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From: <ha...@us...> - 2017-04-24 02:25:31
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Revision: 21535
http://sourceforge.net/p/jmol/code/21535
Author: hansonr
Date: 2017-04-24 02:25:28 +0000 (Mon, 24 Apr 2017)
Log Message:
-----------
Jmol.___JmolVersion="14.15.2" // 4/23/17
new feature: x.split(true)
-- does a white-space token split of the string value of x
new feature: CIP chirality adds P, S, As, Se, Sb, Te, Bi, Po trigonal pyramidal and tetrahedral
code: CIPChirality.java 633 lines all except Rule 4b (Mata)
code: validates on 79 known chirality compounds testing a variety of nuances
bug fix: CIP chirality broken for carbonyl groups
bug fix: CIP chirality E/Z should not be indicated for rings of size < 8
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-04-24 02:19:06 UTC (rev 21534)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-04-24 02:25:28 UTC (rev 21535)
@@ -57,6 +57,8 @@
new feature: CIP chirality adds P, S, As, Se, Sb, Te, Bi, Po trigonal pyramidal and tetrahedral
code: CIPChirality.java 633 lines all except Rule 4b (Mata)
+code: validates on 79 known chirality compounds testing a variety of nuances
+
bug fix: CIP chirality broken for carbonyl groups
bug fix: CIP chirality E/Z should not be indicated for rings of size < 8
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From: <ha...@us...> - 2017-04-24 16:10:14
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Revision: 21543
http://sourceforge.net/p/jmol/code/21543
Author: hansonr
Date: 2017-04-24 16:10:10 +0000 (Mon, 24 Apr 2017)
Log Message:
-----------
Jmol.___JmolVersion="14.15.1" // 4/23/17
new feature: x.split(true)
-- does a white-space token split of the string value of x
new feature: CIP chirality adds P, S, As, Se, Sb, Te, Bi, Po trigonal pyramidal and tetrahedral
bug fix: CIP chirality broken for carbonyl groups
bug fix: CIP chirality E/Z should not be indicated for rings of size < 8
code: CIPChirality.java 633 lines all except Rule 4b (Mata)
code: validates on 78 known chirality compounds testing a variety of nuances
code: CIP optimizations
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-04-24 15:48:45 UTC (rev 21542)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-04-24 16:10:10 UTC (rev 21543)
@@ -49,7 +49,7 @@
# 10. Run jmol/tools build-release.xml
#
-Jmol.___JmolVersion="14.15.2" // 4/23/17
+Jmol.___JmolVersion="14.15.1" // 4/23/17
new feature: x.split(true)
-- does a white-space token split of the string value of x
@@ -56,12 +56,13 @@
new feature: CIP chirality adds P, S, As, Se, Sb, Te, Bi, Po trigonal pyramidal and tetrahedral
-code: CIPChirality.java 633 lines all except Rule 4b (Mata)
-code: validates on 79 known chirality compounds testing a variety of nuances
-
bug fix: CIP chirality broken for carbonyl groups
bug fix: CIP chirality E/Z should not be indicated for rings of size < 8
+code: CIPChirality.java 633 lines all except Rule 4b (Mata)
+code: validates on 78 known chirality compounds testing a variety of nuances
+code: CIP optimizations
+
JmolVersion="14.14.1" // 4/19/17
new feature: CALCULATE CHIRALITY {atom set}
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From: <ha...@us...> - 2017-04-27 04:55:53
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Revision: 21559
http://sourceforge.net/p/jmol/code/21559
Author: hansonr
Date: 2017-04-27 04:55:50 +0000 (Thu, 27 Apr 2017)
Log Message:
-----------
CIP validates for Rules 1-5 for 86 compounds -- 763 lines
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-04-27 04:34:08 UTC (rev 21558)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-04-27 04:55:50 UTC (rev 21559)
@@ -49,7 +49,7 @@
# 10. Run jmol/tools build-release.xml
#
-Jmol.___JmolVersion="14.15.1" // 4/23/17
+Jmol.___JmolVersion="14.15.1" // 4/26/17
new feature: x.split(true)
-- does a white-space token split of the string value of x
@@ -59,8 +59,7 @@
bug fix: CIP chirality broken for carbonyl groups
bug fix: CIP chirality E/Z should not be indicated for rings of size < 8
-code: CIPChirality.java 633 lines all except Rule 4b (Mata)
-code: validates on 78 known chirality compounds testing a variety of nuances
+code: CIPChirality.java 763 lines Rules 1-5 validated on 86 compounds
- see https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol-datafiles/cip/
code: CIP optimizations
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From: <ha...@us...> - 2017-04-29 19:09:30
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Revision: 21575
http://sourceforge.net/p/jmol/code/21575
Author: hansonr
Date: 2017-04-29 19:09:27 +0000 (Sat, 29 Apr 2017)
Log Message:
-----------
Jmol.___JmolVersion="14.15.2" // 4/29/17
bug fix: CIP chirality adds axial chirality (M/P[Ra/Sa], m/p[ra/sa]) for cumulenes
bug fix: CIP chirality adds atropisomer chirality (M/P[Ra/Sa], m/p[ra/sa]) for biaryls
