diff --git a/.github/workflows/docker_build.yml b/.github/workflows/docker_build.yml
index 178f886..4f1be86 100644
--- a/.github/workflows/docker_build.yml
+++ b/.github/workflows/docker_build.yml
@@ -23,10 +23,11 @@ jobs:
                      calculate_net_charge, generate_conformers,
                      mol2_to_pdbqt, nmr4md, openbabel,
                      remove_terminal_residue_name_prefixes,
-                     rename_residues_mol, combine_structure,
+                     rename_residues, combine_structure,
                      remove_terminal_residue_name_prefixes, molgan,
                      pdbbind_refined, onionnet-sfct, smina, pdbfixer,
-                     fix_pdb_atom_column, extract_protein, extract_ligand_protein, generate_conformers]  # No username for pdbind_refined
+                     fix_pdb_atom_column, extract_protein, extract_ligand_protein, generate_conformers,
+                     onionnet, combine_pdb]  # No username for pdbind_refined
         # skip data/ and cwl_adapters/file_format_conversions/biosimspace/
     runs-on: [ubuntu-latest]
 
diff --git a/cwl_adapters/autodock_vina.cwl b/cwl_adapters/autodock_vina.cwl
new file mode 100644
index 0000000..ad4167d
--- /dev/null
+++ b/cwl_adapters/autodock_vina.cwl
@@ -0,0 +1,221 @@
+
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.1  # See `loadContents: true` below!
+
+class: CommandLineTool
+
+label: Wrapper of the AutoDock Vina software.
+
+doc: |-
+  This class performs docking of the ligand to a set of grids describing the target protein via the AutoDock Vina software.
+
+baseCommand: vina # NOTE: Only version >=1.2 supports --batch!
+arguments:
+# Need to parse box.pdb and pass in each number separately.
+# REMARK BOX CENTER:     0.102     0.019    -0.004 SIZE:    30.195    31.940    27.005
+# - "--dir" # Need to explicitly pass --dir . in --batch mode
+# - "."
+- "--center_x"
+- $(inputs.input_box_path.contents.split("\n")[0].split(" ").filter(function(s) {return !isNaN(parseFloat(s))})[0])
+- "--center_y"
+- $(inputs.input_box_path.contents.split("\n")[0].split(" ").filter(function(s) {return !isNaN(parseFloat(s))})[1])
+- "--center_z"
+- $(inputs.input_box_path.contents.split("\n")[0].split(" ").filter(function(s) {return !isNaN(parseFloat(s))})[2])
+- "--size_x"
+- $(inputs.input_box_path.contents.split("\n")[0].split(" ").filter(function(s) {return !isNaN(parseFloat(s))})[3])
+- "--size_y"
+- $(inputs.input_box_path.contents.split("\n")[0].split(" ").filter(function(s) {return !isNaN(parseFloat(s))})[4])
+- "--size_z"
+- $(inputs.input_box_path.contents.split("\n")[0].split(" ").filter(function(s) {return !isNaN(parseFloat(s))})[5])
+# NOTE: Cannot use a single javascript expression to create the entire arguments list because CWL treats it as a string:
+# "the `arguments` field is not valid because value is a str"
+#  ${
+#    var words = inputs.input_box_path.contents.split("\n")[0].split(" ");
+#    var nums = words.filter(function(s) {return !isNaN(parseFloat(s))});
+#    var args = {};
+#    args.push("--dir"); // Need to explicitly pass --dir . in --batch mode
+#    args.push(".");
+#    args.push("--center_x");
+#    args.push(nums[0]);
+#    args.push("--center_y");
+#    args.push(nums[1]);
+#    args.push("--center_z");
+#    args.push(nums[2]);
+#    args.push("--size_x");
+#    args.push(nums[3]);
+#    args.push("--size_y");
+#    args.push(nums[4]);
+#    args.push("--size_z");
+#    args.push(nums[5]);
+#    return args;
+#  }
+
+hints:
+  DockerRequirement:
+    dockerPull: jakefennick/autodock_vina
+
+requirements:
+  InlineJavascriptRequirement: {}
+
+inputs:
+  input_ligand_pdbqt_path:
+    label: Path to the input PDBQT ligand
+    doc: |-
+      Path to the input PDBQT ligand
+      Type: string
+      File type: input
+      Accepted formats: pdbqt
+      Example file: https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/data/vina/vina_ligand.pdbqt
+    type: File
+    format:
+    - edam:format_1476
+    inputBinding:
+      prefix: --ligand
+
+  input_receptor_pdbqt_path:
+    label: Path to the input PDBQT receptor
+    doc: |-
+      Path to the input PDBQT receptor
+      Type: string
+      File type: input
+      Accepted formats: pdbqt
+      Example file: https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/data/vina/vina_receptor.pdbqt
+    type: File
+    format:
+    - edam:format_1476
+    inputBinding:
+      #position: 2
+      prefix: --receptor
+
+  input_box_path:
+    label: Path to the PDB containing the residues belonging to the binding site
+    doc: |-
+      Path to the PDB containing the residues belonging to the binding site
+      Type: string
+      File type: input
+      Accepted formats: pdb
+      Example file: https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/data/vina/vina_box.pdb
+    type: File
+    format:
+    - edam:format_1476
+#    inputBinding:
+#      position: 3
+#      prefix: --input_box_path
+    loadContents: true  # requires cwlVersion: v1.1
+    # See https://www.commonwl.org/v1.1/CommandLineTool.html#Changelog
+    # Curiously, cwlVersion: v1.0 allows loadContents for outputs, but not inputs.
+
+  output_pdbqt_path:
+    label: Path to the output PDBQT file
+    doc: |-
+      Path to the output PDBQT file
+      Type: string
+      File type: output
+      Accepted formats: pdbqt
+      Example file: https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/reference/vina/ref_output_vina.pdbqt
+    type: string
+    format:
+    - edam:format_1476
+    inputBinding:
+      prefix: --out
+    default: system.pdbqt
+
+  output_log_path:
+    label: Path to the log file
+    doc: |-
+      Path to the log file
+      Type: string
+      File type: output
+      Accepted formats: log
+      Example file: https://github.com/bioexcel/biobb_vs/raw/master/biobb_vs/test/reference/vina/ref_output_vina.log
+    type: string
+    format:
+    - edam:format_2330
+    default: system.log
+
+  cpu:
+    label: The number of CPUs to use
+    doc: |-
+      The number of CPUs to use
+      Type: int
+    type: int?
+    format:
+    - edam:format_2330
+    inputBinding:
+      prefix: --cpu
+    default: 1
+
+  exhaustiveness:
+    label: exhaustiveness of the global search (roughly proportional to time).
+    doc: |-
+      exhaustiveness of the global search (roughly proportional to time).
+      Type: int
+    type: int?
+    format:
+    - edam:format_2330
+    inputBinding:
+      prefix: --exhaustiveness
+    default: 8
+
+  num_modes:
+    label: maximum number of binding modes to generate
+    doc: |-
+      Tmaximum number of binding modes to generate
+      Type: int
+    type: int?
+    format:
+    - edam:format_2330
+    inputBinding:
+      prefix: --num_modes
+    default: 9 
+
+  min_rmsd:
+    label: The minimum RMSD between output poses     
+    doc: |-
+      The minimum RMSD between output poses
+      Type: int
+    type: int?
+    format:
+    - edam:format_2330
+    inputBinding:
+      prefix: --min_rmsd
+    default: 1
+
+  energy_range:
+    label: maximum energy difference between the best binding mode and the worst one displayed (kcal/mol).
+    doc: |-
+      maximum energy difference between the best binding mode and the worst one displayed (kcal/mol).
+      Type: int
+    type: int?
+    format:
+    - edam:format_2330
+    inputBinding:
+      prefix: --energy_range
+    default: 3
+
+outputs:
+  output_pdbqt_path:
+    label: Path to the output PDBQT file
+    doc: |-
+      Path to the output PDBQT file
+    type: File
+    outputBinding:
+      glob: $(inputs.output_pdbqt_path)
+    format: edam:format_1476
+
+  output_log_path:
+    label: Path to the log file
+    doc: |-
+      Path to the log file
+    type: File
+    outputBinding:
+      glob: $(inputs.output_log_path)
+    format: edam:format_2330
+
+stdout: $(inputs.output_log_path)
+
+$namespaces:
+  edam: https://edamontology.org/
+
+$schemas:
+- https://raw.githubusercontent.com/edamontology/edamontology/master/EDAM_dev.owl
diff --git a/cwl_adapters/combine_pdb.cwl b/cwl_adapters/combine_pdb.cwl
new file mode 100644
index 0000000..5dac17f
--- /dev/null
+++ b/cwl_adapters/combine_pdb.cwl
@@ -0,0 +1,72 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+
+class: CommandLineTool
+
+label: A tool that employs MDAnalysis to combine two PDB structures in a single PDB file.
+
+doc: |-
+  A tool that employs MDAnalysis to combine two PDB structures in a single PDB file.
+
+baseCommand: ['python', '/combine_pdb.py']
+
+hints:
+  DockerRequirement:
+    dockerPull: ndonyapour/combine_pdb
+
+inputs:
+  input_structure1:
+    label: Input PDB structure 1 file path
+    doc: |-
+      Input PDB structure 1 file path
+      Type: string
+      File type: input
+      Accepted formats: pdb
+    type: File
+    format:
+    - edam:format_1476
+    inputBinding:
+      prefix: --input_structure1
+
+  input_structure2:
+    label: Input PDB structure 2 file path
+    doc: |-
+      Input PDB structure 2 file path
+      Type: string
+      File type: input
+      Accepted formats: pdb
+    type: File
+    format:
+    - edam:format_1476
+    inputBinding:
+      prefix: --input_structure2
+
+  output_structure_path:
+    label: Output combined PDB file path
+    doc: |-
+      Output combined PDB file path
+      Type: string
+      File type: output
+      Accepted formats: pdb
+      Example file: https://github.com/bioexcel/biobb_structure_utils/raw/master/biobb_structure_utils/test/reference/utils/ref_cat_pdb.pdb
+    type: string
+    format:
+    - edam:format_1476
+    inputBinding:
+      prefix: --output_structure_path
+    default: system.pdb
+outputs:
+  output_structure_path:
+    label: Output protein file path
+    doc: |-
+      Output protein file path
+    type: File
+    outputBinding:
+      glob: $(inputs.output_structure_path)
+    format: edam:format_1476
+
+$namespaces:
+  edam: https://edamontology.org/
+
+$schemas:
+- https://raw.githubusercontent.com/edamontology/edamontology/master/EDAM_dev.owl
diff --git a/cwl_adapters/convert_pdb.cwl b/cwl_adapters/convert_pdb.cwl
new file mode 100644
index 0000000..94ead7f
--- /dev/null
+++ b/cwl_adapters/convert_pdb.cwl
@@ -0,0 +1,129 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+
+class: CommandLineTool
+
+label: This class is a wrapper of the Open Babel tool.
+
+doc: |-
+  Small molecule format conversion for structures or trajectories. Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. Visit the official page.
+
+baseCommand: obabel
+#Usage:
+#obabel[-i<input-type>] <infilename> [-o<output-type>] -O<outfilename> [Options]
+#...
+#Options, other than -i -o -O -m, must come after the input files.
+arguments: [$(inputs.input_path), "-h", "-o", "pdb", "-O", $(inputs.output_pdb_path)]
+# NOTE: These arguments must be given individually; they cannot be concatenated together.
+# (e.g. -xrhn) Otherwise, all but the first argument will be silently ignored!
+
+# pdb format options
+# Read Options e.g. -as
+#   s  Output single bonds only
+#   b  Disable bonding entirely
+#   c  Ignore CONECT records
+
+# Write Options, e.g. -xo
+#   n  Do not write duplicate CONECT records to indicate bond order
+#   o  Write origin in space group label (CRYST1 section)
+
+hints:
+  DockerRequirement:
+    dockerPull: quay.io/biocontainers/biobb_chemistry:4.0.0--pyhdfd78af_1
+
+requirements:
+  InlineJavascriptRequirement: {}
+
+inputs:
+  first_molecule:
+    label: Index of the first molecule (1-based)
+    doc: |-
+      Input Index of the first molecule (1-based)
+      Type: string?
+    type: string?
+    format:
+    - edam:format_2330 # 'Textual format'
+    inputBinding:
+      prefix: -f
+
+  last_molecule:
+    label: Index of the last molecule (1-based)
+    doc: |-
+      Input Index of the last molecule (1-based)
+      Type: string?
+    type: string?
+    format:
+    - edam:format_2330 # 'Textual format'
+    inputBinding:
+      prefix: -l
+
+  input_path:
+    label: Path to the input file
+    doc: |-
+      Path to the input file
+      Type: string
+      File type: input
+      Accepted formats: dat, ent, fa, fasta, gro, inp, log, mcif, mdl, mmcif, mol, mol2, pdb, pdbqt, png, sdf, smi, smiles, txt, xml, xtc
+      Example file: https://github.com/bioexcel/biobb_chemistry/raw/master/biobb_chemistry/test/data/babel/babel.smi
+    type: File
+    format:
+    - edam:format_1637
+    - edam:format_1476
+    - edam:format_1929
+    - edam:format_1929
+    - edam:format_2033
+    - edam:format_3878
+    - edam:format_2030
+    - edam:format_1477
+    - edam:format_3815
+    - edam:format_1477
+    - edam:format_3815
+    - edam:format_3816
+    - edam:format_1476
+    - edam:format_1476
+    - edam:format_3603
+    - edam:format_3814
+    - edam:format_1196
+    - edam:format_1196
+    - edam:format_2033
+    - edam:format_2332
+    - edam:format_3875
+
+  output_pdb_path:
+    label: Path to the output file
+    doc: |-
+      Path to the output file
+      Type: string
+      File type: output
+      Accepted formats: pdb
+    type: string
+    format:
+    - edam:format_1476 # pdb
+    default: system.pdb
+
+  arg1:
+    label: Additional arguments
+    doc: |-
+      Additional arguments
+      Type: string?
+    type: string?
+    format:
+    - edam:format_2330 # 'Textual format'
+    inputBinding:
+      position: 1
+
+outputs:
+  output_pdb_path:
+    label: Path to the output file
+    doc: |-
+      Path to the output file
+    type: File
+    outputBinding:
+      glob: $(inputs.output_pdb_path)
+    format: edam:format_1476 # pdb
+
+$namespaces:
+  edam: https://edamontology.org/
+
+$schemas:
+- https://raw.githubusercontent.com/edamontology/edamontology/master/EDAM_dev.owl
diff --git a/cwl_adapters/onionnet-sfct.cwl b/cwl_adapters/onionnet-sfct.cwl
index 3cf2fb4..d4a8be4 100644
--- a/cwl_adapters/onionnet-sfct.cwl
+++ b/cwl_adapters/onionnet-sfct.cwl
@@ -9,7 +9,7 @@ baseCommand: ["python", "/OnionNet-SFCT/scorer.py"]
 
