diff --git a/README.md b/README.md
index c2e0a5f..991d347 100644
--- a/README.md
+++ b/README.md
@@ -1,5 +1,3 @@
-<img align="right" width="230" src="assets/logo.png" />
-
 [![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://moleculehub.github.io/OpenBabel.jl/dev/)
 [![Code Style: Blue](https://img.shields.io/badge/code%20style-blue-4495d1.svg)](https://github.com/JuliaDiff/BlueStyle)
 [![Aqua QA](https://raw.githubusercontent.com/JuliaTesting/Aqua.jl/master/badge.svg)](https://github.com/JuliaTesting/Aqua.jl)
diff --git a/assets/logo.png b/assets/logo.png
deleted file mode 100644
index d1b706c..0000000
Binary files a/assets/logo.png and /dev/null differ
diff --git a/docs/src/api/energy.md b/docs/src/api/energy.md
index 23e65ba..3ae25f6 100644
--- a/docs/src/api/energy.md
+++ b/docs/src/api/energy.md
@@ -2,26 +2,55 @@
 
 These macros perform energy calculations, geometry optimizations, and advanced molecular computations.
 
-## Energy Calculations
+## Calculate Energy
 
 ```@docs
 @calculate_energy
-@minimize_energy
-@add_partial_charges
 ```
 
-## Structure Generation
+### Usage Examples
 
-```@docs
-@canonicalize
-@generate_conformers
+Calculate energy using different force fields:
+
+```julia
+# MMFF94 forcefield (default)
+@chain begin
+    @read_file("molecules.smi", "smi")
+    @gen_3D_coords("fast")
+    @calculate_energy("MMFF94")
+    @output_as("energies.sdf", "sdf")
+    @execute
+end
+
+# UFF forcefield
+@chain begin
+    @read_file("molecules.smi", "smi")
+    @gen_3D_coords("med")
+    @calculate_energy("UFF")
+    @output_as("uff_energies.sdf", "sdf")
+    @execute
+end
 ```
 
-## Usage Examples
+Energy ranking workflow:
 
-### Energy Minimization Workflow
+```julia
+@chain begin
+    @read_file("conformers.sdf", "sdf")
+    @calculate_energy("MMFF94")
+    @sort_by("Energy")  # Sort by ascending energy (most stable first)
+    @output_as("energy_ranked.sdf", "sdf")
+    @execute
+end
+```
+
+## Minimize Energy
 
-Optimize molecular geometries using different forcefields:
+```@docs
+@minimize_energy
+```
+
+### Usage Examples
 
 ```julia
 # MMFF94 forcefield (default)
@@ -29,7 +58,6 @@ Optimize molecular geometries using different forcefields:
     @read_file("molecules.smi", "smi")
     @gen_3D_coords("fast")
     @minimize_energy("MMFF94")
-    @calculate_energy("MMFF94")
     @output_as("optimized.sdf", "sdf")
     @execute
 end
@@ -44,19 +72,26 @@ end
 end
 ```
 
-### Available Forcefields
+Complete energy minimization workflow:
 
-| Forcefield | Description | Best for |
-|------------|-------------|----------|
-| `MMFF94` | Merck Molecular Force Field | General organic molecules |
-| `MMFF94s` | MMFF94 static | Static conformations |
-| `UFF` | Universal Force Field | Broad chemical space |
-| `GAFF` | General AMBER Force Field | Drug-like molecules |
-| `Ghemical` | Ghemical Force Field | Quick calculations |
+```julia
+@chain begin
+    @read_file("molecules.smi", "smi")
+    @gen_3D_coords("fast")
+    @minimize_energy("MMFF94")
+    @calculate_energy("MMFF94")
+    @output_as("optimized.sdf", "sdf")
+    @execute
+end
+```
 
-### Partial Charge Calculation
+## Add Partial Charges
 
-Add partial charges using different methods:
+```@docs
+@add_partial_charges
+```
+
+### Usage Examples
 
 ```julia
 # Gasteiger charges (default)
@@ -78,7 +113,7 @@ end
 end
 ```
 
-### Available Charge Methods
+Available charge methods:
 
 | Method | Description | Accuracy | Speed |
 |--------|-------------|----------|-------|
@@ -88,7 +123,32 @@ end
 | `eqeq` | EQEq charges | Medium | Fast |
 | `eem` | Electronegativity Equalization | Medium | Medium |
 
-### Conformer Generation
+## Canonicalize
+
+```@docs
+@canonicalize
+```
+
+### Usage Examples
+
+Standardize molecular representation:
+
+```julia
+@chain begin
+    @read_file("compounds.smi", "smi")
+    @canonicalize()
+    @output_as("canonical_structures.smi", "smi")
+    @execute
+end
+```
+
+## Generate Conformers
+
+```@docs
+@generate_conformers
+```
+
+### Usage Examples
 
 Generate multiple conformations:
 
@@ -103,9 +163,19 @@ Generate multiple conformations:
 end
 ```
 