bug fix: CIP chirality adds cumulene E/Z chirality
-- 816 lines
-- validation data are at https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol-datafiles/cip/
-- validates for 160 structures (some duplicates; both cip_examples.zip and stereo_test_cases.sdf)
-- validates for all cases considered:
-- simple R/S and E/Z
-- small-ring removal of E/Z
-- parallel-strand Rule 4b and Rule 5 (Mata)
-- pseudochiral r/s and m/p
-- odd and even cumulenes
-- atropisomers
-- P, S, As, Se, Sb, Te, Bi, Po trigonal pyramidal and tetrahedral
-- imine and diazine E/Z chirality
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-04-29 19:00:44 UTC (rev 21574)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-04-29 19:09:27 UTC (rev 21575)
@@ -64,6 +64,8 @@
-- pseudochiral r/s and m/p
-- odd and even cumulenes
-- atropisomers
+ -- P, S, As, Se, Sb, Te, Bi, Po trigonal pyramidal and tetrahedral
+ -- imine and diazine E/Z chirality
JmolVersion="14.15.1" // 4/28/17
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From: <ha...@us...> - 2017-05-07 00:37:50
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Revision: 21585
http://sourceforge.net/p/jmol/code/21585
Author: hansonr
Date: 2017-05-07 00:37:48 +0000 (Sun, 07 May 2017)
Log Message:
-----------
Jmol.___JmolVersion="14.15.3"
bug fix: use of the less preferred name of Jmol token that has two optional
forms ("fix" vs "fixed") as a VAR does not assign that variable name
bug fix: set cartoonRibose misses the C1'-O4' and O3'-P(+1) edges
bug fix: JVXL reader not reading Gaussian files with "1" in the third line, 5th field
bug fix: CIP chirality
test: load "$2,2'-dibromobiphenyl"; calculate chirality; print {*}.chirality.join("")
bug fix: CIP chirality nearly fully validated on ACD/Labs AY-236 set, with some unimplemented aspects:
var skip = ({27 229}) || // E/Z only; missing chirality
({95 96 98 99 100 101 102 103 104 108 109 110 111 112 200}) || // trigonal planar, square planar, or hypervalent
({32 33}) || // helicene
({201 202})|| // spirocyclic central (redundant) atom designation missing (axial designation option)
({212 213})|| // chiral conformation 1,4-benzene in a ring
({38 84}) || // ignore -- 38: Mancude for cyclopentadienyl; 84: unknown error with P compound
({203}) || // // chiral bridgehead amine
Issue: Full implementation of the rules requires a slight modification of Rule 1b.
Specifically, aromatic duplicate atoms must reference the sphere of their own parent, not their
duplicated atom.
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-05-07 00:35:31 UTC (rev 21584)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-05-07 00:37:48 UTC (rev 21585)
@@ -72,6 +72,12 @@
({212 213})|| // chiral conformation 1,4-benzene in a ring
({38 84}) || // ignore -- 38: Mancude for cyclopentadienyl; 84: unknown error with P compound
({203}) || // // chiral bridgehead amine
+
+Issue: Full implementation of the rules requires a slight modification of Rule 1b.
+Specifically, aromatic duplicate atoms must reference the sphere of their own parent, not their
+duplicated atom.
+
+
Three structures appear to be in error in the IUPAC Blue Book 2013.
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From: <ha...@us...> - 2017-05-13 21:55:35
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Revision: 21592
http://sourceforge.net/p/jmol/code/21592
Author: hansonr
Date: 2017-05-13 21:55:33 +0000 (Sat, 13 May 2017)
Log Message:
-----------
Jmol.___JmolVersion="14.15.4" // 2017-05-13
bug fix: INVERTSELECTED ATOM not documented; functionality of INVERTSTEREO SELECTED folded into it, and INVERTSELECTED STEREO deprecated
-- inverts ring or chain stereochemistry
-- adds that keyword ATOM is optional, so INVERTSELECTED @2 works
bug fix: @n for "atom n" not working in several contexts where {atoms} works.
bug fix: CIP full implementation; simplified algorithm - 984 lines
bug fix: CIP Rule 1b modification to ensure aromatic rings do not result in false positive for R/S (binap2)
-- specifically that the duplicate atom is given the root distance of its parent, not its duplicated atom
bug fix: CIP chiral bridgehead N designations missing
bug fix: CIP Assignment of auxiliary r/s not functional (AY-236.201,202)
bug fix: CIP basic "mancude" atom number adjustment for heteroatoms
-- implemented for benzenoids (benzene, pyridine, pyrazine) and fused benzenoids only
new feature: set debugHigh
-- same as set loglevel 6 - debugging only
-- debugging only; not considered significant enough to increment minor version
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-05-13 21:54:38 UTC (rev 21591)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-05-13 21:55:33 UTC (rev 21592)
@@ -61,7 +61,7 @@
-- inverts ring or chain stereochemistry
-- adds that keyword ATOM is optional, so INVERTSELECTED @2 works
-bug fix: @n for "atom n" not working in several contexts where {atoms} works.
+bug fix: @n for "atom n" not working in several script-checking contexts where {atoms} works.
bug fix: CIP full implementation; simplified algorithm - 984 lines
bug fix: CIP Rule 1b modification to ensure aromatic rings do not result in false positive for R/S (binap2)
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From: <ha...@us...> - 2017-05-14 19:04:55
|
Revision: 21601
http://sourceforge.net/p/jmol/code/21601
Author: hansonr
Date: 2017-05-14 19:04:52 +0000 (Sun, 14 May 2017)
Log Message:
-----------
Jmol.___JmolVersion="14.15.5"
code: CIP: additional simplification;
code: CIP status: implementation complete, including:
All subrules implemented fully: 1a, 1b, 2, 3, 4a, 4b, 4c, 5
R/S, E/Z, M/P, r/s, seqCis/seqTrans (as Z/E)
benzenoid (including fused benzenoid heteroaromatic) Mancude ring "Kekule weighted" atom number adjustments
proposed Rule 1b amendment:
A duplicate atom in a Kekule-weighted system is given a root distance equal to
its sphere, not the sphere of its duplicated atom.
IUPAC Blue Book 2103 errors:
,"147":"r,,,R,,,,r,,,S" // chiral phosphine -- disagrees with BB P-93.5.1.1.2 for S vs R
{
"id" : "148"
"name_pname_pin" : "bis[(1r,4r)-4-methylcyclohexyl]phosphane"
"ref_pname_pin" : "P-93.5.1.1.2"
"stereo" : ",r,,,R,,,,r,,,R,,,"
}
,"148":"r,,,S,,,,r,,,R,,,,s,,,s" // r,,,S,,,,r,,,S,,,,s,,,S Jmol disagrees with BB P-93.5.1.1.2 or R and S p. 1243
{
"id" : "149"
"name_pname_pin" : "bis[(1r,4r)-4-methylcyclohexyl]-(1s,4s)-4-methylcyclohexylphosphane"
"ref_pname_pin" : "P-93.5.1.1.2"
"stereo" : ",r,,,S,,,,r,,,S,,,,s,,,S,,,"
}
,"202":"RR" // // p. 1265 disagrees with BB P-93.5.3.5 for RR vs. SS
{
"id" : "203"
"name_pname_pin" : "(5S,8R,11S)-1,12-dioxatrispiro[4.2.2.4^{11}.2^{8}.2^{5}]nonadecane"
"ref_pname_pin" : "P-93 5.3.5"
}
,"227":"SrSEErS" // disagrees with BB P-93.5.7.2 for S vs. r
{
"id" : "228"
"name_pname_pin" : "(1E)-1-{(1'S,1r,4s)-[1,1'-bi(cyclohexan)]-3'-en-4-yl}-N-[(1r,4r)-4-phenylcyclohexyl]methan-1-imine"
"ref_pname_pin" : "P-93.5.7.2"
"stereo" : "S,,,,,,,r,S,,,,,,,E,,r,r,,,,,,,,,,,,"
}
,"230":"@3D RrRsR" // p 1282 disagrees with BB P-93.6
{
"id" : "231"
"name_pname_pin" : "(2R)-1-[(1r,4R)-4-methylcyclohexyl]-3-[(1s,4S)-4-methylcyclohexyl]propan-2-ol"
"ref_pname_pin" : "P-93.6"
"stereo" : ",,,,r,,,R,,,,s,,,R,,,"
}
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-05-14 18:49:17 UTC (rev 21600)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-05-14 19:04:52 UTC (rev 21601)
@@ -55,8 +55,62 @@
# instead of the occupancies I tried to assign in jmol.
-Jmol.___JmolVersion="14.15.4" // 2017-05-13
+Jmol.___JmolVersion="14.15.5"
+
+code: CIP: additional simplification;
+code: CIP status: implementation complete, including:
+ All subrules implemented fully: 1a, 1b, 2, 3, 4a, 4b, 4c, 5
+ R/S, E/Z, M/P, r/s, seqCis/seqTrans (as Z/E)
+ benzenoid (including fused benzenoid heteroaromatic) Mancude ring "Kekule weighted" atom number adjustments
+ proposed Rule 1b amendment:
+ A duplicate atom in a Kekule-weighted system is given a root distance equal to
+ its sphere, not the sphere of its duplicated atom.
