repo stringlengths 2 99 | file stringlengths 13 225 | code stringlengths 0 18.3M | file_length int64 0 18.3M | avg_line_length float64 0 1.36M | max_line_length int64 0 4.26M | extension_type stringclasses 1
value |
|---|---|---|---|---|---|---|
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/filter/filter_classes/filter_children_classes/vande_waterbeemd_filter.py | """VandeWaterbeemd Filter
This runs a VandeWaterbeemd filter for drugs which are likely to be blood
brain barrier permeable. VandeWaterbeemd filter filters molecules for
Molecular weight (MW), and Polar Sureface Area (PSA).
To pass the VandeWaterbeemd filter a ligand must have:
Molecular Weight: less than 450 dalt... | 2,715 | 34.272727 | 88 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/filter/filter_classes/filter_children_classes/ghose_modified_filter.py | """Ghose Filter
This runs a Ghose filter for drug-likeliness. Ghose filter filters molecules
by Molecular weight (MW), the number of atoms, and the logP value.
The upper bound of MW is relaxed from 480Da to 500Da. This is
less restrictive and works in conjunction with Lipinski. This is also
to retro-match AutoGrow 3.1.... | 3,978 | 34.846847 | 85 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/filter/filter_classes/filter_children_classes/ghose_filter.py | """Ghose Filter
This runs a Ghose filter for drug-likeliness. Ghose filter filters molecules
by Molecular weight (MW), the number of atoms, and the logP value.
We protonate the mol in this filter because hydrogens affect
atom count. Our Ghose implementation counts hydrogens in against
the total number of atoms.
To pa... | 3,772 | 33.614679 | 85 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/filter/filter_classes/filter_children_classes/__init__.py | """
This imports all of the filters within the FilterClasses file. This is very
important as the filters will not work if this doesn't exist.
This is a dynamic and modular way of doing these imports.
Code is taken from:
https://stackoverflow.com/questions/1057431/how-to-load-all-modules-in-a-folder
"""
from os.path... | 526 | 26.736842 | 92 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/filter/filter_classes/filter_children_classes/pains_filter.py | """#PAINS Filter
This will filter a ligand using a PAINS filter. PAINS eliminates of Pan Assay
Interference Compounds using substructure a search.
This will include PAINS_A, PAINS_B, and PAINS_C filtering.
This script relies on the RDKit predefined FilterCatalog. FilterCatalog is
maintained by RDKit.
If using th... | 4,056 | 35.881818 | 86 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/filter/filter_classes/filter_children_classes/nih_filter.py | """#NIH Filter
This will filter a ligand using the NIH filter to remove ligands with
undersirable functional groups.
This script relies on the RDKit predefined FilterCatalog. FilterCatalog is
maintained by RDKit.
If using the NIH filter please cite: Jadhav A, et al. Quantitative Analyses of
Aggregation, Autofluoresce... | 2,926 | 31.164835 | 86 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/convert_files/conversion_to_3d.py | """
Run file type conversions from .smi to .sdf to .pdb
"""
import __future__
import glob
import sys
import os
from os.path import basename
import rdkit
import rdkit.Chem as Chem
from func_timeout import func_timeout
# Disable the unnecessary RDKit warnings
rdkit.RDLogger.DisableLog("rdApp.*")
# Some pathing to all... | 19,850 | 36.243902 | 105 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/convert_files/__init__.py | 1 | 0 | 0 | py | |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/convert_files/gypsum_dl/run_gypsum_dl.py | #!/usr/bin/env python
# Copyright 2018 Jacob D. Durrant
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable l... | 9,808 | 30.041139 | 98 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/convert_files/gypsum_dl/__init__.py | 2 | 0.5 | 1 | py | |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/convert_files/gypsum_dl/gypsum_dl/ChemUtils.py | # Copyright 2018 Jacob D. Durrant
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writ... | 8,444 | 34.93617 | 111 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/convert_files/gypsum_dl/gypsum_dl/Utils.py | # Copyright 2018 Jacob D. Durrant
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writ... | 5,886 | 28.883249 | 84 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/convert_files/gypsum_dl/gypsum_dl/__init__.py | # Copyright 2018 Jacob D. Durrant
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writ... | 904 | 33.807692 | 74 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/convert_files/gypsum_dl/gypsum_dl/MolContainer.py | # Copyright 2018 Jacob D. Durrant
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writ... | 11,036 | 35.667774 | 115 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/convert_files/gypsum_dl/gypsum_dl/Parallelizer.py | # Copyright 2018 Jacob D. Durrant
