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

javascript/lib/binana.interactions._pi_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 {fabs} from './binana._utils.shim.js';

javascript/lib/binana.interactions._salt_bridges.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';
@@ -30,24 +30,28 @@ export var get_salt_bridges = function (ligand, receptor, cutoff) {
 				}
 				var key = 'SALT-BRIDGE_' + structure;
 				for (var index of receptor_charge.indices) {
-					pdb_salt_bridges.add_new_atom (receptor.all_atoms [index].copy_of ());
+					var idx = int (index);
+					var atom = receptor.all_atoms [idx];
+					pdb_salt_bridges.add_new_atom (atom.copy_of ());
 				}
 				for (var index of ligand_charge.indices) {
-					pdb_salt_bridges.add_new_atom (ligand.all_atoms [index].copy_of ());
+					var idx = int (index);
+					var atom = ligand.all_atoms [idx];
+					pdb_salt_bridges.add_new_atom (atom.copy_of ());
 				}
 				hashtable_entry_add_one (salt_bridges, key);
 				salt_bridge_labels.append (tuple ([('[' + ' / '.join ((function () {
 					var __accu0__ = [];
 					for (var index of ligand_charge.indices) {
-						__accu0__.append (ligand.all_atoms [index].string_id ());
+						__accu0__.append (ligand.all_atoms [int (index)].string_id ());
 					}
-					return __accu0__;
+					return py_iter (__accu0__);
 				}) ())) + ']', ('[' + ' / '.join ((function () {
 					var __accu0__ = [];
 					for (var index of receptor_charge.indices) {
-						__accu0__.append (receptor.all_atoms [index].string_id ());
+						__accu0__.append (receptor.all_atoms [int (index)].string_id ());
 					}
-					return __accu0__;
+					return py_iter (__accu0__);
 				}) ())) + ']']));
 			}
 		}

javascript/lib/binana.interactions.default_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
 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.interactions.default_params';
 export var CLOSE_CONTACTS_DIST1_CUTOFF = 2.5;

javascript/lib/binana.interactions.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 * as _closest from './binana.interactions._closest.js';
@@ -22,7 +22,7 @@ __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, PI_PADDING_DIST, PI_PI_INTERACTING_DIST_CUTOFF, PI_STACKING_ANGLE_TOLERANCE, SALT_BRIDGE_DIST_CUTOFF, T_STACKING_ANGLE_TOLERANCE, T_STACKING_CLOSEST_DIST_CUTOFF} from './binana.interactions.default_params.js';
 import {_set_default} from './binana._utils.shim.js';
 import * as default_params from './binana.interactions.default_params.js';
-export {CLOSE_CONTACTS_DIST2_CUTOFF, _cat_pi, PI_PADDING_DIST, _flexibility, CATION_PI_DIST_CUTOFF, _closest, _electrostatic_energies, default_params, HYDROPHOBIC_DIST_CUTOFF, CLOSE_CONTACTS_DIST1_CUTOFF, SALT_BRIDGE_DIST_CUTOFF, _hydrophobics, T_STACKING_ANGLE_TOLERANCE, _close, _ligand_atom_types, HYDROGEN_HALOGEN_BOND_ANGLE_CUTOFF, ACTIVE_SITE_FLEXIBILITY_DIST_CUTOFF, ELECTROSTATIC_DIST_CUTOFF, _set_default, PI_PI_INTERACTING_DIST_CUTOFF, _salt_bridges, HYDROGEN_HALOGEN_BOND_DIST_CUTOFF, T_STACKING_CLOSEST_DIST_CUTOFF, PI_STACKING_ANGLE_TOLERANCE, _hydrogen_halogen_bonds, _pi_pi};
+export {HYDROPHOBIC_DIST_CUTOFF, default_params, T_STACKING_ANGLE_TOLERANCE, HYDROGEN_HALOGEN_BOND_ANGLE_CUTOFF, PI_PADDING_DIST, _pi_pi, _salt_bridges, PI_STACKING_ANGLE_TOLERANCE, ACTIVE_SITE_FLEXIBILITY_DIST_CUTOFF, _hydrophobics, _electrostatic_energies, _flexibility, _hydrogen_halogen_bonds, T_STACKING_CLOSEST_DIST_CUTOFF, CLOSE_CONTACTS_DIST1_CUTOFF, CLOSE_CONTACTS_DIST2_CUTOFF, SALT_BRIDGE_DIST_CUTOFF, _ligand_atom_types, _closest, _close, CATION_PI_DIST_CUTOFF, PI_PI_INTERACTING_DIST_CUTOFF, HYDROGEN_HALOGEN_BOND_DIST_CUTOFF, _set_default, _cat_pi, ELECTROSTATIC_DIST_CUTOFF};
 var __name__ = 'binana.interactions';
 export var get_cation_pi = function (ligand, receptor, cutoff, pi_padding) {
 	if (typeof cutoff == 'undefined' || (cutoff != null && cutoff.hasOwnProperty ("__kwargtrans__"))) {;