+
+IUPAC Blue Book 2103 errors:
+
+,"147":"r,,,R,,,,r,,,S" // chiral phosphine -- disagrees with BB P-93.5.1.1.2 for S vs R
+{
+ "id" : "148"
+ "name_pname_pin" : "bis[(1r,4r)-4-methylcyclohexyl]phosphane"
+ "ref_pname_pin" : "P-93.5.1.1.2"
+ "stereo" : ",r,,,R,,,,r,,,R,,,"
+ }
+
+,"148":"r,,,S,,,,r,,,R,,,,s,,,s" // r,,,S,,,,r,,,S,,,,s,,,S Jmol disagrees with BB P-93.5.1.1.2 or R and S p. 1243
+{
+ "id" : "149"
+ "name_pname_pin" : "bis[(1r,4r)-4-methylcyclohexyl]-(1s,4s)-4-methylcyclohexylphosphane"
+ "ref_pname_pin" : "P-93.5.1.1.2"
+ "stereo" : ",r,,,S,,,,r,,,S,,,,s,,,S,,,"
+ }
+
+,"202":"RR" // // p. 1265 disagrees with BB P-93.5.3.5 for RR vs. SS
+{
+ "id" : "203"
+ "name_pname_pin" : "(5S,8R,11S)-1,12-dioxatrispiro[4.2.2.4^{11}.2^{8}.2^{5}]nonadecane"
+ "ref_pname_pin" : "P-93 5.3.5"
+ }
+
+,"227":"SrSEErS" // disagrees with BB P-93.5.7.2 for S vs. r
+{
+ "id" : "228"
+ "name_pname_pin" : "(1E)-1-{(1'S,1r,4s)-[1,1'-bi(cyclohexan)]-3'-en-4-yl}-N-[(1r,4r)-4-phenylcyclohexyl]methan-1-imine"
+ "ref_pname_pin" : "P-93.5.7.2"
+ "stereo" : "S,,,,,,,r,S,,,,,,,E,,r,r,,,,,,,,,,,,"
+ }
+
+,"230":"@3D RrRsR" // p 1282 disagrees with BB P-93.6
+{
+ "id" : "231"
+ "name_pname_pin" : "(2R)-1-[(1r,4R)-4-methylcyclohexyl]-3-[(1s,4S)-4-methylcyclohexyl]propan-2-ol"
+ "ref_pname_pin" : "P-93.6"
+ "stereo" : ",,,,r,,,R,,,,s,,,R,,,"
+ }
+
+
+JmolVersion="14.15.4" // 2017-05-13
+
bug fix: INVERTSELECTED ATOM not documented; functionality of INVERTSTEREO SELECTED folded into it, and INVERTSELECTED STEREO deprecated
-- inverts ring or chain stereochemistry
-- adds that keyword ATOM is optional, so INVERTSELECTED @2 works
@@ -65,7 +119,7 @@
bug fix: CIP full implementation; simplified algorithm - 984 lines
bug fix: CIP Rule 1b modification to ensure aromatic rings do not result in false positive for R/S (binap2)
- -- specifically that the duplicate atom is given the root distance of its parent, not its duplicated atom
+ -- specifically that the duplicate atom is given a root distance equal to its sphere, not that of its duplicated atom
bug fix: CIP chiral bridgehead N designations missing
bug fix: CIP Assignment of auxiliary r/s not functional (AY-236.201,202)
bug fix: CIP basic "mancude" atom number adjustment for heteroatoms
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From: <ha...@us...> - 2017-07-20 11:24:37
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Revision: 21664
http://sourceforge.net/p/jmol/code/21664
Author: hansonr
Date: 2017-07-20 11:24:34 +0000 (Thu, 20 Jul 2017)
Log Message:
-----------
Jmol.___JmolVersion="14.20.3" // 2017.07.20
bug fix: CIPChirality tests for CIP1966#31,#32 douple spirans and C3 compounds
bug fix: CIPChirality for Rule 2 using atomic masses and not for duplicate atoms
bug fix: MOL file reading where isotope is indicated in atom line and V item
bug fix: MOL reader fails for H1, D, T isotopes indicated as symbols along with isotope difference
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-07-20 04:58:30 UTC (rev 21663)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-07-20 11:24:34 UTC (rev 21664)
@@ -56,7 +56,7 @@
# TODO: fix UNDO
-Jmol.___JmolVersion="14.20.3"
+Jmol.___JmolVersion="14.20.3" // 2017.07.20
bug fix: CIPChirality tests for CIP1966#31,#32 douple spirans and C3 compounds
bug fix: CIPChirality for Rule 2 using atomic masses and not for duplicate atoms
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From: <ha...@us...> - 2021-08-18 02:17:40
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Revision: 22222
http://sourceforge.net/p/jmol/code/22222
Author: hansonr
Date: 2021-08-18 02:17:38 +0000 (Wed, 18 Aug 2021)
Log Message:
-----------
Jmol.___JmolVersion="14.31.52"
also 15.1.52
bug fix: JavaScript does not return to correct scrpt level after DELAY
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2021-08-18 02:12:55 UTC (rev 22221)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2021-08-18 02:17:38 UTC (rev 22222)
@@ -57,7 +57,12 @@
# TODO: isosurface cavity delivers nonsense volume due to unclosed surface
-Jmol.___JmolVersion="14.31.51"
+Jmol.___JmolVersion="14.31.52"
+ also 15.1.52
+
+bug fix: JavaScript does not return to correct scrpt level after DELAY
+
+JmolVersion="14.31.51"
also 15.1.51 (take 2)
new feature: ISOSURFACE DENSITY option
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From: <ha...@us...> - 2021-09-24 15:45:17
