sdf2xyz2sdf: How to exploit TINKER power in cheminformatics projects

Research output: Non-textual formComputer programmeResearch

  • Paolo Tosco (Developer)
  • Thomas Balle (Developer)

sdf2xyz2sdf is an open-source software aimed at converting SDF files into TINKER XYZ files (and viceversa) while performing automatic assignment of MMFF94 atom types, bond types and charges.
The sdf2xyz2sdf package consists of two programs:

sdf2xyz2sdf depends on OpenBabel for MMFF atom type and charge assignment. Since input to sdf2tinkerxyz is entered through standard input, and output from tinkerxyz2sdf is printed on standard output, it is possible to pipe output from OpenBabel into sdf2tinkerxyz, or to pipe tinkerxyz2sdf output into OpenBabel, so that virtually any format conversion from/to TINKER XYZ may be accomplished.
Interestingly, also ionic heteroaromatic rings which could not be assigned proper charges by the original TINKER-MMFF code are correctly accounted for by sdf2xyz2sdf.
Original languageEnglish
Publication date2011
Publication statusPublished - 2011

Bibliographical note

Publication describing this software, CURIS id: 33803838

ID: 34403188