PyPI - tmquick - Versions diffs - 1.0.3__tar.gz → 1.0.6__tar.gz - Mend

tmquick 1.0.3tar.gz → 1.0.6tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

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{tmquick-1.0.3/tmquick.egg-info → tmquick-1.0.6}/PKG-INFO RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tmquick
-Version: 1.0.3
+Version: 1.0.6
 Summary: TrajMapQuick: Towards Fast Trajectory Map Analysis and Visualization
 Author: Wande M. Oluyemi (PhD), Adeniyi T. Adewumi (PhD), Shadrach C. Eze, Stephen C. Nnemolisa,  @ Research Laboratory for Rational Design of Drugs and Biomaterials (ResLaR Labs), Afe Babalola University, Ado-Ekiti Nigeria
 Project-URL: Homepage, https://github.com/SHEDOOMTC/TrajMapQuick.git
@@ -42,12 +42,12 @@ We have also extended the code to allow for automatic detection of regions with
 See **[Github](https://github.com/SHEDOOMTC/TrajMapQuick/blob/main/README.md)**
 ## **Installation**
+### **From Source**
 ```bash
 # Clone the repo
-git clone https://github.com/SHEDOOMTC/TrajMapQuick.git
-cd TrajMapQuick
+git clone https://github.com/SHEDOOMTC/TrajMapQuick.git && cd TrajMapQuick
 # In conda environment with pip
 conda create -n tmq python=3.10
@@ -61,31 +61,45 @@ conda activate tmq
 Use tmq --help to see the arguments
 ```
+### **From PyPI**
+```bash
+pip install tmquick
+conda install -c conda-forge mdtraj
+```
 ## **Commands**
 ```bash
-#TrajMapQuick uses a two levell subcommand from the global "tmq" command
-tmq  shift  : Extract matrices, compute residue-residue shifts and make plots: For more, use tmq shift --help
+#TrajMapQuick uses a four levell subcommand from the global "tmq" command
+tmq  shift  : Extract matrices, compute residue-residue shifts and make plots:
+ For more, use tmq shift --help
-tmq hotspot : Detect hotspots in residue shifts and create plots: For more, use tmq hotspot --help
+tmq hotspot : Detect hotspots in residue shifts and create plots:
+  For more, use tmq hotspot --help
-tmq diff      Computes difference between two matrices and creates the difference map: For more, use tmq diff --help
+tmq diff:     Computes difference between two matrices and creates
+  the difference map: For more, use tmq diff --help
-tmq average   Computes average of n matrices and creates the average map: For more, use tmq average --help
+tmq average   Computes average of n matrices and creates the average map:
+  For more, use tmq average --help
 ```
 ## **Usage (CLI)**
 ```bash
 # For tmq shift, arguments are passed into the flags for trajectory, topology etc.
-tmq shift --traj traj.pdb --top top.parmtop --str 1 --resr 1-300 --resrs 110-125 --cent backbone --plot --out shift_output
+tmq shift --traj traj.pdb --top top.parmtop --str 1 --resr 1-300 \
+ --resrs 110-125 --cent backbone --out shift_output
-#for tmq hotspot, arguments are passed similiarly, except that the region of shift is not provided
+#for tmq hotspot, arguments are passed similiarly, the region of shift is not provided
-tmq hotspot --traj traj.pdb --top top.parmtop --str 1 --resr 1-300 --cent backbone --out hotspot_output
+tmq hotspot --traj traj.pdb --top top.parmtop --str 1 --resr 1-300 \
+  --cent backbone --out hotspot_output
 ```
 ## **Usage (Python API)**
-The core modules in the tmq library are clearly demonstrated in the **[Python_API.ipynb](./Notebooks/Python_API.ipynb)** file
+The core modules in the tmq library are clearly demonstrated in the
+  **[Python_API.ipynb](./Notebooks/Python_API.ipynb)** file
 ```python
 #Typical modules are loaded and then used as explained in the jupyter notebook above:
@@ -120,7 +134,7 @@ jupyter notebook Python_API.ipynb
 All library requirements are pre-installed installed via pip or conda and are available for use in CLI or via Python API
 ## **Examples**
-Three trajectories and topologies files are included in the **[Test](./Test)** directory for users to try out the codes. Trajectory 1 has only 125 frames (from apo strucuture of PDB ID: 8EM8 with 789 residues) while others have 250 frames (from apo and bound strucutres of BACE1, with 389 residues). To get the full sized trajectories, see [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.20681326.svg)](https://doi.org/10.5281/zenodo.20681326)
+Three trajectories and topologies files are included in the **[Test](./Test)** directory for users to try out the codes. Trajectory 1 has only 125 frames (from apo strucuture of PDB ID: 8EM8 with 789 residues) while others have 250 frames (from apo and bound strucutres of BACE1, with 389 residues). To get the full sized trajectories, see [![DOI](https://img.shields.io/badge/DOI-10.5281%2Fzenodo.20681326-3C5A99?logo=zenodo&logoColor=white)](https://doi.org/10.5281/zenodo.20681326)
 See the full examples on **[Github](https://github.com/SHEDOOMTC/TrajMapQuick/blob/main/README.md)**
@@ -154,9 +168,12 @@ For questions or issues, please contact us @ [Reslar Labs](reslarscience@gmail.c
 If you use TrajMapQuick, please cite: SHEDOOMTC. (2026). TrajMapQuick: Towards Fast Trajectory Map Analysis and Visualization (v1.0). Zenodo. https://doi.org/10.5281/zenodo.20681061
 **Software:**
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.20681061.svg)](https://doi.org/10.5281/zenodo.20681061)
+[![DOI](https://img.shields.io/badge/DOI-10.5281%2Fzenodo.20681061-3C5A99?logo=zenodo&logoColor=white)](https://doi.org/10.5281/zenodo.20681061)
 **Dataset:**
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.20681326.svg)](https://doi.org/10.5281/zenodo.20681326)
+[![DOI](https://img.shields.io/badge/DOI-10.5281%2Fzenodo.20681326-3C5A99?logo=zenodo&logoColor=white)](https://doi.org/10.5281/zenodo.20681326)

{tmquick-1.0.3 → tmquick-1.0.6}/README.md RENAMED Viewed

@@ -13,51 +13,9 @@ We have also extended the code to allow for automatic detection of regions with
 - **Hotspot Detection and Plotting:** This automatically probes and detects regions of high fluctuations and computes the residual shift for each region for downstream processing.
 - **Hotspot Annotation:** An RMSF like plot is also generated with the key hotspots highlight for visual confirmation and inspection.
-## **Project Structure**
-<pre>
-TrajMapQuick/
-├── README.md                     # Project overview, installation, usage
-├── requirements.txt              # Python dependencies
-├── setup.py                      # Packaging configuration
-├── environment.yml               # Build config
-├── pyproject.toml                # Build config
