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Commit d93c4e09 authored by jdurrant's avatar jdurrant
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Updated license notices, etc.

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CHANGES.md
View file @ d93c4e09
Changes
=======
WIP
---
2.1 WIP
-------
1. Can select multiple interactions at once.
2. PNG file included in download from "Save" button. Also, log.txt file, for
......@@ -31,41 +31,20 @@ WIP
19. output_csv option now also prints csv file containing same information as json.
20. Possible to toggle ribbon on and off.
21. Updated documentation.
22. chain and resid now included in output PDB files.
23. Throws a warning when using Python 2. Only Python 3 now offically supported.
TODO:
Hydrogen bonds w/o hydrogens added. Need to be more judicious. Remove certain
bonds per this heuristic:
* For oxygen and sulfur, sum of actual neighbors and hydrogen bonds cannot be >
two. Remember to account for water molecules. Pick based on distance, dihedral
angle. =O not marked as donor, so don't need to worry about that.
* Nitrogen cannot donate to more than actual neighbors + hydrogen bonds > 4, as
above.
* chain and resid now included in output PDB files.
Tests on all operating systems (including mobile).
Be sure to compress javascript
MAke sure not javascript is external.
Clean up examples directory
Tests both python2 and python3
Test should also test version of protein without hydrogens, and make sure you
get all interactions tested. Metal, halogen, hydrogen with S.
finish README.md on file loading component.
PDBQT in webapp looks strange?
*** Makesure can loadin multipleligands. Probably need to rewritecodethat
triggersbinana run. Also, can run if restart.
And you need a message explaining the difference between delete/extract.
Push updated documentation somewhere.
2.0
---
......
javascript/compile.sh
View file @ d93c4e09
# This file is part of BINANA, released under the Apache 2.0 License. See
# LICENSE.md or go to https://opensource.org/licenses/Apache-2.0 for full
# details. Copyright 2021 Jacob D. Durrant.
# This script only works if transcrypt is installed.
# pip install transcrypt
......@@ -7,7 +11,7 @@ rm -rf ../python/__target__/ ./lib/
# Compile the python file.
cd ../python/
# --nomin
transcrypt --build --nomin --ecom --verbose binana.py
transcrypt --build --ecom --verbose binana.py
cd -
# Move the javascript library to the lib directory.
......
javascript/lib/__future__.js
View file @ d93c4e09
// Transcrypt'ed from Python, 2021-11-27 01:23:32
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__ = '__future__';
export var all_feature_names = [];
'use strict';import{AssertionError,AttributeError,BaseException,DeprecationWarning,Exception,IndexError,IterableError,KeyError,NotImplementedError,RuntimeWarning,StopIteration,UserWarning,ValueError,Warning,__JsIterator__,__PyIterator__,__Terminal__,__add__,__and__,__call__,__class__,__envir__,__eq__,__floordiv__,__ge__,__get__,__getcm__,__getitem__,__getslice__,__getsm__,__gt__,__i__,__iadd__,__iand__,__idiv__,__ijsmod__,__ilshift__,__imatmul__,__imod__,__imul__,__in__,__init__,__ior__,__ipow__,
__irshift__,__isub__,__ixor__,__jsUsePyNext__,__jsmod__,__k__,__kwargtrans__,__le__,__lshift__,__lt__,__matmul__,__mergefields__,__mergekwargtrans__,__mod__,__mul__,__ne__,__neg__,__nest__,__or__,__pow__,__pragma__,__proxy__,__pyUseJsNext__,__rshift__,__setitem__,__setproperty__,__setslice__,__sort__,__specialattrib__,__sub__,__super__,__t__,__terminal__,__truediv__,__withblock__,__xor__,abs,all,any,assert,bool,bytearray,bytes,callable,chr,copy,deepcopy,delattr,dict,dir,divmod,enumerate,filter,float,
getattr,hasattr,input,int,isinstance,issubclass,len,list,map,max,min,object,ord,pow,print,property,py_TypeError,py_iter,py_metatype,py_next,py_reversed,py_typeof,range,repr,round,set,setattr,sorted,str,sum,tuple,zip}from"./org.transcrypt.__runtime__.js";var __name__="__future__";export var all_feature_names=[];
//# sourceMappingURL=__future__.map
\ No newline at end of file
javascript/lib/binana._cli_params._get_params.js
View file @ d93c4e09
......@@ -2,86 +2,15 @@
// LICENSE.md or go to https://opensource.org/licenses/Apache-2.0 for full
// details. Copyright 2020 Jacob D. Durrant.
