Various updates.

CHANGES.md

@@ -14,21 +14,23 @@ WIP
 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_bond_dist_cutoff
-    hydrogen_halogen_bond_angle_cutoff
+10. changed hydrogen_bond_angle_cutoff parameter name to
+    hydrogen_halogen_bond_angle_cutoff. Added OTHER HALOGEN DIST HERE PARAM
+    HERE.
 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.
 13. Improved ability to detect salt bridges and hydrogen bonds even if protein
     and ligand models do not have hydrogen atoms.
-14. Speed improvements
+14. Speed and memory improvements
 15. Revised file input system. Can now also specify PDB ID, extract delete
     non-protein residues, etc.
 16. Sulfur can now be a hydrogen bond donor and acceptor.
 17. If input structure has mmultiple frames, keepsfirst one.
 18. JSON file now includes distances and angles.
 19. output_csv option now also prints csv file containing same information as json.
+20. Possible to toggle ribbon on and off.
+21. Updated documentation.
 
 TODO:
 
@@ -40,37 +42,42 @@ bonds per this heuristic:
   angle. =O not marked as donor, so don't need to worry about that.
 * Nitrogen cannot donate to more than actual neighbors + hydrogen bonds > 4, as
   above.
-
-Are water molecules able to be hydrogen bond donors?
+* chain and resid now included in output PDB files.
 
 Tests on all operating systems (including mobile).
 
 Be sure to compress javascript
 
-Halogen bonds mention in all documentation?
+MAke sure not javascript is external.
 
-Test should also test version of protein without hydrogens, and make sure you
-get all interactions tested. Metal, halogen, hydrogen with S.
+DOCUMENTATION:
 
-METAL_COORDINATION_CUTOFF. Get into web app (DONE), documentation, parameters, etc.
+1. Halogen bonds mention in all documentation?
+2. METAL_COORDINATION_CUTOFF. Get into web app (DONE), documentation,
+   parameters, etc.
+3. Make sure all documentation/examples account for get_all_interactions
+   (updated for metal coordination, halogen bonds)
+4. Make sure output_csv parameter documented.
 
-Make sure all documentation/examples account for get_all_interactions (updated for metal coordination, halogen bonds)
-
-finish README.md on file loading component.
+hydrogen_halogen_bond_angle_cutoff
+halogen_bond_dist_cutoff
+metal_coordination_dist_cutoff
+output_csv
 
-Check all docstrings on functions.
+(COMMAND_LINE_USE updated)
 
-PDBQT in webapp looks strange?
 
-SDF on ligand works?
+Test should also test version of protein without hydrogens, and make sure you
+get all interactions tested. Metal, halogen, hydrogen with S.
 
-Makesure can loadin multipleligands. Probably need to rewritecodethat triggersbinana run. Also, can run if restart.
+finish README.md on file loading component.
 
-Make sure output_csv parameter documented.
+PDBQT in webapp looks strange?
 
-// And you need a message explaining difference between delete/extract. Also,
-// converting files hasn't been implemented.
+*** Makesure can loadin multipleligands. Probably need to rewritecodethat
+triggersbinana run. Also, can run if restart.
 
+And you need a message explaining the difference between delete/extract. 
 
 2.0
 ---

javascript/lib/__future__.js

-// Transcrypt'ed from Python, 2021-11-20 02:43:22
+// Transcrypt'ed from Python, 2021-11-23 00:01:21
 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 = [];

javascript/lib/binana._cli_params._get_params.js

@@ -2,7 +2,7 @@
 // LICENSE.md or go to https://opensource.org/licenses/Apache-2.0 for full
 // details. Copyright 2020 Jacob D. Durrant.
 
-// Transcrypt'ed from Python, 2021-11-20 02:43:20
+// Transcrypt'ed from Python, 2021-11-23 00:01:20
 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';

javascript/lib/binana._structure.atom.js

@@ -2,14 +2,17 @@
 // LICENSE.md or go to https://opensource.org/licenses/Apache-2.0 for full
 // details. Copyright 2020 Jacob D. Durrant.
 
