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revision 1.81, Wed Feb 21 13:21:42 2007 UTC revision 1.84, Thu May 17 23:44:51 2007 UTC
# Line 274  Line 274 
274              my $extra = join " ", @extraData;              my $extra = join " ", @extraData;
275              # Get the full taxonomy.              # Get the full taxonomy.
276              my $taxonomy = $fig->taxonomy_of($genomeID);              my $taxonomy = $fig->taxonomy_of($genomeID);
277                # Get the version. If no version is specified, we default to the genome ID by itself.
278                my $version = $fig->genome_version($genomeID);
279                if (! defined($version)) {
280                    $version = $genomeID;
281                }
282                # Get the DNA size.
283                my $dnaSize = $fig->genome_szdna($genomeID);
284              # Open the NMPDR group file for this genome.              # Open the NMPDR group file for this genome.
285              my $group;              my $group;
286              if (open(TMP, "<$FIG_Config::organisms/$genomeID/NMPDR") &&              if (open(TMP, "<$FIG_Config::organisms/$genomeID/NMPDR") &&
# Line 286  Line 293 
293              }              }
294              close TMP;              close TMP;
295              # Output the genome record.              # Output the genome record.
296              $loadGenome->Put($genomeID, $accessCode, $fig->is_complete($genomeID), $genus,              $loadGenome->Put($genomeID, $accessCode, $fig->is_complete($genomeID),
297                               $group, $species, $extra, $taxonomy);                               $dnaSize, $genus, $group, $species, $extra, $version, $taxonomy);
298              # Now we loop through each of the genome's contigs.              # Now we loop through each of the genome's contigs.
299              my @contigs = $fig->all_contigs($genomeID);              my @contigs = $fig->all_contigs($genomeID);
300              for my $contigID (@contigs) {              for my $contigID (@contigs) {
# Line 517  Line 524 
524              Trace("Loading features for genome $genomeID.") if T(3);              Trace("Loading features for genome $genomeID.") if T(3);
525              $loadFeature->Add("genomeIn");              $loadFeature->Add("genomeIn");
526              # Get the feature list for this genome.              # Get the feature list for this genome.
527              my $features = $fig->all_features_detailed($genomeID);              my $features = $fig->all_features_detailed_fast($genomeID);
528              # Sort and count the list.              # Sort and count the list.
529              my @featureTuples = sort { $a->[0] cmp $b->[0] } @{$features};              my @featureTuples = sort { $a->[0] cmp $b->[0] } @{$features};
530              my $count = scalar @featureTuples;              my $count = scalar @featureTuples;
# Line 530  Line 537 
537              # Loop through the features.              # Loop through the features.
538              for my $featureTuple (@featureTuples) {              for my $featureTuple (@featureTuples) {
539                  # Split the tuple.                  # Split the tuple.
540                  my ($featureID, $locations, undef, $type) = @{$featureTuple};                  my ($featureID, $locations, undef, $type, $minloc, $maxloc, $assignment, $user, $quality) = @{$featureTuple};
541                  # Check for duplicates.                  # Check for duplicates.
542                  if ($featureID eq $oldFeatureID) {                  if ($featureID eq $oldFeatureID) {
543                      Trace("Duplicate feature $featureID found.") if T(1);                      Trace("Duplicate feature $featureID found.") if T(1);
# Line 538  Line 545 
545                      $oldFeatureID = $featureID;                      $oldFeatureID = $featureID;
546                      # Count this feature.                      # Count this feature.
547                      $loadFeature->Add("featureIn");                      $loadFeature->Add("featureIn");
548                        # Fix the quality. It is almost always a space, but some odd stuff might sneak through, and the
549                        # Sprout database requires a single character.
550                        if (! defined($quality) || $quality eq "") {
551                            $quality = " ";
552                        }
553                      # Begin building the keywords. We start with the genome ID, the                      # Begin building the keywords. We start with the genome ID, the
554                      # feature ID, the taxonomy, and the organism name.                      # feature ID, the taxonomy, and the organism name.
555                      my @keywords = ($genomeID, $featureID, $fig->genus_species($genomeID),                      my @keywords = ($genomeID, $featureID, $fig->genus_species($genomeID),
556                                      $fig->taxonomy_of($genomeID));                                      $fig->taxonomy_of($genomeID));
                     # Get the functional assignment and aliases.  
                     my $assignment = $fig->function_of($featureID);  
557                      # Create the aliases.                      # Create the aliases.