-### Complete Energy Workflow
+## Available Forcefields
 
-Comprehensive energy calculation pipeline:
+| Forcefield | Description | Best for |
+|------------|-------------|----------|
+| `MMFF94` | Merck Molecular Force Field | General organic molecules |
+| `MMFF94s` | MMFF94 static | Static conformations |
+| `UFF` | Universal Force Field | Broad chemical space |
+| `GAFF` | General AMBER Force Field | Drug-like molecules |
+| `Ghemical` | Ghemical Force Field | Quick calculations |
+
+## Complete Workflows
+
+### Comprehensive Energy Calculation Pipeline
 
 ```julia
 @chain begin
@@ -124,8 +194,6 @@ end
 
 ### Drug Discovery Pipeline
 
-Typical computational chemistry workflow for drug discovery:
-
 ```julia
 @chain begin
     @read_file("drug_candidates.smi", "smi")
diff --git a/docs/src/api/filtering.md b/docs/src/api/filtering.md
index e5ff651..ec6798f 100644
--- a/docs/src/api/filtering.md
+++ b/docs/src/api/filtering.md
@@ -2,103 +2,229 @@
 
 These macros filter, sort, and manipulate molecular datasets based on structural patterns and properties.
 
-## Pattern Matching
+## Match SMARTS String
 
 ```@docs
 @match_smarts_string
+```
+
+### Usage Examples
+
+Filter molecules containing benzene rings:
+
+```julia
+@chain begin
+    @read_file("database.smi", "smi")
+    @match_smarts_string("c1ccccc1")  # Aromatic benzene ring
+    @output_as("benzene_compounds.smi", "smi")
+    @execute
+end
+```
+
+Common SMARTS patterns:
+
+| Pattern | Description |
+|---------|-------------|
+| `c1ccccc1` | Benzene ring |
+| `[OH]` | Hydroxyl group |
+| `[NH2]` | Primary amine |
+| `C=O` | Carbonyl group |
+| `[#6]=[#8]` | Carbon double bonded to oxygen |
+| `[R]` | Any atom in a ring |
+
+## Don't Match SMARTS String
+
+```@docs
 @dont_match_smarts_string
 ```
 
-## Sorting and Deduplication
+### Usage Examples
+
+Exclude molecules with specific functional groups:
+
+```julia
+@chain begin
+    @read_file("compounds.smi", "smi")
+    @dont_match_smarts_string("[OH]")  # Remove alcohols
+    @output_as("no_alcohols.smi", "smi")
+    @execute
+end
+```
+
+## Sort By
 
 ```@docs
 @sort_by
+```
+
+### Usage Examples
+
+```julia
+@chain begin
+    @read_file("molecules.sdf", "sdf")
+    @add_properties(["MW"])
+    @sort_by("MW")  # Ascending order
+    @output_as("sorted_by_mw.sdf", "sdf")
+    @execute
+end
+```
+
+## Sort By Reverse
+
+```@docs
 @sort_by_reverse
+```
+
+### Usage Examples
+
+Sort by logP in descending order:
+
+```julia
+@chain begin
+    @read_file("molecules.sdf", "sdf")
+    @add_properties(["logP"])
+    @sort_by_reverse("logP")  # Descending order
+    @output_as("high_logp_first.sdf", "sdf")
+    @execute
+end
+```
+
+## Remove Duplicate Molecules
+
+```@docs
 @remove_duplicate_mols
 ```
 
-## Structural Modifications
+### Usage Examples
+
+Remove duplicate structures:
+
+```julia
+@chain begin
+    @read_file("raw_data.smi", "smi")
+    @remove_duplicate_mols()
+    @output_as("unique_molecules.smi", "smi")
+    @execute
+end
+```
+
+## Convert Dative Bonds
 
 ```@docs
 @convert_dative_bonds
-@remove_hydrogens
-@set_atom_order_canonical
-@separate_fragments
 ```
 
