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# import requests
# import numpy as np
# import pandas as pd
# from utils import *
# from pathlib import Path
# from bs4 import BeautifulSoup
# from add_sasa import *
# def addModbaseModels(dataframe, path_to_input_files, path_to_output_files):
# if len(dataframe) != 0:
# # GET MODBASE MODELS
# # Get IDs from data to retrieve only their models from MODBASE
# dataframe.reset_index(inplace=True, drop=True)
# existing_modbase_models = list(Path(path_to_output_files / 'modbase_structures').glob("*"))
# existing_modbase_models = [str(i) for i in existing_modbase_models]
# existing_modbase_models = [i.split('/')[-1].split('.')[0] for i in existing_modbase_models]
# existing_modbase_models_ind = list(Path(path_to_output_files / 'modbase_structures_individual').glob("*"))
# existing_modbase_models_ind = [str(i) for i in existing_modbase_models_ind]
# existing_modbase_models_ind = [i.split('/')[-1].split('.')[0] for i in existing_modbase_models_ind]
# modbase_reduced = pd.DataFrame(columns = ['uniprotID', 'target_begin', 'target_end', 'quality_score',
# 'model_id', 'coordinates','AAonPDB', 'coordVAR'])
# print('Retrieving ModBase models...\n')
# modbase = pd.DataFrame(
# columns=['uniprotID', 'target_begin', 'target_end', 'quality_score', 'model_id',
# 'coordinates', 'AAonPDB', 'coordVAR'])
# no_modbase = pd.DataFrame(
# columns=['uniprotID', 'target_begin', 'target_end', 'quality_score', 'model_id',
# 'coordinates', 'AAonPDB', 'coordVAR'])
# # Get model files associated with each UniProtID
# existing_free_sasa = list(Path(path_to_output_files / 'freesasa_files').glob("*"))
# existing_free_sasa = [str(i) for i in existing_free_sasa]
# existing_free_sasa = [i.split('/')[-1].split('.')[0] for i in existing_free_sasa]
# keep_cols = dataframe.columns
# for i in dataframe.index:
# coordDict = {}
# protein = dataframe.at[i, 'uniprotID']
# varPos = int(dataframe.at[i, 'pos'])
# wt = dataframe.at[i, 'wt']
# mut = dataframe.at[i, 'mut']
# datapoint = dataframe.at[i, 'datapoint']
# if protein not in existing_modbase_models:
# print('Downloading Modbase models for ', protein)
# url = 'https://salilab.org/modbase/retrieve/modbase/?databaseID=' + protein
# req = requests.get(url)
# name = path_to_output_files / 'modbase_structures' / f'{protein}.txt'
# with open(name, 'wb') as f:
# f.write(req.content)
# else:
# print('Model exists for', protein)
# name = Path(path_to_output_files / 'modbase_structures' / f'{protein}.txt')
# with open(name, encoding="utf8") as f:
# a = open(name, 'r').read()
# soup = BeautifulSoup(a, 'lxml')
# if soup.findAll('pdbfile') != []:
# for pdb in soup.findAll('pdbfile'):
# model_id = str(pdb.contents[1])[10:-11]
# if model_id not in existing_modbase_models_ind:
# with open(path_to_output_files / 'modbase_structures_individual' / f'{model_id}.txt', 'w', encoding="utf8") as individual:
# individual.write(str('UniProt ID: ' + protein))
# individual.write('\n')
# individual.write(str(pdb.contents[3])[10:-11].strip())
# run_freesasa(
# Path(path_to_output_files / 'modbase_structures_individual' / f'{model_id.lower()}.txt'),
# Path(path_to_output_files / 'freesasa_files' / f'{model_id.lower()}.txt'),
# include_hetatms=True,
# outdir=None, force_rerun=False, file_type='pdb')
# filename = Path(path_to_output_files / 'freesasa_files' / f'{model_id.lower()}.txt')
# st.write('filename', filename)
# st.write('varPos', varPos)
# st.write('wt', wt)
# st.write('protein', protein)
# st.write('path_to_output_files', path_to_output_files)
# dataframe.loc[i, 'sasa'] = sasa(protein, varPos, wt, 1, filename, path_to_output_files, file_type='pdb')
# st.write('sasa', dataframe.loc[i, 'sasa'] )
# st.write('model_id', model_id)
# with open(path_to_output_files / 'modbase_structures_individual'/ f'{model_id}.txt', encoding="utf8") as m:
# lines = m.readlines()
# quality_score = -999
# for ind_line in lines:
# if ind_line[0:10] == 'UniProt ID':
# uniprot_id = ind_line.split(':')[1].strip()
# if ind_line[0:23] == 'REMARK 220 TARGET BEGIN':
# target_begin = ind_line[40:43].strip()
# if ind_line[0:21] == 'REMARK 220 TARGET END':
# target_end = ind_line[40:43].strip()
# coordDict, AAonPDB, coordVAR = {},np.NaN,np.NaN