// Transcrypt'ed from Python, 2021-11-27 01:23:31
var binana = {};
import {AssertionError, AttributeError, BaseException, DeprecationWarning, Exception, IndexError, IterableError, KeyError, NotImplementedError, RuntimeWarning, StopIteration, UserWarning, ValueError, Warning, __JsIterator__, __PyIterator__, __Terminal__, __add__, __and__, __call__, __class__, __envir__, __eq__, __floordiv__, __ge__, __get__, __getcm__, __getitem__, __getslice__, __getsm__, __gt__, __i__, __iadd__, __iand__, __idiv__, __ijsmod__, __ilshift__, __imatmul__, __imod__, __imul__, __in__, __init__, __ior__, __ipow__, __irshift__, __isub__, __ixor__, __jsUsePyNext__, __jsmod__, __k__, __kwargtrans__, __le__, __lshift__, __lt__, __matmul__, __mergefields__, __mergekwargtrans__, __mod__, __mul__, __ne__, __neg__, __nest__, __or__, __pow__, __pragma__, __proxy__, __pyUseJsNext__, __rshift__, __setitem__, __setproperty__, __setslice__, __sort__, __specialattrib__, __sub__, __super__, __t__, __terminal__, __truediv__, __withblock__, __xor__, abs, all, any, assert, bool, bytearray, bytes, callable, chr, copy, deepcopy, delattr, dict, dir, divmod, enumerate, filter, float, getattr, hasattr, input, int, isinstance, issubclass, len, list, map, max, min, object, ord, pow, print, property, py_TypeError, py_iter, py_metatype, py_next, py_reversed, py_typeof, range, repr, round, set, setattr, sorted, str, sum, tuple, zip} from './org.transcrypt.__runtime__.js';
import * as __module_binana__ from './binana.js';
__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, HALOGEN_BOND_DIST_CUTOFF, HYDROGEN_BOND_DIST_CUTOFF, HYDROGEN_HALOGEN_BOND_ANGLE_CUTOFF, HYDROPHOBIC_DIST_CUTOFF, LIGAND, METAL_COORDINATION_CUTOFF, OUTPUT_CSV, OUTPUT_DIR, OUTPUT_FILE, OUTPUT_JSON, PI_PADDING_DIST, PI_PI_INTERACTING_DIST_CUTOFF, PI_STACKING_ANGLE_TOLERANCE, RECEPTOR, SALT_BRIDGE_DIST_CUTOFF, TEST, T_STACKING_ANGLE_TOLERANCE, T_STACKING_CLOSEST_DIST_CUTOFF} from './binana.interactions.default_params.js';
var __name__ = 'binana._cli_params._get_params';
export var sep = '/';
export var CommandLineParameters = __class__ ('CommandLineParameters', [object], {
__module__: __name__,
params: dict ({}),
get is_num () {return __get__ (this, function (self, num) {
try {
return float (num);
}
catch (__except0__) {
if (isinstance (__except0__, ValueError)) {
return num;
}
else {
throw __except0__;
}
}
});},
get __init__ () {return __get__ (this, function (self, parameters) {
self.params ['close_contacts_dist1_cutoff'] = CLOSE_CONTACTS_DIST1_CUTOFF;
self.params ['close_contacts_dist2_cutoff'] = CLOSE_CONTACTS_DIST2_CUTOFF;
self.params ['electrostatic_dist_cutoff'] = ELECTROSTATIC_DIST_CUTOFF;
self.params ['active_site_flexibility_dist_cutoff'] = ACTIVE_SITE_FLEXIBILITY_DIST_CUTOFF;
self.params ['hydrophobic_dist_cutoff'] = HYDROPHOBIC_DIST_CUTOFF;
self.params ['hydrogen_bond_dist_cutoff'] = HYDROGEN_BOND_DIST_CUTOFF;
self.params ['hydrogen_halogen_bond_angle_cutoff'] = HYDROGEN_HALOGEN_BOND_ANGLE_CUTOFF;
self.params ['halogen_bond_dist_cutoff'] = HALOGEN_BOND_DIST_CUTOFF;
self.params ['pi_padding_dist'] = PI_PADDING_DIST;
self.params ['pi_pi_interacting_dist_cutoff'] = PI_PI_INTERACTING_DIST_CUTOFF;
self.params ['pi_stacking_angle_tolerance'] = PI_STACKING_ANGLE_TOLERANCE;
self.params ['T_stacking_angle_tolerance'] = T_STACKING_ANGLE_TOLERANCE;
self.params ['T_stacking_closest_dist_cutoff'] = T_STACKING_CLOSEST_DIST_CUTOFF;
self.params ['cation_pi_dist_cutoff'] = CATION_PI_DIST_CUTOFF;
self.params ['salt_bridge_dist_cutoff'] = SALT_BRIDGE_DIST_CUTOFF;
self.params ['metal_coordination_dist_cutoff'] = METAL_COORDINATION_CUTOFF;
self.params ['receptor'] = RECEPTOR;
self.params ['ligand'] = LIGAND;
self.params ['output_dir'] = OUTPUT_DIR;
self.params ['output_file'] = OUTPUT_FILE;
self.params ['output_json'] = OUTPUT_JSON;
self.params ['output_csv'] = OUTPUT_CSV;
self.params ['test'] = TEST;
for (var index = 0; index < len (parameters); index++) {
var item = parameters [index];
if (len (item) > 0 && item [0] == '-') {
var key = item.py_replace ('-', '');
var value = self.is_num (parameters [index + 1]);
if (__in__ (key, list (self.params.py_keys ()))) {
self.params [key] = value;
parameters [index] = '';
parameters [index + 1] = '';
}
}
}
self.error = '';
for (var index = 1; index < len (parameters); index++) {
var item = parameters [index];
if (item != '') {
self.error = (self.error + item) + ' ';
}
}
if (self.params ['output_dir'] != '' && self.params ['output_dir'].__getslice__ (-(1), null, 1) != sep) {
self.params ['output_dir'] = self.params ['output_dir'] + sep;
}
var single_output_files = [tuple (['output_file', 'pdb']), tuple (['output_json', 'json']), tuple (['output_csv', 'csv'])];
for (var [single_output_file, ext] of single_output_files) {
if (self.params ['output_dir'] != '' && self.params [single_output_file] == '') {
self.params [single_output_file] = (self.params ['output_dir'] + 'output.') + ext;
}
}
});},
