This log contains changes made from rastop 1.3.1 to rastop 2.0. Numerous
changes were adapted from rasmol 2.7.2 and 2.7.2.1 from Herbert Bernstein.
[12/01] PV, all files.
- Added DepthCue.
- Doubled colour shades (HICOLOR).
- "Prepared" rotation, translation, and zoom commands.
- Added commands "scale","colour axes world","reset worlddepth",
"show worlddepth", "colour dots none", and "position world".
- repres.c: Added code to the Richards-Connolly surface.
- Changed management of dot color.
[10/01] PV
- Added command position.
- Added help html command.
[09/01] PV
- pixutil.c: Corrected bug in CommonVectStep.
- command.c: Corrected zoom command.
[08/01] PV
- transfor.c,script.c: Normalized Range for calculating translation
offsets. This changes classical translation scripting (see rastop
help).
- command.c: Added with corrections the "set stereo"
command modification from rasmol 2.7.2.1 by H. Bernstein -
see other stereotok as well.
- render.c: Inverted left and right image - the last and correct
image is now the left one. Adjusted IdentifyAtom function for picking in
stereo.
- FindDisulphideBridges(): Corrected bug on slist.
- molecule.c/.h: Added function ReclaimAllBonds.
- transfor.c/.h: Added function PrepareBondRotate.
- command.c: Corrected bug on INVERT in rotate bond command.
- vector.c: Corrected SubstractAtom.
- Replace BondsSelected by RotBondsList.
- vector.c: Added function ZeroMatrix.
- All: Added triple coordinate system.
- All: Improved way to calculate centre rotation.
- Command.c: Modified ExecuteShowCommand.
- abstree.c: Modified DescribeObj.
- Corrected inversion in RotYMatrix.
- render.c: Corrected Y axis labeling.
- command.c: Added DescribeWorld function.
[07/01] PV
- All project: Fixed Filemodified variable.
- Put ShadePower scripting values like in RasMol 2.7.2.1 [H. Bernstein].
- command.c: Added ExecuteResetCommand() function.
- render.c (DrawFrame) Corrected SlabInten.
- (mostly) command.c: Wrote saving and opening of rsm files.
- multiple.c: Added with changes function ReRadius() from rasmol
2.7.2.1.
- transfor.c: Modified InitialTransform to adjust zoom factor upon
loading.
- render.c: Modifid ResizeScreen function.
- transfer.c: Modified DrawWorld() to prevent conflict with maxzoom
during cliboard manipulations.
- script.c: Added macro IsZero(x).
- All: variable RefreshState: Found deep conflict between refreshing,
saving,and fast drawing. Modifications may not be ok in 8-bit mode
(ColourMap).
- Added corrections from rasmol 2.7.2.1 by Herbert Bernstein:
- molecule.c: SimpleAtomType(), ComplexSimpleAtomType(): Corrected
bug with ElemnDesc.
[14/04/01] HJB script.c
Correct error in writing scripts with partial use of spacefill.
Thanks to Steven Vik <svik@mail.smu.edu> for reporting the
problem.
[02/04/01] HJB abstree.c, abstree.h
Increase space for atom names from 4 to 12 characters.
[02/04/01] HJB infile.c
Increase limit on atom names for CIF from 4 to 12 characters.
[02/04/01] HJB several
Make dial indices symbolic (PV: Not fully done yet!)
[21/08/00] HJB command.h
Add space after "__huge"
[23/02/00] HJB infile.c
Fix *- for - typo in XYZ and MOL2 input of coordinates
[05/01] PV
- Clipping is not reset anymore upon "reset" in order to
respect the world construction when new molecules are loaded.
The old way of bringing clips to the center of the molecule
does not seem logical.
- Added command "reset ligth", "reset slab", and "reset depth".
- Added commands "refresh off" and "refresh on".
- Cmndline.c: Added function ProcessWheelDial().
- ResizeScreen: Corrected background redrawing in Displaymode.
- DefineColourMap: Darkened DisplayMode Background.
- Added variable SRange and fixed stereo mode.
- Finished code for slab and back-clipping (all files). Added code
for commands "slab world <number>" and "slab world origin",
and equivalent for depth mode.
- Finished code for manipulation of rotation centers; made
center visible in display mode; added centre command syntax
from rasmol 2.7.2.1.
- Added commands:
"centre world": Translate world origin to centre of screen,
world is translated at the same time;
"centre origin": Bring center to world origin
"centre origin centre": Translate world origin to actual
rotation center; this is a "world" destructive command!
[04/01] PV
- Added new panes to status bar.
- command.c: errorcount versus rastop 1.3.1, corrected bug in
executecommand.
- Corrected ExecuteTitleCommand() and SetTitle() for new titles.
- Changed edit menu; put accelerator key to "enter rasmol
command".
- Modified command panel, added world button.
- Modified DisplayMode.
- Added commands "molecule hide" and "molecule Sow" (see comdline
and pickatoms + all molset->visible references).
- DisplayRibbons(): Corrected alignement of DNA helix.
[03/01] PV
- Added fast drawing (variable FastDraw).
- Added variable DrawWorldAxes.
[02/01] PV
- Added variables WAxe[], Zo[], ZRange, and DRange.
- transfor.c: Added functions PrepareWorldTransform(), ResetWorldAxes.
- vector.c/.h: Added function CopyMatrix3(), IdentityMatrix3().
- Adjusted ReSizeScreen() code.
- Added zoom to comndline.c in rotate all mode; Corrected a few
bugs in ProcessMouseMove().
- Introduced molecule offsets MOffset[] to position molecules during
all transformations; X/Y/ZOffset are equivalent integers used
for calculating rendering.
- Changed DialValue for translation to modulo[2] (free translation).
[01/01] PV
- Added code for preferences.
- Added code for default script in default representation.
- rasview.cpp rasdoc.cpp: Corrected Windows 2000 bug.
- Passed conditions on RegisterAlloc() into the function.
- Added bond rotation code, renamed wbrotate.c brotate.c (all the
world-rotate code is tranfered into transfor.c).
Added ChangeBondOrder(), removed NewBond, removed RotBond mode, and
added PickRBond picking mode.
Added command "bond <number> <number>
single/double/triple/unbound".
Added command "set picking bond rotate" and "set
picking rotate bond".
Removed function RemoveBond(); Attempted to correct erroneous hbond
and ssbond in BondRotate() by simply destroying bond lists!
- Added code for picking lightsource in picking mode.
- Added PickLight mode;
- Added F1 help.
- Added new icons in toolbar.
- Adjusted WriteScriptFile();
- Modified WriteScriptDots();
- Renamed DeleteSurface() DeleteDotSurface();
- Renamed CalculateSurface() CalculateDotSurface();
- Added function WriteScriptSurface() in script.c;
- Corrected bug in WriteScriptAtomSets().
[12/00] PV
- Removed ProcessDoc() function; added ResetUserBox().
- rasview.c cmndline.c/.h SetPickMode()
Added code for cursor mode.
- command.c transfor.c molecule.h (and others)
Added PreviousTok and code for saving previous selection.
Added flag2 for RAtom (flag is full).
- command.c rasdoc.c/.h rastop.c multiple.c (and others)
Added code for handling rsm files by rasmol;
Added ErrorCount and ErrorFlag to handle wrong scriptfiles.
- graphic.h SetCanvasTitle() SetTitle() ExecuteTitleCommand()
SelectMolecule(): changed title code.
- All: Removed (rastop) variable MoleculeFileName.
Put "strcpy(Info.filename,DataFileName);" uniquely in
ProcessFile()with correction for "inline" files in DivertoData().
- Transfered new 2.7.2 FetchFile function to ProcessFile()
- Confusion on attribution of DataFileFormat. Only attribution in
processfile() is conserved.
- DrawFrameOne() transfor.h: Replaced ApplyTransform() by
ApplyTransformOne().
[11/00] PV
- multiple.c command.c
Transfered ZapDatabase() into multiple.c; changed name to Zapmolecule();
created new Zapdatabase() for zapping all molecules. Added command
"zap molecule", "zap selected" and "zap all" with "zap" synonymous of
"zap all".
- WriteVRMLWireframe(): typing bug corrected.
- transfor.c/.h wbrotate.c/.h: Transfered WorldRotate to Transfor.c
- All: Added rasmol 2.7.2 code for multiple molecules
- IdentifyAtom(): Corrected bug with UseDepthPlane
- transfor.c: Changed carbon cpk color to white when no hydrogen.
Changed default cartoonheight.
[10/00] PV
- pixutil.h/c rastop.cpp
Changed cylinder code. Added code to draw cylinders with flat cap.
Code still needs some fixings.
- pixutil.h/c repres.c
Completed cartoons code.
- rasview.cpp rasdoc.cpp mainframe.cpp pannel.h/.cpp
Reorganized automode.
- LightX, LightY, LightZ, LightLength, ColConst, DefaultTok,
LightsourceTok, HeadlightTok
Added multidirectional lightsource.
- command.c
Corrected bug in parsing of shadepower command.
