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BIOVIA Direct Administration Guide

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BIOVIA Direct Administration Guide ADMINISTRATION 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 are commercial 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 Dassault Systèmes 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 BIOVIA software, acknowledge the source in an appropriate format. BIOVIA may grant permission to republish or reprint its copyrighted materials. Requests should be submitted to BIOVIA Support, either through electronic mail to [email protected], or in writing to: BIOVIA Support 5005 Wateridge Vista Drive, San Diego, CA 92121 USA Structure of a Domain Index 117 Contents Example Objects 117 Permissions Required for BIOVIA Direct Users 120 About This Guide 1 Dropping and Recreating Domain Indexes 120 Introduction to Direct 1 Storing Structures that Cannot be Indexed or Audience and Prerequisite Knowledge 1 Searched 121 Related BIOVIA Direct documents 1 Maintaining Tables and Indexes 124 Setting the Cartridge C$DIRECT2016 Routine Index Maintenance 124 Environment 3 Scan for Duplicate Molecules 124 The BIOVIA Chemical Environment 3 Scan for Duplicate Reactions 126 Overview of BIOVIA Global Chemical Scan the Substructure Search Keys 129 Environment 4 Update the Inverted Key Index 129 Writing Global Environment Information to a File 4 Update a Fastsearch Index 130 Editing the Global Environment Information 5 Validate the Fastsearch Index 130 Loading Global Environment Files 5 Rebuild a Domain Index 131 Using Multiple Processors with SSS and RSS Rebuild the Fastsearch Index 132 Searches 6 Rebuild the FLEXMATCH or RXNFLEXMATCH Customizing Environment Information 6 Index 132 The BIOVIA Periodic Table 6 Rebuild the Molecular Formula Index 132 Format of the BIOVIA Ptable 7 Rebuild the Substructure Search Keys 132 The Direct Default Ptable 7 Truncate a Domain Index 133 Customize the BIOVIA Ptable 8 Analyze a Domain Index 133 The BIOVIA Salts Definition File 9 Recreate Invalid Domain Indexes 133 Customize the Salts Definition 13 Optional Index Management Tasks 134 Customize the Sgroupfields Definition 14 Add Fastsearch to a Domain Index 134 Allowed Sgroup Field Names and Data Add Substructure Search Keys to a Domain Types 16 Index 135 Modifying the Sgroupfields Definition 16 Add a Modification Date Column to a Table 135 Customize the Isotopedata Definition 17 Add a molfile or Chime String Column to a Table 136 The Direct Default Isotopedata Definition File 17 Add a rxnfile or Chime String Column to a Table 136 Customize the Isotopedata Definition 109 Add a Molecular Formula Column to a Table 137 Creating and Managing Indexes and Tables 110 Add a Molecule Name Column to a Table 138 Creating Molecule Indexes and Tables 110 Add a Molecular Weight Column to a Table 139 Molecule Index Without Generic Structures 110 Add a Molecule Text Keys Column to a Table 140 Markush Molecule Index 111 Add an InChI key or SMILES String Column Creating Molecule Tables 112 to a Table 140 Examples 112 Alter Duplicate Checking Behavior 141 Create a Table to Contain Molecules 113 Alter Inverted Keys Chunk Size 142 Add a Domain Index to the Molecule Table 113 Recompute the Molecular Formula 142 Domain Index Creation 114 Recompute the Molecular Weight Values 142 Creating and Managing Reaction Tables and Validate the Molecular Formula Index 142 Indexes 114 Validate Molecular Weights 143 Creating Reaction Tables 114 Remove Fastsearch from a Domain Index 143 Create a Table to Contain Reactions 115 Remove Substructure Search Keys from a Insert Reactions into a Table 115 Domain Index 143 Add a Domain Index to the Reactions Rename a Domain Index 143 Table 115 Drop a Domain Index 143 If CREATE INDEX Fails 116 Enable NEMA Keys for Exact-match Streams Replication 172 Searching 144 Streams Configuration and Administration 172 Disable NEMA Keys for Exact-match Limitations on Replication 173 Searching 144 Command Reference 174 Running Routine Index Maintenance Procedures Automatically 144 Cartridge Management Functions and Procedures 174 Example 145 MDLAUX.CARTRIDGESCHEMA 174 Atom-To-Atom Maps 150 MDLAUX.CREATEBOOSTFILE 174 Using the Automapper 150 MDLAUX.CREATELOGFILE 175 Create a Status Information Table 150 MDLAUX.ERRORS 176 Use the Automapper 150 MDLAUX.GETENVFILE 177 Lock and Commit 151 MDLAUX.GETEXTPROCPID 178 Examine the Automap Status 151 MDLAUX.GETPROPERTY 178 Local Partitioned Index 153 MDLAUX.INDEXPARAMETERS 178 Creating a Partitioned Domain Index 153 MDLAUX.KILLEXTPROC 179 Creating Indexes on Large Partitions 154 MDLAUX.LOGTABLE 180 Adding a New Partition 154 