get okay_to_proceed () {return __get__ (this, function (self) {
return self.params ['receptor'] != '' && self.params ['ligand'] != '';
});}
});
'use strict';var binana={};import{AssertionError,AttributeError,BaseException,DeprecationWarning,Exception,IndexError,IterableError,KeyError,NotImplementedError,RuntimeWarning,StopIteration,UserWarning,ValueError,Warning,__JsIterator__,__PyIterator__,__Terminal__,__add__,__and__,__call__,__class__,__envir__,__eq__,__floordiv__,__ge__,__get__,__getcm__,__getitem__,__getslice__,__getsm__,__gt__,__i__,__iadd__,__iand__,__idiv__,__ijsmod__,__ilshift__,__imatmul__,__imod__,__imul__,__in__,__init__,__ior__,
__ipow__,__irshift__,__isub__,__ixor__,__jsUsePyNext__,__jsmod__,__k__,__kwargtrans__,__le__,__lshift__,__lt__,__matmul__,__mergefields__,__mergekwargtrans__,__mod__,__mul__,__ne__,__neg__,__nest__,__or__,__pow__,__pragma__,__proxy__,__pyUseJsNext__,__rshift__,__setitem__,__setproperty__,__setslice__,__sort__,__specialattrib__,__sub__,__super__,__t__,__terminal__,__truediv__,__withblock__,__xor__,abs,all,any,assert,bool,bytearray,bytes,callable,chr,copy,deepcopy,delattr,dict,dir,divmod,enumerate,
filter,float,getattr,hasattr,input,int,isinstance,issubclass,len,list,map,max,min,object,ord,pow,print,property,py_TypeError,py_iter,py_metatype,py_next,py_reversed,py_typeof,range,repr,round,set,setattr,sorted,str,sum,tuple,zip}from"./org.transcrypt.__runtime__.js";import*as __module_binana__ from"./binana.js";__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,HALOGEN_BOND_DIST_CUTOFF,
HYDROGEN_BOND_DIST_CUTOFF,HYDROGEN_HALOGEN_BOND_ANGLE_CUTOFF,HYDROPHOBIC_DIST_CUTOFF,LIGAND,METAL_COORDINATION_CUTOFF,OUTPUT_CSV,OUTPUT_DIR,OUTPUT_FILE,OUTPUT_JSON,PI_PADDING_DIST,PI_PI_INTERACTING_DIST_CUTOFF,PI_STACKING_ANGLE_TOLERANCE,RECEPTOR,SALT_BRIDGE_DIST_CUTOFF,TEST,T_STACKING_ANGLE_TOLERANCE,T_STACKING_CLOSEST_DIST_CUTOFF}from"./binana.interactions.default_params.js";var __name__="binana._cli_params._get_params";export var sep="/";export var CommandLineParameters=__class__("CommandLineParameters",
[object],{__module__:__name__,params:dict({}),get is_num(){return __get__(this,function(self,num){try{return float(num)}catch(__except0__){if(isinstance(__except0__,ValueError))return num;else throw __except0__;}})},get __init__(){return __get__(this,function(self,parameters){self.params["close_contacts_dist1_cutoff"]=CLOSE_CONTACTS_DIST1_CUTOFF;self.params["close_contacts_dist2_cutoff"]=CLOSE_CONTACTS_DIST2_CUTOFF;self.params["electrostatic_dist_cutoff"]=ELECTROSTATIC_DIST_CUTOFF;self.params["active_site_flexibility_dist_cutoff"]=
ACTIVE_SITE_FLEXIBILITY_DIST_CUTOFF;self.params["hydrophobic_dist_cutoff"]=HYDROPHOBIC_DIST_CUTOFF;self.params["hydrogen_bond_dist_cutoff"]=HYDROGEN_BOND_DIST_CUTOFF;self.params["hydrogen_halogen_bond_angle_cutoff"]=HYDROGEN_HALOGEN_BOND_ANGLE_CUTOFF;self.params["halogen_bond_dist_cutoff"]=HALOGEN_BOND_DIST_CUTOFF;self.params["pi_padding_dist"]=PI_PADDING_DIST;self.params["pi_pi_interacting_dist_cutoff"]=PI_PI_INTERACTING_DIST_CUTOFF;self.params["pi_stacking_angle_tolerance"]=PI_STACKING_ANGLE_TOLERANCE;
self.params["T_stacking_angle_tolerance"]=T_STACKING_ANGLE_TOLERANCE;self.params["T_stacking_closest_dist_cutoff"]=T_STACKING_CLOSEST_DIST_CUTOFF;self.params["cation_pi_dist_cutoff"]=CATION_PI_DIST_CUTOFF;self.params["salt_bridge_dist_cutoff"]=SALT_BRIDGE_DIST_CUTOFF;self.params["metal_coordination_dist_cutoff"]=METAL_COORDINATION_CUTOFF;self.params["receptor"]=RECEPTOR;self.params["ligand"]=LIGAND;self.params["output_dir"]=OUTPUT_DIR;self.params["output_file"]=OUTPUT_FILE;self.params["output_json"]=
OUTPUT_JSON;self.params["output_csv"]=OUTPUT_CSV;self.params["test"]=TEST;for(var index=0;index<len(parameters);index++){var item=parameters[index];if(len(item)>0&&item[0]=="-"){var key=item.py_replace("-","");var value=self.is_num(parameters[index+1]);if(__in__(key,list(self.params.py_keys()))){self.params[key]=value;parameters[index]="";parameters[index+1]=""}}}self.error="";for(var index=1;index<len(parameters);index++){var item=parameters[index];if(item!="")self.error=self.error+item+" "}if(self.params["output_dir"]!=
""&&self.params["output_dir"].__getslice__(-1,null,1)!=sep)self.params["output_dir"]=self.params["output_dir"]+sep;var single_output_files=[tuple(["output_file","pdb"]),tuple(["output_json","json"]),tuple(["output_csv","csv"])];for(var [single_output_file,ext]of single_output_files)if(self.params["output_dir"]!=""&&self.params[single_output_file]=="")self.params[single_output_file]=self.params["output_dir"]+"output."+ext})},get okay_to_proceed(){return __get__(this,function(self){return self.params["receptor"]!=
""&&self.params["ligand"]!=""})}});
//# sourceMappingURL=binana._cli_params._get_params.map
\ No newline at end of file
javascript/lib/binana._start.js
View file @ d93c4e09
......@@ -2,47 +2,13 @@
// LICENSE.md or go to https://opensource.org/licenses/Apache-2.0 for full
// details. Copyright 2020 Jacob D. Durrant.
