============================================================================== === TO DO ================================================================== ============================================================================== do base-P distance, etc <-- what could "etc" mean?... --> GUI for defining measures? new func? avgall() should call getAll() instead of get() on AtomSpecs different selenoMet bond lengths & angles? expand "isprepro" to generic "ispre AAA"? determine SSs geometrically if no SSBOND headers avail (or even if so)? output residue info for both ends of SSs? base-P perp devs in geom kin req(resname) for rnabb special cases w/ substituted heavy atoms ============================================================================== === CHANGE LOG ============================================================= ============================================================================== ### 1.08 ### VBC - Added -hydrogen flag and StdLengths to measure a few of the standard hydrogen lengths. - Added s-s distance to disulfide output. - Added angles around s-s bond to disulfide output. ### 1.07 ### DAK - Fixed major bug with base-P perp calculation: I had miscalculated projection onto a vector by not scaling dot products by magnitude of that vector! - Added generic projection() function for projecting point onto vector (which should actually work now that perp bug is fixed...) - Minor change to help file on how hets are processed: accepted if recognized as protein or nucleic acid; ignored otherwise unless -hets supplied - Made VBC's bad-omega kin output account for cis peptides and only work for omega, not other dihedrals - Tried to add -allalt functionality but ran into logical difficulties (how to handle >1 measurement when 1 has alt but other(s) don't?) & aborted, but along the way made minor improvements to robustness to input & code readability - Added -ideals flag for printing ideal mean & sigma for each measurement ### 1.06 ### DAK: - Added recognition of bases with another heavy atom substituted for O2' as RNA - Reverted to evaluating HETATMs listed as nucleic acids even if doHets boolean is false (which is the default), but the most common non-oligomeric residues ([ACTGU][MDT]P, e.g. ATP) are now excluded (see above), so we should be OK - Changed help file to note past changes to cbdev (now matches Prekin) VBC: - Added prototype for visualization for bad omega(peptide plane) dihedrals. ### 1.05 ### dak - Fixed bug where HETATMs listed as nucleic acids (e.g. ATP) would still get evaluated even if doHets boolean was false (which is the default) - Actually removed [ACTGU][MDT]P, e.g. ATP, from the nucleic acids list, so now they won't get evaluated even if doHets boolean is true. Rationale: they're never in oligomers! - Changed definition for omega from i,i+1 to i-1,i to correspond with common terminology for cis vs. trans peptides (e.g. Pro) - Added proper chi3 definition for Pro to Measurement: CB-CG-CD-N - Fixed bug that I had apparently added in at some point which required all atoms in a length, angle, or dihedral have the same alt conf. That's unnecessary b/c Model.getState() already gets the default state of ' ' (or 'A' if there is an alt conf). - Added -alt=X flag for measuring geometry of other alts like 'B' ### 1.04 ### dak - Allowed "for" to be followed by multiple specifiers, e.g. "for deoxy 2'", and to apply to any resname by default if none specified, as opposed to before where a residue name was strictly required. - Replaced kludgy ignoreDNA/RNA variables with "for oxy/rna" and "for deoxy/ dna", so "-rna -dna" is now handled logically. - Hard coded "for oxy/rna" and "for deoxy/dna" into Parkinson & Gelbin resource files as well as dnabb and rnabb builtins. - Revamped parsing of -res=#,#-#,... flag to allow a sequence of ranges. - Builtin chi3 now works on selenoMet (has 'SE ' atom). - Added disulfide support: "for disulf", "disulfides"/"disulf"/"ss" superbuiltin, chi2',chi1',phi',psi' builtins, alternate chi2/3 defs, ... - Made geom kin springs & fans unpickable (Jane's request via Vince) - Added balls for Cbeta devs >0.25A to geometry kin output - Implemented Prekin-like aa type specificity for cbdev builtin; both programs now output the same numbers - Changed some geom kin flags (mainly deleted them to make things cleaner!) - Made Dangle automatically pull build # out of buildnum.props ... - Made Dangle only deploy Disulfide info to Models if any Measurements actually involve disulfides - Added some modified bases to RNA residue "whitelist" for Swati ... - Fixed bug with Disulfide prep (see above) - Added alternative chi definition for FHU and PSU (different base atoms) ### 1.03 ### gjk - Added Gelbin....DNA.txt to resources (source file for DNA parameters) - Modified Dangle.java to incorporate DNA instead of skipping it dak - Fixed bug where "-dna" also evaluated RNA. Now, "-dna" ignores RNA and "-rna" ignores DNA. Both simultaneously evaulates both but (WARNING!) still acts weird, especially with "-validate" or "-outliers"! - Added "dnabb" superbuiltin analogous to "rnabb" - Made Dangle.java automatically pull version # out of version.props - Minor readability changes ### 1.02 ### dak - Added builtins like cbdev - hadev, nhdev, codev - for diagnosing RDC-based peptide distortions ### 1.01 ### dak - Added infrastructure for "for 2'" additions to the Parkinson RNA resource file (pucker-specific bond lengths and angles) - Also set up for future incorp'n of "for deoxy ..." DNA ideal values ### 1.00 ### dak - Made Dangle its own program & package separate from chiropraxis