_letters=self.atom_name.__getslice__(0,2,1).strip().upper();if(two_letters=="BR")self.element="BR";else if(two_letters=="CL")self.element="CL";else if(two_letters=="BI")self.element="BI";else if(two_letters=="AS")self.element="AS";else if(two_letters==
-"AG")self.element="AG";else if(two_letters=="LI")self.element="LI";else if(two_letters=="MG")self.element="MG";else if(two_letters=="MN")self.element="MN";else if(two_letters=="RH")self.element="RH";else if(two_letters=="ZN")self.element="ZN";else if(two_letters=="FE")self.element="FE";else{self.element=self.atom_name;self.element=self.element.py_replace("0","");self.element=self.element.py_replace("1","");self.element=self.element.py_replace("2","");self.element=self.element.py_replace("3","");self.element=
-self.element.py_replace("4","");self.element=self.element.py_replace("5","");self.element=self.element.py_replace("6","");self.element=self.element.py_replace("7","");self.element=self.element.py_replace("8","");self.element=self.element.py_replace("9","");self.element=self.element.py_replace("@","");self.element=self.element.__getslice__(0,1,1).strip().upper()}}self.pdb_index=line.__getslice__(6,12,1).strip();self.residue=line.__getslice__(16,20,1);self.residue=" "+self.residue.__getslice__(-3,null,
-1);try{self.resid=int(line.__getslice__(23,26,1))}catch(__except0__){}self.chain=line.__getslice__(21,22,1);if(self.chain==" ")self.chain="X";if(self.residue.strip()=="")self.residue=" MOL"})}});
+// Transcrypt'ed from Python, 2021-11-05 16:24:09
+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 {r_just, round_to_thousandths_to_str} from './binana._utils.shim.js';
+import {Point} from './binana._structure.point.js';
+import * as __module_binana__ from './binana.js';
+__nest__ (binana, '', __module_binana__);
+var __name__ = 'binana._structure.atom';
+export var Atom =  __class__ ('Atom', [object], {
+	__module__: __name__,
+	get __init__ () {return __get__ (this, function (self) {
+		self.atom_name = '';
+		self.residue = '';
+		self.coordinates = Point (99999, 99999, 99999);
+		self.element = '';
+		self.pdb_index = '';
+		self.line = '';
+		self.atom_type = '';
+		self.indecies_of_atoms_connecting = [];
+		self.charge = 0;
+		self.resid = 0;
+		self.chain = '';
+		self.structure = '';
+		self.comment = '';
+	});},
+	get copy_of () {return __get__ (this, function (self) {
+		var theatom = Atom ();
+		theatom.atom_name = self.atom_name;
+		theatom.residue = self.residue;
+		theatom.coordinates = self.coordinates.copy_of ();
+		theatom.element = self.element;
+		theatom.pdb_index = self.pdb_index;
+		theatom.line = self.line;
+		theatom.atom_type = self.atom_type;
+		theatom.indecies_of_atoms_connecting = self.indecies_of_atoms_connecting.__getslice__ (0, null, 1);
+		theatom.charge = self.charge;
+		theatom.resid = self.resid;
+		theatom.chain = self.chain;
+		theatom.structure = self.structure;
+		theatom.comment = self.comment;
+		return theatom;
+	});},
+	get string_id () {return __get__ (this, function (self) {
+		var to_return = '';
+		if (self.chain.strip () != '') {
+			var to_return = (to_return + self.chain.strip ()) + ':';
+		}
+		var to_return = (((((((to_return + self.residue.strip ()) + '(') + str (self.resid)) + '):') + self.atom_name.strip ()) + '(') + str (self.pdb_index)) + ')';
+		return to_return;
+	});},
+	get create_pdb_line () {return __get__ (this, function (self, index) {
+		var output = 'ATOM ';
+		var output = ((output + r_just (str (index), 6)) + r_just (self.atom_name, 5)) + r_just (self.residue, 4);
+		var output = output + r_just (round_to_thousandths_to_str (self.coordinates.x), 18);
+		var output = output + r_just (round_to_thousandths_to_str (self.coordinates.y), 8);
+		var output = output + r_just (round_to_thousandths_to_str (self.coordinates.z), 8);
+		var output = output + r_just (self.element, 24);
+		return output;
+	});},
+	get number_of_neighbors () {return __get__ (this, function (self) {
+		return len (self.indecies_of_atoms_connecting);
+	});},
+	get add_neighbor_atom_index () {return __get__ (this, function (self, index) {
+		if (!(__in__ (index, self.indecies_of_atoms_connecting))) {
+			self.indecies_of_atoms_connecting.append (index);
+		}
+	});},
+	get side_chain_or_backbone () {return __get__ (this, function (self) {
+		if (self.atom_name.strip () == 'CA' || self.atom_name.strip () == 'C' || self.atom_name.strip () == 'O' || self.atom_name.strip () == 'N') {
+			return 'BACKBONE';
+		}
+		else {
+			return 'SIDECHAIN';
+		}
+	});},
+	get read_pdb_line () {return __get__ (this, function (self, line) {
+		self.line = line;
+		self.atom_name = line.__getslice__ (11, 16, 1).strip ();
+		if (len (self.atom_name) == 1) {
+			self.atom_name = self.atom_name + '  ';
+		}
+		else if (len (self.atom_name) == 2) {
+			self.atom_name = self.atom_name + ' ';
+		}
+		else if (len (self.atom_name) == 3) {
+			self.atom_name = self.atom_name + ' ';
+		}
+		self.coordinates = Point (float (line.__getslice__ (30, 38, 1)), float (line.__getslice__ (38, 46, 1)), float (line.__getslice__ (46, 54, 1)));
+		self.atom_type = line.__getslice__ (77, 79, 1).strip ().upper ();
+		if (line.__getslice__ (69, 76, 1).strip () != '') {
+			self.charge = float (line.__getslice__ (69, 76, 1));
+		}
+		else {
+			self.charge = 0.0;
+		}
+		if (self.element == '') {
+			var two_letters = self.atom_name.__getslice__ (0, 2, 1).strip ().upper ();
+			if (two_letters == 'BR') {
+				self.element = 'BR';
+			}
+			else if (two_letters == 'CL') {
+				self.element = 'CL';
+			}
+			else if (two_letters == 'BI') {
+				self.element = 'BI';
+			}
+			else if (two_letters == 'AS') {
+				self.element = 'AS';
+			}
+			else if (two_letters == 'AG') {
+				self.element = 'AG';
+			}
+			else if (two_letters == 'LI') {
+				self.element = 'LI';
+			}
+			else if (two_letters == 'MG') {
+				self.element = 'MG';
+			}
+			else if (two_letters == 'MN') {
+				self.element = 'MN';
+			}
+			else if (two_letters == 'RH') {
+				self.element = 'RH';
+			}
+			else if (two_letters == 'ZN') {
+				self.element = 'ZN';
+			}
+			else if (two_letters == 'FE') {
+				self.element = 'FE';
+			}
+			else {
+				self.element = self.atom_name;
+				self.element = self.element.py_replace ('0', '');
+				self.element = self.element.py_replace ('1', '');
+				self.element = self.element.py_replace ('2', '');
+				self.element = self.element.py_replace ('3', '');
+				self.element = self.element.py_replace ('4', '');
+				self.element = self.element.py_replace ('5', '');
+				self.element = self.element.py_replace ('6', '');
+				self.element = self.element.py_replace ('7', '');
+				self.element = self.element.py_replace ('8', '');
+				self.element = self.element.py_replace ('9', '');
+				self.element = self.element.py_replace ('@', '');
+				self.element = self.element.__getslice__ (0, 1, 1).strip ().upper ();
+			}
+		}
+		self.pdb_index = line.__getslice__ (6, 12, 1).strip ();
+		self.residue = line.__getslice__ (16, 20, 1);
+		self.residue = ' ' + self.residue.__getslice__ (-(3), null, 1);
+		try {
+			self.resid = int (line.__getslice__ (23, 26, 1));
+		}
+		catch (__except0__) {
+			// pass;
+		}
+		self.chain = line.__getslice__ (21, 22, 1);
+		if (self.chain == ' ') {
+			self.chain = 'X';
+		}
+		if (self.residue.strip () == '') {
+			self.residue = ' MOL';
+		}
+	});}
+});
 
 //# sourceMappingURL=binana._structure.atom.map
\ No newline at end of file

javascript/lib/binana._structure.point.js

@@ -2,11 +2,55 @@
 // LICENSE.md or go to https://opensource.org/licenses/Apache-2.0 for full
 // details. Copyright 2020 Jacob D. Durrant.
