SIOS user manual
Contents
1. Ready Y You must then select the button Rebuild All and after Shop has rebuilt all search hits by attaching the removed fragments of the original molecule to their anchor points SIOS will be executed and you will see a window like this Y Shop Interface to Other Software SIOS IE ER _ Metasite 3 Volsurf Plus Moka Exit start L I Click on any checkbutton to select which program do you want to run If during SIOS installation you didn t enter some of the programs installation folders you will not be able to select them now III MetaSite3 options window Whenever you click to select on Metasite the Metasite options windows appears see picture below v Metasite options ales S 7 B x E ampute Site of Metabolism Tad Predict Metabolites e ampute MBI Choose type Choose type Steren Choose CVYPs LIVER LIVER x YES CYP3A4 x SKIH x SKIH HO i CYPI4A4 m Dr choose CYPs Or choose CYPs Choose reactions MBI 3a4 threshold Unselect all 5 00 SULPHOXIDIC 8 OXIDATION MBI exposure threshold 3 S DEALKYLATION E OLEFINIC_EPOXIDATION Export results as ANILINIC_H DROX LATION csv DESULPHURATION SDF HTML Output filename Jujetasite3METABOLITESF ile coy Output filename Metasite3MBIFile csv Export results as Metabolite minimum mass 4 SDF no x HTML Ignore redundant MIM Output filename x WES set o MIM Metasite3sOME o2. man perl or perldoc perl If you have access to the Internet point your browser at http www perl org the Perl Home Page MIEL JS Shep Taw 2 C gt i R zT A ZoomB SSH EX Secu a Fe T t H Skype SSH JSSHSec Secur z Papelera de rec ig Inicio e a ETT E E T BH 2Explo T T ES 15 36 If everything went OK you should see a message with the version and license b Installing Perl interpreter in Linux systems Even though most Linux operative systems do already have installed some version of a Perl interpreter we recommend installing ActivePerl for Linux available for free from ActiveState web site http www activestate com Included in ActiveState s ActivePerl precompiled binaries for there is Perl Package Manager ppm which really makes it easy to install the required Tk Perl module If you still prefer to use the preinstalled Perl in your Linux check which version if any is installed by opening a Linux console and writing perl v If there is a Perl interpreter installed this will print the version Any version from 5 8 or higher including 5 10 will be OK II 2 Installing required Perl modules Unfortunately we ve not yet finished We need to install Gf they re not already installed one Perl module that give some extra functionality to Perl Its named Tk tested with Tk version 804 028 and is a graphic library that allows Perl applications to have windows I
3. HO system s global options Import options Temp folder Generate conformations Protonation fust software shop2012 4948 sios NO AS IS System library vw YES MEUTRALIZE ustisoftware metasite3 system mel o NORMALIZE User library HMetasite3 Output File MaetasiteaFile ms3 Close window save options You can select which type of MetaSite3 computation to perform on the rebuilt Shop search hits click in the checkbuttons marked as red circles in the above picture besides Compute Site of Metabolism SOM Predict Metabolites and or Compute MBI to select these tasks Once one task is selected you will see the checkbutton checked and the text will have a darker grey background colour For each task you can choose type Skin Liver or select one or more cytochromes Cytochromes list is a multiple selection list Control click or Shift Click or drag select allows the user to select more than one cytochrome For each Metasite3 task the user can select to export the results of that task to one file marked as a blue line in the above picture and choose the filename The predict metabolites task has a list of possible reactions to apply to the substrate to generate the metabolites all are selected by default but the user can modify it to apply only some of them The lower block of the window contains import and global options which are set for all tasks There user
4. II 4 Running tasks Once finished configuration of tasks to be run simply click button Start in the main SIOS windows and wait a few seconds minutes until you see a message indicating that all tasks have been finished Then if you chose the option Process output file when you bound SIOS to Shop Shop will display the chosen txt or html file in a window Otherwise users can use Volsurf or Metasite to load the vs or ms3 output files stored in results folder Results from Moka can be viewed with any text editor Annex A sios conf file explained Users can find a sample sios conf file included in SIOS package Its contents are similar to Lines with a hash symbol at the beginning are NOT used OS Linux LOG_FILE home guillemp shop_script LOG log MOKA _DIR usr software moka VSPLUS DIR usr software vsplus 0 9 26 Linux VSPLUS USER MODELS DIR home guillemp shop script VSPLUS USER MODELS FILE home guillemp shop script libfile0000 TestUserModel VSPLUS USER MODELS FILE home guillemp shop script libfile0001 TestUserModel2 METASITE3 DIR usr software metasite3 ZMETASITE3 USER LIBRARY usr software metasite3 pepe mel SHOP DIR usr software shop2012 4940 RESULTS DIR usr software shop2012 4940 DISABLE CACO2 DISABLE PB DISABLE SKIN DISABLE SOLY DISABLE VD Any line beginning with a hash will be ignored by SIOS and can be used to include comments or simply to disable some option Each line contains a