-├── LICENSE                       # MIT license
-├── Manifest.in
-├── tmq/                          # Source codes and CLI wrappers lives here
-│   ├── cli.py/                   # Main command line launcher
-│   ├── __init__.py               # Main launcher for the python API
-│   ├── core/                     # Python package folder
-│   │   ├── __init__.py
-│   │   ├── traj2pdb.py           # Converts trajectory to pdb
-│   │   ├── pdb2csv.py            # Converts pdb to distance matrix
-│   │   ├── trajmap.py            # plots the trajectory map
-│   │   ├── csv2shift.py          # Core shift logic for a given loop
-│   │   ├── shift2graph.py        # Makes shift plots for a given loop
-│   │   ├── hotspot.py            # Automatic detection of regions with peak fluctuations
-│   │   ├── diff2graph.py         # Computes and plot difference map for two trajectories
-│   │   └── average_trajmap.py    # Computes and plot average map for two trajectories
-│   ├── commands/                 # Main wrapper for the CLI
-│   │   ├── __init__.py
-│   │   ├── traj2pdb_cli.py       # CLI wrapper
-│   │   ├── pdb2csv_cli.py        # CLI wrapper
-│   │   ├── trajmap_cli.py        # CLI wrapper
-│   │   ├── csv2shift_cli.py      # CLI wrapper
-│   │   ├── shift2graph_cli.py    # CLI wrapper
-│   │   ├── hotspot_cli.py        # CLI wrapper
-│   │   ├── diff2graph_cli.py     # CLI wrapper
-│   │   └── average_trajmap_cli.py# CLI wrapper
-│   └── utils                     # Holds functions
-│   │   ├── __init__.py
-│   │   └── utils.py              # utility functions
-├── docs/                         # docstrings for the modules
-├── assets/                       # Container for images
-├── Tests/                        # Containers for test trajectories and topologies
-└── Conda/                        # Backup YAML files
-</pre>
 ## **Installation**
+### **From Source**
 ```bash
 # Clone the repo
 git clone https://github.com/SHEDOOMTC/TrajMapQuick.git && cd TrajMapQuick
@@ -74,30 +32,44 @@ conda activate tmq
 Use tmq --help to see the arguments
 ```
+### **From PyPI**
+```bash
+pip install tmquick
+conda install -c conda-forge mdtraj
+```
 ## **Commands**
 ```bash
 #TrajMapQuick uses a four levell subcommand from the global "tmq" command
-tmq  shift  : Extract matrices, compute residue-residue shifts and make plots: For more, use tmq shift --help
+tmq  shift  : Extract matrices, compute residue-residue shifts and make plots:
+ For more, use tmq shift --help
-tmq hotspot : Detect hotspots in residue shifts and create plots: For more, use tmq hotspot --help
+tmq hotspot : Detect hotspots in residue shifts and create plots:
+  For more, use tmq hotspot --help
-tmq diff      Computes difference between two matrices and creates the difference map: For more, use tmq diff --help
+tmq diff:     Computes difference between two matrices and creates
+  the difference map: For more, use tmq diff --help
-tmq average   Computes average of n matrices and creates the average map: For more, use tmq average --help
+tmq average   Computes average of n matrices and creates the average map:
+  For more, use tmq average --help
 ```
 ## **Usage (CLI)**
 ```bash
 # For tmq shift, arguments are passed into the flags for trajectory, topology etc.
-tmq shift --traj traj.pdb --top top.parmtop --str 1 --resr 1-300 --resrs 110-125 --cent backbone --out shift_output
+tmq shift --traj traj.pdb --top top.parmtop --str 1 --resr 1-300 \
+ --resrs 110-125 --cent backbone --out shift_output
-#for tmq hotspot, arguments are passed similiarly, except that the region of shift is not provided
+#for tmq hotspot, arguments are passed similiarly, the region of shift is not provided
-tmq hotspot --traj traj.pdb --top top.parmtop --str 1 --resr 1-300 --cent backbone --out hotspot_output
+tmq hotspot --traj traj.pdb --top top.parmtop --str 1 --resr 1-300 \
+  --cent backbone --out hotspot_output
 ```
 ## **Usage (Python API)**
-The core modules in the tmq library are clearly demonstrated in the **[Python_API.ipynb](./Notebooks/Python_API.ipynb)** file
