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zinph
2020-01-26 18:42:57 -05:00
parent 4784da6f77
commit 1c84b966db
8 changed files with 391 additions and 100 deletions
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SIME.py
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@@ -12,6 +12,7 @@
import os
import re
import os.path
import datetime
from molvs import standardize_smiles
from random import *
from rdkit import Chem
@@ -24,61 +25,67 @@ from operator import itemgetter
class SIME:
def __init__(self):
def __init__(self, structural_motifs_file, sugars_file, max_repeat_motifs, minimal_sugars, library_size, enumerate_all_SMs, enumerate_all_sugars):
## self.info = {} # to record number of compounds for each length
self.total_numcompounds = 0
self.load_sugars()
self.load_extenders()
self.library_size = int(input('Desired Library Size (numbers only) :'))
## self.SM_info = {}
self.smile_file_name = self.create_directory()+'/mcrl'
self.max_repeat = int(input('Maximum occurrence of the same structural motifs per scaffold (number only) :'))
self.min_sugar = int(input('Minimal number of sugars per scaffold (number only) :'))
self.ext_question = input('Generate all possible stereocenters for extender structural motifs at joining carbons? y or n :')
self.sugar_question = input('Generate all possible stereocenters for sugars at joining carbons? y or n :')
self.total_numcompounds = 0
self.structural_motifs_file = structural_motifs_file
self.sugars_file = sugars_file
self.max_repeat_motifs = max_repeat_motifs
self.minimal_sugars = minimal_sugars
self.library_size = library_size
self.enumerate_all_SMs = enumerate_all_SMs
self.enumerate_all_sugars = enumerate_all_sugars
date_stamp = datetime.datetime.utcnow().strftime("%Y-%m-%d-%H-%M-%S")
self.smile_file_name = 'LIBRARIES/'+date_stamp+'_mcrl'
self.info_manager = open(self.smile_file_name + '_info','a+')
self.info_manager.write('Desired Library Size (numbers only) :'+ self.library_size + '\n')
self.info_manager.write('Maximum occurrence of the same structural motifs per scaffold (number only) :'+ str(self.max_repeat) + '\n')
self.info_manager.write('Minimal number of sugars per scaffold (number only) :'+ str(self.min_sugar) + '\n')
self.info_manager.write('Generate all possible stereocenters for extender structural motifs at joining carbons? y or n :y'+ self.ext_question + '\n')
self.info_manager.write('Generate all possible stereocenters for sugars at joining carbons? y or n :' + self.sugar_question + '\n')
self.info_manager.write(f'Desired Library Size (numbers only) : {self.library_size}\n')
self.info_manager.write(f'Maximum occurrence of the same structural motifs per scaffold (number only) : {self.max_repeat_motifs}\n')
self.info_manager.write(f'Minimal number of sugars per scaffold (number only) :{self.minimal_sugars}\n')
self.info_manager.write(f'Generate all possible stereocenters for extender structural motifs at joining carbons? {self.enumerate_all_SMs}\n')
self.info_manager.write(f'Generate all possible stereocenters for sugars at joining carbons? {self.enumerate_all_sugars}\n')
def create_directory(self):
old_directory = os.getcwd()
newfolder = input('Peferred Directory Name for Output Files: ')
new_directory = os.path.join(old_directory, newfolder)
while os.path.exists(new_directory):
print('This folder exists or input is invalid. Try again.')
newfolder = input('Peferred Directory Name for Output Files: ')
new_directory = os.path.join(old_directory,newfolder)
os.mkdir(new_directory)
return new_directory
self.load_sugars()
self.load_extenders()
# def create_directory(self):
# old_directory = os.getcwd()
# newfolder = input('Peferred Directory Name for Output Files: ')
# new_directory = os.path.join(old_directory, newfolder)
# while os.path.exists(new_directory):
# print('This folder exists or input is invalid. Try again.')
# newfolder = input('Peferred Directory Name for Output Files: ')
# new_directory = os.path.join(old_directory,newfolder)
# os.mkdir(new_directory)
# return new_directory
def load_sugars(self):
f = open('Data/sugars','r')
original_sugars = f.read().splitlines()
if self.sugar_question.lower() == 'no' or self.sugar_question.lower() == 'n':
self.sugars = [r.replace('[*R*]','') for r in original_sugars]
if self.sugars_file == None:
with open('Data/sugars', 'r') as f:
original_sugars = f.read().splitlines()
else:
original_sugars = self.sugars_file.read().splitlines()
if self.enumerate_all_sugars.lower() == 'yes':
sugars = []
for i in original_sugars:
sugars.append(self.ENUMERATE_sugar_stereocenters(i))
self.sugars = [r.replace('[*R*]','') for r in list(chain(*sugars))]
else:
self.sugars = [r.replace('[*R*]','') for r in original_sugars]
self.make_full_sugar_list() # make self.full_list by adding hydroxyl to self.sugars
self.info_manager.write('\n\nSugars\n'+'\n'.join(original_sugars)+'\n')
def load_extenders(self):
f = open('Data/selected_extenders.txt','r')
original_extenders = f.read().splitlines()
if self.ext_question.lower() == 'no' or self.ext_question.lower() == 'n':
self.extenders = [r.replace('[*R*]','') for r in original_extenders]
if self.structural_motifs_file == None:
with open('Data/selected_extenders.txt','r') as f:
original_extenders = f.read().splitlines()
else:
original_extenders = self.structural_motifs_file.read().splitlines()
if self.enumerate_all_SMs.lower() == 'yes':
self.extenders = [r.replace('[*R*]','') for r in self.enumerate_SM_stereocenters(original_extenders)]
else:
self.extenders = [r.replace('[*R*]','') for r in original_extenders]
self.info_manager.write('\n\nStructural Motifs\n'+'\n'.join(original_extenders)+'\n')
self.info_manager.close()
@@ -87,7 +94,7 @@ class SIME:
'''
self.full_list contains all the sugars and hydroxyl groups.
'''
hydroxyl = ['[C@H](O)','[C@@H](O)']
hydroxyl = ["[C@H](O)","[C@@H](O)"]
self.full_list = self.sugars.copy()
self.full_list += hydroxyl # contains all sugars and hydroxyl groups
@@ -96,10 +103,9 @@ class SIME:
'''
Take in sugar strings that start and end with [*R*], and return a list of sugars with two different stereoceters for the joining carbon.
'''
sugar_stereocenters = []
# if the stereocenter of the joining carbon isn't defined
if smile[5] is 'C':
if smile[5] is "C":
# template = smile[0:5] + '[C@H]' + smile[6:]
template = smile.replace(smile[5], "[C@@H]", 1)
sugar_stereocenters.append(template)
@@ -109,48 +115,51 @@ class SIME:
sugar_stereocenters.append(smile)
if "@" in smile[:10]:
if "@@" in smile[:10]: # for clockwise
template = smile.replace('@@', '@', 1)
template = smile.replace("@@", "@", 1)
else:
template = smile.replace('@', '@@', 1)
template = smile.replace("@", "@@", 1)
sugar_stereocenters.append(template)
return sugar_stereocenters
def locate_SM_replace_points(self, smile):
def remove_SM_digits(self, smile):
'''
Take a string, and locate places for replacement. They are indicated by [1*], [2*], etc.... Return the string with all these joints replaced with [*]s.
Take a string, and locate places for replacement. They are indicated by [1*], [2*], etc....
Return the string with all these joints replaced with [*]s.
'''
numbers = set(re.findall(r'\d+', smile))
possible_joints = ['['+str(m) +'*]' for m in numbers]
possible_joints = ["["+str(m) +"*]" for m in numbers]
for each in possible_joints:
smile = smile.replace(each, '[*]')
smile = smile.replace(each, "[*]")
return smile
def generate_templates_withextenders(self, smile):
'''
Generate all possible templates. Takes in a smile string (structural core). This function only deals with extenders or structural motifs.
Then, insert all possible extenders at those joint positions.