 hints:
   DockerRequirement:
-    dockerPull: polusai/onionnet-sfct-tool:1.0.0
+    dockerPull: polusai/onionnet-sfct-tool@sha256:8b51dd5e9d1218a4033cb6126c44aed0ea67a7ad4cfcf49ee4703fce7520c6be
 
 requirements:
   InlineJavascriptRequirement: {}
diff --git a/cwl_adapters/onionnet_featurize.cwl b/cwl_adapters/onionnet_featurize.cwl
new file mode 100644
index 0000000..42a977c
--- /dev/null
+++ b/cwl_adapters/onionnet_featurize.cwl
@@ -0,0 +1,70 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.0
+class: CommandLineTool
+
+label: Generate the features for the protein-ligand complexes using OnionNet V1
+
+baseCommand: ["conda", "run", "-n", "py37", "python", "/onionnet/generate_features.py"]
+arguments: ["-inp", "input.dat"]
+
+hints:
+  DockerRequirement:
+    dockerPull: ndonyapour/onionnet
+
+requirements:
+  - class: InlineJavascriptRequirement
+  # This enables staging input files and dynamically generating a file
+  # containing the file paths on the fly.
+  - class: InitialWorkDirRequirement 
+    listing: |
+      ${
+        var dat_file_contents = "";
+        for (var i = 0; i < inputs.pdb_paths.length; i++) {
+          dat_file_contents += inputs.pdb_paths[i].path + "\n";
+        }
+        // Note: Uses https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent
+        // and https://www.commonwl.org/user_guide/topics/creating-files-at-runtime.html
+        // "If the value is a string literal or an expression which evaluates to a string, 
+        // a new file must be created with the string as the file contents."
+        return ([{"entryname": "input.dat", "entry": dat_file_contents}]);
+      }
+
+inputs:
+  pdb_paths:
+    label: The path of input pdb files
+    type: File[]
+    format: 
+    - edam:format_1476 # PDB
+
+  num_of_cpus:
+    label: number of CPUs to use.
+    type: int?
+    format:
+    - edam:format_2330
+    inputBinding:
+      prefix: -nt
+    default: 1
+
+  output_feature_file:
+    label: the output file name containing the features.
+    type: string?
+    format:
+    - edam:format_3752
+    inputBinding:
+      prefix: -out
+    default: "output.csv"
+
+outputs:
+  output_feature_file:
+    type: File
+    format: edam:format_3752
+    outputBinding:
+      glob: $(inputs.output_feature_file)
+
+$namespaces:
+  edam: https://edamontology.org/
+  cwltool: http://commonwl.org/cwltool#
+
+$schemas:
+- https://raw.githubusercontent.com/edamontology/edamontology/master/EDAM_dev.owl
diff --git a/cwl_adapters/onionnet_score.cwl b/cwl_adapters/onionnet_score.cwl
new file mode 100644
index 0000000..6accd62
--- /dev/null
+++ b/cwl_adapters/onionnet_score.cwl
@@ -0,0 +1,113 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.0
+class: CommandLineTool
+
+label: OnionNet (version1) for rescoring of docking poses
+
+baseCommand: ["conda", "run", "-n", "py37", "python", "/onionnet/predict.py"]
+
+hints:
+  DockerRequirement:
+    dockerPull: ndonyapour/onionnet
+
+requirements:
+  InlineJavascriptRequirement: {}
+
+inputs:
+  input_feature_file:
+    label: feature csv file for protein-ligand complexes
+    type: File?
+    format:
+    - edam:format_3752
+    inputBinding:
+      prefix: -fn
+
+  scaler:
+    label: the standard scaler file.
+    type: string?
+    format:
+    - edam:format_2330
+    inputBinding:
+      prefix: -scaler
+    default: "/onionnet/models/StandardScaler.model"
+
+  weights:
+    label: the trained DNN model file.
+    type: string?
+    format:
+    - edam:format_2330
+    inputBinding:
+      prefix: -weights
+    default: "/onionnet/models/CNN_final_model_weights.h5"
+
+  output_score_file:
+    label: the predicted pKa values file
+    type: string?
+    format:
+    - edam:format_3752
+    inputBinding:
+      prefix: -out
+    default: "predicted_pKa.csv"
+
+  onionnet_score:
+    type: string?
+
+outputs:
+  output_score_file:
+    type: File
+    outputBinding:
+      glob: $(inputs.output_score_file)
+    format: edam:format_3752
+
+  onionnet_score:
+    label: Estimated Free Energy of Binding (onionnet score)
+    doc: |-
+      Estimated Free Energy of Binding
+    type: float[]
+    outputBinding:
+      glob: $(inputs.output_score_file)
+      loadContents: true
+      outputEval: |
+        ${
+          const lines = self[0].contents.split("\n");
+          // Remove blank lines
+          var non_blank_lines = lines.filter(function(line) {return line.trim() !== '';});
+          var onionnet_dGs = [];   
+
+          // Calculate the binding free energy from pKa, 
+          // See https://github.com/PolusAI/mm-workflows/blob/1c2284e5bf517b90950c2f7af574caff3aa536d8/examples/scripts/generate_conformers.py#L31
+          // Calculate pKa = -log(Kd), See https://en.wikipedia.org/wiki/Dissociation_constant,
+          // Calculate the binding free energy from Kd so we can make the correlation plots. dG = RT*ln(Kd/c)
+          // See https://en.wikipedia.org/wiki/Binding_constant
+          const ideal_gas_constant = 8.31446261815324;  // J/(Mol*K)
+          const kcal_per_joule = 4184;
+          // NOTE: Unfortunately, the temperature at which experimental Kd binding data was taken
+          // is often not recorded. Thus, we are forced to guess. The two standard guesses are
+          // physiological body temperature (310K) or room temperature (298K).
+          const temperature = 298;
+          const RT = (ideal_gas_constant / kcal_per_joule) * temperature;
+          // NOTE: For performance, simulations are often done in a very small unit cell, and
+          // thus at a very high concentration. The size of the unit cell bounds the volume.
+          // For shorter simulations where the ligand has not explored the entire box, it may
+          // be less. See the Yank paper for a method of calculating the correct volumes.
+          const standard_concentration = 1;  // Units of mol / L, but see comment above.  
+
+          for (var i = 1; i < non_blank_lines.length; i++) {
+            // The correct lines of output score file should be of the form
+            // pKa_predicted 
+            // /var/lib/cwl/stg19c300d1-f7fd-4a38-80d2-0f5615e3eb8f/complex_pdbs.pdb,7.441
+            var pKa_string = non_blank_lines[i].split(",").filter(function(s) {return !isNaN(parseFloat(s))})[0];
+            var Kd = (10 ** - parseFloat(pKa_string));
+            var dG = RT * Math.log(Kd / standard_concentration);
+            onionnet_dGs.push(dG);
+          }
+          return onionnet_dGs;
+        }
+
+$namespaces:
+  edam: https://edamontology.org/
+  cwltool: http://commonwl.org/cwltool#
+
+$schemas:
+- https://raw.githubusercontent.com/edamontology/edamontology/master/EDAM_dev.owl
diff --git a/cwl_adapters/rename_residues_mol2.cwl b/cwl_adapters/rename_residues_mol2.cwl
new file mode 100644
index 0000000..8be5d22
--- /dev/null
+++ b/cwl_adapters/rename_residues_mol2.cwl
@@ -0,0 +1,79 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+
+class: CommandLineTool
+
+label: Change the labels of residues
+
+doc: |
+  Change the labels of residues
+
+baseCommand: ["python", "/rename_residues.py"]
+
+hints:
+  DockerRequirement:
+    dockerPull: ndonyapour/rename_residues
+
+inputs:
+  input_path:
+    type: File
+    format:
+    - edam:format_3816 # mol2
+    inputBinding:
+      prefix: --input_path
+
+  output_path:
+    label: Path to the output file
+    doc: |-
+      Path to the output file
+    type: string
+    format:
+    - edam:format_3816 # mol2
+    inputBinding:
+      prefix: --output_path
+    default: system.mol2
+
+  residue_name:
+    label: The new residue name to which all residues should be changed 
+    doc: |-
+      The new residue name to which all residues should be changed
+    type: string
+    format:
+    - edam:format_2330
+    inputBinding:
+      prefix: --residue_name 
+ 
+  column_index:
+    label: The index of column of the line
+    doc: |-
+     The index of column of the line
+    type: int?
+    format:
+    - edam:format_2330
+    inputBinding:
+      prefix: --column_index
+
+  line_start_column_idxs:
+    label: A dictionary string indicating the line start and corresponding column indice 
+    doc: |-
+      A dictionary string indicating the line start and corresponding column indice
+    type: string?
+    format:
+    - edam:format_2330
+    inputBinding:
+      prefix: --line_start_column_idxs
+outputs:
+  output_path:
+    label: Path to the output file
+    doc: |-
+      Path to the output file
+    type: File
+    format: edam:format_3816 # mol2
+    outputBinding:
+      glob: $(inputs.output_path)
+
+$namespaces:
+  edam: https://edamontology.org/
+
+$schemas:
+- https://raw.githubusercontent.com/edamontology/edamontology/master/EDAM_dev.owl
\ No newline at end of file
diff --git a/cwl_adapters/rename_residues_pdb.cwl b/cwl_adapters/rename_residues_pdb.cwl
new file mode 100644
index 0000000..72d5f36
--- /dev/null
+++ b/cwl_adapters/rename_residues_pdb.cwl
@@ -0,0 +1,76 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+
+class: CommandLineTool
+
+label: Change the labels of residues
+
+doc: |
+  Change the labels of residues
+
+baseCommand: ["python", "/rename_residues.py"]
+
+hints:
+  DockerRequirement:
+    dockerPull: ndonyapour/rename_residues
+
+inputs:
+  input_path:
+    label: Input pdb file
+    type: File
+    format:
+    - edam:format_1476 # pdb
+    inputBinding:
+      prefix: --input_path
+
+  output_path:
+    label: Output pdb file
+    type: string?
+    format:
+    - edam:format_1476 # pdb
+    inputBinding:
+      prefix: --output_path
+    default: system.pdb
+
+  residue_name:
+    label: The new residue name to which all residues should be changed 
+    doc: |-
+      The new residue name to which all residues should be changed
+    type: string
+    format:
+    - edam:format_2330
+    inputBinding:
+      prefix: --residue_name 
+ 
+  column_index:
+    label: The index of column of the line
+    doc: |-
+     The index of column of the line
+    type: int?
+    format:
+    - edam:format_2330
+    inputBinding:
+      prefix: --column_index
+
+  line_start_column_idxs:
+    label: A dictionary string indicating the line start and corresponding column indice 
+    doc: |-
+      A dictionary string indicating the line start and corresponding column indice
+    type: string?
+    format:
+    - edam:format_2330
+    inputBinding:
+      prefix: --line_start_column_idxs
+
+outputs:
+  output_path:
+    type: File
+    format: edam:format_1476
+    outputBinding:
+      glob: $(inputs.output_path)
+
+$namespaces:
+  edam: https://edamontology.org/
+
+$schemas:
+- https://raw.githubusercontent.com/edamontology/edamontology/master/EDAM_dev.owl
\ No newline at end of file
diff --git a/cwl_adapters/smina_docking.cwl b/cwl_adapters/smina_docking.cwl
index 78b2614..a16c623 100644
--- a/cwl_adapters/smina_docking.cwl
+++ b/cwl_adapters/smina_docking.cwl
@@ -33,7 +33,6 @@ inputs:
     - edam:format_3815
     - edam:format_3816
     inputBinding:
-      position: 1
       prefix: -r
 
   ligand_file:
@@ -50,7 +49,6 @@ inputs:
     - edam:format_3815
     - edam:format_3816
     inputBinding:
-      position: 2
       prefix: -l
 
   ligand_box:
@@ -67,14 +65,24 @@ inputs:
     - edam:format_3815
     - edam:format_3816
     inputBinding:
-      position: 3
       prefix: --autobox_ligand
 
