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 @@
// 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';
......
......@@ -2,7 +2,7 @@
// LICENSE.md or go to https://opensource.org/licenses/Apache-2.0 for full
// details. Copyright 2020 Jacob D. Durrant.
// Transcrypt'ed from Python, 2021-11-05 16:24:09
// Transcrypt'ed from Python, 2021-11-09 00:25:33
var __future__ = {};
var binana = {};
var math = {};
......@@ -21,7 +21,20 @@ __nest__ (binana, '', __module_binana__);
import {HYDROGEN_HALOGEN_BOND_ANGLE_CUTOFF, HYDROGEN_HALOGEN_BOND_DIST_CUTOFF} from './binana.interactions.default_params.js';
import {_set_default} from './binana._utils.shim.js';
var __name__ = 'binana.interactions._hydrogen_halogen_bonds';
export var max_donor_X_dist = dict ({'H': 1.3, 'I': 2.04 * 1.4, 'BR': 1.86 * 1.4, 'Br': 1.86 * 1.4, 'CL': 1.71 * 1.4, 'Cl': 1.71 * 1.4, 'F': 1.33 * 1.4});
export var _mimic_set_minus = function (set1, set2) {
for (var s2 of set2) {
var set1 = (function () {
var __accu0__ = [];
for (var s of set1) {
if (s [0] != s2 [0]) {
__accu0__.append (s);
}
}
return __accu0__;
}) ();
}
return set1;
};
export var get_hydrogen_or_halogen_bonds = function (ligand, receptor, dist_cutoff, angle_cutoff, hydrogen_bond) {
if (typeof dist_cutoff == 'undefined' || (dist_cutoff != null && dist_cutoff.hasOwnProperty ("__kwargtrans__"))) {;
var dist_cutoff = null;
......@@ -32,45 +45,56 @@ export var get_hydrogen_or_halogen_bonds = function (ligand, receptor, dist_cuto
if (typeof hydrogen_bond == 'undefined' || (hydrogen_bond != null && hydrogen_bond.hasOwnProperty ("__kwargtrans__"))) {;
var hydrogen_bond = true;
};
var central_atoms = (hydrogen_bond ? ['H'] : ['I', 'BR', 'Br', 'CL', 'Cl', 'F']);
var dist_cutoff = _set_default (dist_cutoff, HYDROGEN_HALOGEN_BOND_DIST_CUTOFF);
var angle_cutoff = _set_default (angle_cutoff, HYDROGEN_HALOGEN_BOND_ANGLE_CUTOFF);
var hbonds = dict ({});
var pdb_hbonds = Mol ();
var hbonds_labels = [];
var dist_cutoff = _set_default (dist_cutoff, HYDROGEN_HALOGEN_BOND_DIST_CUTOFF);
var angle_cutoff = _set_default (angle_cutoff, HYDROGEN_HALOGEN_BOND_ANGLE_CUTOFF);
var lig_and_recep_have_hydrogens = ligand.has_hydrogens && receptor.has_hydrogens;
var ligand_receptor_dists = _get_ligand_receptor_dists (ligand, receptor);
var close_donors_acceptors = (function () {
var __accu0__ = [];
for (var [ligand_atom, receptor_atom, dist] of ligand_receptor_dists) {
if (dist < dist_cutoff && __in__ (ligand_atom.element, ['O', 'N']) && __in__ (receptor_atom.element, ['O', 'N'])) {
var hydrogens = [];
for (var atm_index of ligand.all_atoms.py_keys ()) {
var element = ligand.all_atoms [atm_index].element;
if (__in__ (element, central_atoms)) {
var dist = ligand.all_atoms [atm_index].coordinates.dist_to (ligand_atom.coordinates);
if (dist < max_donor_X_dist [element]) {
ligand.all_atoms [atm_index].comment = 'LIGAND';
hydrogens.append (ligand.all_atoms [atm_index]);
__accu0__.append ([ligand_atom, receptor_atom]);
}
}
return __accu0__;
}) ();
for (var [ligand_atom, receptor_atom] of close_donors_acceptors) {
var hbond_detected = false;
var lig_atm_hbond_infs = ligand.is_hbond_donor_acceptor (ligand_atom, hydrogen_bond);
var recep_atm_hbond_infs = receptor.is_hbond_donor_acceptor (receptor_atom, hydrogen_bond);
for (var lig_atm_hbond_inf of lig_atm_hbond_infs) {
if (hbond_detected) {
break;
}
for (var atm_index of receptor.all_atoms.py_keys ()) {
var element = receptor.all_atoms [atm_index].element;
if (__in__ (element, central_atoms)) {
var dist = receptor.all_atoms [atm_index].coordinates.dist_to (receptor_atom.coordinates);
if (dist < max_donor_X_dist [element]) {
receptor.all_atoms [atm_index].comment = 'RECEPTOR';
hydrogens.append (receptor.all_atoms [atm_index]);
var __left0__ = lig_atm_hbond_inf;
var lig_donor_or_accept = __left0__ [0];
var lig_center_atom = __left0__ [1];
for (var recep_atm_hbond_inf of recep_atm_hbond_infs) {
var __left0__ = recep_atm_hbond_inf;
var accept_donor_or_accept = __left0__ [0];
var accept_center_atom = __left0__ [1];
if (lig_donor_or_accept == accept_donor_or_accept) {
continue;
}
var center_atom = (lig_donor_or_accept == 'DONOR' ? lig_center_atom : accept_center_atom);
if (lig_and_recep_have_hydrogens && hydrogen_bond) {
var angle = angle_between_three_points (ligand_atom.coordinates, center_atom.coordinates, receptor_atom.coordinates);
if (fabs (180 - (angle * 180.0) / math.pi) > angle_cutoff) {
continue;
}
}