-## Data Processing
+### Usage Examples
+
+Convert dative bonds to standard representation:
+
+```julia
+@chain begin
+    @read_file("complexes.sdf", "sdf")
+    @convert_dative_bonds()
+    @output_as("converted_bonds.sdf", "sdf")
+    @execute
+end
+```
+
+## Remove Hydrogens
 
 ```@docs
-@ignore_bad_molecules
-@start_with_index
+@remove_hydrogens
 ```
 
-## Usage Examples
+### Usage Examples
 
-### SMARTS Pattern Filtering
+Remove explicit hydrogens:
 
-Filter molecules containing benzene rings:
+```julia
+@chain begin
+    @read_file("molecules.sdf", "sdf")
+    @remove_hydrogens()
+    @output_as("implicit_h.sdf", "sdf")
+    @execute
+end
+```
+
+## Set Atom Order Canonical
+
+```@docs
+@set_atom_order_canonical
+```
+
+### Usage Examples
+
+Standardize atom ordering:
 
 ```julia
 @chain begin
-    @read_file("database.smi", "smi")
-    @match_smarts_string("c1ccccc1")  # Aromatic benzene ring
-    @output_as("benzene_compounds.smi", "smi")
+    @read_file("molecules.sdf", "sdf")
+    @set_atom_order_canonical()
+    @output_as("canonical_order.sdf", "sdf")
     @execute
 end
 ```
 
-Exclude molecules with specific functional groups:
+## Separate Fragments
+
+```@docs
+@separate_fragments
+```
+
+### Usage Examples
+
+Split salts and complexes:
 
 ```julia
 @chain begin
-    @read_file("compounds.smi", "smi")
-    @dont_match_smarts_string("[OH]")  # Remove alcohols
-    @output_as("no_alcohols.smi", "smi")
+    @read_file("salts.sdf", "sdf")
+    @separate_fragments()
+    @output_as("fragments.sdf", "sdf")
     @execute
 end
 ```
 
-### Common SMARTS Patterns
+## Ignore Bad Molecules
 
-| Pattern | Description |
-|---------|-------------|
-| `c1ccccc1` | Benzene ring |
-| `[OH]` | Hydroxyl group |
-| `[NH2]` | Primary amine |
-| `C=O` | Carbonyl group |
-| `[#6]=[#8]` | Carbon double bonded to oxygen |
-| `[R]` | Any atom in a ring |
+```@docs
+@ignore_bad_molecules
+```
 
-### Sorting by Properties
+### Usage Examples
 
-Sort molecules by molecular weight:
+Skip invalid molecular structures:
 
 ```julia
 @chain begin
-    @read_file("molecules.sdf", "sdf")
-    @add_properties(["MW"])
-    @sort_by("MW")  # Ascending order
-    @output_as("sorted_by_mw.sdf", "sdf")
+    @read_file("raw_data.smi", "smi")
+    @ignore_bad_molecules()
+    @output_as("valid_molecules.smi", "smi")
     @execute
 end
 ```
 
-Sort by logP in descending order:
+## Start With Index
+
+```@docs
+@start_with_index
+```
+
+### Usage Examples
 
 ```julia
 @chain begin
-    @read_file("molecules.sdf", "sdf")
-    @add_properties(["logP"])
-    @sort_by_reverse("logP")  # Descending order
-    @output_as("high_logp_first.sdf", "sdf")
+    @read_file("huge_database.sdf", "sdf")
+    @start_with_index(1000)  # Begin from molecule 1000
+    @add_properties(["MW", "logP"])
+    @sort_by("MW")
+    @output_as("subset_processed.sdf", "sdf")
     @execute
 end
 ```
 
-### Data Cleaning Workflow
+## Complete Workflows
 
-Complete data cleaning and processing pipeline:
+### Data Cleaning Pipeline
 
 ```julia
 @chain begin
@@ -114,17 +240,16 @@ Complete data cleaning and processing pipeline:
 end
 ```
 
-### Processing Large Datasets
-
-Start processing from a specific molecule index:
+### Structure-Based Filtering
 
 ```julia
 @chain begin
-    @read_file("huge_database.sdf", "sdf")
-    @start_with_index(1000)  # Begin from molecule 1000
+    @read_file("compounds.smi", "smi")
+    @match_smarts_string("c1ccccc1")     # Keep aromatic compounds
+    @dont_match_smarts_string("[OH]")    # Remove alcohols
     @add_properties(["MW", "logP"])
-    @sort_by("MW")
-    @output_as("subset_processed.sdf", "sdf")
+    @sort_by_reverse("logP")
+    @output_as("filtered_aromatics.sdf", "sdf")
     @execute
 end
 ```
\ No newline at end of file
diff --git a/docs/src/api/io.md b/docs/src/api/io.md
index 2bc1c4c..a1fc35b 100644
--- a/docs/src/api/io.md
+++ b/docs/src/api/io.md
@@ -2,42 +2,58 @@
 
 These macros handle the fundamental input and output operations for molecular data files.
 