+  local_only:
+    label: try local minimization only rather than docking
+    type: boolean?
+    inputBinding:
+      prefix: --local_only
+
+  score_only:
+    label: Do not do any conformational search; simply rescore.
+    type: boolean?
+    inputBinding:
+      prefix: --score_only
+
   scoring:
     label: scoring function option, default is vina, options can be (vina, vinardo, or a customized scoring function) 
     type: string?
     inputBinding:
-      position: 4
       prefix: --scoring
     default: "vina"
 
@@ -83,7 +91,6 @@ inputs:
     type: string?
     format: edam:format_1476
     inputBinding:
-      position: 5
       prefix: -o
     default: "docked.pdb"
 
diff --git a/docker/dockerBuild.sh b/docker/dockerBuild.sh
index 368b8fa..5cfed75 100755
--- a/docker/dockerBuild.sh
+++ b/docker/dockerBuild.sh
@@ -27,7 +27,6 @@ sudo docker build --no-cache --pull -f Dockerfile_mol2_to_pdbqt -t jakefennick/m
 sudo docker build --no-cache --pull -f Dockerfile_nmr4md -t jakefennick/nmr4md .
 sudo docker build --no-cache --pull -f Dockerfile_openbabel -t ndonyapour/openbabel .
 sudo docker build --no-cache --pull -f Dockerfile_remove_terminal_residue_name_prefixes -t jakefennick/remove_terminal_residue_name_prefixes .
-sudo docker build --no-cache --pull -f Dockerfile_rename_residues_mol -t jakefennick/rename_residues_mol .
 sudo docker build --no-cache --pull -f Dockerfile_combine_structure -t ndonyapour/combine_structure .
 sudo docker build --no-cache --pull -f Dockerfile_molgan -t ndonyapour/molgan .
 sudo docker build --no-cache --pull -f Dockerfile_onionnet-sfct -t polusai/onionnet-sfct-tool:1.0.0 .
@@ -37,6 +36,9 @@ sudo docker build --no-cache --pull -f Dockerfile_extract_protein -t ndonyapour/
 sudo docker build --no-cache --pull -f Dockerfile_extract_ligand_protein -t mrbrandonwalker/extract_ligand_protein .
 sudo docker build --no-cache --pull -f Dockerfile_fix_pdb_atom_column -t ndonyapour/fix_pdb_atom_column .
 sudo docker build --no-cache --pull -f Dockerfile_generate_conformers -t ndonyapour/generate_conformers .
+sudo docker build --no-cache --pull -f Dockerfile_onionnet -t ndonyapour/onionnet .
+sudo docker build --no-cache --pull -f Dockerfile_combine_pdb -t ndonyapour/combine_pdb .
+sudo docker build --no-cache --pull -f Dockerfile_rename_residues -t ndonyapour/rename_residues .
 
 sudo docker build --no-cache --pull -f Dockerfile_pdbbind_refined -t pdbbind_refined_v2020 .  # NOTE: no username
 cd ../..
diff --git a/dockerPull.sh b/dockerPull.sh
index d635d77..0ff87fa 100755
--- a/dockerPull.sh
+++ b/dockerPull.sh
@@ -19,7 +19,6 @@ docker pull jakefennick/mol2_to_pdbqt
 docker pull jakefennick/nmr4md
 docker pull ndonyapour/openbabel
 docker pull jakefennick/remove_terminal_residue_name_prefixes
-docker pull jakefennick/rename_residues_mol
 docker pull ndonyapour/molgan
 docker pull cyangnyu/onionnet-sfct
 docker pull cyangnyu/smina
@@ -30,4 +29,7 @@ docker pull ndonyapour/pdbfixer
 docker pull ndonyapour/extract_protein
 docker pull mrbrandonwalker/extract_ligand_protein
 docker pull ndonyapour/fix_pdb_atom_column
-docker pull ndonyapour/generate_conformers
\ No newline at end of file
+docker pull ndonyapour/generate_conformers
+docker pull ndonyapour/onionnet
+docker pull ndonyapour/combine_pdb
+docker pull ndonyapour/rename_residues
diff --git a/examples/config_ci.json b/examples/config_ci.json
index 467efbd..a31fa5b 100644
--- a/examples/config_ci.json
+++ b/examples/config_ci.json
@@ -10,7 +10,8 @@
         "vs_demo_2_weekly",
         "vs_demo_3_weekly",
         "vs_demo_4_weekly",
-        "docking_rescoring_weekly"
+        "docking_rescoring_weekly",
+        "docking_rescoring_onionnet"
     ],
     // NOTE: Most of the workflows in this list have free variables because they are subworkflows
     // i.e. if you try to run them, you will get "Missing required input parameter"
diff --git a/examples/docking/convert_ligand_mol2_to_pdbqt_obabel.wic b/examples/docking/convert_ligand_mol2_to_pdbqt_obabel.wic
index a18ae51..f4de973 100644
--- a/examples/docking/convert_ligand_mol2_to_pdbqt_obabel.wic
+++ b/examples/docking/convert_ligand_mol2_to_pdbqt_obabel.wic
@@ -1,7 +1,12 @@
+inputs:
+  input_path:
+    type: File
+    format:
+    - edam:format_3816 
 steps:
   - id: convert_pdbqt
     in:
-      input_path: !* conformer.mol2
+      input_path: input_path
 #    out:
 #    - output_pdb_path: !& ligand_keywords.pdbqt
         # NOTE: There is no way to preserve the order of the atoms. Indeed, the
diff --git a/examples/docking/docking.wic b/examples/docking/docking.wic
index 10cf0f0..07c4402 100644
--- a/examples/docking/docking.wic
+++ b/examples/docking/docking.wic
@@ -9,9 +9,9 @@ steps:
 # NOTE: Searching for conformers tends to cause the ligand to curl up into a ball.
 # Although this lowers its energy in isolation, the decreased surface area tends
 # to weaken the binding free energy! (as reported by autodock vina)
-    flc.wic:
-      in:
-        sdf_path: sdf_path
+  flc.wic:
+    in:
+      sdf_path: sdf_path
 #    minimize_ligand_only.wic:
 
 # NOTE: We converted to mol2 format above because it allows explicit charges.
@@ -22,92 +22,96 @@ steps:
 
 # NOTE: Rename all residues to MOL before calling acpypye. Otherwise, acpype crashes with:
 # "ERROR: more than one residue detected '{'UNL', 'MOL'}'"
-    python3_mol2_to_mol2:
-      in:
-        script: !ii /rename_residues_mol.py # NOTE: Initial / required
-        input_mol2_path: !* ligand_min.mol2
-      out:
-      - output_mol2_path: !& conformer.mol2
+  rename_residues_mol2:
+    in:
+      input_path: !* ligand_min.mol2
+      output_path: !ii conformer.mol2
+      residue_name: !ii MOL
+      column_index: !ii 7
+    out:
+    - output_path: !& conformer.mol2
 