- render.c repress.c pixutil.c
Fixed use of InvertY with LightDot and switched to ORIGINAL lighting.
This log summarizes changes from RasTop version 1.3 to RasTop version 1.3.1
[03/01] PV
- mainframe: Changed font generation;
changed selectbar initialization.
- Added profile "Selection" for the select bar.
- render.c/IdentifyAtom(): Made atoms behind the depth plane not
identified.
(thanks to Ian Gibbons for reporting the bug and other
suggestions)
- command.c: Added ErrorCount, ErrorFlag and MAXERROR.
- mainframe: Removed function OnDropFile to allow dropping of pdb files.
- rasview/rasdoc: Added macro STOPTIMER and STARTTIMER
- pannel.ccp/h: Changed auto by spin. Made variable m_autostatus
private.
- Changed two icons in the resources.
- transfor.c: Changed carbon cpk color to white when no hydrogen.
- script.c: Corrected output error in WriteAtomSelection.
- command.c: Corrected bug in parsing of shadepower command.
- script.c: Added exittok at the end of saved script.
- rasview/rasdoc: Corrected bug in drawing and removed unuseful code.
- repres.c: Corrected drawing of ribbons at large zoom.
- render.c/displayboxes: Corrected bug on axe position when moving
center.
- transfor.h: Removed duplicated variables
- SetPickMode, CentreTranform: Changed RedrawFlag.
- Switch Help command to mainframe and activate help on F1
Consult also RasMol changeLog and RasMol2.7.1 changeLog.
This log contains all changes made to RasMol
source independently of RasTop. Initial work was done on version 2.6.4,
but was quickly updated to the newer version 2.7.1 by Herbert Beirnstein.
[21/09/99] PV command.c
Changed output for one-letter-code sequence in series of 50
characters with a space each subgroup of 10.
[21/09/99] PV command.c (ExecuteCommand())
Added command "trace dots <value>" allowing trace dots
representations of varied radii.
[21/09/99] PV command.c / render.h /
render.c / transfor.h .c
Added four new picking modes:
- select an atom: PickAtome
- select a group: PickGroup
- select a chain: PickChain
- modify bonding/add multiple bonds: PickBond
Allowed picking parameter shift = -1 when Ctrl key is down to deselect
an atom (a group, a chain) from the current selection.
[21/09/99] PV cmndline.c (ProcessCharacter())
Added <Esc> character to interupt script pausing.
[21/09/99] PV pixutils.c
Set ARCSIZE to 32768 under MSWIN, allowing drawing cylinders with
radii up to 250 RasMol Units. Current implementation gives a maximum
of 75 RU at maximum zooming. Mac implementation should be verified.
[21/09/99] PV script.c
Completed scripting for "trace dots <value>", backfade,
shadow,and stereo.
[21/09/99] PV
Compiling problems with RasMol 2.7.1 files (VisualC++ 5.0)
- declared InterruptPauseCommand() and ResumePauseCommand()
in command.h
- declared TestDisulphideBridge() in molecule.h
- explicited all conversions long to short in infile.c /*casting*/
- excluded all unreferenced variables in infile.c /*unreferenced*/
- included graphics.h in molecule.c
- fixed casting in drawstar() and clipstar() in pixutils.c
- declared DefineShade() in transfor header
- fixed casting and referencing in script.c
- declared LoadDotsFile() in repres header
- declared SetFontStroke() in pixutil header
- missing WritePOVRay3File() declaration in script header
- declared cif_free_handle() in cif header
- missing declaration of cif_parse in cif.h
[22/09/99] PV repres.c
Fixed bug in DisplayRibbon() that produced cartoon like structure in
ribbons covering only parts of chains or mixing ribbon types.
[22/09/99] PV abstree.h .c
Fisrt step for saving atomsets & identifiers in RasMol scripts (SetSize
to 100 and SymEntry and SymbolTable in header).
[22/09/99] PV repres.h command.c
Improved label picking mode (LabelFormat to store the current label
string,the command "label {<string>}" is disabled in
picking mode but save the format).
[24/09/99] PV cmndline.c
Correlated mouse binding to global variable MouseMode;
Removed EnableMenus(state==1) in ResetCommandLine();
Fixed mouse binding with INVERT on y values;
Fixed bug on capture status on mouse-up;
Added MM_PREV to mouse binding for deselection;
Fixed INVERT on y value for mouseup!
[28/09/99] PV transfor.c
Fixed bug (?) with stars, making them mutually exclusive with spheres.
Adjusted bondmode in EnableWireframe().
[29/09/99] PV molecule.c
Fixed bug in FindCisBonds() (no zeroing of last group cisbondflag);
Added ability to convert triple bond to single (CreateBondOrder())
[01/10/99] PV command.c
Fixed initialization SeqFormat and CalcBondsFlag (ExecuteConnectCommand);
Fixed bug in coloring strands (missing strandtok).
[07/10/99] PV command.c abstree.c script.c render.c
Changed coordinates and phipsi output, modified output for showcommand;
Adjusted threshold in DisplaySelected.
[07/10/99] PV cif.c
Fixed memory allocation bug (VisualC++?) in cif_make_handle;
[07/14/99] PV abstree.c transfor.c
Added shortcuts for direct evaluations of atomsets (BuildAtomSet(),
SelectZoneExpr()); gain up to 15 seconds of computer time on very
large molecules.
Added variable ModelInclude to select either in one model or in all
models;
[17/10/99] PV command.c
Modified CommandError output (shortened file name).
[19/10/99] PV
Release RasTop1.1
-------------------------------------------------------------------------
[20/10/99] PV script.c
Added temporary output on command line when null file in WriteScriptFile,
which edits a rasmol header file.
[22/10/99] PV command.c transform.c .h
Added function ReadAtomSelection() which escapes the parser under
the form:"select (< or >) x1[-x2],...,xi[-x(i+1)](> or <)"
where '<' starts or continues an atom selection, '>' continues or stops
the current selection, - indicates a bloc of consecutive atoms, and xi
are atomnos. Required DisplaySelectCount() to be global.
[27/10/99] PV command.c script.c .h graphics.h
Added function WriteAtomSelection() and WriteScriptPosition();
Added commands "clipboard selected", "clipboard
position" "clipboard
image" and "clipboard paste" and corresponding functions:
ClipboardImage( )
ClipboardPosition( )
ClipboardSelection( )
ClipboardPaste( )
[29/10/99] PV command.c script.c .h graphics.h
Added function WriteScriptAtomSets() to write atom sets to the script.
[02/11/99] PV repres.h transfor.h
Added variables DotR,DotG,DotB,DotDensity, and UseDotColPot for
saving dot characteristics.
[09/11/99] PV command.h/.c
Added MoleculeFileName variable and SaveRsmMolecule() function;
Modified save command to address "save <filename>" to
SaveRsmMolecule().
[09/11/99] PV rasmol.h command.c
Added ProcessDoc and SaveDoc functions which allows add-ons (like
RasTop)to react to newly loaded molecules, zapping, and saving of
molecular data.
[22/11/99] PV molecule.c script.c
Modified CreateNewBond() to prevent pdb files without atom description;
Adjusted ProcessFile() and FetchFile() to allow attribution
of DataFileFormat when no Database is created.
Modified output of WriteScriptHBonds();
[12/08/99] PV command.c
ResumePauseCommand( ), added '\r' to terminate curline (bug? resulted in
non opening of subscripts when LF/CR in the script file).
[12/08/99] PV rasmol.h command.c
Added function RefreshView() in rasmol.h to replace RefreshScreen() in
command.c to allow refreshscreeen from inside RasMol.
[12/09/99] PV command.c
Added Beginwait/endwait in ProcessFile().
[12/10/99] PV command.c token.c
Added CopyTok for "copy" command equivalent to
"clipboard" and shorcut for "paste" command.
Added SELECTION as an homonymous keyword to SELECTED
-------------------------------------------------------------------------
Started version 1.3.
[12/14/99] PV transform.c and others
Added function CentreTransform() to either move the origin in the molecule
or move the molecule to the origin (origin = True ). Added variables
Cenx,y,z, which mesure distance centre-origin. Changed DrawTwinVector to
ClipTwinVector in DisplayWireFrame() (render.c).
[12/14/99] PV
Added variables ShiftS and UseAutoDepthCue that adjust DepthCue
with slabbing.
[12/17/99] PV render.c
Added centre correction in DisplayBoxes().
[12/18/99] PV
Added code for backclipping based on ZOffset. New variable UseDepthPlane
and DialValue[8].
[12/20/99] PV script.c
Added more precision to rotate, translate, zoom, and slab commands in
WriteScriptFile() and WriteScriptPosition(). This is important
for passing cliboard content and saving centre. Fixed centre scripting.
[01/03/00] PV transfor.c
Fixed bug (and modified) function Power() to handle Specpower.
[01/14/00] PV molecule.c
Set Info.filename as alternative title.
[01/16/00] PV transfor.h/.c token.h/.c script.c
Added ShadePower in DefineColourMap(), which brings some interesting
shade variations. Added ShadePowerTok and command "set shade x" with
x between -20 to 20.
