linuxinstallation& configurationguide

LINUX INSTALLATION &CONFIGURATION GUIDE

BIOVIA DIRECT 2017

Copyright Notice

©2016 Dassault Systèmes. All rights reserved. 3DEXPERIENCE, the Compass icon and the 3DS logo,CATIA, SOLIDWORKS, ENOVIA, DELMIA, SIMULIA, GEOVIA, EXALEAD, 3D VIA, BIOVIA and NETVIBES arecommercial trademarks or registered trademarks of Dassault Systèmes or its subsidiaries in the U.S.and/or other countries. All other trademarks are owned by their respective owners. Use of any DassaultSystèmes or its subsidiaries trademarks is subject to their express written approval.

Acknowledgments and References

To print photographs or files of computational results (figures and/or data) obtained using BIOVIAsoftware, acknowledge the source in an appropriate format.

BIOVIAmay grant permission to republish or reprint its copyrighted materials. Requests should besubmitted to BIOVIA Support, either through electronic mail to [email protected], or in writingto:

BIOVIA Support5005Wateridge Vista Drive, San Diego, CA 92121 USA

ContentsAbout This Guide 5Introduction to BIOVIA Direct 5How to Use this Installation Guide 5Prerequisite Knowledge 5Related BIOVIA Documents 5

Before You Install Direct 7Installation Modes 7Pre-Installation Software Checklist 7Server Software 7Program Fonts 7

Pre-Installation Required Tasks Checklist 7Prepare the System Tasks 8Required Oracle Tasks 8

Preparing the System Tasks 9Verify Disk Space 9Create the BIOVIA Home Directory 10Verify JRE is Installed 10

Installing in an Oracle RAC Environment 10Information Required to Install Direct onOracle 11Install Direct 12Direct Installation Tasks Checklist 12Using the Java Installer 12Installation from File Archive 12Post-Installation Tasks 12

Required Permissions 13Introduction to the Direct Installer 13Requirements and Recommendations 13Decompressing the Installer 13Verify and Set DISPLAY 14Test the X Environment 15

Running Direct Installer in GUI Mode for Linuxor Solaris 15Install the Files 16Create the Direct Schema and Install theDirect Cartridge 17TWO_TASK Environment Variable 17Installation Log Files 18

Running the Installer in Silent Mode for Linux 18Running the Installer in Silent Mode for Solaris 21Direct Post-Installation Tasks 23Check Installation Requirements for OracleUser SYS 23Verify the Installation 23Modify the UniProtConverter Script 24Enable Accounts to Run the Cartridge 24

Install Direct in Additional Oracle Instances 26Set Up the Direct Demonstration Databases 27Introduction to the Sample Databases 27Demonstration Database Task Checklist 27Create Oracle Schema for DCSAMPLESDatabase Tables 27Import the Oracle DCSAMPLES.DMP File 28Isentris Data Source Definition Files 30Verify Demonstration Database and TablesInstallation 31Molecule Verification 31Reaction Verification 33

Direct File Configuration on Linux and Solaris 35Direct Directory Hierarchy 35Files and Directories 35Case Sensitivity 35Explanation of Directories and Files 35

Uninstalling Direct 38Alert Users That Direct Will Be Unavailable 38Close Any Applications That Use Direct 38Back Up Direct Files 38Uninstall the Direct Files 38Drop the Direct Schema 38Drop the Demonstration Database Schema 39Configure Multiple Direct Versions on theSame System 40Direct Cartridge 40User Account Issues with Multiple CartridgeVersions 40Configuring an extproc Listener 41About the extproc Listener 41Test an extproc Listener 42Configure an extproc Listener Using OracleTools 42Add PLSExtProc Listener to the Defaultlistener.ora File 43Add the EXTPROC_CONNECTION_DATAService to tnsnames.ora 44

Manually Configure the extproc Listener 45Edit the listener.ora File 45Check the tnsnames.ora File 46Stop and Restart the Oracle Listener 47

Set Up an Oracle RAC Environment 47Install Direct 48Configure the listener.ora File 49Configure the tnsnames.ora file 49

Configure a Separate extproc Listener 51Edit the tnsnames.ora File 51

Edit the listener.ora File and Start the NewListener 52Create the Public Database Link 52Manual Installation of the Direct Schema 53Install Direct Files from the File Archive 53Manual Installation Tasks 53Modify the UniProtConverter Script 53Customizing SETPATH 54Run mdlsysactions.sql 54Create the C$DIRECT2017 Schema 55Edit mdllibdef.sql 55Test the Oracle extproc Listener 56Load the Direct Packages 56Test the Direct Installation 57

Maintaining an Installation During a MajorOracle Upgrade 58Upgrade Issues 58Protect Your Direct Data During an OracleUpgrade 58Upgrade Scenario 1 - Upgrade in Place 58Upgrade Scenario 2 - Backup, Upgrade, andRestore 58

About This GuideThis guide explains installation and configuration for BIOVIA Direct 2016 on 64-bit computers that runthe Red Hat Linux, SUSE Linux or Sun Solaris operating environment. For information on how toadminister the data cartridge, see the BIOVIA Direct Administration Guide.

Introduction to BIOVIA DirectDirect:

n Uses the extensibility features of Oracle Server to incorporate chemical searching capabilities intoOracle.

n Allows you to use Oracle SQL to register to and search on tables that contain molecule and reactioncolumns.

How to Use this Installation GuideThis section explains:

Prerequisite KnowledgeThis guide assumes that you are familiar with:

n Oracle database administration and one of the following operating systems:n Red Hat Linux operating system and Red Hat Linux system administration.n SUSE Linux Enterprise Server operating system and SUSE Linux system administration.n Oracle Solaris operating system and Solaris system administration.

Related BIOVIA Documents

Document Purpose

Direct 2016 System Requirements System requirements to run Direct 2016

BIOVIA Direct Secure extproc ListenerConfiguration

How to set up a secure extproc listener

BIOVIA Direct Administration Guide How to administer the Direct cartridge

BIOVIA Direct Developers Guide

BIOVIA Direct Reference

How to develop applications using Direct

BIOVIA Direct Migration Guide How to migrate Direct 6, 7, or 8 databases to Direct Version 9+

BIOVIA Chemical Representation

BIOVIA DirectDirect 8 to Direct 9Chemistry Migration Guide

Reference information on BIOVIA-Chemical Representation

Reference information on the harmonized chemistry availablewith Direct

BIOVIA Direct Error Messages Guide Error messages that might occur using Direct, when upgradingdatabases, and common Oracle errors.

About This Guide |

Document Purpose

CTFile Formats Describes the file formats used to represent structures.

Available for download at https://community.3dsbiovia.com.

| BIOVIA Direct • Linux Installation & Configuration Guide

https://community.3dsbiovia.com/

Before You Install Direct

IMPORTANT! Direct now supports both Oracle versions 11 and 12. Do not use instance_name or SIDbecause these do not direct to known good instances and SID is deprecated. Administrators mustspecify the Oracle service namewhen they install Direct.

Installation ModesThere are threemethods for installing the Unix version of Direct. Run the Java installer in GUI mode,which requires X Windows, or in silent modewhich does not require X Windows. The Java installer is inone of the following files depending on your operating system:

n Direct-16_1_0_LinuxInstaller.tar.gz (Linux)n Direct-16_1_0_SolarisInstaller.tar.gz (Solaris)

A zipped archive containing all files required by Direct is also included. These files must be installedmanually:n directfiles.tar.gz

Use the Java installer if possible, as it handles customization of certain files, creates the BIOVIA schemain Oracle and runs the Oracle installation scripts. For more information see Running the Installer in GUIMode or Running the Installer in Silent Mode.

If the Java installer will not run on your system because ofmissing libraries, you must then install Directmanually. For more information seeManual Installation of the Direct Schema.

Pre-Installation Software ChecklistThe pre-installation software checklist explains the software that you must install before you can installDirect on a host computer running the Red Hat Linux, SUSE Linux, or Oracle Solaris operation system.

See also

Direct 2016 System Requirements

Server SoftwareInstall the version of Oracle Server specified in theDirect 2016 System Requirements. Direct is notsupported on any Oracle version other than those listed in the hardware and software requirements forOracle.

Program FontsThe following system fonts are required to render images:

n Arialn Courier New

If one or both of these fonts are not present, images might not render correctly.

Pre-Installation Required Tasks ChecklistUse this task checklist to verify that you have performed the required pre-installation tasks necessary tocorrectly install and configure Direct.

Before You Install Direct |

Prepare the System Tasks

Do This Details Done

Back up all disks used in the installation.

Verify hardware and software. See theDirect 2016 System Requirements.

Verify that sufficient disk space is available. See Verify that sufficient disk space is available.

Create the BIOVIA Home directory. See Create the BIOVIA Home directory.

Required Oracle TasksDirect 9.1 SP1 and later adds support for Oracle 12c, which includes support for OracleMultitenant /pluggable databases.

To install Direct into multitenant databases, use the same instructions for installing Directinto anotherOracle instance on the samemachine into the same Oracle Home. The instructions are in ManualInstallation of the Direct Schema.

For more information, contact BIOVIA Support.

Notes:

n Oracle does not support SELinux security enforcement, and you must disable the SELinux securityenforcement before installing Direct.

n Direct will not work on Oracle 12.1.0.1.0 due to bug 18169693. Users will need to install patch18169693 for Linux/Unix/Solaris or use 12.0.1.2.

Do this Details Done

1. Verify that thereis an existingOracle databaseinstance.

For more information, see theDirect 2016 System Requirements.

2. Verify that anOracle tablespaceand temporarytablespace existsand is available.

For more information, see theDirect 2016 System Requirements.

3. Verify that yourOracle DBAaccount is valid.

Log in to SQL*Plus using your DBA user name and password (withoutspecifying a DB alias), for example: sqlplus system/manager.

Note: If your DBA login fails, check that the PATH, ORACLE_HOME,and ORACLE_SID are correct, and that the DBA user name andpassword are valid.


mailto:[email protected]

Do this Details Done

4. Verify that youhave a runningexternalprocedure(extproc) listener.

You cannot create the Direct schema until an extproc listener has beenconfigured for Direct.

Note: The PATH in you listener must include the Direct 2017 bin11directory for Oracle 11 or Direct 2017 bin12 directory for Oracle 12.Because of this requirement, if you have and existing Direct 6, 7, 8extproc listener, it might not be sufficient for Direct 2017.

For information on testing and configuring an extproc listener, seeConfiguring an extproc Listener.

(Optional) Set up asecure extproclistener.

See BIOVIA Direct Secure Extproc Listener Configuration.

This document is available in the BIOVIADirect_Direct_Documentation.zip file.

If you choose to set up a secure extproc listener, you should do so afteryou install the Direct files. This allows you to use the BIOVIA templatesprovided for this task.

(Optional) Verify thatthe TNS_ADMINenvironment variableis set.

Perform this task if you set up a secure extproc listener. See BIOVIADirect Secure extproc Listener Configuration Guide.

Preparing the System Tasks

Verify Disk SpaceDisk storage space required for use with Direct.

Note: The disk space values that follow do not include space for Oracle databases.

On Red HatLinux

n 290MB (this number includes Direct files, the necessary JVM files, and theuninstaller)

n 360MB of additional temporary space is needed during installation.

On SUSE Linux n 290MB (this number includes Direct files, the necessary JVM files, and theuninstaller)


On OracleSolaris

n 760MB (this number includes Direct files, the necessary JVM files, and theuninstaller)


To view the space that is available on the disk

1. Open a terminal window.

2. Issue the command that follows, specifying the drive on which you will install Direct:$ df –k path_name

Before You Install Direct |

Where path_name is the location where you will install Direct, for example, /opt/BIOVIA. Theavailable disk space is displayed in kilobytes.

For information about disk space and tablespace requirements, see theDirect 2016 SystemRequirements.

Create the BIOVIA Home DirectoryThe BIOVIA Home directory is a directory for BIOVIA software. The recommended pathname for theBIOVIA Home directory is /opt/BIOVIA.

Use the procedure that follows to create the BIOVIA Home directory /opt/BIOVIA if it does notalready exist.

