Minor bug fixes

app/fn.py

@@ -23,6 +23,7 @@ from rdkit.Chem import Crippen, Descriptors, rdMolDescriptors, Lipinski, rdmolop
 import requests
 
 from app import static
+from app.main import COL_ALIASES
 
 sys.path.append(str(Path(RDConfig.RDContribDir) / 'SA_Score'))
 import sascorer
@@ -393,18 +394,9 @@ def read_molecule_file(in_file, allowed_extentions):
 
 def create_result_table_html(summary_df, result_info, opts=(), progress=gr.Progress(track_tqdm=True)):
     html_df = summary_df.copy().drop(columns=['mol'])
-    column_aliases = {
-        'out_path': 'Pose',
-        'ligand_conf_path': 'Pose',
-        'ID1': 'Compound ID',
-        'ID2': 'Target ID',
-        'X1': 'Fragment SMILES',
-        'X1^': 'Compound SMILES',
-        'name': 'Complex Name',
-    }
     output_dir = Path(result_info['output_dir'])
     job_type = result_info['type']
-    html_df.rename(columns=column_aliases, inplace=True)
+    html_df.rename(columns=COL_ALIASES, inplace=True)
     html_df['Pose'] = html_df['Pose'].apply(lambda x: str(output_dir / job_type / x))
     # drop remaining columns ending with '_path'
     hidden_cols = [col for col in html_df.columns if col.endswith('_path')]

app/main.py

@@ -54,6 +54,15 @@ POCKET_EXTRACT_OPTS = {
     }
 }
 
+COL_ALIASES = {
+    'out_path': 'Pose',
+    'ligand_conf_path': 'Pose',
+    'ID1': 'Compound ID',
+    'ID2': 'Target ID',
+    'X1': 'Fragment SMILES',
+    'X1^': 'Compound SMILES',
+    'name': 'Complex Name',
+}
 
 def gr_error_wrapper(func):
     def wrapper(*args, **kwargs):
@@ -73,7 +82,6 @@ def query_job_status(job_id):
             job = job_db.job_lookup(job_id)
             if job:
                 if job['status'] == "RUNNING":
-                    sleep(5)
                     yield {
                         pred_lookup_status: f'''
 Your  job (ID: **{job['id']}**) started at **{job['start_time']}** and is **RUNNING...**
@@ -82,21 +90,17 @@ It might take a few minutes up to a few hours depending on the input size and th
 You may keep the page open and wait for job completion, or close the page and revisit later to look up the job status 
 using the job id. You will also receive an email notification once the job is done.
 ''',
-                        pred_lookup_btn: gr.Button(visible=False),
-                        pred_lookup_stop_btn: gr.Button(visible=True)
                     }
                 if job['status'] == "COMPLETED":
                     stop = True
-                    msg = f"Your GenFBDD job (ID: {job['id']}) has been COMPLETED"
-                    msg += f" at {job['end_time']}" if job.get('end_time') else ""
-                    msg += f" and the results will expire by {job['expiry_time']}." if job.get('expiry_time') else "."
+                    msg = f"Your GenFBDD job (ID: {job['id']}) has been **COMPLETED**"
+                    msg += f" at **{job['end_time']}**" if job.get('end_time') else ""
+                    msg += f" and the results will **EXPIRE** by **{job['expiry_time']}**." if job.get('expiry_time') else "."
                     msg += f' Redirecting to the Results page...'
 
                     gr.Info(msg)
                     yield {
                         pred_lookup_status: msg,
-                        pred_lookup_btn: gr.Button(visible=True),
-                        pred_lookup_stop_btn: gr.Button(visible=False),
                         tabs: gr.Tabs(selected='result'),
                         result_state: job
                     }
@@ -110,7 +114,6 @@ using the job id. You will also receive an email notification once the job is do
                         pred_lookup_status: msg,
                         pred_lookup_btn: gr.Button(visible=True),
                         pred_lookup_stop_btn: gr.Button(visible=False),
-                        tabs: gr.Tabs(selected='job'),
                     }
             else:
                 stop = (retry > 2)
@@ -120,13 +123,12 @@ using the job id. You will also receive an email notification once the job is do
                     msg = f'Job ID {job_id} not found after {retry} retries. Please double-check the job ID.'
                 gr.Info(msg)
                 retry += 1
-                sleep(5)
                 yield {
                     pred_lookup_status: msg,
-                    pred_lookup_btn: gr.Button(visible=True),
-                    pred_lookup_stop_btn: gr.Button(visible=False),
-                    tabs: gr.Tabs(selected='job'),
+                    pred_lookup_btn: gr.Button(visible=stop),
+                    pred_lookup_stop_btn: gr.Button(visible=stop),
                 }
+            sleep(5)
 
         except Exception as e:
             raise gr.Error(f'Failed to retrieve job status due to error: {str(e)}')
@@ -211,8 +213,8 @@ def dock_link(
     config = OmegaConf.load('configs/gen_fbdd_v1.yaml')
     device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')
     print(f'Using device: {device}')
-    date_time = datetime.now().strftime("%Y-%m-%d_%H-%M-%S.%f")
-    out_dir = f'results/{date_time}'
+    date_time = datetime.now().strftime("%Y-%m-%d_%H-%M-%S")
+    out_dir = f'results/{date_time}_{job_id}'
     frag_lib['X2'] = prot
     frag_lib['ID2'] = Path(prot).stem
 
@@ -333,189 +335,184 @@ with gr.Blocks(theme=THEME, title='GenFBDD', css=static.CSS, delete_cache=(3600,
     run_state = gr.State(value={})
     session_state = gr.State(value={})
 
