“A command-line interface (CLI) is a mechanism for interacting with a computer
operating system or software by typing commands to perform specific tasks.
Command-line tools of ChemAxon: tips and tricks
György Pirok
Solutions for Cheminformatics
Command-line interface “A command-line interface (CLI) is a mechanism for interacting with a computer operating system or software by typing commands to perform specific tasks.” (Wikipedia)
msketch The msketch tool starts MarvinSketch applications opening a selected molecule of the file specified as input parameter.
mview caffeine.mol
msketch caffeine.mol
mview The mview tool starts MarvinView application opening the file specified as input parameter.
mview caffeine.mol
mview dsstox.sdf
mview The layout of molecules in mview can be customized by command line parameters. The example below forces to open and SDfile in a matrix view. mview dsstox.sdf --gridbag
It is possible to display only a part of a large file. mview nci.smiles –s 15000 –n 400
The number of displayed columns and rows can be set as parameters as well. mview nci.smiles –c 10 –r 10
These settings are particularly useful when molecules are piped into mview for display as it will be shown later.
molconvert The molconvert script can be used to convert a structure file to an other format. molconvert mrv caffeine.mol –o caffeine.mrv
Merge the molecules of the Molfiles in the current directory to a single SMILES file. The structures are aromatized and explicit hydrogens are removed. molconvert smiles:a-H *.mol –o output.smiles
Merge the SMILES files in the current directory to a single SDfile. The structures are dearomatized, and 2D atom coordinates are calculated. molconvert -2 sdf:-a *.smiles –o output.sdf
molconvert, convert2image Generate jpeg image in 100x150 resolution having yellow background. Many options are available to customize the generated molecule image. molconvert jpeg caffeine.mol –o caffeine.jpg
Batch image generation is possible with the convert2image script that creates a series of numbered images. The script is downloadable from the ChemAxon forum. convert2image "jpeg:w300,h300,mono" molecules.sdf
cxcalc The cxcalc command-line application provides access to plugin functions. The first example below shows general help and lists all available calculations, the second displays calculation specific help. cxcalc -h cxcalc logD -h
Calculated values of a molecule file are usually printed in the form of an indexed table, but the index and table headers can be turned off. cxcalc pKa in.mrv cxcalc -N ih logP in.sdf
cxcalc Enumerate random members of a Markush library. cxcalc -N ih randomMarkushEnumerations -m 50 markush.mrv
Calculate the lowest energy conformer of each molecule of a large file in batch mode and display the results in MarvinView during the calculation. cxcalc lowestEnergyConformer in.smiles | mview --gridbag -
Determine the IUPAC names of the molecules and store them as SDfile fields. cxcalc -S -t NAME -o out.sdf name in.smiles
evaluate The evaluate script provides a command line interface for complex calculations via the Chemical Terms language of ChemAxon. More than a hundred functions can be combined to examine chemical compounds. Determine the number of non-heteroaromatic rings. evaluate –e 'ringCount() – heteroaromaticRingCount()' in.mrv
Calculate an indicator for scaffold hopping. evaluate –e 'dissimilarity("ChemicalFingerprint", actives) - dissimilarity("PharmacophoreFingerprint", actives) > 0.5' in.mrv
Calculate Lipinski's oral drug-likeness flag for each molecule. evaluate –e '(mass() 2' nci.smiles
Find molecules containing carboxyl group having a given pKa value. jcsearch -e "pka('acidic',hm(1)) > 4" -q "[H][O:1]C=[O:2]" nci25k.smiles
standardize Standardizer converts molecules by a list of actions and is usually used as a molecule canonicalization engine integrated with databases. However, the standardize command-line tool provides and easy to use batch conversion interface for files. Merge aromatized molecules of multiple files into a single SMILES file. standardize *.sdf *.mrv -c 'aromatize' –o output.smiles
Remove small components (counterions) and neutralize the remaining molecules. Actions can be listed by two periods as separator. standardize in.mrv -c 'keepone..neutralize' –f mrv –o out.mrv
Convert all nitro groups to the ionic form. standardize in.sdf -c '[O:3]=[N:1]=[O:2]>>[O-:3][N+:1]=[O:2]'
standardize Map reactions by an MCS-based mapping algorithm. standardize in.smiles -c 'mapreaction' –o out.smiles
Convert alias atoms to abbreviated groups by the alias labels and ungroup them after. standardize in.sdf -c 'aliastogroup..sgroups:expand' –f sdf –o out.sdf
Canonicalize molecules acconding to a list of actions specified in an XML configuration file. standardize in.mrv -c config.xml –f sdf –o out.sdf
Retrieve core ring systems using two transforms and pipe the results to MarvinView for display. standardize in.smiles -c '[*R0:1]>>..[*:1]!@[*:2]>>[*:2].[*:1]' | mview -
react Generate reaction products from reactants using virtual reactions with the react program can be used to convert a structure file format to another. Reaction is specified as the –r option. $ react -r '[H:2][C:1]=[O:3]>>[H:2][C:1][O:3][H:4]' "O=Cc1ccccc1" OCc1ccccc1
IUPAC and traditional names are handled by ChemAxon tools as a native format providing outstanding usability for chemists. react –r esterification.smarts '2-hydroxybenzoicacid' 'acetic acid' aspirin
Combinatorial libraries can be produced by multimolecular reactions using the reactants from files. react –m comb –r acyl.rxn alcohols.sdf acidhalides.smiles -o esters.smiles
Summary Command-line interfaces are high performance applications and are available for all ChemAxon products. Only few could be mentioned here. They serve as easy to use tools for those who work with structure files and they shine the most when used in batch mode.
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