Lines Matching refs:atom
11 # bug fix: bfactor min/max was ignoring first atom
77 # bug fix: NWChem reader not reading files with lower-case-only atom names
151 # bug fix: GAMESS reader vibrations use wrong atom coordinates
232 # new feature: draw ID xxx SYMOP [n or "-x,y,z"] [optional {atom or position}]
294 # new feature: set picking Label now allows label offset by holding SHIFT down while dragging atom
580 # new feature: print {xxx}.label.all("xxxx") -- forces array even if only one atom (like "{xxx}.lab…
638 # string, point, axis-angle/plane/quaternion, atom bitset, bond bitset,
767 # new feature: inline FOR(varName;{atom expression};math expression)
787 # bug fix: various tweaks of atom properties business.
795 # new feature: consistent set of atom properties now accessible via:
815 # The full set of atom properties can be checked this way:
836 # yes yes adpmax the maximum anisotropic displacement parameter for the selected atom
837 # yes yes adpmin the minimum anisotropic displacement parameter for the selected atom
839 # yes yes yes atomID special atom IDs for PDB atoms assigned by Jmol
840 # yes D yes atomIndex atom 0-based index; a unique number for each atom regardless of the number …
841 # yes yes a yes atomName atom name
843 # yes yes B yes atomType atom type (mol2, AMBER files) or atom name (other file types) -- Jmol 11.…
850 # yes yes color the atom color
854 # yes yes file file number containing this atom
871 # yes f yes phi protein group PHI angle for atom\'s residue (Jmol 11.3.41)
874 # yes p yes psi protein group PSI angle for the atom\'s residue (Jmol 11.3.41)
883 # yes u yes surfacedistance shortest distance to a surface atom
885 # o yes symmetry list of crystallographic symmetry operators generating this atom
891 # yes yes yes valence the valence of an atom (sum of bonds, where double bond counts as 2 and tri…
905 # code: extensive rewrite of Eval in terms of getting and setting atom properties
907 # new feature: consistent set of atom properties now accessible via:
921 # code: ver efficient and flexible atom label compiler class modelset.LabelToken
1018 # --sets _vibrationName from file's atom set collection name
1094 # new feature: label %G -- group index, like atom index, 0-based for entire collection
1106 # new feature: \? in atom name escapes ? wildcard. Still no * in names,
1150 # bug fix -- Spartan reader adding " in front of atom label
1526 # new feature: user-definable atom selector for extended select:
1530 # new feature: user-definable atom selector functions.
1531 # _x is used for the selected atom (not _atom) as for
1571 # bug fix: AMBER atom type IM and IP not recognized
1587 # new feature: settable atom elements, atomType, and atomName
1588 # {atomno=3}.element = 6 # set atom 3 to carbon
1590 # note -- this will reset the atom color to its standard CPK value.
1607 # code: better algorithm for atom types in Mol2Reader
1608 # code: faster loading -- no "pre" definition of atom sets
1616 # new feature: mol2 format reads force field atom types for AMBER, CFF91, GAFF, ESFF, CHARMM, COMPA…
1666 # selects within a set of atom types (defined currently only for mol2 and AMBER topology file type…
1668 # defaults to atom name if no types are indicated
1766 # bug fix: CML reader not assigning atom labels
1791 # bug fix: ramachandran and quaternion derivative not indicating structure due to dropping last atom
1808 # bug fix: getProperty("atominfo",{atom expression}) not working for "atominfo[0].xxx
1809 # bug fix: getProperty("modelinfo",{atom expression}) not working
2123 # new feature: quaternion({atom expression}) -- returns calculated
2160 # new feature: show atom(s)
2182 # bug fix: hover will find atom in hidden frame.
2203 # bug fix -- if last helix is last atom, SHOW STRUCTURE fails to identify it.
2296 # bug fix: load trajectory for cases with different atom counts.
2413 # new feature: full math on individual atom properties using
2493 # -- atom picking:
2518 # bug fix: draw ARROW {atom center} {xyz} draws arrow the wrong way
2524 # new feature: draw VECTOR {atom center} {dx dy dz}
2566 # bug fix: quaternions created with extraneous atom lines
2600 # *.XX an atom name, such as .CA
2601 # !.XX not a specific atom name
2634 # *.XX an atom name, such as .CA
2772 # bug fix: hover appears when a load script leaves an atom very close to (0,0) in the window
2799 # new feature: minimization FIX {atom expression}
2824 # new feature: minimize CLEAR # flushes logged info and saved atom info
2908 # new feature: delete {atom expression} NEEDS TESTING
2911 # bug fix: zap {atom expression} for not including all atoms in a model in the selection
2917 # new feature: zap {atom expression} # zaps models associated with given atoms.
