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info_gen.py
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'''
Generating files for finial analysis.
mol_2_info --- Take source folder's .mol2 files, then generate 2 target folders, one for the pickle files
containing 'vor' and 'atoms' objects, one for the images.
'''
import sys
import os
import argparse
import pickle
import skimage
from bionoi import Bionoi
from skimage.io import imshow
import numpy as np
from os import listdir
from os.path import isfile, join
def get_args():
parser = argparse.ArgumentParser('python')
parser.add_argument('-dpi',
default=256,
required=False,
help='image quality in dpi')
parser.add_argument('-size', default=256,
required=False,
help='image size in pixels, eg: 128')
parser.add_argument('-alpha',
default=0.5,
required=False,
help='alpha for color of cells')
parser.add_argument('-colorby',
default="residue_type",
choices=["atom_type", "residue_type", "residue_num"],
required=False,
help='color the voronoi cells according to {atom_type, residue_type, residue_num}')
parser.add_argument('-imageType',
default=".jpg",
choices=[".jpg", ".png"],
required=False,
help='the type of image {.jpg, .png}')
return parser.parse_args()
def mol_2_info(mol, sourceFolder, targetFolderPkl, targetFolderImg, args):
"""
mol2File: a path of a sinle .mol2 file as input
args: input arguments
targetFolderPkl: path to pickle file of a dictionary containing vor objects and
atoms objects of the .mol2 file from 6 different directions. The dirctions are already predefined.
targetFolderImg: path to save the images of 6 different directions
"""
dpi = args.dpi
size = args.size
alpha = args.alpha
colorby = args.colorby
imageType = args.imageType
if not os.path.exists(targetFolderPkl):
os.makedirs(targetFolderPkl)
if not os.path.exists(targetFolderImg):
os.makedirs(targetFolderImg)
# path of the source .mol2 file
molPath = sourceFolder + mol
#print(molPath)
# remove file extension
molName = mol.split('.')[0]
# the dictionary containing 6 sub-dictionaries for 6 dirctions:
# xoy_p, xoy_n, yoz_p, yoz_n, zox_p, zox_n
dict ={}
# the directions tuple
dirs = ('xoy_+', 'xoy_-', 'yoz_+', 'yoz_-', 'zox_+', 'zox_-')
i = 0
for dir in dirs:
atoms, vor, image = Bionoi(mol=molPath,bs_out='',size=size,dpi=dpi,alpha=alpha,colorby=colorby,proj_direction=i+1)
dict[dirs[i]] = {'atoms':atoms, 'vor':vor}
#save the images
skimage.io.imsave(targetFolderImg+molName+dir+imageType, image)
# increment direction index
i = i + 1
#imshow(image)
#print('dict:',dict)
# dump the dictionary into a pickle file
pklFile = open(targetFolderPkl+molName+'.pickle','wb')
pickle.dump(dict, pklFile)
def mol_2_info_folder(sourceFolder, targetFolderPkl, targetFolderImg, args):
"""
Run mol_2_info() on entire folder
"""
fileList = [f for f in listdir(sourceFolder) if isfile(join(sourceFolder, f))]
print('converting {} of files in folder {}'.format(len(fileList),sourceFolder))
print('pickle files saved in folder {}'.format(targetFolderPkl))
print('images saved in folder {}'.format(targetFolderImg))
for mol in fileList:
mol_2_info(mol, sourceFolder, targetFolderPkl, targetFolderImg, args)
#print('processed:', mol)
def control_vs_heme_gen(args):
"""
Generate files for control_vs_heme task.
"""
sourceFolder = '../control_vs_heme_mols/train/control/'
targetFolderPkl = '../analyse/mols_pkl/control_vs_heme/train/control/'
targetFolderImg = '../analyse/images/control_vs_heme/train/control/'
mol_2_info_folder(sourceFolder, targetFolderPkl, targetFolderImg, args)
sourceFolder = '../control_vs_heme_mols/train/heme/'
targetFolderPkl = '../analyse/mols_pkl/control_vs_heme/train/heme/'
targetFolderImg = '../analyse/images/control_vs_heme/train/heme/'
mol_2_info_folder(sourceFolder, targetFolderPkl, targetFolderImg, args)
sourceFolder = '../control_vs_heme_mols/val/control/'
targetFolderPkl = '../analyse/mols_pkl/control_vs_heme/val/control/'
targetFolderImg = '../analyse/images/control_vs_heme/val/control/'
mol_2_info_folder(sourceFolder, targetFolderPkl, targetFolderImg, args)
sourceFolder = '../control_vs_heme_mols/val/heme/'
targetFolderPkl = '../analyse/mols_pkl/control_vs_heme/val/heme/'
targetFolderImg = '../analyse/images/control_vs_heme/val/heme/'
mol_2_info_folder(sourceFolder, targetFolderPkl, targetFolderImg, args)
sourceFolder = '../control_vs_heme_mols/test/control/'
targetFolderPkl = '../analyse/mols_pkl/control_vs_heme/test/control/'
targetFolderImg = '../analyse/images/control_vs_heme/test/control/'
mol_2_info_folder(sourceFolder, targetFolderPkl, targetFolderImg, args)
sourceFolder = '../control_vs_heme_mols/test/heme/'
targetFolderPkl = '../analyse/mols_pkl/control_vs_heme/test/heme/'
targetFolderImg = '../analyse/images/control_vs_heme/test/heme/'
mol_2_info_folder(sourceFolder, targetFolderPkl, targetFolderImg, args)
def control_vs_nucleotide_gen(args):
"""
Generate files for control_vs_nucleotide task.