// Transcrypt'ed from Python, 2021-11-27 01:23:31
var __future__ = {};
var binana = {};
var math = {};
import {AssertionError, AttributeError, BaseException, DeprecationWarning, Exception, IndexError, IterableError, KeyError, NotImplementedError, RuntimeWarning, StopIteration, UserWarning, ValueError, Warning, __JsIterator__, __PyIterator__, __Terminal__, __add__, __and__, __call__, __class__, __envir__, __eq__, __floordiv__, __ge__, __get__, __getcm__, __getitem__, __getslice__, __getsm__, __gt__, __i__, __iadd__, __iand__, __idiv__, __ijsmod__, __ilshift__, __imatmul__, __imod__, __imul__, __in__, __init__, __ior__, __ipow__, __irshift__, __isub__, __ixor__, __jsUsePyNext__, __jsmod__, __k__, __kwargtrans__, __le__, __lshift__, __lt__, __matmul__, __mergefields__, __mergekwargtrans__, __mod__, __mul__, __ne__, __neg__, __nest__, __or__, __pow__, __pragma__, __proxy__, __pyUseJsNext__, __rshift__, __setitem__, __setproperty__, __setslice__, __sort__, __specialattrib__, __sub__, __super__, __t__, __terminal__, __truediv__, __withblock__, __xor__, abs, all, any, assert, bool, bytearray, bytes, callable, chr, copy, deepcopy, delattr, dict, dir, divmod, enumerate, filter, float, getattr, hasattr, input, int, isinstance, issubclass, len, list, map, max, min, object, ord, pow, print, property, py_TypeError, py_iter, py_metatype, py_next, py_reversed, py_typeof, range, repr, round, set, setattr, sorted, str, sum, tuple, zip} from './org.transcrypt.__runtime__.js';
import {fabs} from './binana._utils.shim.js';
import * as shim from './binana._utils.shim.js';
import * as __module_binana__ from './binana.js';
__nest__ (binana, '', __module_binana__);
import * as __module_math__ from './math.js';
__nest__ (math, '', __module_math__);
import {from_files} from './binana.load_ligand_receptor.js';
import {get_all_interactions} from './binana.interactions.js';
import {_write_main} from './binana.output.js';
import * as __module___future____ from './__future__.js';
__nest__ (__future__, '', __module___future____);
var __name__ = 'binana._start';
export var textwrap = shim;
export var VERSION = '2.0';
export var _get_all_interactions = function (parameters) {
var max_cutoff = max ((function () {
var __accu0__ = [];
for (var i of parameters.params.py_items ()) {
if (__in__ ('dist', i [0]) && __in__ ('cutoff', i [0])) {
__accu0__.append (i [1]);
}
}
return py_iter (__accu0__);
}) ()) + 15;
var __left0__ = from_files (parameters.params ['ligand'], parameters.params ['receptor'], max_cutoff);
var ligand = __left0__ [0];
var receptor = __left0__ [1];
var pi_padding = parameters.params ['pi_padding_dist'];
var all_interacts = get_all_interactions (ligand, receptor, parameters.params ['close_contacts_dist1_cutoff'], parameters.params ['close_contacts_dist2_cutoff'], parameters.params ['electrostatic_dist_cutoff'], parameters.params ['active_site_flexibility_dist_cutoff'], parameters.params ['hydrophobic_dist_cutoff'], parameters.params ['hydrogen_bond_dist_cutoff'], parameters.params ['hydrogen_halogen_bond_angle_cutoff'], parameters.params ['halogen_bond_dist_cutoff'], parameters.params ['pi_pi_interacting_dist_cutoff'], parameters.params ['pi_stacking_angle_tolerance'], parameters.params ['T_stacking_angle_tolerance'], parameters.params ['T_stacking_closest_dist_cutoff'], parameters.params ['cation_pi_dist_cutoff'], parameters.params ['salt_bridge_dist_cutoff'], parameters.params ['metal_coordination_dist_cutoff'], pi_padding);
for (var key of all_interacts ['cat_pi'] ['counts'].py_keys ()) {
all_interacts ['pi_pi'] ['counts'] [key] = all_interacts ['cat_pi'] ['counts'] [key];
}
_write_main (parameters, ligand, receptor, all_interacts ['closest'], all_interacts ['close'], all_interacts ['hydrophobics'], all_interacts ['hydrogen_bonds'], all_interacts ['halogen_bonds'], all_interacts ['salt_bridges'], all_interacts ['metal_coordinations'], all_interacts ['pi_pi'], all_interacts ['cat_pi'], all_interacts ['electrostatic_energies'], all_interacts ['active_site_flexibility'], all_interacts ['ligand_atom_types']);
};
export var _intro = function () {
print ('\n [- END INTRO -]\n');
};
'use strict';var __future__={};var binana={};var math={};import{AssertionError,AttributeError,BaseException,DeprecationWarning,Exception,IndexError,IterableError,KeyError,NotImplementedError,RuntimeWarning,StopIteration,UserWarning,ValueError,Warning,__JsIterator__,__PyIterator__,__Terminal__,__add__,__and__,__call__,__class__,__envir__,__eq__,__floordiv__,__ge__,__get__,__getcm__,__getitem__,__getslice__,__getsm__,__gt__,__i__,__iadd__,__iand__,__idiv__,__ijsmod__,__ilshift__,__imatmul__,__imod__,
