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 !

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.
Neutral Loss(es) - List of molecular formulas of neutral losses separated by semicolon (one list is used for all isomers i.e. the symbol '/' cannot be used in this column).
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)
list of neutral losses separated by semicolon (one list is used for all isomers i.e. the symbol '/' cannot be used in this column)
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")
"CHEBI: <number>" (ChEBI ID; example: "CHEBI: 4031")
"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:

Database	Content	Location
D₁₉	19 proteinogenic amino acids (20 including isobars)	20_amino_acids.txt
D₁₉ (nl)	19 proteinogenic amino acids (20 including isobars) with neutral losses	20_amino_acids_nl.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
D₂₉₁	291 NRP building blocks (525 including isobars)	db291.txt
ketide blocks	19 ketide building blocks (22 including isobars)	inhouse_siderophores_blocks.txt
custom		Download Template for Excel