Solvent eXtraction Database
Contents
1. Solvent eXtraction Database manual SXD user manual Three modes of functioning are available e Adminisitrator mode database management and creation deletion of users accounts e Operator mode supply SXD using an electronic form e User mode search and exploitation of the information from SXD Administrator manual 1 Home Main page shows the functions available to the administrator Solvent eXtraction Database Administration a 5 wew all niomat aout users show all mol files create 3 new weer show all graphs delete anew user chow all structures show all temporary files view all sdf files sorted by users change the news remove all temporary files vwitw admin temporary files Import sdf filets into database Export database to sdf file Verw oll records Delete entries Disconnect 2 Users The administrator creates or deletes the users accounts The list of the users of SXD can be visualized 3 Database This part is related to the management of the SXD Solvent eXtraction Database Administration Home BB rewind By erevious JR next Wena i B 277 results found Import sdi Export sot En t Dalat Delate this record 20 tracture CAS Humber Peta CsHS604 648 90 BO 05 b2 6 Abbreviation s Reaction Symbol Hame RN Regt paca l fi Concentrations Units Min Max Single 30 File name Sh2. includes the plots By default for any textual field in the query the search is performed as word 12 mon Example the search for benzene in the Name field results in benzene chloro benzene etc For any numerical field in the query values if a exact value is written the search is performed automatically for the range of 1 Example If 100 is written in the temperature field the search engine selects all records where temperature is included in the range of 99 to 101 The program recognizes automatically a correspondence between different unities for the temperature and pressure Thus for the query containing 25 and C in the fields Temperature and T Unit fields respectively the search engine retrieves the records corresponding to 25 C and to 298 K Unities used for temperature Symbol Unity C Celsius degree K Kelvin degree Unities used for pressure Symbol Unity atm Atmosphere bar Bar Pa Pascal psi Pound per square inch mmHg Millimetres of mercury As soon as the query form is completed click on the Search button to perform the search To refine the search the user can modify the query by clicking the Edit query button or create a new one using the New query button The SXD search engine applies both structural and alphanumerical search procedures The retrieved information is given in a table containing i an index of the record in the database ii the 2
3. 3 Curves comparison tools This option allows the user to place the curves from the different records in one plot This procedure is launched using the Compare graph button in the Graphs section in any record having at least one plot 16 Solvent extraction Database Graph Plots RegIND graph plot x Axis Y Axis Element Organic phase Water phase I 1 l f pH Cs org mM Cs Dichloromethane cs on cscl Redraw graph In the new window the user has to select the filtering criteria related to axis names cation and composition of aqueous and organic phases The filtered results are presented in the table containing the number of record in SXD the numbers of a plot and a curve on a given plot if there are some as well as the filtering criteria If the initial plot contains several curves the user can select some of them using the Redraw graph and Clear unselected buttons The user can switch on off the filtering criteria using corresponding checkboxes The View filtering results button visualizes the list of records which satisfy the selected criteria table Filtering results Csr orgmM Filter on F Filter on m Filter on Filter on View fillers results In order to place curves from different records in the same plot the user should select the curves to be c
4. 50F submit copy rename remove 4 all S0F Help All fles J This page presents the list of all SD files stored in the user s files sdf directory on the server The buttons remove rename and copy serve for corresponding manipulations with the files To edit a file one should click the corresponding file name in the list If a file contains several records the user can select one of them from the additional window see below all SDF This file contains 276 molecules Please chose one to modify Since a file or an extraction system is selected a new window containing an electronic form appears The textual and numerical data are entered by filling the corresponding fields To edit the structure of the extractant one should click on the extractant picture then use 2D editor JAVA applet In order to draw the graphs the data are placed in the field XY Data 7 236 0 0 Remarks nee The X and Y values must be entered corresponding to the 10 05 0 508 ascending order of X 11 55 0 899 Only unique values of X are permitted al Having finished the input of the X Y values use the Redraw graph button to visualize the graph The SXD software allows the user to input an unlimited number of curves on each plot as well as an unlimited number of plots for each record To add a curve or a plot use 4dd plot or Add graph menus Use the valid your entry button to save the
5. export either one record only or several records from X record to Y record or all records Selecting X Y interval is advised when the number of exported records is very big this allows administrator to create several SD files instead of one huge file The program creates the SD file on the server followed by its automatic download to the client machine When the download procedure is finished the file created on the server can be deleted using a corresponding Delete button 3 2 3 Edit This function allows administrator to edit selected records from the database One can select one record using the Rewind Previous Next and End buttons then clicking on the Edit button In a current record all fields can be modified except of ID RegIND The modified record is saved since it is submitted to the database 3 2 4 Del all This function allows administrator to delete all records For security reasons administrator login and password are requested Warning There s no way to undo this operation 3 2 5 Delete this record This function allows administrator to delete the selected record from the database The program presents the detailed report showing if the procedure was successful Warning There s no way to undo this operation 4 SD files This option allows the administrator to show and to download the SD files stored on the files sdf operators directories on the server Files submitted by operat