for (var hydrogen of hydrogens) {
if (fabs (180 - (angle_between_three_points (ligand_atom.coordinates, hydrogen.coordinates, receptor_atom.coordinates) * 180.0) / math.pi) <= angle_cutoff) {
var hbonds_key = (((('HDONOR_' + hydrogen.comment) + '_') + receptor_atom.side_chain_or_backbone ()) + '_') + receptor_atom.structure;
var comment = (lig_donor_or_accept == 'ACCEPTOR' ? 'RECEPTOR' : 'LIGAND');
var hbonds_key = (((('HDONOR_' + comment) + '_') + receptor_atom.side_chain_or_backbone ()) + '_') + receptor_atom.structure;
pdb_hbonds.add_new_atom (ligand_atom.copy_of ());
pdb_hbonds.add_new_atom (hydrogen.copy_of ());
pdb_hbonds.add_new_atom (center_atom.copy_of ());
pdb_hbonds.add_new_atom (receptor_atom.copy_of ());
hashtable_entry_add_one (hbonds, hbonds_key);
hbonds_labels.append (tuple ([ligand_atom.string_id (), hydrogen.string_id (), receptor_atom.string_id (), hydrogen.comment]));
}
hbonds_labels.append (tuple ([ligand_atom.string_id (), center_atom.string_id (), receptor_atom.string_id (), comment]));
var hbond_detected = true;
break;
}
}
}
......
......@@ -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';
......
......@@ -2,7 +2,7 @@
// LICENSE.md or go to https://opensource.org/licenses/Apache-2.0 for full
// details. Copyright 2020 Jacob D. Durrant.
// Transcrypt'ed from Python, 2021-11-05 16:24:09
// Transcrypt'ed from Python, 2021-11-09 00:25:33
var binana = {};
import {AssertionError, AttributeError, BaseException, DeprecationWarning, Exception, IndexError, IterableError, KeyError, NotImplementedError, RuntimeWarning, StopIteration, UserWarning, ValueError, Warning, __JsIterator__, __PyIterator__, __Terminal__, __add__, __and__, __call__, __class__, __envir__, __eq__, __floordiv__, __ge__, __get__, __getcm__, __getitem__, __getslice__, __getsm__, __gt__, __i__, __iadd__, __iand__, __idiv__, __ijsmod__, __ilshift__, __imatmul__, __imod__, __imul__, __in__, __init__, __ior__, __ipow__, __irshift__, __isub__, __ixor__, __jsUsePyNext__, __jsmod__, __k__, __kwargtrans__, __le__, __lshift__, __lt__, __matmul__, __mergefields__, __mergekwargtrans__, __mod__, __mul__, __ne__, __neg__, __nest__, __or__, __pow__, __pragma__, __proxy__, __pyUseJsNext__, __rshift__, __setitem__, __setproperty__, __setslice__, __sort__, __specialattrib__, __sub__, __super__, __t__, __terminal__, __truediv__, __withblock__, __xor__, abs, all, any, assert, bool, bytearray, bytes, callable, chr, copy, deepcopy, delattr, dict, dir, divmod, enumerate, filter, float, getattr, hasattr, input, int, isinstance, issubclass, len, list, map, max, min, object, ord, pow, print, property, py_TypeError, py_iter, py_metatype, py_next, py_reversed, py_typeof, range, repr, round, set, setattr, sorted, str, sum, tuple, zip} from './org.transcrypt.__runtime__.js';
import {hashtable_entry_add_one, list_alphebetize_and_combine} from './binana._utils.utils.js';
......
......@@ -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';
......
......@@ -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__);
}) ())) + ']']));
}
}
......
......@@ -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;
......
......@@ -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__"))) {;
......
......@@ -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) {
......
......@@ -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;
......
......@@ -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) {
......
......@@ -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) {
......
......@@ -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';
......
......@@ -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';
......
......@@ -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';
......
......@@ -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}));
......
......@@ -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';
......
source activate Python36
# Clean up old files.
ls | grep -v "compile_and_copy_here.sh" | awk '{print "rm " $1}' | bash
# Compile the python to javascript. Assumes transcrypt installed.
cd ../../../javascript/
./compile.sh
cd -
# Clean up old files.
ls | grep -v "compile_and_copy_here.sh" | awk '{print "rm " $1}' | bash
# Copy over compiled files.
cp ../../../javascript/lib/* ./
// 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;
......
// 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';
......
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