javascript/lib/binana.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 _get_params from './binana._cli_params._get_params.js';
@@ -13,7 +13,7 @@ import * as load_ligand_receptor from './binana.load_ligand_receptor.js';
 import * as fs from './binana.fs.js';
 import * as __module_binana__ from './binana.js';
 __nest__ (binana, '', __module_binana__);
-export {fs, output, _get_params, interactions, load_ligand_receptor, _start};
+export {fs, _get_params, _start, output, interactions, load_ligand_receptor};
 var __name__ = '__main__';
 export var _sys = binana.sys;
 export var run = function (args) {

javascript/lib/binana.load_ligand_receptor.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';
@@ -13,7 +13,7 @@ import * as __module_math__ from './math.js';
 __nest__ (math, '', __module_math__);
 import * as __module_binana__ from './binana.js';
 __nest__ (binana, '', __module_binana__);
-export {_Point, _Mol, _math_functions};
+export {_math_functions, _Point, _Mol};
 var __name__ = 'binana.load_ligand_receptor';
 export var _ligand_receptor_dists = null;
 export var _ligand_receptor_aromatic_dists = null;

javascript/lib/binana.output._directory.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 * as shim from './binana._utils.shim.js';
@@ -10,7 +10,7 @@ import * as __module_binana__ from './binana.js';
 __nest__ (binana, '', __module_binana__);
 import * as vmd_state from './binana.output._directory.vmd_state.js';
 import * as pdbs from './binana.output._directory.pdbs.js';
-export {vmd_state, pdbs, shim};
+export {pdbs, vmd_state, shim};
 var __name__ = 'binana.output._directory';
 export var os = shim;
 export var make_directory_output = function (parameters, closest, close, active_site_flexibility, hydrophobics, hydrogen_bonds, halogen_bonds, pi_pi, cat_pi, salt_bridges, ligand, receptor) {

javascript/lib/binana.output._directory.pdbs.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
 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.output._directory.pdbs';
 export var output_dir_pdbs = function (pdb_closest_contacts, parameters, pdb_close_contacts, pdb_contacts_alpha_helix, pdb_contacts_beta_sheet, pdb_contacts_other_2nd_structure, pdb_back_bone, pdb_side_chain, pdb_hydrophobic, pdb_hbonds, pdb_halbonds, pdb_pistack, pdb_pi_T, pdb_pi_cat, pdb_salt_bridges, ligand, receptor) {

javascript/lib/binana.output._directory.vmd_state.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';

javascript/lib/binana.output._log.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 00:25:34
 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 * as json from './binana._utils.shim.js';

javascript/lib/binana.output.dictionary.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 00:25:34
 var binana = {};
 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';