[01/16/00] PV cmndline.c PerformMouseFunc()
Corrected MM_CLIP to access clipping with the mouse;
Added MM_DEPT to access backclipping (depth) with the mouse.
[01/16/00] PV
Completed 32-bits version. Code a bit messy, especially for
clipboard and background operations. Will probably not compile on
other compilers. bmp file saving not done in 32 bits.
Added code for command "set dot <value>" which adjusts
the size of the dots in a rather rough way.
[01/17/00] PV script.c
Corrected bug in WriteScriptAtoms().
[01/17/00] PV render.c
Solved problem in regenerating background in 32 bits in ReSizeScreen().
[01/17/00] PV command.c ExecutePauseCommand()
Added a RFRefresh for refreshing RasTop screen.
[01/28/00] PV render.c ResetRender()
(Bug?) Finally found old problem with shadows in RasTop. Missing
a ResetVoxelData() on zapping. This is a potential source of problems
when successively opening scripts containing shadows in RasMol.
[01/30/00] PV command.c
Added command "select view" and corresponding code, which allows to
select a part of a molecule based on screen display.
[01/31/00] PV command.c
Added code for selecting atom areas with mouse:
- changed PickAtom() function name in PickAtoms();
- changed PicAtome identifier in PickAtom;
- added function SelectArea() and DisplayArea();
- added code for command "select view";
[02/02/00] PV pixutil.c render.c
Added function ClipDashLine();
Changed display of cells with dashed lines in DisplayBoxes().
[06/01/00] PV
Finish help; Release version 1.3
Changes from RasMol 2.7.0.1 to create RasMol 2.7.1:
[15/07/99] HJB documentation
Add Dunix binaries. Thanks to David Atkinson
[06/07/99] HJB all
Release 2.7.1
[05/07/99] HJB documentation
Cut-off date for Release 2.7.1 documentation changes.
[22/06/99] HJB all source
Cut-off date for Release 2.7.1 code changes.
[22/06/99] HJB command.c
Save fact that a data file was loaded inline. Add
processing for star command, all new options for
bondmode [all | none | not bonded ]
[22/06/99] HJB infile.c
Update DataFileFormat after autorecognition.
[22/06/99] HJB molecule.h
Add MarkAtoms to hold new bondmode flags.
[22/06/99] HJB pixutils.c, render.c
Add code for new star command.
[22/06/99] HJB script.c
Add logic to write star command output. Report data
loaded as CIF or as inline correctly. Warn users
that inline data is not being written out. Check
inversion of Y-axis on POVRAY3. Thanks to Curt
Haltiwanger for suggesting marking non-bonded atoms
on wireframe displays.
[22/06/99] HJB transfor.c
Add code for new star command, new bondmode options.
[18/06/99] HJB pixutils.h, pixutils.c
Change name of DisplayString to DisplayRasString to
avoid a conflict with X libraries. Add FontWid array
to hold character widths (FontSize for FS, FontSize/4
+1 + maximum x position for PS). Add FontStroke logic to
write cylinders instead of lines when FontStroke is not
zero.
[18/06/99] HJB render.c
Change name of DisplayString to DisplayRasString to
avoid a conflict with X libraries.
[18/06/99] HJB repres.c
When FonstStroke is non-zero, don't offset character
color by (ColourMask>>1), to allow room for color
adjustments in cylinder drawing.
[18/06/99] HJB script.c
Add logic to write PS flag for proportional spacing
on set fontsize, and logic to write set fontstroke n.
[18/06/99] HJB tokens.c, tokens.h
Add tokens for BlueTint (BlueTintTok), Brown (BrownTok),
FontStroke (FontStrokeTok), FS (FSTok), Gold (GoldTok),
Gray or Grey (GrayTok), GreenTint (GreenTintTok), HotPink
(HotPinkTok), Pick as an alternative for Picking
(PickingTok), Pink (PinkTok), PinkTint (PinktintTok),
SeaGreen (SeaGreenTok), SkyBlue (SlyBlueTok),
YellowTint (YellowTintTok)
[13/06/99] HJB command.c
Change processing of load inline command to work from
the currently opened script, saving the file position.
Accept HEADER and DATA_... as commands in a script,
processing that line and all subsequent lines as a
data file, unless a prior load inline command was already
done
[12/06/99] HJB infile.c
When processing a PDB file, test for DATA_... until
a non-comment, non-blank line is found. Revert
to CIF processing if DATA_... is found.
[11/06/99] HJB infile.c
In PDB format input extract EXPDTA for Info.technique.