5. MTA TipJar Te i interpolate data into templates with a minim Perl extension for Tivoli TME10 M 3 k per 804 027 r6 Tk a Graphical User Interface Toolkit heel 4 l Entry that reflects its state in the background MEA Mie Tk Airports A widget to select airports Saaie ia Tk Applicat MainWindow Widget with special features Tk autobind automatically bind a widget to an ALT key Tk Autoscroll i space invaders like scrolling T E Tk BarberP i A rotating barber pole ES pue Tk Browser Perl library browser N J 2 Tk Calculat 152 Hewlett Packard RPN Calculators MEL ISS Shap nit Tl r aniacFia additional Tb can iac mathade far daalina ww Draw AI Status Detalls Tk lle Tk a Graphical User Interface Toolkit a f Version 804 027 r6 ZoomB SSH Released 2007 07 05 EX Secu Author Nick Ing Simmons lt nick ing simmons net gt CPAN http search cpan org dist Tk 804 027 D p E 6978 packages 6978 listed 45 installed O to install O to remove Install Area site z z Skype SSH SSHSec Secur Lz Papelera de rec Inicio S mbolo d 48 2SSHS v 3 Bloc v SHOP 2 0 8 2 Explo v FA 2 Peric v Z comillas d ES amp 16 07 b Installing Tk in Linux Linux users that don t have Tk Perl module installed will need to this If you installed ActivePerl for Linux you have also the Perl Package Manager try executing ppm in a
6. KEY in upper case followed by an and a VALUE The KEY must be in uppercase and exactly as displayed above The equal sign and VALUE are not mandatory for all KEY but when they are they must contain either one of several fixed options indicated between brackets separated by the symbol I For instance OS KEY lines can be OS Linux or OS windows and it will be indicated as OS Linuxlwindows VALUES can be of type COMPLETE PATH TO FILE COMPLETE PATH TO FOLDER or COMPLETE PATH TO FILE MODELNAME The first two lines that any sios conf file must contain are OS z Linuxlwindows LOG FILE COMPLETE PATH TO FILE These need to be in this order first the OS then the LOG FILE so that every time SIOS is executed and reads sios conf file it can print its options in the log file for later inspection MOKA_DIR VSPLUS_DIR and METASITE3_DIR are the options that point to the folder where each program if available is installed The folder must be written WITHOUT any double quotes but including any empty spaces that the path might have The folder path must not end in or for Windows VSPLUS USER MODELS DIR if included must point to the folder that contains Volsurf Plus user models files If VSPLUS USER MODELS DIR is included in sios conf sios conf must contain at least one VSPLUS USER MODELS FILE line Each VSPLUS USER MODELS FILE line has the following syntax VSPLUS USER MODELS FILE 2Z COMPLE
7. can be executed by itself or it can be bound to Shop so that it s run just after Shop performs one task In order to bind SIOS to one Shop task run the graphical client Shop Install Folder gt shop run and select Menu Edit gt Preferences gt Scripting Tab Scroll down to Template Rebuild All then click on checkbutton Call script and browse through the filesystem to Shop Install Folder gt bin run_sios bash or Shop Install Folder gt bin run_sios bat if you re running Windows hdd SHOP Settings x General settings Scripting On action Template rebuild all Call script Ihop2012 4949 bin run sios bash 5 Process output fle Apply Cancel L A You could also select Process output file so that Shop displays any txt or html file after SIOS has been executed III Running SIOS SIOS can be executed both as a standalone application interface simple write in console run sios bash or run sios bat followed by the complete path to a multimol2 file or as an application bound to Shop s task Template Rebuild AII as explained above How can you trigger Shop s Template Rebuild All task First you need to connect to a Shop server and select the database you want to search Then select menu Query gt Load Query and choose an sdf or mol2 file containing a whole molecule Shop automatically detects that the loaded query doesn t have any anchor points and loads a 3D interface for
8. complete path to file libfile usr software shop sios sios log log Is Moka installed which folder ELLA No Set default to disable CACO2 VS calculation Ww Yes gt 5 Ww esten T Set default to disable PB VS calculation No PN Yes Set default to disable SKIN VS calculation Is Metasite installed which folder No Ww Yes Set default to disable SOLY VS calculation t x Do you want to use a user made Metasite library Set default to disable VD VS calculation Ww Enter Metasite library complete path to mel file L Install Ww This installation program has two main tasks create and copy SIOS files to the right place in your machine In order to be able to install SIOS users have to choose and fill these fields in a predetermined order First users must choose their operative system Linux or Windows and write down where is Shop installed and where do they want SIOS results to be stored as well as the location and name of SIOS log file Every time you click on Linux or Windows Shop installation folder Sios results folder and Sios log file change to their default values for the selected operative system but once the operative system 1s selected the user can modify them at will Also users can select which programs are installed on their machine Moka Volsurf Plus and or Metasite3 All configuration options specific of one pro
