In ICM, a pipe (|) is a way to efficiently send the output of one command or program directly as input to another command or program without creating an intermediate file. All the available scripts for piping tables are in the $ICMHOME/molpipe directory.

Setting up your ICM Environment

In ICM scripting, setshell is a command used to execute shell commands within an ICM session. It allows you to interact with the operating system’s command-line environment (e.g., Bash on Linux/macOS) from within an ICM script.

Use 'setshell' to set the path to your version of ICM:

./setshell /usr/local/icm/icm64

or set a PATH to $ICMHOME/molpipe

Available Scripts

Read (from SDF,SMILES,MOLT,MOLCART)

molrdsdf.icm
molrdsmi.icm
molrdmolt.icm
molrdmolcart.icm

Write/Convert (SDF,SMILES,MOLT,ICB)

mol2sdf.icm
mol2smi.icm
mol2molt.icm
mol2icb.icm

Misc

molcount.icm : counts number of molecules in the input
molhead.icm : show first top number of molecules
molgrep.icm : grep by substructure
molmkindex.icm : generate ICM index file from the pipe

Filter/Properties

molcharge.icm : set formal charges
molfilter.icm : filter by properties
molcalcprop.icm : calculate properties
molenantiomers.icm : generate enantiomers
molstandard.icm : removes salt/applies 2D depiction/removed explicit hydrogen/normalize chemical group drawing

Unique/Centers

moluniq.icm : generates non-redundant subset from the input file
molcluster.icm : selects centers from the input pipe

Compare

molcompare.icm : compare two SD files

View the result in GUI

molview.icm

Examples

molcount.icm myfile.sdf  #  counts the number of chemical
cat myfile.sdf | molcount.icm   # the same but reads the input from file

molgrep.icm c1cccnc1 t.sdf | molhead.icm   # view first hits
molgrep.icm c1cccnc1 t.sdf | molcount.icm   # count matches
molgrep.icm c1cccnc1 t.sdf | molcharge.icm -proc=3 | molto3d.icm -proc=3 | mol2sdf.icm > t_hits_3d.sdf

# calculate number of racemic centers and enumerate enantiomers
molrdsdf.icm input.sdf | molcalcprop.icm "Icm::Nof(mol,chiral,3)[1]" nof_rac | molenantiomers.icm | molview.icm

# create 3D conformers and create index from the result (confgen.sh is just a wrapper around _confGen script )
confgen.sh out.sdf - | molmkindex.icm confout   # will create confout.sdf and confout.inx

# Lipinksi filter
# read SDF, apply Lipinski filter and convert output to smiles

molrsdf.icm file.sdf | molfilter.icm "MolWeight(mol)<=500 & MolLogP(mol)<=5 & Nof_HBD(mol) <= 5 & Nof_HBA(mol)<=10" | mol2smi.icm