decimer 2.2.2__tar.gz → 2.3.0__tar.gz

decimer-2.3.0/.github/ISSUE_TEMPLATE/Bug_Report.yml

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+name: DECIMER issue template
+description: >-
+  To report any DECIMER Image Transformer related issue please use this
+  template. Please report data/security related issue by directly sending us an
+  email.
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thanks for taking the time to fill out this bug report!
+  - type: markdown
+    attributes:
+      value: >
+        Please make sure that this is a bug. As per our [GitHub
+        Policy](https://github.com/Kohulan/DECIMER-Image_Transformer/blob/master/ISSUES.md).    
+  - type: dropdown
+    id: issue-type
+    attributes:
+      label: Issue Type
+      description: What type of issue would you like to report?
+      multiple: false
+      options:
+        - Bug
+        - Build/Install
+        - Performance
+        - Support
+        - Feature Request
+        - Documentation Feature Request
+        - Questions
+    validations:
+      required: true
+  - type: dropdown
+    id: source
+    attributes:
+      label: Source
+      description: DECIMER Image Transformer installed from
+      options:
+        - GitHub (source)
+        - PyPi
+    validations:
+      required: true
+  - type: input
+    id: decimerversion
+    attributes:
+      label: DECIMER Image Transformer Version
+      description: null
+      placeholder: 'ex,. 2.0.0'
+    validations:
+      required: true
+  - type: input
+    id: OS
+    attributes:
+      label: OS Platform and Distribution
+      description: null
+      placeholder: 'e.g., Linux Ubuntu 16.04'
+    validations:
+      required: false
+  - type: input
+    id: Python
+    attributes:
+      label: Python version
+      description: null
+      placeholder: 'e.g., 3.9'
+    validations:
+      required: false
+  - type: textarea
+    id: what-happened
+    attributes:
+      label: Current Behaviour?
+      description: 'Also tell us, what did you expect to happen?'
+      placeholder: Tell us what you see!
+      value: A bug happened!
+    validations:
+      required: true
+  - type: textarea
+    id: screenshot
+    attributes:
+      label: Which images caused the issue? (This is mandatory for images related issues)
+      description: Please ensure that an image depicting the cause of the bug or the inaccuracy of the prediction is included.
+      placeholder: Attach the image
+    validations:
+      required: false
+  - type: textarea
+    id: code-to-reproduce
+    attributes:
+      label: Standalone code to reproduce the issue
+      description: >-
+        Provide a reproducible test case that is the bare minimum necessary to
+        generate the problem. If possible, please share a link to
+        Colab/Jupyter/any notebook.
+      placeholder: Tell us what you see!
+      value: null
+      render: shell
+    validations:
+      required: true
+  - type: textarea
+    id: logs
+    attributes:
+      label: Relevant log output
+      description: >-
+        Please copy and paste any relevant log output. This will be
+        automatically formatted into code, so no need for backticks.
+      render: shell
+  - type: checkboxes
+    id: terms
+    attributes:
+      label: Code of Conduct
+      description: >-
+        By submitting this issue, you agree to follow our [Code of
+        Conduct](https://github.com/Kohulan/DECIMER-Image_Transformer/blob/master/CODE_OF_CONDUCT.md)
+      options:
+        - label: I agree to follow this project's Code of Conduct
+          required: true

decimer-2.3.0/.github/workflows/Check_errors.yml

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+# This is a basic workflow to help you get started with Actions
+
+name: Error checking and testing
+
+# Controls when the workflow will run
+on:
+  # Triggers the workflow on push or pull request events but only for the main branch
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.10']
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v1
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install basic dependencies
+        run: |
+          python -m pip install --upgrade pip
+      - name: Test with tox
+        run: |
+          pip install -e .
+          pip install tox
+          tox

decimer-2.3.0/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+.vscode
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+.DS_Store

decimer-2.3.0/.readthedocs.yml

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+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+
+# Optionally build your docs in additional formats such as PDF
+formats:
+  - pdf
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+  version: "3.8"
+  install:
+    - requirements: docs/requirements.txt

decimer-2.3.0/Benchmark/README.md

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+# Benchmark results
+
+This is a collection of scripts for running the benchmarks described in our publication.
+
+_________________
+
+## In order to replicate the benchmark results, it is necessary to install RDKit.
+
+```
+conda install -c rdkit rdkit
+``` 
+
+## The slight distortions (shearing, rotation) are applied to the benchmark images by running:
+
+```
+python distort_images $input_directory $output_directory
+```
+
+## Run DECIMER and save the results in a file:
+```
+python run_decimer_save_results.py $image_dir $benchmark_ID
+```
+
+- The results of the benchmark run are going to be save in $benchmark_ID.txt which contains the image names and the results (SMILES representation of the depicted molecule)
+- Per line: $image_name \t $SMILES
+
+## Evaluate the benchmark results:
+```
+python evaluate_benchmarks.py $benchmark_ID.txt $reference_file_directory
+```
+- $benchmark_ID.txt is the output generated by run_decimer_save_results.py
+- $reference_file_directory is the path of a directory that contains SD- or mol-files as provided in the benchmark datasets