__imul__,__in__,__init__,__ior__,__ipow__,__irshift__,__isub__,__ixor__,__jsUsePyNext__,__jsmod__,__k__,__kwargtrans__,__le__,__lshift__,__lt__,__matmul__,__mergefields__,__mergekwargtrans__,__mod__,__mul__,__ne__,__neg__,__nest__,__or__,__pow__,__pragma__,__proxy__,__pyUseJsNext__,__rshift__,__setitem__,__setproperty__,__setslice__,__sort__,__specialattrib__,__sub__,__super__,__t__,__terminal__,__truediv__,__withblock__,__xor__,abs,all,any,assert,bool,bytearray,bytes,callable,chr,copy,deepcopy,delattr,
dict,dir,divmod,enumerate,filter,float,getattr,hasattr,input,int,isinstance,issubclass,len,list,map,max,min,object,ord,pow,print,property,py_TypeError,py_iter,py_metatype,py_next,py_reversed,py_typeof,range,repr,round,set,setattr,sorted,str,sum,tuple,zip}from"./org.transcrypt.__runtime__.js";import{fabs}from"./binana._utils.shim.js";import*as shim from"./binana._utils.shim.js";import*as __module_binana__ from"./binana.js";__nest__(binana,"",__module_binana__);import*as __module_math__ from"./math.js";
__nest__(math,"",__module_math__);import{from_files}from"./binana.load_ligand_receptor.js";import{get_all_interactions}from"./binana.interactions.js";import{_write_main}from"./binana.output.js";import*as __module___future____ from"./__future__.js";__nest__(__future__,"",__module___future____);var __name__="binana._start";export var textwrap=shim;export var VERSION="2.1";export var _get_all_interactions=function(parameters){var max_cutoff=max(function(){var __accu0__=[];for(var i of parameters.params.py_items())if(__in__("dist",
i[0])&&__in__("cutoff",i[0]))__accu0__.append(i[1]);return py_iter(__accu0__)}())+15;var __left0__=from_files(parameters.params["ligand"],parameters.params["receptor"],max_cutoff);var ligand=__left0__[0];var receptor=__left0__[1];var pi_padding=parameters.params["pi_padding_dist"];var all_interacts=get_all_interactions(ligand,receptor,parameters.params["close_contacts_dist1_cutoff"],parameters.params["close_contacts_dist2_cutoff"],parameters.params["electrostatic_dist_cutoff"],parameters.params["active_site_flexibility_dist_cutoff"],
parameters.params["hydrophobic_dist_cutoff"],parameters.params["hydrogen_bond_dist_cutoff"],parameters.params["hydrogen_halogen_bond_angle_cutoff"],parameters.params["halogen_bond_dist_cutoff"],parameters.params["pi_pi_interacting_dist_cutoff"],parameters.params["pi_stacking_angle_tolerance"],parameters.params["T_stacking_angle_tolerance"],parameters.params["T_stacking_closest_dist_cutoff"],parameters.params["cation_pi_dist_cutoff"],parameters.params["salt_bridge_dist_cutoff"],parameters.params["metal_coordination_dist_cutoff"],
pi_padding);for(var key of all_interacts["cat_pi"]["counts"].py_keys())all_interacts["pi_pi"]["counts"][key]=all_interacts["cat_pi"]["counts"][key];_write_main(parameters,ligand,receptor,all_interacts["closest"],all_interacts["close"],all_interacts["hydrophobics"],all_interacts["hydrogen_bonds"],all_interacts["halogen_bonds"],all_interacts["salt_bridges"],all_interacts["metal_coordinations"],all_interacts["pi_pi"],all_interacts["cat_pi"],all_interacts["electrostatic_energies"],all_interacts["active_site_flexibility"],
all_interacts["ligand_atom_types"])};export var _intro=function(){print("\n [- END INTRO -]\n")};
//# sourceMappingURL=binana._start.map
\ No newline at end of file
javascript/lib/binana._structure.atom.js
View file @ d93c4e09
......@@ -2,231 +2,21 @@
// LICENSE.md or go to https://opensource.org/licenses/Apache-2.0 for full
// details. Copyright 2020 Jacob D. Durrant.
// Transcrypt'ed from Python, 2021-11-27 01:23:32
var binana = {};
var math = {};
var re = {};
import {AssertionError, AttributeError, BaseException, DeprecationWarning, Exception, IndexError, IterableError, KeyError, NotImplementedError, RuntimeWarning, StopIteration, UserWarning, ValueError, Warning, __JsIterator__, __PyIterator__, __Terminal__, __add__, __and__, __call__, __class__, __envir__, __eq__, __floordiv__, __ge__, __get__, __getcm__, __getitem__, __getslice__, __getsm__, __gt__, __i__, __iadd__, __iand__, __idiv__, __ijsmod__, __ilshift__, __imatmul__, __imod__, __imul__, __in__, __init__, __ior__, __ipow__, __irshift__, __isub__, __ixor__, __jsUsePyNext__, __jsmod__, __k__, __kwargtrans__, __le__, __lshift__, __lt__, __matmul__, __mergefields__, __mergekwargtrans__, __mod__, __mul__, __ne__, __neg__, __nest__, __or__, __pow__, __pragma__, __proxy__, __pyUseJsNext__, __rshift__, __setitem__, __setproperty__, __setslice__, __sort__, __specialattrib__, __sub__, __super__, __t__, __terminal__, __truediv__, __withblock__, __xor__, abs, all, any, assert, bool, bytearray, bytes, callable, chr, copy, deepcopy, delattr, dict, dir, divmod, enumerate, filter, float, getattr, hasattr, input, int, isinstance, issubclass, len, list, map, max, min, object, ord, pow, print, property, py_TypeError, py_iter, py_metatype, py_next, py_reversed, py_typeof, range, repr, round, set, setattr, sorted, str, sum, tuple, zip} from './org.transcrypt.__runtime__.js';
import {fabs} from './binana._utils.shim.js';
import * as shim from './binana._utils.shim.js';
import * as __module_binana__utils__ from './binana._utils.js';
__nest__ (binana, '_utils', __module_binana__utils__);
import * as __module_re__ from './re.js';
__nest__ (re, '', __module_re__);
import {protein_resnames, to_deg, two_leter_atom_names} from './binana._structure.consts.js';
import {angle_between_three_points} from './binana._utils._math_functions.js';
import {r_just, round_to_thousandths_to_str} from './binana._utils.shim.js';
import {Point} from './binana._structure.point.js';
import * as __module_binana__ from './binana.js';
__nest__ (binana, '', __module_binana__);
import * as __module_math__ from './math.js';
__nest__ (math, '', __module_math__);
var __name__ = 'binana._structure.atom';
export var Atom = __class__ ('Atom', [object], {
__module__: __name__,
get __init__ () {return __get__ (this, function (self) {
self.atom_name = '';
self.residue = '';
self.coordinates = Point (99999, 99999, 99999);
self.element = '';
self.pdb_index = '';
self.all_atoms_index = -(1);
self.line = '';
self.atom_type = '';
self.indecies_of_atoms_connecting = [];
self.charge = 0;
self.resid = 0;
self.chain = '';
self.structure = '';
self.comment = '';
});},
get copy_of () {return __get__ (this, function (self) {
var theatom = Atom ();
theatom.atom_name = self.atom_name;
theatom.residue = self.residue;
theatom.coordinates = self.coordinates.copy_of ();
theatom.element = self.element;
theatom.pdb_index = self.pdb_index;
theatom.line = self.line;
theatom.atom_type = self.atom_type;
theatom.indecies_of_atoms_connecting = self.indecies_of_atoms_connecting.__getslice__ (0, null, 1);
theatom.charge = self.charge;
theatom.resid = self.resid;
theatom.chain = self.chain;
theatom.structure = self.structure;
theatom.comment = self.comment;
theatom.all_atoms_index = self.all_atoms_index;
return theatom;
});},
get string_id () {return __get__ (this, function (self) {
var to_return = '';
if (self.chain.strip () != '') {
var to_return = (to_return + self.chain.strip ()) + ':';
}
var to_return = (((((((to_return + self.residue.strip ()) + '(') + str (self.resid)) + '):') + self.atom_name.strip ()) + '(') + str (self.pdb_index)) + ')';
return to_return;
});},
get create_pdb_line () {return __get__ (this, function (self, index) {
var output = 'ATOM ';
var output = ((((output + r_just (str (index), 6)) + r_just (self.atom_name, 5)) + r_just (self.residue, 4)) + r_just (self.chain, 2)) + r_just (str (self.resid), 4);
output += r_just (round_to_thousandths_to_str (self.coordinates.x), 12);
output += r_just (round_to_thousandths_to_str (self.coordinates.y), 8);
output += r_just (round_to_thousandths_to_str (self.coordinates.z), 8);
output += r_just (self.element, 24);
return output;
});},
get number_of_neighbors () {return __get__ (this, function (self) {
return len (self.indecies_of_atoms_connecting);
});},
get add_neighbor_atom_index () {return __get__ (this, function (self, index) {
if (!__in__ (index, self.indecies_of_atoms_connecting)) {
self.indecies_of_atoms_connecting.append (index);
}
});},
get side_chain_or_backbone () {return __get__ (this, function (self) {
if (__in__ (self.atom_name.strip (), ['CA', 'C', 'O', 'N'])) {
return 'BACKBONE';
}
else {
return 'SIDECHAIN';
}
});},
get read_pdb_line () {return __get__ (this, function (self, line) {
self.line = line;
self.atom_name = line.__getslice__ (11, 16, 1).strip ();
if (len (self.atom_name) == 1) {
self.atom_name = self.atom_name + ' ';
}
else if (__in__ (len (self.atom_name), [2, 3])) {
self.atom_name = self.atom_name + ' ';
}
self.coordinates = Point (float (line.__getslice__ (30, 38, 1)), float (line.__getslice__ (38, 46, 1)), float (line.__getslice__ (46, 54, 1)));
self.atom_type = line.__getslice__ (76, 79, 1).strip ().upper ();
self.charge = (line.__getslice__ (69, 76, 1).strip () != '' ? float (line.__getslice__ (69, 76, 1)) : 0.0);
self.residue = line.__getslice__ (16, 20, 1);
self.residue = ' ' + self.residue.__getslice__ (-(3), null, 1);
if (self.element == '') {
var element = line.__getslice__ (76, null, 1).strip ().upper ();
if (element != '') {
var two_letters = re.sub ('[^A-Z]', '', element).__getslice__ (0, 2, 1);
}
else {
var two_letters = self.atom_name.__getslice__ (0, 2, 1).strip ().upper ();
}
if (__in__ (two_letters, two_leter_atom_names) && !__in__ (self.residue.__getslice__ (-(3), null, 1), protein_resnames)) {
self.element = two_letters;
}
else {
self.element = self.atom_name;
self.element = self.element.py_replace ('0', '');
self.element = self.element.py_replace ('1', '');
self.element = self.element.py_replace ('2', '');
self.element = self.element.py_replace ('3', '');
self.element = self.element.py_replace ('4', '');
self.element = self.element.py_replace ('5', '');
self.element = self.element.py_replace ('6', '');
self.element = self.element.py_replace ('7', '');
self.element = self.element.py_replace ('8', '');
self.element = self.element.py_replace ('9', '');
self.element = self.element.py_replace ('@', '');
self.element = self.element.__getslice__ (0, 1, 1).strip ().upper ();
}
}
self.pdb_index = line.__getslice__ (6, 12, 1).strip ();
try {
self.resid = int (line.__getslice__ (23, 26, 1));
}
catch (__except0__) {
// pass;
}
self.chain = line.__getslice__ (21, 22, 1);
if (self.chain == ' ') {
self.chain = 'X';
}
if (self.residue.strip () == '') {
self.residue = ' MOL';
}
});},
get _has_sp3_geometry_if_protein () {return __get__ (this, function (self, resname) {