558                      for my $alias ($fig->feature_aliases($featureID)) {                      for my $alias ($fig->feature_aliases($featureID)) {
559                          $loadFeatureAlias->Put($featureID, $alias);                          $loadFeatureAlias->Put($featureID, $alias);
# Line 645  Line 655 
655                      my $cleanWords = $sprout->CleanKeywords($keywordString);                      my $cleanWords = $sprout->CleanKeywords($keywordString);
656                      Trace("Keyword string for $featureID: $cleanWords") if T(4);                      Trace("Keyword string for $featureID: $cleanWords") if T(4);
657                      # Create the feature record.                      # Create the feature record.
658                      $loadFeature->Put($featureID, 1, $type, $assignment, $cleanWords);                      $loadFeature->Put($featureID, 1, $user, $quality, $type, $assignment, $cleanWords);
659                      # This part is the roughest. We need to relate the features to contig                      # This part is the roughest. We need to relate the features to contig
660                      # locations, and the locations must be split so that none of them exceed                      # locations, and the locations must be split so that none of them exceed
661                      # the maximum segment size. This simplifies the genes_in_region processing                      # the maximum segment size. This simplifies the genes_in_region processing
# Line 778  Line 788 
788              # Get the subsystem object.              # Get the subsystem object.
789              my $sub = $fig->get_subsystem($subsysID);              my $sub = $fig->get_subsystem($subsysID);
790              # Only proceed if the subsystem has a spreadsheet.              # Only proceed if the subsystem has a spreadsheet.
791              if (! $sub->{empty_ss}) {              if (defined($sub) && ! $sub->{empty_ss}) {
792                  Trace("Creating subsystem $subsysID.") if T(3);                  Trace("Creating subsystem $subsysID.") if T(3);
793                  $loadSubsystem->Add("subsystemIn");                  $loadSubsystem->Add("subsystemIn");
794                  # Create the subsystem record.                  # Create the subsystem record.
# Line 991  Line 1001 
1001          # Create a hash for storing property IDs.          # Create a hash for storing property IDs.
1002          my %propertyKeys = ();          my %propertyKeys = ();
1003          my $nextID = 1;          my $nextID = 1;
1004            # Get the attributes we intend to store in the property table.
1005            my @propKeys = $fig->get_group_keys("NMPDR");
1006          # Loop through the genomes.          # Loop through the genomes.
1007          for my $genomeID (sort keys %{$genomeHash}) {          for my $genomeID (sort keys %{$genomeHash}) {
1008              $loadProperty->Add("genomeIn");              $loadProperty->Add("genomeIn");
1009              Trace("Generating properties for $genomeID.") if T(3);              Trace("Generating properties for $genomeID.") if T(3);
1010              # Get the genome's features. The feature ID is the first field in the              # Initialize a counter.
             # tuples returned by "all_features_detailed". We use "all_features_detailed"  
             # rather than "all_features" because we want all features regardless of type.  
             my @features = map { $_->[0] } @{$fig->all_features_detailed($genomeID)};  
             my $featureCount = 0;  
1011              my $propertyCount = 0;              my $propertyCount = 0;
1012              # Get the properties for this genome's features.              # Get the properties for this genome's features.
1013              my $attributes = GetGenomeAttributes($fig, $genomeID, \@features);              my @attributes = $fig->get_attributes("fig|$genomeID%", \@propKeys);
1014              Trace("Property hash built for $genomeID.") if T(3);              Trace("Property list built for $genomeID.") if T(3);
1015              # Loop through the features, creating HasProperty records.              # Loop through the results, creating HasProperty records.
1016              for my $fid (@features) {              for my $attributeData (@attributes) {
1017                  # Get all attributes for this feature. We do this one feature at a time                  # Pull apart the attribute tuple.
1018                  # to insure we do not get any genome attributes.                  my ($fid, $key, $value, $url) = @{$attributeData};
                 my @attributeList = @{$attributes->{$fid}};  
                 if (scalar @attributeList) {  
                     $featureCount++;  
                 }  
                 # Loop through the attributes.  
                 for my $tuple (@attributeList) {  
                     $propertyCount++;  
                     # Get this attribute value's data. Note that we throw away the FID,  
                     # since it will always be the same as the value if "$fid".  
                     my (undef, $key, $value, $url) = @{$tuple};  
1019                      # Concatenate the key and value and check the "propertyKeys" hash to                      # Concatenate the key and value and check the "propertyKeys" hash to
