Before removing cruft from old hydrogen/halogen-bond code.

CHANGES.md

@@ -17,10 +17,25 @@ WIP
 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.
+13. Improved ability to detect salt bridges even if protein and ligand models do not have hydrogen atoms. TODO: Try to detect hydrogen bonds too.
+
+TODO:
 
 Halogen bonds mention in all documentation?
 Halogen bonds counted twice? Good to check. In the chart in log file.
 
+CAPTURE WARNINGS. Also, move no-hydrogen warning to below table to be less
+obtrusive.
+
+Consider "S" as donor/acceptors? Need to investigate.
+
+Much of hydrogen-bond detecting code should go into mol. Also, use protein
+definitions where possible, like you do for electrostatics. But in case of
+hydrogen bonds detecvt only on the ffly (otherwise too many).
+
+
+Test should also test version of protein without hydrogens
+
 2.0
 ---
 

javascript/lib/__future__.js

-// Transcrypt'ed from Python, 2021-11-05 16:24:09
+// Transcrypt'ed from Python, 2021-11-09 00:25:33
 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, 2021-11-05 16:24:08
+// Transcrypt'ed from Python, 2021-11-09 00:25:32
 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._start.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, 2021-11-05 16:24:08
+// Transcrypt'ed from Python, 2021-11-09 00:25:32
 var __future__ = {};
 var binana = {};
 var math = {};

javascript/lib/binana._structure.atom.js

@@ -2,13 +2,21 @@
 // LICENSE.md or go to https://opensource.org/licenses/Apache-2.0 for full
 // details. Copyright 2020 Jacob D. Durrant.
 
-// Transcrypt'ed from Python, 2021-11-05 16:24:09
+// Transcrypt'ed from Python, 2021-11-09 00:25:33
 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 * as shim from './binana._utils.shim.js';
+import * as __module_binana__utils__ from './binana._utils.js';
+__nest__ (binana, '_utils', __module_binana__utils__);
+import {angle_between_three_points} from './binana._utils._math_functions.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__);
+import * as __module_math__ from './math.js';
+__nest__ (math, '', __module_math__);
 var __name__ = 'binana._structure.atom';
 export var Atom =  __class__ ('Atom', [object], {
 	__module__: __name__,
@@ -55,22 +63,22 @@ export var Atom =  __class__ ('Atom', [object], {
 	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);
+		output += r_just (round_to_thousandths_to_str (self.coordinates.x), 18);
+		output += r_just (round_to_thousandths_to_str (self.coordinates.y), 8);
+		output += r_just (round_to_thousandths_to_str (self.coordinates.z), 8);
+		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))) {
+		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') {
+		if (__in__ (self.atom_name.strip (), ['CA', 'C', 'O', 'N'])) {
 			return 'BACKBONE';
 		}
 		else {
@@ -164,6 +172,29 @@ export var Atom =  __class__ ('Atom', [object], {
 		if (self.residue.strip () == '') {
 			self.residue = ' MOL';
 		}
+	});},
+	get has_sp3_geometry () {return __get__ (this, function (self, parent_mol) {
+		var ncrs = (function () {
+			var __accu0__ = [];
+			for (var i of self.indecies_of_atoms_connecting) {
+				__accu0__.append (parent_mol.all_atoms [i].coordinates);
+			}
+			return __accu0__;
+		}) ();
+		var ccr = self.coordinates;
+		var to_deg = 180.0 / math.pi;
+		var angles = [angle_between_three_points (ncrs [0], ccr, ncrs [1]) * to_deg];
+		if (len (ncrs) > 2) {
+			angles.append (angle_between_three_points (ncrs [0], ccr, ncrs [2]) * to_deg);
+			angles.append (angle_between_three_points (ncrs [1], ccr, ncrs [2]) * to_deg);
+		}
+		if (len (ncrs) > 3) {
+			angles.append (angle_between_three_points (ncrs [0], ccr, ncrs [3]) * to_deg);
+			angles.append (angle_between_three_points (ncrs [1], ccr, ncrs [3]) * to_deg);
+			angles.append (angle_between_three_points (ncrs [2], ccr, ncrs [3]) * to_deg);
+		}
+		var average_angle = sum (angles) / float (len (angles));
+		return fabs (average_angle - 109.0) < 5.0;
 	});}
 });
 

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, 2021-11-05 16:24:08
+// Transcrypt'ed from Python, 2021-11-09 00:25:32
 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, 2021-11-05 16:24:08
+// Transcrypt'ed from Python, 2021-11-09 00:25:32
 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';
@@ -84,8 +84,7 @@ export var dihedral = function (point1, point2, point3, point4) {
 	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;
+	return math.atan2 (dot_product (b1XMagb2, b2Xb3), dot_product (b1Xb2, b2Xb3));
 };
 export var angle_between_three_points = function (point1, point2, point3) {
 	var vector1 = vector_subtraction (point1, point2);
@@ -96,12 +95,8 @@ 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 > 1.0) {
-		var dot_prod = 1.0;
-	}
-	if (dot_prod < -(1.0)) {
-		var dot_prod = -(1.0);
-	}
+	var dot_prod = min (dot_prod, 1.0);
+	var dot_prod = max (dot_prod, -(1.0));
 	return math.acos (dot_prod);
 };
 export var return_normalized_vector = function (vector) {

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, 2021-11-05 16:24:09
+// Transcrypt'ed from Python, 2021-11-09 00:25:33
 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, 2021-11-05 16:24:08
+// Transcrypt'ed from Python, 2021-11-09 00:25:32
 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, 2021-11-05 16:24:09
+// Transcrypt'ed from Python, 2021-11-09 00:25:33
 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, 2021-11-05 16:24:10
+// Transcrypt'ed from Python, 2021-11-09 00:25:34
 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 {OpenFile, _utils, shim};
+export {_utils, shim, OpenFile};
 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, 2021-11-05 16:24:09
+// Transcrypt'ed from Python, 2021-11-09 00:25:33
 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';
@@ -40,14 +40,14 @@ export var _detect_pi_cat = function (mol_with_aromatic, mol_with_pos_charge, cu
 						for (var index of charged.indices) {
 							__accu0__.append (mol_with_pos_charge.all_atoms [index].string_id ());
 						}
-						return __accu0__;
+						return py_iter (__accu0__);
 					}) ())) + ']';
 					var aromatic_mol_lbls = ('[' + ' / '.join ((function () {
 						var __accu0__ = [];
 						for (var index of aromatic.indices) {
 							__accu0__.append (mol_with_aromatic.all_atoms [index].string_id ());
 						}
-						return __accu0__;
+						return py_iter (__accu0__);
 					}) ())) + ']';
 					if (name_of_charged == 'LIGAND') {
 						cat_pi_labels.append (tuple ([charged_mol_lbls, aromatic_mol_lbls]));

