Create Molecule Table
There are several ways to go about creating a library of molecules in a Molecule Table.
- Molecules with 3D coordinates in the format SDF or Mol2 can be imported
directly to a Molecule Table. SDF and Mol2 are both plain text formats, and
you can have several molecules one after the other in a Mol2 or SDF file.
Each molecule will get its own row in a Molecule Table. One Mol2/SDF file
will turn into one Molecule Table (Using Import Molecules with 3D Coordinates).
- Molecules with 2D coordinates in the format SDF or Mol2 (the z-coordinate
set to zero for all atoms) can be imported directly to a Molecule Table. SDF
and Mol2 are both plain text formats, and you can have several molecules one
after the other in a Mol2 or SDF file. Each molecule will get its own row in
a Molecule Table (Using the Import Molecules from SMILES or 2D option).
- Molecules given in SMILES notation can be imported directly to a Molecule
Table. Several SMILES can be listed in the same .smi file, one SMILES string
per line. If the SMILES string is followed by a text string, this will be
used as the name of the molecule on import. Each molecule will get its own
row in a Molecule Table (Using the Import Molecules from SMILES or 2D option).
Example of how a .smi file with eight molecules from the ZINC database could look:
Cc1ccc(o1)C(F)(F)F ZINC15442277
Cc1[nH]c(cn1)C(F)(F)F ZINC31176470
Cc1c[nH]nc1C(F)(F)F ZINC00066375
c1cnn(c1)CC(F)(F)F ZINC12396097
C1CN[C@H](C1(F)F)C(=O)[O-] ZINC36458630
COC(=O)C(C(=O)OC)F ZINC00158096
c1cc2c(c(c1)F)c(=O)c2=O ZINC00367517
[C@H]([C@@H](C(=O)N)F)(C(=O)[O-])[NH3+] ZINC01568479
- If you have molecules in a Molecule Project that you would like to have in a
Molecule Table, use the Extract Ligands tool from the Toolbox (Extract ligands).
- If you have a Molecule Table that you would like to extend with extra
molecules:
- The molecules should be found in a Molecule Table or Molecule Project.
- Select the molecules in the Molecule Table or Molecule Project in which they currently are found.
- Use the right-click context menu (or Ctrl-C) to copy the molecules.
- Go to the Molecule Table you would like to extend, and select any row.
- Use the right-click context menu (or Ctrl-V) to paste the molecules to the table.
- If you are building a molecule library from molecules copy-pasted from a 2D
sketcher:
- Paste the molecules to a Molecule Project as usual (Copy-paste of SMILES strings).
- Inspect the molecules in 3D and make corrections to them if necessary.
- When you have pasted all the molecules you wish to have in a Molecule Table, use the Extract Ligands tool to transfer them to a table (Extract ligands).
- If you wish to add them to another table, you can select all rows in the extracted Molecule Table (Ctrl-A), and copy-paste them into another Molecule Table, as described above.