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writ... | 30,734 | 36.944444 | 223 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/convert_files/gypsum_dl/gypsum_dl/MyMol.py | # Copyright 2018 Jacob D. Durrant
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writ... | 32,750 | 36.048643 | 100 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/convert_files/gypsum_dl/gypsum_dl/MolObjectHandling.py | # Copyright 2018 Jacob D. Durrant
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writ... | 10,436 | 30.627273 | 128 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/convert_files/gypsum_dl/gypsum_dl/Start.py | # Copyright 2018 Jacob D. Durrant
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writ... | 22,182 | 35.848837 | 222 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/convert_files/gypsum_dl/gypsum_dl/Test/Tester.py | # Copyright 2018 Jacob D. Durrant
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writ... | 7,621 | 32.429825 | 90 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/convert_files/gypsum_dl/gypsum_dl/Test/__init__.py | 0 | 0 | 0 | py | |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/convert_files/gypsum_dl/gypsum_dl/Steps/__init__.py | # Copyright 2018 Jacob D. Durrant
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writ... | 1,071 | 33.580645 | 74 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/convert_files/gypsum_dl/gypsum_dl/Steps/ThreeD/GenerateAlternate3DNonaromaticRingConfs.py | # Copyright 2018 Jacob D. Durrant
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writ... | 12,269 | 38.967427 | 124 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/convert_files/gypsum_dl/gypsum_dl/Steps/ThreeD/Minimize3D.py | # Copyright 2018 Jacob D. Durrant
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writ... | 7,568 | 38.421875 | 87 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/convert_files/gypsum_dl/gypsum_dl/Steps/ThreeD/__init__.py | # Copyright 2018 Jacob D. Durrant
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writ... | 984 | 35.481481 | 74 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/convert_files/gypsum_dl/gypsum_dl/Steps/ThreeD/Convert2DTo3D.py | # Copyright 2018 Jacob D. Durrant
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writ... | 4,645 | 32.666667 | 85 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/convert_files/gypsum_dl/gypsum_dl/Steps/ThreeD/PrepareThreeD.py | # Copyright 2018 Jacob D. Durrant
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writ... | 2,581 | 31.275 | 76 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/convert_files/gypsum_dl/gypsum_dl/Steps/SMILES/EnumerateDoubleBonds.py | # Copyright 2018 Jacob D. Durrant
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writ... | 11,736 | 36.61859 | 93 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/convert_files/gypsum_dl/gypsum_dl/Steps/SMILES/DurrantLabFilter.py | # Copyright 2018 Jacob D. Durrant
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writ... | 6,203 | 30.653061 | 86 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/convert_files/gypsum_dl/gypsum_dl/Steps/SMILES/AddHydrogens.py | # Copyright 2018 Jacob D. Durrant
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writ... | 6,779 | 34.129534 | 88 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/convert_files/gypsum_dl/gypsum_dl/Steps/SMILES/EnumerateChiralMols.py | # Copyright 2018 Jacob D. Durrant
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writ... | 8,191 | 36.067873 | 87 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/convert_files/gypsum_dl/gypsum_dl/Steps/SMILES/MakeTautomers.py | # Copyright 2018 Jacob D. Durrant
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writ... | 15,760 | 33.563596 | 87 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/convert_files/gypsum_dl/gypsum_dl/Steps/SMILES/PrepareSmiles.py | # Copyright 2018 Jacob D. Durrant
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writ... | 6,193 | 32.663043 | 87 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/convert_files/gypsum_dl/gypsum_dl/Steps/SMILES/DeSaltOrigSmiles.py | # Copyright 2018 Jacob D. Durrant
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writ... | 3,703 | 31.491228 | 82 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/convert_files/gypsum_dl/gypsum_dl/Steps/SMILES/__init__.py | # Copyright 2018 Jacob D. Durrant
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writ... | 985 | 35.518519 | 74 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/convert_files/gypsum_dl/gypsum_dl/Steps/SMILES/dimorphite_dl/dimorphite_dl.py | # Copyright 2020 Jacob D. Durrant
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writ... | 56,465 | 37.861666 | 209 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/convert_files/gypsum_dl/gypsum_dl/Steps/SMILES/dimorphite_dl/__init__.py | # This file included so this directory can be loaded as a Python module.