-    # script_init_frame = gr.HTML(static.PROTEIN_VIEW_IFRAME)
     with gr.Tabs() as tabs:
         with gr.Tab(label='Start', id='start'):
-            gr.Markdown('''
-                # GenFBDD - A Fragment-Based Drug Design Protocol Based on SOTA Molecular Generative Models
-                
-                Given a fragment library and a target protein, GenFBDD blindly docks the fragments to the 
-                protein and generates linkers connecting the selected fragments, generating novel scaffolds 
-                or drug-like molecules with desirable binding conformations.
-            ''')
-            with gr.Row():
-                with gr.Column(variant='panel'):
-                    gr.Markdown('## Chemical Fragment Library')
-                    # Fragment settings
-                    frag_lib_dropdown = gr.Dropdown(
-                        label='Select a Preset Fragment Library',
-                        choices=list(FRAG_LIBS.keys()),
-                        value='',
-                    )
-                    # with gr.Row():
-                    #     gr.File(label='Example SDF fragment library',
-                    #             value='data/examples/fragment_library.sdf', interactive=False)
-                    #     gr.File(label='Example CSV fragment library',
-                    #             value='data/examples/fragment_library.csv', interactive=False)
-                    frag_lib_upload_btn = gr.UploadButton(
-                        label='OR Upload Your Own Library', variant='primary', interactive=True,
-                    )
-
-                    frag_lib_file = gr.File(
-                        value=None, label='Fragment Library File (Original)',
-                        file_count='single', file_types=['.sdf', '.csv'],
-                        interactive=False, visible=False
-                    )
-                    frag_lib_orig_df = gr.State(value=pd.DataFrame(columns=['X1', 'ID1', 'mol']))
-                    frag_lib_mod_df = gr.State(value=pd.DataFrame(columns=['X1', 'ID1', 'mol']))
-                    # TODO: Tabulator with gr.HTML() for fragment library preview
-                    frag_lib_view = gr.DataFrame(
-                        value=pd.DataFrame(columns=['X1', 'ID1']), elem_id='frag_lib_view',
-                        visible=True, interactive=False,
-                    )
-
-                    with gr.Group():
-                        frag_lib_process_opts = gr.CheckboxGroup(
-                            label='Fragment Preparation Options',
-                            info='1) All fragments consisting of multiple fragments will be split into individual '
-                                 'fragments. 2) All fragments consisting of a single heavy atom will be discarded. '
-                                 '3) All fragments will then be processed in the order of the selected options. '
-                                 '4) Finally, fragments will be deduplicated based on their SMILES.',
-                            choices=list(FRAG_LIB_PROCESS_OPTS.keys()),
-                            value=['Dehalogenate Fragments', 'Discard Inorganic Fragments'],
-                            interactive=True,
-                        )
-                        frag_lib_process_btn = gr.Button(
-                            value='Process Fragments', variant='primary', interactive=True,
-                        )
-                    # Fragment library preview
-
-                with gr.Column(variant='panel'):
-                    gr.Markdown('## Target Protein Structure')
-                    # Protein settings
-                    with gr.Row(equal_height=True):
-                        prot_query_dropdown = gr.Dropdown(
-                            label='Select a Protein Structure Query Strategy',
-                            choices=[
-                                'PDB ID',
-                                'UniProt ID',
-                                'FASTA Sequence',
-                            ],
-                            interactive=True,
-                            scale=4
+            with gr.Column(variant='panel'):
+                gr.Markdown('''
+                    # GenFBDD - A Fragment-Based Drug Design Protocol Based on SOTA Molecular Generative Models
+                    
+                    Given a fragment library and a target protein, GenFBDD blindly docks the fragments to the 
+                    protein and generates linkers connecting the selected fragments, generating novel scaffolds 
+                    or drug-like molecules with desirable binding conformations.
+                ''')
+                with gr.Row():
+                    with gr.Column(variant='panel'):
+                        gr.Markdown('## Chemical Fragment Library')
+                        # Fragment settings
+                        frag_lib_dropdown = gr.Dropdown(
+                            label='Select a Preset Fragment Library',
+                            choices=list(FRAG_LIBS.keys()),
+                            value='',
                         )
-                        prot_query_input = gr.Textbox(
-                            show_label=False, placeholder='Enter the protein query here',
-                            scale=3, interactive=True
+                        frag_lib_upload_btn = gr.UploadButton(
+                            label='OR Upload Your Own Library', variant='primary', interactive=True,
                         )
 
-                    with gr.Row():
-                        prot_query_btn = gr.Button(
-                            value='Query', variant='primary',
-                            scale=1, interactive=True
+                        frag_lib_file = gr.File(
+                            value=None, label='Fragment Library File (Original)',
+                            file_count='single', file_types=['.sdf', '.csv'],
+                            interactive=False, visible=False
                         )
-                        prot_upload_btn = gr.UploadButton(
-                            label='OR Upload Your PDB/FASTA File', variant='primary',
-                            file_types=['.pdb', '.fasta'],
-                            scale=2,  interactive=True,
+                        frag_lib_orig_df = gr.State(value=pd.DataFrame(columns=['X1', 'ID1', 'mol']))
+                        frag_lib_mod_df = gr.State(value=pd.DataFrame(columns=['X1', 'ID1', 'mol']))
+                        # TODO: Tabulator with gr.HTML() for fragment library preview
+                        frag_lib_view = gr.DataFrame(
+                            value=pd.DataFrame(columns=['X1', 'ID1']), elem_id='frag_lib_view',
+                            visible=True, interactive=False,
                         )
 