 # NOTE: minimize before calling acpype so 1. tleap complains less about close contacts:
 # /usr/local/bin/teLeap: Warning!
 # Close contact of 1.418311 angstroms between .R<UNL 1>.A<CG 8> and .R<UNL 1>.A<HD2 30>
 # and 2. acpype doesn't complain about 'ERROR: Atoms TOO alone (> 3.0 Ang.)'
 # (acpype suggests using --force, but it's better to just minimize.)
-    acpype:
-    # NOTE: We are using our own acpypye CWL adapter (NOT the biobb version) so
-    # we have the choice of using charges from the mol2 file.
-      in:
-        input_path: !* conformer.mol2 # Do NOT use pose_ligand.pdb
-      out:
-      - output_itp_path: !& ligand_GMX.itp
-        # NOTE: Although we don't need the *.itp topology file yet, we
-        # need to use these coordinates with autodock because they are
-        # sorted to agree with the *.itp topology include file.
-        # Otherwise, we will get the grompp atom name warning (see below).
-      - output_gro_path: !& ligand_GMX.gro
-      - output_top_path: !& ligand_GMX.top
-        #charge_method: user # take charges from mol2 file
+  acpype:
+  # NOTE: We are using our own acpypye CWL adapter (NOT the biobb version) so
+  # we have the choice of using charges from the mol2 file.
+    in:
+      input_path: !* conformer.mol2 # Do NOT use pose_ligand.pdb
+    out:
+    - output_itp_path: !& ligand_GMX.itp
+      # NOTE: Although we don't need the *.itp topology file yet, we
+      # need to use these coordinates with autodock because they are
+      # sorted to agree with the *.itp topology include file.
+      # Otherwise, we will get the grompp atom name warning (see below).
+    - output_gro_path: !& ligand_GMX.gro
+    - output_top_path: !& ligand_GMX.top
+      #charge_method: user # take charges from mol2 file
 # NOTE: acpype doesn't add forcefield or water topology #include lines.
-    bash_top:
-      in:
-        script: !ii /gmx_add_topology_includes.sh # NOTE: Initial / required
-        input_top_path: !* ligand_GMX.top
-      out:
-      - output_top_path: !& ligand_GMX_includes.top
-    zip_top:
-      in:
-        input_top_path: !* ligand_GMX_includes.top
-        input_itp_path: !* ligand_GMX.itp
-      out:
-      - output_top_zip_path: !& ligand_GMX.zip
+  bash_top:
+    in:
+      script: !ii /gmx_add_topology_includes.sh # NOTE: Initial / required
+      input_top_path: !* ligand_GMX.top
+    out:
+    - output_top_path: !& ligand_GMX_includes.top
+  zip_top:
+    in:
+      input_top_path: !* ligand_GMX_includes.top
+      input_itp_path: !* ligand_GMX.itp
+    out:
+    - output_top_zip_path: !& ligand_GMX.zip
 
 # Docking
-    convert_ligand_mol2_to_pdbqt_obabel.wic:
-#    convert_ligand_mol2_to_pdbqt_mdanalysis.wic: # generates ligand_rigid.pdbqt only
+  convert_ligand_mol2_to_pdbqt_obabel.wic:
+    in:
+      input_path: !* conformer.mol2
+#  - convert_ligand_mol2_to_pdbqt_mdanalysis.yml: # generates ligand_rigid.pdbqt only
 
-    autodock_vina_run:
-      in:
-        input_ligand_pdbqt_path: !* ligand_flex.pdbqt
-        #input_ligand_pdbqt_path: !* ligand_rigid.pdbqt
-        input_receptor_pdbqt_path: !* pdb.pdbqt
-        input_box_path: !* box.pdb
-      out:
-      - output_pdbqt_path: !& poses_ligand.pdbqt
-      - output_log_path: !& vina.log
-    extract_model_pdbqt:
-      in:
-        input_pdbqt_path: !* poses_ligand.pdbqt
-        output_pdbqt_path: !ii pose_ligand.pdbqt
-        config: !ii
-          model: 1 # NOTE: score, rmsd l.b., rmsd u.b. stored in REMARK lines
-      out:
-      - output_pdbqt_path: !& pose_ligand.pdbqt
-    convert_xyz:
-      in:
-        input_path: !* pose_ligand.pdbqt
-        output_xyz_path: !ii pose_ligand.xyz
-      out:
-      - output_xyz_path: !& pose_ligand.xyz
+  autodock_vina_run:
+    in:
+      input_ligand_pdbqt_path: !* ligand_flex.pdbqt
+      #input_ligand_pdbqt_path: !* ligand_rigid.pdbqt
+      input_receptor_pdbqt_path: !* pdb.pdbqt
+      input_box_path: !* box.pdb
+    out:
+    - output_pdbqt_path: !& poses_ligand.pdbqt
+    - output_log_path: !& vina.log
+  extract_model_pdbqt:
+    in:
+      input_pdbqt_path: !* poses_ligand.pdbqt
+      output_pdbqt_path: !ii pose_ligand.pdbqt
+      config: !ii
+        model: 1 # NOTE: score, rmsd l.b., rmsd u.b. stored in REMARK lines
+    out:
+    - output_pdbqt_path: !& pose_ligand.pdbqt
+  convert_xyz:
+    in:
+      input_path: !* pose_ligand.pdbqt
+      output_xyz_path: !ii pose_ligand.xyz
+    out:
+    - output_xyz_path: !& pose_ligand.xyz
 # Molecular Dynamics combine receptor & ligand
-    append_ligand:
-      in:
-        input_itp_path: !* ligand_GMX.itp
-        input_top_zip_path: !* receptor.zip
-      out:
-      - output_top_zip_path: !& complex_vac.zip
-    combine_structure:
-      in:
-        input_structure1: !* receptor.xyz  # receptor_hydrogens.pdb
-        input_structure2: !* pose_ligand.xyz
-      out:
-      - output_structure_path: !& complex_vac.pdb
+  append_ligand:
+    in:
+      input_itp_path: !* ligand_GMX.itp
+      input_top_zip_path: !* receptor.zip
+    out:
+    - output_top_zip_path: !& complex_vac.zip
+  combine_structure:
+    in:
+      input_structure1: !* receptor.xyz  # receptor_hydrogens.pdb
+      input_structure2: !* pose_ligand.xyz
+    out:
+    - output_structure_path: !& complex_vac.pdb
 
 wic:
    graphviz:
      label: Cheminformatics + Docking + Initial Topology Setup
    steps:
-     (2, python3_mol2_to_mol2):
+     (2, rename_residues_mol2):
        wic:
          graphviz:
            label: Rename Ligand\nResidues to MOL
diff --git a/examples/docking/gen_topol_params.wic b/examples/docking/gen_topol_params.wic
index 1efb759..430d236 100644
--- a/examples/docking/gen_topol_params.wic
+++ b/examples/docking/gen_topol_params.wic
@@ -18,12 +18,10 @@ steps:
 #      input_path: !* ligand.pdbqt
 #    out:
 #    - output_mol2_path: !& pose.mol2
-  python3_mol2_to_mol2:
+  rename_residues_mol2:
     in:
-      script: !ii /rename_residues_mol.py # NOTE: Initial / required
-#      input_mol2_path: !* pose.mol2
-#    out:
-#    - output_mol2_path: !& pose_mol.mol2
+      residue_name: !ii MOL
+      column_index: !ii 7
 # NOTE: minimize before calling acpype so 1. tleap complains less about close contacts:
 # /usr/local/bin/teLeap: Warning!
 # Close contact of 1.418311 angstroms between .R<UNL 1>.A<CG 8> and .R<UNL 1>.A<HD2 30>
@@ -89,7 +87,7 @@ wic:
       wic:
         graphviz:
           label: Convert to\nmol2 format
-    (2, python3_mol2_to_mol2):
+    (2, rename_residues_mol2):
       wic:
         graphviz:
           label: Rename Residues\nto MOL
diff --git a/examples/docking/ligand_modeling_docking.wic b/examples/docking/ligand_modeling_docking.wic
index b9a26ec..dbb9d51 100644
--- a/examples/docking/ligand_modeling_docking.wic
+++ b/examples/docking/ligand_modeling_docking.wic
@@ -9,9 +9,9 @@ steps:
 # NOTE: Searching for conformers tends to cause the ligand to curl up into a ball.
 # Although this lowers its energy in isolation, the decreased surface area tends
 # to weaken the binding free energy! (as reported by autodock vina)
-    flc.wic:
-      in:
-        sdf_path: sdf_path
+  flc.wic:
+    in:
+      sdf_path: sdf_path
 #    minimize_ligand_only.wic:
 #      in:
 #        sdf_path: sdf_path
@@ -24,36 +24,41 @@ steps:
 
 # NOTE: Rename all residues to MOL before calling acpypye. Otherwise, acpype crashes with:
 # "ERROR: more than one residue detected '{'UNL', 'MOL'}'"
-    python3_mol2_to_mol2:
-      in:
-        script: !ii /rename_residues_mol.py # NOTE: Initial / required
-        input_mol2_path: !* ligand_min.mol2
-      out:
-      - output_mol2_path: !& conformer.mol2
+  rename_residues_mol2:
+    in:
+      input_path: !* ligand_min.mol2
+      output_path: !ii conformer.mol2
+      residue_name: !ii MOL
+      column_index: !ii 7
+    out:
+    - output_path: !& conformer.mol2
+
 
