CycloBranch
Building Blocks Editor

Building Blocks Editor

The editor is opened using the command "Tools -> Building Blocks Editor" from the Main Window. Use F1 to open this help.

Changes in the editor do not impact the settings of the engine until they are saved !

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Building Blocks Editor

Toolbar

New Database (CTRL + N)

Create a new database of building blocks.

Open Database (CTRL + O)

Open a database of building blocks.

Save Database (CTRL + S)

Save the database of building blocks.

Save Database As... (CTRL + D)

Save the database of building blocks with another file name.

Import Database (CTRL + I)

Import a database of building blocks.

Close (Esc)

Close window.

Insert Row (Insert)

Insert a new row at the bottom of the table.

Remove Selected Rows (Delete)

Remove checked rows.

Select All (CTRL + A)

Select all rows.

Unselect Rows (CTRL + U)

Unselect all rows.

HTML Documentation (F1)

Show HTML documentation.

Text Filter

See details here.

Columns

  • Name(s) - Name of a building block (or more blocks corresponding to isomers separated by '/').
  • Acronym(s) - Acronym of a building block (or more blocks corresponding to isomers separated by '/').
  • Residue Summary - Residue summary formula of a building block.
  • Monoisotopic Residue Mass - Monoisotopic mass corresponding to a block. The value is recalculated when the summary formula is changed.
  • Reference(s) - Reference id of a building block (or more blocks corresponding to isomers separated by '/'). See Format of Building Blocks Databases.
  • Preview - A link to a reference database (e.g., ChemSpider) generated from the fields acronym and reference. The link is generated automatically and cannot be edited manually.

The numbers of '/' must be equal in a row in the fields Name, Acronym and Reference. The names and acronyms must not contain the characters '[' or ']'.


Format of Building Block Databases

The database of building blocks is a text file (*.txt) containing a list of building blocks (one building block per line). Each line contains the following items separated by tabulars:

  • name of a block (or more blocks corresponding to isomers separated by '/')
  • acronym of a block (or more blocks corresponding to isomers separated by '/')
  • residue summary formula of a block (important: an exact mass of the block is calculated from this value)
  • mass corresponding to the block (the value is ignored; the mass is automatically calculated from the residue summary formula)
  • reference id (or more blocks corresponding to isomers separated by '/')

The numbers of '/' must be equal on a line in the fields name, acronym and reference id. The names and acronyms must not contain the characters '[' or ']'. A line starting with the hash '#' is a comment which is not processed.

Reference ids can be written in the following formats (without quotes):

  • "CSID: <number>" (ChemSpider ID; example: "CSID: 13539649")
  • "CID: <number>" (PubChem ID; example: "CID: 12439044")
  • "PDB: <pdb_code>" (PDB code; example: "PDB: UAL")
  • "<smiles> in CSID: <number>" (smiles in ChemSpider ID; example: "C(C(CN)NC(C)=O)(=O)O in CSID: 8570696")
  • "<smiles> in CID: <number>" (smiles in PubChem ID; example: "C1=C(C(=CC2=C1N3C(C(=C2)N)NC(CC3)C(O)=O)O)O in CID: 5289234")
  • "<smiles> in: <norine_id>" (smiles in Norine; example: "C1=C(C(=CC2=C1N3C(C(N)C2)NCCC3C(O)=O)O)O in: NOR00903")

Format of Ketide Building Blocks

The identification of linear and cyclic polyketides requires an additional annotation of building blocks. A name of a building block eliminating 2 hydrogens instead of the water molecule must start with the string "(-2H) " without quotes. Corresponding residue summary formulas must be entered in the column "Residue Summary" (i.e., 2 hydrogens or the water molecule must be deducted manually).


List of Available Building Block Databases

The following pre-defined databases of building blocks are available in "BrickDatabases" folder:

DatabaseContentLocation
D1919 proteinogenic amino acids (20 including isobars)20_amino_acids.txt
D33 (v1)33 NRP building blocks (42 including isobars)db33_v1.txt
D33 (v2)33 NRP building blocks (132 including isobars)db33_v2.txt
D287 (v1)287 NRP building blocks (412 including isobars)db287_v1.txt
D287 (v2)287 NRP building blocks (521 including isobars)db287_v2.txt
D287 (v3)287 NRP building blocks (523 including isobars)db287_v3.txt
D291291 NRP building blocks (525 including isobars)db291.txt
ketide blocks19 ketide building blocks (22 including isobars)inhouse_siderophores_blocks.txt
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