3040 # bug fix: save/restore of atom data incorrect when user has set propertyAtomNumberField or propert…
3043 # bug fix: undocumented .vdw atom property was equivalent to .valence
3059 # bug fix: DATA command assigning property to last atom in structure fails
3131 # atom labels and 3D echos then scale properly.
3218 # bug fix: restore of state does not reset user-defined atom properties
3437 # bug fix: no special atom checks for PDB symmetry files
3604 # coding efficiencies in atom iterators
3667 # For many property types, the qualifier is an atom set
3668 # If the atom set is not given, those properties default to {visible}
3682 # sets the bound box around the specified atom expression
3709 # three {x y z} points, draw point references, or atom expressions
3811 # new feature: Jmol math allows direct string replacement in select atom expressions:
3821 # new feature: set atom properties using an array instead of a DATA statement:
3830 # new feature: set atom properties from space-separated string:
3879 # in povray is based on the signed distance from the slab to the atom center.
3888 # bug fix: hover state not properly showing specific-atom hover labels.
3956 # PDB remediated atom name upgrade -- NEEDS CAREFUL CHECKING
3984 # adds support for "xx'" atom designations in PDB and variable names
4063 # new feature: settable atom properties (preliminary):
4075 # new feature: set atom properties using {xxxx}.x =
4082 # new feature: set atom properties using an array instead of a DATA statement:
4155 # new feature: _1 parameter for "first atom" in second expression of connect:
4214 # print "atom " + i + " " + {atomno=i}.ident + " is at " + {atomno=i}.xyz
4347 # scales with the model, so arrow head:atom size ratio remains constant
4469 # Residue indexes in order correspond to the groupID of an atom:
4661 …" {mmm nnn 1|0} range x.x where x.x is a maximum distance away from closest atom in the base cell
4899 # bug fix for select @x not functioning where x = {atom expression} or x = "atom expression"
4900 # bug fix for {atom expression}.ident nonfunctional
4921 # adds "structure" command -- structure [helix|sheet|turn|none] (atom expression)
4974 # zoomTo (atom expression) 0
4978 # zoomTo (atom expression) 0+n
4979 # zoomTo (atom expression) 0-n
4980 # zoomTo (atom expression) 0*n
4981 # zoomTo (atom expression) 0/n
4985 # moveTo timeSec {x y z w} (atom expression) 0 [zoom factor]
4987 # moveTo timeSec {x y z w} 0 transX transY (atom expression) 0 [zoom factor]
5145 # the model is "molecular" -- the base atom coordinates are correct
5359 # allows comparison of user-defined atom properties in SELECT:
5377 # introduces user-definable atom properties that can be used
5387 # allows isosurface mapping of general atom properties:
5448 # x = {*}.atoms.max #the last atom
5504 # operands are atom expressions, in which case these operate directly on the
5505 # atom sets and return a new atom set, just like in SELECT.
5523 # When you set a variable to a value, and that value is a point, plane, or atom expression,
5532 # atom expressions:
5601 # atom expressions or XYZ coordinates and returns a decimal number for
5603 # When more than one atom is involved, average positions are used.
5605 # Note that when more than one atom is involved in a set,
5612 # from each molecule 1 atom to the average molecule 2 position"
5679 # %x1 atom property "x" for atom 1
5680 # %x2 atom property "x" for atom 2
5681 # %x3 atom property "x" for atom 3
5682 # %x4 atom property "x" for atom 4
5699 # Use {} in IF, SET and %{} for designating atom expressions.
5718 # atom expression.
5720 # x = {carbon}[3] # the third carbon atom
5726 # select (carbon)[3] # the third carbon atom
5737 # atom expressions {1,2,3} and coordinates {x y z}, and this seems to me the
5738 # simplest way to do it. (Comma means "or" in atom expressions.) In all other
5756 # atom-based data back to the user with whatever formatting is desired.
5758 # x2 = {atomno=3).label("atom %a\t" + (atomno=3).xyz)
5789 # You can select atoms from an atom expression using [n].
5792 # x = {atom expression}[3].ident
5793 # x = {atom expression}[3][0].xyz # 3 and after (average position)
5794 # x = {atom expression}[3][5].x # 3-5 (average x)
5799 # You can select bonds from an atom expression
5801 # x = {atom expression}.bonds.ident
5802 # x = {atom expression}.bonds[3].ident
5815 # %x1 atom property "x" for atom 1
5816 # %x2 atom property "x" for atom 2
5818 # The special atom properties %D1 and %D2 give sequential numbers for the
5822 # x = {atom expression}.bonds[3].label("%# %3ORDER %TYPE %a1 %a2 %6.3LENGTH")
5856 # full state support for "tainting" atom positions using translateSelected or invertSelected
5867 # x = (some atom expression).atomProperty -- takes an average if more than one atom