In CIF format input accept _audit_block_code for the
entry ID, _exptl.method, _diffrn_radiation.probe or
_diffrn_radiation_probe for Info.technique. Preserve
low order bits of coordinates in xtrl, yrtl, ztrl. On
PDB output, report Info.technique in EXPDTA and reinsert
low-order bits for coordinates.
[10/06/99] HJB abstree.c
Add code to report coordinates for show selected cordinates
[10/06/99] HJB command.c
Recognize new commands, picking coordinates,
show selected cordinates. Update default title produced
by title command.
[10/06/99] HJB molecule.h
Add new Info fields for date and technique. Extend
identcode to 80 columns. Add CRD to Selection enum type.
Add prototype for ReviseTitle.
[10/06/99] HJB render.h, render.c
Add code to report coordinates for picking coordinates,
define PickCoord symbol.
[10/06/99] HJB tokens.h, tokens.c
Add code recognize COORD, COORDS, COORDINATE, COORDINATES for
new CoordTok, DATA_... for CIFDataTok, HEADER for HeaderTok
[09/06/99] HJB molecule.c
Put PDB entry ID and EXPDTA info into canvas title, report
EXPDTA data from Info.technique on reading file.
[06/06/99] HJB infile.c
Restore the origin on PDB and other outputs.
[06/06/99] HJB script.c
Change script output to include centering and
change various coordinate outputs to restore
origins the z-axis orientation.
[06/06/99] HJB command.c
Add command centre [CenX,CenY,CenZ] to center by offsets
from centre of gravity.
[03/06/99] HJB render.c
Remove call to TranslateToCentre, hold centering
in CenX, CenY and CenZ, decoupled from dials,
add RFRotate to ReDrawFlag on centering. Thanks to
Bohdan Schneider for pointing out the problems with
centering.
[03/06/99] HJB transfor.c
Remove TranslateToCentre, remove processing of CenX,
CenY and CenZ from dial values, and put it into
computation of ptr->x,y,z
 Changes
after release of RasMol_2.7.0.1:
[27/04/99] HJB README.html, Changelog.html, INSTALL.html, manual
Add navigation links at top and bottom of each page.
Add links for gzipped versions of raswin.hlp, rasmol.hlp.
Thanks to E. Martz and Kjeld Olesen.
[27/04/99] HJB INSTALL.html, manual
Replace empty copy of INSTALL.html in doc/, correct
embedded html in manual. Thanks to Kurt Giles.
Changes from RasMol_2.7.0 to create RasMol_2.7.0.1:
[22/04/99] HJB
Announce RasMol 2.7.0.1 on pdb-l@rcsb.org,
rasmol@lists.umass.edu, mmciflist@ndbdev.rutgers.edu
[11/04/99] HJB *.c, *.h
Update all comment blocks for new version and date
[11/04/99] HJB abstree.h
Realign Pred... to agree with ...Tok to correct
misaligned introduced by HJB (not AM) during merge of 2.6x1
into 2.7.0.
[11/04/99] HJB tokens.h
Fix definition of IsPredTok
[09/04/99] HJB molecule,h
Make residue identification case-insensitive.
Changes from RasMol_2.6.4, RasMol2.6x1 and RasMol_2.6_CIF.2 to
create RasMol_2.7.0:
[30/03/99] HJB all
Cleanup and release of version 2.7.0
[23/03/99] HJB abstree.c
Add code to select on alternate conformers. Increase
accuracy of torsion angle calculation.
[23/03/99] HJB command.c, command.h
Make InitHelpFile generally available, change to
WriteString for reporting CisBondCutOff for use on mac,
report models on show selected.
[23/03/99] HJB rasmol.c, raswin.c, rasmac.c
Add suggestion for help notice to initial text lines.
[23/03/99] HJB script.c
In order to support mac introduce WriteBuffer and
change all fprintf(outFile, ... to WriteBuffer, provide
code from fisipl for Ramachandran printer plot. Handle
signs of torsion angles. Thanks to F. C. Bernstein.
[23/03/99] HJB tokens.h, tokens.c
Add RamPrintTok, RPP, RDF, etc., hook POVRAY3 to the
new POVray code.
[20/03/99] HJB *.h, *.c
In general, the RasMol_2.6_CIF.2 version was used as a base
and upgraded with the RasMol_2.6.4 changes. The exceptions
are below
[20/03/99] HJB infile.c
Cell parameters are read with the double routine ReadDecValue
from 2.6_CIF.2, rather than ReadValue2 from 2.6.4
Changes
from RasMol_2.6 to create RasMol_2.6x1:
[15/2/98] AM abstree.c, abstree.h
Add PredCisBond, DescribeObj, CalcPhiAngle, CalcPsiAngle,
CalcOmegaAngle, shift torsion angle calculations 180
degrees.