6. D structure of the extractant iii the extracted metal and iv the diluent 13 Solvent eXtraction Database Home Supply SXD Searching xD Edit query Results found a a RegiND Metal ligand m nitro briflueromethy benzene In order to see the content of retrieved records the user has to select one or several records from the list or to use the Select all records button then to click the View selected results button As soon as a new record appears the user can pass from one selected record to another one using the Rewind Previous Next and End buttons The Extractant Phases Exp conditions Graphs Numeric properties and References buttons provide a rapid access to different parts of the given record The PDF button allows one to create a PDF file corresponding to one selected record 2 Filtering This option allows one to group the records according to certain filter criteria see Figure below For example the user can select the records related to extraction of a given cation by different ligands under similar conditions temperature pressure pH diluent 14 Solvent eXtraction Database Supply SXD Searching XD Search by form J Filtering Choose constant parameters C extractant Name Extractant Formula C Extractant Mw Hames of Cobxtractant s gt Anion C Fomula C Name C Hame C salt C salt D Mi
7. data Remark If your browser displays a message asking if you want to close the window you should answer yes Some browsers ask for a confirmation before running the JavaScript commands used in the SXD code The Submit button serves to submit the prepared SD file to the administrator It should be noted that the data submitted by the operators must be validated by the administrator before being loaded to the database The selected SD file is located in the files submit directory on the server All files in that directory are accessible via the Submitted files part 1 3 Submitted files This page presents the list of all SD files submitted to the administrator and located in the files submit directory on the server The Cancel option moves the selected file into the SD File part in order to modify it Then the operator will have to re submit the file when the modifications are done Any file can be removed renamed or visualized using the corresponding buttons As soon as the administrator validates a given SD file it is copied in the files succes directory or in the files error directory and hence it will disappear from this list of submitted files 1 4 Submit results 10 Solvent eXtraction Database Home Supply SD Searching SxD Help MOL files J SDF files Submitted files Submit results All files These files were suocefully Imported ln the database dovnload J re
8. move 1 167 8SB0F download J remove 2 169 1 sdf download J remove 3 17 1 sdf download J remove 4 174 1 sdf dovnload J remove 5 19 50F download remove 6 70 1 sdf download J remove 7 all 1 sdf These files are incomplete flaw note Submit rename remove 1 testib sdf This part concerns the files which have been examined by the administrator The top frame shows the list of the files which have been successfully imported in the database Those files are stored on the server in the sdf succes directory and they can be visualized removed or downloaded using the corresponding buttons The bottom frame shows the list of the files which have been rejected by the administrator and stored on the server in the sdf error directory To read the administrators comments use the View note button Operator can edit the SD file clicking the corresponding file name and re submit it using the Submit button 1 5 All files This part presents the list of all the MOL and SD files used for the alimentation of SXD The submitted SD files are not given in thas list 1 6 Remarks The graph structure and temp are temporary directories to which the user has no access The query directory is related to the user s part it is used to save the search query submitted to the database search engine see user manual for the details 11 User manual This part is related to
9. n concentrator C Min concentration C Max concentration C Max concentration Single Concentration C Sindle concentration The user can choose a threshold for the number of records in the sub set using the Choose minimum number of result fields By default that number is equal to 20 which means that the sub sets containing less than 20 records will be ignored The filtering procedure results in i an histogram showing the number of records for each sub set and ii a table specifying the name and the values of common properties for each sub set Solvent extraction Database Supply SXD Searching XD Search by form Filtering e p ee chloroform fas a al cots benzene flao e a benzoylinflucroacetone Ees benzene fa CCN C S A A ep e O ebon tetrachionde fe e e 2 thenoyltri voroacetone cot2e lentoroform l7 15 Using the View data set button the user can visualize the content of the selected sub sets as a table containing internal number of records in SXD the 2D structure of extractants the name of the cation and some thermodynamics properties logK and logD Solvent eXtraction Database Supply SD Searching SXD Search by form Filtering Eiltering short report 33 records Regino fextractant Metal E type k value Lago The View detailed report with selected results button shows content of the selected records
10. ompared from the table Filtering results and to use the Add to graph button 17 Organic phase Water phase CDichloromethane csconecse Pichoromethane cscompacse Cichloramethane csconpeesc i eE ls ompecse x AXIS Y Axis Element h 1 pH Cs org mM s h ph esetorg m css Cs Cs org mM When the selected records appear in the Plots table the user visualises an ensemble of curves with the Redraw graph button Solvent extraction Database Plots RegIND graph plot ix Axis Y Axis Element Organic phase water phase M ji pH Cs Jorg mM Cs Dichloromethane jCs OH Cscl ie 1 pH Cs Jorg mM Cs Dichloromethane jCs OH Cscl 18