 # Docking
-    convert_ligand_mol2_to_pdbqt_obabel.wic:
-#    convert_ligand_mol2_to_pdbqt_mdanalysis.wic: # generates ligand_rigid.pdbqt only
-    autodock_vina_run:
-      in:
-        input_ligand_pdbqt_path: !* ligand_flex.pdbqt
-        #input_ligand_pdbqt_path: !* ligand_rigid.pdbqt
-        input_receptor_pdbqt_path: !* pdb.pdbqt
-        input_box_path: !* box.pdb
-      out:
+  convert_ligand_mol2_to_pdbqt_obabel.wic:
+    in:
+      input_path: !* conformer.mol2
+#  - convert_ligand_mol2_to_pdbqt_mdanalysis.yml: # generates ligand_rigid.pdbqt only
+  autodock_vina_run:
+    in:
+      input_ligand_pdbqt_path: !* ligand_flex.pdbqt
+      #input_ligand_pdbqt_path: !* ligand_rigid.pdbqt
+      input_receptor_pdbqt_path: !* pdb.pdbqt
+      input_box_path: !* box.pdb
+    out:
 #      - output_pdbqt_path: !& poses_ligand.pdbqt
-      - output_log_path: !& vina.log
-    split_pdbqt:
+    - output_log_path: !& vina.log
+  split_pdbqt:
 #      in:
 #        input_path: !* poses_ligand.pdbqt # Scalar type
-      out:
-      - output_pdb_path: !& ligand_nested_split.pdbqt
+    out:
+    - output_pdb_path: !& ligand_nested_split.pdbqt
 
 wic:
   graphviz:
     label: Perform Ligand\nModeling & Docking
   steps:
-    (2, python3_mol2_to_mol2):
+    (2, rename_residues_mol2):
       wic:
         graphviz:
           label: Rename Residues\nto MOL
diff --git a/examples/onionnet/autodock_onionnet.wic b/examples/onionnet/autodock_onionnet.wic
new file mode 100644
index 0000000..8d887f0
--- /dev/null
+++ b/examples/onionnet/autodock_onionnet.wic
@@ -0,0 +1,255 @@
+## Protein-ligand docking and docking poses re-ranking
+##
+## input: pdb structures from PDBbind refined dataset
+## output: 
+##    1. Docking  
+##    2. Scoring the best pose using OnionNet
+
+steps:
+  extract_pdbbind_refined:
+    in:
+      # https://pandas.pydata.org/docs/reference/api/pandas.DataFrame.query.html
+      # The query() method uses a slightly modified Python syntax by default.
+      # For example, the & and | (bitwise) operators have the precedence of their
+      # boolean cousins, and and or. This is syntactically valid Python, however
+      # the semantics are different.
+      query: !ii '(Kd_Ki == "Kd") and (value < 0.001)'
+      max_row: !ii 1 #25 # Use 1 for CI
+      convert_Kd_dG: !ii True
+      output_txt_path: !ii binding_data.txt
+    out:
+    - output_txt_path: !& binding_data.txt
+    - output_pdb_paths: !& pdbbind_pdbs
+    - output_sdf_paths: !& pdbbind_sdfs
+    - experimental_dGs: !& exp_dGs
+    - pdb_ids: !& pdbids
+  extract_protein:
+    scatter: [input_pdb_path]
+    in:
+      input_pdb_path: !* pdbbind_pdbs
+      output_pdb_path: !ii pdbbind_protein.pdb
+    out:
+    - output_pdb_path: !& pdbbind_protein.pdb
+  config_tag_pdb:
+    scatter: [pdb_id]
+    in:
+      pdb_id: !* pdbids
+      filter: !ii False
+    out: 
+    - output_config_string: !& pdb_id_str
+  pdb:
+    scatter: [config]
+    in:
+      output_pdb_path: !ii rcsb_protein.pdb
+      config: !* pdb_id_str
+    out:
+    - output_pdb_path: !& rcsb_protein.pdb
+  pdb_fixer:
+    in:
+      input_pdb_path: !* pdbbind_protein.pdb
+      input_helper_pdb_path: !* rcsb_protein.pdb # Note: PDBFixer utilizes sequence information from this file
+      output_pdb_path: !ii pdbbind_pdbfixer.pdb
+      add_atoms: !ii heavy
+      add_residues: !ii True
+      replace_nonstandard: !ii True
+      keep_heterogens: !ii none
+    scatter: [input_pdb_path, input_helper_pdb_path]
+    scatterMethod: dotproduct
+    out:
+    - output_pdb_path: !& pdbbind_pdbfixer.pdb
+  setup_pdb.wic:
+    scatter: [input_pdb_path]
+    in:
+      input_pdb_path: !* pdbbind_pdbfixer.pdb
+      pdb_path: !ii pdb.pdbqt
+      box_path: !ii box.pdb
+      box_buffer: !ii 20 # Angstroms
+      water_type: !ii spce
+      forcefield: !ii amber99sb-ildn
+    out:
+    - pdb_path: !& pdb.pdbqt
+    - box_path: !& box.pdb
+
+  # assign partial charges (ligand)
+  convert_mol2:
+    scatter: [input_path]
+    in:
+      input_path: !* pdbbind_sdfs
+
+  rename_residues_mol2:
+    scatter: [input_path]
+    in:
+      output_path: !ii ligand.mol2
+      residue_name: !ii MOL
+      column_index: !ii 7
+    out: 
+    - output_path: !& ligand.mol2
+
+  convert_ligand_mol2_to_pdbqt_obabel.wic:
+    scatter: [input_path]
+  autodock_vina:
+    scatter: [input_ligand_pdbqt_path, input_receptor_pdbqt_path, input_box_path]
+    scatterMethod: dotproduct
+    in:
+      input_ligand_pdbqt_path: !* ligand_rigid.pdbqt
+      input_receptor_pdbqt_path: !* pdb.pdbqt
+      input_box_path: !* box.pdb
+      output_pdbqt_path: !ii  poses_ligand.pdbqt
+      output_log_path: !ii vina.log
+      num_modes: !ii 20
+    out:
+    - output_pdbqt_path: !& poses_ligand.pdbqt
+    - output_log_path: !& vina.log'
+
+  extract_model_pdbqt:
+    scatter: [input_pdbqt_path]
+    in: 
+      input_pdbqt_path: !* poses_ligand.pdbqt
+      output_pdbqt_path: !ii pose_ligand.pdbqt
+      config: !ii
+        model: 1 # NOTE: score, rmsd l.b., rmsd u.b. stored in REMARK lines
+    out:
+    - output_pdbqt_path: !& pose_ligand.pdbqt
+
+  convert_pdb:
+    scatter: [input_path]
+    in:
+      input_path: !* pose_ligand.pdbqt
+      output_pdb_path: !ii pose_ligand.pdb
+    out:
+    - output_pdb_path: !& pose_ligand.pdb
+
+  rename_residues_pdb:
+    scatter: [input_path]
+    in:
+      input_path: !* pose_ligand.pdb
+      output_path: !ii ligand.pdb
+      residue_name: !ii LIG
+      line_start_column_idxs: !ii '{"ATOM": 3, "HETATM": 3, "TER": 2}'
+    out:
+    - output_path: !& ligand.pdb
+
+  combine_pdb:
+    scatter: [input_structure1, input_structure2]
+    scatterMethod: dotproduct
+    in:
+      input_structure1: !* pdbbind_pdbfixer.pdb
+      input_structure2: !* ligand.pdb
+      output_structure_path: !ii complex_pdb.pdb
+    out:
+    - output_structure_path: !& complex_pdb.pdb
+
+  onionnet_featurize:
+    in:
+      pdb_paths: !* complex_pdb.pdb
+      output_feature_file: !ii output_features.csv
+    out:
+    - output_feature_file: !& output_features.csv
+ 
+  onionnet_score:
+    in:
+      input_feature_file: !* output_features.csv
+      output_score_file: !ii predicted_pKa.csv
+      onionnet_score: !ii onionnet_score
+    out:
+    - output_score_file: !& predicted_pKa.csv
+    - onionnet_score: !& onionnet_score
+
+  scatter_plot:
+    in:
+      xs: !* exp_dGs
+      ys: !* onionnet_score
+      output_png_path: !ii dG_exp_wpred.png
+    out:
+    - output_png_path: !& dG_exp_wpred.png
+
+  check_linear_fit:
+    in:
+      xs: !* exp_dGs
+      ys: !* onionnet_score
+      # Use massive tolerances because the re-docking performance of classical scoring functions (Vina) are unreliable.
+      tol_quad: !ii 0.18
+      slope_min: !ii -10
+      slope_max: !ii 10
+
+wic:
+  graphviz:
+    label: Virtual Screening Demo
+  steps:
+    (1, extract_pdbbind_refined):
+      wic:
+        graphviz:
+          label: Extract PDBbind Data
+    (2, extract_protein):
+      wic:
+        inlineable: False
+        graphviz:
+          label: Extract protein
+    (3, config_tag_pdb):
+      wic:
+        inlineable: False
+        graphviz:
+          label: Specify PDB Code
+    (4, pdb):
+      wic:
+        inlineable: False
+        graphviz:
+          label: Download PDB File
+    (5, pdbfixer):
+      wic:
+        inlineable: False
+        graphviz:
+          label: Fix Protein Structure
+    (6, setup_pdb.yml):
+      wic:
+        inlineable: True
+        graphviz:
+          label: Setup PDB
+    (7, convert_mol2):
+      wic:
+        graphviz:
+          label: Convert Ligand\nsdf to mol2
+    (8, rename_residues_mol2):
+      wic:
+         graphviz:
+           label: Rename Ligand\nResidues to MOL
+    (9, convert_ligand_mol2_to_pdbqt_obabel.yml):
+      wic:
+        graphviz:
+          label: Rename Residues\nto MOL
+    (10, autodock_vina):
+      wic:
+        graphviz:
+          label: Docking
+    (11, extract_model_pdbqt):
+       wic:
+         graphviz:
+           label: Extract Best\nDocking Pose
+    (12, convert_pdb):
+      wic:
+        graphviz:
+          label: Convert to\npdb format
+    (13, rename_residues_pdb):
+      wic:
+        graphviz:
+          label: Rename residues to LIG
+    (14, combine_pdb):
+      wic:
+        graphviz:
+          label: Combine Protein & Ligand\nPDB Structures
+    (15, onionnet_featurize):
+      wic:
+        graphviz:
+          label: Generate features for the Docking Poses
+    (16, onionnet_score):
+      wic:
+        graphviz:
+          label: Predict Binding Scores
+    (17, scatter_plot):
+      wic:
+        graphviz:
+          label: Plot Experimental\nvs Predicted Binding
+    (18, check_linear_fit):
+      wic:
+        graphviz:
+          label: True if fitted slope is between slope_min and slope_max
\ No newline at end of file
diff --git a/examples/rescoring/docking_rescoring.wic b/examples/onionnet/docking_rescoring.wic
similarity index 98%
rename from examples/rescoring/docking_rescoring.wic
rename to examples/onionnet/docking_rescoring.wic
index 97c7b1a..0c2e958 100644
--- a/examples/rescoring/docking_rescoring.wic
+++ b/examples/onionnet/docking_rescoring.wic
@@ -6,7 +6,6 @@
 ##    2. scoring file (vina score, sfct correction, combined_score for re-ranking docking poses)
 
 steps:
-#
 - id: extract_pdbbind_refined
   in:
     # https://pandas.pydata.org/docs/reference/api/pandas.DataFrame.query.html
@@ -15,7 +14,7 @@ steps:
     # This is syntactically valid Python, however the semantics are different."
     query: !ii '(Kd_Ki == "Kd") and ((value < 0.0001) or ((0.08 < value) and ( value < 0.1)) or ((8 < value) and ( value < 10)) or (1000 < value))'
       # to obtain a broader experimental dGs
-    max_row: !ii 500 # first 500 rows selection.
+    max_row: !ii 100 # first 500 rows selection.
     convert_Kd_dG: !ii True
     output_txt_path: !ii binding_data.txt
   out:
diff --git a/examples/rescoring/docking_rescoring_weekly.wic b/examples/onionnet/docking_rescoring_weekly.wic
similarity index 84%
rename from examples/rescoring/docking_rescoring_weekly.wic
rename to examples/onionnet/docking_rescoring_weekly.wic
index 8e56403..6c847f2 100644
--- a/examples/rescoring/docking_rescoring_weekly.wic
+++ b/examples/onionnet/docking_rescoring_weekly.wic
@@ -8,7 +8,7 @@ wic:
         steps:
           (1, extract_pdbbind_refined):
             in:
-              max_row: !ii 1000  # Default 500
+              max_row: !ii 1000  # Default 100
           (2, random_subset_rows):
             in:
               num_of_samples: !ii 32
\ No newline at end of file
diff --git a/examples/onionnet/replicate_onionnet_paper.wic b/examples/onionnet/replicate_onionnet_paper.wic
new file mode 100644
index 0000000..ec3e460
--- /dev/null
+++ b/examples/onionnet/replicate_onionnet_paper.wic
@@ -0,0 +1,124 @@
+## Protein-ligand dG predcition
+##
+## input: pdb structures from PDBbind refined dataset
+## output: 
+##    1. Predicting protein-ligand pKa using OnionNet 
+
+steps:
+  extract_pdbbind_refined:
+    in:
+      # https://pandas.pydata.org/docs/reference/api/pandas.DataFrame.query.html
+      # The query() method uses a slightly modified Python syntax by default.
+      # For example, the & and | (bitwise) operators have the precedence of their
+      # boolean cousins, and and or. This is syntactically valid Python, however
+      # the semantics are different.
+      query: !ii '(Kd_Ki == "Kd") and (value < 0.001)'
+      max_row: !ii 1 #25 # Use 1 for CI
+      convert_Kd_dG: !ii True
+      output_txt_path: !ii binding_data.txt
+    out:
+    - output_txt_path: !& binding_data.txt
+    - output_pdb_paths: !& pdbbind_pdbs
+    - output_sdf_paths: !& pdbbind_sdfs
+    - experimental_dGs: !& exp_dGs
+    - pdb_ids: !& pdbids
+
+  convert_pdb:
+    scatter: [input_path]
+    in:
+      input_path: !* pdbbind_sdfs
+      output_pdb_path: !ii ligand_pdbbind.pdb
+    out:
+    - output_pdb_path: !& ligand_pdbbind.pdb
+
+  rename_residues_pdb:
+    scatter: [input_path]
+    in:
+      input_path: !* ligand_pdbbind.pdb
+      output_path: !ii ligand.pdb
+      residue_name: !ii LIG # Note, the residue name should be three characters
+      # See: https://www.cgl.ucsf.edu/chimera/1.4/docs/UsersGuide/tutorials/pdbintro.html
+      line_start_column_idxs: !ii '{"ATOM": 3, "HETATM": 3, "TER": 2}'
+    out:
+    - output_path: !& ligand.pdb
+        
+  combine_pdb:
+    scatter: [input_structure1, input_structure2]
+    scatterMethod: dotproduct
+    in:
+      input_structure1: !* pdbbind_pdbs 
+      input_structure2: !* ligand.pdb
+      output_structure_path: !ii complex_pdbs.pdb
+    out:
+    - output_structure_path: !& complex_pdbs.pdb
+
+  onionnet_featurize:
+    in:
+      pdb_paths: !* complex_pdbs.pdb
+      output_feature_file: !ii output_features.csv
+    out:
+    - output_feature_file: !& output_features.csv
+
+  onionnet_score:
+    in:
+      input_feature_file: !* output_features.csv
+      output_score_file: !ii predicted_pKa.csv
+      onionnet_score: !ii onionnet_score
+    out:
+    - output_score_file: !& predicted_pKa.csv
+    - onionnet_score: !& onionnet_score
+
+  scatter_plot:
+    in:
+      xs: !* exp_dGs
+      ys: !* onionnet_score
+      output_png_path: !ii dG_exp_wpred.png
+    out:
+    - output_png_path: !& dG_exp_wpred.png
+
+  check_linear_fit:
+    in:
+      xs: !* exp_dGs
+      ys: !* onionnet_score
+      # Use massive tolerances because the re-docking performance of classical scoring functions (Vina) are unreliable.
+      tol_quad: !ii 0.18
+      slope_min: !ii -10
+      slope_max: !ii 10
+
+wic:
+  graphviz:
+    label: Virtual Screening Demo
+  steps:
+    (1, extract_pdbbind_refined):
+      wic:
+        graphviz:
+          label: Extract PDBbind Data
+
+    (2, convert_pdb):
+      wic:
+        graphviz:
+          label: Convert to PDB 
+    (3, rename_residues_pdb):
+      wic:
+        graphviz:
+          label: Rename residues to LIG
+    (4, combine_pdb):
+      wic:
+        graphviz:
+          label: Combine Protein & Ligand\nPDB Structures
+    (5, onionnet_featurize):
+      wic:
+        graphviz:
+          label: Generate features for the Docking Poses
+    (6, onionnet_score):
+      wic:
+        graphviz:
+          label: Predict Binding Scores
+    (7, scatter_plot):
+      wic:
+        graphviz:
+          label: Plot Experimental\nvs Predicted Binding
+    (8, check_linear_fit):
+      wic:
+        graphviz:
+          label: True if fitted slope is between slope_min and slope_max
\ No newline at end of file
diff --git a/examples/scripts/Dockerfile_combine_pdb b/examples/scripts/Dockerfile_combine_pdb
new file mode 100644
index 0000000..71de53f
--- /dev/null
+++ b/examples/scripts/Dockerfile_combine_pdb
@@ -0,0 +1,7 @@
+FROM condaforge/mambaforge
+# NOT mambaforge-pypy3 (mdanalysis is incompatible with pypy)
+
+RUN mamba install -c conda-forge mdanalysis
+
+ADD combine_pdb.py .
+ADD Dockerfile_combine_pdb .
diff --git a/examples/scripts/Dockerfile_onionnet b/examples/scripts/Dockerfile_onionnet
new file mode 100644
index 0000000..d9132db
--- /dev/null
+++ b/examples/scripts/Dockerfile_onionnet
@@ -0,0 +1,34 @@
+FROM condaforge/mambaforge
+# NOT mambaforge-pypy3 (pandas & rdkit & mdtraj are incompatible with pypy)
+
+# Install requirements
+RUN apt-get update && apt-get install -y wget git
+
+# Create environment
+# Since python 3.10 is already installed in the base image condaforge/mambaforge, 
+# See https://github.com/zhenglz/onionnet#installation 
+# OnionNet uses sklearn.externals.joblib which is removed in sklearn 0.23
+# RUN mamba install -y python=3.7 Doesn't work
+RUN mamba create -n py37 python=3.7
+
+# Activate the conda environment
+SHELL ["conda", "run", "-n", "py37", "/bin/bash", "-c"]
+RUN echo "source activate py37" > ~/.bashrc
+ENV PATH /opt/conda/envs/env/bin:$PATH
+
+# Install the required packages
+RUN mamba install -c conda-forge scipy numpy pandas "scikit-learn<0.23" mdtraj openbabel tensorflow -y
+
+# cleanup
+RUN apt-get clean
+RUN mamba clean --all --yes
+
+# Install onionnet
+RUN git clone https://github.com/zhenglz/onionnet.git
+
+# Download models
+## the default model of onionnet-v1 in github repo is not correct, the actually size is around 600 MB. 
+## The authors provided a google drive link to download it, 
+## but their command wget "https://drive.google.com/uc?export=download&id=1cwJN44TgaVBWYEEb_SGU5JBJp6WbFdM1" -O "CNN_final_model_weights.h5" is not working.
+RUN cd /onionnet/models && rm CNN_final_model_weights.h5 && wget -nv --no-clobber https://huggingface.co/ndonyapour/OnionNet-V1/resolve/main/CNN_final_model_weights.h5
+ADD Dockerfile_onionnet .
\ No newline at end of file
diff --git a/examples/scripts/Dockerfile_rename_residues b/examples/scripts/Dockerfile_rename_residues
new file mode 100644
index 0000000..2481697
--- /dev/null
+++ b/examples/scripts/Dockerfile_rename_residues
@@ -0,0 +1,7 @@
+FROM python
+
+RUN apt-get update && apt-get install -y wget
+RUN apt-get clean
+
+Add rename_residues.py .
+Add Dockerfile_rename_residues .
diff --git a/examples/scripts/combine_pdb.py b/examples/scripts/combine_pdb.py
new file mode 100644
index 0000000..9c00e08
--- /dev/null
+++ b/examples/scripts/combine_pdb.py
@@ -0,0 +1,61 @@
+import sys
+import os
+import argparse
+from typing import Optional
+import numpy as np
+
+import MDAnalysis as mda
+
+
+def parse_arguments() -> argparse.Namespace:
+    """ This function parses the arguments.
+
+    Returns:
+        argparse.Namespace: The command line arguments
+    """
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--input_structure1', type=str)
+    parser.add_argument('--input_structure2', type=str)
+    parser.add_argument('--output_structure_path', type=str)
+    args = parser.parse_args()
+    return args
+
+
+def combine_structure_rdkit(input_structure1_path: str, input_structure2_path: str, output_structure_path: str) -> None:
+    """ Combine two structures into a single PDB file using MDAnalysis
+
+    Args:
+        input_structure1_path (str): The path to the PDB structure 1 
+        input_structure2_path (str): The path to the PDB structure 2 
+        output_structure_path (str): The path to the output combined PDB structure
+    """
+
+    u1 = mda.Universe(input_structure1_path)
+    u2 = mda.Universe(input_structure2_path)
+
+    merged = mda.Merge(u1.atoms, u2.atoms)
+    merged_elements = np.concatenate([u1.atoms.elements, u2.atoms.elements])
+
+    merged.atoms.elements = merged_elements
+    all_atoms = merged.select_atoms("all")
+    all_atoms.write(output_structure_path)
+
+
+def main() -> None:
+    """ Reads the command line arguments and combine two structures into a single PDB file
+    """
+    args = parse_arguments()
+
+    if not os.path.exists(args.input_structure1):
+        print(f'Error: Can not find file {args.input_structure1}')
+        sys.exit(1)
+
+    if not os.path.exists(args.input_structure2):
+        print(f'Error: Can not find file {args.input_structure2}')
+        sys.exit(1)
+
+    combine_structure_rdkit(args.input_structure1, args.input_structure2, args.output_structure_path)
+
+
+if __name__ == '__main__':
+    main()
diff --git a/examples/scripts/rename_residues.py b/examples/scripts/rename_residues.py
new file mode 100644
index 0000000..50a255f
--- /dev/null
+++ b/examples/scripts/rename_residues.py
@@ -0,0 +1,86 @@
+import sys
+import os
+import argparse
+import ast
+from typing import Dict
+
+
+def parse_arguments() -> argparse.Namespace:
+    """ This function parses the arguments.
+
+    Returns:
+        argparse.Namespace: The command line arguments
+    """
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--input_path', type=str)
+    parser.add_argument('--output_path', type=str)
+    parser.add_argument('--residue_name', type=str)
+    parser.add_argument('--column_index', type=int, required=False, default=None)
+    parser.add_argument('--line_start_column_idxs', type=str, required=False, default=None)
+    args = parser.parse_args()
+    return args
+
+
+def rename_residues(input_path: str, output_path: str, residue_name: str,
+                    column_index: int, line_start_column_idxs: str) -> None:
+    """ Modifies the names of residues based on the specified column index or 
+    line start and column indices
+
+    Args:
+        input_path (str): input file path
+        output_path (str): output file path
+        residue_name (str): The new residue name to which all residues should be changed 
+        column_index (int): The index of column
+        line_start_column_idxs (str): A dictionary string indicating the line start and corresponding column indices, 
+        such as '{"ATOM": 3, "HETATM": 3}'.
+    """
+    line_start_column_idxs_dict: Dict[str, int] = {}
+
+    if line_start_column_idxs:
+        # Parse the dictionary string to a dictionary
+        line_start_column_idxs_dict = ast.literal_eval(line_start_column_idxs)
+
+    with open(input_path, mode='r', encoding='utf-8') as f:
+        lines = f.readlines()
+
+    lines_new = []
+    for line in lines:
+        l = line
+        words = l.split()
+        if column_index:
+            if len(words) >= column_index:
+                l = l.replace(words[column_index], residue_name)
+        elif line_start_column_idxs:
+            for line_start, cindex in line_start_column_idxs_dict.items():
+                if words[0] == line_start:
+                    l = l.replace(words[cindex], residue_name)
+
+        lines_new.append(l)
+
+    with open(output_path, mode='w', encoding='utf-8') as f:
+        f.writelines(lines_new)
+
+
+def main() -> None:
+    """ Reads the command line arguments and renames the residues
+    """
+    args = parse_arguments()
+
+    if args.input_path and not os.path.exists(args.input_path):
+        print(f'Error: Can not find file {args.input_path}')
+        sys.exit(1)
+
+    if (args.column_index is None) and (args.line_start_column_idxs is None):
+        print("Error: No column index information is provided")
+        sys.exit(1)
+
+    if (args.column_index) and (args.line_start_column_idxs):
+        print("Error: One of column_index or line_start_column_idxs arguments should be provided")
+        sys.exit(1)
+
+    rename_residues(args.input_path, args.output_path, args.residue_name,
+                    args.column_index, args.line_start_column_idxs)
+
+
+if __name__ == '__main__':
+    main()
diff --git a/examples/scripts/rename_residues_mol.py b/examples/scripts/rename_residues_mol.py
deleted file mode 100644
index 29550fc..0000000
--- a/examples/scripts/rename_residues_mol.py
+++ /dev/null
@@ -1,20 +0,0 @@
-import sys
-
-input_mol2_path = sys.argv[1]
-output_mol2_path = sys.argv[2]
-
-with open(input_mol2_path, mode='r', encoding='utf-8') as f:
-    lines = f.readlines()
-
-lines_new = []
-index = 7  # mol2 file format residue name column index
-for line in lines:
-    l = line
-    words = l.split()
-    if len(words) >= index:  # TODO: and only for ATOM records
-        l = l.replace(words[index], 'MOL')
-
-    lines_new.append(l)
-
-with open(output_mol2_path, mode='w', encoding='utf-8') as f:
-    f.writelines(lines_new)