-## File Input
+## Read File
 
 ```@docs
 @read_file
 ```
 
-## File Output
+### Usage Examples
 
-```@docs
-@output_as
-@write_multiple_files
+Basic file reading with format specification:
+
+```julia
+@chain begin
+    @read_file("molecules.smi", "smi")
+    @output_as("molecules.mol", "mol")
+    @execute
+end
 ```
 
-## Pipeline Execution
+## Output As
 
 ```@docs
-@execute
+@output_as
 ```
 
-## Usage Examples
-
-### Basic File Conversion
+### Usage Examples
 
-Convert SMILES to MOL format:
+Convert and save to different formats:
 
 ```julia
+# SMILES to SDF conversion
 @chain begin
-    @read_file("molecules.smi", "smi")
+    @read_file("compounds.smi", "smi")
+    @gen_3D_coords("fast")
+    @output_as("compounds.sdf", "sdf")
+    @execute
+end
+
+# Multiple format outputs
+@chain begin
+    @read_file("molecules.sdf", "sdf")
     @output_as("molecules.mol", "mol")
     @execute
 end
 ```
 
-### Multiple Output Files
+## Write Multiple Files
+
+```@docs
+@write_multiple_files
+```
 
-Create separate files for each molecule:
+### Usage Examples
 
 ```julia
 @chain begin
@@ -48,7 +64,26 @@ Create separate files for each molecule:
 end
 ```
 
-### Supported File Formats
+## Execute
+
+```@docs
+@execute
+```
+
+### Usage Examples
+
+Execute the processing pipeline:
+
+```julia
+@chain begin
+    @read_file("molecules.smi", "smi")
+    @add_properties(["MW", "logP"])
+    @output_as("processed.sdf", "sdf")
+    @execute  # This executes the entire pipeline
+end
+```
+
+## Supported File Formats
 
 The library supports all Open Babel file formats:
 
@@ -60,4 +95,27 @@ The library supports all Open Babel file formats:
 | XYZ | `.xyz` | XYZ coordinate format |
 | PDB | `.pdb` | Protein Data Bank format |
 
-For a complete list, refer to the [Open Babel documentation](https://openbabel.org/docs/FileFormats/Overview.html).
\ No newline at end of file
+For a complete list, refer to the [Open Babel documentation](https://openbabel.org/docs/FileFormats/Overview.html).
+
+## Complete Workflows
+
+### Basic File Conversion
+
+```julia
+@chain begin
+    @read_file("molecules.smi", "smi")
+    @output_as("molecules.mol", "mol")
+    @execute
+end
+```
+
+### Batch Processing with Multiple Outputs
+
+```julia
+@chain begin
+    @read_file("database.sdf", "sdf")
+    @write_multiple_files()
+    @output_as("molecule", "mol")
+    @execute
+end
+```
\ No newline at end of file
diff --git a/docs/src/api/properties.md b/docs/src/api/properties.md
index 6139fc7..42ef321 100644
--- a/docs/src/api/properties.md
+++ b/docs/src/api/properties.md
@@ -2,35 +2,13 @@
 
 These macros add molecular properties, generate coordinates, and modify molecular metadata.
 
-## Property Calculation
+## Add Properties
 
 ```@docs
 @add_properties
 ```
 
-### Available Descriptors
-
-The `get_available_descriptors()` function returns a list of all molecular descriptors that can be calculated. If this function is not yet implemented, refer to the Open Babel documentation for available descriptors.
-
-## Coordinate Generation
-
-```@docs
-@gen_3D_coords
-@gen_2D_coords
-@center_coords_at_zero
-```
-
-## Metadata Addition
-
-```@docs
-@add_filename
-@add_index
-@add_title
-```
-
-## Usage Examples
-
-### Adding Molecular Properties
+### Usage Examples
 
 Calculate common molecular descriptors:
 
@@ -43,16 +21,7 @@ Calculate common molecular descriptors:
 end
 ```
 