+The core modules in the tmq library are clearly demonstrated in the
+  **[Python_API.ipynb](./Notebooks/Python_API.ipynb)** file
 ```python
 #Typical modules are loaded and then used as explained in the jupyter notebook above:
@@ -122,6 +94,50 @@ cd ./Notebooks/
 jupyter notebook Python_API.ipynb
 ```
+## **Project Structure**
+<pre>
+TrajMapQuick/
+├── README.md                     # Project overview, installation, usage
+├── requirements.txt              # Python dependencies
+├── setup.py                      # Packaging configuration
+├── environment.yml               # Build config
+├── pyproject.toml                # Build config
+├── LICENSE                       # MIT license
+├── Manifest.in
+├── tmq/                          # Source codes and CLI wrappers lives here
+│   ├── cli.py/                   # Main command line launcher
+│   ├── __init__.py               # Main launcher for the python API
+│   ├── core/                     # Python package folder
+│   │   ├── __init__.py
+│   │   ├── traj2pdb.py           # Converts trajectory to pdb
+│   │   ├── pdb2csv.py            # Converts pdb to distance matrix
+│   │   ├── trajmap.py            # plots the trajectory map
+│   │   ├── csv2shift.py          # Core shift logic for a given loop
+│   │   ├── shift2graph.py        # Makes shift plots for a given loop
+│   │   ├── hotspot.py            # Automatic detection of regions with peak fluctuations
+│   │   ├── diff2graph.py         # Computes and plot difference map for two trajectories
+│   │   └── average_trajmap.py    # Computes and plot average map for two trajectories
+│   ├── commands/                 # Main wrapper for the CLI
+│   │   ├── __init__.py
+│   │   ├── traj2pdb_cli.py       # CLI wrapper
+│   │   ├── pdb2csv_cli.py        # CLI wrapper
+│   │   ├── trajmap_cli.py        # CLI wrapper
+│   │   ├── csv2shift_cli.py      # CLI wrapper
+│   │   ├── shift2graph_cli.py    # CLI wrapper
+│   │   ├── hotspot_cli.py        # CLI wrapper
+│   │   ├── diff2graph_cli.py     # CLI wrapper
+│   │   └── average_trajmap_cli.py# CLI wrapper
+│   └── utils                     # Holds functions
+│   │   ├── __init__.py
+│   │   └── utils.py              # utility functions
+├── docs/                         # docstrings for the modules
+├── assets/                       # Container for images
+├── Tests/                        # Containers for test trajectories and topologies
+└── Conda/                        # Backup YAML files
+</pre>
 ## **Requirements**
 - Trajectory processing libraries (mdtraj, biopython)
@@ -133,7 +149,7 @@ jupyter notebook Python_API.ipynb
 All library requirements are pre-installed installed via pip or conda and are available for use in CLI or via Python API
 ## **Examples**
-Three trajectories and topologies files are included in the **[Test](./Test)** directory for users to try out the codes. Trajectory 1 has only 125 frames (from apo strucuture of PDB ID: 8EM8 with 789 residues) while others have 250 frames (from apo and bound strucutres of BACE1, with 389 residues). To get the full sized trajectories, see [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.20681326.svg)](https://doi.org/10.5281/zenodo.20681326)
+Three trajectories and topologies files are included in the **[Test](./Test)** directory for users to try out the codes. Trajectory 1 has only 125 frames (from apo strucuture of PDB ID: 8EM8 with 789 residues) while others have 250 frames (from apo and bound strucutres of BACE1, with 389 residues). To get the full sized trajectories, see [![DOI](https://img.shields.io/badge/DOI-10.5281%2Fzenodo.20681326-3C5A99?logo=zenodo&logoColor=white)](https://doi.org/10.5281/zenodo.20681326)
 The Utility of the shift command (using a 500 frame trajectory) was shown by the figure below:
@@ -190,10 +206,12 @@ For questions or issues, please contact us @ [Reslar Labs](reslarscience@gmail.c