-                    input_prot_file = gr.File(
-                        value=None, label='Protein Structure File (Original)',
-                        interactive=False, visible=False, file_count='single',
-                    )
-                    input_prot_view = gr.HTML(value='<div id="input_protein_view" class="mol-container"></div>')
-
-                    with gr.Group():
-                        pocket_extract_dropdown = gr.Dropdown(
-                            label='Select a Pocket Extraction Method',
-                            choices=list(POCKET_EXTRACT_OPTS.keys()),
-                            info=POCKET_EXTRACT_OPTS[list(POCKET_EXTRACT_OPTS.keys())[0]]['info'],
-                            value=list(POCKET_EXTRACT_OPTS.keys())[0],
-                            interactive=True,
+                        with gr.Group():
+                            frag_lib_process_opts = gr.CheckboxGroup(
+                                label='Fragment Preparation Options',
+                                info='1) All fragments consisting of multiple fragments will be split into individual '
+                                     'fragments. 2) All fragments consisting of a single heavy atom will be discarded. '
+                                     '3) All fragments will then be processed in the order of the selected options. '
+                                     '4) Finally, fragments will be deduplicated based on their SMILES.',
+                                choices=list(FRAG_LIB_PROCESS_OPTS.keys()),
+                                value=['Dehalogenate Fragments', 'Discard Inorganic Fragments'],
+                                interactive=True,
+                            )
+                            frag_lib_process_btn = gr.Button(
+                                value='Process Fragments', variant='primary', interactive=True,
+                            )
+                        # Fragment library preview
+
+                    with gr.Column(variant='panel'):
+                        gr.Markdown('## Target Protein Structure')
+                        # Protein settings
+                        with gr.Row(equal_height=True):
+                            prot_query_dropdown = gr.Dropdown(
+                                label='Select a Protein Structure Query Strategy',
+                                choices=[
+                                    'PDB ID',
+                                    'UniProt ID',
+                                    'FASTA Sequence',
+                                ],
+                                interactive=True,
+                                scale=4
+                            )
+                            prot_query_input = gr.Textbox(
+                                show_label=False, placeholder='Enter the protein query here',
+                                scale=3, interactive=True
+                            )
+
+                        with gr.Row():
+                            prot_query_btn = gr.Button(
+                                value='Query', variant='primary',
+                                scale=1, interactive=True
+                            )
+                            prot_upload_btn = gr.UploadButton(
+                                label='OR Upload Your PDB/FASTA File', variant='primary',
+                                file_types=['.pdb', '.fasta'],
+                                scale=2,  interactive=True,
+                            )
+
+                        input_prot_file = gr.File(
+                            value=None, label='Protein Structure File (Original)',
+                            interactive=False, visible=False, file_count='single',
                         )
-                        selected_pocket = gr.Textbox(visible=False)
-                        selected_ligand = gr.Textbox(visible=False)
-                        pocket_files = gr.Files(visible=False)
-                        pocket_extract_btn = gr.Button(
-                            value='Extract Pocket', variant='primary', interactive=True
-                        )
-                        # Target protein preview
-            with gr.Row():
-                with gr.Column(variant='panel'):
-                    gr.Markdown('## Dock Phase Settings')
-                    dock_n_poses = gr.Slider(
-                        value=5, minimum=1, maximum=20, step=1,
-                        label="Number of conformers to generate per fragment",
-                        interactive=True
-                    )
-                    dock_confidence_cutoff = gr.Slider(
-                        value=-1.0, minimum=-2.0, maximum=0, step=0.1,
-                        label="Confidence cutoff for filtering conformers of docked fragments (>0: high, <=-1.5: low)",
-                        interactive=True
-                    )
-                    with gr.Accordion(label='Advanced Options', open=False):
-                        dock_model = gr.Dropdown(
-                            label='Select a Fragment Docking Model',
-                            choices=['DiffDock-L'],
-                            interactive=True,
+                        input_prot_view = gr.HTML(value='<div id="input_protein_view" class="mol-container"></div>')
+
+                        with gr.Group():
+                            pocket_extract_dropdown = gr.Dropdown(
+                                label='Select a Pocket Extraction Method',
+                                choices=list(POCKET_EXTRACT_OPTS.keys()),
+                                info=POCKET_EXTRACT_OPTS[list(POCKET_EXTRACT_OPTS.keys())[0]]['info'],
+                                value=list(POCKET_EXTRACT_OPTS.keys())[0],
+                                interactive=True,
+                            )
+                            selected_pocket = gr.Textbox(visible=False)
+                            selected_ligand = gr.Textbox(visible=False)
+                            pocket_files = gr.Files(visible=False)
+                            pocket_extract_btn = gr.Button(
+                                value='Extract Pocket', variant='primary', interactive=True
+                            )
+                            # Target protein preview
+                with gr.Row():
+                    with gr.Column(variant='panel'):
+                        gr.Markdown('## Dock Phase Settings')
+                        dock_n_poses = gr.Slider(
+                            value=5, minimum=1, maximum=20, step=1,
+                            label="Number of conformers to generate per fragment",
+                            interactive=True
                         )
-                        dock_steps = gr.Slider(
-                            minimum=20, maximum=40, step=1,
-                            label="Number of Denoising Steps for Docking Fragments",
+                        dock_confidence_cutoff = gr.Slider(
+                            value=-1.0, minimum=-2.0, maximum=0, step=0.1,
+                            label="Confidence cutoff for filtering conformers of docked fragments (>0: high, <=-1.5: low)",
                             interactive=True
                         )
-                with gr.Column(variant='panel'):
-                    gr.Markdown('## Link Phase Settings')
-                    link_frag_pose_strategy = gr.Radio(
-                        label='Select a Fragment-Conformer Linking Strategy',
-                        choices=[
-                            'Link Pairs of Fragment-Conformers Contacting the Pocket',
-                            # 'Link Maximal Fragment-Conformers Spanning the Entire Pocket',
-                        ],
-                        value='Link Pairs of Fragment-Conformers Contacting the Pocket',
-                    )
-                    link_frag_dist_range = RangeSlider(
-                        value=[2, 8], minimum=1, maximum=10, step=1,
-                        label="Fragment-Conformer Distance Range (Å) Eligible for Linking",
-                        interactive=True
-                    )
-                    link_n_mols = gr.Slider(
-                        value=10, minimum=1, maximum=20, step=1,
-                        label="Number of molecules to generate per fragment conformer combination",
-                        interactive=True
-                    )
-                    with gr.Accordion(label='Advanced Options', open=False):
-                        link_model = gr.Dropdown(
-                            label='Select a Linker Generation Model',
-                            choices=['DiffLinker'],
-                            interactive=True,
+                        with gr.Accordion(label='Advanced Options', open=False):
+                            dock_model = gr.Dropdown(
+                                label='Select a Fragment Docking Model',
+                                choices=['DiffDock-L'],
+                                interactive=True,
+                            )
+                            dock_steps = gr.Slider(
+                                minimum=20, maximum=40, step=1,
+                                label="Number of Denoising Steps for Docking Fragments",
+                                interactive=True
+                            )
+                    with gr.Column(variant='panel'):
+                        gr.Markdown('## Link Phase Settings')
+                        link_frag_pose_strategy = gr.Radio(
+                            label='Select a Fragment-Conformer Linking Strategy',
+                            choices=[
+                                'Link Pairs of Fragment-Conformers Contacting the Pocket',
+                                # 'Link Maximal Fragment-Conformers Spanning the Entire Pocket',
+                            ],
+                            value='Link Pairs of Fragment-Conformers Contacting the Pocket',
                         )
-                        link_linker_size = gr.Slider(
-                            minimum=0, maximum=20, step=1,
-                            label="Linker Size",
-                            info="0: automatically predicted; >=1: fixed size",
+                        link_frag_dist_range = RangeSlider(
+                            value=[2, 8], minimum=1, maximum=10, step=1,
+                            label="Fragment-Conformer Distance Range (Å) Eligible for Linking",
                             interactive=True
                         )
-                        link_steps = gr.Slider(
-                            minimum=100, maximum=500, step=10,
-                            label="Number of Denoising Steps for Generating Linkers",
+                        link_n_mols = gr.Slider(
+                            value=10, minimum=1, maximum=20, step=1,
+                            label="Number of molecules to generate per fragment conformer combination",
                             interactive=True
                         )
-            with gr.Row(equal_height=True):
-                email_input =gr.Textbox(
-                    label='Email Address (Optional)',
-                    info="Your email address will be used to notify you of the status of your job. "
-                         "If you cannot receive the email, please check your spam/junk folder.",
-                    type='email'
-                )
-                with gr.Column():
-                    start_clr_btn = gr.ClearButton(
-                        value='Reset Inputs', interactive=True,
-                    )
-                    run_btn = gr.Button(
-                        value='Run GenFBDD', variant='primary', interactive=True,
+                        with gr.Accordion(label='Advanced Options', open=False):
+                            link_model = gr.Dropdown(
+                                label='Select a Linker Generation Model',
+                                choices=['DiffLinker'],
+                                interactive=True,
+                            )
+                            link_linker_size = gr.Slider(
+                                minimum=0, maximum=20, step=1,
+                                label="Linker Size",
+                                info="0: automatically predicted; >=1: fixed size",
+                                interactive=True
+                            )
+                            link_steps = gr.Slider(
+                                minimum=100, maximum=500, step=10,
+                                label="Number of Denoising Steps for Generating Linkers",
+                                interactive=True
+                            )
+                with gr.Row(equal_height=True):
+                    email_input =gr.Textbox(
+                        label='Email Address (Optional)',
+                        info="Your email address will be used to notify you of the status of your job. "
+                             "If you cannot receive the email, please check your spam/junk folder.",
+                        type='email'
                     )
+                    with gr.Column():
+                        start_clr_btn = gr.ClearButton(
+                            value='Reset Inputs', interactive=True,
+                        )
+                        run_btn = gr.Button(
+                            value='Run GenFBDD', variant='primary', interactive=True,
+                        )
         with gr.Tab(label='Results', id='result'):
             # Results
             result_state = gr.State(value={})
@@ -554,9 +551,10 @@ with gr.Blocks(theme=THEME, title='GenFBDD', css=static.CSS, delete_cache=(3600,
                         label='Input Your Job ID', placeholder='e.g., e9dfd149-3f5c-48a6-b797-c27d027611ac',
                         info="Your job ID is a UUID4 string that you receive after submitting a job on the "
                              "page or in the email notification.")
+                    pred_lookup_example = gr.Button('Example', elem_classes=['example'], scale=1)
                     pred_lookup_btn = gr.Button(value='Lookup the Job Status', variant='primary', visible=True)
                     pred_lookup_stop_btn = gr.Button(value='Stop Tracking', variant='stop', visible=False)
-                    pred_lookup_status = gr.Markdown()
+                    pred_lookup_status = gr.Markdown("**Job Status**", container=True)
 
     # Event handlers
     ## Start tab
@@ -755,30 +753,32 @@ with gr.Blocks(theme=THEME, title='GenFBDD', css=static.CSS, delete_cache=(3600,
     )
 
     ### Job Status
-    user_job_lookup = pred_lookup_btn.click(
+    pred_lookup_btn.click(
         fn=lambda: '<div class="loader"></ div>',
         outputs=loader_html,
-    ).success(
+    )
+    user_job_lookup = pred_lookup_btn.click(
         fn=query_job_status,
         inputs=[pred_lookup_id],
-        outputs=[pred_lookup_status, pred_lookup_btn, pred_lookup_stop_btn, tabs, result_state],
+        outputs=[pred_lookup_status, tabs, result_state, pred_lookup_btn, pred_lookup_stop_btn],
         show_progress='minimal',
     ).success(
         lambda: '<div class="loader first-frame"></ div>',
         outputs=loader_html,
     )
 
-    auto_job_lookup =job_valid.success(
+    job_valid.success(
         fn=lambda job: [job['id'], gr.Tabs(selected='job')],
         inputs=[run_state],
         outputs=[pred_lookup_id, tabs],
     ).success(
         lambda: '<div class="loader"></ div>',
         outputs=loader_html,
-    ).success(
+    )
+    auto_job_lookup = job_valid.success(
         fn=query_job_status,
         inputs=pred_lookup_id,
-        outputs=[pred_lookup_status, pred_lookup_btn, pred_lookup_stop_btn, tabs, result_state],
+        outputs=[pred_lookup_status, tabs, result_state, pred_lookup_btn, pred_lookup_stop_btn],
         show_progress='minimal',
         cancels=[user_job_lookup],
     ).success(
@@ -790,12 +790,22 @@ with gr.Blocks(theme=THEME, title='GenFBDD', css=static.CSS, delete_cache=(3600,
         fn=lambda: [gr.Button(visible=True), gr.Button(visible=False)],
         outputs=[pred_lookup_btn, pred_lookup_stop_btn],
         cancels=[user_job_lookup, auto_job_lookup],
-        concurrency_limit=None,
     ).success(
         lambda: '<div class="loader first-frame"></ div>',
         outputs=loader_html,
     )
 
+    pred_lookup_example.click(
+        fn=lambda: '80cf2658-7a1c-48d6-8372-61b978177fe6',
+        outputs=[pred_lookup_id],
+    ).success(
+        fn=query_job_status,
+        inputs=pred_lookup_id,
+        outputs=[pred_lookup_status, tabs, result_state],
+        show_progress='minimal',
+        cancels=[user_job_lookup, auto_job_lookup],
+    )
+
     ### Results
     def update_results(result_info):
         result_dir = Path(result_info['output_dir'])
@@ -882,17 +892,20 @@ with gr.Blocks(theme=THEME, title='GenFBDD', css=static.CSS, delete_cache=(3600,
 
     def generate_result_zip(result_info, compound_mod_df, protein_file):
         result_path = Path(result_info['output_dir'])
-        zip_path = result_path.with_suffix('.zip')
+        filename = f'GenFBDD_{result_path.name}.zip'
+        zip_path = result_path / filename
         cols_to_drop = ['mol', 'Compound', 'protein_path']
         compound_mod_df.drop(columns=[col for col in cols_to_drop if col in compound_mod_df.columns], inplace=True)
+        compound_mod_df.rename(columns=COL_ALIASES, inplace=True)
         compound_mod_df.to_csv(result_path / f'{result_info["type"]}_summary.csv', index=False)
 
         with zipfile.ZipFile(zip_path, 'w') as zip_file:
             for file in result_path.rglob('*'):
-                if file.is_file():  # Skip directories
+                if file.is_file() and file != zip_path:  # Skip directories and the zip file itself
                     archive_path = file.relative_to(result_path)
                     zip_file.write(file, arcname=archive_path)
-            zip_file.write(Path(protein_file), arcname=Path(protein_file).name)
+            if Path(protein_file).name not in zip_file.namelist():
+                zip_file.write(Path(protein_file), arcname=Path(protein_file).name)
 
         return gr.File(str(zip_path), visible=True)
 

app/static.py

@@ -32,6 +32,19 @@ CSS = """
   100%  {transform: translateY(-20px)}
 }
 
+.loader.first-frame {
+  animation: none; /* Stop the main animation */
+}
+
+.loader.first-frame:before {
+    transform: rotate(0deg); /* Explicitly set the rotation to the first frame */
+}
+
+.loader.first-frame:after {
+    animation: none; /* Stop the after animation */
+    transform: translateY(0px); /*reset the translate Y*/
+}
+
 .help-tip {
   position: absolute;
   display: inline-block;

results/2025-01-01_01-01-01_80cf2658-7a1c-48d6-8372-61b978177fe6/docking/1xkk-frag_0_0-confidence-1.02.sdf

@@ -0,0 +1,18 @@
+
+     RDKit          3D
+
+  6  6  0  0  0  0  0  0  0  0999 V2000
+   26.2622   42.5449   56.1505 C   0  0  0  0  0  0  0  0  0  0  0  0
+   27.1354   43.1784   55.2905 C   0  0  0  0  0  0  0  0  0  0  0  0
+   28.4363   42.7134   55.2411 C   0  0  0  0  0  0  0  0  0  0  0  0
+   28.8292   41.6522   56.0312 C   0  0  0  0  0  0  0  0  0  0  0  0
+   27.9789   41.0046   56.8954 C   0  0  0  0  0  0  0  0  0  0  0  0
+   26.6689   41.4757   56.9427 C   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  2  0
+  2  3  1  0
+  3  4  2  0
+  4  5  1  0
+  5  6  2  0
+  6  1  1  0
+M  END
+$$$$

results/2025-01-01_01-01-01_80cf2658-7a1c-48d6-8372-61b978177fe6/docking/1xkk-frag_1_0-confidence0.01.sdf

@@ -0,0 +1,27 @@
+
+     RDKit          3D
+
+ 10 11  0  0  0  0  0  0  0  0999 V2000
+   16.2668   34.0732   40.2359 C   0  0  0  0  0  0  0  0  0  0  0  0
+   17.1893   33.6174   39.3135 C   0  0  0  0  0  0  0  0  0  0  0  0
+   16.8190   33.1721   38.0602 C   0  0  0  0  0  0  0  0  0  0  0  0
+   15.4885   33.1712   37.6893 C   0  0  0  0  0  0  0  0  0  0  0  0
+   15.1263   32.7313   36.4520 N   0  0  0  0  0  0  0  0  0  0  0  0
+   13.8133   32.7391   36.1083 C   0  0  0  0  0  0  0  0  0  0  0  0
+   12.8631   33.1755   36.9728 N   0  0  0  0  0  0  0  0  0  0  0  0
+   13.2229   33.6106   38.1967 C   0  0  0  0  0  0  0  0  0  0  0  0
+   14.5461   33.6226   38.5944 C   0  0  0  0  0  0  0  0  0  0  0  0
+   14.9311   34.0680   39.8521 C   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  2  0
+  2  3  1  0
+  3  4  2  0
+  4  5  1  0
+  5  6  2  0
+  6  7  1  0
+  7  8  2  0
+  8  9  1  0
+  9 10  2  0
+ 10  1  1  0
+  9  4  1  0
+M  END
+$$$$

results/2025-01-01_01-01-01_80cf2658-7a1c-48d6-8372-61b978177fe6/docking/1xkk-frag_2_0-confidence-2.64.sdf

@@ -0,0 +1,18 @@
+
+     RDKit          3D
+
+  6  6  0  0  0  0  0  0  0  0999 V2000
+   20.9568   33.4893   32.6574 C   0  0  0  0  0  0  0  0  0  0  0  0
+   21.2282   32.5448   33.6503 C   0  0  0  0  0  0  0  0  0  0  0  0
+   20.2187   31.7858   34.0602 N   0  0  0  0  0  0  0  0  0  0  0  0
+   18.9740   31.9144   33.5433 C   0  0  0  0  0  0  0  0  0  0  0  0
+   18.7058   32.8340   32.5753 N   0  0  0  0  0  0  0  0  0  0  0  0
+   19.7009   33.6417   32.1141 C   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  2  0
+  2  3  1  0
+  3  4  2  0
+  4  5  1  0
+  5  6  2  0
+  6  1  1  0
+M  END
+$$$$

results/2025-01-01_01-01-01_80cf2658-7a1c-48d6-8372-61b978177fe6/docking/1xkk-frag_3_0-confidence-1.00.sdf

@@ -0,0 +1,13 @@
+
+     RDKit          3D
+
+  4  3  0  0  0  0  0  0  0  0999 V2000
+   23.6319   36.0653   39.6398 C   0  0  0  0  0  0  0  0  0  0  0  0
+   23.6554   37.1918   40.3718 C   0  0  0  0  0  0  0  0  0  0  0  0
+   23.4153   37.1532   41.8222 C   0  0  0  0  0  0  0  0  0  0  0  0
+   22.7765   38.1036   42.3816 O   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  2  0
+  2  3  1  0
+  3  4  2  0
+M  END
+$$$$

results/2025-01-01_01-01-01_80cf2658-7a1c-48d6-8372-61b978177fe6/docking/1xkk-frag_4_0-confidence-0.21.sdf

@@ -0,0 +1,20 @@
+
+     RDKit          3D
+
+  7  7  0  0  0  0  0  0  0  0999 V2000
+   17.2665   32.7344   35.2760 C   0  0  0  0  0  0  0  0  0  0  0  0
+   16.2547   32.0615   36.0235 N   0  0  0  0  0  0  0  0  0  0  0  0
+   15.1769   31.6076   35.2358 C   0  0  0  0  0  0  0  0  0  0  0  0
+   14.0819   32.6551   35.2550 C   0  0  0  0  0  0  0  0  0  0  0  0
+   13.6160   32.7305   36.6158 N   0  0  0  0  0  0  0  0  0  0  0  0
+   14.6282   33.1443   37.5436 C   0  0  0  0  0  0  0  0  0  0  0  0
+   15.9759   32.5381   37.3164 C   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0
+  2  3  1  0
+  3  4  1  0
+  4  5  1  0
+  5  6  1  0
+  6  7  1  0
+  7  2  1  0
+M  END
+$$$$

results/2025-01-01_01-01-01_80cf2658-7a1c-48d6-8372-61b978177fe6/docking/1xkk-frag_5_0-confidence-0.87.sdf

@@ -0,0 +1,18 @@
+
+     RDKit          3D
+
+  6  6  0  0  0  0  0  0  0  0999 V2000
+   36.5702   41.8594   49.2727 C   0  0  0  0  0  0  0  0  0  0  0  0
+   35.1323   42.1045   49.7242 C   0  0  0  0  0  0  0  0  0  0  0  0
+   34.4564   42.5006   48.5574 O   0  0  0  0  0  0  0  0  0  0  0  0
+   34.2725   41.3236   47.8234 C   0  0  0  0  0  0  0  0  0  0  0  0
+   35.5872   40.7310   47.3646 C   0  0  0  0  0  0  0  0  0  0  0  0
+   36.6280   40.8492   48.2949 N   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0
+  2  3  1  0
+  3  4  1  0
+  4  5  1  0
+  5  6  1  0
+  6  1  1  0
+M  END
+$$$$

results/2025-01-01_01-01-01_80cf2658-7a1c-48d6-8372-61b978177fe6/docking/1xkk-frag_6_0-confidence-0.98.sdf

@@ -0,0 +1,18 @@
+
+     RDKit          3D
+
+  6  6  0  0  0  0  0  0  0  0999 V2000
+   17.0738   34.4358   36.4989 C   0  0  0  0  0  0  0  0  0  0  0  0
+   17.3789   33.0388   37.0151 C   0  0  0  0  0  0  0  0  0  0  0  0
+   18.7434   32.6889   36.5261 C   0  0  0  0  0  0  0  0  0  0  0  0
+   19.6063   33.7306   36.1612 N   0  0  0  0  0  0  0  0  0  0  0  0
+   19.3834   35.0538   36.5357 C   0  0  0  0  0  0  0  0  0  0  0  0
+   18.0716   35.2842   37.2889 C   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0
+  2  3  1  0
+  3  4  1  0
+  4  5  1  0
+  5  6  1  0
+  6  1  1  0
+M  END
+$$$$

results/2025-01-01_01-01-01_80cf2658-7a1c-48d6-8372-61b978177fe6/docking/1xkk-frag_7_0-confidence0.25.sdf