-// Transcrypt'ed from Python, 2021-11-20 02:43:21
+// Transcrypt'ed from Python, 2021-11-23 00:01:20
 var binana = {};
 var math = {};
+var re = {};
 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 * as shim from './binana._utils.shim.js';
 import * as __module_binana__utils__ from './binana._utils.js';
 __nest__ (binana, '_utils', __module_binana__utils__);
+import * as __module_re__ from './re.js';
+__nest__ (re, '', __module_re__);
 import {protein_resnames, to_deg, two_leter_atom_names} from './binana._structure.consts.js';
 import {angle_between_three_points} from './binana._utils._math_functions.js';
 import {r_just, round_to_thousandths_to_str} from './binana._utils.shim.js';
@@ -27,6 +30,7 @@ export var Atom =  __class__ ('Atom', [object], {
 		self.coordinates = Point (99999, 99999, 99999);
 		self.element = '';
 		self.pdb_index = '';
+		self.all_atoms_index = -(1);
 		self.line = '';
 		self.atom_type = '';
 		self.indecies_of_atoms_connecting = [];
@@ -51,6 +55,7 @@ export var Atom =  __class__ ('Atom', [object], {
 		theatom.chain = self.chain;
 		theatom.structure = self.structure;
 		theatom.comment = self.comment;
+		theatom.all_atoms_index = self.all_atoms_index;
 		return theatom;
 	});},
 	get string_id () {return __get__ (this, function (self) {
@@ -101,7 +106,13 @@ export var Atom =  __class__ ('Atom', [object], {
 		self.residue = line.__getslice__ (16, 20, 1);
 		self.residue = ' ' + self.residue.__getslice__ (-(3), null, 1);
 		if (self.element == '') {
-			var two_letters = self.atom_name.__getslice__ (0, 2, 1).strip ().upper ();
+			var element = line.__getslice__ (76, null, 1).strip ().upper ();
+			if (element != '') {
+				var two_letters = re.sub ('[^A-Z]', '', element).__getslice__ (0, 2, 1);
+			}
+			else {
+				var two_letters = self.atom_name.__getslice__ (0, 2, 1).strip ().upper ();
+			}
 			if (__in__ (two_letters, two_leter_atom_names) && !__in__ (self.residue.__getslice__ (-(3), null, 1), protein_resnames)) {
 				self.element = two_letters;
 			}
@@ -136,7 +147,58 @@ export var Atom =  __class__ ('Atom', [object], {
 			self.residue = ' MOL';
 		}
 	});},
+	get _has_sp3_geometry_if_protein () {return __get__ (this, function (self, resname) {
+		var atomname = self.atom_name.strip ();
+		if (__in__ (atomname, ['C', 'O', 'N'])) {
+			return false;
+		}
+		if (resname == 'ARG') {
+			if (__in__ (atomname, ['NE', 'NH1', 'NH2'])) {
+				return false;
+			}
+		}
+		else if (resname == 'ASN') {
+			if (__in__ (atomname, ['CG', 'OD1', 'ND2'])) {
+				return false;
+			}
+		}
+		else if (resname == 'ASP') {
+			if (__in__ (atomname, ['CG', 'OD1'])) {
+				return false;
+			}
+		}
+		else if (resname == 'GLN') {
+			if (__in__ (atomname, ['CD', 'OE1', 'NE2'])) {
+				return false;
+			}
+		}
+		else if (resname == 'GLU') {
+			if (__in__ (atomname, ['CD', 'OE1'])) {
+				return false;
+			}
+		}
+		else if (resname == 'HIS') {
+			if (__in__ (atomname, ['CG', 'CD2', 'NE2', 'CE1', 'ND1'])) {
+				return false;
+			}
+		}
+		else if (__in__ (resname, ['PHE', 'TYR'])) {
+			if (__in__ (atomname, ['CE1', 'CZ', 'CE2', 'CD2', 'CG', 'CD1'])) {
+				return false;
+			}
+		}
+		else if (resname == 'TRP') {
+			if (__in__ (atomname, ['CG', 'CD1', 'NE1', 'CE2', 'CD2', 'CE3', 'CZ2', 'CZ3', 'CH2'])) {
+				return false;
+			}
+		}
+		return true;
+	});},
 	get has_sp3_geometry () {return __get__ (this, function (self, parent_mol) {
+		var resname = self.residue.__getslice__ (-(3), null, 1);
+		if (__in__ (resname, protein_resnames)) {
+			return self._has_sp3_geometry_if_protein (resname);
+		}
 		var ncrs = (function () {
 			var __accu0__ = [];
 			for (var i of self.indecies_of_atoms_connecting) {
@@ -161,6 +223,9 @@ export var Atom =  __class__ ('Atom', [object], {
 		}
 		var average_angle = sum (angles) / float (len (angles));
 		return fabs (average_angle - 109.0) < 5.0;
+	});},
+	get belongs_to_protein () {return __get__ (this, function (self) {
+		return __in__ (self.residue.__getslice__ (-(3), null, 1), protein_resnames);
 	});}
 });
 

