Commit 063873b2 authored by jdurrant's avatar jdurrant
Browse files

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

parent 6c2f57df
...@@ -2,7 +2,7 @@ ...@@ -2,7 +2,7 @@
// LICENSE.md or go to https://opensource.org/licenses/Apache-2.0 for full // LICENSE.md or go to https://opensource.org/licenses/Apache-2.0 for full
// details. Copyright 2020 Jacob D. Durrant. // 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 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 {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 {fabs} from './binana._utils.shim.js';
......
...@@ -2,7 +2,7 @@ ...@@ -2,7 +2,7 @@
// LICENSE.md or go to https://opensource.org/licenses/Apache-2.0 for full // LICENSE.md or go to https://opensource.org/licenses/Apache-2.0 for full
// details. Copyright 2020 Jacob D. Durrant. // 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 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 {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'; import {Mol} from './binana._structure.mol.js';
...@@ -30,24 +30,28 @@ export var get_salt_bridges = function (ligand, receptor, cutoff) { ...@@ -30,24 +30,28 @@ export var get_salt_bridges = function (ligand, receptor, cutoff) {
} }
var key = 'SALT-BRIDGE_' + structure; var key = 'SALT-BRIDGE_' + structure;
for (var index of receptor_charge.indices) { 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) { 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); hashtable_entry_add_one (salt_bridges, key);
salt_bridge_labels.append (tuple ([('[' + ' / '.join ((function () { salt_bridge_labels.append (tuple ([('[' + ' / '.join ((function () {
var __accu0__ = []; var __accu0__ = [];
for (var index of ligand_charge.indices) { 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 () { }) ())) + ']', ('[' + ' / '.join ((function () {
var __accu0__ = []; var __accu0__ = [];
for (var index of receptor_charge.indices) { 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__);
}) ())) + ']'])); }) ())) + ']']));
} }
} }
......
...@@ -2,7 +2,7 @@ ...@@ -2,7 +2,7 @@
// LICENSE.md or go to https://opensource.org/licenses/Apache-2.0 for full // LICENSE.md or go to https://opensource.org/licenses/Apache-2.0 for full
// details. Copyright 2020 Jacob D. Durrant. // 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'; 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'; var __name__ = 'binana.interactions.default_params';
export var CLOSE_CONTACTS_DIST1_CUTOFF = 2.5; export var CLOSE_CONTACTS_DIST1_CUTOFF = 2.5;
......
...@@ -2,7 +2,7 @@ ...@@ -2,7 +2,7 @@
// LICENSE.md or go to https://opensource.org/licenses/Apache-2.0 for full // LICENSE.md or go to https://opensource.org/licenses/Apache-2.0 for full
// details. Copyright 2020 Jacob D. Durrant. // 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 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 {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'; import * as _closest from './binana.interactions._closest.js';
...@@ -22,7 +22,7 @@ __nest__ (binana, '', __module_binana__); ...@@ -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 {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 {_set_default} from './binana._utils.shim.js';
import * as default_params from './binana.interactions.default_params.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'; var __name__ = 'binana.interactions';
export var get_cation_pi = function (ligand, receptor, cutoff, pi_padding) { export var get_cation_pi = function (ligand, receptor, cutoff, pi_padding) {
if (typeof cutoff == 'undefined' || (cutoff != null && cutoff.hasOwnProperty ("__kwargtrans__"))) {; if (typeof cutoff == 'undefined' || (cutoff != null && cutoff.hasOwnProperty ("__kwargtrans__"))) {;
......