@@ -0,0 +1,25 @@
+
+     RDKit          3D
+
+  9 10  0  0  0  0  0  0  0  0999 V2000
+   13.7292   32.7591   36.0010 C   0  0  0  0  0  0  0  0  0  0  0  0
+   12.8332   33.1961   36.9363 N   0  0  0  0  0  0  0  0  0  0  0  0
+   13.2567   33.6225   38.1465 C   0  0  0  0  0  0  0  0  0  0  0  0
+   14.6200   33.5956   38.3887 C   0  0  0  0  0  0  0  0  0  0  0  0
+   15.3454   33.9624   39.5126 C   0  0  0  0  0  0  0  0  0  0  0  0
+   16.6770   33.7359   39.2265 C   0  0  0  0  0  0  0  0  0  0  0  0
+   16.7767   33.2491   37.9785 N   0  0  0  0  0  0  0  0  0  0  0  0
+   15.5396   33.1587   37.4589 C   0  0  0  0  0  0  0  0  0  0  0  0
+   15.0625   32.7459   36.2719 N   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  2  0
+  2  3  1  0
+  3  4  2  0
+  4  5  1  0
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+  6  7  1  0
+  7  8  1  0
+  8  9  2  0
+  9  1  1  0
+  8  4  1  0
+M  END
+$$$$

results/2025-01-01_01-01-01_80cf2658-7a1c-48d6-8372-61b978177fe6/docking/1xkk-frag_8_0-confidence-2.04.sdf

@@ -0,0 +1,15 @@
+
+     RDKit          3D
+
+  5  4  0  0  0  0  0  0  0  0999 V2000
+   18.6411   27.9625   28.3005 N   0  0  0  0  0  0  0  0  0  0  0  0
+   17.6342   27.9901   27.7010 C   0  0  0  0  0  0  0  0  0  0  0  0
+   16.3420   28.0158   26.9607 C   0  0  0  0  0  0  0  0  0  0  0  0
+   16.6860   28.2824   25.5126 C   0  0  0  0  0  0  0  0  0  0  0  0
+   15.8377   28.6319   24.7305 O   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  3  0
+  2  3  1  0
+  3  4  1  0
+  4  5  2  0
+M  END
+$$$$

results/2025-01-01_01-01-01_80cf2658-7a1c-48d6-8372-61b978177fe6/docking/1xkk-frag_9_0-confidence-1.02.sdf

@@ -0,0 +1,22 @@
+
+     RDKit          3D
+
+  8  8  0  0  0  0  0  0  0  0999 V2000
+   15.2472   32.9988   34.0231 O   0  0  0  0  0  0  0  0  0  0  0  0
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+   16.8279   30.9188   36.6163 C   0  0  0  0  0  0  0  0  0  0  0  0
+   16.6064   31.5795   35.4089 C   0  0  0  0  0  0  0  0  0  0  0  0
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+  4  5  2  0
+  5  6  1  0
+  6  7  2  0
+  7  8  1  0
+  7  2  1  0
+M  END
+$$$$

results/2025-01-01_01-01-01_80cf2658-7a1c-48d6-8372-61b978177fe6/docking_summary.csv

@@ -0,0 +1,11 @@
+name,ID2,protein_path,ID1,X1,confidence,ligand_conf_path
+1xkk-frag_0,1xkk,/tmp/gradio/1xkk.pdb,frag_0_0,c1ccccc1,-1.0169598,results/2025-01-05_11-14-29.222981/docking/1xkk-frag_0_0-confidence-1.02.sdf
+1xkk-frag_1,1xkk,/tmp/gradio/1xkk.pdb,frag_1_0,c1ccc2ncncc2c1,0.011155255,results/2025-01-05_11-14-29.222981/docking/1xkk-frag_1_0-confidence0.01.sdf
+1xkk-frag_2,1xkk,/tmp/gradio/1xkk.pdb,frag_2_0,c1cncnc1,-2.6432655,results/2025-01-05_11-14-29.222981/docking/1xkk-frag_2_0-confidence-2.64.sdf
+1xkk-frag_3,1xkk,/tmp/gradio/1xkk.pdb,frag_3_0,C=CC=O,-1.0013701,results/2025-01-05_11-14-29.222981/docking/1xkk-frag_3_0-confidence-1.00.sdf
+1xkk-frag_4,1xkk,/tmp/gradio/1xkk.pdb,frag_4_0,CN1CCNCC1,-0.21079868,results/2025-01-05_11-14-29.222981/docking/1xkk-frag_4_0-confidence-0.21.sdf
+1xkk-frag_5,1xkk,/tmp/gradio/1xkk.pdb,frag_5_0,C1COCCN1,-0.8726358,results/2025-01-05_11-14-29.222981/docking/1xkk-frag_5_0-confidence-0.87.sdf
+1xkk-frag_6,1xkk,/tmp/gradio/1xkk.pdb,frag_6_0,C1CCNCC1,-0.9784176,results/2025-01-05_11-14-29.222981/docking/1xkk-frag_6_0-confidence-0.98.sdf
+1xkk-frag_7,1xkk,/tmp/gradio/1xkk.pdb,frag_7_0,c1ncc2cc[nH]c2n1,0.24687979,results/2025-01-05_11-14-29.222981/docking/1xkk-frag_7_0-confidence0.25.sdf
+1xkk-frag_8,1xkk,/tmp/gradio/1xkk.pdb,frag_8_0,N#CCC=O,-2.0430398,results/2025-01-05_11-14-29.222981/docking/1xkk-frag_8_0-confidence-2.04.sdf
+1xkk-frag_9,1xkk,/tmp/gradio/1xkk.pdb,frag_9_0,Oc1ccccc1O,-1.0192447,results/2025-01-05_11-14-29.222981/docking/1xkk-frag_9_0-confidence-1.02.sdf

results/2025-01-01_01-01-01_80cf2658-7a1c-48d6-8372-61b978177fe6/linking/1xkk-frag_3_0-frag_1_0_0.sdf

@@ -0,0 +1,43 @@
+
+ OpenBabel01052512113D
+
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+ 17 18  3  0  0  0  0
+ 17  1  1  0  0  0  0
+ 18 15  1  0  0  0  0
+M  END
+$$$$

results/2025-01-01_01-01-01_80cf2658-7a1c-48d6-8372-61b978177fe6/linking/1xkk-frag_3_0-frag_4_0_0.sdf

@@ -0,0 +1,44 @@
+
+ OpenBabel01052512113D
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+   20.9645   35.4012   41.8838 C   0  0  0  0  0  2  0  0  0  0  0  0
+   22.2321   35.0624   42.3623 C   0  0  0  0  0  3  0  0  0  0  0  0
+   18.4738   34.2265   39.6307 C   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  2  0  0  0  0
+  2  3  1  0  0  0  0
+  3  4  2  0  0  0  0
+  3 13  1  0  0  0  0
+  5  6  1  0  0  0  0
+  6 11  1  0  0  0  0
+  7  8  1  0  0  0  0
+  7  6  1  0  0  0  0
+  8  9  1  0  0  0  0
+  9 10  1  0  0  0  0
+ 11 10  1  0  0  0  0
+ 11 12  1  6  0  0  0
+ 12 16  1  0  0  0  0
+ 14 17  1  0  0  0  0
+ 15 14  2  0  0  0  0
+ 16 19  3  0  0  0  0
+ 17 18  1  0  0  0  0
+ 18 13  2  0  0  0  0
+ 19 15  1  0  0  0  0
+M  END
+$$$$

results/2025-01-01_01-01-01_80cf2658-7a1c-48d6-8372-61b978177fe6/linking/1xkk-frag_3_0-frag_7_0_0.sdf

@@ -0,0 +1,38 @@
+
+ OpenBabel01052512113D
+
+ 16 16  0  0  1  0  0  0  0  0999 V2000
+   23.6319   36.0653   39.6398 C   0  0  0  0  0  2  0  0  0  0  0  0
+   23.6554   37.1918   40.3718 C   0  0  0  0  0  2  0  0  0  0  0  0
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+   13.7292   32.7591   36.0010 C   0  0  0  0  0  3  0  0  0  0  0  0
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+   13.2567   33.6225   38.1465 C   0  0  0  0  0  3  0  0  0  0  0  0
+   14.6200   33.5956   38.3887 C   0  0  2  0  0  3  0  0  0  0  0  0
+   15.3454   33.9624   39.5126 C   0  0  0  0  0  3  0  0  0  0  0  0
+   16.6770   33.7359   39.2265 C   0  0  0  0  0  3  0  0  0  0  0  0
+   16.7767   33.2491   37.9785 N   0  0  0  0  0  0  0  0  0  0  0  0
+   15.5396   33.1587   37.4589 C   0  0  0  0  0  0  0  0  0  0  0  0
+   15.0625   32.7459   36.2719 N   0  0  0  0  0  0  0  0  0  0  0  0
+   20.0922   34.6588   39.4569 C   0  0  0  0  0  1  0  0  0  0  0  0
+   22.5256   35.3420   39.5149 C   0  0  0  0  0  0  0  0  0  0  0  0
+   21.4541   35.0084   39.4530 C   0  0  0  0  0  0  0  0  0  0  0  0
+  1  2  1  0  0  0  0
+  2  3  1  0  0  0  0
+  3  4  2  0  0  0  0
+  5 13  2  0  0  0  0
+  5  6  1  0  0  0  0
+  6  7  2  0  0  0  0
+  8  7  1  6  0  0  0
+  8  9  1  0  0  0  0
+ 10  9  2  0  0  0  0
+ 11 10  1  0  0  0  0
+ 12 11  2  0  0  0  0
+ 12  8  1  0  0  0  0
+ 13 12  1  0  0  0  0
+ 15  1  1  0  0  0  0
+ 16 14  1  0  0  0  0
+ 16 15  3  0  0  0  0
+M  END
+$$$$

results/2025-01-01_01-01-01_80cf2658-7a1c-48d6-8372-61b978177fe6/linking/1xkk-frag_3_0-frag_9_0_0.sdf

@@ -0,0 +1,66 @@
+
+ OpenBabel01052512113D
+
+ 29 31  0  0  1  0  0  0  0  0999 V2000
+   23.6319   36.0653   39.6398 C   0  0  0  0  0  2  0  0  0  0  0  0
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+   23.7128   35.7920   44.0012 C   0  0  0  0  0  1  0  0  0  0  0  0
+   20.7938   35.8588   41.0702 C   0  0  0  0  0  2  0  0  0  0  0  0
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+   16.7891   33.4750   39.3526 C   0  0  0  0  0  3  0  0  0  0  0  0
+   16.9106   33.0342   41.5738 C   0  0  0  0  0  2  0  0  0  0  0  0
+   23.4828   35.8431   42.5132 C   0  0  2  0  0  3  0  0  0  0  0  0
+   16.1604   32.7492   40.3907 C   0  0  0  0  0  0  0  0  0  0  0  0
+   21.2845   34.8221   43.1573 C   0  0  0  0  0  2  0  0  0  0  0  0
+   15.1573   31.8629   40.3610 N   0  0  0  0  0  2  0  0  0  0  0  0
+  1  2  2  0  0  0  0
+  2  3  1  0  0  0  0
+  3  4  2  0  0  0  0
+  3 26  1  0  0  0  0
+  5  6  1  0  0  0  0
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+  6  7  1  0  0  0  0
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+ 17 14  2  0  0  0  0
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+ 24 27  2  0  0  0  0
+ 26 21  1  1  0  0  0
+ 27 25  1  0  0  0  0
+ 29 27  1  0  0  0  0
+M  END
+$$$$

results/2025-01-01_01-01-01_80cf2658-7a1c-48d6-8372-61b978177fe6/linking/1xkk-frag_6_0-frag_1_0_0.sdf

@@ -0,0 +1,46 @@
+
+ OpenBabel01052512113D
+
+ 19 21  0  0  1  0  0  0  0  0999 V2000
+   17.0738   34.4358   36.4989 C   0  0  0  0  0  2  0  0  0  0  0  0
+   17.3789   33.0388   37.0151 C   0  0  1  0  0  3  0  0  0  0  0  0
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+   13.2229   33.6106   38.1967 C   0  0  0  0  0  3  0  0  0  0  0  0
+   14.5461   33.6226   38.5944 C   0  0  0  0  0  0  0  0  0  0  0  0
+   14.9311   34.0680   39.8521 C   0  0  0  0  0  3  0  0  0  0  0  0
+   15.5366   32.0719   33.7144 O   0  0  0  0  0  1  0  0  0  0  0  0
+   13.3826   32.4791   34.7418 C   0  0  0  0  0  2  0  0  0  0  0  0
+   14.4022   32.9100   33.6879 C   0  0  0  0  0  2  0  0  0  0  0  0
+  1  2  1  0  0  0  0
+  1  6  1  0  0  0  0
+  2  9  1  1  0  0  0
+  3  2  1  0  0  0  0
+  4  3  1  0  0  0  0
+  4  5  1  0  0  0  0
+  5  6  1  0  0  0  0
+  8  7  2  0  0  0  0
+  9  8  1  0  0  0  0
+ 10  9  2  0  0  0  0
+ 10 15  1  0  0  0  0
+ 11 10  1  0  0  0  0
+ 12 11  2  0  0  0  0
+ 12 13  1  0  0  0  0
+ 13 14  2  0  0  0  0
+ 14 15  1  0  0  0  0
+ 15 16  2  0  0  0  0
+ 16  7  1  0  0  0  0
+ 18 12  1  0  0  0  0
+ 19 17  1  0  0  0  0
+ 19 18  1  0  0  0  0
+M  END
+$$$$

results/2025-01-01_01-01-01_80cf2658-7a1c-48d6-8372-61b978177fe6/linking/1xkk-frag_6_0-frag_3_0_0.sdf