"""
sourceFolder = '../control_vs_nucleotide_mols/train/control/'
targetFolderPkl = '../analyse/mols_pkl/control_vs_nucleotide/train/control/'
targetFolderImg = '../analyse/images/control_vs_nucleotide/train/control/'
mol_2_info_folder(sourceFolder, targetFolderPkl, targetFolderImg, args)
sourceFolder = '../control_vs_nucleotide_mols/train/nucleotide/'
targetFolderPkl = '../analyse/mols_pkl/control_vs_nucleotide/train/nucleotide/'
targetFolderImg = '../analyse/images/control_vs_nucleotide/train/nucleotide/'
mol_2_info_folder(sourceFolder, targetFolderPkl, targetFolderImg, args)
sourceFolder = '../control_vs_nucleotide_mols/val/control/'
targetFolderPkl = '../analyse/mols_pkl/control_vs_nucleotide/val/control/'
targetFolderImg = '../analyse/images/control_vs_nucleotide/val/control/'
mol_2_info_folder(sourceFolder, targetFolderPkl, targetFolderImg, args)
sourceFolder = '../control_vs_nucleotide_mols/val/nucleotide/'
targetFolderPkl = '../analyse/mols_pkl/control_vs_nucleotide/val/nucleotide/'
targetFolderImg = '../analyse/images/control_vs_nucleotide/val/nucleotide/'
mol_2_info_folder(sourceFolder, targetFolderPkl, targetFolderImg, args)
sourceFolder = '../control_vs_nucleotide_mols/test/control/'
targetFolderPkl = '../analyse/mols_pkl/control_vs_nucleotide/test/control/'
targetFolderImg = '../analyse/images/control_vs_nucleotide/test/control/'
mol_2_info_folder(sourceFolder, targetFolderPkl, targetFolderImg, args)
sourceFolder = '../control_vs_nucleotide_mols/test/nucleotide/'
targetFolderPkl = '../analyse/mols_pkl/control_vs_nucleotide/test/nucleotide/'
targetFolderImg = '../analyse/images/control_vs_nucleotide/test/nucleotide/'
mol_2_info_folder(sourceFolder, targetFolderPkl, targetFolderImg, args)
def heme_vs_nucleotide_gen(args):
"""
Generate files for heme_vs_nucleotide task.
"""
sourceFolder = '../heme_vs_nucleotide_mols/train/0-heme/'
targetFolderPkl = '../analyse/mols_pkl/heme_vs_nucleotide/train/0-heme/'
targetFolderImg = '../analyse/images/heme_vs_nucleotide/train/0-heme/'
mol_2_info_folder(sourceFolder, targetFolderPkl, targetFolderImg, args)
sourceFolder = '../heme_vs_nucleotide_mols/train/1-nucleotide/'
targetFolderPkl = '../analyse/mols_pkl/heme_vs_nucleotide/train/1-nucleotide/'
targetFolderImg = '../analyse/images/heme_vs_nucleotide/train/1-nucleotide/'
mol_2_info_folder(sourceFolder, targetFolderPkl, targetFolderImg, args)
sourceFolder = '../heme_vs_nucleotide_mols/val/0-heme/'
targetFolderPkl = '../analyse/mols_pkl/heme_vs_nucleotide/val/0-heme/'
targetFolderImg = '../analyse/images/heme_vs_nucleotide/val/0-heme/'
mol_2_info_folder(sourceFolder, targetFolderPkl, targetFolderImg, args)
sourceFolder = '../heme_vs_nucleotide_mols/val/1-nucleotide/'
targetFolderPkl = '../analyse/mols_pkl/heme_vs_nucleotide/val/1-nucleotide/'
targetFolderImg = '../analyse/images/heme_vs_nucleotide/val/1-nucleotide/'
mol_2_info_folder(sourceFolder, targetFolderPkl, targetFolderImg, args)
sourceFolder = '../heme_vs_nucleotide_mols/test/0-heme/'
targetFolderPkl = '../analyse/mols_pkl/heme_vs_nucleotide/test/0-heme/'
targetFolderImg = '../analyse/images/heme_vs_nucleotide/test/0-heme/'
mol_2_info_folder(sourceFolder, targetFolderPkl, targetFolderImg, args)
sourceFolder = '../heme_vs_nucleotide_mols/test/1-nucleotide/'
targetFolderPkl = '../analyse/mols_pkl/heme_vs_nucleotide/test/1-nucleotide/'
targetFolderImg = '../analyse/images/heme_vs_nucleotide/test/1-nucleotide/'
mol_2_info_folder(sourceFolder, targetFolderPkl, targetFolderImg, args)
#-----------------------------------------------------------------------------------
if __name__ == "__main__":
args = get_args()
#control_vs_heme_gen(args)
#control_vs_nucleotide_gen(args)
heme_vs_nucleotide_gen(args)