| Name | nmrPype JSON |
| Version |
1.0.8
JSON |
| download |
| home_page | None |
| Summary | Python implementation of Nuclear Magnetic Resonance (NMR) signal analysis program "nmrPipe" |
| upload_time | 2025-02-04 16:01:02 |
| maintainer | None |
| docs_url | None |
| author | Micah Smith |
| requires_python | >=3.10 |
| license | Copyright Notice and Statement for the nmrPype project
Copyright (c) 2023-2024 Micah J. Smith
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:
a. Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
b. Redistributions in binary form must reproduce the above copyright
notice, this list of conditions and the following disclaimer in the
documentation and/or other materials provided with the
distribution.
c. Neither the name of the author nor the names of contributors may
be used to endorse or promote products derived from this software
without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
Copyright Notice and Statement for the nmrglue Project
Copyright (c) 2010-2015 Jonathan J. Helmus
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:
a. Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
b. Redistributions in binary form must reproduce the above copyright
notice, this list of conditions and the following disclaimer in the
documentation and/or other materials provided with the
distribution.
c. Neither the name of the author nor the names of contributors may
be used to endorse or promote products derived from this software
without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. |
| keywords |
nmr
decomposition
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
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|
# nmrPype
Python implementation of command-line program nmrpipe, using linux pipelines to process NMR data.
- **Documentation:** https://phimykah.github.io/nmrpype
- **NMRPipe Website:** https://www.ibbr.umd.edu/nmrpipe
- **Source Code:** https://github.com/PhiMykah/nmrPype
- **Bug Reports:** https://github.com/PhiMykah/nmrPype/issues
Installation
============
Installing nmrPype can be done by through pip:
```sh
# Install prerequisites
pip install numpy scipy
# Install program
pip install nmrPype
```
A virtual environment or conda environment is recommended for using nmrPype.
If using conda, `numpy` and `scipy` can be installed using `conda install`.
### Note
This is made for Python 3.10 or above. Some of the code requires Python 3.10's features such as `match-case` statements.
Python 3.12 is recommended as development is done with 3.12, but testing is done to assure that 3.10 is supported.
Usage
==========
nmrPype can be used in through two methods: Command-line and Script
Command-line
--------------
```
nmrPype -in [inFile] -fn fnName -out [outFile] [-ov]
```
Functions:
```
FT Perform a Fourier transform (FT) on the data
ZF Perform a Zero Fill (ZF) Operation on the data
SP (SINE) Adjustable Sine Bell
PS Perform a Phase Correction (PS) on the data
YTP (TP, XY2YX) 2D Plane Transpose
ZTP (XYZ2ZYX) 3D Matrix Transpose
ATP (XYZA2AYZX) 4D Matrix Transpose (unimplemented)
NULL Null Function, does not apply any function
```
Run the `nmrPype --help` command to see a list of more options.
Script
------
In a Python script or jupyter notebook use the following line:
```py
import nmrPype
```
I recommend setting the import as `pype` for simplification.
### Example
```py
import nmrPype as pype
df = pype.DataFrame("h.fid") # Load NMR data file into script
df.array() # Display spectral data array
```
Building From Source
====================
### Building using Pip
1. Install prerequisites
```sh
pip install numpy scipy
```
2. Clone the repository
```sh
git clone https://github.com/PhiMykah/nmrPype
```
3. Install in development mode with pip:
```sh
cd nmrPype
pip install -e .
```
### Building using Conda
With conda, the environment.yml file can be used to obtain
the development environment.
1. Clone the repository
```sh
git clone https://github.com/PhiMykah/nmrPype
```
2. Copy the source conda environment
```sh
cd nmrPype
conda env create -f environment.yml --name nmrpype
```
- You can set the name to anything you wish, but typically
my convention is to have the environments lowercase
3. Install in development mode with pip:
```
pip install -e .
```
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"description": "# nmrPype\r\nPython implementation of command-line program nmrpipe, using linux pipelines to process NMR data.\r\n\r\n- **Documentation:** https://phimykah.github.io/nmrpype\r\n- **NMRPipe Website:** https://www.ibbr.umd.edu/nmrpipe\r\n- **Source Code:** https://github.com/PhiMykah/nmrPype\r\n- **Bug Reports:** https://github.com/PhiMykah/nmrPype/issues\r\n\r\nInstallation\r\n============\r\nInstalling nmrPype can be done by through pip:\r\n```sh\r\n# Install prerequisites\r\npip install numpy scipy\r\n# Install program\r\npip install nmrPype\r\n``` \r\nA virtual environment or conda environment is recommended for using nmrPype.\r\nIf using conda, `numpy` and `scipy` can be installed using `conda install`.\r\n\r\n### Note\r\n\r\nThis is made for Python 3.10 or above. Some of the code requires Python 3.10's features such as `match-case` statements. \r\n\r\nPython 3.12 is recommended as development is done with 3.12, but testing is done to assure that 3.10 is supported.\r\n\r\nUsage\r\n==========\r\nnmrPype can be used in through two methods: Command-line and Script\r\n\r\nCommand-line\r\n--------------\r\n```\r\nnmrPype -in [inFile] -fn fnName -out [outFile] [-ov]\r\n```\r\nFunctions:\r\n```\r\nFT Perform a Fourier transform (FT) on the data\r\nZF Perform a Zero Fill (ZF) Operation on the data\r\nSP (SINE) Adjustable Sine Bell\r\nPS Perform a Phase Correction (PS) on the data\r\nYTP (TP, XY2YX) 2D Plane Transpose\r\nZTP (XYZ2ZYX) 3D Matrix Transpose\r\nATP (XYZA2AYZX) 4D Matrix Transpose (unimplemented)\r\nNULL Null Function, does not apply any function\r\n```\r\nRun the `nmrPype --help` command to see a list of more options.\r\n\r\nScript\r\n------\r\nIn a Python script or jupyter notebook use the following line:\r\n```py\r\nimport nmrPype\r\n```\r\nI recommend setting the import as `pype` for simplification.\r\n### Example\r\n```py\r\nimport nmrPype as pype\r\n\r\ndf = pype.DataFrame(\"h.fid\") # Load NMR data file into script\r\ndf.array() # Display spectral data array\r\n```\r\n\r\nBuilding From Source\r\n====================\r\n\r\n### Building using Pip\r\n\r\n1. Install prerequisites\r\n```sh\r\npip install numpy scipy\r\n```\r\n2. Clone the repository\r\n```sh\r\ngit clone https://github.com/PhiMykah/nmrPype\r\n```\r\n3. Install in development mode with pip:\r\n\r\n```sh\r\ncd nmrPype\r\npip install -e .\r\n```\r\n\r\n### Building using Conda\r\n\r\nWith conda, the environment.yml file can be used to obtain\r\nthe development environment.\r\n\r\n1. Clone the repository\r\n```sh\r\ngit clone https://github.com/PhiMykah/nmrPype\r\n```\r\n2. Copy the source conda environment\r\n```sh\r\ncd nmrPype\r\nconda env create -f environment.yml --name nmrpype\r\n```\r\n- You can set the name to anything you wish, but typically\r\nmy convention is to have the environments lowercase\r\n\r\n3. Install in development mode with pip:\r\n```\r\npip install -e .\r\n```\r\n\r\n",
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