| 73 | 36 | 72 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/convert_files/gypsum_dl/gypsum_dl/Steps/IO/Web2DOutput.py | # Copyright 2018 Jacob D. Durrant
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writ... | 3,142 | 37.329268 | 96 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/convert_files/gypsum_dl/gypsum_dl/Steps/IO/SaveToPDB.py | # Copyright 2018 Jacob D. Durrant
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writ... | 2,598 | 31.08642 | 104 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/convert_files/gypsum_dl/gypsum_dl/Steps/IO/ProcessOutput.py | # Copyright 2018 Jacob D. Durrant
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writ... | 1,574 | 32.510638 | 75 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/convert_files/gypsum_dl/gypsum_dl/Steps/IO/LoadFiles.py | # Copyright 2018 Jacob D. Durrant
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writ... | 6,751 | 34.166667 | 117 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/convert_files/gypsum_dl/gypsum_dl/Steps/IO/__init__.py | # Copyright 2018 Jacob D. Durrant
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writ... | 1,157 | 35.1875 | 74 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/convert_files/gypsum_dl/gypsum_dl/Steps/IO/SaveToSDF.py | # Copyright 2018 Jacob D. Durrant
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writ... | 2,963 | 31.217391 | 101 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/convert_files/gypsum_dl/gypsum_dl/molvs/resonance.py | # -*- coding: utf-8 -*-
"""
molvs.resonance
~~~~~~~~~~~~~~~
Resonance (mesomeric) transformations.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import logging
from rdkit import Chem
log = logging.getLogger(... | 3,773 | 40.021739 | 201 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/convert_files/gypsum_dl/gypsum_dl/molvs/charge.py | # -*- coding: utf-8 -*-
"""
molvs.charge
~~~~~~~~~~~~
This module implements tools for manipulating charges on molecules. In particular, :class:`~molvs.charge.Reionizer`,
which competitively reionizes acids such that the strongest acids ionize first, and :class:`~molvs.charge.Uncharger`,
which attempts to neutralize i... | 14,678 | 43.213855 | 129 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/convert_files/gypsum_dl/gypsum_dl/molvs/tautomer.py | # -*- coding: utf-8 -*-
"""
molvs.tautomer
~~~~~~~~~~~~~~
This module contains tools for enumerating tautomers and determining a canonical tautomer.
"""
from __future__ import print_function
from __future__ import unicode_literals
from __future__ import division
import copy
import logging
from rdkit import Chem
fro... | 17,504 | 52.53211 | 226 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/convert_files/gypsum_dl/gypsum_dl/molvs/errors.py | # -*- coding: utf-8 -*-
"""
molvs.errors
~~~~~~~~~~~~
This module contains exceptions that are raised by MolVS.
"""
from __future__ import print_function
from __future__ import unicode_literals
from __future__ import division
class MolVSError(Exception):
pass
class StandardizeError(MolVSError):
pass
cl... | 497 | 15.6 | 85 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/convert_files/gypsum_dl/gypsum_dl/molvs/standardize.py | # -*- coding: utf-8 -*-
"""
molvs.standardize
~~~~~~~~~~~~~~~~~
This module contains the main :class:`~molvs.standardize.Standardizer` class that can be used to perform all
standardization tasks, as well as convenience functions like :func:`~molvs.standardize.standardize_smiles` for common
standardization tasks.
"""
... | 13,987 | 40.630952 | 120 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/convert_files/gypsum_dl/gypsum_dl/molvs/validate.py | # -*- coding: utf-8 -*-
"""
molvs.validate
~~~~~~~~~~~~~~
This module contains the main :class:`~molvs.validate.Validator` class that can be used to perform all
:class:`Validations <molvs.validations.Validation>`, as well as the :func:`~molvs.validate.validate_smiles()`
convenience function.
"""
from __future__ impo... | 4,213 | 34.116667 | 119 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/convert_files/gypsum_dl/gypsum_dl/molvs/utils.py | # -*- coding: utf-8 -*-
"""
molvs.utils
~~~~~~~~~~~
This module contains miscellaneous utility functions.
