Commit ce30089f authored by Aymeric BLONDEL's avatar Aymeric BLONDEL
Browse files

Readme.md v2

parent 8f6d1b3c
#Copremo : Python package for COlor PREdiction of MOlecules
# Copremo : Python package for COlor PREdiction of MOlecules
Copremo is a free software within the framework of the project Marches. It is written in python and possesses a GUI. It aims to simulate the absorption and transmittance spectra of dyes and ultimately quantify its color as perceived by any standard human eyes. This color quantification is based on the absorption spectrum obtained by experiment or by quantum computations.
......@@ -14,21 +14,21 @@ The active site of a dye is called a chromophore, it is in this site that electr
Each color is characterized by a point in a colorimetric multi-dimensional reference space. There are several color spaces, e.g. RGB, XYZ, LAB and HTML. Copremo computes these values and provides a color image perceived by the human eye in the presence of daylight.
##Copremo description
## Copremo description
This package is a free software under the GNU GPL License (see below) that can be employed in two different ways:
1. As software with a graphical interface (GUI) in order to predict the color of a compound from one of the three ways listed above (.csv file, .log and .fcuv).
2. As a python package to use in your own programs / scripts.
##License
## License
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with Copremo. If not, see <http://www.gnu.org/licenses/>.
##How to cite Copremo
## How to cite Copremo
If you use Copremo to get publisheable results, please cite: A.Blondel, Copremo, Université de Nantes, 2015.
##Prerequisite
## Prerequisite
L'installation préalable de Copremo nécessite
......@@ -46,7 +46,7 @@ Copremo employs two librariesunder LGPL licence: Colorpy [3] et cclib [4].
Copremo is working on Apple operating systems, on several Linux distribution (fedora, Ubuntu, opensuse) but on Windows 7 (not yet validated interface).
##Installation
## Installation
```
......@@ -81,7 +81,7 @@ Launch the software
```
Copremo GUI shows up.
##How to predict color from a Gaussian computation
## How to predict color from a Gaussian computation
The procedure described below has been used previously in Ref. [1] Considering the dye/pigment of your choice, follow the five steps to vizualize the color induced by the interaction between you molecule and light:
......@@ -93,15 +93,15 @@ The procedure described below has been used previously in Ref. [1] Considering t
The Copremo software has many other options which are explained below using different validation tests.
##Validations
## Validations
###Objective 1:
### Objective 1:
Diluate your dye in a solution and visualize (take a picture) the color of your solution (A)
Perform a spectrophotometric measurement of your diluted compound (B) and extract the data (.csv format). Use Copremo to transform this csv file in order to generate within Corpremo approximation the hexdecimal color value. Compare this value with the color of A.
Realize an electronic transition calculation (cf follow the above protcol), generate the theoretical absorption spectrum (C). Compare the preceived color (A) with B and the predicted color (C) from a theoretical method.
###Validation 1 :
### Validation 1 :
Four dyes synthesized in the laboratory CEISAM were used for the validation of Copremo.
......@@ -114,7 +114,7 @@ These molecules were placed in a UV spectrometer/Visible Shimadzu UV-2501PC usin
* Recover the experimental transmittance spectrum of Ref. [2] using WebPlotDigitizer for each molecule and create a .csv file that is readable by Copremo.
* Compare the results of colors perceived by the human eye when the molecules are in solution (see Table 1 in Ref. [2]) to the Copremo predictions.
###Validation 2 :
### Validation 2 :
Compare Copremo to a similar approach (see Ref. [2]) which has been validated with four solution tests and water. This aims to validate Copremo colorimetric analysis method. We recovered the transmittance spectra of these colored solutions to estimate whether the perceived colors estimated by Copremo were comparable to the one of Ref. [3].
......@@ -124,13 +124,13 @@ Be cautious that .csv files contain normalized transmittance spectra. For Coprem
Copremo allows to find the colors from the experimental transmittance spectrum.
#GUICopremo
# GUICopremo
##Initial and default values
## Initial and default values
The ini file (in ini folder) gathers the intitial parameters. The following parameters might be changed by the user:
##Input files
## Input files
* .csv : La première ligne du fichier csv n'est pas prise en compte. Ensuite deux colonnes de valeurs séparées par un « ; ». La première colonne correspond à la longueur d'onde en nm. La seconde correspond à l'intensité à cette longueur d'onde.
......@@ -140,12 +140,12 @@ The ini file (in ini folder) gathers the intitial parameters. The following para
* .fcuv: Copremo peut également lire les fichiers issus de FCclasses (cf ci-dessous) après conversion des nm en eV,on nommera ce fichier .fcuv.
#Copremo API
# Copremo API
Copremo includes an API (Application Programming Interface) containing two classes Color and Spectral.
##Test of Color class
## Test of Color class
* Test 1 :use Color.py in command line to obtain the hexadecimal value corresponding tp the color of the studied dye, for instance CuSO4 (vérif2).
......@@ -160,11 +160,11 @@ Copremo includes an API (Application Programming Interface) containing two class
```
##Classe Spectral docs
## Classe Spectral docs
Classe Color Doc
##Test of Spectral class
## Test of Spectral class
* Test 1 : use Spectral.py in command line to obtain the spectrum of Color.log file (verif4) in the .uv (Color.log.uv) format. Then just open GUI.
......@@ -179,7 +179,7 @@ Copremo includes an API (Application Programming Interface) containing two class
```
#References
# References
1 :Beck, M. E. (2005), Estimation of physiologically perceived color from TDDFT-derived excitation spectra. Int. J. Quantum Chem., 101: 683–689. doi: 10.1002/qua.20326
2: Beyond λ[lambda]max: Transforming Visible Spectra into 24-Bit Color Values Darren L. Williams, Thomas J. Flaherty, Casie L. Jupe, Stephanie A. Coleman, Kara A. Marquez, and Jamie J. Stanton Journal of Chemical Education 2007 84 (11), 1873
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment