Difference between revisions of "XYZ (format)"
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although no formal specification has been published. Consequently, | although no formal specification has been published. Consequently, | ||
Open Babel attempts to be extremely flexible in parsing XYZ | Open Babel attempts to be extremely flexible in parsing XYZ | ||
| − | format files. Similar formats include [[Tinker | + | format files. Similar formats include [[Tinker XYZ]] and [[UniChem XYZ]] which differ |
| − | XYZ]] and [[UniChem XYZ]] which differ | + | |
slightly in the format of the files. (Notably, [[UniChem XYZ]] uses the | slightly in the format of the files. (Notably, [[UniChem XYZ]] uses the | ||
atomic number rather than element symbol for the first column.) | atomic number rather than element symbol for the first column.) | ||
Revision as of 12:18, 6 January 2006
| Filename Extensions | xyz |
|---|---|
| Chemical MIME Type | chemical/x-xyz |
| Specification URL | None |
| Import | {{{import}}} |
| Export | {{{export}}} |
| Open Babel Version | {{{version}}} |
Options
Read Options e.g. -as
s Output single bonds only
b Disable bonding entirely
Additional Comments
Input Format
The "XYZ" chemical file format is widely supported by many programs, although no formal specification has been published. Consequently, Open Babel attempts to be extremely flexible in parsing XYZ format files. Similar formats include Tinker XYZ and UniChem XYZ which differ slightly in the format of the files. (Notably, UniChem XYZ uses the atomic number rather than element symbol for the first column.)
Line one of the file contains the number of atoms in the file.
Line two of the file contains a title, comment, or filename.
Any remaining lines are parsed for atom information. Lines start with the element symbol, followed by X, Y, and Z coordinates in angstroms separated by whitespace.
Multiple molecules / frames can be contained within one file.
Output Format
The first line written is the number of atoms in the molecule. Line two is the title of the molecule or the filename if no title is defined. Remaining lines define the atoms in the file. The first column is the atomic symbol (right-aligned on the third character), followed by the XYZ coordinates in "10.5" format, in angstroms. This means that all coordinates are printed with five decimal places.
Example File
12 benzene example C 0.00000 1.40272 0.00000 H 0.00000 2.49029 0.00000 C -1.21479 0.70136 0.00000 H -2.15666 1.24515 0.00000 C -1.21479 -0.70136 0.00000 H -2.15666 -1.24515 0.00000 C 0.00000 -1.40272 0.00000 H 0.00000 -2.49029 0.00000 C 1.21479 -0.70136 0.00000 H 2.15666 -1.24515 0.00000 C 1.21479 0.70136 0.00000 H 2.15666 1.24515 0.00000