 
-'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{r_just,round_to_thousandths_to_str}from"./binana._utils.shim.js";import*as __module_binana__ from"./binana.js";__nest__(binana,"",__module_binana__);import*as __module_math__ from"./math.js";__nest__(math,"",__module_math__);
-var __name__="binana._structure.point";export var Point=__class__("Point",[object],{__module__:__name__,x:99999,y:99999,z:99999,get __init__(){return __get__(this,function(self,x,y,z){self.x=x;self.y=y;self.z=z})},get copy_of(){return __get__(this,function(self){return Point(self.x,self.y,self.z)})},get print_coors(){return __get__(this,function(self){print(str(self.x)+"\t"+str(self.y)+"\t"+str(self.z))})},get snap(){return __get__(this,function(self,reso){self.x=round(self.x/reso)*reso;self.y=round(self.y/
-reso)*reso;self.z=round(self.z/reso)*reso})},get dist_to(){return __get__(this,function(self,apoint){return math.sqrt(math.pow(self.x-apoint.x,2)+math.pow(self.y-apoint.y,2)+math.pow(self.z-apoint.z,2))})},get description(){return __get__(this,function(self){return str(self.x)+" "+str(self.y)+" "+str(self.z)})},get magnitude(){return __get__(this,function(self){return self.dist_to(Point(0,0,0))})},get create_pdb_line(){return __get__(this,function(self,index){var output="ATOM ";var output=output+
-r_just(str(index),6)+r_just("X",5)+r_just("XXX",4);var output=output+r_just(round_to_thousandths_to_str(self.x),18);var output=output+r_just(round_to_thousandths_to_str(self.y),8);var output=output+r_just(round_to_thousandths_to_str(self.z),8);var output=output+r_just("X",24);return output})}});
+// Transcrypt'ed from Python, 2021-11-05 16:24:08
+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 {r_just, round_to_thousandths_to_str} from './binana._utils.shim.js';
+import * as __module_binana__ from './binana.js';
+__nest__ (binana, '', __module_binana__);
+import * as __module_math__ from './math.js';
+__nest__ (math, '', __module_math__);
+var __name__ = 'binana._structure.point';
+export var Point =  __class__ ('Point', [object], {
+	__module__: __name__,
+	x: 99999.0,
+	y: 99999.0,
+	z: 99999.0,
+	get __init__ () {return __get__ (this, function (self, x, y, z) {
+		self.x = x;
+		self.y = y;
+		self.z = z;
+	});},
+	get copy_of () {return __get__ (this, function (self) {
+		return Point (self.x, self.y, self.z);
+	});},
+	get print_coors () {return __get__ (this, function (self) {
+		print ((((str (self.x) + '\t') + str (self.y)) + '\t') + str (self.z));
+	});},
+	get snap () {return __get__ (this, function (self, reso) {
+		self.x = round (self.x / reso) * reso;
+		self.y = round (self.y / reso) * reso;
+		self.z = round (self.z / reso) * reso;
+	});},
+	get dist_to () {return __get__ (this, function (self, apoint) {
+		return math.sqrt ((math.pow (self.x - apoint.x, 2) + math.pow (self.y - apoint.y, 2)) + math.pow (self.z - apoint.z, 2));
+	});},
+	get description () {return __get__ (this, function (self) {
+		return (((str (self.x) + ' ') + str (self.y)) + ' ') + str (self.z);
+	});},
+	get magnitude () {return __get__ (this, function (self) {
+		return self.dist_to (Point (0, 0, 0));
+	});},
+	get create_pdb_line () {return __get__ (this, function (self, index) {
+		var output = 'ATOM ';
+		var output = ((output + r_just (str (index), 6)) + r_just ('X', 5)) + r_just ('XXX', 4);
+		var output = output + r_just (round_to_thousandths_to_str (self.x), 18);
+		var output = output + r_just (round_to_thousandths_to_str (self.y), 8);
+		var output = output + r_just (round_to_thousandths_to_str (self.z), 8);
+		var output = output + r_just ('X', 24);
+		return output;
+	});}
+});
 
 //# sourceMappingURL=binana._structure.point.map
\ No newline at end of file

javascript/lib/binana._utils._math_functions.js

@@ -2,16 +2,131 @@
 // LICENSE.md or go to https://opensource.org/licenses/Apache-2.0 for full
 // details. Copyright 2020 Jacob D. Durrant.