var atomname = self.atom_name.strip ();
if (__in__ (atomname, ['C', 'O', 'N'])) {
return false;
}
if (resname == 'ARG') {
if (__in__ (atomname, ['NE', 'NH1', 'NH2'])) {
return false;
}
}
else if (resname == 'ASN') {
if (__in__ (atomname, ['CG', 'OD1', 'ND2'])) {
return false;
}
}
else if (resname == 'ASP') {
if (__in__ (atomname, ['CG', 'OD1'])) {
return false;
}
}
else if (resname == 'GLN') {
if (__in__ (atomname, ['CD', 'OE1', 'NE2'])) {
return false;
}
}
else if (resname == 'GLU') {
if (__in__ (atomname, ['CD', 'OE1'])) {
return false;
}
}
else if (resname == 'HIS') {
if (__in__ (atomname, ['CG', 'CD2', 'NE2', 'CE1', 'ND1'])) {
return false;
}
}
else if (__in__ (resname, ['PHE', 'TYR'])) {
if (__in__ (atomname, ['CE1', 'CZ', 'CE2', 'CD2', 'CG', 'CD1'])) {
return false;
}
}
else if (resname == 'TRP') {
if (__in__ (atomname, ['CG', 'CD1', 'NE1', 'CE2', 'CD2', 'CE3', 'CZ2', 'CZ3', 'CH2'])) {
return false;
}
}
return true;
});},
get has_sp3_geometry () {return __get__ (this, function (self, parent_mol) {
var resname = self.residue.__getslice__ (-(3), null, 1);
if (__in__ (resname, protein_resnames)) {
return self._has_sp3_geometry_if_protein (resname);
}
var ncrs = (function () {
var __accu0__ = [];
for (var i of self.indecies_of_atoms_connecting) {
__accu0__.append (parent_mol.all_atoms [i].coordinates);
}
return __accu0__;
}) ();
var ncrs_len = len (ncrs);
if (ncrs_len <= 1) {
return true;
}
var ccr = self.coordinates;
var angles = [angle_between_three_points (ncrs [0], ccr, ncrs [1]) * to_deg];
if (ncrs_len > 2) {
angles.append (angle_between_three_points (ncrs [0], ccr, ncrs [2]) * to_deg);
angles.append (angle_between_three_points (ncrs [1], ccr, ncrs [2]) * to_deg);
}
if (ncrs_len > 3) {
angles.append (angle_between_three_points (ncrs [0], ccr, ncrs [3]) * to_deg);
angles.append (angle_between_three_points (ncrs [1], ccr, ncrs [3]) * to_deg);
angles.append (angle_between_three_points (ncrs [2], ccr, ncrs [3]) * to_deg);
}
var average_angle = sum (angles) / float (len (angles));
return fabs (average_angle - 109.0) < 5.0;
});},
get belongs_to_protein () {return __get__ (this, function (self) {
return __in__ (self.residue.__getslice__ (-(3), null, 1), protein_resnames);
});}
});
'use strict';var binana={};var math={};var re={};import{AssertionError,AttributeError,BaseException,DeprecationWarning,Exception,IndexError,IterableError,KeyError,NotImplementedError,RuntimeWarning,StopIteration,UserWarning,ValueError,Warning,__JsIterator__,__PyIterator__,__Terminal__,__add__,__and__,__call__,__class__,__envir__,__eq__,__floordiv__,__ge__,__get__,__getcm__,__getitem__,__getslice__,__getsm__,__gt__,__i__,__iadd__,__iand__,__idiv__,__ijsmod__,__ilshift__,__imatmul__,__imod__,__imul__,
__in__,__init__,__ior__,__ipow__,__irshift__,__isub__,__ixor__,__jsUsePyNext__,__jsmod__,__k__,__kwargtrans__,__le__,__lshift__,__lt__,__matmul__,__mergefields__,__mergekwargtrans__,__mod__,__mul__,__ne__,__neg__,__nest__,__or__,__pow__,__pragma__,__proxy__,__pyUseJsNext__,__rshift__,__setitem__,__setproperty__,__setslice__,__sort__,__specialattrib__,__sub__,__super__,__t__,__terminal__,__truediv__,__withblock__,__xor__,abs,all,any,assert,bool,bytearray,bytes,callable,chr,copy,deepcopy,delattr,dict,
dir,divmod,enumerate,filter,float,getattr,hasattr,input,int,isinstance,issubclass,len,list,map,max,min,object,ord,pow,print,property,py_TypeError,py_iter,py_metatype,py_next,py_reversed,py_typeof,range,repr,round,set,setattr,sorted,str,sum,tuple,zip}from"./org.transcrypt.__runtime__.js";import{fabs}from"./binana._utils.shim.js";import*as shim from"./binana._utils.shim.js";import*as __module_binana__utils__ from"./binana._utils.js";__nest__(binana,"_utils",__module_binana__utils__);import*as __module_re__ from"./re.js";
__nest__(re,"",__module_re__);import{protein_resnames,to_deg,two_leter_atom_names}from"./binana._structure.consts.js";import{angle_between_three_points}from"./binana._utils._math_functions.js";import{r_just,round_to_thousandths_to_str}from"./binana._utils.shim.js";import{Point}from"./binana._structure.point.js";import*as __module_binana__ from"./binana.js";__nest__(binana,"",__module_binana__);import*as __module_math__ from"./math.js";__nest__(math,"",__module_math__);var __name__="binana._structure.atom";
export var Atom=__class__("Atom",[object],{__module__:__name__,get __init__(){return __get__(this,function(self){self.atom_name="";self.residue="";self.coordinates=Point(99999,99999,99999);self.element="";self.pdb_index="";self.all_atoms_index=-1;self.line="";self.atom_type="";self.indecies_of_atoms_connecting=[];self.charge=0;self.resid=0;self.chain="";self.structure="";self.comment=""})},get copy_of(){return __get__(this,function(self){var theatom=Atom();theatom.atom_name=self.atom_name;theatom.residue=
