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: 1) sdf2xyz; 2) xyz2sdf; sdf2xyz2sdf depends on OpenBabel for MMFF atom type and charge assignment. Since input to sdf2xyz is entered through standard input, and output from xyz2sdf is printed on standard output, it is possible to pipe output from OpenBabel into sdf2xyz, or to pipe xyz2sdf 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.
sdf2xyz2sdf
TOSCO, Paolo
2010-01-01
Abstract
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: 1) sdf2xyz; 2) xyz2sdf; sdf2xyz2sdf depends on OpenBabel for MMFF atom type and charge assignment. Since input to sdf2xyz is entered through standard input, and output from xyz2sdf is printed on standard output, it is possible to pipe output from OpenBabel into sdf2xyz, or to pipe xyz2sdf 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.
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