MDLAUX.NODROP 181 Splitting a Partition 154 MDLAUX.NOSTRUCT 181 Rebuilding a Partition 155 MDLAUX.PENDINGFASTSEARCH 181 Exchanging Table and Partition 155 MDLAUX.DELETEDFASTSEARCH 182 Direct Index Maintenance Procedures 156 MDLAUX.PREPAREINDEXEXPORT 182 Parallelization of Index Maintenance 156 MDLAUX.RECREATEFASTSEARCH 186 Parallelizing Index Partition Creation and Searching 156 MDLAUX.RECREATEINDEXES 188 Structure of Partitioned Domain Index 157 MDLAUX.RECREATEKEYS 189 Limitations with Partitioned Domain Indexes 158 MDLAUX.REGENAAMAPS 191 Upgrading Indexes 160 MDLAUX.REMOVEBOOSTFILE 193 Upgrading a Direct Table with an Existing MDLAUX.SCANINDEX 193 Domain Index 160 MDLAUX.SETENVFILE 197 Upgrading a Direct Table without an Existing MDLAUX.SETFLAGS('NODATE') 198 Domain Index 160 MDLAUX.SETFLAGS('FORCEV3000') 198 Exporting and Importing 162 MDLAUX.SETPROPERTY 199 Export and Import 162 MDLAUX.SETUP 200 If Import Fails to Create the Domain Index 163 MDLAUX.SHOWBOOSTFILES 201 Importing Data and the Domain Index 164 MDLAUX.UPDATEPENDINGFASTSEARCH 201 Logging Information 167 MDLAUX.UPDATEPENDINGINVERSIONS 203 Logging Index Operations 167 MDLAUX.UPGRADEINDEXES_PREPARE and Logging to a File 167 MDLAUX.UPGRADEINDEXES_UPGRADE 204 Log levels 168 Parameters for Index Creation and Create the MDL_DC_LOGGING Table 168 Maintenance 206 Change the Logging Level 169 Parameters for CREATE INDEX 206 Modify the Logging Table 169 Parameters for ALTER INDEX REBUILD 212 Logging and Performance 169 Parameters for ALTER INDEX 218 Direct Error Messages 170 Performance Tuning 221 Replication 171 BIOVIA Direct Performance 221 Direct and Replication 171 Fastsearch Index Cache and Searching 221 Direct Replication Scripts 171 Oracle Real Application Clusters 222 Configure Chemical Tables for Replication 171 Known Issues with Oracle RAC 222 Direct Index Tables 223 Description of the Direct Index Tables 223 Specifying a MOLREGNO or RXNREGNO Direct SDFile Import Utility 225 Column 240 Syntax of the importSDFile Utility 225 Specifying an extreg Column 240 Processing Options of the importSDFile Utility 225 Specifying a Molecule RDFile Versus a Reaction RDFile 240 Create the Intermediate Table 225 Designating the Molecule Column 240 Import as MOLFILE 226 Specifying the Record Source 240 Import as 2D 226 Controlling Record Order 240 Specify a Table in Another Schema 226 Controlling Included Records 240 Oracle O/S Authentication 226 Renaming Columns 241 Rename SDFile Fields 227 Formatting Columns 241 NOWAIT Option 227 Oracle O/S Authentication 241 ERRORS N Option 227 SQL File Syntax 241 REPORTFIELD Option 227 Error Handling 242 Numeric and Date Field Processing 228 UniProt Converter 244 Error Handling 228 About the UniProt Converter 244 SDFile Import Example 229 Running the UniProt Converter 245 Direct RDFile Import Utility 231 Usage 245 Introduction to the RDFile Import Utility 231 Format of Fields File 246 RDFile Import Utility Operation 231 Operation 246 Tables and Columns 232 Additional Information on UniProt Structure tableprefix Parameter 232 Conversion 247 Handling of Specialized Conventions 233 FEATURE TYPEs 248 Syntax of the importRDFile Program 233 Ignored Types 249 Processing Options of the importRDFile Structure Modifications 249 Program 233 Sgroups 250 Create the Intermediate Table 233 Abbreviation Classes 250 Import Structures in Character(-char) Mode 234 Known Limitations 250 Oracle O/S Authentication 234 Multiple Modifications to a Single Residue 251 NOWAIT Option 234 Crosslinks Involving 3 Residues 251 Numeric and Date Field Processing 234 Creating a Sample Proteins Database 251 Control/C Interrupt 235 Direct Boost Files 252 Error Handling 235 Storing in Boost Files 252 Tables Created by RDFile Import Utility 236 Adding Boost Files to a Molecule or Reaction Duplicate Checking 236 Index 252 Domain Index Creation 236 Location of Boost Files 253 SDFile and RDFile Export Utilities 237 Size of Boost Files 254 Overview of the Export Utilities 237 Boost Files Creation Time 254 Usage 238 Recreating Boost Files 254 ExportSDFile 238 Displaying Boost Files 255 Designating the Molecule Column 238 Removing Boost Files 256 Specifying the Record Source 238 Controlling Record Order 238 Controlling Which Records are Included 238 Renaming Columns 239 Formatting Columns 239 Oracle O/S Authentication 239 ExportRDFile 239 About This Guide This guide explains how to administer BIOVIA Direct on: n Host computers that run the Red Hat Linux operating system n Host computers that run the SUSE Linux operating system n Host computers that run the Oracle Solaris operating system n Intel or Intel-compatible
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