kdock 0.0.2__py3-none-any.whl

kdock/__init__.py

@@ -0,0 +1 @@
+__version__ = "0.0.2"

kdock/_modidx.py

@@ -0,0 +1,131 @@
+# Autogenerated by nbdev
+
+d = { 'settings': { 'branch': 'main',
+                'doc_baseurl': '/kdock',
+                'doc_host': 'https://sky1ove.github.io',
+                'git_url': 'https://github.com/sky1ove/kdock',
+                'lib_path': 'kdock'},
+  'syms': { 'kdock.af3.analyze': { 'kdock.af3.analyze.copy_file': ('af3/analyze.html#copy_file', 'kdock/af3/analyze.py'),
+                                   'kdock.af3.analyze.get_3d_report': ('af3/analyze.html#get_3d_report', 'kdock/af3/analyze.py'),
+                                   'kdock.af3.analyze.get_report': ('af3/analyze.html#get_report', 'kdock/af3/analyze.py'),
+                                   'kdock.af3.analyze.get_summary_df': ('af3/analyze.html#get_summary_df', 'kdock/af3/analyze.py'),
+                                   'kdock.af3.analyze.get_top_cases': ('af3/analyze.html#get_top_cases', 'kdock/af3/analyze.py'),
+                                   'kdock.af3.analyze.process_summary_df': ('af3/analyze.html#process_summary_df', 'kdock/af3/analyze.py'),
+                                   'kdock.af3.analyze.read_summary_json': ('af3/analyze.html#read_summary_json', 'kdock/af3/analyze.py')},
+            'kdock.af3.docker': { 'kdock.af3.docker.docker_multi_full': ('af3/docker.html#docker_multi_full', 'kdock/af3/docker.py'),
+                                  'kdock.af3.docker.docker_multi_infer': ('af3/docker.html#docker_multi_infer', 'kdock/af3/docker.py'),
+                                  'kdock.af3.docker.docker_multi_msa': ('af3/docker.html#docker_multi_msa', 'kdock/af3/docker.py'),
+                                  'kdock.af3.docker.docker_single_full': ('af3/docker.html#docker_single_full', 'kdock/af3/docker.py'),
+                                  'kdock.af3.docker.get_docker_command': ('af3/docker.html#get_docker_command', 'kdock/af3/docker.py')},
+            'kdock.af3.json': { 'kdock.af3.json.assign_atom_names_from_graph': ( 'af3/json.html#assign_atom_names_from_graph',
+                                                                                 'kdock/af3/json.py'),
+                                'kdock.af3.json.dump_json': ('af3/json.html#dump_json', 'kdock/af3/json.py'),
+                                'kdock.af3.json.get_protein_ccd_json': ('af3/json.html#get_protein_ccd_json', 'kdock/af3/json.py'),
+                                'kdock.af3.json.get_protein_ccdcode_json': ('af3/json.html#get_protein_ccdcode_json', 'kdock/af3/json.py'),
+                                'kdock.af3.json.get_protein_json': ('af3/json.html#get_protein_json', 'kdock/af3/json.py'),
+                                'kdock.af3.json.get_protein_smiles_json': ('af3/json.html#get_protein_smiles_json', 'kdock/af3/json.py'),
+                                'kdock.af3.json.mol_to_ccd_text': ('af3/json.html#mol_to_ccd_text', 'kdock/af3/json.py'),
+                                'kdock.af3.json.read_json': ('af3/json.html#read_json', 'kdock/af3/json.py'),
+                                'kdock.af3.json.sdf2ccd': ('af3/json.html#sdf2ccd', 'kdock/af3/json.py'),
+                                'kdock.af3.json.split_nfolder': ('af3/json.html#split_nfolder', 'kdock/af3/json.py')},
+            'kdock.af3.protein_pairs': { 'kdock.af3.protein_pairs.a3m_to_seq': ( 'af3/protein_pairs.html#a3m_to_seq',
+                                                                                 'kdock/af3/protein_pairs.py'),
+                                         'kdock.af3.protein_pairs.copy_a3m': ( 'af3/protein_pairs.html#copy_a3m',
+                                                                               'kdock/af3/protein_pairs.py'),
+                                         'kdock.af3.protein_pairs.dump_json_folder': ( 'af3/protein_pairs.html#dump_json_folder',