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Revision: 22232
http://sourceforge.net/p/jmol/code/22232
Author: hansonr
Date: 2021-09-24 15:45:14 +0000 (Fri, 24 Sep 2021)
Log Message:
-----------
14.31.55
bug fix: UnitCell transform should be included in COMPARE FRAME
bug fix: CifReader fix for lack of case sensitivity in some GEOM_* records for some COD and CCDC files
bug fix: FilesReader fails with zip file pipe
bug fix: Polyhedra SMILES not working for chirality check -- was never fully tested
bug fix: Resolver can fail for certain CIF files resolved to MOL incorrectly
bug fix: TopoCif update
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2021-09-24 15:29:11 UTC (rev 22231)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2021-09-24 15:45:14 UTC (rev 22232)
@@ -59,7 +59,28 @@
Jmol.___JmolVersion="14.31.55"
also 15.1.55
-
+
+bug fix: UnitCell transform should be included in COMPARE FRAME
+bug fix: CifReader fix for lack of case sensitivity in some GEOM_* records for some COD and CCDC files
+bug fix: FilesReader fails with zip file pipe
+bug fix: Polyhedra SMILES not working for chirality check -- was never fully tested
+bug fix: Resolver can fail for certain CIF files resolved to MOL incorrectly
+bug fix: TopoCif update
+
+new feature: COMPARE additions:
+
+ // compare FRAMES
+ // compare {model1} {model2} POLYHEDRA
+ // compare {model1} {model2} SUBSET {polyhedra} POLYHEDRA
+ // compare {model1} {model2} ATOMS @atom1 @atom2 POLYHEDRA
+ // compare FRAMES POLYHEDRA
+
+new feature: compare() additions
+
+ // A, B, int[] map
+ // A, B, int[] map, stddev
+
+
JmolVersion="14.31.54"
also 15.1.54
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From: <ha...@us...> - 2021-09-29 15:05:45
|
Revision: 22234
http://sourceforge.net/p/jmol/code/22234
Author: hansonr
Date: 2021-09-29 15:05:43 +0000 (Wed, 29 Sep 2021)
Log Message:
-----------
Jmol.___JmolVersion="14.31.55"
also 15.1.55
new feature: COMPARE {2.1} {1.1} BONDS SMILES HYDROGEN
- adds HYDROGEN check for aligning methyl and methylene groups properly
bug fix: (-1.4567).format("%5.2f") missing minus sign
bug fix: UnitCell transform should be included in COMPARE FRAME
bug fix: CifReader fix for lack of case sensitivity in some GEOM_* records for some COD and CCDC files
bug fix: FilesReader fails with zip file pipe
bug fix: Polyhedra SMILES not working for chirality check -- was never fully tested
bug fix: Resolver can fail for certain CIF files resolved to MOL incorrectly
bug fix: TopoCif update
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2021-09-29 15:03:03 UTC (rev 22233)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2021-09-29 15:05:43 UTC (rev 22234)
@@ -60,6 +60,10 @@
Jmol.___JmolVersion="14.31.55"
also 15.1.55
+new feature: COMPARE {2.1} {1.1} BONDS SMILES HYDROGEN
+ - adds HYDROGEN check for aligning methyl and methylene groups properly
+
+bug fix: (-1.4567).format("%5.2f") missing minus sign
bug fix: UnitCell transform should be included in COMPARE FRAME
bug fix: CifReader fix for lack of case sensitivity in some GEOM_* records for some COD and CCDC files
bug fix: FilesReader fails with zip file pipe
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From: <ha...@us...> - 2021-12-05 13:51:01
|
Revision: 22272
http://sourceforge.net/p/jmol/code/22272
Author: hansonr
Date: 2021-12-05 13:50:58 +0000 (Sun, 05 Dec 2021)
Log Message:
-----------
Jmol.___JmolVersion="15.2.2" also 14.32.2 - Modelkit
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2021-12-05 05:29:43 UTC (rev 22271)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2021-12-05 13:50:58 UTC (rev 22272)
@@ -81,6 +81,8 @@
modelkit ON
modelkit OFF
+
+ -- note that the modelkit does not have to be ON for the following functionality.
-- configuration options include the following, where (xxx) is optional, CAPS is default:
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From: <ha...@us...> - 2022-01-16 03:28:30
|
Revision: 22299
http://sourceforge.net/p/jmol/code/22299
Author: hansonr
Date: 2022-01-16 03:28:27 +0000 (Sun, 16 Jan 2022)
Log Message:
-----------
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2022-01-16 03:24:21 UTC (rev 22298)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2022-01-16 03:28:27 UTC (rev 22299)
@@ -100,7 +100,7 @@
bug fix: CMLWriter broken; maybe never worked.
bug fix: format() did not allow for decimal places up to 12.