"""
from __future__ import print_function
from __future__ import unicode_literals
from __future__ import division
import functools
from itertools import tee
import six
def memoized_property(fget):
"""Deco... | 787 | 20.888889 | 60 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/convert_files/gypsum_dl/gypsum_dl/molvs/cli.py | # -*- coding: utf-8 -*-
"""
molvs.cli
~~~~~~~~~
This module contains a command line interface for standardization.
"""
from __future__ import print_function
from __future__ import unicode_literals
from __future__ import division
import argparse
import logging
from rdkit import Chem
import sys
from molvs import Stan... | 3,399 | 31.380952 | 143 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/convert_files/gypsum_dl/gypsum_dl/molvs/metal.py | # -*- coding: utf-8 -*-
"""
molvs.metal
~~~~~~~~~~~
This module contains tools for disconnecting metal atoms that are defined as covalently bonded to non-metals.
"""
from __future__ import print_function
from __future__ import unicode_literals
from __future__ import division
import logging
from rdkit import Chem
... | 3,012 | 40.273973 | 197 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/convert_files/gypsum_dl/gypsum_dl/molvs/__init__.py | # -*- coding: utf-8 -*-
"""
MolVS - Molecule Validation and Standardization
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
MolVS is a python tool built on top of RDKit that performs validation and standardization of chemical structures.
"""
from __future__ import print_function
from __future__ import unicode_litera... | 837 | 26.933333 | 115 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/convert_files/gypsum_dl/gypsum_dl/molvs/normalize.py | # -*- coding: utf-8 -*-
"""
molvs.normalize
~~~~~~~~~~~~~~~
This module contains tools for normalizing molecules using reaction SMARTS patterns.
"""
from __future__ import print_function
from __future__ import unicode_literals
from __future__ import division
import logging
from rdkit import Chem
from rdkit.Chem imp... | 9,432 | 52.902857 | 165 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/convert_files/gypsum_dl/gypsum_dl/molvs/fragment.py | # -*- coding: utf-8 -*-
"""
molvs.fragment
~~~~~~~~~~~~~~
This module contains tools for dealing with molecules with more than one covalently bonded unit. The main classes are
:class:`~molvs.fragment.LargestFragmentChooser`, which returns the largest covalent unit in a molecule, and
:class:`~molvs.fragment.FragmentRem... | 11,192 | 44.872951 | 120 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/convert_files/gypsum_dl/gypsum_dl/molvs/validations.py | # -*- coding: utf-8 -*-
"""
molvs.validations
~~~~~~~~~~~~~~~~~
This module contains all the built-in :class:`Validations <molvs.validations.Validation>`.
"""
from __future__ import print_function
from __future__ import unicode_literals
from __future__ import division
import logging
from rdkit import Chem
from .er... | 7,188 | 33.07109 | 123 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/crossover/__init__.py | 1 | 0 | 0 | py | |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/crossover/execute_crossover.py | """Pre-SmileMerge_mcs_Filter
This script should take an input of a randomly selected file containing a list
of smiles.
A random number function will be used to pick 2 non-identical numbers for 0 to
the len(smile_list) Then those numbers are used to grab 2 non-identical
molecules from smile_list Those 2 smiles are tes... | 15,983 | 35.91455 | 140 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/crossover/smiles_merge/smiles_merge.py | """
Run a single crossover event.
"""
import __future__
import rdkit
from rdkit import Chem
from rdkit.Chem import rdFMCS
# Disable the unnecessary RDKit warnings
rdkit.RDLogger.DisableLog("rdApp.*")
import autogrow.operators.crossover.smiles_merge.merge_functions.merge_w_core as MWC
import autogrow.operators.crosso... | 5,464 | 33.808917 | 92 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/crossover/smiles_merge/__init__.py | 0 | 0 | 0 | py | |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/crossover/smiles_merge/merge_functions/dict_and_r_groups.py | """
Dictionary and Dictionary handling functions
"""
import __future__
import copy
import rdkit
from rdkit import Chem
# Disable the unnecessary RDKit warnings
rdkit.RDLogger.DisableLog("rdApp.*")
import autogrow.operators.crossover.smiles_merge.merge_functions.mapping_class as mapping_class
def handle_dicts_and_... | 25,351 | 38.244582 | 155 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/crossover/smiles_merge/merge_functions/alignment_and_breaks.py | """This handles alignment and ring breaks for Crossover"""
import __future__
import random
import copy
import rdkit
from rdkit import Chem
# Disable the unnecessary RDKit warnings
rdkit.RDLogger.DisableLog("rdApp.*")
import autogrow.operators.convert_files.gypsum_dl.gypsum_dl.MolObjectHandling as MOH
# handle_m... | 21,264 | 37.593466 | 86 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/crossover/smiles_merge/merge_functions/merge_w_core.py | """
This script is handles the merging of two molecules and cleans up
the molecule.