 If you use TrajMapQuick, please cite: SHEDOOMTC. (2026). TrajMapQuick: Towards Fast Trajectory Map Analysis and Visualization (v1.0). Zenodo. https://doi.org/10.5281/zenodo.20681061
 **Software:**
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.20681061.svg)](https://doi.org/10.5281/zenodo.20681061)
+[![DOI](https://img.shields.io/badge/DOI-10.5281%2Fzenodo.20681061-3C5A99?logo=zenodo&logoColor=white)](https://doi.org/10.5281/zenodo.20681061)
 **Dataset:**
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.20681326.svg)](https://doi.org/10.5281/zenodo.20681326)
+[![DOI](https://img.shields.io/badge/DOI-10.5281%2Fzenodo.20681326-3C5A99?logo=zenodo&logoColor=white)](https://doi.org/10.5281/zenodo.20681326)

{tmquick-1.0.3 → tmquick-1.0.6}/pyproject.toml RENAMED Viewed

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "tmquick"
-version = "1.0.3"
+version = "1.0.6"
 readme = "readme_pypi.md"
 description = "TrajMapQuick: Towards Fast Trajectory Map Analysis and Visualization"
 authors = [

{tmquick-1.0.3 → tmquick-1.0.6}/readme_pypi.md RENAMED Viewed

@@ -17,12 +17,12 @@ We have also extended the code to allow for automatic detection of regions with
 See **[Github](https://github.com/SHEDOOMTC/TrajMapQuick/blob/main/README.md)**
 ## **Installation**
+### **From Source**
 ```bash
 # Clone the repo
-git clone https://github.com/SHEDOOMTC/TrajMapQuick.git
-cd TrajMapQuick
+git clone https://github.com/SHEDOOMTC/TrajMapQuick.git && cd TrajMapQuick
 # In conda environment with pip
 conda create -n tmq python=3.10
@@ -36,31 +36,45 @@ conda activate tmq
 Use tmq --help to see the arguments
 ```
+### **From PyPI**
+```bash
+pip install tmquick
+conda install -c conda-forge mdtraj
+```
 ## **Commands**
 ```bash
-#TrajMapQuick uses a two levell subcommand from the global "tmq" command
-tmq  shift  : Extract matrices, compute residue-residue shifts and make plots: For more, use tmq shift --help
+#TrajMapQuick uses a four levell subcommand from the global "tmq" command
+tmq  shift  : Extract matrices, compute residue-residue shifts and make plots:
+ For more, use tmq shift --help
-tmq hotspot : Detect hotspots in residue shifts and create plots: For more, use tmq hotspot --help
+tmq hotspot : Detect hotspots in residue shifts and create plots:
+  For more, use tmq hotspot --help
-tmq diff      Computes difference between two matrices and creates the difference map: For more, use tmq diff --help
+tmq diff:     Computes difference between two matrices and creates
+  the difference map: For more, use tmq diff --help
-tmq average   Computes average of n matrices and creates the average map: For more, use tmq average --help
+tmq average   Computes average of n matrices and creates the average map:
+  For more, use tmq average --help
 ```
 ## **Usage (CLI)**
 ```bash
 # For tmq shift, arguments are passed into the flags for trajectory, topology etc.
-tmq shift --traj traj.pdb --top top.parmtop --str 1 --resr 1-300 --resrs 110-125 --cent backbone --plot --out shift_output
+tmq shift --traj traj.pdb --top top.parmtop --str 1 --resr 1-300 \
+ --resrs 110-125 --cent backbone --out shift_output
-#for tmq hotspot, arguments are passed similiarly, except that the region of shift is not provided
+#for tmq hotspot, arguments are passed similiarly, the region of shift is not provided
-tmq hotspot --traj traj.pdb --top top.parmtop --str 1 --resr 1-300 --cent backbone --out hotspot_output
+tmq hotspot --traj traj.pdb --top top.parmtop --str 1 --resr 1-300 \
+  --cent backbone --out hotspot_output
 ```
 ## **Usage (Python API)**
-The core modules in the tmq library are clearly demonstrated in the **[Python_API.ipynb](./Notebooks/Python_API.ipynb)** file
+The core modules in the tmq library are clearly demonstrated in the
+  **[Python_API.ipynb](./Notebooks/Python_API.ipynb)** file
 ```python
 #Typical modules are loaded and then used as explained in the jupyter notebook above:
@@ -95,7 +109,7 @@ jupyter notebook Python_API.ipynb
 All library requirements are pre-installed installed via pip or conda and are available for use in CLI or via Python API
