table of contents
| cif_p1() | cif_p1() |
NAME¶
cif_p1 - Expand atoms in CIF to the P1 space group, preserving molecules (i.e. outputting atoms that are bonded at bond distances from each other).SYNOPSIS¶
cif_p1 --options input1.cif input*.cifDESCRIPTION¶
Expand atoms in CIF to the P1 space group, preserving molecules (i.e. outputting atoms that are bonded at bond distances from each other).OPTIONS¶
--always-continue Continue processing and return successful return status even if errors are diagnosed.-c-, --always-die Stop and return error status if errors are diagnosed.
-1, --one-datablock-output Output all molecules and all alternative conformations to a single output data block.
-1-, --multiple-datablocks-output Separate each molecule and each example of an alternative conformation into a separate data block.
-c, --covalent-sensitivity Set a new covalent sensitivity value (default 0.35).
--simplify-formula Simplify chemical formula and output not the whole P1 cell but only a minimal stoichiometric set of molecules. Should have the same result as 'cif_molecule --preserve-stoichiometry'.
--dont-simplify-formula, --no-simplify-formula Do not simplify formula, output the whole P1 cell (default).
--exclude-zero-occupancies Do not use atoms with 0 occupancies in calculations (default).
--dump-atoms Dump atoms (including symmetry-equivalent) in CIF format, for inspection with some graphics program.
--dont-dump-atoms, --no-dump-atoms Do not dump atoms (default).
-i, --ignore-bumps Detect and warn about close atom "bumps" but do not stop processing.
--dont-ignore-bumps, --no-ignore-bumps Stop processing immediately if bumps are detected (default).
--bump-distance-factor 0.75 A fraction of covalent bond radii sum used to determine when atoms are too close and are considered a bump.
--max-polymer-span 4 A span, in +/- unit cells, in which polymeric molecules (repeating units) will be constructed.
--max-polymer-atoms 100 A maximum allowed count of polymer example atoms: more than this amount of symmetry (translational) equivalent atoms, for each AU atom, will not be written to the output file:
Using --max-polymer-span=0 --max-polymer-atoms=1 essentially switches off the polymer detection.
--split-disorder-groups, --dont-merge-disorder-groups Put examples of disorder group conformations into separate data blocks (default).
--merge-disorder-groups, --dont-split-disorder-groups Put all disorder groups into one data block.
--use-perl-parser Use development CIF parser written in Perl.
--use-c-parser Use faster C/Yacc CIF parser (default).
--debug Print some human-readable debug output.
--no-debug Suppress any debug output (default).
--format "%8.6f" Use the specified format for output coordinate printout.
--audit Print audit information to the generated CIF file (default).
--no-audit Do not print audit information to the generated CIF file.
--continue-on-errors Do not terminate script if errors such as unrecognised atoms are encountered; the output may be incorrect and missing some atoms if this option is used!
--die-on-errors, --dont-continue-on-errors,
--no-continue-on-errors Terminate script immediately if errors are raised (default).
--continue-on-warnings Do not terminate script if warnings are raised (default).
--die-on-warnings Terminate script immediately if warnings are raised.
--continue-on-notes Do not terminate script if notes are raised (default).
--die-on-notes Terminate script immediately if notes are raised.
--verbose Print warning messages in long format.
--no-verbose Print warning messages in concise format (default).
--help, --usage Output a short usage message (this message) and exit.
--version Output version information and exit.