...@@ -2,7 +2,7 @@ ...@@ -2,7 +2,7 @@
// LICENSE.md or go to https://opensource.org/licenses/Apache-2.0 for full // LICENSE.md or go to https://opensource.org/licenses/Apache-2.0 for full
// details. Copyright 2020 Jacob D. Durrant. // 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 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 {AssertionError, AttributeError, BaseException, DeprecationWarning, Exception, IndexError, IterableError, KeyError, NotImplementedError, RuntimeWarning, StopIteration, UserWarning, ValueError, Warning, __JsIterator__, __PyIterator__, __Terminal__, __add__, __and__, __call__, __class__, __envir__, __eq__, __floordiv__, __ge__, __get__, __getcm__, __getitem__, __getslice__, __getsm__, __gt__, __i__, __iadd__, __iand__, __idiv__, __ijsmod__, __ilshift__, __imatmul__, __imod__, __imul__, __in__, __init__, __ior__, __ipow__, __irshift__, __isub__, __ixor__, __jsUsePyNext__, __jsmod__, __k__, __kwargtrans__, __le__, __lshift__, __lt__, __matmul__, __mergefields__, __mergekwargtrans__, __mod__, __mul__, __ne__, __neg__, __nest__, __or__, __pow__, __pragma__, __proxy__, __pyUseJsNext__, __rshift__, __setitem__, __setproperty__, __setslice__, __sort__, __specialattrib__, __sub__, __super__, __t__, __terminal__, __truediv__, __withblock__, __xor__, abs, all, any, assert, bool, bytearray, bytes, callable, chr, copy, deepcopy, delattr, dict, dir, divmod, enumerate, filter, float, getattr, hasattr, input, int, isinstance, issubclass, len, list, map, max, min, object, ord, pow, print, property, py_TypeError, py_iter, py_metatype, py_next, py_reversed, py_typeof, range, repr, round, set, setattr, sorted, str, sum, tuple, zip} from './org.transcrypt.__runtime__.js';
import * as _get_params from './binana._cli_params._get_params.js'; import * as _get_params from './binana._cli_params._get_params.js';
...@@ -13,7 +13,7 @@ import * as load_ligand_receptor from './binana.load_ligand_receptor.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 fs from './binana.fs.js';
import * as __module_binana__ from './binana.js'; import * as __module_binana__ from './binana.js';
__nest__ (binana, '', __module_binana__); __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__'; var __name__ = '__main__';
export var _sys = binana.sys; export var _sys = binana.sys;
export var run = function (args) { export var run = function (args) {
......
...@@ -2,7 +2,7 @@ ...@@ -2,7 +2,7 @@
// LICENSE.md or go to https://opensource.org/licenses/Apache-2.0 for full // LICENSE.md or go to https://opensource.org/licenses/Apache-2.0 for full
// details. Copyright 2020 Jacob D. Durrant. // 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 binana = {};
var math = {}; 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 {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'; ...@@ -13,7 +13,7 @@ import * as __module_math__ from './math.js';
__nest__ (math, '', __module_math__); __nest__ (math, '', __module_math__);
import * as __module_binana__ from './binana.js'; import * as __module_binana__ from './binana.js';
__nest__ (binana, '', __module_binana__); __nest__ (binana, '', __module_binana__);
export {_Point, _Mol, _math_functions}; export {_math_functions, _Point, _Mol};
var __name__ = 'binana.load_ligand_receptor'; var __name__ = 'binana.load_ligand_receptor';
export var _ligand_receptor_dists = null; export var _ligand_receptor_dists = null;
export var _ligand_receptor_aromatic_dists = null; export var _ligand_receptor_aromatic_dists = null;
......
