added app

.gitignore

@@ -0,0 +1,145 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+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/
+docs/_build/
+docs/modules.rst
+docs/cli_help.txt
+
+# 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/
+
+# PyCharmm idea
+.idea/
+
+#VS Code
+.vscode/
+
+# Pytest coverage output
+coverage/
+
+.DS_Store
+.AppleDouble
+.LSOverride

.streamlit/conf.toml

@@ -0,0 +1,2 @@
+[theme]
+base="light"

README.md

@@ -1,12 +1,17 @@
 ---
-title: SynPlanner
-emoji: 🐠
-colorFrom: blue
-colorTo: purple
+title: SynPlanner GUI
+emoji: 🧪
+colorFrom: pink
+colorTo: blue
 sdk: streamlit
 sdk_version: 1.37.0
 app_file: app.py
 pinned: false
+license: mit
+python_version: 3.11.9
 ---
 
-Check out the configuration reference at https://huggingface.co/docs/hub/spaces-config-reference
+# SynPlanner Graphical User Interface (GUI)
+Try the GUI to find reaction paths...
+
+**documentation to be done**

app.py

@@ -0,0 +1,263 @@
+import base64
+import pickle
+import re
+import uuid
+
+import pandas as pd
+import streamlit as st
+from CGRtools.files import SMILESRead
+from streamlit_ketcher import st_ketcher
+from huggingface_hub import hf_hub_download
+from huggingface_hub.utils import disable_progress_bars
+
+
+from synplan.mcts.expansion import PolicyNetworkFunction
+from synplan.mcts.search import extract_tree_stats
+from synplan.mcts.tree import Tree
+from synplan.chem.utils import mol_from_smiles
+from synplan.utils.config import TreeConfig, PolicyNetworkConfig
+from synplan.utils.loading import load_reaction_rules, load_building_blocks
+from synplan.utils.visualisation import generate_results_html, get_route_svg
+
+disable_progress_bars("huggingface_hub")
+
+smiles_parser = SMILESRead.create_parser(ignore=True)
+
+
+def download_button(object_to_download, download_filename, button_text, pickle_it=False):
+    """
+    Issued from
+    Generates a link to download the given object_to_download.
+    Params:
+    ------
+    object_to_download:  The object to be downloaded.
+    download_filename (str): filename and extension of file. e.g. mydata.csv,
+    some_txt_output.txt download_link_text (str): Text to display for download
+    link.
+    button_text (str): Text to display on download button (e.g. 'click here to download file')
+    pickle_it (bool): If True, pickle file.
+    Returns:
+    -------
+    (str): the anchor tag to download object_to_download
+    Examples:
+    --------
+    download_link(your_df, 'YOUR_DF.csv', 'Click to download data!')
+    download_link(your_str, 'YOUR_STRING.txt', 'Click to download text!')
+    """
+    if pickle_it:
+        try:
+            object_to_download = pickle.dumps(object_to_download)
+        except pickle.PicklingError as e:
+            st.write(e)
+            return None
+
+    else:
+        if isinstance(object_to_download, bytes):
+            pass
+
+        elif isinstance(object_to_download, pd.DataFrame):
+            object_to_download = object_to_download.to_csv(index=False).encode('utf-8')
+
+    # Try JSON encode for everything else  # else:  #     object_to_download = json.dumps(object_to_download)
+
+    try:
+        # some strings <-> bytes conversions necessary here
+        b64 = base64.b64encode(object_to_download.encode()).decode()
+
+    except AttributeError:
+        b64 = base64.b64encode(object_to_download).decode()
+
+    button_uuid = str(uuid.uuid4()).replace('-', '')
+    button_id = re.sub('\d+', '', button_uuid)
+
+    custom_css = f""" 
+        <style>
+            #{button_id} {{
+                background-color: rgb(255, 255, 255);
+                color: rgb(38, 39, 48);
+                text-decoration: none;
+                border-radius: 4px;
+                border-width: 1px;
+                border-style: solid;
+                border-color: rgb(230, 234, 241);
+                border-image: initial;
+            }} 
+            #{button_id}:hover {{
+                border-color: rgb(246, 51, 102);
+                color: rgb(246, 51, 102);
+            }}
+            #{button_id}:active {{
+                box-shadow: none;
+                background-color: rgb(246, 51, 102);
+                color: white;
+                }}
+        </style> """
+
+    dl_link = custom_css + f'<a download="{download_filename}" id="{button_id}" href="data:file/txt;base64,{b64}">{button_text}</a><br></br>'
+
+    return dl_link
+
+
+st.set_page_config(page_title="SynPlanner GUI", page_icon="🧪", layout="wide")
+
+intro_text = '''
+This is a demo of the graphical user interface of 
+[SynPlanner](https://github.com/Laboratoire-de-Chemoinformatique/SynPlanner/).
+SynPlanner is a comprehensive tool for reaction data curation, rule extraction, model training and retrosynthetic planning.
+
+More information on SynPlanner is available in the [official docs](https://synplanner.readthedocs.io/en/latest/index.html).
+'''
+
+st.title("`SynPlanner GUI`")
+
+st.write(intro_text)
+
+st.header('Molecule input')
+st.markdown(
+    '''
+    You can provide a molecular structure by either providing:
+    * SMILES string + Enter
+    * Draw it + Apply
+    '''
+)
+
+DEFAULT_MOL = 'c1cc(ccc1Cl)C(CCO)NC(C2(CCN(CC2)c3c4cc[nH]c4ncn3)N)=O'
+molecule = st.text_input("SMILES:", DEFAULT_MOL)
+smile_code = st_ketcher(molecule)
+target_molecule = mol_from_smiles(smile_code)
+
+building_blocks_path = hf_hub_download(
+        repo_id="Laboratoire-De-Chemoinformatique/SynPlanner",