9. you to choose where to place them by clicking on the precise atom see picture below v SS OOOO L OK Cancel This step is crucial it is by selecting where do you want the anchor points using this interface that Shop will be able to re attach the removed fragments displayed in a lighter grey in the above picture to the all search results Template Rebuild All Automatic recognition of molecules missing anchor points is not implemented in the Draw Query tool Menu Query gt Draw query so if you re using it to draw your query you must first draw it choose the mol file name and submit it without any Dummy atoms draw the whole molecule and then discard the wrong query and load the saved file after drawing 1t using Menu Query Load Query Once you ve selected the anchor points do a search on the database and click on any of the results Then select Menu Search gt Rebuild Ligand see picture below SHOP 2 0 File Edit View Query Search Database Help l Goog Database Query 38 ase Descriptor Rebuild ligand v m testTT_dummy mol2 Select i testTT dumm Style chroman 0 2 0 1 1 1 H sS chroman 0 2 0 1 1 1 ome Zoom Zoom Multi Fields lt lt Prev Next gt gt File name b 01 1 1 01 minim 2 mol2 a Rebuild All Rebuild Close Z Ai E n i iy i Ui ij d a O S Similarity Value 0 782 distance Template B Query a
10. Default is that all system models are used If during installation you choose to disable one of the system models its checkbutton will not be selectable Also if during installation one or more customized user models were included they will be listed and selected by default Click on any checkbutton to add remove making predictions on that model be aware that System model projections will anyway be included in the data matrix CSV file Once finished click on Save options button below and the window will disappear You can check at any time later the options you selecting by unselecting and selecting again Volsurf in the main window III 3 Moka options window Whenever you click to select on Moka the Moka options windows appears see picture below r I x w Moka options n add Output file name IMoka_ Predictions tt Automatic tautomer correction 4 YES HO Custom DB model file absolute path L Close window save options _ Here you can set Moka output file name as well as to choose whether to perform automatic tautomer correction check whether your version of Moka supports this feature and if given during SIOS installation it will display the absolute path to the customized DB file that will be used Once finished click on Save options button below and the window will disappear You can check at any time later the options you selecting by unselecting and selecting again Moka in the main window
11. S First of all which operative system Shop client is running under Windows Linux SIOS needs to be installed in the same machine as Shop client II 1 Installing a Perl interpreter a Installing Perl interpreter in Windows systems If Shop client 1s executed from a Windows machine the easiest way 1s to download a precompiled executable of Perl interpreter ActivePerl recommended version is 5 8 but not 5 10 as the newest version lacks some of the required modules needed from the company ActiveState This compiled interpreter is completely for free but ActiveState sells also integrated development tools to help programmers write their own Perl applications Download ActivePerl as an MSI Microsoft Installer package and install it Default installation options are OK Once finished open a System terminal see screenshot below and write perl v and press Enter Gygwin Internet gt Simbolo del sistema Explorer C gt perl u This is perl v5 8 8 built for MSWin32 x86 multi thread with 18 registered patches see perl U for more detail Macopyright 1987 2007 Larry Wall Binary build 822 280952 provided by ActiveState http www ActiveState com Built Jul 31 2007 19 34 48 Perl may be copied only under the terms of either the Artistic License or the GNU General Public License which may be found in the Perl 5 source kit Complete documentation for Perl including FAQ lists should be found on this system using
12. SIOS Shop Interface to Other Software User Manual PhD Guillem Plasencia Gallofr Lead Molecular Design S L I Introduction SIOS Shop Interface to Other Software as its name says is an interface for Shop to access configure and execute other programs Moka Volsurf Plus and Metasite3 from within Shop Using it users can submit within Shop itself the rebuilt search hits to either Moka Volsurf Plus or Metasite3 SIOS makes use of Shop s Scripting feature that allows Shop users to bind the execution of an external program SIOS in the present case to completion of a task in Shop Template Rebuild All in the present case In the particular case of SIOS the execution of this interface must be bound to Template Rebuild All read II Requisites and Installation for more details which means that SIOS will be executed after all Shop s search hits have been rebuilt II Requisites and Installation SIOS is an application written in Perl which is an interpreted programming language Unlike other programming languages interpreted languages rely upon an interpreter to be executed We at Lead Molecular Design offer our registered users SIOS as a Perl application but we do not provide the Perl interpreter to users This means that users in order to run a program written in Perl have to install both the Perl interpreter and the program Here we will explain how to download and install Perl interpreter and SIO