 
-'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{fabs}from"./binana._utils.shim.js";import{Point}from"./binana._structure.point.js";import*as __module_binana__ from"./binana.js";__nest__(binana,"",__module_binana__);import*as __module_math__ from"./math.js";__nest__(math,
-"",__module_math__);var __name__="binana._utils._math_functions";export var planrity=function(point1,point2,point3,point4){var x1=point1.x;var y1=point1.y;var z1=point1.z;var x2=point2.x;var y2=point2.y;var z2=point2.z;var x3=point3.x;var y3=point3.y;var z3=point3.z;var x4=point4.x;var y4=point4.y;var z4=point4.z;var A=y1*(z2-z3)+y2*(z3-z1)+y3*(z1-z2);var B=z1*(x2-x3)+z2*(x3-x1)+z3*(x1-x2);var C=x1*(y2-y3)+x2*(y3-y1)+x3*(y1-y2);var D=-x1*(y2*z3-y3*z2)+-x2*(y3*z1-y1*z3)+-x3*(y1*z2-y2*z1);var distance=
-fabs(A*x4+B*y4+C*z4+D)/math.sqrt(math.pow(A,2)+math.pow(B,2)+math.pow(C,2));var A1=y1*(z2-z4)+y2*(z4-z1)+y4*(z1-z2);var B1=z1*(x2-x4)+z2*(x4-x1)+z4*(x1-x2);var C1=x1*(y2-y4)+x2*(y4-y1)+x4*(y1-y2);var D1=-x1*(y2*z4-y4*z2)+-x2*(y4*z1-y1*z4)+-x4*(y1*z2-y2*z1);var distance1=fabs(A1*x3+B1*y3+C1*z3+D1)/math.sqrt(math.pow(A1,2)+math.pow(B1,2)+math.pow(C1,2));var A2=y1*(z4-z3)+y4*(z3-z1)+y3*(z1-z4);var B2=z1*(x4-x3)+z4*(x3-x1)+z3*(x1-x4);var C2=x1*(y4-y3)+x4*(y3-y1)+x3*(y1-y4);var D2=-x1*(y4*z3-y3*z4)+-x4*
-(y3*z1-y1*z3)+-x3*(y1*z4-y4*z1);var distance2=fabs(A2*x2+B2*y2+C2*z2+D2)/math.sqrt(math.pow(A2,2)+math.pow(B2,2)+math.pow(C2,2));var A3=y4*(z2-z3)+y2*(z3-z4)+y3*(z4-z2);var B3=z4*(x2-x3)+z2*(x3-x4)+z3*(x4-x2);var C3=x4*(y2-y3)+x2*(y3-y4)+x3*(y4-y2);var D3=-x4*(y2*z3-y3*z2)+-x2*(y3*z4-y4*z3)+-x3*(y4*z2-y2*z4);var distance3=fabs(A3*x1+B3*y1+C3*z1+D3)/math.sqrt(math.pow(A3,2)+math.pow(B3,2)+math.pow(C3,2));var final_dist=-1;if(distance<distance1&&distance<distance2&&distance<distance3)var final_dist=
-distance;else if(distance1<distance&&distance1<distance2&&distance1<distance3)var final_dist=distance1;else if(distance2<distance&&distance2<distance1&&distance2<distance3)var final_dist=distance2;else if(distance3<distance&&distance3<distance1&&distance3<distance2)var final_dist=distance3;return final_dist};export var vector_subtraction=function(vector1,vector2){return Point(vector1.x-vector2.x,vector1.y-vector2.y,vector1.z-vector2.z)};export var cross_product=function(pt1,pt2){var response=Point(0,