...@@ -2,7 +2,7 @@ ...@@ -2,7 +2,7 @@
// LICENSE.md or go to https://opensource.org/licenses/Apache-2.0 for full // LICENSE.md or go to https://opensource.org/licenses/Apache-2.0 for full
// details. Copyright 2020 Jacob D. Durrant. // 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 = {}; 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 {AssertionError, AttributeError, BaseException, DeprecationWarning, Exception, IndexError, IterableError, KeyError, NotImplementedError, RuntimeWarning, StopIteration, UserWarning, ValueError, Warning, __JsIterator__, __PyIterator__, __Terminal__, __add__, __and__, __call__, __class__, __envir__, __eq__, __floordiv__, __ge__, __get__, __getcm__, __getitem__, __getslice__, __getsm__, __gt__, __i__, __iadd__, __iand__, __idiv__, __ijsmod__, __ilshift__, __imatmul__, __imod__, __imul__, __in__, __init__, __ior__, __ipow__, __irshift__, __isub__, __ixor__, __jsUsePyNext__, __jsmod__, __k__, __kwargtrans__, __le__, __lshift__, __lt__, __matmul__, __mergefields__, __mergekwargtrans__, __mod__, __mul__, __ne__, __neg__, __nest__, __or__, __pow__, __pragma__, __proxy__, __pyUseJsNext__, __rshift__, __setitem__, __setproperty__, __setslice__, __sort__, __specialattrib__, __sub__, __super__, __t__, __terminal__, __truediv__, __withblock__, __xor__, abs, all, any, assert, bool, bytearray, bytes, callable, chr, copy, deepcopy, delattr, dict, dir, divmod, enumerate, filter, float, getattr, hasattr, input, int, isinstance, issubclass, len, list, map, max, min, object, ord, pow, print, property, py_TypeError, py_iter, py_metatype, py_next, py_reversed, py_typeof, range, repr, round, set, setattr, sorted, str, sum, tuple, zip} from './org.transcrypt.__runtime__.js';
import * as shim from './binana._utils.shim.js'; import * as shim from './binana._utils.shim.js';
...@@ -10,7 +10,7 @@ import * as __module_binana__ from './binana.js'; ...@@ -10,7 +10,7 @@ import * as __module_binana__ from './binana.js';
__nest__ (binana, '', __module_binana__); __nest__ (binana, '', __module_binana__);
import * as vmd_state from './binana.output._directory.vmd_state.js'; import * as vmd_state from './binana.output._directory.vmd_state.js';
import * as pdbs from './binana.output._directory.pdbs.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'; var __name__ = 'binana.output._directory';
export var os = shim; 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) { 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) {
......
...@@ -2,7 +2,7 @@ ...@@ -2,7 +2,7 @@
// LICENSE.md or go to https://opensource.org/licenses/Apache-2.0 for full // LICENSE.md or go to https://opensource.org/licenses/Apache-2.0 for full
// details. Copyright 2020 Jacob D. Durrant. // 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'; 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'; 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) { 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) {
......
...@@ -2,7 +2,7 @@ ...@@ -2,7 +2,7 @@
// LICENSE.md or go to https://opensource.org/licenses/Apache-2.0 for full // LICENSE.md or go to https://opensource.org/licenses/Apache-2.0 for full
// details. Copyright 2020 Jacob D. Durrant. // 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 = {}; 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 {AssertionError, AttributeError, BaseException, DeprecationWarning, Exception, IndexError, IterableError, KeyError, NotImplementedError, RuntimeWarning, StopIteration, UserWarning, ValueError, Warning, __JsIterator__, __PyIterator__, __Terminal__, __add__, __and__, __call__, __class__, __envir__, __eq__, __floordiv__, __ge__, __get__, __getcm__, __getitem__, __getslice__, __getsm__, __gt__, __i__, __iadd__, __iand__, __idiv__, __ijsmod__, __ilshift__, __imatmul__, __imod__, __imul__, __in__, __init__, __ior__, __ipow__, __irshift__, __isub__, __ixor__, __jsUsePyNext__, __jsmod__, __k__, __kwargtrans__, __le__, __lshift__, __lt__, __matmul__, __mergefields__, __mergekwargtrans__, __mod__, __mul__, __ne__, __neg__, __nest__, __or__, __pow__, __pragma__, __proxy__, __pyUseJsNext__, __rshift__, __setitem__, __setproperty__, __setslice__, __sort__, __specialattrib__, __sub__, __super__, __t__, __terminal__, __truediv__, __withblock__, __xor__, abs, all, any, assert, bool, bytearray, bytes, callable, chr, copy, deepcopy, delattr, dict, dir, divmod, enumerate, filter, float, getattr, hasattr, input, int, isinstance, issubclass, len, list, map, max, min, object, ord, pow, print, property, py_TypeError, py_iter, py_metatype, py_next, py_reversed, py_typeof, range, repr, round, set, setattr, sorted, str, sum, tuple, zip} from './org.transcrypt.__runtime__.js';
import {OpenFile} from './binana._utils.shim.js'; import {OpenFile} from './binana._utils.shim.js';
......
