PyPI - tmquick - Versions diffs - 1.0.1__tar.gz → 1.0.2__tar.gz - Mend

tmquick 1.0.1tar.gz → 1.0.2tar.gz

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{tmquick-1.0.1/tmquick.egg-info → tmquick-1.0.2}/PKG-INFO RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tmquick
-Version: 1.0.1
+Version: 1.0.2
 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
@@ -9,7 +9,6 @@ Project-URL: DOI, https://github.com/SHEDOOMTC/TrajMapQuick.git
 Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE.md
-License-File: LICENSE.md:Zone.Identifier
 Requires-Dist: numpy
 Requires-Dist: pandas
 Requires-Dist: matplotlib
@@ -24,7 +23,7 @@ Requires-Dist: mdtraj; extra == "md"
 Dynamic: license-file
 <p align="center">
-  <img src="https://github.com/SHEDOOMTC/TrajMapQuick/blob/main/assets/TrajMapQuick.png" alt="TrajMapQuick Logo" />
+  <img src="https://raw.githubusercontent.com/SHEDOOMTC/TrajMapQuick/main/assets/TrajMapQuick.png" alt="TrajMapQuick Logo" />
 </p>
 ## **Overview**
@@ -39,48 +38,9 @@ We have also extended the code to allow for automatic detection of regions with
 - **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>
+See **[Github](https://github.com/SHEDOOMTC/TrajMapQuick/blob/main/README.md)**
 ## **Installation**
 ```bash
@@ -161,36 +121,15 @@ All library requirements are pre-installed installed via pip or conda and are av
 ## **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)
+See the full examples on **[Github](https://github.com/SHEDOOMTC/TrajMapQuick/blob/main/README.md)**
-The Utility of the shift command (using a 500 frame trajectory) was shown by the figure below:
-![test_traj_2_shift_graph.png](https://github.com/SHEDOOMTC/TrajMapQuick/blob/main/assets/test_traj_2_shift_graph.png)
-**And that of the hotspot command by:**
-![test_traj_2_hotspot_graph.png](https://github.com/SHEDOOMTC/TrajMapQuick/blob/main/assets/test_traj_2_hotspot_graph.png)
-To reproduce the figures above, download the full length trajectory (500 frames) from Zenodo [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.20681326.svg)](https://doi.org/10.5281/zenodo.20681326) and run the codes below on the CLI
-```bash
-#The exact codes used to produce the results above
-tmq shift -tr traj_9NSR_500.nc -to topol_9NSR.prmtop -st 1 -rr 1-378 -rs 272-285 -ce backbone -ma 5 -o out
-tmq hotspot -tr traj_9NSR_500.nc -to topol_9NSR.prmtop -st 1 -rr 1-378 -ce backbone -o out
-```
 ## **Improvements (Speed, Throughput and Reliability)**
 **1.** Batch processing over the CLI and Python API
-**2.** A major improvement of TrajMapQuick over TrajMap is the speed across varying **residue lengths** and **number of frames**. We evaluated a 1000 frame trajectory (at 100 frame interval) over 800 residues (at 100 residue interval) in TrajMapQuick for both subcommands (shift & hotspot). The **performance plots below:**
-![performance plots](https://github.com/SHEDOOMTC/TrajMapQuick/blob/main/assets/Performance_shift_hotspot.png?raw=true)
+**2.** A major improvement of TrajMapQuick over TrajMap is the speed across varying **residue lengths** and **number of frames**. We evaluated a 1000 frame trajectory (at 100 frame interval) over 800 residues (at 100 residue interval) in TrajMapQuick for both subcommands (shift & hotspot).
-shows clear scaling with number of residues and frames, with completion time between **2-5 mins**. Compared to TrajMapQuick, a single 500 frame calculations across 800 residues took around **10 minutes** in TrajMap, besides the manual editing of input parameters.
+See full details on **[Github](https://github.com/SHEDOOMTC/TrajMapQuick/blob/main/README.md)**
 **3.** The choice to select either the CA or backbone for shift calculations.

{tmquick-1.0.1 → tmquick-1.0.2}/README.md RENAMED Viewed

@@ -1,5 +1,5 @@
 <p align="center">
-  <img src="https://github.com/SHEDOOMTC/TrajMapQuick/blob/main/assets/TrajMapQuick.png" alt="TrajMapQuick Logo" />
+  <img src="https://raw.githubusercontent.com/SHEDOOMTC/TrajMapQuick/main/assets/TrajMapQuick.png" alt="TrajMapQuick Logo" />
 </p>
 ## **Overview**
@@ -14,48 +14,9 @@ We have also extended the code to allow for automatic detection of regions with
 - **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>
+See **[Github](https://github.com/SHEDOOMTC/TrajMapQuick/blob/main/README.md)**
 ## **Installation**
 ```bash
@@ -136,36 +97,15 @@ All library requirements are pre-installed installed via pip or conda and are av
 ## **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)
+See the full examples on **[Github](https://github.com/SHEDOOMTC/TrajMapQuick/blob/main/README.md)**
-The Utility of the shift command (using a 500 frame trajectory) was shown by the figure below:
-![test_traj_2_shift_graph.png](https://github.com/SHEDOOMTC/TrajMapQuick/blob/main/assets/test_traj_2_shift_graph.png)
-**And that of the hotspot command by:**
-![test_traj_2_hotspot_graph.png](https://github.com/SHEDOOMTC/TrajMapQuick/blob/main/assets/test_traj_2_hotspot_graph.png)
-To reproduce the figures above, download the full length trajectory (500 frames) from Zenodo [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.20681326.svg)](https://doi.org/10.5281/zenodo.20681326) and run the codes below on the CLI
-```bash
-#The exact codes used to produce the results above
-tmq shift -tr traj_9NSR_500.nc -to topol_9NSR.prmtop -st 1 -rr 1-378 -rs 272-285 -ce backbone -ma 5 -o out
-tmq hotspot -tr traj_9NSR_500.nc -to topol_9NSR.prmtop -st 1 -rr 1-378 -ce backbone -o out
-```
 ## **Improvements (Speed, Throughput and Reliability)**
 **1.** Batch processing over the CLI and Python API
-**2.** A major improvement of TrajMapQuick over TrajMap is the speed across varying **residue lengths** and **number of frames**. We evaluated a 1000 frame trajectory (at 100 frame interval) over 800 residues (at 100 residue interval) in TrajMapQuick for both subcommands (shift & hotspot). The **performance plots below:**
-![performance plots](https://github.com/SHEDOOMTC/TrajMapQuick/blob/main/assets/Performance_shift_hotspot.png?raw=true)
+**2.** A major improvement of TrajMapQuick over TrajMap is the speed across varying **residue lengths** and **number of frames**. We evaluated a 1000 frame trajectory (at 100 frame interval) over 800 residues (at 100 residue interval) in TrajMapQuick for both subcommands (shift & hotspot).
-shows clear scaling with number of residues and frames, with completion time between **2-5 mins**. Compared to TrajMapQuick, a single 500 frame calculations across 800 residues took around **10 minutes** in TrajMap, besides the manual editing of input parameters.
+See full details on **[Github](https://github.com/SHEDOOMTC/TrajMapQuick/blob/main/README.md)**
 **3.** The choice to select either the CA or backbone for shift calculations.