+                                                                                       'kdock/af3/protein_pairs.py'),
+                                         'kdock.af3.protein_pairs.generate_pair_df': ( 'af3/protein_pairs.html#generate_pair_df',
+                                                                                       'kdock/af3/protein_pairs.py'),
+                                         'kdock.af3.protein_pairs.get_colabfold_cmd': ( 'af3/protein_pairs.html#get_colabfold_cmd',
+                                                                                        'kdock/af3/protein_pairs.py'),
+                                         'kdock.af3.protein_pairs.get_multi_protein_json': ( 'af3/protein_pairs.html#get_multi_protein_json',
+                                                                                             'kdock/af3/protein_pairs.py'),
+                                         'kdock.af3.protein_pairs.get_protein_subjson': ( 'af3/protein_pairs.html#get_protein_subjson',
+                                                                                          'kdock/af3/protein_pairs.py')},
+            'kdock.core.data': { 'kdock.core.data.Collins': ('core/data.html#collins', 'kdock/core/data.py'),
+                                 'kdock.core.data.Collins.get_antibiotics_2k': ( 'core/data.html#collins.get_antibiotics_2k',
+                                                                                 'kdock/core/data.py'),
+                                 'kdock.core.data.Collins.get_antibiotics_39k': ( 'core/data.html#collins.get_antibiotics_39k',
+                                                                                  'kdock/core/data.py'),
+                                 'kdock.core.data.Collins.get_antibiotics_enzyme': ( 'core/data.html#collins.get_antibiotics_enzyme',
+                                                                                     'kdock/core/data.py'),
+                                 'kdock.core.data.Kras': ('core/data.html#kras', 'kdock/core/data.py'),
+                                 'kdock.core.data.Kras.get_mirati_g12d': ('core/data.html#kras.get_mirati_g12d', 'kdock/core/data.py'),
+                                 'kdock.core.data.Kras.get_mirati_g12d_raw': ( 'core/data.html#kras.get_mirati_g12d_raw',
+                                                                               'kdock/core/data.py'),
+                                 'kdock.core.data.Kras.get_seq': ('core/data.html#kras.get_seq', 'kdock/core/data.py'),
+                                 'kdock.core.data.fetch_csv': ('core/data.html#fetch_csv', 'kdock/core/data.py')},
+            'kdock.core.ligand': { 'kdock.core.ligand.compress_fp': ('core/ligand.html#compress_fp', 'kdock/core/ligand.py'),
+                                   'kdock.core.ligand.get_fp': ('core/ligand.html#get_fp', 'kdock/core/ligand.py'),
+                                   'kdock.core.ligand.get_rdkit': ('core/ligand.html#get_rdkit', 'kdock/core/ligand.py'),
+                                   'kdock.core.ligand.get_rdkit_3d': ('core/ligand.html#get_rdkit_3d', 'kdock/core/ligand.py'),
+                                   'kdock.core.ligand.get_rdkit_all': ('core/ligand.html#get_rdkit_all', 'kdock/core/ligand.py'),
+                                   'kdock.core.ligand.get_rdkit_df': ('core/ligand.html#get_rdkit_df', 'kdock/core/ligand.py'),
+                                   'kdock.core.ligand.get_same_mol_group': ('core/ligand.html#get_same_mol_group', 'kdock/core/ligand.py'),
+                                   'kdock.core.ligand.hash_fp': ('core/ligand.html#hash_fp', 'kdock/core/ligand.py'),
+                                   'kdock.core.ligand.plot_drug': ('core/ligand.html#plot_drug', 'kdock/core/ligand.py'),
+                                   'kdock.core.ligand.preprocess': ('core/ligand.html#preprocess', 'kdock/core/ligand.py'),
+                                   'kdock.core.ligand.rdkit_conformer': ('core/ligand.html#rdkit_conformer', 'kdock/core/ligand.py'),
+                                   'kdock.core.ligand.remove_hi_corr': ('core/ligand.html#remove_hi_corr', 'kdock/core/ligand.py'),
+                                   'kdock.core.ligand.tanimoto': ('core/ligand.html#tanimoto', 'kdock/core/ligand.py'),
+                                   'kdock.core.ligand.tanimoto_numba': ('core/ligand.html#tanimoto_numba', 'kdock/core/ligand.py')},
+            'kdock.core.plot': { 'kdock.core.plot.plot_2d': ('core/plot.html#plot_2d', 'kdock/core/plot.py'),
+                                 'kdock.core.plot.plot_corr': ('core/plot.html#plot_corr', 'kdock/core/plot.py'),
+                                 'kdock.core.plot.reduce_feature': ('core/plot.html#reduce_feature', 'kdock/core/plot.py'),
+                                 'kdock.core.plot.set_sns': ('core/plot.html#set_sns', 'kdock/core/plot.py')},
+            'kdock.core.protein': { 'kdock.core.protein.apply_mut_complex': ( 'core/protein.html#apply_mut_complex',
+                                                                              'kdock/core/protein.py'),
+                                    'kdock.core.protein.apply_mut_single': ('core/protein.html#apply_mut_single', 'kdock/core/protein.py'),
+                                    'kdock.core.protein.compare_seq': ('core/protein.html#compare_seq', 'kdock/core/protein.py'),
+                                    'kdock.core.protein.get_uniprot_features': ( 'core/protein.html#get_uniprot_features',
+                                                                                 'kdock/core/protein.py'),
+                                    'kdock.core.protein.get_uniprot_kd': ('core/protein.html#get_uniprot_kd', 'kdock/core/protein.py'),
+                                    'kdock.core.protein.get_uniprot_seq': ('core/protein.html#get_uniprot_seq', 'kdock/core/protein.py'),
+                                    'kdock.core.protein.get_uniprot_type': ('core/protein.html#get_uniprot_type', 'kdock/core/protein.py')},
+            'kdock.core.utils': { 'kdock.core.utils.copy_files': ('core/utils.html#copy_files', 'kdock/core/utils.py'),
+                                  'kdock.core.utils.get_box': ('core/utils.html#get_box', 'kdock/core/utils.py'),
+                                  'kdock.core.utils.get_rec_lig': ('core/utils.html#get_rec_lig', 'kdock/core/utils.py'),
+                                  'kdock.core.utils.rglob': ('core/utils.html#rglob', 'kdock/core/utils.py'),
+                                  'kdock.core.utils.view_complex': ('core/utils.html#view_complex', 'kdock/core/utils.py'),
+                                  'kdock.core.utils.view_mol': ('core/utils.html#view_mol', 'kdock/core/utils.py')},
+            'kdock.gnina.dock': { 'kdock.gnina.dock.extract_gnina_dock': ( 'gnina/gnina_docking.html#extract_gnina_dock',
+                                                                           'kdock/gnina/dock.py'),
+                                  'kdock.gnina.dock.gnina_dock': ('gnina/gnina_docking.html#gnina_dock', 'kdock/gnina/dock.py'),
+                                  'kdock.gnina.dock.setup_gnina_docker': ( 'gnina/gnina_docking.html#setup_gnina_docker',
+                                                                           'kdock/gnina/dock.py'),
+                                  'kdock.gnina.dock.setup_gnina_local': ( 'gnina/gnina_docking.html#setup_gnina_local',
+                                                                          'kdock/gnina/dock.py')},
+            'kdock.gnina.rescore': { 'kdock.gnina.rescore.ChainSelect': ( 'gnina/gnina_af3_rescore.html#chainselect',
+                                                                          'kdock/gnina/rescore.py'),
+                                     'kdock.gnina.rescore.ChainSelect.__init__': ( 'gnina/gnina_af3_rescore.html#chainselect.__init__',