...@@ -2,7 +2,7 @@ ...@@ -2,7 +2,7 @@
// LICENSE.md or go to https://opensource.org/licenses/Apache-2.0 for full // LICENSE.md or go to https://opensource.org/licenses/Apache-2.0 for full
// details. Copyright 2020 Jacob D. Durrant. // 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 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 {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'; import * as json from './binana._utils.shim.js';
......
...@@ -2,7 +2,7 @@ ...@@ -2,7 +2,7 @@
// LICENSE.md or go to https://opensource.org/licenses/Apache-2.0 for full // LICENSE.md or go to https://opensource.org/licenses/Apache-2.0 for full
// details. Copyright 2020 Jacob D. Durrant. // 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 binana = {};
var re = {}; 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 {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';
......
...@@ -2,7 +2,7 @@ ...@@ -2,7 +2,7 @@
// LICENSE.md or go to https://opensource.org/licenses/Apache-2.0 for full // LICENSE.md or go to https://opensource.org/licenses/Apache-2.0 for full
// details. Copyright 2020 Jacob D. Durrant. // 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 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 {AssertionError, AttributeError, BaseException, DeprecationWarning, Exception, IndexError, IterableError, KeyError, NotImplementedError, RuntimeWarning, StopIteration, UserWarning, ValueError, Warning, __JsIterator__, __PyIterator__, __Terminal__, __add__, __and__, __call__, __class__, __envir__, __eq__, __floordiv__, __ge__, __get__, __getcm__, __getitem__, __getslice__, __getsm__, __gt__, __i__, __iadd__, __iand__, __idiv__, __ijsmod__, __ilshift__, __imatmul__, __imod__, __imul__, __in__, __init__, __ior__, __ipow__, __irshift__, __isub__, __ixor__, __jsUsePyNext__, __jsmod__, __k__, __kwargtrans__, __le__, __lshift__, __lt__, __matmul__, __mergefields__, __mergekwargtrans__, __mod__, __mul__, __ne__, __neg__, __nest__, __or__, __pow__, __pragma__, __proxy__, __pyUseJsNext__, __rshift__, __setitem__, __setproperty__, __setslice__, __sort__, __specialattrib__, __sub__, __super__, __t__, __terminal__, __truediv__, __withblock__, __xor__, abs, all, any, assert, bool, bytearray, bytes, callable, chr, copy, deepcopy, delattr, dict, dir, divmod, enumerate, filter, float, getattr, hasattr, input, int, isinstance, issubclass, len, list, map, max, min, object, ord, pow, print, property, py_TypeError, py_iter, py_metatype, py_next, py_reversed, py_typeof, range, repr, round, set, setattr, sorted, str, sum, tuple, zip} from './org.transcrypt.__runtime__.js';
import {OpenFile as _openFile} from './binana._utils.shim.js'; import {OpenFile as _openFile} from './binana._utils.shim.js';
...@@ -13,7 +13,7 @@ import * as pdb_file from './binana.output.pdb_file.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 _log from './binana.output._log.js';
import * as dictionary from './binana.output.dictionary.js'; import * as dictionary from './binana.output.dictionary.js';
import * as _directory from './binana.output._directory.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'; 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) { 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})); 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}));
......
...@@ -2,7 +2,7 @@ ...@@ -2,7 +2,7 @@
// LICENSE.md or go to https://opensource.org/licenses/Apache-2.0 for full // LICENSE.md or go to https://opensource.org/licenses/Apache-2.0 for full
// details. Copyright 2020 Jacob D. Durrant. // 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 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 {AssertionError, AttributeError, BaseException, DeprecationWarning, Exception, IndexError, IterableError, KeyError, NotImplementedError, RuntimeWarning, StopIteration, UserWarning, ValueError, Warning, __JsIterator__, __PyIterator__, __Terminal__, __add__, __and__, __call__, __class__, __envir__, __eq__, __floordiv__, __ge__, __get__, __getcm__, __getitem__, __getslice__, __getsm__, __gt__, __i__, __iadd__, __iand__, __idiv__, __ijsmod__, __ilshift__, __imatmul__, __imod__, __imul__, __in__, __init__, __ior__, __ipow__, __irshift__, __isub__, __ixor__, __jsUsePyNext__, __jsmod__, __k__, __kwargtrans__, __le__, __lshift__, __lt__, __matmul__, __mergefields__, __mergekwargtrans__, __mod__, __mul__, __ne__, __neg__, __nest__, __or__, __pow__, __pragma__, __proxy__, __pyUseJsNext__, __rshift__, __setitem__, __setproperty__, __setslice__, __sort__, __specialattrib__, __sub__, __super__, __t__, __terminal__, __truediv__, __withblock__, __xor__, abs, all, any, assert, bool, bytearray, bytes, callable, chr, copy, deepcopy, delattr, dict, dir, divmod, enumerate, filter, float, getattr, hasattr, input, int, isinstance, issubclass, len, list, map, max, min, object, ord, pow, print, property, py_TypeError, py_iter, py_metatype, py_next, py_reversed, py_typeof, range, repr, round, set, setattr, sorted, str, sum, tuple, zip} from './org.transcrypt.__runtime__.js';
import {OpenFile} from './binana._utils.shim.js'; import {OpenFile} from './binana._utils.shim.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'; 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'; var __name__ = 'math';
export var pi = Math.PI; export var pi = Math.PI;
......
// 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__'; var __name__ = 'org.transcrypt.__runtime__';
export var __envir__ = {}; export var __envir__ = {};
__envir__.interpreter_name = 'python'; __envir__.interpreter_name = 'python';
......
// 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 {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'; import {translate} from './re.translate.js';
export {translate}; export {translate};
......
// Transcrypt'ed from Python, 2021-11-05 16:24:10 // Transcrypt'ed from Python, 2021-11-09 00:25:34
var re = {}; 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 {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'; import * as __module_re__ from './re.js';
......
...@@ -4,9 +4,25 @@ ...@@ -4,9 +4,25 @@
# this file contains the Atom class for binana.py # this file contains the Atom class for binana.py
import math
import binana import binana
from binana._structure.point import Point from binana._structure.point import Point
from binana._utils.shim import r_just, round_to_thousandths_to_str 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 Class Atom defines an atom
...@@ -81,10 +97,10 @@ class Atom: ...@@ -81,10 +97,10 @@ class Atom:
+ r_just(self.residue, 4) + r_just(self.residue, 4)
) )
output = output + r_just(round_to_thousandths_to_str(self.coordinates.x), 18) 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 += 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 += r_just(round_to_thousandths_to_str(self.coordinates.z), 8)
output = output + r_just(self.element, 24) output += r_just(self.element, 24)
return output return output
# Returns the number of an atom's nearest neighbors # Returns the number of an atom's nearest neighbors
...@@ -96,19 +112,14 @@ class Atom: ...@@ -96,19 +112,14 @@ class Atom:
# Param self (Atom) # Param self (Atom)
# Param index (float): index of atom to be added # Param index (float): index of atom to be added
def add_neighbor_atom_index(self, index): 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) self.indecies_of_atoms_connecting.append(index)
# Returns whether the atom is part of the backbone or a sidechain # Returns whether the atom is part of the backbone or a sidechain
# Only really applies to proteins, assuming standard atom names # Only really applies to proteins, assuming standard atom names
# Param self (Atom) # Param self (Atom)
def side_chain_or_backbone(self): def side_chain_or_backbone(self):
if ( if self.atom_name.strip() in ["CA", "C", "O", "N"]:
self.atom_name.strip() == "CA"
or self.atom_name.strip() == "C"
or self.atom_name.strip() == "O"
or self.atom_name.strip() == "N"
):
return "BACKBONE" return "BACKBONE"
else: else:
return "SIDECHAIN" return "SIDECHAIN"
...@@ -205,3 +216,25 @@ class Atom: ...@@ -205,3 +216,25 @@ class Atom:
if self.residue.strip() == "": if self.residue.strip() == "":
self.residue = " MOL" self.residue = " MOL"
# TODO: Might make more sense to put this in mol.