# if (int(varPos) > int(target_begin)) & (int(varPos) < int(target_end)):
# coordDict = {}
# for ind_line in lines:
# if ind_line[0:27] == 'REMARK 220 MODPIPE MODEL ID':
# model_id = ind_line[40:].strip()
# if ind_line[0:15].strip() == 'REMARK 220 MPQS':
# quality_score = ind_line[40:].strip()
# if ind_line[0:4] == 'ATOM' and ind_line[13:15] == 'CA':
# position = int(ind_line[22:26].strip())
# chain = ind_line[20:22].strip()
# aminoacid = threeToOne(ind_line[17:20])
# coords = [ind_line[31:38].strip(), ind_line[39:46].strip(), ind_line[47:54].strip()]
# coordDict[position] = coords
# if position == int(varPos):
# AAonPDB = aminoacid
# coordVAR = str(coords)
# if ind_line[0:3] == 'TER':
# break
# try:
# k = pd.Series(
# [uniprot_id, target_begin, target_end,quality_score, model_id, coordDict, AAonPDB, coordVAR])
# new_row = {'uniprotID': uniprot_id, 'target_begin': target_begin,
# 'target_end': target_end, 'quality_score': quality_score,
# 'model_id': model_id, 'coordinates': coordDict,
# 'AAonPDB': AAonPDB, 'coordVAR': coordVAR}
# modbase_reduced = modbase_reduced.append(new_row, ignore_index=True)
# modbase_reduced = modbase_reduced[['uniprotID', 'quality_score', 'model_id', 'coordinates', 'AAonPDB', 'coordVAR']]
# modbase = dataframe.merge(modbase_reduced, on='uniprotID', how='left')
# modbase.quality_score = modbase.quality_score.astype(float)
# modbase = modbase.sort_values(by=['datapoint', 'quality_score'], ascending=False)
# modbase.reset_index(inplace=True, drop=True)
# modbase.fillna(np.NaN, inplace=True)
# modbase.replace({'\'?\', ': '',
# ', \'?\'': '',
# '(': '', ')': '',
# '[\'?\']': np.NaN,
# '[]': np.NaN,
# 'nan-nan': np.NaN,
# '': np.NaN}, inplace=True)
# except NameError:
# print('This file doesnt have Quality Score. Replacer: -999', model_id)
# else:
# new_row = {'uniprotID': uniprot_id, 'wt': wt,
# 'pos': varPos, 'mut': mut, 'datapoint': datapoint }
# no_modbase = no_modbase.append(new_row, ignore_index=True)
# else:
# new_row = {'uniprotID': uniprot_id, 'wt': wt,
# 'pos': varPos, 'mut': mut, 'datapoint': datapoint }
# no_modbase = no_modbase.append(new_row, ignore_index=True)
# no_modbase_no_Coord = modbase[pd.isna(modbase['coordVAR'])]
# no_modbase = pd.concat([no_modbase, no_modbase_no_Coord])
# modbase = modbase[~pd.isna(modbase['coordVAR'])]
# no_modbase = no_modbase[keep_cols]
# return modbase, no_modbase
import requests
import numpy as np
import pandas as pd
from utils import *
from pathlib import Path
from bs4 import BeautifulSoup
from add_sasa import *
def addModbaseModels(dataframe, path_to_input_files, path_to_output_files):
if len(dataframe) != 0:
# GET MODBASE MODELS
# Get IDs from data to retrieve only their models from MODBASE
dataframe.reset_index(inplace=True, drop=True)
existing_modbase_models = list(Path(path_to_output_files / 'modbase_structures').glob("*"))
existing_modbase_models = [str(i) for i in existing_modbase_models]
existing_modbase_models = [i.split('/')[-1].split('.')[0] for i in existing_modbase_models]
existing_modbase_models_ind = list(Path(path_to_output_files / 'modbase_structures_individual').glob("*"))
existing_modbase_models_ind = [str(i) for i in existing_modbase_models_ind]
existing_modbase_models_ind = [i.split('/')[-1].split('.')[0] for i in existing_modbase_models_ind]
modbase_reduced = pd.DataFrame(columns = ['uniprotID', 'target_begin', 'target_end', 'quality_score',
'model_id', 'coordinates','AAonPDB', 'coordVAR'])
print('Retrieving ModBase models...\n')
modbase = pd.DataFrame(
columns=['uniprotID', 'target_begin', 'target_end', 'quality_score', 'model_id',
'coordinates', 'AAonPDB', 'coordVAR'])
no_modbase = pd.DataFrame(
columns=['uniprotID', 'target_begin', 'target_end', 'quality_score', 'model_id',
'coordinates', 'AAonPDB', 'coordVAR'])
# Get model files associated with each UniProtID
existing_free_sasa = list(Path(path_to_output_files / 'freesasa_files').glob("*"))
existing_free_sasa = [str(i) for i in existing_free_sasa]
existing_free_sasa = [i.split('/')[-1].split('.')[0] for i in existing_free_sasa]
keep_cols = dataframe.columns
for i in dataframe.index:
coordDict = {}
protein = dataframe.at[i, 'uniprotID']
varPos = int(dataframe.at[i, 'pos'])