javascript/lib/binana.output.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 {OpenFile as _openFile} from './binana._utils.shim.js';
@@ -13,7 +13,7 @@ import * as pdb_file from './binana.output.pdb_file.js';
 import * as _log from './binana.output._log.js';
 import * as dictionary from './binana.output.dictionary.js';
 import * as _directory from './binana.output._directory.js';
-export {_directory, _openFile, dictionary, _json, pdb_file, _log};
+export {_openFile, _directory, _json, dictionary, pdb_file, _log};
 var __name__ = 'binana.output';
 export var _write_main = function (parameters, ligand, receptor, closest, close, hydrophobics, hydrogen_bonds, halogen_bonds, salt_bridges, pi_pi, cat_pi, electrostatic_energies, active_site_flexibility, ligand_atom_types) {
 	var json_output = binana.output.dictionary.collect (closest, close, hydrophobics, hydrogen_bonds, halogen_bonds, salt_bridges, pi_pi, cat_pi, electrostatic_energies, active_site_flexibility, ligand_atom_types, __kwargtrans__ ({ligand_rotatable_bonds: ligand.rotatable_bonds_count}));

javascript/lib/binana.output.pdb_file.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 {OpenFile} from './binana._utils.shim.js';

javascript/lib/math.js

-// 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, 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__ = 'math';
 export var pi = Math.PI;

javascript/lib/org.transcrypt.__runtime__.js

-// Transcrypt'ed from Python, 2021-11-05 16:24:08
+// Transcrypt'ed from Python, 2021-11-09 00:25:32
 var __name__ = 'org.transcrypt.__runtime__';
 export var __envir__ = {};
 __envir__.interpreter_name = 'python';

javascript/lib/re.js

-// Transcrypt'ed from Python, 2021-11-05 16:24:09
+// Transcrypt'ed from Python, 2021-11-09 00:25:34
 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 {translate} from './re.translate.js';
 export {translate};

javascript/lib/re.translate.js

-// Transcrypt'ed from Python, 2021-11-05 16:24:10
+// Transcrypt'ed from Python, 2021-11-09 00:25:34
 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 * as __module_re__ from './re.js';

python/binana/_structure/atom.py

@@ -4,9 +4,25 @@
 
 # this file contains the Atom class for binana.py
 
+import math
 import binana
 from binana._structure.point import Point
 from binana._utils.shim import r_just, round_to_thousandths_to_str
+from binana._utils._math_functions import angle_between_three_points
+
+# __pragma__ ('skip')
+# Python
+from math import fabs
+
+# __pragma__ ('noskip')
+
+
+"""?
+# Transcrypt
+import binana._utils
+from binana._utils import shim
+from binana._utils.shim import fabs
+?"""
 
 """
 Class Atom defines an atom
@@ -81,10 +97,10 @@ class Atom:
             + r_just(self.residue, 4)
         )
 
-        output = output + r_just(round_to_thousandths_to_str(self.coordinates.x), 18)
-        output = output + r_just(round_to_thousandths_to_str(self.coordinates.y), 8)
-        output = output + r_just(round_to_thousandths_to_str(self.coordinates.z), 8)
-        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
 
     # Returns the number of an atom's nearest neighbors
@@ -96,19 +112,14 @@ class Atom:
     # Param self (Atom)
     # Param index (float): index of atom to be added
     def add_neighbor_atom_index(self, index):
-        if not (index in self.indecies_of_atoms_connecting):
+        if index not in self.indecies_of_atoms_connecting:
             self.indecies_of_atoms_connecting.append(index)
 
     # Returns whether the atom is part of the backbone or a sidechain
     # Only really applies to proteins, assuming standard atom names
     # Param self (Atom)
     def side_chain_or_backbone(self):
-        if (
-            self.atom_name.strip() == "CA"
-            or self.atom_name.strip() == "C"
-            or self.atom_name.strip() == "O"
-            or self.atom_name.strip() == "N"
-        ):
+        if self.atom_name.strip() in ["CA", "C", "O", "N"]:
             return "BACKBONE"
         else:
             return "SIDECHAIN"
@@ -205,3 +216,25 @@ class Atom:
 
         if self.residue.strip() == "":
             self.residue = " MOL"
+
+    # TODO: Might make more sense to put this in mol.
+    def has_sp3_geometry(self, parent_mol):
+        ncrs = [
+            parent_mol.all_atoms[i].coordinates
+            for i in self.indecies_of_atoms_connecting
+        ]
+        ccr = self.coordinates
+        to_deg = 180.0 / math.pi
+        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)
+
+        average_angle = sum(angles) / float(len(angles))
+
+        return fabs(average_angle - 109.0) < 5.0