11. ors are not listed here 5 Other files This option allows the administrator to visualize and to download different types of files stored on the server It concerns the files corresponding to 2D structures MOL and PNG to graphs PNG and to some temporary files 6 Tools This menu bring together the following functions 6 1 Change the news Here the administrator writes a message informing all users about the date of the last update of SXD or the maintenance periods Being posted that message appears at the user home page 6 2 Remove all temporary files This function allows administrator to delete all temporary files stored on the server Remark Only files from disconnected users are deleted 6 3 View all admin temporary files This function allows administrator to see the content of his temporary directory Operator manual This part is related to the Supply SXD menu The operator s interface includes 5 sub menus MOL files SD files Submitted files Submit results and All files Operators feed SXD using an electronic form The submitted data are stored on the server as SD files Each operator has his directory containing several sub directories Bg votre repertoire The SXD feeding proceeds in two steps i drawing or importing the 2D structure of extractant using the Mol files menu and ii an input of experimental extraction data using the SD files menu 1 1 MOL files This option allow
12. ort Name Ligand Class Name s of CoExtractant s Buelecmsy BuCalnfdisrene flex Dievelohencv 1 B crown amp B 3 1 Records visualisation The Rewind Previous Next and End buttons allows user to pass from one record to another one 3 2 Database management 3 2 1 Import sdf This option allows one to feed the database by importing the SD files submitted by operators The administrator can vizualize the list of all submitted SD files Selecting one file opens the following page Solvent eXtraction Database Administration File entree sdf From User test hls file Copy this file to submitted files user directory Back to the sof list Back to database view One SD file can contain information about several extraction systems each of whose represents a potential record of SXD Administrator verifies the content of each record using the View button If the data are correct the record s are imported in SXD using the Import or the Import all button If the SD file is not incorrect Administrator uses the Reject this file button to send his comments and the SD file to the operator 3 2 2 Export sdf This function allow administrator to export the records from the database to the SD file For confidentiality reasons it is protected with login and password which by default are the same as the login and password of the administrator The administrator can
13. s the user to input 2D chemical structures of the extractant molecule There are two possibilities 7 to import a MOL file using the Enter the MOL file you want to import button and ii to draw the structure using the JAVA applet included in SXD Solvent eXtraction Database Supply SXD Searching SXD Help files SDE files Submitted filas Submit results all files Enter the MOL file you vant to import Prone clicks fact dioweoed telstra de iy thek here te launch Isis Drow 7 4 Click here to draw a ntr mol These are your MOL files convert to SDF J remove BETA PICOLINE moal convert to SDF remove GAMMA PICOLINE mol convert to SOF remove RO 2P 0 0H mal convert to SDF remove 1 1 DLANTIPYRYLHEPTANE nmal convert to SOF remove naph moal convert to SDF remove BETA MERCAPTOCINNAMAMIDE mol In order to import MOL file click the browse button then choose a file on your computer and click the Import your file button The MOL file is uploaded in the files mol directory on the server and appear in the list These are your MOL files To draw directly the structure click the Click here to draw a new mol button which leads to Opening a window containing the 2D structures editor JAVA applet As soon as the structure is drawn write down a corresponding file name in the field situated on the bottom of the window then click the Ok bu
14. the Searching SXD menu of the user interface There are two ways to retrieve an information from the database Search by form The user prepares a query using an electronic form Filtering The user groups the records according to selected parameters 1 Search by form The first page contains the search form Once prepared the query is automatically saved which allows the user to refine the next search The New query option clears the form To prepare a query the user fills one or more fields in the form which corresponds to the Boolean AND The SXD search engine also includes some functions giving a certain flexibility in query preparation For example it is possible to input an incomplete name for a textual fields or a range of values for numeric fields The following functions are available Operator Function Example Replaces any number of unspecified characters calixYoarene B Replaces only one unspecified character c lix 4 arene lt Searches of values less than the target value lt 100 Searches of values larger than the target value gt 100 Searches of values in the range between x and y 100 200 exists Searches all records where a given field 1s filled exists Remarks The wildcard and are applied only for textual variables The operators lt gt and are applied only for numerical variables Ifthe option Graph exists is selected the program searches the records which
15. tton Remark 1 In order to be able to use the JAVA applet the JAVA Runtime Environnement JRE must be installed on your computeur If the JRE is not installed a download dialog window will appear Otherwise the user has to download the JRE from the JAVA website http java sun com getjava 2 In case of a security warning the user should give the permission to run the JAVA progam 3 For more information about JAVA applet visits the website http www chemaxon com marvin chemaxon marvin help sketch index html As soon as a new MOL file 1s drawn or imported its name will appear in the frame These are your MOL files showing the list of users MOL files stored on the server Selecting the file from that allows user to visualize and to edit structure using the Edit button The Remove button deletes a given MOL file Having created the 2D structure the user has to use the Convert to SDF option which creates a SD file containing only the chemical structures All of the other fields are empty and will be filled using electronic forms 1 2 SDF files Solvent eXtraction Database Home Supply SXD Searching SD MOL files SDF files Submitted files Submit results Enterthe SDF file you vrant to import These are your SDF files submit copy J rename remove 1 test lt df submit copy rename remove 2 1 80F submit copy J rename remove 3 2
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