1020                      # see if we already have an ID for it. We use a tab for the separator                      # see if we already have an ID for it. We use a tab for the separator
1021                      # character.                      # character.
# Line 1035  Line 1033 
1033                      # Create the HasProperty entry for this feature/property association.                      # Create the HasProperty entry for this feature/property association.
1034                      $loadHasProperty->Put($fid, $propertyID, $url);                      $loadHasProperty->Put($fid, $propertyID, $url);
1035                  }                  }
             }  
1036              # Update the statistics.              # Update the statistics.
1037              Trace("$propertyCount attributes processed for $featureCount features.") if T(3);              Trace("$propertyCount attributes processed.") if T(3);
             $loadHasProperty->Add("featuresIn", $featureCount);  
1038              $loadHasProperty->Add("propertiesIn", $propertyCount);              $loadHasProperty->Add("propertiesIn", $propertyCount);
1039          }          }
1040      }      }
# Line 1611  Line 1607 
1607    
1608  The following relations are loaded by this method.  The following relations are loaded by this method.
1609    
     DrugProject  
     ContainsTopic  
     DrugTopic  
     ContainsAnalysisOf  
1610      PDB      PDB
1611      IncludesBound      DocksWith
1612      IsBoundIn      IsProteinForFeature
     BindsWith  
1613      Ligand      Ligand
     DescribesProteinForFeature  
     FeatureConservation  
1614    
1615  The source information for these relations is taken from flat files in the  The source information for these relations is taken from attributes. The
1616  C<$FIG_Config::drug_directory>. The file C<master_tables.list> contains  C<PDB> attribute links a PDB to a feature, and is used to build B<IsProteinForFeature>.
1617  a list of drug project names paired with file names. The named file (in the  The C<zinc_name> attribute describes the ligands. The C<docking_results>
1618  same directory) contains all the data for the project.  attribute contains the information for the B<DocksWith> relationship. It is
1619    expected that additional attributes and tables will be added in the future.
1620    
1621  =over 4  =over 4
1622    
# Line 1646  Line 1636 
1636      # Get the genome hash.      # Get the genome hash.
1637      my $genomeHash = $self->{genomes};      my $genomeHash = $self->{genomes};
1638      # Create load objects for the tables we're loading.      # Create load objects for the tables we're loading.
     my $loadDrugProject = $self->_TableLoader('DrugProject');  
     my $loadContainsTopic = $self->_TableLoader('ContainsTopic');  
     my $loadDrugTopic = $self->_TableLoader('DrugTopic');  
     my $loadContainsAnalysisOf = $self->_TableLoader('ContainsAnalysisOf');  
1639      my $loadPDB = $self->_TableLoader('PDB');      my $loadPDB = $self->_TableLoader('PDB');
     my $loadIncludesBound = $self->_TableLoader('IncludesBound');  
     my $loadIsBoundIn = $self->_TableLoader('IsBoundIn');  
     my $loadBindsWith = $self->_TableLoader('BindsWith');  
1640      my $loadLigand = $self->_TableLoader('Ligand');      my $loadLigand = $self->_TableLoader('Ligand');
1641      my $loadDescribesProteinForFeature = $self->_TableLoader('DescribesProteinForFeature');      my $loadIsProteinForFeature = $self->_TableLoader('IsProteinForFeature');
1642      my $loadFeatureConservation = $self->_TableLoader('FeatureConservation');      my $loadDocksWith = $self->_TableLoader('DocksWith');
1643      if ($self->{options}->{loadOnly}) {      if ($self->{options}->{loadOnly}) {
1644          Trace("Loading from existing files.") if T(2);          Trace("Loading from existing files.") if T(2);
1645      } else {      } else {
1646          Trace("Generating drug target data.") if T(2);          Trace("Generating drug target data.") if T(2);
1647          # Load the project list. The file comes in as a list of chomped lines,          # First comes the "DocksWith" relationship. This will give us a list of PDBs.
1648          # and we split them on the TAB character to make the project name the          # We can also encounter PDBs when we process "IsProteinForFeature". To manage
1649          # key and the file name the value of the resulting hash.          # this process, PDB information is collected in a hash table and then
1650          my %projects = map { split /\t/, $_ } Tracer::GetFile("$FIG_Config::drug_directory/master_tables.list");          # unspooled after both relationships are created.
1651          # Create hashes for the derived objects: PDBs, Features, and Ligands. These objects          my %pdbHash = ();
1652          # may occur multiple times in a single project file or even in multiple project          Trace("Generating docking data.") if T(2);
1653          # files.          # Get all the docking data. This may cause problems if there are too many PDBs,
1654          my %ligands = ();          # at which point we'll need another algorithm. The indicator that this is
1655          my %pdbs = ();          # happening will be a timeout error in the next statement.
1656          my %features = ();          my @dockData = $fig->query_attributes('$key = ? AND $value < ?',
1657          my %bindings = ();                                                ['docking_results', $FIG_Config::dockLimit]);
1658          # Set up a counter for drug topics. This will be used as the key.          Trace(scalar(@dockData) . " rows of docking data found.") if T(3);
1659          my $topicCounter = 0;          for my $dockData (@dockData) {
1660          # Loop through the projects. We sort the keys not because we need them sorted, but              # Get the docking data components.
1661          # because it makes it easier to infer our progress from trace messages.              my ($pdbID, $docking_key, @valueData) = @{$dockData};
1662          for my $project (sort keys %projects) {              # Fix the PDB ID. It's supposed to be lower-case, but this does not always happen.
1663              Trace("Processing project $project.") if T(3);              $pdbID = lc $pdbID;
1664              # Only proceed if the download file exists.              # Strip off the object type.
1665              my $projectFile = "$FIG_Config::drug_directory/$projects{$project}";              $pdbID =~ s/pdb://;
1666              if (! -f $projectFile) {              # Extract the ZINC ID from the docking key. Note that there are two possible
1667                  Trace("Project file $projectFile not found.") if T(0);              # formats.
1668              } else {              my (undef, $zinc_id) = $docking_key =~ /^docking_results::(ZINC)?(\d+)$/;
1669                  # Create the project record.              if (! $zinc_id) {
1670                  $loadDrugProject->Put($project);                  Trace("Invalid docking result key $docking_key for $pdbID.") if T(0);
1671                  # Create a hash for the topics. Each project has one or more topics. The                  $loadDocksWith->Add("errors");
1672                  # topic is identified by a URL, a category, and an identifier.              } else {
1673                  my %topics = ();                  # Get the pieces of the value and parse the energy.
1674                  # Now we can open the project file.                  # Note that we don't care about the rank, since
1675                  Trace("Reading project file $projectFile.") if T(3);                  # we can sort on the energy level itself in our database.
1676                  Open(\*PROJECT, "<$projectFile");                  my ($energy, $tool, $type) = @valueData;
1677                  # Get the first record, which is a list of column headers. We don't use this                  my ($rank, $total, $vanderwaals, $electrostatic) = split /\s*;\s*/, $energy;
1678                  # for anything, but it may be useful for debugging.                  # Ignore predicted results.
1679                  my $headerLine = <PROJECT>;                  if ($type ne "Predicted") {
1680                  # Loop through the rest of the records.                      # Count this docking result.
1681                  while (! eof PROJECT) {                      if (! exists $pdbHash{$pdbID}) {
1682                      # Get the current line of data. Note that not all lines will have all                          $pdbHash{$pdbID} = 1;
1683                      # the fields. In particular, the CLIBE data is fairly rare.                      } else {
1684                      my ($authorOrganism, $category, $tag, $refURL, $peg, $conservation,                          $pdbHash{$pdbID}++;
1685                          $pdbBound, $pdbBoundEval, $pdbFree, $pdbFreeEval, $pdbFreeTitle,                      }
1686                          $protDistInfo, $passAspInfo, $passAspFile, $passWeightInfo,                      # Write the result to the output.
1687                          $passWeightFile, $clibeInfo, $clibeURL, $clibeTotalEnergy,                      $loadDocksWith->Put($pdbID, $zinc_id, $electrostatic, $type, $tool,
1688                          $clibeVanderwaals, $clibeHBonds, $clibeEI, $clibeSolvationE)                                          $total, $vanderwaals);
                        = Tracer::GetLine(\*PROJECT);  
                     # The tag contains an identifier for the current line of data followed  
                     # by a text statement that generally matches a property name in the  
                     # main database. We split it up, since the identifier goes with  
                     # the PDB data and the text statement is part of the topic.  
                     my ($lineID, $topicTag) = split /\s*,\s*/, $tag;  
                     $loadDrugProject->Add("data line");  
                     # Check for a new topic.  
                     my $topicData = "$category\t$topicTag\t$refURL";  
                     if (! exists $topics{$topicData}) {  
                         # Here we have a new topic. Compute its ID.  
                         $topicCounter++;  
                         $topics{$topicData} = $topicCounter;  
                         # Create its database record.  
                         $loadDrugTopic->Put($topicCounter, $refURL, $category, $authorOrganism,  
                                             $topicTag);  
                         # Connect it to the project.  
