Spaces:
Paused
Paused
File size: 3,224 Bytes
56793c5 |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 |
# -*- coding: utf-8
"""Utility functions."""
import sys
import os
import glob
import tempfile
import shutil
from pathlib import Path
from typing import Tuple
from rdkit import Chem
from jdk import install as _jre_install, _JRE_DIR
def install_jre(version: int = 19):
"""Install a Java Runtime Environment."""
path = get_jre_in_dir(_JRE_DIR, version)
if len(path) == 0:
# Could not find JRE, install it
_ = _jre_install(version, jre=True)
path = get_jre_in_dir(_JRE_DIR, version)
return path
def make_temp_jre() -> Tuple[str, str]:
"""Copy the installed JRE to a temporary file.
Allows multiprocessing capacities.
:return: a tuple of (path to temp dir, path to the JRE)
"""
# Path of JRE installation
install_path = [path for path in Path(install_jre()).parents
if path.as_posix().endswith('jre') and not path.as_posix().endswith('.jre')][0]
# Path of temp dir
outdir = mktempdir()
# Make copy into dir
shutil.copytree(install_path, os.path.join(outdir, 'jre'))
# Find JRE in temp dir
path = get_jre_in_dir(outdir)
return outdir, path
def get_jre_in_dir(dir: str):
"""Recursively search the directory to find a JRE."""
paths = glob.glob(os.path.join(dir, '**', 'server',
'jvm.dll' if sys.platform == "win32" else 'libjvm.so'
), recursive=True)
path = [path for path in paths if f'jre-{version}' in path]
if len(path):
return path[0]
return None
def install_java(version: int = 19):
"""Install a Java Runtime Environment."""
path = get_java_in_dir(_JRE_DIR, version)
if path is None:
# Could not find JRE, install it
_ = _jre_install(version, jre=True)
path = get_java_in_dir(_JRE_DIR, version)
return path
def get_java_in_dir(dir: str, version: int):
"""Recursively search the directory to find a JRE."""
paths = glob.glob(os.path.join(dir, '**', 'bin',
'java.exe' if sys.platform == "win32" else 'java'
), recursive=True)
path = [path for path in paths if f'jdk-{version}' in path]
if len(path):
return os.path.abspath(path[0])
return None
def mktempdir(suffix: str = None) -> str:
"""Return the path to a writeable temporary directory."""
dir = tempfile.mkdtemp(suffix=suffix)
return dir
def mktempfile(suffix: str = None) -> str:
"""Return the path to a writeable temporary file."""
file = tempfile.mkstemp(suffix=suffix)
os.close(file[0])
return file[1]
def needsHs(mol: Chem.Mol) -> bool:
"""Return if the molecule lacks hydrogen atoms or not.
:param mol: RDKit Molecule
:return: True if the molecule lacks hydrogens.
"""
for atom in mol.GetAtoms():
nHNbrs = 0
for nbr in atom.GetNeighbors():
if nbr.GetAtomicNum() == 1:
nHNbrs += 1
noNeighbors = False
if atom.GetTotalNumHs(noNeighbors) > nHNbrs:
return True
return False
|