Feb 16 2024
[ Chemical Search | Molecular Editor | convert to 3D | Grid View | Convert Chemical | convert to 3D and preserve | Add Property Column | Extract Ligand | Druglikeness | Chemical Monitor | SMILES | APF Model | Chemical Rotate | Remove salt | Fingerprints | Distance to Ring | H-bond acceptors ]Frequently asked questions regarding small molecules, ICM-Chemistry tools and MolCart
You can search MolCart or Chemical Tables using the ICM Chemical Search Window. This window can be displayed by going to:
Use the molecule editor
or look for the ICM molecular editor button at the top of the graphical user interface.
To change the layout of a chemical table (eg converting a table to grid view).
To do this:
To read a chemical table into ICM:
To add a chemical property to the table.
You can extract a ligand from an ICM object or PDB file by:
When building a molecule in the ICM Molecular Editor (Tools/Chemistry) properties such as druglikeness are calculated on the fly. The properties can also be added by inserting a column into a chemical table (right click on column header/ insert column/ Function = Chemical). These values should be used as a guide and druglikeness is a prediction based on drug-like properties. A druglikeness value less than zero indicates that the compound may have some non-drug-like properties.
If you do not see the chemical monitor in the ICM Molecule Editor - Go to:
See Convert Smiles to 2D section.
_setAPFparams is in the distribution since 3.6-0;
icm _apf3Dqsar train=trainingSet.sdf activity=LogIC50 table=testSet.sdf
Training and test set compounds should be all pre-aligned, for example by aligning training set actives using APF multiple chemical alignment, and then superimposing the test compounds onto aligned actives using APF superposition. Any external alignment method can be used as well. The field containing activity data in the training set SDF is specified by activity= argument.
The script also can take alignments in icm multiple object format *.ob, in which case SDFs are only used for input/output of activity data and can be just 2D:
icm _apf3Dqsar train=trainingSet.sdf align=trainingSet3Daligned.ob activity=LogIC50 predict=testSet3Daligned.ob table=testSet.sdf
The results are written to testSet_predict.sdf output file. Some statistics is reported along the way. If testSet.sdf contains activity (i.e. LogIC50) column like the training set, RMSD and R2 will be reported as well.
See this description in the command line manual:
You can do this in the menu option Chemistry/Standardize and check the remove salt option.
To export our default binary fingerprints the Descriptor function can be used as below:
It will return array of binary 0/1 strings of length 1536.
If you need to just measure the distance from the center of the ring to the atom it can be done lile this:
ring atoms are selected into as_graph and the distance is measured from the center of the mass to atom 'c3'
Distance( Matrix( Mean(Xyz(as_graph ) ) ) Xyz( a_//c3 ) )
to visualize this you can create a dummy atom in the center of the ring
# create a single atom with coordinates in the center of the ring read mol Chemical( "C|3D:" + Sum(Sarray( Mean(Xyz(as_graph )))",") ) name="cent_ring" # display it display xstick a_cent_ring.m # display distance make distance append refresh a_cent_ring.m/1/c1 a_//c3 display
The number of hydrogen bond acceptors is calculated as a sum of number of lone pairs on the following atoms:
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