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, 2021-11-05 16:24:09
+// Transcrypt'ed from Python, 2021-11-09 00:25:33
 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, 2021-11-05 16:24:09
+// Transcrypt'ed from Python, 2021-11-09 00:25:33
 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, 2021-11-05 16:24:09
+// Transcrypt'ed from Python, 2021-11-09 00:25:33
 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, 2021-11-05 16:24:09
+// Transcrypt'ed from Python, 2021-11-09 00:25:33
 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, 2021-11-05 16:24:09
+// Transcrypt'ed from Python, 2021-11-09 00:25:33
 var __future__ = {};
 var binana = {};
 var math = {};
@@ -21,7 +21,20 @@ __nest__ (binana, '', __module_binana__);
 import {HYDROGEN_HALOGEN_BOND_ANGLE_CUTOFF, HYDROGEN_HALOGEN_BOND_DIST_CUTOFF} from './binana.interactions.default_params.js';
 import {_set_default} from './binana._utils.shim.js';
 var __name__ = 'binana.interactions._hydrogen_halogen_bonds';
-export var max_donor_X_dist = dict ({'H': 1.3, 'I': 2.04 * 1.4, 'BR': 1.86 * 1.4, 'Br': 1.86 * 1.4, 'CL': 1.71 * 1.4, 'Cl': 1.71 * 1.4, 'F': 1.33 * 1.4});
+export var _mimic_set_minus = function (set1, set2) {
+	for (var s2 of set2) {
+		var set1 = (function () {
+			var __accu0__ = [];
+			for (var s of set1) {
+				if (s [0] != s2 [0]) {
+					__accu0__.append (s);
+				}
+			}
+			return __accu0__;
+		}) ();
+	}
+	return set1;
+};
 export var get_hydrogen_or_halogen_bonds = function (ligand, receptor, dist_cutoff, angle_cutoff, hydrogen_bond) {
 	if (typeof dist_cutoff == 'undefined' || (dist_cutoff != null && dist_cutoff.hasOwnProperty ("__kwargtrans__"))) {;
 		var dist_cutoff = null;
@@ -32,45 +45,56 @@ export var get_hydrogen_or_halogen_bonds = function (ligand, receptor, dist_cuto
 	if (typeof hydrogen_bond == 'undefined' || (hydrogen_bond != null && hydrogen_bond.hasOwnProperty ("__kwargtrans__"))) {;
 		var hydrogen_bond = true;
 	};
-	var central_atoms = (hydrogen_bond ? ['H'] : ['I', 'BR', 'Br', 'CL', 'Cl', 'F']);
-	var dist_cutoff = _set_default (dist_cutoff, HYDROGEN_HALOGEN_BOND_DIST_CUTOFF);
-	var angle_cutoff = _set_default (angle_cutoff, HYDROGEN_HALOGEN_BOND_ANGLE_CUTOFF);
 	var hbonds = dict ({});
 	var pdb_hbonds = Mol ();
 	var hbonds_labels = [];
+	var dist_cutoff = _set_default (dist_cutoff, HYDROGEN_HALOGEN_BOND_DIST_CUTOFF);
+	var angle_cutoff = _set_default (angle_cutoff, HYDROGEN_HALOGEN_BOND_ANGLE_CUTOFF);
+	var lig_and_recep_have_hydrogens = ligand.has_hydrogens && receptor.has_hydrogens;
 	var ligand_receptor_dists = _get_ligand_receptor_dists (ligand, receptor);
+	var close_donors_acceptors = (function () {
+		var __accu0__ = [];
 		for (var [ligand_atom, receptor_atom, dist] of ligand_receptor_dists) {
 			if (dist < dist_cutoff && __in__ (ligand_atom.element, ['O', 'N']) && __in__ (receptor_atom.element, ['O', 'N'])) {
-			var hydrogens = [];
-			for (var atm_index of ligand.all_atoms.py_keys ()) {
-				var element = ligand.all_atoms [atm_index].element;
-				if (__in__ (element, central_atoms)) {
-					var dist = ligand.all_atoms [atm_index].coordinates.dist_to (ligand_atom.coordinates);
-					if (dist < max_donor_X_dist [element]) {
-						ligand.all_atoms [atm_index].comment = 'LIGAND';
-						hydrogens.append (ligand.all_atoms [atm_index]);
+				__accu0__.append ([ligand_atom, receptor_atom]);
 			}
 		}
+		return __accu0__;
+	}) ();
+	for (var [ligand_atom, receptor_atom] of close_donors_acceptors) {
+		var hbond_detected = false;
+		var lig_atm_hbond_infs = ligand.is_hbond_donor_acceptor (ligand_atom, hydrogen_bond);
+		var recep_atm_hbond_infs = receptor.is_hbond_donor_acceptor (receptor_atom, hydrogen_bond);
+		for (var lig_atm_hbond_inf of lig_atm_hbond_infs) {
+			if (hbond_detected) {
+				break;
 			}
-			for (var atm_index of receptor.all_atoms.py_keys ()) {
-				var element = receptor.all_atoms [atm_index].element;
-				if (__in__ (element, central_atoms)) {
-					var dist = receptor.all_atoms [atm_index].coordinates.dist_to (receptor_atom.coordinates);
-					if (dist < max_donor_X_dist [element]) {
-						receptor.all_atoms [atm_index].comment = 'RECEPTOR';
-						hydrogens.append (receptor.all_atoms [atm_index]);
+			var __left0__ = lig_atm_hbond_inf;
+			var lig_donor_or_accept = __left0__ [0];
+			var lig_center_atom = __left0__ [1];
+			for (var recep_atm_hbond_inf of recep_atm_hbond_infs) {
+				var __left0__ = recep_atm_hbond_inf;
+				var accept_donor_or_accept = __left0__ [0];
+				var accept_center_atom = __left0__ [1];
+				if (lig_donor_or_accept == accept_donor_or_accept) {
+					continue;
 				}
+				var center_atom = (lig_donor_or_accept == 'DONOR' ? lig_center_atom : accept_center_atom);
+				if (lig_and_recep_have_hydrogens && hydrogen_bond) {
+					var angle = angle_between_three_points (ligand_atom.coordinates, center_atom.coordinates, receptor_atom.coordinates);
+					if (fabs (180 - (angle * 180.0) / math.pi) > angle_cutoff) {
+						continue;
 					}
 				}
-			for (var hydrogen of hydrogens) {
-				if (fabs (180 - (angle_between_three_points (ligand_atom.coordinates, hydrogen.coordinates, receptor_atom.coordinates) * 180.0) / math.pi) <= angle_cutoff) {
-					var hbonds_key = (((('HDONOR_' + hydrogen.comment) + '_') + receptor_atom.side_chain_or_backbone ()) + '_') + receptor_atom.structure;
+				var comment = (lig_donor_or_accept == 'ACCEPTOR' ? 'RECEPTOR' : 'LIGAND');
+				var hbonds_key = (((('HDONOR_' + comment) + '_') + receptor_atom.side_chain_or_backbone ()) + '_') + receptor_atom.structure;
 				pdb_hbonds.add_new_atom (ligand_atom.copy_of ());
-					pdb_hbonds.add_new_atom (hydrogen.copy_of ());
+				pdb_hbonds.add_new_atom (center_atom.copy_of ());
 				pdb_hbonds.add_new_atom (receptor_atom.copy_of ());
 				hashtable_entry_add_one (hbonds, hbonds_key);
-					hbonds_labels.append (tuple ([ligand_atom.string_id (), hydrogen.string_id (), receptor_atom.string_id (), hydrogen.comment]));
-				}
+				hbonds_labels.append (tuple ([ligand_atom.string_id (), center_atom.string_id (), receptor_atom.string_id (), comment]));
+				var hbond_detected = true;
+				break;
 			}
 		}
 	}

javascript/lib/binana.interactions._hydrophobics.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, 2021-11-05 16:24:09
+// Transcrypt'ed from Python, 2021-11-09 00:25:33
 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._ligand_atom_types.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, 2021-11-05 16:24:09
+// Transcrypt'ed from Python, 2021-11-09 00:25:33
 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';