decimer-2.3.0/Benchmark/TEST.txt

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+DECIMER_test_0.png	C1=CC=C(C=C1)CC2=C(C3=CC=C(C=C3)OS(=O)(=O)C(F)(F)F)C4=C(C=CC=C4)O2
+DECIMER_test_1.png	CCCCC1=CC=CC=C1
+github_issue_test.png	CC(CC1=CC2=C(C=C1)OCO2)NC

decimer-2.3.0/Benchmark/distort_images.py

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+import sys
+import os
+from multiprocessing import Pool
+import numpy as np
+from skimage.io import imread, imsave
+import imgaug.augmenters as iaa
+
+
+def distort_image(input_image_path: str, output_image_path: str) -> None:
+    """
+    This function takes the path of an input image and the desired output image path (both str).
+    It rotates the input image randomly (-5° or +5°) and applies shearing (in x or y-direction with an
+    angle of -9° or 9°) as described by Clevert et al (Img2Mol (preprint)).
+    I was a bit confused about the "shearing factor" of +/- 0.1 described by Clevert et al. Normally the transformation
+    is done with a shearing angle. I assume here that the correponding angle is 0.1*90° = 9° as 90° is the extreme case
+    where the image turns into a horizontal or vertical line.
+    This seems reasonable as it results in a mild distortion as described by the authors.
+
+    Args:
+            input_image_path (str): Path of input image
+            output_image_path (str): Path where the output image is saved
+    """
+    image = imread(input_image_path)
+    # Add a one-pixel-layer of white pixels so that we can simply take that as a reference what to fill
+    # the blank space with when we apply the transformations
+    image = np.pad(image, pad_width=1, mode="constant", constant_values=255)
+    augmentation = iaa.Sequential(
+        [
+            iaa.Affine(rotate=[-5, 5], mode="edge", fit_output=True),
+            iaa.OneOf(
+                [
+                    iaa.geometric.ShearX([-9, 9], mode="edge", fit_output=True),
+                    iaa.geometric.ShearY([-9, 9], mode="edge", fit_output=True),
+                ]
+            ),
+        ]
+    )
+    image = augmentation(images=[image])[0]
+    imsave(fname=output_image_path, arr=image)
+    return
+
+
+def main():
+    """This script takes an input directory with images of chemical structure depictions, applies a random
+    rotation (-5° or +5°) as well as shearing (angle drawn from [-0.1, 0.1]) to every input image. These
+    distortions are supposed to imitate the image modifications described by Clevert et al (Img2Mol (preprint))"""
+    input_dir = os.path.abspath(sys.argv[1])
+    output_dir = os.path.abspath(sys.argv[2])
+    if not os.path.exists(output_dir):
+        os.mkdir(output_dir)
+    starmap_iterable = [
+        (os.path.join(input_dir, image_name), os.path.join(output_dir, image_name))
+        for image_name in os.listdir(input_dir)
+        if image_name[-3:].lower() == "png"
+    ]
+    with Pool(5) as p:
+        _ = p.starmap(distort_image, starmap_iterable)
+
+
+if __name__ == "__main__":
+    if len(sys.argv) != 3:
+        print("Usage: {} input_dir output_dir".format(sys.argv[0]))
+    else:
+        main()

