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# SimpeleNMR # SimpeleNMR aims to be simple, automatic, batch processor for (semi) quantitative NMR spectra. Features include: * Agilent/Varian VNMR, Bruker (Avance II and newer), and PicoSpin files * 1D spectra (regular/arrayed), limited 2D spectra support (JRES/basic absolute value processing). * Zero fill, exponential, sine, gaussian window functions * Phased/magnitude/power mode spectra * Automatic or manual phasing * 1st/2nd order and smooth baseline correction * Output in ImatraNMR .is/isz, txt, csv, matlab, wav (FID only). * Open source, BSD 3-clause license. ## Installation ## Requirements: * Python3 * NumPy * SciPy * scikit-learn * Matplotlib * Cython (only for building from scratch) In Debian based distros, you can start with: ``` #!bash apt-get install python3 python3-virtualenv python3-pip ``` Safest way is to use pip and install the package in a dedicated virtualenv to avoid any conflicts with other packages. First create a new virtualenv and activate it: ``` #!bash virtualenv --python=python3 some_env_name source some_env_name/bin/activate ``` Finally dowload the wheel package and use pip to install it: ``` #!bash pip install simpelenmr-1.5.2-cp35-cp35m-linux_x86_64.whl ``` Now you can use simpeleNMR whenever the virtualenv is activated. ``` #!bash # activate env source some_env_name/bin/activate # do stuff -> profit # deactivate if you want to use some other venv deactivate ``` you can also install without virtualenv, but remeber to use pip3 and add .local/bin/ to your path etc: ``` #!bash pip3 install simpelenmr-1.5.2-cp35-cp35m-linux_x86_64.whl --user ``` # Example processing # SimpeleNMR is a console program and takes arguments in the following syntax: ``` simpele INPUTMODE FORMAT INPUTFILE [OPTIONS] ``` So, for example a single (s) Varian (vn) fid file can be processed with default settings with following command: ``` simpele s vn oil.fid ``` In more realistic scenario, some processing options are supplied in the form of a processing config file. An example of such file (example.sconf) could be: ``` zerofill = default apo_lb = 1.0 phase = auto autophase_mode = default baseline_corr = 2 ``` And now processing using example.sconf: ``` simpele s vn oil.fid -c example.sconf ``` The resulting spectrum (example_oil.isz) can be viewed using simp_view, bundled with SimpeleNMR: ``` simp_view oil.isz -png oil ``` # Quick reference # This file lists configuration options in SimpeleNMR 1.4.6 and is supplementary to the full user guide. Config parameter list ## Basic ## ``` proc = [1d|2d] ``` ## Window functions and zerofill ## ``` zerofill = <POINTS> zerofill2d = <POINTS> apo_lb = <HZ> apo2d_lb = <HZ> apo_gauss = <STDEVS> apo2d_gauss = <STDEVS> apo_gauss_mean = <MEAN> apo2d_gauss_mean = <MEAN> apo_sine = <SCALE> apo2d_sine = <SCALE> ``` ## Phasing ## ``` phase = [auto|default|manual|av|pow] ph0 = <degrees> ph1 = <degrees> autophase_mode = [1|2|3|4|5|zero|default] autophase_copyblock = [first|last] autophase_blcorr = [1|2|3] ``` ## 1D postprocess ## ``` baseline_corr = [1|2|3|drift|second|smooth] baseline_corr_window = <POINTS_PERCENT> trim = <TRIM_PERCENT> align = <STATRTPPM> -> <ENDPPM> @ <REFERENCE> ``` ## 2D postprocess ## ``` rotate = [y|n] fold = [y|n] project_f2 = [sky|y|n] ``` # Building it yourself# This is useful if your are not on 64-bit linux with Python 3.5, so the readymade wheel archives do not work. First clone or download the repo, and create a new virtualenv if needed & activate it. Then go to the repo dir, build & install the wheel package ``` #!bash # make sure you have cython pip install cython # build python3 setup.py bdist_wheel # install pip install dist/simpelenmr-1.5.2-cp35-cp35m-linux_x86_64.whl ``` # License # BSD 3-Clause. See: https://opensource.org/licenses/BSD-3-Clause Copyright 2017 Valtteri Mäkelä Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. 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. 3. Neither the name of the copyright holder nor the names of its 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 HOLDER 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.