@@ -0,0 +1,62 @@
+
+ OpenBabel01052512113D
+
+ 27 29  0  0  1  0  0  0  0  0999 V2000
+   17.0738   34.4358   36.4989 C   0  0  0  0  0  2  0  0  0  0  0  0
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+   25.0812   34.2399   40.3120 C   0  0  0  0  0  0  0  0  0  0  0  0
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+   26.9955   33.0667   40.5446 C   0  0  0  0  0  3  0  0  0  0  0  0
+   20.2216   36.0776   40.6807 C   0  0  0  0  0  0  0  0  0  0  0  0
+   19.3932   37.1576   41.0659 C   0  0  0  0  0  3  0  0  0  0  0  0
+  1  2  1  0  0  0  0
+  1  6  1  0  0  0  0
+  3  2  1  0  0  0  0
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+  5  6  1  0  0  0  0
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+ 25 17  2  0  0  0  0
+ 26 27  2  0  0  0  0
+ 26 16  1  0  0  0  0
+ 27 20  1  0  0  0  0
+M  END
+$$$$

results/2025-01-01_01-01-01_80cf2658-7a1c-48d6-8372-61b978177fe6/linking/1xkk-frag_6_0-frag_4_0_0.sdf

@@ -0,0 +1,49 @@
+
+ OpenBabel01052512113D
+
+ 19 24  0  0  1  0  0  0  0  0999 V2000
+   17.0738   34.4358   36.4989 C   0  0  0  0  0  2  0  0  0  0  0  0
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+  1  6  1  0  0  0  0
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+  9 10  1  0  0  0  0
+  9  8  1  0  0  0  0
+ 10 11  1  0  0  0  0
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+ 14  7  1  0  0  0  0
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+ 15 17  1  0  0  0  0
+ 15 16  1  0  0  0  0
+ 17 16  1  0  0  0  0
+ 18 14  1  0  0  0  0
+ 19 18  3  0  0  0  0
+M  END
+$$$$

results/2025-01-01_01-01-01_80cf2658-7a1c-48d6-8372-61b978177fe6/linking/1xkk-frag_6_0-frag_7_0_0.sdf

@@ -0,0 +1,44 @@
+
+ OpenBabel01052512113D
+
+ 18 20  0  0  1  0  0  0  0  0999 V2000
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+   17.3789   33.0388   37.0151 C   0  0  1  0  0  3  0  0  0  0  0  0
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+   16.6770   33.7359   39.2265 C   0  0  0  0  0  3  0  0  0  0  0  0
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+   15.5396   33.1587   37.4589 C   0  0  0  0  0  0  0  0  0  0  0  0
+   15.0625   32.7459   36.2719 N   0  0  0  0  0  2  0  0  0  0  0  0
+   13.3021   32.3378   34.6672 C   0  0  0  0  0  2  0  0  0  0  0  0
+   13.2782   34.7143   33.8299 C   0  0  0  0  0  1  0  0  0  0  0  0
+   13.8699   33.3178   33.6224 C   0  0  0  0  0  2  0  0  0  0  0  0
+  1  6  1  0  0  0  0
+  2  1  1  6  0  0  0
+  2 13  1  0  0  0  0
+  3  2  1  0  0  0  0
+  4  3  1  0  0  0  0
+  4  5  1  0  0  0  0
+  5  6  1  0  0  0  0
+  7 15  1  0  0  0  0
+  7  8  2  0  0  0  0
+  8  9  1  0  0  0  0
+  9 10  1  0  0  0  0
+ 10 11  1  0  0  0  0
+ 12 11  2  0  0  0  0
+ 13 12  1  0  0  0  0
+ 14 13  1  0  0  0  0
+ 14 10  2  0  0  0  0
+ 15 14  1  0  0  0  0
+ 16  7  1  0  0  0  0
+ 18 17  1  0  0  0  0
+ 18 16  1  0  0  0  0
+M  END
+$$$$

results/2025-01-01_01-01-01_80cf2658-7a1c-48d6-8372-61b978177fe6/linking/1xkk-frag_6_0-frag_9_0_0.sdf

@@ -0,0 +1,49 @@
+
+ OpenBabel01052512113D
+
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+   16.6064   31.5795   35.4089 C   0  0  0  0  0  0  0  0  0  0  0  0
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+   17.9775   30.9644   32.0475 C   0  0  0  0  0  1  0  0  0  0  0  0
+   18.4760   33.1867   33.2194 C   0  0  0  0  0  0  0  0  0  0  0  0
+   20.7208   33.7271   33.9372 C   0  0  0  0  0  2  0  0  0  0  0  0
+   17.5118   32.0121   33.0543 C   0  0  2  0  0  3  0  0  0  0  0  0
+   18.0312   34.3106   33.4089 O   0  0  0  0  0  0  0  0  0  0  0  0
+   19.7669   32.8674   33.2778 N   0  0  0  0  0  2  0  0  0  0  0  0
+   20.8215   33.4047   35.4326 C   0  0  0  0  0  2  0  0  0  0  0  0
+  1  2  1  0  0  0  0
+  1  6  1  0  0  0  0
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+ 14 13  1  0  0  0  0
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+ 17 21  1  0  0  0  0
+ 18 15  1  6  0  0  0
+ 18 16  1  0  0  0  0
+ 18 14  1  0  0  0  0
+ 20 17  1  0  0  0  0
+ 21  4  1  0  0  0  0
+M  END
+$$$$

results/2025-01-01_01-01-01_80cf2658-7a1c-48d6-8372-61b978177fe6/linking_summary.csv

@@ -0,0 +1,7 @@
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results/job_db.json

@@ -0,0 +1,15 @@
+{
+  "_default": {
+    "1": {
+      "id": "80cf2658-7a1c-48d6-8372-61b978177fe6",
+      "type": "linking",
+      "status": "COMPLETED",
+      "output_dir": "results/2025-01-01_01-01-01_80cf2658-7a1c-48d6-8372-61b978177fe6",
+      "protein_structure_file": "results/2025-01-01_01-01-01_80cf2658-7a1c-48d6-8372-61b978177fe6/1xkk.pdb",
+      "start_time": 1735693261,
+      "end_time": 1735693321,
+      "expiry_time": 1893459721,
+      "ip": "1.1.1.1"
+    }
+  }
+}