"""
import __future__
import copy
import rdkit
from rdkit import Chem
# Disable the unnecessary RDKit warnings
rdkit.RDLogger.DisableLog("rdApp.*")
import autogrow.operators.convert_files.gypsum_dl.gypsum_dl.MolObjectHandling as MOH
... | 13,928 | 40.088496 | 99 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/crossover/smiles_merge/merge_functions/mapping_class.py | """
This script holds the Mapping class.
This is used when mapping most common substructure (MCS)
to combine two molecules.
"""
import __future__
import random
import copy
class Mapping(object):
"""
# Notes on terminology:
-most common substructure (MCS): The substructure shared between
... | 15,165 | 41.481793 | 88 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/crossover/smiles_merge/merge_functions/__init__.py | 1 | 0 | 0 | py | |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/mutation/__init__.py | 1 | 0 | 0 | py | |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/mutation/execute_mutations.py | """
This function should contain all the info for executing the mutation functions
"""
import __future__
import random
import copy
import autogrow.operators.mutation.smiles_click_chem.smiles_click_chem as SmileClickClass
#######################################
# Functions for creating molecular models
###########... | 8,245 | 41.287179 | 141 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/mutation/smiles_click_chem/__init__.py | 1 | 0 | 0 | py | |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/mutation/smiles_click_chem/smiles_click_chem.py | """SMILECLICK Class"""
import __future__
import random
import os
import json
import copy
import rdkit
from rdkit import Chem
from rdkit.Chem import AllChem
# Disable the unnecessary RDKit warnings
rdkit.RDLogger.DisableLog("rdApp.*")
import autogrow.operators.convert_files.gypsum_dl.gypsum_dl.MolObjectHandling as M... | 53,667 | 42.03769 | 145 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/operators/mutation/smiles_click_chem/reaction_libraries/all_rxns/fix.py | """
Developers script for merging robust_rxns and click_chem_rxns
into all_rxns... This script renumbers a rxn_libraries numbering
"""
import sys
def renumber_file(old_path, new_path, new_rxn_num):
"""
This is a developers tool to renumber a rxn_library .json file
Must provide the following:
... | 2,288 | 35.333333 | 79 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/docking/concatenate_files.py | """
This script compresses files which makes it easier to transfer data To
decompress the files use the script in
$PATH/autogrow4/accessory_scripts/file_concatenation_and_compression.py .
"""
import __future__
import glob
import os
import gzip
import shutil
def compress_file(file_name):
"""
Compress ... | 5,893 | 30.021053 | 87 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/docking/__init__.py | 1 | 0 | 0 | py | |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/docking/execute_docking.py | """
This script handles the docking and file conversion for docking.
"""
import __future__
import os
from autogrow.docking.docking_class.get_child_class import get_all_subclasses
from autogrow.docking.docking_class.docking_class_children import *
from autogrow.docking.docking_class.parent_dock_class import ParentDock... | 8,035 | 35.035874 | 168 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/docking/delete_failed_mol.py | """
delete_failed_mol.py deletes all files associated with a ligand
This is done to clean up failed attempts to dock.
"""
#######################
# Delete extra ligands #
########################
import glob
import os
def delete_all_associated_files(pdb_filename):
"""Delete files associated with a compound
... | 920 | 20.418605 | 63 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/docking/docking_class/get_child_class.py | """
An object for auto-detecting and creating jobs with the proper templates.
You'll need to import the base class first
"""
def get_all_subclasses(base_class):
"""
Method for getting all child classes from a parent object. Taken from:
http://stackoverflow.com/questions/3862310/how-can-i-find-all-subclass... | 772 | 27.62963 | 102 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/docking/docking_class/parent_pdbqt_converter.py | """
This script holds the parent class for file conversion for docking.