-bug fix: POSCAR reader treating "T" constraing as "tritium"
+bug fix: POSCAR reader treating "T" constraint as "tritium"
bug fix: XCrystDen reader not reading animation properly
JmolVersion="14.32.11"
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From: <ha...@us...> - 2022-01-24 04:50:01
|
Revision: 22315
http://sourceforge.net/p/jmol/code/22315
Author: hansonr
Date: 2022-01-24 04:49:58 +0000 (Mon, 24 Jan 2022)
Log Message:
-----------
Jmol.___JmolVersion="14.32.16"
also 15.2.16
new feature: (JavaScript API) Jmol.setCallback(jmolApplet0, "xxx", function() {......})
-- where "xxx" is one of the allowed callbacks, namely (case insensitive):
ANIMFRAME, APPLETREADY, ATOMMOVED, AUDIO, CLICK, DRAGDROP, ECHO,
ERROR, EVAL, HOVER, IMAGE, LOADSTRUCT, MEASURE, MESSAGE, MINIMIZATION,
MODELKIT, PICK, RESIZE, SCRIPT, SELECT, SERVICE, STRUCTUREMODIFIED, SYNC
-- allows anonymous function setting for callbacks rather than using JmolScript SET xxxCallback "funcName"
new feature: (JavaScript) Info = { .... , errorCallback: function{....},...}
-- allows setting of functions rather than function names in Info parameters
new feature: (JavaScript) Info = { .... , errorCallback: function{....},...}
-- allows setting of functions rather than function names in Info parameters
new feature: Drag-Drop into Java AppConsole assumed to be script and run
new feature: Drag-Drop into JavaScript output console assumed to be script and run
new feature: Drag-Drop into JavaScript input console displayed
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2022-01-24 04:49:32 UTC (rev 22314)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2022-01-24 04:49:58 UTC (rev 22315)
@@ -97,7 +97,7 @@
new feature: Drag-Drop into JavaScript input console displayed
-
+
JmolVersion="14.32.15"
also 15.2.15
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From: <ha...@us...> - 2022-03-08 04:13:25
|
Revision: 22361
http://sourceforge.net/p/jmol/code/22361
Author: hansonr
Date: 2022-03-08 04:13:22 +0000 (Tue, 08 Mar 2022)
Log Message:
-----------
(that is, on an axis or plane)
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2022-03-08 03:52:48 UTC (rev 22360)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2022-03-08 04:13:22 UTC (rev 22361)
@@ -83,8 +83,8 @@
new feature: set picking dragAtom TRUE now recognizes symmetry for crystal structures
-- drags atoms only if symmetry-allowed
+ (that is, on an axis or plane)
-- does not move atoms if they are in fixed special positions
- (that is, on an axis or plane)
new feature: {1/2 1/2 1/2}.symop("invariant")
-- similar to @@1.symop("invariant")
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From: <ha...@us...> - 2022-03-14 03:06:58
|
Revision: 22370
http://sourceforge.net/p/jmol/code/22370
Author: hansonr
Date: 2022-03-14 03:06:55 +0000 (Mon, 14 Mar 2022)
Log Message:
-----------
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2022-03-14 02:21:32 UTC (rev 22369)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2022-03-14 03:06:55 UTC (rev 22370)
@@ -70,8 +70,8 @@
-Jmol.___JmolVersion="15.2.34"
- also 14.32.34
+Jmol.___JmolVersion="14.32.34"
+ also 15.2.34
bug fix: PWMatReader constraints default 1 1 1
bug fix: PWMatReader resolver fix
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From: <ha...@us...> - 2022-03-31 15:09:19
|
Revision: 22392
http://sourceforge.net/p/jmol/code/22392
Author: hansonr
Date: 2022-03-31 15:09:17 +0000 (Thu, 31 Mar 2022)
Log Message:
-----------
Jmol.___JmolVersion="14.32.45" // also 15.2.45
bug fix: PDBReader fails to treat chain case for filter biomolecule
bug fix: PDBReader can fail when making connections with filter biomolecule
bug fix: attempted LOAD of nonexistant PNGJ file (*.png) can crash Jmol
bug fix: CIFWriter and PWMATWriter do not round coordinates very close to 1.0000
new feature: SCALE command
-- a special category of ECHO
-- also ECHO "%SCALE (units)"
-- draws a |---| scale in the specified location
-- adjusts by decades -- 0.01, 0.1, 1, 10, 100, etc.
-- SCALE ON
-- turns scale on at bottom left
-- units dynamic, corresponding to SET measurementUnits
-- SCALE OFF
-- turns scale off
-- SCALE (units)
-- optional fixed units, where (units) can be one of:
"nanometers" ("nm")
"picometers" ("pm")
"angstroms" ("a" or "ang")
"bohr" ("atomicunits" or "au")
-- when perspectiveDepth TRUE, is for center of visible depth based on screen width
-- like FRANK, persists through file loading and ZAP
-- additional relevant options same as for SET ECHO command
-- examples:
SCALE angstroms bottom center
new feature: COLOR SCALE ...
-- sets the color of the scale
new feature: FONT SCALE ...
-- sets the font of the scale
new default properties: Jmol application (Java and JavaScript) adds two additional preferences:
-- antialiasDisplay TRUE
-- measurementUnits "angstroms"
-- PreferencesDialog will set these as "JmolDefaults"
new feature: ECHO "%SCALE (units)"
-- same as SCALE (units) ...