javascript/lib/binana._structure.consts.js

@@ -2,7 +2,7 @@
 // LICENSE.md or go to https://opensource.org/licenses/Apache-2.0 for full
 // details. Copyright 2020 Jacob D. Durrant.
 
-// Transcrypt'ed from Python, 2021-11-20 02:43:21
+// Transcrypt'ed from Python, 2021-11-23 00:01:20
 var math = {};
 import {AssertionError, AttributeError, BaseException, DeprecationWarning, Exception, IndexError, IterableError, KeyError, NotImplementedError, RuntimeWarning, StopIteration, UserWarning, ValueError, Warning, __JsIterator__, __PyIterator__, __Terminal__, __add__, __and__, __call__, __class__, __envir__, __eq__, __floordiv__, __ge__, __get__, __getcm__, __getitem__, __getslice__, __getsm__, __gt__, __i__, __iadd__, __iand__, __idiv__, __ijsmod__, __ilshift__, __imatmul__, __imod__, __imul__, __in__, __init__, __ior__, __ipow__, __irshift__, __isub__, __ixor__, __jsUsePyNext__, __jsmod__, __k__, __kwargtrans__, __le__, __lshift__, __lt__, __matmul__, __mergefields__, __mergekwargtrans__, __mod__, __mul__, __ne__, __neg__, __nest__, __or__, __pow__, __pragma__, __proxy__, __pyUseJsNext__, __rshift__, __setitem__, __setproperty__, __setslice__, __sort__, __specialattrib__, __sub__, __super__, __t__, __terminal__, __truediv__, __withblock__, __xor__, abs, all, any, assert, bool, bytearray, bytes, callable, chr, copy, deepcopy, delattr, dict, dir, divmod, enumerate, filter, float, getattr, hasattr, input, int, isinstance, issubclass, len, list, map, max, min, object, ord, pow, print, property, py_TypeError, py_iter, py_metatype, py_next, py_reversed, py_typeof, range, repr, round, set, setattr, sorted, str, sum, tuple, zip} from './org.transcrypt.__runtime__.js';
 import * as __module_math__ from './math.js';

javascript/lib/binana._structure.mol.js

@@ -2,7 +2,7 @@
 // LICENSE.md or go to https://opensource.org/licenses/Apache-2.0 for full
 // details. Copyright 2020 Jacob D. Durrant.
 