[15/2/98] AM command.c
Add FindCisBonds, CisBondCutOff, show of selected chains,
groups, atoms, show and write of phi-psi angles
[15/2/98] AM molecule.h, molecule.c
Add CIS bond logic
[15/2/98] AM rasmol.h, rasmol.c
Add USE_FD_SET_TYPE option
[15/2/98] AM script.h, script.c
Add WritePhiPsiAngles, code for POV-Ray version 3
[15/2/98] AM tokens.h
Add CisBondedTok, RamachanTok, CisAngleTok, PhiPsiTok,
define PHIPSI, CISANGLE, RAMACHAN, CISBONDED
Changes
from RasMol_2.6 to create RasMol_2.6.4:
[8/2/99] RS command.c, rasmol.c, scripts.c, rastxt.c, raswin.c
rasmac.c
Final fixup and release of version 2.6.4
[27/12/98] RS *.h, *.c
Remove all non-ANSI-C prototypes and ensure use of ( void )
for empty argument lists. Upgrade all procedure delcarations.
Convert to use of MSWIN.
[27/12/98] RS abstree.c
Redo torsion angel calculation.
[27/12/98] RS applemac.c
Convert to Apple's new routine names
[27/12/98] RS cmndline.c, cmndline.h
New routine for mouse, keyboard, dials
[27/12/98] RS command.c, command.h
Move routines for mouse, keyboard, dials to cmndline.c.
Redo ParseColour. Reorganize command parsing
[27/12/98] RS infile.c
Change references to MMIO to MMIOLIB. Pass fp and buffer
to FetchRecord as argument. Add ReadValue2, ProcessPDBBond,
ProcessPDBUnitCell. Fix recognition of END. Use
InvalidateCmndline and UnusedArgument. Write MODEL and
ENDMDL records when appropriate
[27/12/98] RS molecule.c
Reorganize FindResNo as a character-oriented search tree
Add Cache.
[27/12/98] RS rasmac.c
Convert to Apple's new routine names
[27/12/98] RS rastxt.c
New text-only main program
[27/12/98] RS repres.c
Add LabelTermnii
[27/12/98] RS tranfor.c
Add TranslateToCentre
[27/12/98] RS transfor.h
Reorganize the logic defining DefaultAmbient, making
the default value 0.4 instead of 0.6, except for E&S, which
is still .05.
[27/12/98] RS tokens.c
New routine for character-oriented search tree for tokens.
[01/08/97] RS infile.c
Decreased the maximum valid alpha carbon to alpha carbon
distance to 4.2 Angstroms from 7.0 Angstroms. Thanks to
Kostas Sfyrakis and Harren Jhoti.
[15/04/97] RS molecule.c repres.c
Fixed a bizarre feature in the OpenVMS compiler that complained
about "a=*b" as "=*" operator is an obsoltete form and may not
be portable. Special thanks to Remington Stone.
[28/11/96] RS rasmol.h rasmol.c
Several minor fixes to compile RasMol under VMS. Special
thanks to Adam Ralph (and CCP4).
Changes
from RasMol_2.6_CIF(Rev 1) to create RasMol_2.6_CIF(Rev 2):
[24/2/99] HJB Release of RasMol_2.6_CIF(Rev 2) at
http://www/bernstein-plus-sons.com/software/rasmol
and announce to mailing lists.
[21/2/99] HJB cif.h
Add prototypes of cif_make_handle, cif_read_file,
cif_make_file, cif_save_character to avoid compiler warnings
[21/2/99] HJB cif_ctonum.c
Remove unneeded values.h
[21/2/99] HJB cif_ctonum.h
Correct prototype
[21/2/99] HJB infile.c
Add cif_ctonum.h, define LoadCIFMolecule prototype,
initialize ch, add return to avoid compiler warnings.
[21/2/99] HJB abstree.c, cif.c, cif_ctonum.c, command.c,
infile.c, molecule.c
Use string_case.h instead of for IBMPC,
VMS and APPLEMAC.
[21/2/99] HJB rasmol.h
Update version, add some definitions from R. Sayle's
2.6.4 in preparation for 2.7.0.
[21/2/99] HJB rasmac.c, rasmol.c, raswin.c
Update reported date on startup.
[21/2/99] HJB render.c
Add cif_fract.h to avoid compiler warnings.
[21/2/99] HJB string_case.c
Replace garbled version, provide string_case.h.
[21/2/99] HJB script.c
Initialize first, last, radius, to avoid compiler warnings
[21/2/99] HJB transfor.c
Initialize min and max to avoid compiler warnings.