This is used as the basis for all file conversion classes.
"""
import __future__
class ParentPDBQTConverter(object):
"""
Docking
Inputs:
:param class object: a class to initialize on
"""
def __init__(self, vars=None, rece... | 2,221 | 30.742857 | 79 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/docking/docking_class/parent_dock_class.py | """
This script holds the parent class for docking.
This is used as the basis for all docking classes.
"""
import __future__
class ParentDocking(object):
"""
Docking
Inputs:
:param class object: a class to initialize on
"""
def __init__(self, vars=None, receptor_file=None,
fi... | 2,657 | 32.225 | 79 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/docking/docking_class/__init__.py | 1 | 0 | 0 | py | |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/docking/docking_class/docking_class_children/vina_docking.py | """
The child classes from ParentExample
"""
import __future__
import os
import sys
import glob
import autogrow.docking.delete_failed_mol as Delete
import autogrow.docking.ranking.ranking_mol as Ranking
from autogrow.docking.docking_class.parent_dock_class import ParentDocking
import autogrow.docking.scoring.execute_... | 21,978 | 36.315789 | 113 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/docking/docking_class/docking_class_children/quick_vina_2_docking.py | """
The child classes from ParentExample
"""
import __future__
import os
import sys
from autogrow.docking.docking_class.docking_class_children.vina_docking import VinaDocking
class QuickVina2Docking(VinaDocking):
"""
RUN QuickVina2 Docking
Inputs:
:param class ParentDocking: Parent docking class to... | 4,016 | 32.198347 | 90 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/docking/docking_class/docking_class_children/__init__.py |
"""
This imports all of the filters within the FilterClasses file. This is very
important as the filters will not work if this doesn't exist.
This is a dynamic and modular way of doing these imports.
Code is taken from:
https://stackoverflow.com/questions/1057431/how-to-load-all-modules-in-a-folder
"""
from os.path... | 524 | 26.631579 | 92 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/docking/docking_class/docking_file_conversion/convert_with_mgltools.py | """
The child classes from ParentExample
"""
import __future__
import os
import subprocess
import rdkit.Chem as Chem
import autogrow.docking.delete_failed_mol as Delete
import autogrow.operators.convert_files.gypsum_dl.gypsum_dl.MolObjectHandling as MOH
from autogrow.docking.docking_class.parent_pdbqt_converter imp... | 14,188 | 38.745098 | 96 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/docking/docking_class/docking_file_conversion/convert_with_obabel.py | """
The child classes from ParentExample
"""
import __future__
import os
import subprocess
import datetime
import rdkit.Chem as Chem
import autogrow.docking.delete_failed_mol as Delete
import autogrow.operators.convert_files.gypsum_dl.gypsum_dl.MolObjectHandling as MOH
from autogrow.docking.docking_class.parent_pdb... | 14,937 | 38.834667 | 86 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/docking/docking_class/docking_file_conversion/__init__.py |
"""
This imports all of the filters within the filter_children_classes file.
This is very important as the filters will not work if this doesn't exist.
This is a dynamic and modular way of doing these imports.
Code is taken from:
https://stackoverflow.com/questions/1057431/how-to-load-all-modules-in-a-folder
"""
f... | 535 | 25.8 | 92 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/docking/scoring/__init__.py | 1 | 0 | 0 | py | |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/docking/scoring/execute_scoring_mol.py | """
This function handles the scoring/rescoring of docked molecules.
"""
import __future__
from autogrow.docking.docking_class.get_child_class import get_all_subclasses
# importing scoring_functions is necessary to find rescoring modules
import autogrow.docking.scoring.scoring_classes.scoring_functions
from autogrow... | 11,825 | 33.782353 | 119 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/docking/scoring/scoring_classes/__init__.py | 1 | 0 | 0 | py | |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/docking/scoring/scoring_classes/parent_scoring_class.py | """
This script holds the parent class for scoring/rescoring.
This is used as the basis for all scoring/rescoring classes.
"""
import __future__
class ParentScoring(object):
"""
This is a script containing all of the scoring functions.
"""
def get_name(self):
"""
Returns the current cl... | 748 | 23.966667 | 70 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/docking/scoring/scoring_classes/scoring_functions/nn1.py | """
This script contains the class NN1 that rescores Vina type docking
using the program NNScore1.
