Difference between revisions of "Jreader"

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<span style="color:#FF8C00">  '' Ongoing discussion on the jmol-users @ lists.sourceforge.net and private communication between Damien Jeannerat and Angel Herraez (if you want to join, you are welcome)'' </span>
 
  
[http://www3.uah.es/nmr_e_data/reader/reader.htm ''J-reader''] is webtool that can be accessed through the web or [[Jreader#Installation |installed]] on a local computer.
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[http://www3.uah.es/nmr_e_data/reader/reader.htm ''J_reader''] is a webtool for reading and editing NMReDATA files that can be accessed through the web or [[Jreader#Installation |installed]] on a local computer.
In both cases, the programs is running on the users's computer. Not data (structure, etc.) are send to any server via the net.
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In both cases, the program is running on the users's computer. No data (structure, etc.) are sent to any server via the net.
  
 
'''This page is under construction and will be improved...'''
 
'''This page is under construction and will be improved...'''
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=== Main features ===
 
=== Main features ===
  
*display the structure(s)  
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*Display the structure(s)  
*display the data in the signal assignment tags (NMREDATA_ASSIGMENT )  
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*Display the data in the signal assignment tags (NMREDATA_ASSIGMENT)  
*display the data in the J-coupoing assignment tags (NMREDATA_J)   
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*Display the data in the J-coupling assignment tags (NMREDATA_J)   
*for each NMREDATA_1D tag, display the 1D spectrum (pop-up window) and add as overlay the data found in the tag (chemical shifts, couplings, multiplicity, on top of the spectrum, labels, integral, etc.)
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*For each NMREDATA_1D tag, display the 1D spectrum if available in JCAMP format; additionally, the data found in the tag (chemical shifts, couplings) are displayed on top of the structure display.
*for each and NMREDATA_2D tag, display the 2D spectrum (pop-up window) and add on top the spectral data found in the tag (list of correlations vertical and horizontal lines for each "label" and dits when the correlation was listed in the tag)
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<!--
 +
*For each NMREDATA_2D tag, display the 2D spectrum (pop-up window) and add on top the spectral data found in the tag (list of correlations vertical and horizontal lines for each "label" and dits when the correlation was listed in the tag)
 +
-->
 +
 
 +
This work was presented at the [[ Symposium2019 | 1st NMReDATA symposium in Sept. 2019]].
  
 
===2D to 3D conversion===
 
===2D to 3D conversion===
JSmol can display 3D structures (<jmolSmiles text="example">aspirin</jmolSmiles>), but as now the NMReDATA .SDF files include "flat" structures.
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JSmol can display 3D structures (<jmolSmiles text="example">aspirin</jmolSmiles>), but for now the NMReDATA .SDF files include "flat" structures.
  
A first step, we could say that when there is no 3D structure in the sdf file, we use Jmol the build-in addition of H and “optimized” 3D structure, allow to save it, just to get started. I think that renumbering the atoms for proper reference will not be impossible…(via a reference table if direct correction of the NMREDATA_ASSIGNMENT table is not possible. We will see later if other tools should be used to generate a 3D or if we can develop more the ones in J-mol to make the process better (user) controlled.
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J_reader allows to start from the 2D model, add the implicit hydrogens and generate an “optimized” 3D structure that may be added to the original NMReDATA file and later saved to disk. The assignments and couplings are remapped accordingly on the 3D model.
  
Difficulties - when H atoms are implicit, renumbering is necessary - it could be done...
 
 
=== Installation ===
 
=== Installation ===
 
For local installation:
 
For local installation:
  
1) download the last (?) version of the JSmol package - testing was done with version ???
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<!--
 +
1) Download the last version of the [https://sourceforge.net/projects/jmol/files/ Jmol package] - testing was done with version 14.29.46
 +
 
 +
: 1a) From the downloaded <code>Jmol-xx.xx.xx-binary.zip</code>, extract <code>jsmol.zip</code>
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: 1b) From <code>jsmol.zip</code>, extract everything or just the needed parts (see below)
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 +
2) Download [http://www3.uah.es/nmr_e_data/J_reader.zip the J_reader package] that contains [http://www3.uah.es/nmr_e_data/reader/reader.htm the web application] and ancillary files. Extract everything.
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: This download does not include any of the sample files used for demonstration by the web application.
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-->
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Download [http://www3.uah.es/nmr_e_data/J_reader.zip the J_reader package] that contains a copy of [http://www3.uah.es/nmr_e_data/reader/reader.htm the web application] and ancillary files. Extract everything.
 +
: This download uses JSmol, a part of the full [https://sourceforge.net/projects/jmol/files Jmol distribution], version 14.29.46.
 +
: It does not include any of the sample files used for demonstration by the web application.
 +
 