[10/1/99] HJB Release of RasMol_2.6_CIF(Rev 1) at
http://www.bernstein-plus-sons.com/software/rasmol
and announce to mmCIF mailing list.
[9/1/99] HJB cif.c
Change toupper calls to ToUpper calls.
[8/1/99] HJB command.c
Add argument to CreateMoleculeBonds to force zapping
on connect.
[8/1/99] HJB infile.c
Log requested bonds which cannot be made in NullBonds
and report to users, add RightJustify to right-justify
residue names, recognize _atom_site_disorder_group
for small molecule alternate conformerse, recognize bonds
which don't have either atom names or atom numbers.
[8/1/99] HJB molecule.c
Add argument to CreateMoleculeBonds to force zapping
on connect.
[8/1/99] HJB molecule.h
Add argument to CreateMoleculeBonds to force zapping
on connect, add NullBonds to log requested bonds which
cannot be made.
[8/1/99] HJB mswin31.c
Use VERSION to construct window title.
[8/1/99] HJB outfile.c
Use VERSION to construct Postscript output file header.
[8/1/99] HJB rasmac.c
Use VERSION to report version on startup.
[8/1/99] HJB rasmol.c
Use VERSION to report version on startup.
[8/1/99] HJB raswin.c
Use VERSION to report version on startup.
[8/1/99] HJB script.c
Use VERSION to construct various output file headers.
[8/1/99] HJB x11win.c
Use VERSION to construct window title.
Changes
from RasMol_2.6 to create RasMol_2.6_CIF:
[22/12/98] HJB Preliminary release of RasMol_2.6_CIF at
http://www.bernstein-plus-sons.com/software/rasmol
[19/12/98] HJB command.c
correct handling of internal help files under windows,
and allow for unix help files on a mac.
[18/12/98] HJB Makefile.in, Imakefile
Update for CIF support.
[09/12/98] HJB infile.c
Cummulative changes for fractional coordinates,
CIF.
[09/12/98] HJB command.c
Changes for alt, model labels, colour schemes,
CIF.
[09/12/98] HJB molecule.h
Cummulative changes for fractional coordinates,
new colour schemes, CIF.
[09/12/98] HJB molecule.c
Cummulative changes for fractional coordinates,
new colour schemes, CIF.
[09/12/98] HJB x11win.c
Update comments, menus and version text.
[09/12/98] HJB mswin31.c
Update comments, output file commentary.
[09/12/98] HJB outfile.c
Update comments, output file commentary.
[09/12/98] HJB script.c
Update comments, output file commentary.
[09/12/98] HJB rasmol.c
Update comments, output file commentary.
[04/12/98] HJB pixutils.c
Update comments, code to stripe bonds for alternate
conformers.
[04/12/98] HJB pixutils.h
Update comments, protytpes to stripe bonds for alternate
conformers.
[04/12/98] HJB rasmac.c
Update comments, adjust code for current Metrowerks
compiler.
[04/12/98] HJB raswin.c
Update comments, adjust code for current Metrowerks
compiler.
[04/12/98] HJB tokens.h
Update comments, tokens for alt, model colours.
[04/12/98] HJB transfor.c
Update comments, add code for alt, model colours.
[04/12/98] HJB transfor.h
Update comments, prototypes for alt, model colours.
[23/11/98] HJB abstree.c
Add code for %A, %M specifiers, divide u/l case.
[22/11/98] HJB cif_fract.c
New routine, derived from cif2pdb by H.J. Bernstein
and F. C. Bernstein.
[22/11/98] HJB cif_fract.h.
New header for cif_fact.c.
[22/11/98] HJB cif_stx.c
New routine, derived from P. Ellis CBFlib parser.
[23/11/98] HJB render.c
Update comments, add code to stripe bonds for alternate
conformers.
[23/11/98] HJB repres.c
Update comments, add code to stripe bonds for alternate
conformers.
[09/09/98] HJB cif_ctonum.c
New routine, derived from ciftbx by S. R. Hall
and H. J. Bernstein.
[09/09/98] HJB cif_ctonum.h
New header for cif_ctonum.c.
[18/08/98] HJB cif.h
New header for cif.c, derived from CBFlib by P. Ellis
and H. J. Bernstein.
[18/08/98] HJB cif.c
New routine derived from CBFlib by P. Ellis and
H. J. Bernstein.
[14/08/98] HJB rasmol.c
Added hooks for termio for Linux. These changes
are similar to, but not identical to the FreeBSD hooks.
See the linux conditionals. -- H. J. Bernstein
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