"""
import __future__
import glob
import os
import sys
from autogrow.docking.scoring.scoring_classes.parent_scoring_class import ParentScoring
from autogrow.docking.scoring.scoring_classes.scoring_functions.vina import... | 9,094 | 29.726351 | 87 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/docking/scoring/scoring_classes/scoring_functions/nn2.py | """
This script contains the class NN2 that rescores Vina type docking
using the program NNScore2.
"""
import __future__
import glob
import os
import sys
from autogrow.docking.scoring.scoring_classes.parent_scoring_class import ParentScoring
from autogrow.docking.scoring.scoring_classes.scoring_functions.vina import... | 9,200 | 29.366337 | 89 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/docking/scoring/scoring_classes/scoring_functions/__init__.py |
"""
This imports all of the filters within the filter_children_classes file.
This is very important as the filters will not work if this doesn't exist.
This is a dynamic and modular way of doing these imports.
Code is taken from:
https://stackoverflow.com/questions/1057431/how-to-load-all-modules-in-a-folder
"""
f... | 535 | 25.8 | 92 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/docking/scoring/scoring_classes/scoring_functions/vina.py | """
This script contains the class VINA.
This is used to score Vina type docking such as QuickVina2 and Vina
"""
import __future__
import glob
import os
from autogrow.docking.scoring.scoring_classes.parent_scoring_class import ParentScoring
class VINA(ParentScoring):
"""
This will Score a given ligand for i... | 6,699 | 31.682927 | 87 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/docking/scoring/scoring_classes/scoring_functions/lig_efficiency.py | """
This script contains the class LigEfficiency.
This is used to rescore a fitness metric by the number of non-hydrogen atoms.
"""
import __future__
import rdkit
import rdkit.Chem as Chem
# Disable the unnecessary RDKit warnings
rdkit.RDLogger.DisableLog("rdApp.*")
from autogrow.docking.scoring.scoring_classes.pare... | 4,609 | 28.741935 | 87 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/docking/scoring/nn_score_exe/__init__.py | 2 | 0.5 | 1 | py | |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/docking/scoring/nn_score_exe/nnscore1/NNScore.py | # If you use NNScore in your research, please cite the following reference:
# NNScore: A Neural-Network-Based Scoring Function for the Characterization of
# Protein-Ligand Complexes. Jacob D. Durrant, J. Andrew McCammon. Journal of
# Chemical Information and Modeling, 2010, 50 (10), pp 1865-1871.
import __future__
im... | 42,353 | 39.530144 | 707 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/docking/scoring/nn_score_exe/nnscore1/__init__.py | 2 | 0.5 | 1 | py | |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/docking/scoring/nn_score_exe/nnscore2/__init__.py | 2 | 0.5 | 1 | py | |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/docking/scoring/nn_score_exe/nnscore2/NNScore2.py | # NNScore 2.02 is released under the GNU General Public License (see
# http://www.gnu.org/licenses/gpl.html). If you have any questions, comments,
# or suggestions, please don't hesitate to contact me, Jacob Durrant, at
# durrantj [at] pitt [dot] edu. If you use NNScore 2.02 in your work, please
# cite [REFERENCE HERE]... | 3,563,328 | 1,504.419941 | 171,630 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/docking/ranking/__init__.py | 1 | 0 | 0 | py | |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/docking/ranking/ranking_mol.py | """
This script runs the ranking and selection of ligands.
"""
import __future__
import os
import random
import rdkit
import rdkit.Chem as Chem
from rdkit.Chem.rdMolDescriptors import GetMorganFingerprint
from rdkit import DataStructs
# Disable the unnecessary RDKit warnings
rdkit.RDLogger.DisableLog("rdApp.*")
imp... | 15,237 | 38.785901 | 129 | py |
reinforced-genetic-algorithm | reinforced-genetic-algorithm-main/autogrow/docking/ranking/selecting/roulette_selection.py | """
This script is use to select molecules using a roulette selector
"""
import __future__
import numpy.random as rn
def spin_roulette_selector(usable_list_of_smiles, number_to_chose,
docking_or_diversity):
"""
make a list of ligands chosen by a random weighted roulette selection,
... | 3,389 | 34.3125 | 85 | py |
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