tmquick 1.0.3__tar.gz → 1.0.4__tar.gz

{tmquick-1.0.3/tmquick.egg-info → tmquick-1.0.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tmquick
-Version: 1.0.3
+Version: 1.0.4
 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:
 

{tmquick-1.0.3 → tmquick-1.0.4}/README.md

@@ -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)
 

{tmquick-1.0.3 → tmquick-1.0.4}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "tmquick"
-version = "1.0.3"
+version = "1.0.4"
 readme = "readme_pypi.md"
 description = "TrajMapQuick: Towards Fast Trajectory Map Analysis and Visualization"
 authors = [

{tmquick-1.0.3 → tmquick-1.0.4}/readme_pypi.md

@@ -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:
 

{tmquick-1.0.3 → tmquick-1.0.4/tmquick.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tmquick
-Version: 1.0.3
+Version: 1.0.4
 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: