SchemaSpy Analysis of scope - Columns | Generated by SchemaSpy |
Generated by SchemaSpy on Wed Oct 09 10:41 PDT 2013 |
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scop contains 265 columns - click on heading to sort:
Table | Column | Type | Size | Nulls | Auto | Default | Comments |
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aerospaci | aerospaci | double | 22 | √ | null | ASTRAL AEROSPACI score; same as SPACI for versions where not used | |
aerospaci | effective_r_factor | double | 22 | effective R factor | |||
aerospaci | effective_resolution | double | 22 | effective resolution in angstroms | |||
aerospaci | id | int unsigned | 10 | √ | |||
aerospaci | method_summary | text | 65535 | ||||
aerospaci | pdb_entry_id | int unsigned | 10 | ||||
aerospaci | procheck1 | tinyint unsigned | 3 | √ | null | Morris Ramachandran class from PROCHECK | |
aerospaci | procheck2 | tinyint unsigned | 3 | √ | null | Morris Chi-1 class from PROCHECK | |
aerospaci | procheck3 | tinyint unsigned | 3 | √ | null | Morris H-bond class from PROCHECK | |
aerospaci | r_factor | double | 22 | √ | null | R factor, or null if not known or not applicable | |
aerospaci | release_id | int unsigned | 10 | SCOP release for which these scores were used | |||
aerospaci | resolution | double | 22 | √ | null | resolution in angstroms, or null if not known or not applicable | |
aerospaci | spaci | double | 22 | ASTRAL SPACI score | |||
aerospaci | summary_procheck | double | 22 | summary PROCHECK score | |||
aerospaci | summary_whatcheck | double | 22 | summary WHAT_CHECK score | |||
aerospaci | whatcheck1 | double | 22 | √ | null | Packing score from WHAT_CHECK | |
aerospaci | whatcheck2 | double | 22 | √ | null | Ramachandran score from WHAT_CHECK | |
aerospaci | whatcheck3 | double | 22 | √ | null | Chi angles score from WHAT_CHECK | |
aerospaci | whatcheck4 | double | 22 | √ | null | Backbone score from WHAT_CHECK | |
astral_chain | id | int unsigned | 10 | √ | |||
astral_chain | raf_id | int unsigned | 10 | ||||
astral_chain | seq_id | int unsigned | 10 | ||||
astral_chain | sid | varchar | 5 | e.g., 1jmcA | |||
astral_chain | source_id | int unsigned | 10 | ||||
astral_chain_link_domain | chain_id | int unsigned | 10 | ||||
astral_chain_link_domain | domain_id | int unsigned | 10 | ||||
astral_chain_subset_id | astral_chain_id | int unsigned | 10 | ||||
astral_chain_subset_id | pct_identical | int unsigned | 10 | ||||
astral_chain_subset_id | release_id | int unsigned | 10 | ||||
astral_domain | header | text | 65535 | FASTA header excluding sid | |||
astral_domain | id | int unsigned | 10 | √ | |||
astral_domain | node_id | int unsigned | 10 | ||||
astral_domain | seq_id | int unsigned | 10 | ||||
astral_domain | sid | varchar | 8 | e.g., d1dlwa_ or e1o7d.1B | |||
astral_domain | source_id | int unsigned | 10 | ||||
astral_domain | style_id | int unsigned | 10 | ||||
astral_domain_subset_blast_e | astral_domain_id | int unsigned | 10 | ||||
astral_domain_subset_blast_e | blast_log10_e | double | 22 | ||||
astral_domain_subset_blast_e | release_id | int unsigned | 10 | ||||
astral_domain_subset_blast_e | style_id | int unsigned | 10 | ||||
astral_domain_subset_id | astral_domain_id | int unsigned | 10 | ||||
astral_domain_subset_id | pct_identical | int unsigned | 10 | ||||
astral_domain_subset_id | release_id | int unsigned | 10 | ||||
astral_domain_subset_id | style_id | int unsigned | 10 | ||||
astral_seq | id | int unsigned | 10 | √ | |||
astral_seq | is_reject | tinyint unsigned | 3 | due to length or number of Xs | |||
astral_seq | seq | text | 65535 | lower case, except for X separating genetic domain | |||
astral_seq_blast | blast_log10_e | double | 22 | log10 of the BLAST E-value, or -9999 for E-value of 0 | |||
astral_seq_blast | id | int unsigned | 10 | √ | |||
astral_seq_blast | pct_identical | double unsigned | 22 | as reported by seqcmp, 0-100 | |||
astral_seq_blast | release_id | int unsigned | 10 | √ | null | ||
astral_seq_blast | seq1_id | int unsigned | 10 | ||||
astral_seq_blast | seq1_length | int unsigned | 10 | length of local alignment, including gaps | |||
astral_seq_blast | seq1_start | int unsigned | 10 | 0-indexed start of hit | |||
astral_seq_blast | seq2_id | int unsigned | 10 | ||||
astral_seq_blast | seq2_length | int unsigned | 10 | length of local alignment, including gaps | |||
astral_seq_blast | seq2_start | int unsigned | 10 | 0-indexed start of hit | |||
astral_seq_blast | source_id | int unsigned | 10 | ||||
astral_seq_blast | style1_id | int unsigned | 10 | ||||
astral_seq_blast | style2_id | int unsigned | 10 | ||||
astral_seq_blast_gap | gap_length | int unsigned | 10 | length of gap | |||
astral_seq_blast_gap | gap_start | int unsigned | 10 | 0-indexed start of gap | |||
astral_seq_blast_gap | hit_id | int unsigned | 10 | ||||
astral_seq_blast_gap | id | int unsigned | 10 | √ | |||
astral_seq_hmm_pfam | hmm_length | int unsigned | 10 | length of hit in HMM | |||
astral_seq_hmm_pfam | hmm_start | int unsigned | 10 | start of hit in HMM, 0-indexed | |||
astral_seq_hmm_pfam | id | int unsigned | 10 | √ | |||
astral_seq_hmm_pfam | length | int unsigned | 10 | length of hit in ASTRAL sequence | |||
astral_seq_hmm_pfam | log10_e | double | 22 | log10 of E-value reported by hmmer, or -999 for E=0 | |||
astral_seq_hmm_pfam | pfam_id | int unsigned | 10 | ||||
astral_seq_hmm_pfam | score | double | 22 | raw score of hit reported by hmmer | |||
astral_seq_hmm_pfam | seq_id | int unsigned | 10 | ||||
astral_seq_hmm_pfam | start | int unsigned | 10 | start of hit in ASTRAL sequence, 0-indexed | |||
astral_seq_hmm_pfam_gap | gap_length | int unsigned | 10 | length of gap | |||
astral_seq_hmm_pfam_gap | gap_start | int unsigned | 10 | 0-indexed start of gap | |||
astral_seq_hmm_pfam_gap | hit_id | int unsigned | 10 | ||||
astral_seq_hmm_pfam_gap | id | int unsigned | 10 | √ | |||
astral_seq_source | description | text | 65535 | ||||
astral_seq_source | id | int unsigned | 10 | √ | |||
astral_seq_style | description | text | 65535 | ||||
astral_seq_style | id | int unsigned | 10 | √ | |||
hmmer_release | id | int unsigned | 10 | √ | |||
hmmer_release | version | text | 65535 | ||||
link_pdb | node_id | int unsigned | 10 | ||||
link_pdb | pdb_chain_id | int unsigned | 10 | ||||
link_pfam | node_id | int unsigned | 10 | ||||
link_pfam | pfam_accession | varchar | 8 | ||||
link_species | node_id | int unsigned | 10 | ||||
link_species | species_id | int unsigned | 10 | ||||
link_uniprot | node_id | int unsigned | 10 | ||||
link_uniprot | uniprot_accession | varchar | 6 | ||||
pdb_author | alias_for | int unsigned | 10 | √ | null | ||
pdb_author | id | int unsigned | 10 | √ | |||
pdb_author | name | text | 65535 | full name | |||
pdb_chain | chain | varchar | 1 | case sensitive | |||
pdb_chain | id | int unsigned | 10 | √ | |||
pdb_chain | is_polypeptide | tinyint unsigned | 3 | 0=no, 1=yes | |||
pdb_chain | pdb_release_id | int unsigned | 10 | ||||
pdb_chain_compound | pdb_chain_id | int unsigned | 10 | ||||
pdb_chain_compound | pdb_compound_id | int unsigned | 10 | ||||
pdb_chain_gene | pdb_chain_id | int unsigned | 10 | ||||
pdb_chain_gene | pdb_gene_id | int unsigned | 10 | ||||
pdb_chain_source | pdb_chain_id | int unsigned | 10 | ||||
pdb_chain_source | pdb_source_id | int unsigned | 10 | ||||
pdb_compound | description | text | 65535 | √ | null | ||
pdb_compound | id | int unsigned | 10 | √ | |||
pdb_entry | code | varchar | 4 | 4-letter code e.g., 1jmc | |||
pdb_entry | deposition_date | date | 10 | date structure was deposited, from HEADER line | |||
pdb_entry | description | text | 65535 | from TITLE | |||
pdb_entry | id | int unsigned | 10 | √ | |||
pdb_entry | is_literature_reference | tinyint unsigned | 3 | 0=real PDB, 1=SCOP-only | |||
pdb_entry | obsolete_date | date | 10 | √ | null | date obsoleted or withdrawn by PDB; null if still active | |
pdb_entry | obsoleted_by | int unsigned | 10 | √ | null | non-null if obsoleted by another structure | |
pdb_entry | release_date | date | 10 | date structure was first released by PDB, from REVDAT 1 line | |||
pdb_gene | gene_name | text | 65535 | √ | null | ||
pdb_gene | id | int unsigned | 10 | √ | |||
pdb_headers | class | text | 65535 | ||||
pdb_headers | id | int unsigned | 10 | √ | |||
pdb_headers | keywords | text | 65535 | ||||
pdb_headers | pdb_release_id | int unsigned | 10 | ||||
pdb_headers | title | text | 65535 | ||||
pdb_heterogen | description | text | 65535 | √ | null | ||
pdb_heterogen | id | int unsigned | 10 | √ | |||
pdb_local | is_raf_calculated | tinyint unsigned | 3 | 0=no, 1=yes | |||
pdb_local | pdb_path | text | 65535 | √ | null | absolute path to file | |
pdb_local | pdb_release_id | int unsigned | 10 | ||||
pdb_local | snapshot_date | date | 10 | snapshot containing the PDB file for this release | |||
pdb_local | xml_path | text | 65535 | √ | null | absolute path to xml | |
pdb_method | description | text | 65535 | full EXPDTA record | |||
pdb_method | id | int unsigned | 10 | √ | |||
pdb_method | is_theory | tinyint unsigned | 3 | 0=no, 1=yes | |||
pdb_method | is_xray | tinyint unsigned | 3 | 0=no, 1=yes | |||
pdb_method | summary | text | 65535 | summary of method, e.g. XRAY | |||
pdb_model | pdb_entry_id | int unsigned | 10 | ||||
pdb_release | file_date | date | 10 | √ | null | PDB datestamp on file (if known), to track silent updates by PDB | |
pdb_release | has_valid_procheck | tinyint unsigned | 3 | 0=no, 1=yes | |||
pdb_release | has_valid_whatcheck | tinyint unsigned | 3 | 0=no, 1=yes | |||
pdb_release | id | int unsigned | 10 | √ | |||
pdb_release | method_id | int unsigned | 10 | √ | null | experimental method listed in EXPDTA record, or null if not available | |
pdb_release | pdb_entry_id | int unsigned | 10 | ||||
pdb_release | procheck1 | tinyint unsigned | 3 | √ | null | Morris Ramachandran class from PROCHECK | |
pdb_release | procheck2 | tinyint unsigned | 3 | √ | null | Morris Chi-1 class from PROCHECK | |
pdb_release | procheck3 | tinyint unsigned | 3 | √ | null | Morris H-bond class from PROCHECK | |
pdb_release | r_factor | double | 22 | √ | null | R factor, or null if not known or not applicable | |
pdb_release | replaced_by | int unsigned | 10 | √ | null | non-null if replaced by a later version | |
pdb_release | resolution | double | 22 | √ | null | resolution in angstroms, or null if not known or not applicable | |
pdb_release | revision_date | date | 10 | date this version was released, from REVDAT line | |||
pdb_release | spaci | double | 22 | √ | null | ASTRAL SPACI score, or null if not calculated | |
pdb_release | whatcheck1 | double | 22 | √ | null | Packing score from WHAT_CHECK | |
pdb_release | whatcheck2 | double | 22 | √ | null | Ramachandran score from WHAT_CHECK | |
pdb_release | whatcheck3 | double | 22 | √ | null | Chi angles score from WHAT_CHECK | |
pdb_release | whatcheck4 | double | 22 | √ | null | Backbone score from WHAT_CHECK | |
pdb_release_author | id | int unsigned | 10 | √ | |||
pdb_release_author | pdb_author_id | int unsigned | 10 | ||||
pdb_release_author | pdb_release_id | int unsigned | 10 | ||||
pdb_release_heterogen | pdb_heterogen_id | int unsigned | 10 | ||||
pdb_release_heterogen | pdb_release_id | int unsigned | 10 | ||||
pdb_source | common_name | text | 65535 | √ | null | ||
pdb_source | id | int unsigned | 10 | √ | |||
pdb_source | is_synthetic | tinyint unsigned | 3 | ||||
pdb_source | ncbi_taxid | text | 65535 | √ | null | ||
pdb_source | scientific_name | text | 65535 | ||||
pdb_source | strain_name | text | 65535 | √ | null | ||
pdb_source_species | pdb_source_id | int unsigned | 10 | ||||
pdb_source_species | species_id | int unsigned | 10 | ||||
pfam | accession | text | 65535 | ||||
pfam | description | text | 65535 | ||||
pfam | id | int unsigned | 10 | √ | |||
pfam | length | int unsigned | 10 | length of model | |||
pfam | name | text | 65535 | ||||
pfam | pfam_type_id | int unsigned | 10 | √ | null | ||
pfam | release_id | int unsigned | 10 | ||||
pfam | trusted_cutoff | double | 22 | ||||
pfam_equiv | new_pfam_id | int unsigned | 10 | ||||
pfam_equiv | old_pfam_id | int unsigned | 10 | ||||
pfam_local | pfama_global_hmm_file | text | 65535 | ||||
pfam_local | release_id | int unsigned | 10 | ||||
pfam_release | hmmer_release_id | int unsigned | 10 | √ | null | ||
pfam_release | id | int unsigned | 10 | √ | |||
pfam_release | release_date | date | 10 | ||||
pfam_release | version | text | 65535 | ||||
pfam_type | description | text | 65535 | ||||
pfam_type | id | int unsigned | 10 | √ | |||
raf | first_release_id | int unsigned | 10 | √ | null | first SCOP release in which this raf was used, or null for working copy | |
raf | id | int unsigned | 10 | √ | |||
raf | last_release_id | int unsigned | 10 | √ | null | last SCOP release in which this raf was used, or null for working copy | |
raf | line | text | 65535 | full line of text, including header | |||
raf | pdb_chain_id | int unsigned | 10 | ||||
raf | raf_version_id | int unsigned | 10 | ||||
raf_version | header_length | int unsigned | 10 | ||||
raf_version | id | int unsigned | 10 | √ | |||
raf_version | version | text | 65535 | √ | null | e.g., 0.02 | |
scop_comment | description | text | 65535 | the comment | |||
scop_comment | id | int unsigned | 10 | √ | |||
scop_comment | is_autogenerated | tinyint unsigned | 3 | autogenerated (not by Alexey)? | |||
scop_comment | node_id | int unsigned | 10 | node being commented on | |||
scop_curation_type | description | text | 65535 | ||||
scop_curation_type | id | int unsigned | 10 | √ | |||
scop_history | change_type_id | int unsigned | 10 | type of change | |||
scop_history | id | int unsigned | 10 | √ | |||
scop_history | new_node_id | int unsigned | 10 | √ | null | node it turns into, if applicable | |
scop_history | old_node_id | int unsigned | 10 | node being replaced | |||
scop_history | release_id | int unsigned | 10 | release where change occurred | |||
scop_history | time_occurred | datetime | 19 | √ | null | timestamp | |
scop_history_type | abbreviation | text | 65535 | in history.obs; e.g., mrg | |||
scop_history_type | description | text | 65535 | e.g., merge | |||
scop_history_type | id | int unsigned | 10 | √ | |||
scop_index | long_term | text | 65535 | ||||
scop_index | node_id | int unsigned | 10 | ||||
scop_index | short_term | text | 65535 | ||||
scop_level | abbreviation | text | 65535 | abbreviation to use in parseable files | |||
scop_level | description | text | 65535 | long description, e.g., Class | |||
scop_level | id | int unsigned | 10 | √ | |||
scop_level | is_autoexpanded | tinyint unsigned | 3 | Automatically expand this level in browser? | |||
scop_level | is_hidden | tinyint unsigned | 3 | Show this level in browser? | |||
scop_level | master_abbreviation | text | 65535 | abbreviation used in the master file | |||
scop_level | plural | text | 65535 | plural description, e.g., Classes | |||
scop_node | curation_type_id | int unsigned | 10 | √ | null | ||
scop_node | description | text | 65535 | ||||
scop_node | id | int unsigned | 10 | √ | |||
scop_node | level_id | int unsigned | 10 | SCOP level | |||
scop_node | parent_node_id | int unsigned | 10 | √ | null | null if no parent | |
scop_node | release_id | int unsigned | 10 | √ | null | release in which this node appears, or null for working copy | |
scop_node | sccs | text | 65535 | SCOP concise classification string, e.g., a.1.1.1 | |||
scop_node | sid | text | 65535 | √ | null | SCOP domain identifier, e.g., d1dlwa_ (null if not domain) | |
scop_node | sunid | int | 10 | SCOP unique identifier, e.g., 14982; unique within each release | |||
scop_node_pdbstyle | file_path | text | 65535 | ||||
scop_node_pdbstyle | last_update_id | int unsigned | 10 | SCOP release in which coordinates were last updated | |||
scop_node_pdbstyle | node_id | int unsigned | 10 | ||||
scop_node_thumbnail | chain_large | int unsigned | 10 | √ | null | ||
scop_node_thumbnail | chain_small | int unsigned | 10 | √ | null | ||
scop_node_thumbnail | domain_large | int unsigned | 10 | √ | null | ||
scop_node_thumbnail | domain_small | int unsigned | 10 | √ | null | ||
scop_node_thumbnail | domain_tiny | int unsigned | 10 | √ | null | ||
scop_node_thumbnail | main | int unsigned | 10 | √ | null | default, or primary view | |
scop_node_thumbnail | node_id | int unsigned | 10 | ||||
scop_node_thumbnail | structure_large | int unsigned | 10 | √ | null | ||
scop_node_thumbnail | structure_small | int unsigned | 10 | √ | null | ||
scop_release | freeze_date | date | 10 | date PDB was frozen for classification | |||
scop_release | id | int unsigned | 10 | √ | must be in release order | ||
scop_release | is_comprehensive | tinyint unsigned | 3 | does this include ~all PDB entries prior to freeze date? | |||
scop_release | is_public | tinyint unsigned | 3 | 0=no, 1=yes | |||
scop_release | release_date | date | 10 | date this version was released | |||
scop_release | version | text | 65535 | e.g., 1.73 | |||
scop_subset_level | level_node_id | int unsigned | 10 | ||||
scop_subset_level | rep_node_id | int unsigned | 10 | ||||
species | common_name | text | 65535 | √ | null | ||
species | details | text | 65535 | √ | null | ||
species | id | int unsigned | 10 | √ | |||
species | ncbi_taxid | int unsigned | 10 | √ | null | ||
species | scientific_name | text | 65535 | ||||
thumbnail | height | int unsigned | 10 | ||||
thumbnail | id | int unsigned | 10 | √ | |||
thumbnail | image_path | text | 65535 | ||||
thumbnail | width | int unsigned | 10 | ||||
uniprot | entry_name | text | 65535 | full name | |||
uniprot | id | int unsigned | 10 | √ | |||
uniprot | is_swissprot | tinyint unsigned | 3 | ||||
uniprot | long_id | varchar | 12 | ||||
uniprot | seq_date | date | 10 | ||||
uniprot | seq_version | int unsigned | 10 | ||||
uniprot_accession | accession | varchar | 6 | ||||
uniprot_accession | uniprot_id | int unsigned | 10 | ||||
uniprot_pfam | pfam_id | int unsigned | 10 | ||||
uniprot_pfam | uniprot_id | int unsigned | 10 |