 ## **Examples**
-Three trajectories and topologies files are included in the **[Test](./Test)** directory for users to try out the codes. Trajectory 1 has only 125 frames (from apo strucuture of PDB ID: 8EM8 with 789 residues) while others have 250 frames (from apo and bound strucutres of BACE1, with 389 residues). To get the full sized trajectories, see [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.20681326.svg)](https://doi.org/10.5281/zenodo.20681326)
+Three trajectories and topologies files are included in the **[Test](./Test)** directory for users to try out the codes. Trajectory 1 has only 125 frames (from apo strucuture of PDB ID: 8EM8 with 789 residues) while others have 250 frames (from apo and bound strucutres of BACE1, with 389 residues). To get the full sized trajectories, see [![DOI](https://img.shields.io/badge/DOI-10.5281%2Fzenodo.20681326-3C5A99?logo=zenodo&logoColor=white)](https://doi.org/10.5281/zenodo.20681326)
 See the full examples on **[Github](https://github.com/SHEDOOMTC/TrajMapQuick/blob/main/README.md)**
@@ -129,9 +143,12 @@ For questions or issues, please contact us @ [Reslar Labs](reslarscience@gmail.c
 If you use TrajMapQuick, please cite: SHEDOOMTC. (2026). TrajMapQuick: Towards Fast Trajectory Map Analysis and Visualization (v1.0). Zenodo. https://doi.org/10.5281/zenodo.20681061
 **Software:**
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.20681061.svg)](https://doi.org/10.5281/zenodo.20681061)
+[![DOI](https://img.shields.io/badge/DOI-10.5281%2Fzenodo.20681061-3C5A99?logo=zenodo&logoColor=white)](https://doi.org/10.5281/zenodo.20681061)
 **Dataset:**
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.20681326.svg)](https://doi.org/10.5281/zenodo.20681326)
+[![DOI](https://img.shields.io/badge/DOI-10.5281%2Fzenodo.20681326-3C5A99?logo=zenodo&logoColor=white)](https://doi.org/10.5281/zenodo.20681326)

{tmquick-1.0.3 → tmquick-1.0.6/tmquick.egg-info}/PKG-INFO RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tmquick
-Version: 1.0.3
+Version: 1.0.6
 Summary: TrajMapQuick: Towards Fast Trajectory Map Analysis and Visualization
 Author: Wande M. Oluyemi (PhD), Adeniyi T. Adewumi (PhD), Shadrach C. Eze, Stephen C. Nnemolisa,  @ Research Laboratory for Rational Design of Drugs and Biomaterials (ResLaR Labs), Afe Babalola University, Ado-Ekiti Nigeria
 Project-URL: Homepage, https://github.com/SHEDOOMTC/TrajMapQuick.git
@@ -42,12 +42,12 @@ We have also extended the code to allow for automatic detection of regions with
 See **[Github](https://github.com/SHEDOOMTC/TrajMapQuick/blob/main/README.md)**
 ## **Installation**
+### **From Source**
 ```bash
 # Clone the repo
-git clone https://github.com/SHEDOOMTC/TrajMapQuick.git
-cd TrajMapQuick
+git clone https://github.com/SHEDOOMTC/TrajMapQuick.git && cd TrajMapQuick
 # In conda environment with pip
 conda create -n tmq python=3.10
@@ -61,31 +61,45 @@ conda activate tmq
 Use tmq --help to see the arguments
 ```
+### **From PyPI**
+```bash
+pip install tmquick
+conda install -c conda-forge mdtraj
+```
 ## **Commands**
 ```bash
-#TrajMapQuick uses a two levell subcommand from the global "tmq" command
-tmq  shift  : Extract matrices, compute residue-residue shifts and make plots: For more, use tmq shift --help
+#TrajMapQuick uses a four levell subcommand from the global "tmq" command
+tmq  shift  : Extract matrices, compute residue-residue shifts and make plots:
+ For more, use tmq shift --help
-tmq hotspot : Detect hotspots in residue shifts and create plots: For more, use tmq hotspot --help
+tmq hotspot : Detect hotspots in residue shifts and create plots:
+  For more, use tmq hotspot --help
-tmq diff      Computes difference between two matrices and creates the difference map: For more, use tmq diff --help
+tmq diff:     Computes difference between two matrices and creates
+  the difference map: For more, use tmq diff --help
-tmq average   Computes average of n matrices and creates the average map: For more, use tmq average --help
+tmq average   Computes average of n matrices and creates the average map:
+  For more, use tmq average --help
 ```
 ## **Usage (CLI)**
 ```bash
 # For tmq shift, arguments are passed into the flags for trajectory, topology etc.
-tmq shift --traj traj.pdb --top top.parmtop --str 1 --resr 1-300 --resrs 110-125 --cent backbone --plot --out shift_output
+tmq shift --traj traj.pdb --top top.parmtop --str 1 --resr 1-300 \
+ --resrs 110-125 --cent backbone --out shift_output
-#for tmq hotspot, arguments are passed similiarly, except that the region of shift is not provided
+#for tmq hotspot, arguments are passed similiarly, the region of shift is not provided
-tmq hotspot --traj traj.pdb --top top.parmtop --str 1 --resr 1-300 --cent backbone --out hotspot_output
+tmq hotspot --traj traj.pdb --top top.parmtop --str 1 --resr 1-300 \
+  --cent backbone --out hotspot_output
 ```
 ## **Usage (Python API)**
-The core modules in the tmq library are clearly demonstrated in the **[Python_API.ipynb](./Notebooks/Python_API.ipynb)** file
+The core modules in the tmq library are clearly demonstrated in the
+  **[Python_API.ipynb](./Notebooks/Python_API.ipynb)** file
 ```python
 #Typical modules are loaded and then used as explained in the jupyter notebook above:
@@ -120,7 +134,7 @@ jupyter notebook Python_API.ipynb
 All library requirements are pre-installed installed via pip or conda and are available for use in CLI or via Python API
 ## **Examples**
-Three trajectories and topologies files are included in the **[Test](./Test)** directory for users to try out the codes. Trajectory 1 has only 125 frames (from apo strucuture of PDB ID: 8EM8 with 789 residues) while others have 250 frames (from apo and bound strucutres of BACE1, with 389 residues). To get the full sized trajectories, see [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.20681326.svg)](https://doi.org/10.5281/zenodo.20681326)
+Three trajectories and topologies files are included in the **[Test](./Test)** directory for users to try out the codes. Trajectory 1 has only 125 frames (from apo strucuture of PDB ID: 8EM8 with 789 residues) while others have 250 frames (from apo and bound strucutres of BACE1, with 389 residues). To get the full sized trajectories, see [![DOI](https://img.shields.io/badge/DOI-10.5281%2Fzenodo.20681326-3C5A99?logo=zenodo&logoColor=white)](https://doi.org/10.5281/zenodo.20681326)
 See the full examples on **[Github](https://github.com/SHEDOOMTC/TrajMapQuick/blob/main/README.md)**
@@ -154,9 +168,12 @@ For questions or issues, please contact us @ [Reslar Labs](reslarscience@gmail.c
 If you use TrajMapQuick, please cite: SHEDOOMTC. (2026). TrajMapQuick: Towards Fast Trajectory Map Analysis and Visualization (v1.0). Zenodo. https://doi.org/10.5281/zenodo.20681061
 **Software:**
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.20681061.svg)](https://doi.org/10.5281/zenodo.20681061)
+[![DOI](https://img.shields.io/badge/DOI-10.5281%2Fzenodo.20681061-3C5A99?logo=zenodo&logoColor=white)](https://doi.org/10.5281/zenodo.20681061)
 **Dataset:**
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.20681326.svg)](https://doi.org/10.5281/zenodo.20681326)
+[![DOI](https://img.shields.io/badge/DOI-10.5281%2Fzenodo.20681326-3C5A99?logo=zenodo&logoColor=white)](https://doi.org/10.5281/zenodo.20681326)