1. Log in as root on the host computer where you will be installing Direct.2. Create the BIOVIA home directory:

# cd /opt# mkdir BIOVIA

3. Optionally, change the owner and group:# chown user:group BIOVIA

4. Change the permissions on the BIOVIA directory so that all users have read access:# chmod a+rx BIOVIA

5. Log out as root.

Verify JRE is InstalledThe UniProt Converter Utility is written in Java and requires a Java Runtime Environment (JRE).

The script UniProtConverter uses the JRE installed by the Direct installer, in a directory parallel todirect2016. You can also install your own JRE, version 1.6 or later. Download the Oracle JRE fromOracleWeb site at http://java.com/en/download/manual.jsp.

See also

Modify the UniProtConverter script

Installing in an Oracle RAC EnvironmentDirect supports Oracle Real Application Cluster (RAC). If you are installing Direct in an Oracle RACenvironment, you must:

1. Configure and test the listener on each RAC node.2. Install the product once, using a file path that is visible to and known by the same name on all

nodes.3. Create the Direct schema once.4. Test the installation separately on each RAC node.

See also

Setting Up an Oracle RAC Environment


Information Required to Install Direct on Oracle

Parameter Example Value for your site

Operating system

License key1 rc6xd4ef8

BIOVIA Home2 /opt/BIOVIA/

Product BIN directory> /opt/BIOVIA/direct2016/bin11

n Disk space required on RedHat Linux

n Disk space required on SUSELinux

n Disk space required onOracle Solaris

n 230MB (for the Direct datacartridge)230MB temporary space (requiredfor installation)

n 230MB (for the Direct datacartridge)230MB temporary space (requiredfor installation)

n 250MB (for the Direct datacartridge)

n 250MB temporary space (requiredfor installation)

Oracle environment

Oracle home directory2 /usr/ora11201/oracle/11.2.0

Oracle SYSTEM and SYS username and password2

system/password

sys/password

Oracle Service Name2 server4

Password for the cartridgeschema2

password

Port number for the listener2, 4 1521

Default Oracle tablespace forthe cartridge schema2

USER

Temporary Oracle tablespacefor the cartridge schema2

TEMP

1 The license key for Direct is listed in an email from BIOVIA sent to the Ship To contact at your site. Thelicense key is not case sensitive.2 This can vary at your particular site.3 This is the location of the mdldirect.so file for your version of Oracle. This is used in setting theLD_LIBRARY_PATH for the extproc listener. Use bin11with Oracle 11 and bin12with Oracle 12.4 This port number can be found in the listener.ora file. Port number 1521 is the Oracle default.

Information Required to Install Direct on Oracle |

Install DirectThis chapter explains the tasks required to install Direct on a Linux host computer.

Direct Installation Tasks Checklist

Using the Java InstallerUse this checklist if you are installing Direct using the Java installer.

Task Details Done

1. Copy the installer from the BIOVIA Download site ontothe hard drive.

See Decompress the Directinstaller.

2. Install the Direct files. See Install the Direct files.

3. Create the Direct schema. See Create the Direct schema.

Installation from File ArchiveUse this checklist if you are installing Direct manually using the file archive.

Task Details Done

1. Copy the file archive from the BIOVIA Download site ontothe hard drive and install the Direct files.

See Install Direct Files fromthe File Archive.

2. Install Direct manually. SeeManual Installation ofthe Direct Schema.

Post-Installation Tasks

Task Details Done

1. Enable specific accounts torun Direct.

See Enable specific accounts to run the Direct cartridge.

2. Check the installationrequirements for the SYSuser.

See Check the installation requirements for the Oracle SYSuser.

3. Verify the installation. See Verify the Direct installation.

4. Modify theUniProtConversion script.

SeeModify the UniProtConverter script.

5. (Optional) Install Direct intoadditional Oracle instances.

See Install Direct in additional Oracle instances.

6. (Optional butrecommended) Create asecure extproc listener.

For information on setting up a secure extproc listener, seethe BIOVIA Direct Secure extproc ListenerConfigurationGuide.


Required PermissionsDuring the installation of Direct, specific tasks require specific Oracle or system administrator privileges.The following table lists the tasks and the permissions required to perform the tasks.

Task Owner Permission required

Install the Direct files User who owns the Directfiles.

Administrator privileges

Install the Directcartridge

User who owns theDirectfiles

Read and Execute permissions on installerprogram file

Create the Directschema

Database Administrator DBA system permissions

Introduction to the Direct Installer

Note: If you are installing manually from the file archive, skip this section and proceed to ManualInstallation of the Direct Schema.

The DirectDirect installer is an X11-based GUI installer, and must be run from a computer or X terminalcapable of displaying X windows. The installer provides you the following options to:

n Install the Direct filesn Configure and test the extproc listenern Create the Direct schema and install the Direct Cartridgen You can install examples only.

Requirements and Recommendationsn Note the Direct file installation path, for example, /opt/BIOVIA).n Local display must be able to open an xtermwindow, or its equivalent, from the target computer.

Note: The DISPLAY environment variable must be set properly to ensure that X windows opened bythe installer appears on the local display.

See also

Worksheet

Verify and set DISPLAY

Decompressing the Installer1. Navigate to the directory containing the downloaded installation files. You need one of the following

files:Direct-16_1_0_SolarisInstaller.tar.gz

Direct-16_1_0_LinuxInstaller.tar.gz

2. Decompress the downloaded installer using the gunzip utility:$ gunzip Direct-16_1_0_SolarisInstaller.tar.gzgunzip Direct-16_1_0_LinuxInstaller.tar.gz

Installing Direct |

3. Extract the installer from the .tar file:$ tar xvf Direct-16_1_0_SolarisInstaller.tar$ tar xvf Direct-16_1_0_LinuxInstaller.tar

4. Change permissions on the .bin file:$ chmod +x Install.bin

Tip: You can use the Direct installer to perform multiple functions. For this reason it is recommendedthat you do not remove the installer after installation.

Verify and Set DISPLAYThe installer runs in an X11 environment, and requires that you set the DISPLAY variable to ensure theinstaller window displays properly. You must set the variable correctly in your session before you startthe installer.

Use the procedures that follow to check that your X window environment is set correctly. If you need toset the DISPLAY variable, you must set DISPLAY each time you log into a new session before you runthe installer.

Permissions required: Log in on the target computer as the user who will own the files, for example,user direct.

Set DISPLAY locally

1. Check to see if the DISPLAY variable is set:$ echo $DISPLAY

2. If necessary, set DISPLAY to your local computer environment, for example:$ export DISPLAY=":0.0"

Set DISPLAY on a remote computer

1. Check to see if the DISPLAY variable is set:$ echo $DISPLAY

2. Ensure that DISPLAY is set to the remote computer or terminal from which you are working, forexample:$ export DISPLAY=terminal1.xyz.com:0.0

Notes:

n If you have connected to the server with SSH protocol and DISPLAY is set to localhost:10.0 orsimilar, this is a tunneling address. Do not change.

n If you are connecting to an X display via non-X11 client software, such as VNC or Microsoft RemoteDesktop, enter the name of the X display, not the name of your client computer.

n Some X emulators, for example, WRQ Reflection X, use display numbers other than 0 (zero).Examine the display number in the emulator management dialog, and use that number in place of0 immediately after the colon in the previous export command.

n If you are not the owner of the X display, permissions might not allow you to open the windows.To correct the permissions problem, enter an appropriate xauth command or by restart thedisplay as the correct user. Use of xhost is not recommended as it is not secure.


Set DISPLAY and XAUTHORITY on Linux

Direct installer user interface requires an X-windows session. If you use the sudo command to acquireroot privileges instead of logging in as root, you might need to set the DISPLAY and XAUTHORITYenvironment variables, and to grant read access on the .Xauthority file in your home directory in orderfor the installer to create an X-windows display. For example:

1. Check to see if the DISPLAY variable is set:$ echo $DISPLAYlocalhost:10.0

2. Check you are in your home directory, for example:$ pwd/home/hsmith

3. Change the permissions level on the .Xauthority file:$ chmod o+r .Xauthority

4. Switch user to root for example:$ sudo -s

5. Enter:# export DISPLAY=localhost:10.0# export XAUTHORITY=/home/hsmith/.Xauthority

6. Test the your settings by opening an xterm.# xterm

See also

Running the Direct Installer

Install the Direct files.

Test the X EnvironmentBefore you run the Direct installer, BIOVIA recommends you test your X environment. As a test, enterthe command that follows:

On Solaris:$ /usr/X/bin/xterm &

On Linux:$ /usr/bin/X11/xterm &

If the X window fails to display, do not run the installer until you have fixed the problem.

Running Direct Installer in GUI Mode for Linux or SolarisIf you already have a working Direct installation and aremodifying it, proceed to Install Direct inadditional Oracle instances.

The installation process is:

n Install the Direct filesn Create the Direct schema and install the Direct Cartridge

Installing Direct |

Note: A running extproc listener configured for Direct is required to install the schema. You canconfigure the listener before or after installing the Direct files. The listener, the Direct files, and theDirect schema are all required to use the Direct cartridge. For more information on testing andconfiguring an extproc listener, see the Configuring an extproc Listener.

See also

BIOVIA Direct Secure Extproc Listener Configuration Guide.

Install the Files

IMPORTANT! Oracle does not support SELinux security enforcement, and you must disable theSELinux security enforcement before installing Direct.

Note: If you are installing Direct in an Oracle RAC environment, see Installing in an Oracle RACEnvironment before installing the product.

Verify that the user can write to the installation directory.

Permissions required: Log in with your valid user credentials.

1. Verify that the DISPLAY environment variable has been set to allow X windows to display. See Verifyand set DISPLAY for more information.

2. Navigate to the installer.3. Run the Oracle environment setup script:

$ . /Oracle_environment_script

where Oracle_environment_script is the path name to your site-specific Oracle environmentsetup script, for example, /usr/ora11201/bin/oraenv. If you are not sure where the Oracleenvironment script is located, enter:

$ which oraenv

4. Run the installer.$ ./Install.bin

Notes:

n If an error message appears during installation, note the error, click OK, and cancel theinstallation. You must correct the error before reinstalling.

n If the installer fails to display anything, this is a symptom that the user home directory is notwritable.

n If the error “Try running the installer with the -console or -silent flag”

displays, it indicates that the installer cannot create an xtermwindow. To resolve theproblem, you must adjust your environment set up so an Xterm window can be created.

5. Click Next at the Introduction screen.6. Agree to the license agreement, and then click Next.7. In the Installation Tasks dialog:

a. Check the Install BIOVIA Direct Files check box if necessary.b. Check the Create Direct Schema check box if necessary.c. Type in the license key for the product that you are licensed to install, and then click Next.


8. In the Choose Install Folder dialog, accept the default BIOVIA home directory /opt/BIOVIA, or clickChoose to navigate to another directory, and then click Next.

Notes:

n The BIOVIA home directory must exist before you install the Direct files.n If you did not uninstall Direct 7.0, /opt/symyx displays. To install Direct, you must click Choose

and select /opt/BIOVIA.

Create the Direct Schema and Install the Direct Cartridge

IMPORTANT! If you have not yet configured your extproc listener, click Exit Installation at this time.After you have a configured extproc listener running, restart the Direct installer to create the Directschema. For more information, see Configuring an extproc Listener.

Note: If you will create the schema in an Oracle RAC environment, see Setting Up an Oracle RACEnvironment.

Direct installs the data cartridge into the schema c$direct2016. You must enter a password for thec$direct2016 schema.

1. In theOracle Connection Information dialog:a. Verify the populated information, and the correct if necessary.b. For the DBAUsername and Password, enter the system username and password, and then click

Next.

2. In the Schema Connection Information dialog:

a. Choose a schema password. This is the password for the C$DIRECT2017 schema.b. Accept the default tablespace that appears, or select a tablespace from the drop-down list.

Note: If you use an X terminal emulator to run the Unix installer by connecting from aMicrosoft Windows computer, selecting a tablespacemight be difficult to operate. You cannavigate to a tablespace by entering the first letter of the name.

c. Accept the temporary tablespace name, or select a tablespace name from the drop-down list,and click Next.