+        filename="building_blocks_em_sa_ln.smi",
+        subfolder="building_blocks",
+        local_dir="."
+    )
+
+ranking_policy_weights_path = hf_hub_download(
+        repo_id="Laboratoire-De-Chemoinformatique/SynPlanner",
+        filename="ranking_policy_network.ckpt",
+        subfolder="uspto/weights",
+        local_dir="."
+    )
+
+reaction_rules_path = hf_hub_download(
+        repo_id="Laboratoire-De-Chemoinformatique/SynPlanner",
+        filename="uspto_reaction_rules.pickle",
+        subfolder="uspto",
+        local_dir="."
+    )
+
+st.header('Launch calculation')
+st.markdown(
+    '''If you modified the structure, please ensure you clicked on `Apply` (bottom right of the molecular editor).'''
+)
+st.markdown(f"The molecule SMILES is actually: ``{smile_code}``")
+
+st.subheader('Planning options')
+
+st.markdown(
+    '''
+    The description of each option can be found in the 
+    [Retrosynthetic Planning Tutorial](https://synplanner.readthedocs.io/en/latest/tutorial_files/retrosynthetic_planning.html#Configuring-search-tree).
+    '''
+)
+
+col_options_1, col_options_2 = st.columns(2, gap="medium")
+
+with col_options_1:
+    search_strategy_input = st.selectbox(label='Search strategy', options=('Expansion first', 'Evaluation first',), index=0)
+    ucb_type = st.selectbox(label='Search strategy', options=('uct', 'puct', 'value'), index=0)
+    c_ucb = st.number_input("C coefficient of UCB", value=0.1, placeholder="Type a number...")
+
+with col_options_2:
+    max_iterations = st.slider('Total number of MCTS iterations', min_value=50, max_value=300, value=100)
+    max_depth = st.slider('Maximal number of reaction steps', min_value=3, max_value=9, value=6)
+    min_mol_size = st.slider('Minimum size of a molecule to be precursor', min_value=0, max_value=7, value=0)
+
+search_strategy_translator = {
+    "Expansion first": "expansion_first",
+    "Evaluation first": "evaluation_first",
+}
+search_strategy = search_strategy_translator[search_strategy_input]
+
+submit_planning = st.button('Start retrosynthetic planning')
+
+if submit_planning:
+    with st.status("Downloading data"):
+        st.write("Downloading building blocks")
+        building_blocks = load_building_blocks(building_blocks_path, standardize=False)
+        st.write('Downloading reaction rules')
+        reaction_rules = load_reaction_rules(reaction_rules_path)
+        st.write('Loading policy network')
+        policy_config = PolicyNetworkConfig(weights_path=ranking_policy_weights_path)
+        policy_function = PolicyNetworkFunction(policy_config=policy_config)
+
+    tree_config = TreeConfig(
+        search_strategy=search_strategy,
+        evaluation_type="rollout",
+        max_iterations=max_iterations,
+        max_depth=max_depth,
+        min_mol_size=min_mol_size,
+        init_node_value=0.5,
+        ucb_type=ucb_type,
+        c_ucb=c_ucb,
+        silent=True
+    )
+
+    tree = Tree(
+        target=target_molecule,
+        config=tree_config,
+        reaction_rules=reaction_rules,
+        building_blocks=building_blocks,
+        expansion_function=policy_function,
+        evaluation_function=None,
+    )
+
+    mcts_progress_text = "Running retrosynthetic planning"
+    mcts_bar = st.progress(0, text=mcts_progress_text)
+    for step, (solved, node_id) in enumerate(tree):
+        mcts_bar.progress(step / max_iterations, text=mcts_progress_text)
+
+    res = extract_tree_stats(tree, target_molecule)
+
+    st.header('Results')
+    if res["solved"]:
+        st.balloons()
+
+        st.subheader("Examples of found retrosynthetic routes")
+
+        image_counter = 0
+        visualised_node_ids = set()
+        for n, node_id in enumerate(sorted(set(tree.winning_nodes))):
+            if image_counter == 3:
+                break
+            if n % 2 == 0 and node_id not in visualised_node_ids:
+                visualised_node_ids.add(node_id)
+                image_counter += 1
+                num_steps = len(tree.synthesis_route(node_id))
+                route_score = round(tree.route_score(node_id), 3)
+                st.image(get_route_svg(tree, node_id), caption=f"Route {node_id}; {num_steps} steps; Route score: {route_score}")
+
+        stat_col, download_col = st.columns(2, gap="medium")
+
+        with stat_col:
+            st.subheader("Statistics")
+            df = pd.DataFrame(res, index=[0])
+            st.write(df[["target_smiles", "num_routes", "num_nodes", "num_iter", "search_time"]])
+
+        with download_col:
+            st.subheader("Downloads")
+            html_body = generate_results_html(tree, html_path=None, extended=True)
+            dl_html = download_button(html_body, 'results_synplanner.html', 'Download results as a HTML file')
+
+            dl_csv = download_button(pd.DataFrame(res, index=[0]), 'results_synplanner.csv',
+                                     'Download statistics as a csv file')
+            st.markdown(dl_html + dl_csv, unsafe_allow_html=True)
+
+    else:
+        st.write("Found no reaction path.")
+
+st.divider()
+st.header('Restart from the beginning?')
+if st.button("Restart"):
+    st.rerun()

pre-requirements.txt

@@ -0,0 +1,2 @@
+--find-links https://download.pytorch.org/whl/torch_stable.html
+torch==2.2.2+cpu

requirements.txt

@@ -0,0 +1,3 @@
+streamlit
+streamlit_ketcher
+git+https://github.com/Laboratoire-de-Chemoinformatique/SynPlanner.git