 +
The files should be arranged according to this schema:
 +
* <code>reader.htm</code>  (the interface)
 +
* <code>combined.js</code>  (utilities; contains code from jsTree, jQueryModal, AlertifyJS)
 +
* <code>combined.css</code>  (ditto)
 +
* <code>img/</code>  icons used in the page
 +
* <code>JSmol.min.js</code>    (main file of the JSmol library)
 +
* <code>php/jsmol.php</code>  (a component from JSmol library)
 +
* <code>js/JSmolJSV.js</code>  (a component from JSmol library; other files in that folder are not needed)
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* <code>j2s/</code>  (components forming the JSmol library; includes about 1300 files and subfolders)
  
2) save [http://www3.uah.es/nmr_e_data/reader/reader.htm the main page]
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The application works well from a web server; from local disk, it will work at least in some browsers. When running locally, due to security policy of the browsers, loading of data files is restricted to the folder where the htm file is (sometimes it works as well for subfolders and parent folders). Additionally, some browsers will require setting internal parameters (in <code>about:config</code> or equivalent feature), like <code>security.fileuri.strict_origin_policy = false</code> or <code>privacy.file_unique_origin = false</code>
  
 
=== Funding ===
 
=== Funding ===
 
This development was funded, in part, by the University of Geneva, Gr. D. Jeannerat, in spring 2019.
 
This development was funded, in part, by the University of Geneva, Gr. D. Jeannerat, in spring 2019.
=== Main features ===
 
This work was presented at the [[ Symposium2019 | 1st NMReDATA symposium in sept 2019]].
 
  
 
=== Acknowledgements ===
 
=== Acknowledgements ===
 
We thank Marion Pupier for multiple examples of NMR records used for this work.
 
We thank Marion Pupier for multiple examples of NMR records used for this work.
 +
 +
<!--
 
=== Technical test pages ===
 
=== Technical test pages ===
  
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[[jmol testpage2 | Demo page by Angel Herraez]].
 
[[jmol testpage2 | Demo page by Angel Herraez]].
 +
-->

Latest revision as of 19:20, 28 October 2019

J_reader is a webtool for reading and editing NMReDATA files that can be accessed through the web or installed on a local computer. In both cases, the program is running on the users's computer. No data (structure, etc.) are sent to any server via the net.

This page is under construction and will be improved...

Main features

  • Display the structure(s)
  • Display the data in the signal assignment tags (NMREDATA_ASSIGMENT)
  • Display the data in the J-coupling assignment tags (NMREDATA_J)
  • For each NMREDATA_1D tag, display the 1D spectrum if available in JCAMP format; additionally, the data found in the tag (chemical shifts, couplings) are displayed on top of the structure display.

This work was presented at the 1st NMReDATA symposium in Sept. 2019.

2D to 3D conversion

JSmol can display 3D structures (example), but for now the NMReDATA .SDF files include "flat" structures.

J_reader allows to start from the 2D model, add the implicit hydrogens and generate an “optimized” 3D structure that may be added to the original NMReDATA file and later saved to disk. The assignments and couplings are remapped accordingly on the 3D model.

Installation

For local installation:

Download the J_reader package that contains a copy of the web application and ancillary files. Extract everything.

This download uses JSmol, a part of the full Jmol distribution, version 14.29.46.
It does not include any of the sample files used for demonstration by the web application.

The files should be arranged according to this schema:

  • reader.htm (the interface)
  • combined.js (utilities; contains code from jsTree, jQueryModal, AlertifyJS)
  • combined.css (ditto)
  • img/ icons used in the page
  • JSmol.min.js (main file of the JSmol library)
  • php/jsmol.php (a component from JSmol library)
  • js/JSmolJSV.js (a component from JSmol library; other files in that folder are not needed)
  • j2s/ (components forming the JSmol library; includes about 1300 files and subfolders)

The application works well from a web server; from local disk, it will work at least in some browsers. When running locally, due to security policy of the browsers, loading of data files is restricted to the folder where the htm file is (sometimes it works as well for subfolders and parent folders). Additionally, some browsers will require setting internal parameters (in about:config or equivalent feature), like security.fileuri.strict_origin_policy = false or privacy.file_unique_origin = false

Funding

This development was funded, in part, by the University of Geneva, Gr. D. Jeannerat, in spring 2019.

Acknowledgements

We thank Marion Pupier for multiple examples of NMR records used for this work.