                         $loadContainsTopic->Put($project, $topicCounter);  
                         $loadDrugTopic->Add("topic");  
                     }  
                     # Now we know the topic ID exists in the hash and the topic will  
                     # appear in the database, so we get this topic's ID.  
                     my $topicID = $topics{$topicData};  
                     # If the feature in this line is new, we need to save its conservation  
                     # number.  
                     if (! exists $features{$peg}) {  
                         $loadFeatureConservation->Put($peg, $conservation);  
                         $features{$peg} = 1;  
                     }  
                     # Now we have two PDBs to deal with-- a bound PDB and a free PDB.  
                     # The free PDB will have data about docking points; the bound PDB  
                     # will have data about docking. We store both types as PDBs, and  
                     # the special data comes from relationships. First we process the  
                     # bound PDB.  
                     if ($pdbBound) {  
                         $loadPDB->Add("bound line");  
                         # Insure this PDB is in the database.  
                         $self->CreatePDB($pdbBound, lc "$pdbFreeTitle (bound)", "bound", \%pdbs, $loadPDB);  
                         # Connect it to this topic.  
                         $loadIncludesBound->Put($topicID, $pdbBound);  
                         # Check for CLIBE data.  
                         if ($clibeInfo) {  
                             $loadLigand->Add("clibes");  
                             # We have CLIBE data, so we create a ligand and relate it to the PDB.  
                             if (! exists $ligands{$clibeInfo}) {  
                                 # This is a new ligand, so create its record.  
                                 $loadLigand->Put($clibeInfo);  
                                 $loadLigand->Add("ligand");  
                                 # Make sure we know this ligand already exists.  
                                 $ligands{$clibeInfo} = 1;  
                             }  
                             # Now connect the PDB to the ligand using the CLIBE data.  
                             $loadBindsWith->Put($pdbBound, $clibeInfo, $clibeURL, $clibeHBonds, $clibeEI,  
                                                 $clibeSolvationE, $clibeVanderwaals);  
                         }  
                         # Connect this PDB to the feature.  
                         $loadDescribesProteinForFeature->Put($pdbBound, $peg, $protDistInfo, $pdbBoundEval);  
                     }  
                     # Next is the free PDB.  
                     if ($pdbFree) {  
                         $loadPDB->Add("free line");  
                         # Insure this PDB is in the database.  
                         $self->CreatePDB($pdbFree, lc $pdbFreeTitle, "free", \%pdbs, $loadPDB);  
                         # Connect it to this topic.  
                         $loadContainsAnalysisOf->Put($topicID, $pdbFree, $passAspInfo,  
                                                      $passWeightFile, $passWeightInfo, $passAspFile);  
                         # Connect this PDB to the feature.  
                         $loadDescribesProteinForFeature->Put($pdbFree, $peg, $protDistInfo, $pdbFreeEval);  
                     }  
                     # If we have both PDBs, we may need to link them.  
                     if ($pdbFree && $pdbBound) {  
                         $loadIsBoundIn->Add("connection");  
                         # Insure we only link them once.  
                         my $bindingKey =  "$pdbFree\t$pdbBound";  
                         if (! exists $bindings{$bindingKey}) {  
                             $loadIsBoundIn->Add("newConnection");  
                             $loadIsBoundIn->Put($pdbFree, $pdbBound);  
                             $bindings{$bindingKey} = 1;  
1689                          }                          }
1690                      }                      }
1691                  }                  }
1692                  # Close off this project.          Trace("Connecting features.") if T(2);
1693                  close PROJECT;          # Loop through the genomes.
1694            for my $genome (sort keys %{$genomeHash}) {
1695                Trace("Generating PDBs for $genome.") if T(3);
1696                # Get all of the PDBs that BLAST against this genome's features.
1697                my @attributeData = $fig->get_attributes("fig|$genome%", 'PDB::%');
1698                for my $pdbData (@attributeData) {
1699                    # The PDB ID is coded as a subkey.
1700                    if ($pdbData->[1] !~ /PDB::(.+)/i) {
1701                        Trace("Invalid PDB ID \"$pdbData->[1]\" in attribute table.") if T(0);
1702                        $loadPDB->Add("errors");
1703                    } else {
1704                        my $pdbID = $1;
1705                        # Insure the PDB is in the hash.
1706                        if (! exists $pdbHash{$pdbID}) {
1707                            $pdbHash{$pdbID} = 0;
1708                        }
1709                        # The score and locations are coded in the attribute value.
1710                        if ($pdbData->[2] !~ /^([^;]+)(.*)$/) {
1711                            Trace("Invalid PDB data for $pdbID and feature $pdbData->[0].") if T(0);
1712                            $loadIsProteinForFeature->Add("errors");
1713                        } else {
1714                            my ($score, $locData) = ($1,$2);
1715                            # The location data may not be present, so we have to start with some
1716                            # defaults and then check.
1717                            my ($start, $end) = (1, 0);
1718                            if ($locData) {
1719                                $locData =~ /(\d+)-(\d+)/;
1720                                $start = $1;
1721                                $end = $2;
1722                            }
1723                            # If we still don't have the end location, compute it from
1724                            # the feature length.
1725                            if (! $end) {
1726                                # Most features have one location, but we do a list iteration
1727                                # just in case.
1728                                my @locations = $fig->feature_location($pdbData->[0]);
1729                                $end = 0;
1730                                for my $loc (@locations) {
1731                                    my $locObject = BasicLocation->new($loc);
1732                                    $end += $locObject->Length;
1733                                }
1734                            }
1735                            # Decode the score.
1736                            my $realScore = FIGRules::DecodeScore($score);
1737                            # Connect the PDB to the feature.
1738                            $loadIsProteinForFeature->Put($pdbData->[0], $pdbID, $start, $realScore, $end);
1739              }              }
1740          }          }
1741      }      }
1742            }
1743            # We've got all our PDBs now, so we unspool them from the hash.
1744            Trace("Generating PDBs. " . scalar(keys %pdbHash) . " found.") if T(2);
1745            my $count = 0;
1746            for my $pdbID (sort keys %pdbHash) {
1747                $loadPDB->Put($pdbID, $pdbHash{$pdbID});
1748                $count++;
1749                Trace("$count PDBs processed.") if T(3) && ($count % 500 == 0);
1750            }
1751            # Finally we create the ligand table. This information can be found in the
1752            # zinc_name attribute.
1753            Trace("Loading ligands.") if T(2);
1754            # The ligand list is huge, so we have to get it in pieces. We also have to check for duplicates.
1755            my $last_zinc_id = "";
1756            my $zinc_id = "";
1757            my $done = 0;
1758            while (! $done) {
1759                # Get the next 10000 ligands. We insist that the object ID is greater than
1760                # the last ID we processed.
1761                Trace("Loading batch starting with ZINC:$zinc_id.") if T(3);
1762                my @attributeData = $fig->query_attributes('$object > ? AND $key = ? ORDER BY $object LIMIT 10000',
1763                                                           ["ZINC:$zinc_id", "zinc_name"]);
1764                Trace(scalar(@attributeData) . " attribute rows returned.") if T(3);
1765                if (! @attributeData) {
1766                    # Here there are no attributes left, so we quit the loop.
1767                    $done = 1;
1768                } else {
1769                    # Process the attribute data we've received.
1770                    for my $zinc_data (@attributeData) {
1771                        # The ZINC ID is found in the first return column, prefixed with the word ZINC.
1772                        if ($zinc_data->[0] =~ /^ZINC:(\d+)$/) {
1773                            $zinc_id = $1;
1774                            # Check for a duplicate.
1775                            if ($zinc_id eq $last_zinc_id) {
1776                                $loadLigand->Add("duplicate");
1777                            } else {
1778                                # Here it's safe to output the ligand. The ligand name is the attribute value
1779                                # (third column in the row).
1780                                $loadLigand->Put($zinc_id, $zinc_data->[2]);
1781                                # Insure we don't try to add this ID again.
1782                                $last_zinc_id = $zinc_id;
1783                            }
1784                        } else {
1785                            Trace("Invalid zinc ID \"$zinc_data->[0]\" in attribute table.") if T(0);
1786                            $loadLigand->Add("errors");
1787                        }
1788                    }
1789                }
1790            }
1791            Trace("Ligands loaded.") if T(2);
1792        }
1793      # Finish the load.      # Finish the load.
1794      my $retVal = $self->_FinishAll();      my $retVal = $self->_FinishAll();
1795      return $retVal;      return $retVal;
# Line 1875  Line 1876 
1876      return $retVal;      return $retVal;
1877  }  }
1878    
 =head3 CreatePDB  
   
 C<< $loader->CreatePDB($pdbID, $title, $type, \%pdbHash); >>  
   
 Insure that a PDB record exists for the identified PDB. If one does not exist, it will be  
 created.  
   
 =over 4  
   
 =item pdbID  
   
 ID string (usually an unqualified file name) for the desired PDB.  
   
 =item title  
   
 Title to use if the PDB must be created.  
   
 =item type  
   
 Type of PDB: C<free> or C<bound>  
   
 =item pdbHash  
   
 Hash containing the IDs of PDBs that have already been created.  
   
 =item pdbLoader  
   
 Load object for the PDB table.  
   
 =back  
   
 =cut  
   
 sub CreatePDB {  
     # Get the parameters.  
     my ($self, $pdbID, $title, $type, $pdbHash, $pdbLoader) = @_;  
     $pdbLoader->Add("PDB check");  
     # Check to see if this is a new PDB.  
     if (! exists $pdbHash->{$pdbID}) {  
         # It is, so we create it.  
         $pdbLoader->Put($pdbID, $title, $type);  
         $pdbHash->{$pdbID} = 1;  
         # Count it.  
         $pdbLoader->Add("PDB-$type");  
     }  
 }  
   
1879  =head3 TableLoader  =head3 TableLoader
1880    
1881  Create an ERDBLoad object for the specified table. The object is also added to  Create an ERDBLoad object for the specified table. The object is also added to
# Line 2024  Line 1978 
1978      # Return the load statistics.      # Return the load statistics.
1979      return $retVal;      return $retVal;
1980  }  }
1981    
1982  =head3 GetGenomeAttributes  =head3 GetGenomeAttributes
1983    
1984  C<< my $aHashRef = GetGenomeAttributes($fig, $genomeID, \@fids); >>  C<< my $aHashRef = GetGenomeAttributes($fig, $genomeID, \@fids); >>
1985    
1986  Return a hash of attributes keyed on feature ID. This method gets all the attributes  Return a hash of attributes keyed on feature ID. This method gets all the NMPDR-related
1987  for all the features of a genome in a single call, then organizes them into a hash.  attributes for all the features of a genome in a single call, then organizes them into
1988    a hash.
1989    
1990  =over 4  =over 4
1991    
# Line 2060  Line 2016 
2016      my ($fig, $genomeID, $fids) = @_;      my ($fig, $genomeID, $fids) = @_;
2017      # Declare the return variable.      # Declare the return variable.
2018      my $retVal = {};      my $retVal = {};
2019        # Get a list of the attributes we care about.
2020        my @propKeys = $fig->get_group_keys("NMPDR");
2021      # Get the attributes.      # Get the attributes.
2022      my @aList = $fig->get_attributes("fig|$genomeID%");      my @aList = $fig->get_attributes("fig|$genomeID%", \@propKeys);
2023      # Initialize the hash. This not only enables us to easily determine which FIDs to      # Initialize the hash. This not only enables us to easily determine which FIDs to
2024      # keep, it insures that the caller sees a list reference for every known fid,      # keep, it insures that the caller sees a list reference for every known fid,
2025      # simplifying the logic.      # simplifying the logic.

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