wt = dataframe.at[i, 'wt']
mut = dataframe.at[i, 'mut']
datapoint = dataframe.at[i, 'datapoint']
if protein not in existing_modbase_models:
print('Downloading Modbase models for ', protein)
url = 'https://salilab.org/modbase/retrieve/modbase/?databaseID=' + protein
req = requests.get(url)
name = path_to_output_files / 'modbase_structures' / f'{protein}.txt'
with open(name, 'wb') as f:
f.write(req.content)
else:
print('Model exists for', protein)
name = Path(path_to_output_files / 'modbase_structures' / f'{protein}.txt')
with open(name, encoding="utf8") as f:
a = open(name, 'r').read()
soup = BeautifulSoup(a, 'lxml')
if soup.findAll('pdbfile') != []:
for pdb in soup.findAll('pdbfile'):
model_id = str(pdb.contents[1])[10:-11]
if model_id not in existing_modbase_models_ind:
with open(path_to_output_files / 'modbase_structures_individual' / f'{model_id}.txt', 'w', encoding="utf8") as individual:
individual.write(str('UniProt ID: ' + protein))
individual.write('\n')
individual.write(str(pdb.contents[3])[10:-11].strip())
run_freesasa(
Path(path_to_output_files / 'modbase_structures_individual' / f'{model_id.lower()}.txt'),
Path(path_to_output_files / 'freesasa_files' / f'{model_id.lower()}.txt'),
include_hetatms=True,
outdir=None, force_rerun=False, file_type='pdb')
filename = Path(path_to_output_files / 'freesasa_files' / f'{model_id.lower()}.txt')
sasa_val = sasa(protein, varPos, wt, 1, filename, path_to_output_files, file_type='pdb')
with open(path_to_output_files / 'modbase_structures_individual'/ f'{model_id}.txt', encoding="utf8") as m:
lines = m.readlines()
quality_score = -999
for ind_line in lines:
if ind_line[0:10] == 'UniProt ID':
uniprot_id = ind_line.split(':')[1].strip()
if ind_line[0:23] == 'REMARK 220 TARGET BEGIN':
target_begin = ind_line[40:43].strip()
if ind_line[0:21] == 'REMARK 220 TARGET END':
target_end = ind_line[40:43].strip()
coordDict, AAonPDB, coordVAR = {},np.NaN,np.NaN
if (int(varPos) > int(target_begin)) & (int(varPos) < int(target_end)):
coordDict = {}
for ind_line in lines:
if ind_line[0:27] == 'REMARK 220 MODPIPE MODEL ID':
model_id = ind_line[40:].strip()
if ind_line[0:15].strip() == 'REMARK 220 MPQS':
quality_score = ind_line[40:].strip()
if ind_line[0:4] == 'ATOM' and ind_line[13:15] == 'CA':
position = int(ind_line[22:26].strip())
chain = ind_line[20:22].strip()
aminoacid = threeToOne(ind_line[17:20])
coords = [ind_line[31:38].strip(), ind_line[39:46].strip(), ind_line[47:54].strip()]
coordDict[position] = coords
if position == int(varPos):
AAonPDB = aminoacid
coordVAR = str(coords)
if ind_line[0:3] == 'TER':
break
try:
k = pd.Series(
[uniprot_id, target_begin, target_end,quality_score, model_id, coordDict, AAonPDB, coordVAR, sasa_val])
new_row = {'uniprotID': uniprot_id, 'target_begin': target_begin,
'target_end': target_end, 'quality_score': quality_score,
'model_id': model_id, 'coordinates': coordDict,
'AAonPDB': AAonPDB, 'coordVAR': coordVAR, 'sasa':sasa_val}
modbase_reduced = modbase_reduced.append(new_row, ignore_index=True)
modbase_reduced = modbase_reduced[['uniprotID', 'quality_score', 'model_id', 'coordinates', 'AAonPDB', 'coordVAR', 'sasa']]
modbase = dataframe.merge(modbase_reduced, on='uniprotID', how='left')
modbase.quality_score = modbase.quality_score.astype(float)
modbase = modbase.sort_values(by=['datapoint', 'quality_score'], ascending=False)
modbase.reset_index(inplace=True, drop=True)
modbase.fillna(np.NaN, inplace=True)
modbase.replace({'\'?\', ': '',
', \'?\'': '',
'(': '', ')': '',
'[\'?\']': np.NaN,
'[]': np.NaN,
'nan-nan': np.NaN,
'': np.NaN}, inplace=True)
except NameError:
print('This file doesnt have Quality Score. Replacer: -999', model_id)
else:
new_row = {'uniprotID': uniprot_id, 'wt': wt,
'pos': varPos, 'mut': mut, 'datapoint': datapoint }
no_modbase = no_modbase.append(new_row, ignore_index=True)
else:
new_row = {'uniprotID': uniprot_id, 'wt': wt,
'pos': varPos, 'mut': mut, 'datapoint': datapoint }
no_modbase = no_modbase.append(new_row, ignore_index=True)
no_modbase_no_Coord = modbase[pd.isna(modbase['coordVAR'])]
no_modbase = pd.concat([no_modbase, no_modbase_no_Coord])
modbase = modbase[~pd.isna(modbase['coordVAR'])]
no_modbase = no_modbase[keep_cols]
return modbase, no_modbase |