3. Review the pre-installation summary, and then click Install to install Direct.

If you need to make changes after reviewing the summary, click Previous. After you click Install, nochanges can bemade. During the installation, the installer displays a message when the schema anduser are created.

4. At the Installation Complete screen,select Next.5. Review the Release Notes information, and then select Done to complete the Direct installation.

Proceed to Direct Post-Installation Tasks.

TWO_TASK Environment VariableIf you use SQL*PLUS and your Oracle instance is configured with no default direct connection, you mightneed to define the TWO_TASK environment variable to prevent installation failures. The first indication ofan installation failure is that a blank error screen appears.

Installing Direct |

You can verify that you need to set the TWO_TASK variable by attempting to log in to SQL*Pluswithout specifying a DB Alias, for example: $ sqlplus username/password

The login will fail with the following Oracle error:

ORA-12162: TNS:net service name is incorrectly specified

Review the installation log for more information on the problem. Contact BIOVIA Support if moreassistance is needed.

If the TWO_TASK=<TNS_connection_alias_for_OracleSID> environment variable has been set,the setting is passed to the SQL*Plus environment forcing the package-installation part of the Directinstaller to connect to the Oracle Service Name identified by the specified TNS alias. However, otherparts of the installer continue to connect directly to the Oracle Service Name you specified in the installerdialog box.

IMPORTANT! If the TWO_TASK environment variable is defined, you must specify the same OracleService Name used in the set up dialog. Installation failure results if the Oracle Service Names are notthe same.

Installation Log FilesThe Direct installer writes two .log files to the /opt/BIOVIA directory.

n BIOVIA_Direct_2016_InstallLog.log contains installation details and any errors that occur.n sqlerr_YYYMMDD.log contains the output of SQL*Plus sessions used by the installer and includes

messages and any errors that occur.

Review the log files for errors and possible solutions. Rerun the installer if necessary. You can ignore Javawarning messages that appear in the log file.

If you are troubleshooting an installation problem, check the final operation logged to the file. If the logfile does not contain the following line near the end of the file, the installation is incomplete.

BIOVIA_Direct_2016_InstallLog.log, MDLAUXOP.SETENVFILE('MOLSKEYDEFS',NULL).

Additionally, there should be no Oracle errors in the final section of the log file after the string Usercreated.

Recovering from an installation failure

If your installation fails, but creates the c$direct2016 schema, or if you receive an ORA-904 errormessage during the installation verification, you can install the Direct packages:

1. Log into SQL*Plus as user c$direct2016/password.2. Issue the following command:

@mdlinst_all.sql

3. Exit SQL*Plus.

Running the Installer in Silent Mode for LinuxRun the silent installer for Direct 2017 on Linux systems by the account that will own the files. Inaddition, manually enter the command to run the silent installer or the dashes may bemisinterpretedas parameters and the installation will fail.

Before running the silent install, onemust drop the user c$direct2016 if it exists from the Database:


n Log in to sqlplus as admin:drop user c$direct2016 cascade:

When you unzip the Linux installer, Direct-16_1_LinuxInstaller.tar.gz, there are two properties file withthe installer. The contents of the full install properties file are:#These are properties for a Silent Install on Linux that must be changedaccording to end user system configuration.#This is for a full install.#Do Not edit the following properties#Task=install#INSTALL_TYPE=FULL#INSTALL_REG_TYPE=$INSTALL_TYPE$#Task1=Listener#MAKE_HDW=linux############################USER_SUPPLIED_KEY=<license key>ORACLE_PORT=<Port_Number>Task=installDBA_USERNAME=<DB_Username>TABLE_TEMP=<Temp_Tablespace>IS_DESTINATION=<Install_Dir>INSTALL_TYPE=FULLTABLE_SPACE=<Tablespace_Name>USER_MAGIC_FOLDER_10=<Install_Dir>USER_PASSWORD=<DB_Password>SCHEMA_PASSWORD=<Schema_Password>INSTALL_REG_TYPE=$INSTALL_TYPE$ORACLE_HOME=<DB_Home>USER_INSTALL_DIR=<Install_Dir>ORADBA_PWD=<DB_Password>DBA_PASSWORD=<DB_Password>ORACLE_SID=<DB_Service_Name>Task1=ListenerMAKE_HDW=linux

To use the silent installer, the following properties need to be changed for Linux full install, according toyour system configuration:ORACLE_PORT=<Port_Number>DBA_USERNAME=<DB_Username>IS_DESTINATION=<Install_Dir>USER_MAGIC_FOLDER_10=<Install_Dir>USER_PASSWORD=<DB_Password>SCHEMA_PASSWORD=<Schema_Password>ORACLE_HOME=<DB_Home>USER_INSTALL_DIR=<Install_Dir>ORADBA_PWD=<DB_Password>DBA_PASSWORD=<DB_Password>ORACLE_SID=<DB_Service Name>

To install files only, use the linux_filesonly_silent.properties#These are properties for a Silent Install on Linux that must be changedaccording to end user system configuration.#This is for a files only install.#Do Not edit the following properties

Installing Direct |

#Task=install#INSTALL_REG_TYPE=$INSTALL_TYPE$#MAKE_HDW=linux############################USER_SUPPLIED_KEY=<license key>Task=installIS_DESTINATION=<Install_Dir>USER_MAGIC_FOLDER_10=<Install_Dir>USER_INSTALL_DIR=<Install_Dir>INSTALL_REG_TYPE=$INSTALL_TYPE$MAKE_HDW=linux

IMPORTANT! IS_DESTINATION, USER_MAGIC_FOLDER_10, USER_INSTALL_DIR must all be directed tothe same destination. USER_PASSWORD, ORADBA_PWD, DBA_PASSWORDmust all be the same.

To run the silent install, pass the following from the command line/bash shell:

./Install.bin –i silent –f linux_full_silent.properties

A log file is generated in the user installation directory to check for errors that occurred duringinstallation.

To Uninstall:./direct2016/Uninstall_BIOVIA*/"Uninstall BIOVIA Direct 2017"

Examples

The following properties for a Silent Files Only Install on Linux that must be changed according to enduser system configuration.#This is for a files only install.#Do Not edit the following properties#Task=install#INSTALL_REG_TYPE=$INSTALL_TYPE$#MAKE_HDW=linux############################

USER_SUPPLIED_KEY=<license key>Task=installIS_DESTINATION=/home/bioviaUSER_MAGIC_FOLDER_10=/home/bioviaUSER_INSTALL_DIR=/home/biovia/INSTALL_REG_TYPE=$INSTALL_TYPE$MAKE_HDW=linux

The following properties for a full Silent Install on Linux that must be changed according to end usersystem configuration.#This is for a full install.#Do Not edit the following properties#Task=install#INSTALL_TYPE=FULL#INSTALL_REG_TYPE=$INSTALL_TYPE$#Task1=Listener#MAKE_HDW=linux


############################

USER_SUPPLIED_KEY=<license key>ORACLE_PORT=1521Task=installDBA_USERNAME=systemTABLE_TEMP=TEMPIS_DESTINATION=/home/biovia/INSTALL_TYPE=FULLTABLE_SPACE=USERSUSER_MAGIC_FOLDER_10=/home/biovia/USER_PASSWORD=PASSWORDSCHEMA_PASSWORD=directpwINSTALL_REG_TYPE=$INSTALL_TYPE$ORACLE_HOME=/opt/oracle/11.2_server_64bitUSER_INSTALL_DIR=/home/biovia/ORADBA_PWD=PASSWORDDBA_PASSWORD=PASSWORDORACLE_SID=orclTask1=ListenerMAKE_HDW=linux

Running the Installer in Silent Mode for Solaris

Notes:

When launching the DIrect Installer on a Solaris system, the following error might appear:/Install.bin: !: not found

You can ignore this error. The Installer should launch normally. For further information on this Oracleerror, see http://docs.oracle.com/cd/E19960-01/html/821-2486/gkpcl.html.

When you unzip the Solaris installer, Direct-16_1_SolarisInstaller.tar.gz, there are two properties file withthe installer.

The contents of the full install properties file are:#These are properties for a Silent Install on Solaris that must be changedaccording to end user system configuration.#This is for a full install.#Do Not edit the following properties#Task=install#INSTALL_TYPE=FULL#INSTALL_REG_TYPE=$INSTALL_TYPE$#Task1=Listener#MAKE_HDW=solaris############################USER_SUPPLIED_KEY=<license key>ORACLE_PORT=<Port_Number>Task=installDBA_USERNAME=<DB_Username>TABLE_TEMP=<Temp_Tablespace>IS_DESTINATION=<Install_Dir>INSTALL_TYPE=FULLTABLE_SPACE=<Tablespace_Name>

Installing Direct |

http://docs.oracle.com/cd/E19960-01/html/821-2486/gkpcl.html

USER_MAGIC_FOLDER_10=<Install_Dir>USER_PASSWORD=<DB_Password>SCHEMA_PASSWORD=<Schema_Password>INSTALL_REG_TYPE=$INSTALL_TYPE$ORACLE_HOME=<DB_Home>USER_INSTALL_DIR=<Install_Dir>ORADBA_PWD=<DB_Password>DBA_PASSWORD=<DB_Password>ORACLE_SID=<DB_Service_Name>Task1=ListenerMAKE_HDW=solaris

To use the silent installer, the following properties need to be changed for Solaris full install, according toyour system configuration:ORACLE_PORT=<Port_Number>DBA_USERNAME=<DB_Username>IS_DESTINATION=<Install_Dir>USER_MAGIC_FOLDER_10=<Install_Dir>USER_PASSWORD=<DB_Password>SCHEMA_PASSWORD=<DB_Password>ORACLE_HOME=<DB_Home>USER_INSTALL_DIR=<Install_Dir>ORADBA_PWD=<DB_Password>DBA_PASSWORD=<DB_Password>ORACLE_SID=<DB_Service Name>

To install files only, use the solaris_filesonly_silent.properties#These are properties for a Silent Install on SOlaris that must be changedaccording to end user system configuration.#This is for a files only install.#Do Not edit the following properties#Task=install#INSTALL_REG_TYPE=$INSTALL_TYPE$#MAKE_HDW=solaris############################USER_SUPPLIED_KEY=<license key>Task=installIS_DESTINATION=<Install_Dir>USER_MAGIC_FOLDER_10=<Install_Dir>USER_INSTALL_DIR=<Install_Dir>INSTALL_REG_TYPE=$INSTALL_TYPE$MAKE_HDW=solaris

IMPORTANT! IS_DESTINATION, USER_MAGIC_FOLDER_10, USER_INSTALL_DIR must all be directed tothe same destination. USER_PASSWORD, ORADBA_PWD, DBA_PASSWORDmust all be the same.

To run the silent install, pass the following from the command line/bash shell:

./Install.bin –i silent –f solaris_full_silent.properties

A log file is generated in the user installation directory to check for errors that occurred duringinstallation.

For Uninstall:./direct2016/Uninstall_BIOVIA*/Uninstall\ BIOVIA\ Direct\ 2016


Direct Post-Installation TasksAfter you complete the post-installation tasks, you must set up the demonstration database if you planto use the example applications.

See also

Setting Up the Direct Demonstration Databases

Check Installation Requirements for Oracle User SYSDirect requires that the Oracle user SYSwith the AS SYSDBA option complete the following operationsbefore Direct is run:n GRANT EXECUTE ON DBMS_LOCK TO PUBLIC

Direct uses the DBMS_LOCK package to control multiple-user access to domain indexmaintenance routines.

n GRANT SELECT ON ALL_SECONDARY_OBJECTS TO PUBLIC

n Create procedure SYS.MDLINSERTSECOBJ and grant EXECUTE on it to PUBLIC

When the Oracle import utility (imp or impdp imports a dump file containing secondary tables,Oracle marks the tables as SECONDARY in the ALL_TABLES view but does not add them to the ALL_SECONDARY_OBJECTS view. This procedure adds the tables to the ALL_SECONDARY_OBJECTS view.

BIOVIA provides a script mdlsysactions.sql, located in /opt/BIOVIA/direct2016/sql, that runsall three commands.

See also

Run the script mdlsysactions.sql

BIOVIA Direct Administration Guide > Creating and Managing Molecule Tables and Indexes >Guidelines for Creating Molecule Tables

BIOVIA Direct Administration Guide > Creating and Managing Molecule Tables and Indexes >Guidelines for Creating Reaction Tables

Verify the InstallationVerify that Direct displays the banner.

1. Log in to the host computer.2. At the command line, start SQL*Plus and log in as C$DIRECT2017with the password configured for

this user, for example:$ sqlplus 'c$direct2016/abcd'

3. Issue the SQL statement that follows:SQL> SELECT MDLAUX.VERSION FROM DUAL;

If the Direct cartridge is installed and configured correctly, a banner screen similar to the screen thatfollows appears:

VERSION--------------------------------------------------------------------------

--BIOVIA Direct

Revision 2017 (Linux Oracle12c) (16.1.0.153)

Copyright (c) Dassault Systèmes, 1999-2016

Installing Direct |

4. Exit SQL*Plus:SQL> EXIT

Modify the UniProtConverter ScriptThis procedure is required to use the UniProt Converter Utility.

You must use a 64-bit version of the Java Runtime Environment (JRE), and then modify theUniProtConverter script with the correct JRE installation path:

1. Open and edit the file install_directory/BIOVIA/direct2016/bin11/UniProtConverter. Use bin11with Oracle 11 andbin12with Oracle 12.

2. Change the value of the environment variable JAVA to the location of your 64-bit JRE.

For example, JREinstall_directory/java/jre1.2.6.0_20.

3. Save and close the file.

Enable Accounts to Run the Cartridge

Note: Ensure that there are no tables named mol and rxn. The following task requires that you runthe package procedure mdlauxop.setup, which defines the synonyms, including mol and rxn. If atable exists with these reserved words, running the package will fail.Verify that your databases do notcontain reserved words in the name before you continue with this task. For more information aboutreserved words, see your Oracle documentation.

Permissions required: Log in as a cartridge user other than the cartridge owner. This user must havebeen granted CREATE SYNONYM privileges.

Tip: Perform this task for each Direct user at your site. An Oracle account is a Direct user if thataccount is used to run Oracle SQL commands that make use of Direct functions or operators. In somecases, this could be the Oracle account in which a chemical database is stored (such as ACD20092), orit might be an account used to access a chemical database (such as JOHNSMITH).

1. Start SQL*Plus.$ sqlplus >username/password

where username and password are the user name and the password for the Direct cartridge useryou want to enable.

2. Enable the cartridge synonyms.SQL> EXECUTE C$DIRECT2017.MDLAUXOP.SETUP;

If this command is correctly executed, the following message displays:PL/SQL procedure successfully completed.

Note: For each user of the cartridge except user C$DIRECT2017, run EXECUTE

C$DIRECT2017.MDLAUXOP.SETUP.

3. List synonyms in the cartridge:SQL> SELECT SYNONYM_NAME FROM USER_SYNONYMS ORDER BY SYNONYM_NAME;

The ORDER BY SYNONYM_NAME part of this command is optional.


A list of 90 synonyms displays for the Direct installation.SYNONYM_NAME-------------------------CDCAUXCDCAUXOPCHIMECHIME_STRINGCHIME_STRING_SEGFLEXMATCHFLEXMATCHHIGHLIGHTFLEXMATCHTIMEOUTFMLALIKEFMLAMATCHFMLA_EQFMLA_LIKEHASNOSTRUCTSHELMINCHIINCHIKEYISGENERICISNOSTRUCTISOTOPICFORMULAISSEQUENCEIUPACNAMEMAKECLOBMDLAUXMDLAUXOPMDLIXUTLMOLMOLCHIMEMOLFILEMOLFILE_STRINGMOLFILE_STRING_SEGMOLFMLAMOLIMAGEMOLKEYSMOLNEMAKEYMOLSIMMOLWTMOLWTMAXMOLWTMINMOLWTRANGEMONOISOTOPICMASSNCOMPONENTSNUMRANGENUMSPECIFICSOVERLAPOVERLAPCOUNTOVERLAPTIMEOUTPCTOVERLAPRDCAUXRDCAUXOP

Installing Direct |

READBINARYFILEREADFILEREADMOLRSSRSSCOUNTRSSHIGHLIGHTRSSTIMEOUTRXNRXNAUTOMAPRXNAUTOMAPCHANGERXNAUTOMAPSTATUSRXNCHIMERXNCTRSIMRXNFILERXNFLEXMATCHRXNFLEXMATCHTIMEOUTRXNIMAGERXNKEYSRXNMOLRXNMOLSIMRXNSIMRXNSTRINGSEGMENTSEQUENCESEARCHSEQUENCETEXTSIMILARSIMILARITYSMILESSSSSSSCOUNTSSSHIGHLIGHTSSSSEQUENCEIDSSSSTIMEOUTSSS_HIGHLIGHT_CHIMESSS_HIGHLIGHT_MOLFILESTRINGSEGMENTTEMPCLOBWRITEBINARYFILEWRITEFILEWRITEMOLWRITETEMPCLOB90 rows selected.

4. Exit SQL*Plus:SQL> EXIT

Install Direct in Additional Oracle InstancesTo install Direct into an additional Oracle instance, follow the procedures in Configuring Multiple DirectVersions on the Same System.


Set Up the Direct Demonstration Databases

Note: If you plan to use the example applications, you must perform the procedures in this chapter toview themolecules and reactions through the cartridge.

Introduction to the Sample DatabasesThe Oracle 11 Data Pump dump file DCSAMPLES.DMP contains an export of the DCSAMPLES schema. Itincludes a 2D molecule table (SAMPLE2D), a reaction database containing a reaction table (SAMPLERX_REACTION) and hierarchical data tables, a generic structure table (SAMPLEGEN) and a biopolymersequence table (SAMPLEBIO).

Beginning in Direct 9.1, the dump file includes a molecule table named SAMPLEMOLwhich contains thecontents of SAMPLE2D, SAMPLEGEN andSAMPLEBIO along with several new structures containingexamples of dative, hydrogen, haptic and markush bonds.

Demonstration Database Task ChecklistUse this checklist to verify that you have performed all the tasks that are required to correctly set up thedemonstration reaction table and molecule database for Direct. The procedures that you perform areexplained in the corresponding sections.

DoThis Details Done

Create a newOracle schema to contain the DCSAMPLESdatabase tables.

See the procedure that follows.

Import the Oracle DCSAMPLES.DMP file. See Import the OracleDCSAMPLES.DMP file.

Test the SAMPLE2D database. SeeMolecule verification.

Test the SAMPLERX database. See Reaction verification.

Each of these tasks is explained in detail in the sections that follow.

Create Oracle Schema for DCSAMPLES Database TablesTo load the sample database:

1. Connect to Oracle as a database administrator and create a schema to hold the sample databases.The examples assume that the schema is named DCSAMPLES, however, you can choose any name.To load the databases:connect system/******create user dcsamples identified by dcsamplesdefault tablespace usersquota unlimited on userstemporary tablespace temp;grant create session to dcsamples;grant alter session to dcsamples;grant resource to dcsamples;

Setting Up the Direct Demonstration Databases |

grant connect to dcsamples;grant create synonym to dcsamples;grant create table to dcsamples;grant create view to dcsamples;grant create trigger to dcsamples;grant create sequence to dcsamples;

2. Connect to the new sample database schema, for example, DCSAMPLES, and enable it for use withDirect by executing C$DIRECT2017.MDLAUXOP.SETUP. For example:connect dcsamples/dcsamplesexecute c$direct2016.mdlauxop.setup;

The .dmp file was created using the Oracle Data Pump Export utility. This utility does not accept adirectory path name. The utility uses an Oracle "directory" object to specify the directory where thedump file is located.

3. Contact your Oracle database administrator and determine what Oracle directory object should beused to import the dump file, and copy the dump file to the location on the disk corresponding to theOracle directory object.

The DBA system user might need to create a directory object for you, for example:connect system/*****create or replace directory dpump_dir as '/var/tmp';grant read,write on directory dpump_dir to public;

Import the Oracle DCSAMPLES.DMP FileUsing the Oracle Data Pump Import utility (impdp), import the file DCSAMPLES.DMP.

Note: If you did not name your schema DCSAMPLES in Step 1, use the REMAP_SCHEMA parameter toremap the schema DCSAMPLES stored in the .dmp file to your schema name. If your defaulttablespace name is not USERS, use the REMAP_TABLESPACE parameter to remap the tablespaceUSERS stored in the .dmp file to your tablespace name.

For example, in a terminal window:

n To import the .dmp file into the schema DCSAMPLES and a tablespace named USERSwhich alreadyexist, enter:$ impdp dcsamples/dcsamples directory=dpump_dir dumpfile=DCSAMPLES.DMP

n To import the .dmp file into the schema DCSAMPLESwith the default tablespace named WORK_TABSPACE, enter:$ impdp dcsamples/dcsamples directory=dpump_dir dumpfile=DCSAMPLES.DMPremap_tablespace=users:work_tabspace

n To import the .dmp file into schema OURSAMPLES, with the default tablespace named WORK_TABSPACE, enter:$ impdp dcsamples/dcsamples directory=dpump_dir dumpfile=DCSAMPLES.DMPremap_schema=dcsamples:oursamples remap_tablespace=users:work_tabspace

Once imported, the five databases contain the following objects:

Database and objects Description

2D Generic structure, and Biopolymer structure Molecule database



SAMPLEMOL Main molecule table

SAMPLEMOL_IX Direct molecule domain index on CTAB

2D Molecule database

SAMPLE2D Main molecule table

SAMPLE2D_IX Direct molecule domain index on CTAB

SAMPLE2D_ACTIVITY Subtable of activities

SAMPLE2D_ALTERNATE_NAMES Subtable of alternate names

SAMPLE2D_BOILING_POINT Subtable of boiling points

SAMPLE2D_MELTING_POINT Subtable ofmelting points

Reaction database

SAMPLERX_REACTION Main table of reaction variations

SAMPLERX_REACTION_IX Direct reaction domain index on RCTAB

SAMPLERX_REACTANT_MOLREGNO Subtable of links to SAMPLERX_MOLTABLE

SAMPLERX_PRODUCT_MOLREGNO Subtable of links to SAMPLERX_MOLTABLE

SAMPLERX_VARIATION Subtable of reaction variations

SAMPLERX_CITATION Subtable of links to SAMPLERX_DOC

SAMPLERX_SYSNO Subtable of links to SAMPLERX_SYSTEXT

SAMPLERX_RXNREF Subtable of reaction scheme data

SAMPLERX_REACTANT Subtable of reactant data and links to SAMPLERX_MOLTABLE

SAMPLERX_PRODUCT Subtable of product data and links to SAMPLERX_MOLTABLE

SAMPLERX_STEPNO Subtable of synthesis steps

SAMPLERX_CONDITION Subtable of searchable condition data

SAMPLERX_AUXMOL Subtable of solvent, catalyst and reagent data andlinks to SAMPLERX_MOLECULE

SAMPLERX_SYSTEXT Text descriptions of reaction keywords

SAMPLERX_DOC Literature references

SAMPLERX_AUTHOR Subtable of separate author names

SAMPLERX_MOLTABLE Molecules that participate as reactants, products,solvents, catalysts, or reagents



SAMPLERX_MOL_IX Direct molecule domain index on CTAB

SAMPLERX_CAS Subtable of CAS numbers

SAMPLERX_NAME Subtable ofmolecule names

The following tables are present because they are used in the reaction database data model, howeverfor SAMPLERX, they do not contain data.

SAMPLERX_CHEMNAME

SAMPLERX_CONTENT_RELEASE

SAMPLERX_DISCRETE

SAMPLERX_KEYWORD

SAMPLERX_MOLCITATION

SAMPLERX_POLYMER_INFO

SAMPLERX_POLYMER_NAME

SAMPLERX_PROT_GP

SAMPLERX_REACTIONSCHEME

SAMPLERX_SOLID_SUPPORT_NAME

SAMPLERX_SS_CONDITION

SAMPLERX_SS_KEYPHRASE

Generic structure molecule database

SAMPLEGEN Generic structure table

SAMPLEGEN_IX Direct molecule domain index on CTAB

See the file testsamplegen.sql for examples of searching.

Biopolymer sequence molecule database

SAMPLEBIO Biopolymer structure table

SAMPLEBIO_IX Direct molecule domain index on CTAB

See the file testsamplegen.sql for examples of searching.

Isentris Data Source Definition FilesIsentris data source definition files for these databases are also included:n DIRECT_DCSAMPLES_RELATIONAL.XML

n DIRECT_DCSAMPLES_IDS.XML


The first file defines an Isentris relational datasource. It must be edited to change the values for theusername, password, HOST, PORT and SID. The username and password are both set to"dcsamples", there are no defaults for the Oracle connection parameters.

The second file defines a set of Integrating Data Source (IDS) connectors for these databases. The filedoes not need to be edited. This file is intended for demonstration purposes only. The connectors donot match the format used for BIOVIA databases, such as the ChemInform Reaction Librarydatabase.

Copy both files into the ISENTRIS_HOME/system/config/datasource/dsfiles directory. Forexample:$ c:\BIOVIA\isentris4.0\system\config\datasource\dsfiles

1. After copying, edit the file DIRECT_DCSAMPLES_RELATIONAL.XML:a. Change the username and password to the correct values for the account created when you

created a newOracle schema.

Note: If you created the account as DCSAMPLES/DCSAMPLES, no change is required.

b. Change the HOST string to the appropriate name for the computer running Oracle.c. Change the PORT string to the port number on which the appropriate Oracle listener is listening.

This is generally 1521.d. Change the SID string to the Oracle SID for the database.

You can also replace SID=<your-SID>with service_name=<your-service-name>.

2. After you havemade your changes, save and close the file.

Verify Demonstration Database and Tables Installation

Molecule Verification

Tips:

n The following tests (and more) are listed in the testsample2d.sql file located in the/opt/BIOVIA/direct2016/examples directory.

n You can run this file instead of running the following tests manually.

Permissions required: Log in to SQL*Plus as the owner of the schema, for example,dcsamples/dcsamples.

Test the SAMPLE2D database

Verify that the SSS operator is working correctlySQL> SELECT COUNT(*) FROM SAMPLE2D WHERE SSS(CTAB,'/opt/BIOVIA/direct2016/examples/molfiles/sssquery.mol')=1;

If the command executes correctly, the following message displays:COUNT(*)--------

52

Display cartridge errorsSQL> SELECT MDLAUX.ERRORS FROM DUAL;


If the command executes correctly, the following message displays:ERRORS-------------

Verify that theMOLSIM operator is working correctlySQL> SELECT COUNT(*) FROM SAMPLE2D

2> WHERE MOLSIM(CTAB, 'C1CCNCC1', 'NORMAL')>40;

If the command executes correctly, the following message displays:COUNT(*)

----------3

Verify that the FLEXMATCH operator is working correctly

SQL> SELECT CDBREGNO FROM SAMPLE2DWHERE FLEXMATCH(CTAB,'C1CCCCC1','ALL')=1;

If the command executes correctly, the following message displays:CDBREGNO

27

Verify that the INSERT statement works correctly

INSERT INTO SAMPLE2D(CDBREGNO,CTAB,MOLNAME,CORP_ID) VALUES (1000,MOL('C1CCCCC1'),'INS1','INS1');

If the command executes correctly, the following message displays:1 row created.

Verify that the UPDATE statement works correctlySQL> UPDATE SAMPLE2D SET MOLNAME='INS1' WHERE CDBREGNO=3;

If the command executes correctly, the following message displays:1 row updated.

Verify that the DELETE statement works correctlyDELETE FROM SAMPLE2D WHERE CDBREGNO=2;

If the command executes correctly, the following message displays:1 row deleted.

Rollback changesSQL> ROLLBACK;

If the command executes correctly, the following message displays:Rollback complete.

Display record countSQL> SELECT COUNT(*) FROM SAMPLE2D;

If the command executes correctly, the following message displays:


COUNT(*)----------

382

Reaction Verification

Tip: The following tests are listed in the testsamplerx.sql file located in the/opt/BIOVIA/examples directory. You can run the file or run the tests manually.

Note: The example reaction files must bemade read-accessible from the operating system accountunder which the Oracle extproc listener run. Errors occur if this is not done.

Permissions required: Log in to SQL*Plus as the owner of the schema, for example,dcsamples/dcsamples.

Test the SAMPLERX table

Verify that the RSS operator is working correctly.

1. Start SQL*Plus and log in as the owner of the schema, for example:C:\> sqlplus dcsamples/dcsamples

2. Verify the RSS operator is working:SQL> SELECT RXNMDLNUMBER FROM SAMPLERX_REACTION WHERE RSS(RCTAB,'/opt/BIOVIA/direct2016/examples/rxnfiles/rssq1.rxn')=1;

Note: When typing rssq1.rxn, make sure that you type a one (1) not a lowercase L.

If the command executes correctly, the following message displays:MDLNUMBER--------------RXCI92065766

Display cartridge errorsSQL> SELECT MDLAUX.ERRORS FROM DUAL;

If the command executes correctly, the following message displays:ERRORS

Verify that the RXNSIM operator is working correctlySQL> SELECT RXNMDLNUMBER FROM SAMPLERX_REACTION WHERE RXNSIM(RCTAB,'/opt/BIOVIA/direct2016/examples/rxnfiles/query2.rxn', '80 20')=1 ORDER BYRXNMDLNUMBER;

If the command executes correctly, the following message displays:RXNMDLNUMBER--------------RXIC92000009RXIC92000010RXIC92000013RXIC92000014


RXIC92050814RXIC930032316 rows selected.

Verify that the RXNFLEXMATCH operator is working correctlySQL> SELECT RXNMDLNUMBER FROM SAMPLERX_REACTION WHERE RXNFLEXMATCH(RCTAB,'/opt/BIOVIA/direct2016/examples/rxnfiles/query.rxn', 'match=all')=1;

If the command executes correctly, the following message displays:MDLNUMBER--------------RXCI94006733

Verify that the INSERT statement works correctlySQL> INSERT INTO SAMPLERX_REACTION (RXNMDLNUMBER,RCTAB) VALUES('NEW',RXN('/opt/BIOVIA/direct2016/examples/rxnfiles/newrxn1.rxn'));

If the command executes correctly, the following message displays:1 row created.

Verify that the reaction was insertedSQL> SELECT RXNMDLNUMBER FROM SAMPLERX_REACTION WHERE RXNFLEXMATCH(RCTAB,'/opt/BIOVIA/direct2016/examples/rxnfiles/newrxn1.rxn','match=all')=1;

If the command executes correctly, the following message displays:RXNMDLNUMBER----------------------------NEW

Rollback changesSQL> ROLLBACK;

If the command executes correctly, the following message displays:Rollback complete.SQL> EXIT


Direct File Configuration on Linux and SolarisThis chapter explains the configuration of Direct cartridge files on Red Hat Linux, SUSE Linux, or OracleSolaris host computers.

Direct Directory HierarchyWhen you install Direct cartridge files on Linux or Solaris computers, the installation program places filesinto the directory hierarchy shown below.

Files and DirectoriesThis section explains:

n The case sensitivity and limitations in using file names and directory names on Linux.n Direct cartridge directories and files.

Case SensitivityReferences to file names and directory names on Linux and Solaris are case sensitive.

Do not include spaces in the names of files that are created by or used by the cartridge, such asmdldirect.so. File and directory names that contain spaces can cause erratic program behavior. Toimprove readability, use underscores in file names and directory names.

Explanation of Directories and Files

Directory or file Contents

$ORACLE_HOME/network/admin

listener.ora

tnsnames.ora

Oracle directory

Oracle network system configuration listener files thatmust be present for use with the extproc listener

/opt/BIOVIA Most BIOVIA software is in this directory

/opt/BIOVIA/direct2016 All of the Direct cartridge files

/opt/BIOVIA/direct2016/bin11 Binary executable files for the Oracle 11g installation

/opt/BIOVIA/direct2016/bin12 Binary executable files for the Oracle 12c installation

Direct File Configuration on Linux and Solaris |


directupgrade

mdldirect.so

exportRDFileexportSDFile

importRDFile

importSDFile

UniProtConverter

This directory also containsBIOVIA Foundation .so files, such as:pilot.so, pilotCore.so,ppChemNema.so,ppChemSageCoords.so,ppOpenEye.so

The utility to use when migrating Direct 6, 7, or 8databases.

Primary shared object library that contains the Directcartridge routines, and the import and export utilities forSDFiles and RDFiles.

Shell script use to run the UniProt Converter Utility

/opt/BIOVIA/direct2016/examples Sample applications and demonstration databases

DCSAMPLES.DMP Demonstration database import file

direct_dcsamples_ids.xml

direct_dcsamples_relational.xml

Files for use with BIOVIA Isentris applications

rdcapps.sql SQL script that runs sample applications to read a RDFileand create a cross-reference trigger

readme_dcsamples.txt Instructions on setting up the DCSAMPLES dump file

testsample2d.sqltestsamplerx.sqltestsamplebio.sqltestsamplegen.sql

Script to test the SAMPLE2D databaseScript to test the SAMPLERX databaseScript for examples of searching biopolymer structuresScript for examples of searching and enumeration ofgeneric structures

molfiles Directory containing molecule files used intestsamplerx.sql

rxnfiles Directory containing reaction files used intestsamplerx.sql

secure_extproc Direct that contains example files of the listener.oraand tnsnames.ora files

/opt/BIOVIA/direct2016/lib Shared objects

ccatlib.soCheshire.jarCheshireJNI.jarojdbc14.jarUniProtConverter.jar

Cheshire shared library (used by UniProt Converter)

/opt/BIOVIA/direct2016/sql Direct SQL files



/opt/BIOVIA/direct2016/Uninstall_BIOVIA Direct

Uninstall BIOVIADirect

Direct uninstaller

Direct File Configuration on Linux and Solaris |

Uninstalling Direct

Alert Users That Direct Will Be UnavailableNotify any users who use Direct that they will be unable to access the program.

Close Any Applications That Use DirectPrior to uninstalling, close any applications that use Direct.

Back Up Direct FilesBack up all files prior to unintalling Direct.

Uninstall the Direct Files

Permissions required: Log in as the user who installed Direct, for example, user direct.

1. Navigate to the directory where Direct was installed, for example:

$ cd /opt/BIOVIA

2. Run the uninstaller.

For Linux:$./direct2016/Uninstall_BIOVIA*/"Uninstall BIOVIA Direct 2016"

For Solaris:./direct2016/Uninstall_BIOVIA*/Uninstall\ BIOVIA\ Direct\ 2016

3. In the Uninstall Direct dialog, click Uninstall.

IMPORTANT! It is not possible to uninstall only part of Direct. If you have files that you havemodified in any of the files in the directories under /opt/BIOVIA/direct2016, be sure to save acopy of the file before you click Uninstall. The uninstaller removes the direct2016 directory andall the subdirectories and files.

4. Click Done to complete the uninstalling Direct.

This completes uninstalling Direct.

The next steps are:

1. Drop the Direct schema2. Drop the demonstration database schema

Drop the Direct Schema

Permissions required: Log in to SQL*Plus as the Oracle system user who configured the schema.

1. Run the Oracle environment setup script:$ . /Oracle_environment_script


where /Oracle_environment_script is the pathname to your site-specific Oracle environmentsetup script, for example, /usr/ora11201/bin/oraenv. If you are not sure where the Oracleenvironment script is located, enter which oraenv.

2. Log in to SQL*Plus:$ sqlplus username/password

3. Drop the c$direct2016 user and the schema objects:SQL> drop user c$direct2016 cascade;

4. Exit SQL*Plus.SQL> exit

Drop the Demonstration Database SchemaIf you created the demonstration databases, as described in Setting Up the Direct DemonstrationDatabases, you can now drop the demonstration database schema.

Permissions required: Log in to SQL*Plus as the Oracle system user who configured the schema.

1. Log in to SQL*Plus:$ sqlplus username/password

2. Drop the demonstration database schema:SQL> drop user dcsamples cascade;

where dcsamples is the name of the schema.

3. Exit SQL*Plus.SQL> exit

Uninstalling Direct |

Configure Multiple Direct Versions on the Same SystemYou can install multiple versions of Direct on the same system in the same instance or in differentinstances. You must ensure that the Oracle extproc listener is able to locate all of the correct Directcartridge components. This may require configuring multiple extproc listeners.

Direct CartridgeA cartridge installation consists of an Oracle schema that contains package and type definitions, ashared library file (mdldirect.so)loaded by Oracle, and additional shared libraries and files requiredby mdldirect.so.

The PL/SQL portion of different versions of the cartridge can be installed in different Oracle schemas inthe same instance or in different Oracle instances. The cartridge installer specifies the Oracle schemaname for that particular release, and each release uses a unique schema name.

When an application invokes an Direct cartridge function, Oracle decides which version of Direct to runbased on the schema in which the:

n Operators are definedn Domain index type is defined

These functions are then dispatched to the Oracle external procedure listener, which activates an Directcartridge shared library routine.

Every version of Direct 9.0 or later must have different PATH environment variables defined wheninvoked by the extproc listener. If you are installing Direct 2017 and already have a Direct 9.x installed,you must configure a separate extproc listener for each of these.

If you are installing Direct 2017 (a 64-bit program) and have a 32-bit version of Direct, such as Direct 6.3,installed you must configure a separate extproc listener for each of these. This assumes you are using a32-bit Oracle client to access a 64-bit Oracle server.

To configure a separate extproc listener for Direct 2017when you already have an extproc listener, seeConfiguring a Separate extproc Listener for Direct.

Refer to Configuring an extproc Listener to set up an extproc listener if you do not already have one.

User Account Issues with Multiple Cartridge VersionsAn Oracle user account can only be set up to run one Direct cartridge version at a time. This means thatall the Oracle databases stored in one schemamust use the same cartridge version.

End-user accounts that do not own databases must have the Direct cartridge synonyms definedexplicitly. To set up an Oracle account for a specific cartridge version, the user needs to execute theMDLAUXOP.SETUP procedure. For example:SQL> execute c$direct2016.mdlauxop.setup;

Thereafter, the synonyms of this user will invoke only the Direct cartridge, regardless of the presence ofother versions of Direct in the Oracle instance.

| BIOVIA Direct 2017 • Linux Installation & Configuration Guide

Configuring an extproc ListenerThis section describes how to configure an extproc listener in the same process as the database listener.For more security, you can set up a secure extproc listener. For information on setting up a secureextproc listener, see the BIOVIA Direct Secure extproc Listener Configuration Guide.

The database listener and the extproc listener, if it is a separate listener, should be configured to restartif the system is rebooted.

About the extproc ListenerThe Oracle external procedures feature allows you to call programs that have been compiled into thenative shared library format of the operating system. A shared library is a shared object or .so file.

The first time an Oracle service task sees an external procedure call, it looks for a extproc listener whichshould be running in the background.

At this point, the extproc listener spawns an executable program called extproc. The extproc programloads the dynamic library and then invokes the desired routine in the shared library. It then returns itsresults back to PL/SQL.

The activation of the library (.so) file depends on the following:

n A correct and fully accessible path defined for the library object. The Linux account that runs theextproc listener must have pass-through (execute) rights on all the directories and read plus executerights on the shared library files.

n Correct LD_LIBRARY_PATH set in the .profile file of the Linux account used to run the extproclistener service so that the Oracle extproc program can find thematching 64-bit Oracle run-timelibraries.

n The correct setting in listener.ora for the PROGRAM (extproc) so that word size is 64-bit. The 64-bit extproc program is called “extproc”.

n The correct setting of LD_LIBRARY_PATH such that all of the libraries needed by the .so can befound. These include the correct word size Oracle libraries and libraries that the cartridge productreferences in the direct2016/bin11 or bin12.

n The correct setting for EXTPROC_DLLS (for example, ENVS=”EXTPROC_DLLS=ANY”) so that thespecific .so, or alternatively, any .so file, is permitted to run.

Note: BIOVIA Direct 2016 requires a 64-bit extproc listener with an LD_LIBRARY_PATH that includesdirect2016/bin11, or bin12which contains BIOVIA Pipeline Pilot Server shared objects used byDirect. You must ensure that the listener LD_LIBRARY_PATH does not include any other sharedobjects that have the same name, and that other applications in Oracle using this listener can coexistwith these shared objects.

If this is not feasible, you can either configure a secure extproc listener as described above, or you canconfigure Direct to use a separate 64-bit extproc listener as described in Configuring a Separateextproc Listener for Direct.

If you have an existing Direct installation you must configure a separate extproc listener because theshared objects used by the current and previous versions have the same names.

For more information on setting up a secure extproc listener, see the BIOVIA Direct Secure extprocListener Configuration Guide.

Configuring an extproc Listener |

Test an extproc ListenerAfter the Direct files have been installed and configured in a manual installation, you must test yourextproc listener.

Run the following test procedure on your existing exproc listener to determine whether you need a fullor partial reconfiguration for Direct.

Note: Your existing Direct 6.x, 7.x or 8.x extproc listener might not be sufficient to for Direct. If this isthe case, review Configuring an extproc Listener Using Oracle Tools, Manually Configure the extprocListener, or the Configuring a Separate extproc Listener for Direct.

Permissions required: Start and log into SQL*Plus as an Oracle DBAwith CREATE LIBRARY privileges.

1. Run the Oracle environment setup script.$ . /Oracle_environment_script

where Oracle_environment_script is the pathname to your site-specific Oracle environmentsetup script, for example, /usr/ora11201/bin/oraenv. If you are not sure where the Oracleenvironment script is located, enter which oraenv.

2. Open a Command Prompt window and navigate to the directory that contains the Direct SQL files,for example:$ cd /opt/BIOVIA/direct2016/sql

3. Start SQL*Plus and log in as the user C$DIRECT2017:$ 'c$direct2016/password'

where password is the password for the user C$DIRECT2017.

4. Run the mdltestlistener.sql file:SQL> @mdltestlistener.sql

The output should resemble the following example:Library created.Grant succeeded.Package created.No errors.Package body created. No errors.RUNRPC-----------------------------------------------------Package dropped.

If this procedure was successful, continue with the section Manually Configure the extproc Listener, andperform Steps 1-5. If the procedure was not successful, a full reconfiguration is necessary, and thisprocess is explained in the sections that follow.

Configure an extproc Listener Using Oracle Tools

Note: An extproc listener configured for Direct is required.

BIOVIA recommends that you use the Oracle Tools if you are setting up an extproc listener for the firsttime. Alternatively, you can use the procedureManually Configure the extproc Listener.


You can configure the Oracle default database listener.ora file to include the external procedureinformation by using the Oracle Net Manager tool.

Note: To use the Oracle Tools to configure the listener.ora and tnsnames.ora files, an XWindows System display is required. If you do not have an X display, seeManually Configure theextproc Listener.

Add PLSExtProc Listener to the Default listener.ora File

Permissions required: Log in as a user who has permission to add a listener.ora file.

1. Open a terminal window, and verify that the DISPLAY environment variable has been set to allow Xwindows to display. For more information, Verify and set DISPLAY.

2. Start Oracle Net Manager, for example:$ . /usr/oracle/bin/oraenv$ netmgr

3. In the left pane of the Net Manager window, navigate to Local > Listeners > listener_name.4. A new tab named Address2 displays.

In right pane of the Listening Locations window from Address1 tab, click Add Address.

5. In theNetwork Address dialog:a. From the Protocol drop-down list, select IPC.b. Enter the Set Key value EXTPROC0. From the drop-down list at the top of screen, select Other

Services.6. For Oracle 11gR1, select >Add Service and add the following values:

Note: Use bin11with Oracle 11 and bin12with Oracle 12.

Program Name: extproc

Environment: "EXTPROC_DLLS=ANY,LD_LIBRARY_PATH=/usr/ora_home/lib:/opt/BIOVIA/direct2016/bin11"

where:

/usr/ora_home is the location of your Oracle instance.

7. For Oracle 11gR2, select Add Service, and add the following values:

8. Note: Use bin11with Oracle 11 and bin12with Oracle 12.

a. Program Name: extprocb. Environment: "EXTPROC_DLLS=ANY,LD_LIBRARY_PATH=/usr/ora_

home/lib:/opt/BIOVIA/direct2016/bin11"

where:

/usr/ora_home is the location of your Oracle instance.c. PLSExtProc

d. Oracle Home Directory: enter the path to your Oracle installation, for example, /usr/oracle.e. From the File menu, select Save Network Configuration.

9. Exit the Net Manager window, and click Save Configuration.10. Using a text editor, verify that the tool has added the new settings to the listener.ora file.


Add the EXTPROC_CONNECTION_DATA Service to tnsnames.oraThe tnsnames.ora file must also bemodified to supply extproc connection information before thelistener.ora file can be used. You can modify the tnsnames.ora file by using the Net ConfigurationAssistant.

Permissions required: Log in as a user who has permission to modify the tnsnames.ora file.

1. In a terminal window, start theNet Configuration Assistant, for example:$ . /usr/oracle/bin/oraenv$ netca

1. From theWelcome dialog, select Local Net Service Name configuration, and then Next.2. From the Listener Configuration, Listener dialog, select Add, and then Next.3. Change the Service Name: value to PLSExtProc, and select Next.4. In the Select Protocols dialog, if necessary, select IPC, and then Next.5. In the IPC Protocols dialog, enter the IPC Key Value: EXTPROC0, and select Next.6. In the Net Configuration, Test dialog, select No, do not Test, and then Next.7. From the Net Service Name dialog, change theNet Service Name: value to EXTPROC_CONNECTION_

DATA, and select Next.8. Select Nowhen asked “Would you like to configure another net service name?”, and then Next.9. Select Next at the net service name Configuration Completewindow.10. Select Finish to exit Net Configuration Assistant.11. Use a text editor to verify that the EXTPROC_CONNECTION_DATA service entry in the

tnsnames.ora file is correct. For example:EXTPROC_CONNECTION_DATA =DESCRIPTION =

(ADDRESS_LIST =(ADDRESS = (PROTOCOL = IPC)(KEY = EXTPROC0)))

(CONNECT_DATA =(SERVICE_NAME = PLSExtProc)))

12. Stop and restart the listener. For details, see Stop and restart the Oracle listener.13. To test the extproc listener, open a terminal window, and type tnsping:

$ tnsping EXTPROC_CONNECTION_DATATNS Ping Utility for Linux: Version 11.2.0.3.0 - Production on 11-AUG-201313:20:10Copyright (c) 1997, 2009, Oracle. All rights reserved.Used parameter files:/usr/oracle/network/admin/sqlnet.oraUsed TNSNAMES adapter to resolve the aliasAttempting to contact (DESCRIPTION =(ADDRESS_LIST = (ADDRESS = (PROTOCOL =IPC) (KEY = EXTPROC0))) (CONNECT_DATA = (SID=PLSExtProc)(PRESENTATION=R0)))OK (10 msec)


Manually Configure the extproc Listener

Note: An extproc listener configured for Direct is required.

If you are setting up an extproc listener for the first time, BIOVIA recommends that you proceed toConfiguring an extproc Listener Using Oracle Tools. You can also use the following manual procedure.

For information on setting up a secure extproc listener, see the BIOVIA Direct Secure extproc ListenerConfiguration Guide.

Edit the listener.ora File

Permissions required: Log in as user with sufficient privileges to modify Oracle files.

1. Navigate to the directory where Oracle is installed, for example, /usr/oracle.2. Change directories to /network/admin to located the listener.ora file.3. Open the listener.ora file in an editor.4. Locate the SID_LIST entry for your listener service, for example:

(SID_LIST =(SID_DESC =(GLOBAL_DBNAME = ORCL)(ORACLE_HOME = /usr/oracle)(SID_NAME = ORCL)

5. Insert an additional SID_DESC entry (shown in bold) to describe the extproc service. Or, if the entryalready exists, modify it as appropriate by using the syntax of the following example. For an Oracle11gR2, see the example that follows. Use bin11with Oracle 11 and bin12with Oracle 12.SID_LIST_LISTENER =(SID_LIST =

(SID_DESC =(SID_NAME = orcl)(ORACLE_HOME = /usr/oracle)

)(SID_DESC =

(SID_NAME = PLSExtProc)(ORACLE_HOME = /usr/oracle)(PROGRAM = extproc)(ENVS = "EXTPROC_DLLS=ANY,LD_LIBRARY_

PATH=/usr/oracle/lib:/opt/BIOVIA/direct2016/bin11))

)

If your test of the extproc listener was successful, you do not need to change your tnsnames.orafile, and you can proceed to Stop and restart the Oracle listener.

If your test of the extproc listener was not successful, you must continue with the following Steps,then proceed to Check the tnsnames.ora file, and then start and stop you listener.

6. Locate the DESCRIPTION_LIST for your listener service:(DESCRIPTION_LIST =

(DESCRIPTION_LIST =(ADDRESS_LIST =(ADDRESS = PROTOCOL = TCP)(HOST = your-system-name)(PORT = your-system-

port-number)


))

)

7. Add an ADDRESS_LIST entry (shown in bold) for the extproc service:(DESCRIPTION_LIST =

(DESCRIPTION_LIST =(ADDRESS_LIST =(ADDRESS = PROTOCOL = TCP)(HOST = your-system-name)(PORT = your-system-

port-number)))(ADDRESS_LIST =(ADDRESS = (PROTOCOL = IPC)(KEY = EXTPROC0))))

)

where:

n /usr/oracle indicates the location of ORACLE_HOME at your site.n your-system-name indicates the host name of your computer.n PORT = your-system-port-number indicates that the port number used at your site.n KEY = EXTPROC0 indicates name of the extproc service. This must match the KEY specified in

the tnsnames.ora file, and this KEYmust be unique within the entire Oracle configuration onthat computer.

Example of listener.ora file: The following lines show the extproc modification in and Oracle11gR2 default listener file.SID_LIST_LISTENER =

(SID_LIST =(SID_DESC =

(SID_NAME = orcl)(ORACLE_HOME = /usr/oracle)

)(SID_DESC =(SID_NAME = PLSExtProc)(ORACLE_HOME = /usr/oracle)(PROGRAM

= extproc)(ENVS = "EXTPROC_DLLS=ANY,LD_LIBRARY_PATH=/usr/oracle/lib:/opt/BIOVIA/direct2016/bin11))

)LISTENER =

(DESCRIPTION_LIST =(DESCRIPTION =

(ADDRESS_LIST =(ADDRESS = (PROTOCOL = TCP)(HOST = localhost.localdomain)(PORT =

1522)))(ADDRESS_LIST =

(ADDRESS = (PROTOCOL = IPC)(KEY = EXTPROC0)))

))

Check the tnsnames.ora FileEdit the tnsnames.ora file if the information supplied below is not included in the file.



1. Navigate to the directory where Oracle is installed, for example, /usr/oracle.2. Open /network/adminwhere you find the tnsnames.ora file.3. Open the tnsnames.ora file in an editor.4. Ensure that the tnsnames.ora file contains the data that follows. If necessary, edit this file.

EXTPROC_CONNECTION_DATA =(DESCRIPTION =(ADDRESS_LIST =(ADDRESS = (PROTOCOL = IPC)(KEY = >EXTPROC0)))(CONNECT_DATA =(SID = PLSExtProc)))

where the KEY that you use for the extproc service (for example, EXTPROC0) must match the KEYspecified in the listener.ora file. See Edit the listener.ora file.

Stop and Restart the Oracle Listener

Note: Only the user who has started the listener is authorized to stop it. For this reason, you shouldperform this part of the installation logged in as that user. Typically, this is the user name of the Oracleaccount. The output of the following command lists this user in the first column:ps -ef | grep tnslsnr

Permissions required: Log in as the owner of the listener process.

1. Run the Oracle environment setup script, for example:$ . /usr/oracle/bin/oraenv

2. Stop the listener:$ lsnrctl stop

3. Restart the listener:$ lsnrctl start listener_name

4. Rerun the listener test.

Set Up an Oracle RAC EnvironmentThe tasks for setting up Direct in a Oracle RAC (Real Application Clusters) environment are:

n Install the Filesn Configure the extproc Listenern Verify the Listener is Workingn Create and populate the Direct Scheman Verify the installation on each RAC node


Install Direct1. Download and install the Direct 2016 files.

IMPORTANT! The path to the Oracle LIB directory and the path to the Direct installation must bethe same on all RAC nodes. Do not locate Direct executables in different directories or on differentdevices.BIOVIA recommends placing Oracle and Direct on a shared disk. If you do not use a shareddisk, copy the required files into locations that can be accessed on all nodes using the samepathnames.

2. Exit the installer after the Direct files are installed.3. Configure the extproc listener for an Oracle RAC environment.

For details, see the following sections, Configure the listener.ora file in an Oracle RAC environmentand Configure the tnsnames.ora file in an Oracle RAC environment .

4. Navigate to the /sql directory in the installation path, for example,/opt/BIOVIA/direct2016/sql.

5. Open the mdllibdef.sql file in a text editor, and change 'directory/mdldirect.dll' to thecorrect full path name on your system, for example,'/opt/BIOVIA/direct2016/bin11/mdldirect.so'.

6. Verify that the listener is working correctly on each node by running mdltestlistener.sql. Forexample:$ sqlplus dba_user/dba_password@racnode1 @mdltestlistener.sqlSQL> exit$ sqlplus dba_user/dba_password@racnode2 @mdltestlistener.sqlSQL> exit....$ sqlplus dba_user/dba_password@racnodeN @mdltestlistener.sqlSQL> exit

7. Open the mkdirect.sql file in a text editor, and modify the file as follows:8. Modify the tablespace name if necessary.9. Replace the V in the CREATE and GRANT commands with 2016, which is the version of Direct. For

example, change create user c$directV identified by abdc to:create user c$direct2016 identified by abcd

10. Change abdc in the above command to a new schema password.11. Save and close this file.12. Start SQL*Plus, log into the database as a DBA user, and execute the following SQL script:

SQL>mkdirect.sqlSQL> exit

13. Log into Oracle as C$DIRECT2017, and then execute mdlinst_all.sql.SQL> @mdlinst_all.sqlSQL> exit

Verify the installation by running MDLAUX.VERSION FROM DUAL on each node, for example:$ sqlplus 'c$direct2016/password@racnode1'SQL> select mdlaux.version from dual;SQL> exit$ sqlplus 'c$direct2016/password@racnode2'SQL> select mdlaux.version from dual;SQL> exit


....$ sqlplus 'c$direct2016/password@racnodeN'SQL> select mdlaux.version from dual;SQL> exit

Configure the listener.ora FileConfigure your Oracle RAC nodes manually or using the Oracle Configuration and Management Tools.The examples shown below provide the information that is required for each node.

The requirements for the listener.ora file in an Oracle RAC environment are similar to the single-node steps (see Configuring an extproc Listener Using Oracle Tools or Manually Configure the extprocListener. That is, you must add the program=extproc, key=extproc0, envs=”EXTPROC_DLLS=ANY,LD_LIBRARY_PATH=... information to incorporate the Oracle bin and Direct librarydirectories. The difference is that the listener.ora file must be configured for all nodes. The followingexample illustrates what each node configuration should look like:# listener.ora.rac1 Network Configuration File:/usr/oracle/network/admin/listener.ora.rac1# Generated by Oracle configuration tools.SID_LIST_LISTENER11201_RAC1 =

(SID_LIST =(SID_DESC =

(SID_NAME = PLSExtProc)(ORACLE_HOME = /usr/oracle)(PROGRAM = extproc)

(ENVS="EXTPROC_DLLS=ANY,LD_LIBRARY_PATH=/usr/oracle/lib:/opt/BIOVIA/bin11"))

)LISTENER11201_RAC1 =

(DESCRIPTION_LIST =(DESCRIPTION =

(ADDRESS = (PROTOCOL = TCP)(HOST = rac1-vip)(PORT = 1522)(IP = FIRST))(ADDRESS = (PROTOCOL = IPC)(KEY = EXTPROC0))

))

where rac1-vip is the name of the Oracle RAC node.

Configure the tnsnames.ora fileThe tnsnames.ora file references several database listeners in an Oracle RAC environment, but theextproc_connection_data block is the same as a single-node system (see Check the tnsnames.oraor Add the EXTPROC_CONNECTION_DATA service to tnsnames.ora). For example:EXTPROC_CONNECTION_DATA =

(DESCRIPTION =(ADDRESS_LIST =

(ADDRESS = (PROTOCOL = IPC)(KEY = EXTPROC0)))(CONNECT_DATA =

(SID = PLSExtProc))

)D1120A =

(DESCRIPTION =


(ADDRESS = (PROTOCOL = TCP)(HOST = rac1-vip)(PORT = 1522))(LOAD_BALANCE = yes)(CONNECT_DATA =

(SERVER = DEDICATED)(SERVICE_NAME = D1120A)

))

where rac1-vip is the name of the node.

After editing tnsnames.ora, stop and restart the listener on each node.


Configure a Separate extproc ListenerOracle uses the TNSNAMES.ORA entry for EXTPROC_CONNECTION_DATA as the default agent to serviceextproc calls. However, users can also define a distinct, named agent to use for a particular product likeDirect. This can be used to provide a customized LD_LIBRARY_PATH variable for the listener or toenable the co-existence of 32-bit and 64-bit extprocs. Also, it can be a useful debugging technique in thesituation where the listener setup is not working properly.

Use this procedure if you already have your listener configured with an LD_LIBRARY_PATH that cannotbe changed to include direct2016/bin11 or bin12without affecting other applications, or youalready have your listener configured to access 32-bit external procedures such as Direct 7.0. To access32-bit external procedures such as Direct 7.0, and you need to add the ability to access the 64-bit Direct2016.

IMPORTANT! If you copy sample code from this PDF document and paste it into a text editor, the textmight change from the original. To ensure that the text is valid and usable, you might need to restoreindents, remove extra spaces, and retype characters for single and double quotes.

This section explains how to set up a separate agent, for example EXTPROC_CONNECTION_DATA_64. Toset up a named agent, you must:

1. Edit the tnsnames.ora file to define an alias for the new agent.2. Edit the listener.ora file to define a new service.3. Start the new listener service.4. Create a public database link that uses the new alias name in the USING clause.5. Manually install the Direct schema, see the procedures in Manual Installation Tasks.6. Alter theMDLDIRECT library object to use the database link in the AGENT clause. See Test the Oracle

extproc listener.

Edit the tnsnames.ora File


1. Navigate to the directory where Oracle is installed, for example, /usr/ora11201.2. Change directories to /network/admin to located the tnsnames.ora file.3. Open the tnsnames.ora file in an editor.4. Add an extproc_connection_data entry for the new agent that will service Direct extproc

connections as shown in the following example:extproc_connection_data_direct2016 =(DESCRIPTION =(ADDRESS = (PROTOCOL = IPC)(KEY = DIRECT2016))(CONNECT_DATA = (SID = DIRECT2016)))

a. Choose a unique name for the agent, for example, extproc_connection_data_direct2016.

Note: The namemust not be extproc_connection_data.

b. Chose a unique name for the Key= parameter, for example, DIRECT2016. This must match thename of the KEY= parameter you will add to the listener.ora file.

Configuring a Separate extproc Listener for Direct |

c. Chose a unique name for the SID= parameter, for example, DIRECT2016. This must match thename of the SID_NAME= parameter you will add to the listener.ora file.

5. Save and exit the tnsnames.ora file.

Edit the listener.ora File and Start the New Listener


1. Navigate to the directory where Oracle is installed, for example, /usr/oracle.2. Change directories to /network/admin to locate the listener.ora file.3. Open the listener.ora file in an editor.4. Edit the listener.ora file to define the new service. For example, add the following to the file:

DIRECT2016 =(description_list =

(description =(address_list =

(address = (protocol=IPC)(key=DIRECT2016)))

))

sid_list_direct2016 =(sid_list =

(sid_desc =(SID_NAME = DIRECT2016)(ORACLE_HOME = /usr/oracle)(PROGRAM = extproc)

(ENVS="EXTPROC_DLLS=ANY,LD_LIBRARY_PATH=/usr/oracle/lib:/opt/BIOVIA/direct2016/bin11")

))

LOG_DIRECTORY_DIRECT2016=/opt/BIOVIA/direct2016LOG_FILE_DIRECT2016=direct_agent.logSTART_WAIT_TIME_DIRECT2016=10

5. At the command line, start the new service:$ lsnrctl start DIRECT2016

Create the Public Database Link1. At the command line, start SQL*Plus, and log in as a DBA system user.2. Create a public database link that uses that alias name in the USING clause.

SQL> CREATE PUBLIC DATABASE LINK AGENT_LINK_DIRECT2016 USING 'extproc_connection_data_direct2016';

3. Exit SQL*Plus.

For information on creating or replacing library mdldirect.so, see Edit the script mdllibdef.sqlStep 5 in the second example.


Manual Installation of the Direct SchemaThis section explains the tasks you must perform to create a complete Direct installation after you haveinstalled the Direct files using the Direct installer or from the file archive.

If you have installed the Direct files using the Direct installer, skip to the step Manual Installation Tasks.To install the Direct files from the file archive, proceed to Install Direct Files from the File Archive.

Install Direct Files from the File Archive1. Create the BIOVIA home directory if it does not already exist, if the directory already exists proceed

to step 2. This directory may be located anywhere but BIOVIA recommends that it be /opt/BIOVIA.For example:$ mkdir -p /opt/BIOVIA

2. Navigate to the BIOVIA home directory (created in step 1) and create the directory to hold the filesused by Direct, this should be named direct2016:$ cd /opt/BIOVIA

$ mkdir direct2016

3. Navigate to the directory created in step 2 and and copy your downloaded directfiles.tar.gz file tothis directory:$ cd direct2016

$ cp location-of-downloaded-file/directfiles.tar.gz .

4. Decompress the downloaded file using the gunzip utility:gunzip directfiles.tar.gz

5. Extract the Direct files from the .tar file:$ tar xvf directfiles.tar

6. Change permissions on the files in the bin11, bin12 and lib directories, Oracle’s extproc listenerprocess must be able to read and execute these files:$ chmod +rx bin11/* bin12/* lib/*

Manual Installation Tasks

Note: The Directinstallation contains the directory /sql. This directory contains the SQL scripts thatare needed to create the C$DIRECT2017 schema and to create the Direct packages. You need accessto this directory in order to complete the tasks in this section.

Modify the UniProtConverter ScriptThis procedure is required to use the UniProt Converter Utility.

You must use a 64-bit version of the Java Runtime Environment (JRE), and then modify theUniProtConverter script with the correct JRE installation path:

1. Open and edit the file install_directory/BIOVIA/direct2016/bin11/UniProtConverter. Use bin11with Oracle 11 andbin12with Oracle 12.

Manual Installation of the Direct Schema |

2. Change the value of the environment variable JAVA to the location of your 64-bit JRE.

For example, JREinstall_directory/java/jre1.2.6.0_20.


Customizing SETPATHIn a manual installation, the files setpath and setpath.cshmust be customized.

To customize the setpath or setpath.csh file

1. Open a text editor and edit the setpath or setpath.csh file.

setpath files are placed into the following directory by the installer:( Use bin11with Oracle 11 andbin12with Oracle 12.)install_directory/direct2016/bin11

orinstall_directory/direct2016/bin12

2. Replace strings of four letters with path or value customized for the installation:

AAAA Oracle Service Name

ZZZZ Oracle home directory

BBBB BIOVIA home directory, for example, /opt/BIOVIA

XXXX Oracle version 11 or 12, depending on your installation

YYYY 2016, the Direct version


4. To verify that the file has been modified correctly, source the file in sh, ksh or bash using

. setpath

or in csh use:source setpath.csh

Then use ldd to ensure that none of the dependencies of mdldirect.so aremissing. There shouldnot be any shared objects which are not found:ldd mdldirect.so

Run mdlsysactions.sql

Permissions required: SYS user permissions in order to run the mdlsysactions.sql file.

1. Unpackage the Direct files onto your server.2. Navigate to the directory that contains the Direct SQL files, for example:

$ cd /opt/BIOVIA/direct2016/sql

3. Start SQL*Plus and log in as SYS:$ sqlplus sys/password as sysdba

where password is the password for the SYS account.

4. Run the mdlsysactions.sql file:@mdlsysactions.sql

5. Log out of SQL*Plus.


Create the C$DIRECT2017 SchemaThe C$DIRECT2017 schemamust first be created before the Direct packages can be created. The filemkmdlichem.sql is a template that you can use to create the C$DIRECT2017 schema. You must firstmodify the file to define parameters for your site:

1. Navigate to the directory that contains the Direct SQL files, for example,/opt/BIOVIA/direct2016/sql.

2. Locate and make a copy of the file mkdirect.sql. For example, you might save the file asmkdirect_backup.sql.

3. Open the original file, mkdirect.sql, in a text editor.4. Search the file for the tablespace name USERS. There are two occurrences of this tablespace name.5. Change the two occurrences of the tablespace name USERS to the tablespace name that you plan to

use as the default tablespace for the C$DIRECT2017 user.6. (Optional) Search the file for the tablespace name TEMP.7. Change the tablespace name TEMP to the temporary tablespace name that you plan to use for the

C$DIRECT2017 account.8. Search the file for the string “c$directV”. There are 11 occurrences of this string.9. Change all 11 occurrences of the string “c$directV” to “c$direct2016”.10. Save and close the file.11. Start SQL*Plus and log in using a DBA system account:

$ sqlplus username/password

where username is the name of the DBA system account, and password is the password for thataccount.

12. Run the mkdirect.sql file:SQL> @mkdirect.sql

13. Log out of SQL*Plus.

Edit mdllibdef.sqlYou must edit the script mdllibdef.sql to specify the full path to the mdldirect.so, and include anAGENT specification with the same name as the public database link created in Create the publicdatabase link. This directs Oracle to use the 64-bit listener instead of the 32-bit listener when startingDirect.

1. Navigate to the directory that contains the Direct SQL files, for example/opt/BIOVIA/direct2016/sql.

2. Locate and make a copy of the file mdllibdef.sql. For example, you might save the file asmdllibdef_backup.sql.

3. Open the original file, mdllibdef.sql, in a text editor.4. Locate the following section in the file:

create or replace library mdldirect is'directory/mdldirect.dll';

5. Change the path from ‘directory/mdldirect.dll’ to the full path of the file mdldirect.so,and, optionally, include an AGENT specification with the same name as the public database linkcreated in Create the public database link. For example:create or replace library mdldirect is'/opt/BIOVIA/direct2016/bin11/mdldirect.so';


or

create or replace library mdldirect is'/opt/BIOVIA/direct2016/bin11/mdldirect.so'agent 'agent_link_direct2016';


Test the Oracle extproc Listener

Note: Verify that you have completed the procedures in Create the C$DIRECT2017 schema and Editthe script mdllibdef.sql before you begin this procedure.

1. Open a Command Prompt window and navigate to the directory that contains the Direct SQL files,for example:$ cd /opt/BIOVIA/direct2016/sql

2. Start SQL*Plus and log in as the user C$DIRECT2017:$ sqlplus 'c$direct2016/password'


3. Run the mdltestlistener.sql file:SQL> @mdltestlistener.sql

The output should resemble the following example:Library created.Grant succeeded.Package created.No errors.Package body created. No errors.RUNRPC---------------------------------------------------------------------Package dropped.

Note: If you get errors, your Oracle extproc listener definition must be fixed before you can proceed.Ensure that your listener test is successful before you continue with the installation. For moreinformation, see Configuring an extproc Listener.

Load the Direct PackagesAfter you have created the C$DIRECT2017 schema, and have successfully created an Oracle extproclistener, you can load the Direct packages.

During the Direct files installation, the installer placed the scriptmdlinst_all.sql in the /sql directory.

1. Open a terminal window and navigate to the directory that contains the Direct SQL files, forexample:$ cd /opt/BIOVIA/direct2016/sql



3. Run the mdlinst_all.sql file, for example:SQL> @mdlinst_all.sql


You will see numerous messages. However, there should be no Oracle errors.

Note: If you see Oracle errors, run the script mdluninst.sql to uninstall the packages, correctthe problem, and then run the mdlinst_all.sql script again. If you cannot correct the Oracleerror conditions, contact BIOVIA Support.

Test the Direct InstallationTo test the validity of your installation, verify that the objects are valid and that the cartridge can startup:



2. Execute the following SQL SELECT command:SQL> select distinct status from user_objects;

This command should display a single row of output:VALID

If there is a row of output that displays as INVALID then the installation was not successful.

3. To display the product banner, run the following command:SQL> select mdlaux.version from dual;

If the Direct cartridge is installed and configured correctly, a banner screen similar to the screen thatfollows appears:

VERSION--------------------------------------------------------------------------

--BIOVIA Direct

Revision 2017 (Linux Oracle12c) (16.1.0.153)

(c) Copyright Dassault Systèmes, Inc. 1999-2016

4. Exit SQL*Plus:SQL> exit


Maintaining an Installation During a Major Oracle Upgrade

Upgrade IssuesThe Direct executables are Oracle-version specific, so when you upgrade your database to a newOracleversion, the Direct installation no longer runs.

n Direct requires MDLAUX.PREPAREINDEXEXPORT before you perform a database export to efficientlyperform an import.

n The Oracle import does not restore the Direct schema properly and as a result the import mightresult in invalid objects.

n The Oracle import might not import the C$DIRECT2017 schema before it imports schemas that havedomain indexes which depend on the Direct schema existing in order for the import to work properly.

Protect Your Direct Data During an Oracle Upgraden From Direct, run MDLAUX.PREPAREINDEXEXPORT in each schema that has a Direct domain index

before you export the Oracle database for backup.n Before performing a major Oracle upgrade and after completing Step 1, uninstall Direct.

There two upgrade scenarios:

1. Upgrade in place (no backup and restore).2. Backup (full export), upgrade, and restore (full import).

Upgrade Scenario 1 - Upgrade in Place 58Upgrade Scenario 2 - Backup, Upgrade, and Restore 58

Upgrade Scenario 1 - Upgrade in Place1. Uninstall Direct.

This must be done before the Oracle upgrade.2. Upgrade to the new version of Oracle.3. Reinstall Direct.4. For each schema that owns a domain index:

a. Execute c$direct2016.mdlauxop.setup to define the Direct synonyms.b. Select mdlaux.recreateindexes from dual.

Direct now functions properly in the upgraded Oracle version.

Upgrade Scenario 2 - Backup, Upgrade, and RestoreBackup with the old version of Oracle, upgrade Oracle, and then restore the database with the newversion of Oracle.

1. Run MDLAUX.PREPAREINDEXEXPORT in each schema that has a Direct domain index.2. Export the ORACLE database.3. Uninstall Direct.4. Install the new version of Oracle.5. Restore the Oracle database infrastructure (that is, restore any schemas that do not have Direct

domain indexes).


6. Install Direct.7. Run mdlsysactions.sql as sysdba

8. In each schema that will have Direct domain indexes:a. Execute c$direct2016.mdlauxop.setup to define the Direct synonyms.

This step ensures that the version of Direct that you have installed is the version that will beused during import.

b. Import the contents of the schemas that contain domain indexes, using the indexes=y andignore=y options.

c. For each schema that contains Domain indexes, enterSELECT STATUS,DOMIDX_STATUS, DOMINDX_OPSTATUS, ITYP_OWNER FROM USER_INDEXES WHERE INDEX_TYPE='DOMAIN'

If any of the Direct domain indexes do not show all three status columns as VALID, then runMDLAUX.RECREATEINDEXES in that schema. Any Direct domain indexes that are not repaired bythis command needs to be dropped and created again.

Note: The speed of the import and the speed of MDLAUX.RECREATEINDEXES depends onmdlsysactions.sql having been run in the SYS schema. If mdlsysactions.sql is not run,the result can bemany extra hours of runtime.

Maintaining a Direct Installation During a Major Oracle Upgrade |