Sep 13 2018
Chemical structures can be read into ICM from MOL/MOL2, SMILES, and SDF files or you can construct your own structures by drawing them in the ICM Molecular Editor. Chemicals can also be searched and downloaded via the Search Tab using the PDB Chemical Substructure Search, search by PDB Ligand Code, or by searching DrugBank, ChEMBL, SureChEMBL or PubChem.
To read a chemical format file:
If you know the chemical smiles string for the compound you can build the 2D molecule by:
Smiles can be read from a text file into a chemical table by:
Smiles can be read directly into the ICM Molecular Editor:
Multi mol2 3D files can be read by:
Chemicals can be read directly from ChEMBL, SureCHEMBL, PubChem, and DrugBank
To extract a 2D chemical representation from a PDB file into a chemical spreadsheet.
The ability to read large SDF files (e.g. >100K chemicals) depends on the memory of your computer. A work around for this is available in ICM.
To extract the 3D coordinates of a chemical into a chemical spreadsheet e.g for 3D QSAR or after chemical superposition.
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