decimer-2.3.0/Benchmark/evaluate_benchmarks.py

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+import sys
+import os
+from rdkit import Chem, DataStructs
+
+
+def compare_molecules_inchi_match(
+    input_file_path: str, reference_directory: str
+) -> None:
+    """
+    This function checks if the molecules in the DECIMER results to a set of reference
+    mol-files using Standard InChI.
+
+    Args:
+            input_file (str): Path of file that contains image names and SMILES as created by run_decimer_save_results.py
+            reference_directory (str): Path of directory with mol/sd files as they come with the benchmark datasets
+    """
+    """"""
+    # We assume that the input file has the structure $img_name\t$smiles\n per line
+    tanimoto_list = []
+    perfect_match_count = 0
+    with open(input_file_path, "r") as input_file:
+        lines = input_file.readlines()
+        # assert len(os.listdir(reference_directory)) == len(lines)
+        for line in lines:
+            ID, smiles = line.split("\t")
+            smiles = smiles[:-1]  # Delete \n at the end
+            # Generate mol objects
+            input_mol = Chem.MolFromSmiles(smiles)
+            if input_mol:
+                for format in [".mol", ".sdf", ".MOL"]:
+                    if os.path.exists(
+                        os.path.join(reference_directory, ID[:-4] + format)
+                    ):
+                        reference_mol_suppl = Chem.SDMolSupplier(
+                            os.path.join(reference_directory, ID[:-4] + format)
+                        )
+
+                # Generate Inchi
+                input_inchi = Chem.inchi.MolToInchi(
+                    input_mol
+                )  # rdmolfiles.MolToSmiles(input_mol, True)
+                for reference_mol in reference_mol_suppl:
+                    if reference_mol:
+                        reference_inchi = Chem.inchi.MolToInchi(
+                            reference_mol
+                        )  # .rdmolfiles.MolToSmiles(reference_mol, True)#
+
+                        # Count perfect InChI string match
+                        if input_inchi == reference_inchi:
+                            perfect_match_count += 1
+
+                        # Generate fingerprints and Tanimoto similarity
+                        reference_fp = Chem.RDKFingerprint(reference_mol)
+                        input_fp = Chem.RDKFingerprint(input_mol)
+                        tanimoto = DataStructs.FingerprintSimilarity(
+                            reference_fp, input_fp
+                        )
+                        tanimoto_list.append(tanimoto)
+                        break
+
+    print(
+        "{} out of {} ({}%)".format(
+            perfect_match_count, len(lines), perfect_match_count / len(lines) * 100
+        )
+    )
+    print("Average Tanimoto: {}".format(sum(tanimoto_list) / len(tanimoto_list)))
+    tanimoto_one_count = len(
+        [tanimoto for tanimoto in tanimoto_list if tanimoto == 1.0]
+    )
+    print(
+        "Tanimoto 1.0 count: {} out of {} ({}%)".format(
+            tanimoto_one_count, len(lines), tanimoto_one_count / len(lines)
+        )
+    )
+
+
+def main():
+    if len(sys.argv) != 3:
+        print(
+            '"Usage of this function: {} decimer_benchmark_results_file directory-with-reference-molfiles'.format(
+                sys.argv[0]
+            )
+        )
+    if len(sys.argv) == 3:
+        compare_molecules_inchi_match(sys.argv[1], sys.argv[2])
+    sys.exit(1)
+
+
+if __name__ == "__main__":
+    main()

decimer-2.3.0/Benchmark/run_decimer_save_results.py

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+import sys
+import os
+
+from DECIMER import predict_SMILES
+
+
+def main():
+    """
+    This script runs Decimer on every image in a given directory (first argument) and saves the
+    results in a text file with a given ID (second argument).
+    """
+    im_path = sys.argv[1]
+    save_ID = sys.argv[2]
+
+    # Don't start from beginning if a benchmark run aborted for some reason
+    with open("{}.txt".format(save_ID), "a+") as output:
+        lines = output.readlines()
+        already_processed = list([line.split("\t")[0] for line in lines])
+
+    for im in os.listdir(im_path):
+        if im not in already_processed:
+            with open("{}.txt".format(save_ID), "a") as output:
+                smiles = predict_SMILES(os.path.join(im_path, im))
+                output.write("{}\t{}\n".format(im, smiles))
+                already_processed.append(im)
+                print(im)
+
+
+if __name__ == "__main__":
+    if len(sys.argv) == 3:
+        main()
+    else:
+        print("Usage: {} image_dir benchmark_ID".format(sys.argv[0]))

decimer-2.3.0/CITATION.cff

@@ -0,0 +1,18 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+authors:
+  - family-names: "Rajan"
+    given-names: "Kohulan"
+    orcid: "https://orcid.org/0000-0003-1066-7792"
+  - family-names: "Zielesny"
+    given-names: "Achim"
+    orcid: "https://orcid.org/0000-0003-0722-4229"
+  - family-names: "Steinbeck"
+    given-names: "Christoph"
+    orcid: "https://orcid.org/0000-0001-6966-0814"  
+title: "DECIMER-V2"
+version: 2.2.0
+doi: 10.5281/zenodo.7655952
+date-released: 2022.05.18
+url: "https://github.com/Kohulan/DECIMER-Image_Transformer-2"
+license: MIT

decimer-2.3.0/CODE_OF_CONDUCT.md

@@ -0,0 +1,128 @@
+# DECIMER Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, religion, or sexual identity
+and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the
+  overall community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or
+  advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email
+  address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+kohulan.rajan@uni-jena.de or otto.brinkhaus@uni-jena.de.
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series
+of actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or
+permanent ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior,  harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within
+the community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.0, available at
+https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.
+
+Community Impact Guidelines were inspired by [Mozilla's code of conduct
+enforcement ladder](https://github.com/mozilla/diversity).
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see the FAQ at
+https://www.contributor-covenant.org/faq. Translations are available at
+https://www.contributor-covenant.org/translations.