Molph4
Published:
Automated Validation pharmacophore model
- This package use results from MOE pharmacophore model screening (*txt, *csv)
- Automation select best pharmacophore model to optimize
Requirements
This module requires the following modules:
Installation
Clone this repository to use
Download the data and pretrained model
Use the following onedrive link:
Update...
Put everything in onedrive folder to “Data” folder:
Finally the folder structure should look like this:
Molph4 (project root)
|__ README.md
|__ ph4
|__ Data
|__ |__ data... (downloaded from onedrive)
| |__ results..
|
|...... ## Usage
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import sys
sys.path.append('./Ph4')
from Postprocessing import pharmacophore_postprocess
from Validation import pharmacophore_validation
from Autoresult import autoph4result
import warnings
warnings.filterwarnings('ignore')
# 0. Database: dekois is data before screening through pharmacophore model
dekois = pd.read_csv("DEKOIS_data.csv").drop(['Unnamed: 0'], axis = 1)
data = pd.read_csv("./Data/cover9/haaa_1.txt")
# 1. Postprocess
postprocess = pharmacophore_postprocess(data = data, model ='haaa_1', ID = 'ID', ref=dekois,
scores = 'rmsd', rescore = 'minmax')
postprocess.fit()
postprocess.df
# 2. Validation
ph4 = pharmacophore_validation(data = postprocess.df, active = "Active", predict = "predict",
scores = "haaa_1_rescore", model ='haaa_1', auc_thresh = 0.5, plottype='auc', figsize =(8.5,5))
ph4.validation()
ph4.table.head()
# 3.Automation pharmacophore validation
import os
dekois = pd.read_csv('DEKOIS_data.csv').drop(['Unnamed: 0'], axis = 1)
path = os.getcwd() + '/Data/'
auto = autoph4result(path = path, ref=dekois, scores = 'rmsd', active = 'Active', ID = 'ID',
rescore = 'minmax', auc_thresh = 0.6, figsize = (9,5))
auto.compare_model_multi()
Contributing
Please visit the Molph4 repository. Pull requests are welcome. For major changes, please open an issue first to discuss what you would like to change. Please make sure to update tests as appropriate.