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2022-03-31 15:03:56 UTC (rev 22391)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2022-03-31 15:09:17 UTC (rev 22392)
@@ -72,6 +72,11 @@
Jmol.___JmolVersion="14.32.45" // also 15.2.45
+bug fix: PDBReader fails to treat chain case for filter biomolecule
+bug fix: PDBReader can fail when making connections with filter biomolecule
+bug fix: attempted LOAD of nonexistant PNGJ file (*.png) can crash Jmol
+bug fix: CIFWriter and PWMATWriter do not round coordinates very close to 1.0000
+
new feature: SCALE command
-- a special category of ECHO
-- also ECHO "%SCALE (units)"
@@ -108,7 +113,6 @@
new feature: ECHO "%SCALE (units)"
-- same as SCALE (units) ...
- -- implementation for SCALE in state for backward-compatibility
JmolVersion="14.32.44" // also 15.2.44
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From: <ha...@us...> - 2022-04-07 06:16:28
|
Revision: 22395
http://sourceforge.net/p/jmol/code/22395
Author: hansonr
Date: 2022-04-07 06:16:25 +0000 (Thu, 07 Apr 2022)
Log Message:
-----------
Jmol.___JmolVersion="14.32.46" // also 15.2.46
bug fix: load PDB filter "BMCHAINS=a" should work -- (lower-case issue)
bug fix: set structureModifiedCallback for attempt to move fixed atom should report "FAILED"
bug fix: {assoc array}.pivot.pivot() not working
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2022-04-07 06:14:35 UTC (rev 22394)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2022-04-07 06:16:25 UTC (rev 22395)
@@ -70,15 +70,12 @@
-Jmol.___JmolVersion="14.32.47" // also 15.2.47
+Jmol.___JmolVersion="14.32.46" // also 15.2.46
bug fix: load PDB filter "BMCHAINS=a" should work -- (lower-case issue)
bug fix: set structureModifiedCallback for attempt to move fixed atom should report "FAILED"
bug fix: {assoc array}.pivot.pivot() not working
-
-JmolVersion="14.32.46" // also 15.2.46
-
new feature: hkl(1 0 0 0.3) to produce plane offset by 0.3 Angstroms from the origin.
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From: <ha...@us...> - 2022-04-08 04:26:17
|
Revision: 22397
http://sourceforge.net/p/jmol/code/22397
Author: hansonr
Date: 2022-04-08 04:26:14 +0000 (Fri, 08 Apr 2022)
Log Message:
-----------
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2022-04-08 03:04:59 UTC (rev 22396)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2022-04-08 04:26:14 UTC (rev 22397)
@@ -70,7 +70,7 @@
-Jmol.___JmolVersion="14.3.47" // also 15.2.47
+Jmol.___JmolVersion="14.32.47" // also 15.2.47
bug fix: removing difference between set fx, fux
-too confusing
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From: <ha...@us...> - 2022-05-17 13:45:58
|
Revision: 22414
http://sourceforge.net/p/jmol/code/22414
Author: hansonr
Date: 2022-05-17 13:45:55 +0000 (Tue, 17 May 2022)
Log Message:
-----------
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2022-05-17 13:40:17 UTC (rev 22413)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2022-05-17 13:45:55 UTC (rev 22414)
@@ -77,7 +77,7 @@
bug fix: MMCIF files with single entries rather than loops could fail
bug fix: MMCIF files with DSSR or RNA3D extensions could fail.
-Jmol.___JmolVersion="14.32.55" // P also 15.2.55
+JmolVersion="14.32.55" // P also 15.2.55
(into Jmol 14 only from Jmol-SwingJS precision branch)
feature change: axes POSITION [x y] "xyz" with symmetry
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From: <ha...@us...> - 2022-07-25 05:50:10
|
Revision: 22435
http://sourceforge.net/p/jmol/code/22435
Author: hansonr
Date: 2022-07-25 05:50:07 +0000 (Mon, 25 Jul 2022)
Log Message:
-----------
bug fix: scale units should be in a state that includes echo "%SCALE" or the SCALE command
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2022-07-25 05:49:07 UTC (rev 22434)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2022-07-25 05:50:07 UTC (rev 22435)
@@ -68,7 +68,7 @@
-Jmol.___JmolVersion="14.32.64" // P also 15.2.64
+Jmol.___JmolVersion="14.32.64" // P also 15.2.64 (reissued)
new feature: ORCA input/output reader
@@ -77,6 +77,7 @@
bug fix: COLOR ECHO TRANSLUCENT missing space char in state
bug fix: certain SCALE objects appear transparent with antialiasDisplay
bug fix: set FONTSIZE by itself crashes Jmol
+bug fix: scale units should be in a state that includes echo "%SCALE" or the SCALE command
JmolVersion="14.32.63" // P also 15.2.63
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From: <ha...@us...> - 2022-11-23 12:34:36
|
Revision: 22489
http://sourceforge.net/p/jmol/code/22489
Author: hansonr
Date: 2022-11-23 12:34:33 +0000 (Wed, 23 Nov 2022)
Log Message:
-----------
Jmol.___JmolVersion="15.2.81" // also 14.32.81
new feature: LCAOCARTOON create "anti-sp3a"
-- adds a small anti-sense back-lobe to an sp3 cartoon.
