ChemAzTech. A Chemistry molecule - Web database - software, to manage products and their structures.
Copyright (C) 2009  Remy Dernat.

This program is free software; you can redistribute it and/or modify
it under the terms of the GNU GPL license as published by
the Free Software Foundation (FSF).

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 licence for more details.

You should have received a copy of the GNU GPL license along with
this program; if not, see http://www.gnu.org/licenses/gpl.html

" Chemical library " like software, created by Remy Dernat

Montpellier, CNRS, IBMM - UMR5247



*********  ROADMAP  *********

Continuous Improvement :
- Secure connections, registration forms to enter and modify products (stripslashes, magic quotes ...) OK with PHPIDS and HTMLPurifier.
- Optimization of molecules storage (all in database except pictures).
- Avoid exec and system call from php script. (babel, python, rm, ls...)


********* CHANGELOG *********
***** Current version:

v0.6b :
- Some minor bugs fixed (picture generation, PHP code adapted for version 5.3).
- Update of fpdi, jmol and jchempaint.

v0.6a :
- Bug fixed in consulting mode (rights problem).

v0.6 :
- Approximate search added (wildcard "%").
- Added the research by quantity, purity, yield or for some other text fields.
- Picture for dangerous commercial product added.
- Evolution/improvement of commercial products.
- New group : could see, modify and delete all products.
- Removal possibility added when you look at a specific product (if the user is a member of group with write access).
- Bug fixed in consulting mode (parcours.php) for user products visibility.
- New script to change the owner of products : you can modify many products at the same time from search mode.
- Update for java applet jchempaint and jmol (and some scripts to call these applets (bug fixed for jmol timeout)).
- 2 scripts added for configuring and installaling (and securing the configuration directory) chemaztech.
- LDAP authentication is now possible
- Added a connection functionality for molecules.

v0.56 :
//Renderer 2D and java choice for user cancelled because of SVG.
- Possibility to generate all the structures directly from research and consulting mode.
- Replacement of PNG by SVG wherever it is possible. Structures are cleaner.
-> SVG Adobe plugin should be used for IE users and imagemagick should be installed on server for PDF and XLS(X) extractions.

v0.55 :
- Search similarities between structures with mychem fingerprints
//- Possibility to import PDB file and transform it to mol file into the db - Cancelled
- Storage of associations of [sdf file] fields when importing to keep history.

v0.54 :
- Management of storage with places and price of products.
- Bug correction in parcours.php when changing user.
- Bug correction in RegDrawStruct.php (calc_inchi function).
- AutoSubmit for RegDrawStruct.php and pre_ajout.php

v0.53 :
- Add excel export with PHPExcel
- Centralization of config file with plugins parameters (+ path)
- Basic management of storage places.
- SDF/SMI export after search if login as admin.
- New type of SDF export with experiment number.
- Added "Check All" button in search result.
- New organization of administrative tasks.
- CSV export after search.
- README - Adding a treshold documentation for phpids :
20 - high security
35 - good security
50 - medium
75 - bad security (default value)
100 - really bad security
250 - no security (use it for debug)

v0.52
- New group profile : READ ONLY.
- Java and javascript detection on client side.
- Change of default stylesheet.
- More user-friendly (many informations)
- Empty structures are ignorees in case of SDF export (except for full SDF export with all properties).
- Bug correction in case of "Add a structure" when no structure present.

v0.51:
- bug correction in affichage.php (data field - rmn)
- more translations.

v0.5:
- Compatibility mol CTAB v3000 see MyChem conversion CTAB = V2000> V3000
- Improved Search by sub-structure (eg, COOH, CH3 ...) SMILES / SMARTS JCP applet
- PHPIDS + HTMLPURIFIER Integration.

v0.48:
- Added a directory with core modif.php ajout.php choix.php pre_ajout.php ...

v0.47:
- Search by sub-structure by means of drawing mode: recovery of drawing smiles and then search by substructure.
- Updating products (structure) from the drawing mode "modify structure" (in affichage.php) update tables compound and destruction of files previously associated (regeneration?).
- Same as above to create a new product: "copy and edit the structure to create a new product"

v0.46:
- Registration of products directly from the drawing mode

v0.45:
- Export SDF with sort mass function.
- Add a new stylesheet more sober.

v0.44:
- Translation into English with a file lang.php (define $ Welcome ...)
- Resize images introduced in various functions and parcours.php
- Tree include (lang, fonctions.inc ...) config (version config_db, style.css)

v0.43:
- Optimization of the 2D display in Java.
- Fixed a bug in deleting molecule.
- Preview of molecules already displayed when consulting parcours.php

v0.42:
- Improvement and bug fixes for PDF export
- Search by substructure.

v0.41:
- Extraction homeless by user or by location
- Fixed the warning in the addition mode and display.
- Fixed a bug in the table structure libraries, on the field visibility.
- Change the owner of a product.

v0.4
- Export SDF.
- Export SDF properties of all structures.
- Modify a group.
- Clean.php: delete all *.mol, *.smi, *.html, *.zip, *.mol2 at once

v0.39:
- Verify the format of mails during registration.
- Import SDF differentiated for regular imports.
- Optimization of the tree file and code.

v0.38:
- Improvement of research: possible group with 'Read All'. Coder research function of the product visibility 'o' and 'u'.
- Improvement Accessed product visibility 'o' (other, see unix rights) for everyone.

v0.37
- Addition of a field called "Lot".
- Addition of a field "biomonitoring".
- Addition of field "visibility".
-> Modified database! Make a control structure.
- The consultation is based on the visibility of the product and user groups.
- Addition of fields to export to "CN".
- Improved PDF export with PDFI (concatenation of all files pdf) pdf image of the structure generated in python on a page.
- Automatic image scaling.

v0.35
- Creation and management of user groups (with possibility to create groups "read-only".)
- Define the level of visibility by Molecule: public, group, user.

v0.34
- Clean.php: possibility to delete the mol, mol2, smi, zip, cdx...
For PNG, you must verify that this is not the structure. Normally, the soft core stores the minimum.
- Bug fixes: import and processing sdf (due date, name of the software, and a table).
- Improvement of display for consultation.
- Improvement of the extraction of image structures by user.
- Improvement of the synchronization.
- Import of SDF is more reliable.

V0.33
- Generation 3D OpenBabel option - gen3D "(real 3D)
Babel --gen3D -imol monfichier.mol-omol2 monfichier.mol2
(more 3D details in mol2)

v0.3:
- Import File (SDF allows import from a solid base Isis / Base).
- Partial rewrite code due to legibility problems.

v0.26
- Possibility to edit info on "my account" as the password, the mail ...
- Possibility for the user to delete one of its molecules
- Generation of specific images for the user.

v0.25:
- Improved combined searches
- By MyChem: Generation of InChI codes and smi
- Solid Export smiles
- Possibility to make a user => administrator level "2" (and vice versa)
- Search by number of manip.
- Export images of structures in a zip file for the user.

v0.2:
- Authentication System
- Interface administrative / chimiothecaire (removal of molecules and cleaning of files / data, user management). Exhaustive extraction of the base.
- ID pre-filled when adding product.
- User Interface (extraction of data with personal image and the base term "user")
- Export massive molecules in a mol file (concatenated).

v0.15:
- Bug fixed when adding "simplifies" and product display.

v0.1:
- Small display changes
- Display = default 2D image
- Modification of several molecules at once via the search mode