-### Available Properties
-
-Get a list of all available descriptors:
-
-```julia
-descriptors = get_available_descriptors()
-println(descriptors)
-```
-
-Common properties include:
+Available properties include:
 - `MW` - Molecular weight
 - `logP` - Partition coefficient
 - `TPSA` - Topological polar surface area
@@ -62,9 +31,22 @@ Common properties include:
 - `atoms` - Number of atoms
 - `bonds` - Number of bonds
 
-### 3D Coordinate Generation
+### Available Descriptors
+
+The `get_available_descriptors()` function returns a list of all molecular descriptors that can be calculated:
+
+```julia
+descriptors = get_available_descriptors()
+println(descriptors)
+```
+
+## Generate 3D Coordinates
+
+```@docs
+@gen_3D_coords
+```
 
-Generate 3D structures with different quality levels:
+### Usage Examples
 
 ```julia
 # Fast generation (good for large datasets)
@@ -76,6 +58,44 @@ Generate 3D structures with different quality levels:
 end
 
 # Higher quality (slower)
+@chain begin
+    @read_file("input.smi", "smi")
+    @gen_3D_coords("slow")
+    @output_as("high_quality_3d.mol", "mol")
+    @execute
+end
+```
+
+## Generate 2D Coordinates
+
+```@docs
+@gen_2D_coords
+```
+
+### Usage Examples
+
+Generate 2D coordinates for visualization:
+
+```julia
+@chain begin
+    @read_file("molecules.smi", "smi")
+    @gen_2D_coords()
+    @output_as("molecules_2d.sdf", "sdf")
+    @execute
+end
+```
+
+## Center Coordinates at Zero
+
+```@docs
+@center_coords_at_zero
+```
+
+### Usage Examples
+
+Center molecular coordinates at the origin:
+
+```julia
 @chain begin
     @read_file("input.smi", "smi")
     @gen_3D_coords("slow")
@@ -85,17 +105,88 @@ end
 end
 ```
 
-### Adding Metadata
+## Add Filename
+
+```@docs
+@add_filename
+```
+
+### Usage Examples
 
-Add indices and filenames to track molecule origins:
+Add the source filename as metadata:
 
 ```julia
 @chain begin
     @read_file("database.sdf", "sdf")
-    @add_index()
     @add_filename()
-    @add_title("Processed Database")
+    @output_as("molecules_with_filename.sdf", "sdf")
+    @execute
+end
+```
+
+## Add Index
+
+```@docs
+@add_index
+```
+
+### Usage Examples
+
+Add molecule indices for tracking:
+
+```julia
+@chain begin
+    @read_file("molecules.sdf", "sdf")
+    @add_index()
     @output_as("indexed_molecules.sdf", "sdf")
     @execute
 end
+```
+
+## Add Title
+
+```@docs
+@add_title
+```
+
+### Usage Examples
+
+```julia
+@chain begin
+    @read_file("molecules.sdf", "sdf")
+    @add_title("Processed Database")
+    @output_as("titled_molecules.sdf", "sdf")
+    @execute
+end
+```
+
+## Complete Workflows
+
+### Property Calculation Pipeline
+
+```julia
+@chain begin
+    @read_file("molecules.smi", "smi")
+    @gen_3D_coords("med")
+    @add_properties(["MW", "logP", "TPSA", "HBD", "HBA"])
+    @add_index()
+    @add_filename()
+    @output_as("full_analysis.sdf", "sdf")
+    @execute
+end
+```
+
+### Coordinate Generation with Metadata
+
+```julia
+@chain begin
+    @read_file("database.sdf", "sdf")
+    @gen_3D_coords("slow")
+    @center_coords_at_zero()
+    @add_index()
+    @add_filename()
+    @add_title("High Quality 3D Structures")
+    @output_as("processed_3d.sdf", "sdf")
+    @execute
+end
 ```
\ No newline at end of file
diff --git a/docs/src/assets/logo.png b/docs/src/assets/logo.png
new file mode 100644
index 0000000..0c2e6c3
Binary files /dev/null and b/docs/src/assets/logo.png differ
diff --git a/docs/src/index.md b/docs/src/index.md
index 7e4035c..fd7e4d2 100644
--- a/docs/src/index.md
+++ b/docs/src/index.md
@@ -1,6 +1,6 @@
 # OpenBabel.jl
 
-A Julia library for reading, writing, and transforming chemical data, powered by [Open Babel](https://github.com/openbabel/openbabel).
+Julia bindings for [Open Babel](https://github.com/openbabel/openbabel) library.
 
 ## Installation