13. TE PATH _TO_FILE gt lt MODELNAME gt Where COMPLETE PATH TO FILE is the path to the libfile containing the model data and MODELNAME is the name of the model exactly as displayed in the column Name of vsmodeller menu Edit gt Library table Please note that COMPLETE PATH TO FILE and MODELNAME are separated by a colon Any customized model included with this method will be automatically selected to be used by default but users can unselect them if they wish so In a similar way METASITE3 USER LIBRARY is the option that has to be used if a user wants SIOS to use a customized Metasite3 library It must point to the COMPLETE PATH TO FILE of a mel file SHOP DIR is not strictly needed by SIOS but it stores the COMPLETE PATH TO FOLDER of Shop installation folder This path was used by install sios to copy SIOS files inside its bin folder RESULTS DIR contains the COMPLETE PATH TO FOLDER where all tasks executed through SIOS will store their result files and log files DISABLE CACO2 DISABLE PB DISABLE VD DISABLE SKIN DISABLE SOLY are parameters that don t use a VALUE Simply include them or delete comment them out with a symbol if you want that SIOS disables by default any of these Volsurf Plus system models they are all selected by default
14. ating system SIOS is running under or where are the programs installed You can see a sample of the contents of a sios conf file and some instructions on how to write one sios conf file yourself in the Annex A e It creates any needed folder for instance the folder where you want all results of predictions sent through SIOS to be stored in or the folder where sios log file will be stored if it s a different one e It creates or copies files sios exe install_sios exe sios conf sios_env bash and run_sios bash for Linux or run_sios bat if it s a Windows operating system into lt Shop installation folder gt bin II 5 Checking SIOS installation If you want to test whether SIOS was correctly installed simply open a command terminal either in Windows or Linux and enter into Shop installation folder gt bin Write run sios bash or run sios bat if you re in Windows followed by the complete path to a multimol2 file provided inside sios package there s a test mol2 file run_sios bash path to test mol2 for Linux run sios bat UNIT path to test mol2 for Windows If installation was successful you should see a window like kd Shop Interface to Other Software 5105 EI x _ Metasite 3 Volsurf Plus Moka Exit start L I Using this method SIOS can be executed as a standalone interface completely independent of Shop to launch MetaSite3 Volsurf Plus or MoKa tasks IL 6 Binding SIOS to Shop SIOS
15. console When the graphical program called Perl Package Manager opens read section II 2a Installing Tk in windows above If you didn t install ActivePerl for Linux because either Perl was already installed or you compiled it yourself then the easiest way to install Tk is using CPAN Comprehensive Perl Archive Network First you need to have superuser rights to install new Perl Modules ask the system administrator to install them for you if you don t have them Once you re superuser write in a Linux console cpan and a cpan shell loads that will look like cpan shell CPAN exploration and modules installation v1 9205 ReadLine support enabled cpan 1 Sometimes it might ask you a few questions like the ones below before giving you access to CPAN shell here are some empty means simply press Return and accept CPAN default Always commit changes to config variables to disk no yes Parameters for the perl Build PL command Parameters for the Build command Do you want to use a different command for Build install Parameters for the Build install command It might also ask you about your country this 1s to select the closest mirror server Write the following line to install Tk cpan 1 gt install Tk and press Enter Is it OK to try to connect to the Internet yes It will take some time to download compile and install everything and at some point you will see several windows appearing
16. don t worry cpan 1s testing Tk windows Once finished read the last messages to check if installation went fine and if it succeeded write cpan 3 quit to leave CPAN shell and return to console shell II 3 Testing installation of required Perl modules To test if Tk and Tk FileDialog modules installation was successful write in a Linux console perl e use Tk You should not see any answer or error message in reply II 4 Installing SIOS a Installing SIOS using the install_sios exe application Once you ve finished installing Perl interpreter and the needed module Tk you re ready to install SIOS Probably you ve already done it but if not download SIOS l z p from http www leadmolecular com web site you need to be a registered user and unzip it into a temporary folder for instance home username tmp using Winzip in Windows or unzip in Linux Open a Linux or Windows console and enter into the temporary directory Write the following line to execute the installation program perl e install_sios pl You will see a window like the one in the screenshot below Kd Shop Interface to Other Software Installation Program BEE Choose your operative system Linux Windows Do you want to use user made VS models Enter Shop installation folder v Vusysofware shop v Enter SIOS Results folder Enter VS model name vust sofware shop sios Enter SIOS Log file name Enter VS model