+                                                                                   'kdock/gnina/rescore.py'),
+                                     'kdock.gnina.rescore.ChainSelect.accept_chain': ( 'gnina/gnina_af3_rescore.html#chainselect.accept_chain',
+                                                                                       'kdock/gnina/rescore.py'),
+                                     'kdock.gnina.rescore.extract_gnina_rescore': ( 'gnina/gnina_af3_rescore.html#extract_gnina_rescore',
+                                                                                    'kdock/gnina/rescore.py'),
+                                     'kdock.gnina.rescore.get_gnina_rescore': ( 'gnina/gnina_af3_rescore.html#get_gnina_rescore',
+                                                                                'kdock/gnina/rescore.py'),
+                                     'kdock.gnina.rescore.get_gnina_rescore_folder': ( 'gnina/gnina_af3_rescore.html#get_gnina_rescore_folder',
+                                                                                       'kdock/gnina/rescore.py'),
+                                     'kdock.gnina.rescore.gnina_rescore_docker': ( 'gnina/gnina_af3_rescore.html#gnina_rescore_docker',
+                                                                                   'kdock/gnina/rescore.py'),
+                                     'kdock.gnina.rescore.gnina_rescore_local': ( 'gnina/gnina_af3_rescore.html#gnina_rescore_local',
+                                                                                  'kdock/gnina/rescore.py'),
+                                     'kdock.gnina.rescore.pdb2sdf': ('gnina/gnina_af3_rescore.html#pdb2sdf', 'kdock/gnina/rescore.py'),
+                                     'kdock.gnina.rescore.prepare_rec_lig': ( 'gnina/gnina_af3_rescore.html#prepare_rec_lig',
+                                                                              'kdock/gnina/rescore.py'),
+                                     'kdock.gnina.rescore.rename_residues': ( 'gnina/gnina_af3_rescore.html#rename_residues',
+                                                                              'kdock/gnina/rescore.py'),
+                                     'kdock.gnina.rescore.split_cif': ('gnina/gnina_af3_rescore.html#split_cif', 'kdock/gnina/rescore.py')},
+            'kdock.px.core': { 'kdock.px.core.get_protein_ligand_df_json': ( 'protenix/protenix.html#get_protein_ligand_df_json',
+                                                                             'kdock/px/core.py'),
+                               'kdock.px.core.get_single_job': ('protenix/protenix.html#get_single_job', 'kdock/px/core.py'),
+                               'kdock.px.core.get_single_protein_ligand_json': ( 'protenix/protenix.html#get_single_protein_ligand_json',
+                                                                                 'kdock/px/core.py'),
+                               'kdock.px.core.get_virtual_screening_json': ( 'protenix/protenix.html#get_virtual_screening_json',
+                                                                             'kdock/px/core.py')},
+            'kdock.px.dock': { 'kdock.px.dock.capture_output': ('protenix/proteinix_dock.html#capture_output', 'kdock/px/dock.py'),
+                               'kdock.px.dock.get_protenix_dock': ('protenix/proteinix_dock.html#get_protenix_dock', 'kdock/px/dock.py'),
+                               'kdock.px.dock.get_protenix_vina_dock': ( 'protenix/proteinix_dock.html#get_protenix_vina_dock',
+                                                                         'kdock/px/dock.py'),
+                               'kdock.px.dock.json2sdf': ('protenix/proteinix_dock.html#json2sdf', 'kdock/px/dock.py')}}}

kdock/af3/analyze.py

@@ -0,0 +1,162 @@
+# AUTOGENERATED! DO NOT EDIT! File to edit: ../../nbs/af3/03_analyze.ipynb.
+
+# %% auto 0
+__all__ = ['read_summary_json', 'get_summary_df', 'process_summary_df', 'get_top_cases', 'get_3d_report', 'get_report',
+           'copy_file']
+
+# %% ../../nbs/af3/03_analyze.ipynb 3
+import json, shutil, pandas as pd
+from pathlib import Path
+import plotly.graph_objects as go
+
+# %% ../../nbs/af3/03_analyze.ipynb 5
+def read_summary_json(json_path):
+    "Read json file to dictionary"
+    json_path = Path(json_path)
+    json_data=json.loads(json_path.read_text())
+        
+    # Flatten the JSON data into a single row
+    row = {"ID": json_path.stem}
+    for key, value in json_data.items():
+        if isinstance(value, list):
+            for idx, sub_value in enumerate(value):
+                if isinstance(sub_value, list):
+                    for sub_idx, sub_sub_value in enumerate(sub_value):
+                        row[f"{key}_{idx}_{sub_idx}"] = sub_sub_value
+                else:
+                    row[f"{key}_{idx}"] = sub_value
+        else:
+            row[key] = value
+    return row
+
+# %% ../../nbs/af3/03_analyze.ipynb 7
+def get_summary_df(output_dir):
+    "Pack the summary json from the output folder to the df"
+    
+    path_list = list(Path(output_dir).rglob('*_summary_confidences.json'))
+    print(len(path_list),'summary_confidences.json files detected')
+    return pd.DataFrame(list(map(read_summary_json,path_list)))
+
+# %% ../../nbs/af3/03_analyze.ipynb 10
+def process_summary_df(df,generate_report=False):
+    "Post process the json-converted pandas df; remove redundant columns; available for pairs"
+    
+    df['ID'] = df.ID.str.replace('_summary_confidences','')
+    df = df.set_index('ID')
+
+    # drop zero std columns: usually contains chain_pair_pae_min_0_0 and has_clash
+    zero_std_cols = df.columns[df.std()<1e-10]
+    df=df.drop(columns=zero_std_cols)
+
+    # drop columns with same values
+    redundant_columns = []
+    
+    # Check for columns equal to `iptm`
+    for col in ['chain_iptm_0', 'chain_iptm_1', 'chain_pair_iptm_0_1', 'chain_pair_iptm_1_0']:
+        if df['iptm'].equals(df[col]):
+            redundant_columns.append(col)
+    
+    # Check for columns equal to `chain_ptm_0`
+    if df['chain_ptm_0'].equals(df['chain_pair_iptm_0_0']):
+        redundant_columns.append('chain_pair_iptm_0_0')
+    
+    # Check for columns equal to `chain_ptm_1`
+    if df['chain_ptm_1'].equals(df['chain_pair_iptm_1_1']):
+        redundant_columns.append('chain_pair_iptm_1_1')
+    
+    # Drop redundant columns
+    df = df.drop(columns=redundant_columns)
+    
+    if generate_report:
+        print('Generating pairplot graph report')
+        sns.pairplot(data=df, corner=True)
+        plt.savefig("af_report.pdf")
+        plt.close()
+        print('Export to af_report.pdf')
+
+    # add iptm and ptm
+    df['iptm_ptm_add'] = df['iptm']+df['ptm']
+
+    # inter error add
+    df['chain_pair_pae_min_add'] = df['chain_pair_pae_min_0_1']+df['chain_pair_pae_min_1_0']
+
+    # rank iptm and ptm and add the rank, this method can ignore the different value range between iptm and ptm
+    df['iptm_rnk'],df['ptm_rnk'] = df.iptm.rank(ascending=False), df.ptm.rank(ascending=False)
+    df['iptm_ptm_rnk_add'] = df['iptm_rnk']+df['ptm_rnk']
+
+    # combine chain_pair_pae_min & iptm rank
+    df['chain_pair_pae_min_add_rnk'] = df['chain_pair_pae_min_add'].rank()
+    df['iptm_pae_add_rnk'] = df['chain_pair_pae_min_add_rnk'] + df['iptm_rnk']
+    
+    return df
+
+# %% ../../nbs/af3/03_analyze.ipynb 12
+def get_top_cases(df,n=30):
+    "Get top cases from the metric"
+    idxs = set()
+    
+    big_cols = ['ranking_score', 'iptm', 'iptm_ptm_add']
+    small_cols = [
+        'iptm_ptm_rnk_add', 
+        'chain_pair_pae_min_add', 
+        'chain_pair_pae_min_0_1', 
+        'chain_pair_pae_min_1_0', 
+        'iptm_pae_add_rnk'
+    ]
+    
+    for col in big_cols: idxs.update(df.nlargest(n, col).index)
+    for col in small_cols: idxs.update(df.nsmallest(n, col).index)
+
+    return list(idxs)
+
+# %% ../../nbs/af3/03_analyze.ipynb 14
+def get_3d_report(df,index_list, x='iptm',y='ptm',z='chain_pair_pae_min_add',save_dir='af_report'):
+    "Generate 3d plot html file given case index and x, y, z colname"
+    annotation = df.index.where(df.index.isin(index_list),'').str.split('_').str[1]
+
+    # Create the 3D scatter plot
+    fig = go.Figure(data=go.Scatter3d(
+        x=df[x],
+        y=df[y],
+        z=df[z],
+        mode='markers+text',
+        text=annotation,  # Annotation using the index
+        textposition="top center",
+        marker=dict(size=8, color='blue', opacity=0.8),
+    ))
+    
+    # Customize layout
+    fig.update_layout(
+        scene=dict(
+            xaxis_title=x,
+            yaxis_title=y,
+            zaxis_title=z,
+        ),
+        title='3D Scatter Plot',
+        autosize=True,
+        height=3000,
+    )
+    
+    fig.write_html(Path(save_dir)/'3d_scatter_plot.html',full_html=True)
+    print('Exported the html to 3d_scatter_plot.html')
+
+# %% ../../nbs/af3/03_analyze.ipynb 16
+def get_report(out_dir,save_dir='af_report'):
+    "Generate summary report based on summary_confidences file; return summary df and top cases"
+    out = get_summary_df(out_dir)
+    out = process_summary_df(out)
+    top_cases = get_top_cases(out)
+    
+    Path(save_dir).mkdir(exist_ok=True)
+    get_3d_report(out,top_cases,save_dir=save_dir)
+    out.to_csv(Path(save_dir)/'summary_confidences.csv')
+    
+    return out, top_cases
+
+# %% ../../nbs/af3/03_analyze.ipynb 18
+def copy_file(idx_name, source_dir, dest_dir):
+    "Copy all model cif generated by AF3 to the new dest folder"
+    source_path = Path(source_dir)/f"{idx_name}/{idx_name}_model.cif"
+    dest_path = Path(dest_dir)/f"{idx_name}_model.cif"
+    shutil.copy(source_path,dest_path)
+    print(f'Copying {str(source_path)} to {str(dest_path)}')

kdock/af3/docker.py

@@ -0,0 +1,120 @@
+# AUTOGENERATED! DO NOT EDIT! File to edit: ../../nbs/af3/01_docker.ipynb.
+
+# %% auto 0
+__all__ = ['get_docker_command', 'docker_single_full', 'docker_multi_full', 'docker_multi_msa', 'docker_multi_infer']
+
+# %% ../../nbs/af3/01_docker.ipynb 3
+from fastcore.meta import delegates
+
+# %% ../../nbs/af3/01_docker.ipynb 6
+def get_docker_command(
+    input_dir="af_input", # Directory for input data
+    output_dir="af_output", # Directory for output results
+    model_dir="af_model", # Directory containing models
+    db_dir="af_database", # Directory for databases. If None, this option is ommitted
+    cache_dir="af_cache", # Directory for JAX compilation cache. If None, this option is omitted
+    gpus=0, # GPU devices to allocate (e.g., 0,1), if None, ommitted
+    docker_name="sky1ove/alphafold3", # Docker image name
+    embedding=False, # If True, includes the --save_embeddings=true flag
+    skip_search=False, # if MSA is precalculated and present in json; If True, includes the --norun_data_pipeline flag
+    search_only=False, # search MSA only; If True, sets skip_search to False and includes the --norun_inference flag
+    json_path=None  # Path to JSON file. If not None, uses json_file instead of input_dir
+):
+
+    "Generate a Docker run command for Alphafold with customizable parameters."