'''
smile_with_stars = [[r] for r in self.locate_SM_replace_points(smile).split('[*]')] # take a string with [*]s and split into different fragments, convert each fragment into a list
counter = 1
# smile_with_stars = [ fragment1, fragment2, fragment3 ,...] all are split at joint positions
# insert self.extenders in between all fragments (except for the first and last blocks).
# so it will be something like [fragment1, [self.extenders], fragment2, [self.extenders], fragment3, [self.extenders] ,...]
for i in range(len(smile_with_stars)-1):
shuffle(self.extenders)
smile_with_stars.insert(counter,self.extenders)
counter+=2
template = [x for x in smile_with_stars if x != ['']]
self.make_compounds(template)
return template
# def generate_templates_withextenders(self, smile):
# '''
# Generate all possible templates. Takes in a smile string (structural core).
# This function only deals with extenders or structural motifs.
# Then, insert all possible extenders at those joint positions.
# '''
# smile_with_stars = [[r] for r in self.remove_SM_digits(smile).split('[*]')] # take a string with [*]s and split into different fragments, convert each fragment into a list
# counter = 1
# # smile_with_stars = [ fragment1, fragment2, fragment3 ,...] all are split at joint positions
# # insert self.extenders in between all fragments (except for the first and last blocks).
# # so it will be something like [fragment1, [self.extenders], fragment2, [self.extenders], fragment3, [self.extenders] ,...]
# for i in range(len(smile_with_stars)-1):
# shuffle(self.extenders)
# smile_with_stars.insert(counter,self.extenders)
# counter+=2
#
# template = [x for x in smile_with_stars if x != ['']]
# self.make_compounds(template)
# return template
def generate_templates_withExtendersNSugars(self,smile):
'''
Generate all possible templates. Takes in a smile string (structural core).
This function deals with both structural motifs and sugars.
Then, insert all possible SMs and sugars at those joint positions.
'''
smile_with_stars = self.string_splitter(self.locate_SM_replace_points(smile), '[*]')
smile_with_stars = self.string_splitter(self.remove_SM_digits(smile), '[*]')
template = []
# create a template holder that will have a list of extenders or sugars at the respective split location points and the rest of the core will remain the same.
# The position of all these fragments (core, extenders, sugars) have to be in the correct order.
@@ -166,40 +175,74 @@ class SIME:
template = [x for x in template if x != ['']] # [stable_fragment1, [possible extender motifs], stable_fragment2, [possible sugar moieties], ...]
SM_template = self.insert_SMs(template) # a list of possible extenders inserted at SM locations
SGR_order = self.generate_dummy_sugar_templates(SM_template,minimal_sugars=self.min_sugar) # At least how many sugars do you want in the macrolide scaffold? because of this, more complications.
SGR_order = self.generate_dummy_sugar_templates(SM_template,minimal_sugars=self.minimal_sugars) # At least how many sugars do you want in the macrolide scaffold? because of this, more complications.
for each in SGR_order:
current_SYMBOLsugar_template = self.add_SYMBOLsugars_to_dummy_templates(each,SM_template) # add the lists of sugars and full_list at the dummy positions
current_SYMBOLsugar_template = self.replace_SYMBOLsugars_with_dummies(each,SM_template) # add the lists of sugars and full_list at the dummy positions
current_sugar_template = self.insert_sugars_to_dummies(current_SYMBOLsugar_template)
self.make_compounds(current_sugar_template)
def make_compounds(self,template):
written = []
def make_compounds(self, template):
max_per_file = 1000000
file_counter = 1
file_temp = self.smile_file_name + '_'+str(file_counter)+'.smiles' # attempts to split files because they get too large. Name of the first file will be "file_" + this variable
file_handler = open(file_temp,'a+')
written = []
for item in product(*template):
if self.max_occurrence(list(item))[1] <= self.max_repeat: # If the count of most common SM is less than or equal to the number set up by the user
if self.total_numcompounds <= self.library_size:
if len(written) < 1000000:
if self.max_occurrence(list(item))[1] <= self.max_repeat_motifs: # If the count of most common SM is less than or equal to the number set up by the user
if self.library_size <= max_per_file:
if self.total_numcompounds <= self.library_size:
temp = ''.join([str(r) for r in item])
m = Chem.MolFromSmiles(temp)
self.total_numcompounds += 1
written.append(temp)
else:
file_handler.write('\n'.join(written)) # write smiles in written list
file_handler.close()
file_counter +=1
file_temp = self.smile_file_name + '_'+str(file_counter)+'.smiles'
file_handler = open(file_temp,'a+')
written = []
else:
break
file_handler.close()
file_handler.close()
self.write_to_file(written, file_counter)
break
elif self.library_size > max_per_file:
if self.total_numcompounds <= self.library_size:
if len(written) <= max_per_file:
temp = ''.join([str(r) for r in item])
self.total_numcompounds += 1
written.append(temp)
else:
self.write_to_file(written, file_counter)
file_counter +=1
written = []
else:
break
def write_to_file(self, compound_list, file_counter):
'''
When total compound is 1000000 or library size, this function will be called
to write compounds to file.