python/binana/_test/expected_output/output.pdb

@@ -8,17 +8,17 @@ REMARK            cation_pi_dist_cutoff        |             6.0
 REMARK         close_contacts_dist1_cutoff     |             2.5            
 REMARK         close_contacts_dist2_cutoff     |             4.0            
 REMARK          electrostatic_dist_cutoff      |             4.0            
-REMARK          hydrogen_halogen_bond_angle_cutoff     |             40.0           
-REMARK          hydrogen_halogen_bond_dist_cutoff      |             4.0            
+REMARK      hydrogen_halogen_bond_angle_cutoff |             40.0           
+REMARK      hydrogen_halogen_bond_dist_cutoff  |             4.0            
 REMARK           hydrophobic_dist_cutoff       |             4.0            
-REMARK                    ligand               | /Users/jdurrant/Documents/Work/durrant_git/binana/binana/test/input/ligand.pdbqt
-REMARK                  output_dir             | /Users/jdurrant/Documents/Work/durrant_git/binana/binana/test/output/
-REMARK                 output_file             | /Users/jdurrant/Documents/Work/durrant_git/binana/binana/test/output/output.pdb
-REMARK                 output_json             | /Users/jdurrant/Documents/Work/durrant_git/binana/binana/test/output/output.json
+REMARK                    ligand               | /Users/jdurrant/Documents/Work/durrant_git/binana/python/binana/_test/input/ligand.pdbqt
+REMARK                  output_dir             | /Users/jdurrant/Documents/Work/durrant_git/binana/python/binana/_test/output/
+REMARK                 output_file             | /Users/jdurrant/Documents/Work/durrant_git/binana/python/binana/_test/output/output.pdb
+REMARK                 output_json             | /Users/jdurrant/Documents/Work/durrant_git/binana/python/binana/_test/output/output.json
 REMARK               pi_padding_dist           |             0.75           
 REMARK        pi_pi_interacting_dist_cutoff    |             7.5            
 REMARK         pi_stacking_angle_tolerance     |             30.0           
-REMARK                   receptor              | /Users/jdurrant/Documents/Work/durrant_git/binana/binana/test/input/receptor.pdbqt
+REMARK                   receptor              | /Users/jdurrant/Documents/Work/durrant_git/binana/python/binana/_test/input/receptor.pdbqt
 REMARK           salt_bridge_dist_cutoff       |             5.5            
 REMARK                     test                |            False           
 REMARK 
@@ -8328,11 +8328,11 @@ REMARK "OTH" indicate receptor contacts whose respective protein residues have
 REMARK the alpha-helix, beta-sheet, or "other" secondary structure. "BAC" and
 REMARK "SID" indicate receptor contacts that are part of the protein backbone
 REMARK and sidechain, respectively. "HYD" indicates hydrophobic contacts
-REMARK between the protein and ligand. "HBN" indicates hydrogen bonds. "SAL"
-REMARK indicates salt bridges. "PIS" indicates pi-pi stacking interactions,
-REMARK "PIT" indicates T-stacking interactions, and "PIC" indicates cation-pi
-REMARK interactions. Protein residue names are unchanged, but the ligand
-REMARK residue is now named "LIG".
+REMARK between the protein and ligand. "HBN" indicates hydrogen bonds. "HAL"
+REMARK indicates halogen bonds. "SAL" indicates salt bridges. "PIS" indicates
+REMARK pi-pi stacking interactions, "PIT" indicates T-stacking interactions,
+REMARK and "PIC" indicates cation-pi interactions. Protein residue names are
+REMARK unchanged, but the ligand residue is now named "LIG".
 REMARK
 ATOM      1  N   ASP            23.366  -3.399  14.662                       N
 ATOM      2  CA  ASP            22.530  -2.226  14.843                       C