Collections:
"babel -... --..." Command - Generic Conversion Options
What are generic conversion options that I can use on "babel" commands for all input and output formats?
✍: FYIcenter.com
"babel" commands supports a number of generic conversion options that applies all input and output formats as listed below:
--addtotitle Append text to the current molecule title --addformula Append the molecular formula after the current molecule title -b Convert dative bonds: e.g., [N+]([O-])=O to N(=O)=O -c Center atomic coordinates at (0,0,0) -C Combine molecules in first file with others having the same name -e Continue after errors -d Delete Hydrogens ---errorlevel 2 Filter the level of errors and warnings displayed: 1 = critical errors only 2 = include warnings too (default) 3 = include informational messages too 4 = include "audit log" messages of changes to data 5 = include debugging messages too -f # For multiple entry input, start import with molecule # as the first entry -F Output the available fingerprint types -h Add hydrogens -H Output usage information -H format-ID Output formatting information and options for format specified -Hall Output formatting information and options for all formats -i<format-ID> Specifies input format, see below for the available formats -j --join Join all input molecules into a single output molecule entry -k Translate computational chemistry modeling keywords (e.g., GAMESS and Gaussian) -m Produce multiple output files, to allow: - Splitting one input file - put each molecule into consecutively numbered output files - Batch conversion - convert each of multiple input files into a specified output format -l # For multiple entry input, stop import with molecule # as the last entry -o format-ID Specifies output format, see below for the available formats -O outfile Specify the output file. This option applies to obabel only. -p Add Hydrogens appropriate for pH (use transforms in phmodel.txt) --property Add or replace a property (e.g., in an MDL SD file) -s SMARTS Convert only molecules matching the SMARTS pattern specified --separate Separate disconnected fragments into individual molecular records -t All input files describe a single molecule --title title Add or replace molecular title -v SMARTS Convert only molecules NOT matching SMARTS pattern specified -z Compress the output with gzip
⇒ "babel" Command Option Argument Syntax
⇐ "babel" Command - From STDIN To STDOUT
2021-07-19, 714🔥, 0💬
Popular Posts:
Molecule Summary: ID: FYI-1000174 SMILES: N#CCCC(Br)(Cc1ccccc1)Cc2 ccccc2Received at FYIcenter.com o...
Molecule Summary: ID: FYI-1001132 SMILES: C1=CC2=C(C3=C(C=CC=N3)C= C2)N=C1Received at FYIcenter.com ...
Molecule Summary: ID: FYI-1002630 Names: InChIKey: HVXLVKLIMXAAGM-SWJSCKDZS A-LSMILES: Cc4ccc3O[Fe](...
Molecule Summary: ID: FYI-1004907 Names: InChIKey: BMOVDKGKUGWFHG-UHFFFAOYS A-NSMILES: CCCc3n[nH]c4c...
How to validate and parse a Molecular Formula? To help you validating and parsing a molecular formul...