+    
+    # Start building the Docker command
+    cmd_parts = ["docker run --rm \\"]
+
+    if json_path:
+        parent_dir=json_path.split('/')[0]
+        cmd_parts.append(f'    --volume "$HOME/{parent_dir}:/root/af_input" \\')
+    else:
+        parent_dir = input_dir.split('/')[0]
+        cmd_parts.append(f'    --volume "$HOME/{parent_dir}:/root/af_input" \\')
+
+    cmd_parts.extend([f'    --volume "$HOME/{output_dir}:/root/af_output" \\',
+                      f'    --volume "$HOME/{model_dir}:/root/models" \\',
+                     ])
+    if db_dir:
+        cmd_parts.append(f'    --volume "$HOME/{db_dir}:/root/public_databases" \\')
+
+    if cache_dir:
+        cmd_parts.append(f'    --volume "$HOME/{cache_dir}:/root/cache" \\')
+
+    if gpus is not None:
+        cmd_parts.append(f'    --gpus "device={gpus}" \\')
+
+    cmd_parts.extend([f'    {docker_name} \\',
+                      '    python run_alphafold.py \\'])
+    
+    if json_path:
+        mount_path= '/'.join(json_path.split('/')[1:])
+        cmd_parts.append(f'    --json_path=/root/af_input/{mount_path} \\')
+    else:
+        len_dir = len(input_dir.split('/')[1:])
+        if len_dir:
+            mount_dir= '/'.join(input_dir.split('/')[1:])
+            cmd_parts.append(f'    --input_dir=/root/af_input/{mount_dir} \\')
+        else:
+            cmd_parts.append('    --input_dir=/root/af_input \\')
+
+    cmd_parts.extend(['    --output_dir=/root/af_output \\',
+                      '    --model_dir=/root/models \\'])
+    
+    if cache_dir:
+        cmd_parts.append('    --jax_compilation_cache_dir=/root/cache \\')
+
+    if embedding:
+        cmd_parts.append('    --save_embeddings=true \\')
+    
+    if search_only:
+        skip_search = False
+        cmd_parts.append('    --norun_inference \\')
+    elif skip_search:
+        cmd_parts.append('    --norun_data_pipeline \\')
+
+    if cmd_parts[-1].endswith('\\'):
+        cmd_parts[-1] = cmd_parts[-1].rstrip(' \\')
+
+    docker_command = "\n".join(cmd_parts)
+    print(docker_command)
+
+# %% ../../nbs/af3/01_docker.ipynb 12
+@delegates(get_docker_command)
+def docker_single_full(json_path,output_dir,cache_dir=False,**kwargs):
+    "Single json task with full pipeline."
+    return get_docker_command(
+        json_path=json_path,
+        output_dir=output_dir,
+        cache_dir=cache_dir,
+        **kwargs)
+
+# %% ../../nbs/af3/01_docker.ipynb 16
+@delegates(get_docker_command)
+def docker_multi_full(input_dir,output_dir,**kwargs):
+    "Folder of json as input with full pipeline."
+    return get_docker_command(
+        input_dir=input_dir,
+        output_dir=output_dir,
+        **kwargs)
+
+# %% ../../nbs/af3/01_docker.ipynb 19
+@delegates(get_docker_command)
+def docker_multi_msa(input_dir,output_dir,search_only=True,**kwargs):
+    "MSA search only, without structure inference; CPU only."
+    return get_docker_command(
+        input_dir=input_dir,
+        output_dir=output_dir,
+        search_only=search_only,
+        **kwargs)
+
+# %% ../../nbs/af3/01_docker.ipynb 22
+@delegates(get_docker_command)
+def docker_multi_infer(input_dir,output_dir,skip_search=True,**kwargs):
+    "Infer only with pre-calculated MSA; GPU is needed."
+    return get_docker_command(
+        input_dir=input_dir,
+        output_dir=output_dir,
+        skip_search=skip_search,
+        **kwargs)