17. gram are blocked until the user clicks on Yes to the question Is PROGRAM NAMES Installed Users have to write the absolute path 1 e usr software metasite3 to the installation folder of each program Here is a short explanation on each field e Choose your operative system click on either Windows or Linux e Enter Shop installation folder write the absolute path to Shop installation folder i e usr software shop e Enter SIOS results folder the absolute path to a folder where SIOS results and SIOS log file will be saved e Enter SIOS log file name the file name of SIOS log file This file will be saved inside SIOS results folder e Is lt PROGRAMS installed which folder click on either Yes or No and don t forget to write the absolute path to the installation folder of the program e Do you want to use a user made Metasite library click on either Yes or No and provide the absolute path to the mel customized file e Do you want to use user made VS models click on either Yes or No For each model you have to provide the exact name of the model as is shown in column Name of table displayed in vsmodeller menu Edit gt Library Control L as well as the absolute path to the libfile corresponding to that model BEWARE all user models have to be stored inside the same folder Once the model name and file have been written click on button Add model to include it and repea
18. n order to check if it s already installed please open a terminal and write perl e use Tk press Enter if you see a message like Can t locate Tk pm in INC it means that most likely you don t have these installed If you don t see any apparent message you have it installed and you can skip the rest of this section a Installing Tk in Windows ActivePerl package comes with its own Perl Package Manager PPM a graphical application that allows users to install Perl modules In order to execute PPM either write ppm ENTER in a terminal or start Perl Package Manager from the Applications Menu Select menu View gt All Packages and scroll down to Tk and right click to select Install see picture on next page Once you re done selecting Tk go to Action gt Install or press the small green right arrow in the top right side PPM will install the required module as well as any additional required modules that these modules might need as a requisite i UO gs Adobe MID Read f 7 Aa Perl Package Manager Gygwin Internet File Edit View Action Help Explorer is a IQ View all packages Ctrl 1 Installed Abstract 5 Timestamp f Simple methods for timestamping al TinyMake A minimalist build language similar in purp TipJar fields f generate constants and accessors for array b E aa uii TipJar MTA outgoing SMTP with exponential random bac E TipJar MT j send e mail via TipJar
19. s can choose whether to calculate conformations or protonation options as 1s neutralize or normalize to a user given pH or even the output filename for the MetaSite3 results file this file can be opened by MetaSite3 Once finished click on Save options button below and the window will disappear You can check at any time later the options you selecting by unselecting and selecting again Metasite in the main window II 2 Volsurf Plus options window Whenever you click to select on Volsurf the Volsurf options windows appears see picture below v volsurf Plus options dii Output S File name VSplusFilevse Output Datamatrx File name VsplusDataMatrikcsv Output Log File name Wspuslog Nonnalize Proton HO v YES pH 0 14 GRID Field Parametrization STATIC DYNAMIC GRID spacing in Angstroms ns KWIK 7 v B system Models Custom User Models El E PB Model m SKIN Model E SOL Model E VD Model L dose window save options E Users can select the name of the Volsurf Plus output file as well as the filename where the data matrix in comma separated format CSV will be stored and the name for the Volsurf Plus log file Users can also select whether to normalize protonation state by assigning themselves a pH value it must be a decimal number don t forget the decimal comma or it might not work They can also choose GRID parameters as well as which System models and or Custom models use
20. t as many times as models you want to include e Set default to disable CACO2 PB SKIN SOLY VD Volsurf Plus calculations SIOS by default will select all Volsurf Plus models to be calculated If there is one or more VS system models that you know beforehand that you will not use you can save yourself a few clicks by just disabling the option to calculate them in SIOS BEWARE Choosing to disable one or more of VS models means that you will never have the option to calculate them using SIOS unless you run install sios again When finished choosing options click on Install button bottom right The program will do a few trivial checks filenames and paths must not be empty for instance and if it finds some problem it will be displayed colouring the form in a darker grey colour If the Install button turns green the configuration for the installation was found to be Ok and the installation itself probably succeeded If it turns red it means there was some problem while creating folders and files associated with the installation read the following section for more information on how to install SIOS by hand b Installing SIOS yourself The application install_sios was written just to make a simple process even easier Here there is an explanation of what install_sios does just in case you need to do it yourself e The most important step is writing the sios conf file that contains necessary information to execute SIOS like the oper
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