self.residue;theatom.coordinates=self.coordinates.copy_of();theatom.element=self.element;theatom.pdb_index=self.pdb_index;theatom.line=self.line;theatom.atom_type=self.atom_type;theatom.indecies_of_atoms_connecting=self.indecies_of_atoms_connecting.__getslice__(0,null,1);theatom.charge=self.charge;theatom.resid=self.resid;theatom.chain=self.chain;theatom.structure=self.structure;theatom.comment=self.comment;theatom.all_atoms_index=self.all_atoms_index;return theatom})},get string_id(){return __get__(this,
function(self){var to_return="";if(self.chain.strip()!="")var to_return=to_return+self.chain.strip()+":";var to_return=to_return+self.residue.strip()+"("+str(self.resid)+"):"+self.atom_name.strip()+"("+str(self.pdb_index)+")";return to_return})},get create_pdb_line(){return __get__(this,function(self,index){var output="ATOM ";var output=output+r_just(str(index),6)+r_just(self.atom_name,5)+r_just(self.residue,4)+r_just(self.chain,2)+r_just(str(self.resid),4);output+=r_just(round_to_thousandths_to_str(self.coordinates.x),
12);output+=r_just(round_to_thousandths_to_str(self.coordinates.y),8);output+=r_just(round_to_thousandths_to_str(self.coordinates.z),8);output+=r_just(self.element,24);return output})},get number_of_neighbors(){return __get__(this,function(self){return len(self.indecies_of_atoms_connecting)})},get add_neighbor_atom_index(){return __get__(this,function(self,index){if(!__in__(index,self.indecies_of_atoms_connecting))self.indecies_of_atoms_connecting.append(index)})},get side_chain_or_backbone(){return __get__(this,
function(self){if(__in__(self.atom_name.strip(),["CA","C","O","N"]))return"BACKBONE";else return"SIDECHAIN"})},get read_pdb_line(){return __get__(this,function(self,line){self.line=line;self.atom_name=line.__getslice__(11,16,1).strip();if(len(self.atom_name)==1)self.atom_name=self.atom_name+" ";else if(__in__(len(self.atom_name),[2,3]))self.atom_name=self.atom_name+" ";self.coordinates=Point(float(line.__getslice__(30,38,1)),float(line.__getslice__(38,46,1)),float(line.__getslice__(46,54,1)));self.atom_type=
line.__getslice__(76,79,1).strip().upper();self.charge=line.__getslice__(69,76,1).strip()!=""?float(line.__getslice__(69,76,1)):0;self.residue=line.__getslice__(16,20,1);self.residue=" "+self.residue.__getslice__(-3,null,1);if(self.element==""){var element=line.__getslice__(76,null,1).strip().upper();if(element!="")var two_letters=re.sub("[^A-Z]","",element).__getslice__(0,2,1);else var two_letters=self.atom_name.__getslice__(0,2,1).strip().upper();if(__in__(two_letters,two_leter_atom_names)&&!__in__(self.residue.__getslice__(-3,
null,1),protein_resnames))self.element=two_letters;else{self.element=self.atom_name;self.element=self.element.py_replace("0","");self.element=self.element.py_replace("1","");self.element=self.element.py_replace("2","");self.element=self.element.py_replace("3","");self.element=self.element.py_replace("4","");self.element=self.element.py_replace("5","");self.element=self.element.py_replace("6","");self.element=self.element.py_replace("7","");self.element=self.element.py_replace("8","");self.element=
self.element.py_replace("9","");self.element=self.element.py_replace("@","");self.element=self.element.__getslice__(0,1,1).strip().upper()}}self.pdb_index=line.__getslice__(6,12,1).strip();try{self.resid=int(line.__getslice__(23,26,1))}catch(__except0__){}self.chain=line.__getslice__(21,22,1);if(self.chain==" ")self.chain="X";if(self.residue.strip()=="")self.residue=" MOL"})},get _has_sp3_geometry_if_protein(){return __get__(this,function(self,resname){var atomname=self.atom_name.strip();if(__in__(atomname,
["C","O","N"]))return false;if(resname=="ARG"){if(__in__(atomname,["NE","NH1","NH2"]))return false}else if(resname=="ASN"){if(__in__(atomname,["CG","OD1","ND2"]))return false}else if(resname=="ASP"){if(__in__(atomname,["CG","OD1"]))return false}else if(resname=="GLN"){if(__in__(atomname,["CD","OE1","NE2"]))return false}else if(resname=="GLU"){if(__in__(atomname,["CD","OE1"]))return false}else if(resname=="HIS"){if(__in__(atomname,["CG","CD2","NE2","CE1","ND1"]))return false}else if(__in__(resname,
["PHE","TYR"])){if(__in__(atomname,["CE1","CZ","CE2","CD2","CG","CD1"]))return false}else if(resname=="TRP")if(__in__(atomname,["CG","CD1","NE1","CE2","CD2","CE3","CZ2","CZ3","CH2"]))return false;return true})},get has_sp3_geometry(){return __get__(this,function(self,parent_mol){var resname=self.residue.__getslice__(-3,null,1);if(__in__(resname,protein_resnames))return self._has_sp3_geometry_if_protein(resname);var ncrs=function(){var __accu0__=[];for(var i of self.indecies_of_atoms_connecting)__accu0__.append(parent_mol.all_atoms[i].coordinates);
return __accu0__}();var ncrs_len=len(ncrs);if(ncrs_len<=1)return true;var ccr=self.coordinates;var angles=[angle_between_three_points(ncrs[0],ccr,ncrs[1])*to_deg];if(ncrs_len>2){angles.append(angle_between_three_points(ncrs[0],ccr,ncrs[2])*to_deg);angles.append(angle_between_three_points(ncrs[1],ccr,ncrs[2])*to_deg)}if(ncrs_len>3){angles.append(angle_between_three_points(ncrs[0],ccr,ncrs[3])*to_deg);angles.append(angle_between_three_points(ncrs[1],ccr,ncrs[3])*to_deg);angles.append(angle_between_three_points(ncrs[2],
ccr,ncrs[3])*to_deg)}var average_angle=sum(angles)/float(