-// Transcrypt'ed from Python, 2021-11-20 02:43:21
+// Transcrypt'ed from Python, 2021-11-23 00:01:20
 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';
@@ -110,6 +110,7 @@ export var Mol =  __class__ ('Mol', [object], {
 					}
 					if (!__in__ (key, atom_already_loaded) || !__in__ (temp_residue, protein_resnames)) {
 						atom_already_loaded.append (key);
+						temp_atom.all_atoms_index = autoindex;
 						self.all_atoms [autoindex] = temp_atom;
 						if (!__in__ (temp_atom.residue.__getslice__ (-(3), null, 1), protein_resnames)) {
 							self.non_protein_atoms [autoindex] = temp_atom;
@@ -292,11 +293,27 @@ export var Mol =  __class__ ('Mol', [object], {
 				}
 				var atom2 = self.non_protein_atoms [atom_index2];
 				if (!__in__ (atom2.residue.__getslice__ (-(3), null, 1), protein_resnames)) {
-					var dist = distance (atom1.coordinates, atom2.coordinates);
-					if (dist < self.bond_length (atom1.element, atom2.element) * 1.2) {
-						atom1.add_neighbor_atom_index (atom_index2);
-						atom2.add_neighbor_atom_index (atom_index1);
-					}
+					self.create_bond_by_distance_between_two_atoms (atom1, atom2);
+				}
+			}
+		}
+	});},
+	get create_bond_by_distance_between_two_atoms () {return __get__ (this, function (self, atom1, atom2) {
+		var dist = distance (atom1.coordinates, atom2.coordinates);
+		if (dist < self.bond_length (atom1.element, atom2.element) * 1.2) {
+			atom1.add_neighbor_atom_index (atom2.all_atoms_index);
+			atom2.add_neighbor_atom_index (atom1.all_atoms_index);
+		}
+	});},
+	get create_bond_by_distance () {return __get__ (this, function (self, atom) {
+		var idx1 = atom.all_atoms_index;
+		var coor1 = atom.coordinates;
+		for (var idx2 of self.all_atoms.py_keys ()) {
+			if (idx1 != idx2) {
+				var other_atom = self.all_atoms [idx2];
+				var dist = distance (coor1, other_atom.coordinates);
+				if (dist < self.bond_length (atom.element, other_atom.element) * 1.2) {
+					atom.add_neighbor_atom_index (other_atom.all_atoms_index);
 				}
 			}
 		}
@@ -431,6 +448,9 @@ export var Mol =  __class__ ('Mol', [object], {
 				charaterizations.append (['DONOR', atom]);
 			}
 		}
+		else if (atom.element == 'O' && num_neighbors == 0) {
+			charaterizations.append (['DONOR', atom]);
+		}
 		else if (atom.element == 'N') {
 			var is_sp3 = (num_neighbors > 1 ? atom.has_sp3_geometry (self) : true);
 			if (is_sp3 && num_neighbors < 4 || !(is_sp3) && num_neighbors < 3) {
@@ -514,8 +534,17 @@ export var Mol =  __class__ ('Mol', [object], {
 			}
 		}
 		else if (num_neighors == 1 || atom.has_sp3_geometry (self)) {
-			var chrg = self.Charged (atom.coordinates, [atom_index], true);
-			self.charges.append (chrg);
+			var is_in_aromatic_ring = any ((function () {
+				var __accu0__ = [];
+				for (var ring of self.aromatic_rings) {
+					__accu0__.append (__in__ (int (atom_index), ring.indices));
+				}
+				return py_iter (__accu0__);
+			}) ());
+			if (!(is_in_aromatic_ring)) {
+				var chrg = self.Charged (atom.coordinates, [atom_index], true);
+				self.charges.append (chrg);
+			}
 		}
 	});},
 	get charges_carboxylate () {return __get__ (this, function (self, atom_index, atom) {
@@ -754,6 +783,13 @@ export var Mol =  __class__ ('Mol', [object], {
 		});}
 	}),
 	get add_aromatic_marker () {return __get__ (this, function (self, indicies_of_ring) {
+		var indicies_of_ring = (function () {
+			var __accu0__ = [];
+			for (var i of indicies_of_ring) {
+				__accu0__.append (int (i));
+			}
+			return __accu0__;
+		}) ();
 		var points_list = [];
 		var total = len (indicies_of_ring);
 		var x_sum = 0.0;
@@ -829,10 +865,8 @@ export var Mol =  __class__ ('Mol', [object], {
 				for (var ring_index_2 = 0; ring_index_2 < len (all_rings); ring_index_2++) {
 					if (ring_index_1 != ring_index_2) {
 						var ring2 = all_rings [ring_index_2];
-						if (len (ring2) != 0) {
-							if (self.set1_is_subset_of_set2 (ring1, ring2) == true) {
-								all_rings [ring_index_2] = [];
-							}
+						if (len (ring2) != 0 && self.set1_is_subset_of_set2 (ring1, ring2) == true) {
+							all_rings [ring_index_2] = [];
 						}
 					}
 				}
@@ -871,7 +905,7 @@ export var Mol =  __class__ ('Mol', [object], {
 					}
 				}
 			}
-			if (is_flat == false) {
+			if (!(is_flat)) {
 				all_rings [ring_index] = [];
 			}
 			if (len (ring) < 5) {
@@ -894,7 +928,7 @@ export var Mol =  __class__ ('Mol', [object], {
 		for (var atom_index of self.all_atoms.py_keys ()) {
 			var atom = self.all_atoms [atom_index];
 			var key = (((atom.residue + '_') + str (atom.resid)) + '_') + atom.chain;
-			if (first == true) {
+			if (first) {
 				var curr_res = key;
 				var first = false;
 			}

javascript/lib/binana._structure.point.js

@@ -2,7 +2,7 @@
 // LICENSE.md or go to https://opensource.org/licenses/Apache-2.0 for full
 // details. Copyright 2020 Jacob D. Durrant.
 
-// Transcrypt'ed from Python, 2021-11-20 02:43:21
+// Transcrypt'ed from Python, 2021-11-23 00:01:20
 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';

javascript/lib/binana._utils._math_functions.js

@@ -2,7 +2,7 @@
 // LICENSE.md or go to https://opensource.org/licenses/Apache-2.0 for full
 // details. Copyright 2020 Jacob D. Durrant.
 
-// Transcrypt'ed from Python, 2021-11-20 02:43:21
+// Transcrypt'ed from Python, 2021-11-23 00:01:20
 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';

javascript/lib/binana._utils.js

@@ -2,7 +2,7 @@
 // LICENSE.md or go to https://opensource.org/licenses/Apache-2.0 for full
 // details. Copyright 2020 Jacob D. Durrant.
 
-// Transcrypt'ed from Python, 2021-11-20 02:43:21
+// Transcrypt'ed from Python, 2021-11-23 00:01:20
 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__ = 'binana._utils';
 

javascript/lib/binana._utils.shim.js

@@ -2,7 +2,7 @@
 // LICENSE.md or go to https://opensource.org/licenses/Apache-2.0 for full
 // details. Copyright 2020 Jacob D. Durrant.
 
-// Transcrypt'ed from Python, 2021-11-20 02:43:21
+// Transcrypt'ed from Python, 2021-11-23 00:01:20
 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__ = 'binana._utils.shim';
 export var fake_fs = dict ({});

javascript/lib/binana._utils.utils.js

@@ -2,7 +2,7 @@
 // LICENSE.md or go to https://opensource.org/licenses/Apache-2.0 for full
 // details. Copyright 2020 Jacob D. Durrant.
 
-// Transcrypt'ed from Python, 2021-11-20 02:43:22
+// Transcrypt'ed from Python, 2021-11-23 00:01:21
 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 {_set_default} from './binana._utils.shim.js';
 var __name__ = 'binana._utils.utils';

javascript/lib/binana.fs.js

@@ -2,7 +2,7 @@
 // LICENSE.md or go to https://opensource.org/licenses/Apache-2.0 for full
 // details. Copyright 2020 Jacob D. Durrant.
 
-// Transcrypt'ed from Python, 2021-11-20 02:43:23
+// Transcrypt'ed from Python, 2021-11-23 00:01:22
 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';
@@ -10,7 +10,7 @@ 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, OpenFile, shim};
+export {OpenFile, _utils, shim};
 var __name__ = 'binana.fs';
 export var save_file = function (filename, text) {
 	var f = OpenFile (filename, 'w');

javascript/lib/binana.interactions._cat_pi.js

@@ -2,7 +2,7 @@
 // LICENSE.md or go to https://opensource.org/licenses/Apache-2.0 for full
 // details. Copyright 2020 Jacob D. Durrant.
 
-// Transcrypt'ed from Python, 2021-11-20 02:43:22
+// Transcrypt'ed from Python, 2021-11-23 00:01:21
 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 {project_point_onto_plane} from './binana._utils._math_functions.js';

javascript/lib/binana.interactions._close.js

@@ -2,7 +2,7 @@
 // LICENSE.md or go to https://opensource.org/licenses/Apache-2.0 for full
 // details. Copyright 2020 Jacob D. Durrant.
 
-// Transcrypt'ed from Python, 2021-11-20 02:43:22
+// Transcrypt'ed from Python, 2021-11-23 00:01:21
 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 {Mol} from './binana._structure.mol.js';

javascript/lib/binana.interactions._closest.js

@@ -2,7 +2,7 @@
 // LICENSE.md or go to https://opensource.org/licenses/Apache-2.0 for full
 // details. Copyright 2020 Jacob D. Durrant.
 
-// Transcrypt'ed from Python, 2021-11-20 02:43:22
+// Transcrypt'ed from Python, 2021-11-23 00:01:21
 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 {Mol} from './binana._structure.mol.js';

javascript/lib/binana.interactions._electrostatic_energies.js

@@ -2,7 +2,7 @@
 // LICENSE.md or go to https://opensource.org/licenses/Apache-2.0 for full
 // details. Copyright 2020 Jacob D. Durrant.
 
-// Transcrypt'ed from Python, 2021-11-20 02:43:22
+// Transcrypt'ed from Python, 2021-11-23 00:01:21
 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 {hashtable_entry_add_one, list_alphebetize_and_combine} from './binana._utils.utils.js';

javascript/lib/binana.interactions._flexibility.js

@@ -2,7 +2,7 @@
 // LICENSE.md or go to https://opensource.org/licenses/Apache-2.0 for full
 // details. Copyright 2020 Jacob D. Durrant.
 
-// Transcrypt'ed from Python, 2021-11-20 02:43:22
+// Transcrypt'ed from Python, 2021-11-23 00:01:21
 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 {Mol} from './binana._structure.mol.js';

javascript/lib/binana.interactions._hydrogen_halogen_bonds.js

@@ -2,7 +2,7 @@
 // LICENSE.md or go to https://opensource.org/licenses/Apache-2.0 for full
 // details. Copyright 2020 Jacob D. Durrant.
 
-// Transcrypt'ed from Python, 2021-11-20 02:43:22
+// Transcrypt'ed from Python, 2021-11-23 00:01:21
 var __future__ = {};
 var binana = {};
 var math = {};
@@ -57,6 +57,162 @@ export var _product = function (lst1, lst2) {
 	}
 	return combos;
 };
+export var _collect_bonds = function (bonds_organized_by_donor, pdb_hbonds, hbonds, hbonds_labels) {
+	var unwrapped_bond_infos = [];
+	for (var donor_key of bonds_organized_by_donor.py_keys ()) {
+		for (var bond_inf of bonds_organized_by_donor [donor_key]) {
+			unwrapped_bond_infos.append (bond_inf);
+		}
+	}
+	var unwrapped_bond_infos = sorted (unwrapped_bond_infos, __kwargtrans__ ({key: (function __lambda__ (i) {
+		return i [0];
+	})}));
+	for (var [idx, lig_donor_or_accept, receptor_atom, ligand_atom, center_atom, dist, angle] of unwrapped_bond_infos) {
+		_update_mol_and_data (pdb_hbonds, hbonds, hbonds_labels, lig_donor_or_accept, receptor_atom, ligand_atom, center_atom, dist, angle);
+	}
+};
+export var _score_angle_deviation_from_sp3_sp2 = function (angle, donor_has_sp3_geometry) {
+	if (donor_has_sp3_geometry === null) {
+		var diff = min (fabs (109 - angle), fabs (120 - angle));
+		var min_angle = 89;
+		var max_angle = 150;
+	}
+	else if (donor_has_sp3_geometry == true) {
+		var diff = fabs (109 - angle);
+		var min_angle = 89;
+		var max_angle = 129;
+	}
+	else {
+		var min_angle = 100;
+		var max_angle = 150;
+		var diff = fabs (120 - angle);
+	}
+	return tuple ([diff, angle < min_angle || angle > max_angle]);
+};
+export var _select_acceptor = function (lig, recep, lig_donor_or_accept) {
+	return (lig_donor_or_accept == 'ACCEPTOR' ? lig : recep);
+};
+export var _remo