{tmquick-1.0.1 → tmquick-1.0.2}/pyproject.toml RENAMED Viewed

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "tmquick"
-version = "1.0.1"
+version = "1.0.2"
 readme = "README.md"
 description = "TrajMapQuick: Towards Fast Trajectory Map Analysis and Visualization"
 authors = [

{tmquick-1.0.1 → tmquick-1.0.2/tmquick.egg-info}/PKG-INFO RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tmquick
-Version: 1.0.1
+Version: 1.0.2
 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
@@ -9,7 +9,6 @@ Project-URL: DOI, https://github.com/SHEDOOMTC/TrajMapQuick.git
 Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE.md
-License-File: LICENSE.md:Zone.Identifier
 Requires-Dist: numpy
 Requires-Dist: pandas
 Requires-Dist: matplotlib
@@ -24,7 +23,7 @@ Requires-Dist: mdtraj; extra == "md"
 Dynamic: license-file
 <p align="center">
-  <img src="https://github.com/SHEDOOMTC/TrajMapQuick/blob/main/assets/TrajMapQuick.png" alt="TrajMapQuick Logo" />
+  <img src="https://raw.githubusercontent.com/SHEDOOMTC/TrajMapQuick/main/assets/TrajMapQuick.png" alt="TrajMapQuick Logo" />
 </p>
 ## **Overview**
@@ -39,48 +38,9 @@ We have also extended the code to allow for automatic detection of regions with
 - **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>
+See **[Github](https://github.com/SHEDOOMTC/TrajMapQuick/blob/main/README.md)**
 ## **Installation**
 ```bash
@@ -161,36 +121,15 @@ All library requirements are pre-installed installed via pip or conda and are av
 ## **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)
+See the full examples on **[Github](https://github.com/SHEDOOMTC/TrajMapQuick/blob/main/README.md)**
-The Utility of the shift command (using a 500 frame trajectory) was shown by the figure below:
-![test_traj_2_shift_graph.png](https://github.com/SHEDOOMTC/TrajMapQuick/blob/main/assets/test_traj_2_shift_graph.png)
-**And that of the hotspot command by:**
-![test_traj_2_hotspot_graph.png](https://github.com/SHEDOOMTC/TrajMapQuick/blob/main/assets/test_traj_2_hotspot_graph.png)
-To reproduce the figures above, download the full length trajectory (500 frames) from Zenodo [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.20681326.svg)](https://doi.org/10.5281/zenodo.20681326) and run the codes below on the CLI
-```bash
-#The exact codes used to produce the results above
-tmq shift -tr traj_9NSR_500.nc -to topol_9NSR.prmtop -st 1 -rr 1-378 -rs 272-285 -ce backbone -ma 5 -o out
-tmq hotspot -tr traj_9NSR_500.nc -to topol_9NSR.prmtop -st 1 -rr 1-378 -ce backbone -o out
-```
 ## **Improvements (Speed, Throughput and Reliability)**
 **1.** Batch processing over the CLI and Python API
-**2.** A major improvement of TrajMapQuick over TrajMap is the speed across varying **residue lengths** and **number of frames**. We evaluated a 1000 frame trajectory (at 100 frame interval) over 800 residues (at 100 residue interval) in TrajMapQuick for both subcommands (shift & hotspot). The **performance plots below:**
-![performance plots](https://github.com/SHEDOOMTC/TrajMapQuick/blob/main/assets/Performance_shift_hotspot.png?raw=true)
+**2.** A major improvement of TrajMapQuick over TrajMap is the speed across varying **residue lengths** and **number of frames**. We evaluated a 1000 frame trajectory (at 100 frame interval) over 800 residues (at 100 residue interval) in TrajMapQuick for both subcommands (shift & hotspot).
-shows clear scaling with number of residues and frames, with completion time between **2-5 mins**. Compared to TrajMapQuick, a single 500 frame calculations across 800 residues took around **10 minutes** in TrajMap, besides the manual editing of input parameters.
+See full details on **[Github](https://github.com/SHEDOOMTC/TrajMapQuick/blob/main/README.md)**
 **3.** The choice to select either the CA or backbone for shift calculations.