-0,0);response.x=pt1.y*pt2.z-pt1.z*pt2.y;response.y=pt1.z*pt2.x-pt1.x*pt2.z;response.z=pt1.x*pt2.y-pt1.y*pt2.x;return response};export var vector_scalar_multiply=function(vector,scalar){return Point(vector.x*scalar,vector.y*scalar,vector.z*scalar)};export var dot_product=function(point1,point2){return point1.x*point2.x+point1.y*point2.y+point1.z*point2.z};export var dihedral=function(point1,point2,point3,point4){var b1=vector_subtraction(point2,point1);var b2=vector_subtraction(point3,point2);var b3=
-vector_subtraction(point4,point3);var b2Xb3=cross_product(b2,b3);var b1Xb2=cross_product(b1,b2);var b1XMagb2=vector_scalar_multiply(b1,b2.magnitude());var radians=math.atan2(dot_product(b1XMagb2,b2Xb3),dot_product(b1Xb2,b2Xb3));return radians};export var angle_between_three_points=function(point1,point2,point3){var vector1=vector_subtraction(point1,point2);var vector2=vector_subtraction(point3,point2);return angle_between_points(vector1,vector2)};export var angle_between_points=function(point1,point2){var new_point1=
-return_normalized_vector(point1);var new_point2=return_normalized_vector(point2);var dot_prod=dot_product(new_point1,new_point2);if(dot_prod>1)var dot_prod=1;if(dot_prod<-1)var dot_prod=-1;return math.acos(dot_prod)};export var return_normalized_vector=function(vector){var dist=distance(Point(0,0,0),vector);return Point(vector.x/dist,vector.y/dist,vector.z/dist)};export var distance=function(point1,point2){var deltax=point1.x-point2.x;var deltay=point1.y-point2.y;var deltaz=point1.z-point2.z;return math.sqrt(math.pow(deltax,
-2)+math.pow(deltay,2)+math.pow(deltaz,2))};export var project_point_onto_plane=function(a_point,plane_coefficients){var a=plane_coefficients[0];var b=plane_coefficients[1];var c=plane_coefficients[2];var d=plane_coefficients[3];var s=a_point.x;var u=a_point.y;var v=a_point.z;var t=(d-a*s-b*u-c*v)/(a*a+b*b+c*c);var x=s+a*t;var y=u+b*t;var z=v+c*t;return Point(x,y,z)};
+// Transcrypt'ed from Python, 2021-11-05 16:24:08
+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 {fabs} from './binana._utils.shim.js';
+import {Point} from './binana._structure.point.js';
+import * as __module_binana__ from './binana.js';
+__nest__ (binana, '', __module_binana__);
+import * as __module_math__ from './math.js';
+__nest__ (math, '', __module_math__);
+var __name__ = 'binana._utils._math_functions';
+export var planrity = function (point1, point2, point3, point4) {
+	var x1 = point1.x;
+	var y1 = point1.y;
+	var z1 = point1.z;
+	var x2 = point2.x;
+	var y2 = point2.y;
+	var z2 = point2.z;
+	var x3 = point3.x;
+	var y3 = point3.y;
+	var z3 = point3.z;