'''
print(compound_list)
file_temp = self.smile_file_name + '_'+str(file_counter)+'.smiles' # attempts to split files because they get too large. Name of the first file will be "file_" + this variable
with open(file_temp,'a+') as file_handler:
file_handler.write('\n'.join(compound_list))
# def make_compounds(self,template):
# written = []
# file_counter = 1
# file_temp = self.smile_file_name + '_'+str(file_counter)+'.smiles' # attempts to split files because they get too large. Name of the first file will be "file_" + this variable
# file_handler = open(file_temp,'a+')
# for item in product(*template):
# if self.max_occurrence(list(item))[1] <= self.max_repeat_motifs: # If the count of most common SM is less than or equal to the number set up by the user
# if self.total_numcompounds <= self.library_size:
# if len(written) < 1000000:
# temp = ''.join([str(r) for r in item])
# # m = Chem.MolFromSmiles(temp)
# self.total_numcompounds += 1
# written.append(temp)
# else:
# file_handler.write('\n'.join(written))
# file_handler.close()
# file_counter +=1
# file_temp = self.smile_file_name + '_'+str(file_counter)+'.smiles'
# file_handler = open(file_temp,'a+')
# written = []
# else:
# file_handler.write('\n'.join(written)) # write smiles in written list
# break
# file_handler.close()
def RS_check(self,smile,ringsize):
@@ -301,10 +344,9 @@ class SIME:
n = the least number of sugars the users want in each macrolide.
Default is one, i.e. there will be at least one sugar in each macrolide.
Generate a list of all possible templates using dummys as 'SUGARS' (intended for only sugars) and 'FULL_LIST (intended for sugars + hydroxy).'
'''
num_sugars = template.count(['[*sugar*]'])
list_with_atLeast_nSugars = n*['SUGARS']+(num_sugars-n)*['FULL_LIST'] # Make a new list with at least "n" "SUGARS" and the rest "FULL_LIST"
list_with_atLeast_nSugars = minimal_sugars*['SUGARS']+(num_sugars-minimal_sugars)*['FULL_LIST'] # Make a new list with at least "n" "SUGARS" and the rest "FULL_LIST"
sugar_lists_in_order = [] # make a new list to hold all possible sugar templates at each position
# now create all different arrangements of sugars, full_list. The positions of these blocks matter.
for i in permutations(list_with_atLeast_nSugars):
@@ -313,7 +355,7 @@ class SIME:
return sugar_lists_in_order
def add_SYMBOLsugars_to_dummy_templates(self, sugar_dummy_order,template_with_sugarinlist):
def replace_SYMBOLsugars_with_dummies(self, sugar_dummy_order,template_with_sugarinlist):
'''
each sugar_dummy_order looks like ('SUGARS', 'FULL_LIST', 'FULL_LIST', 'FULL_LIST')
template_with_sugarinlist looks like = [['1'], [ext1,ext2,...], ['2'],['[*sugar*]'],['3'], [ext1,ext2,...], ['[*sugar*]'],['4'], [ext1,ext2,...], ['5'], [ext1,ext2,...], ['6']]