new feature: LCAOCARTOON create "-anti-sp3a"
-- with prefix minus sign reverses the direction of the orbital and
adds a small back-lobe
new feature: LCAOCARTOON REVERSE [optional TRUE|FALSE] (default TRUE)
-- switches the color of two-lobe orbitals such as px and anti-sp3
-- as for other LCAOCARTOON parameters, REVERSE persists until changes
-- for example:
bug fix: modelkit sets boundbox to default value {-10 -10 -10} to {10 10
10} during adding H atoms
bug fix: minimizer does not fire StructureModifiedCallback; now does,
with mode 3/-3 (coord change)
bug fix: PDBWriter does not properly identify CONECT records
bug fix: invertStereo fails for alkenes
bug fix: Pymol reader fails in relation to parent groups
bug fix: WebExport fails
bug fix: V3000 reader misreads continuation lines
bug fix: Automatic 2D->3D conversion for multi-model files fails (should
minimize just first model)
bug fix: print x.select("properties where properties[2] == 3") does not
work, because "properties" being turned into "property"
bug fix: map.format("JSON") should sort map items
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2022-11-22 21:50:16 UTC (rev 22488)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2022-11-23 12:34:33 UTC (rev 22489)
@@ -69,6 +69,26 @@
\xA0 -- switches the color of two-lobe orbitals such as px and anti-sp3
\xA0 -- as for other LCAOCARTOON parameters, REVERSE persists until changes
\xA0 -- for example:
+
+
+ load $1-bromo-2-butene;
+ lcaocartoon @1 reverse false color green yellow "-anti-sp3a";
+ lcaocartoon @2 reverse true color green yellow "-anti-sp3a";
+
+ same as
+\xA0
+ load $1-bromo-2-butene;
+ lcaocartoon @1 color green yellow "-anti-sp3a";
+ lcaocartoon @2 reverse "-anti-sp3a";
+\xA0
+ same as
+\xA0
+ load $1-bromo-2-butene;
+ lcaocartoon reverse false color green yellow;
+ lcaocartoon @1 create "-anti-sp3a";
+ lcaocartoon reverse;
+ lcaocartoon @2 create "-anti-sp3a";
+
bug fix: modelkit sets boundbox to default value {-10 -10 -10} to {10 10 10} during adding H atoms
bug fix: minimizer does not fire StructureModifiedCallback; now does, with mode 3/-3 (coord change)
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From: <ha...@us...> - 2023-09-13 21:23:21
|
Revision: 22561
http://sourceforge.net/p/jmol/code/22561
Author: hansonr
Date: 2023-09-13 21:23:18 +0000 (Wed, 13 Sep 2023)
Log Message:
-----------
Jmol.___JmolVersion="16.1.39" // (legacy) also 16.1.40 (swingJS)
new feature: string.push("xx")
-- appends a string to a string
new feature: string.pop()
-- pops a character off a string
new feature: {atomset}.atoms and {atomset}.label("%[atoms]")
-- same as {atomset}.label("[%n]%r:%c.%a")
-- specifically does not include altloc
-- can be used to identify associated altlocs efficiently
-- example use:
history off
load =5pol
altlocKeys = {}
altlocAtoms = {};
theatoms = {altloc!=''}
for (var a in theatoms){
var name = a.atom;
if (!altlocKeys[name]) {
altlocKeys[name] = "";
altlocAtoms[name] = ({});
}
altlocKeys[name].push(a.altloc);
altlocAtoms[name] |= a.atomIndex;
}
history on
resulting in the creation of the arrays altlocKeys and altlocAtoms, which
group alternate location codes and atom sets by atom name:
{
"[8RP]201:A.C1": "D",
...
"[MET]23:B.SD" : "CD"
}
and
{
"[8RP]201:A.C1" : ({2093}),
...
"[MET]23:B.SD" : ({1039 1040})
}
new feature: AMS reader
- version extension of ADF reader
bug fix: patch #40 ADF/AMS output support (Diego Gayaga)
- support for ADF output files was not working
- for geometry optimizations, only the initial geometry was grabbed
without actually being able to visualize the optimized structure.
Moreover, vibrational displacements were being applied to this initial structure,
which was not consistent.
- newer versions of the ADF code are now named Amsterdam Modeling Suite (AMS)
instead of ADF; these files were also not properly supported.
- bonding energy as a model property is also added.
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2023-09-12 17:24:17 UTC (rev 22560)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2023-09-13 21:23:18 UTC (rev 22561)
@@ -68,11 +68,13 @@
-- pops a character off a string
new feature: {atomset}.atoms and {atomset}.label("%[atoms]")
- -- string label format that does not include altloc or # atomnumber extension
+ -- same as {atomset}.label("[%n]%r:%c.%a")
+ -- specifically does not include altloc
-- can be used to identify associated altlocs efficiently
- -- example use (initial closing parenthesis means "don't record script history"
+ -- example use:
- )load =5pol
+ history off
+ load =5pol
altlocKeys = {}
altlocAtoms = {};
theatoms = {altloc!=''}
@@ -85,8 +87,39 @@
altlocKeys[name].push(a.altloc);
altlocAtoms[name] |= a.atomIndex;
}
+ history on
+
+ resulting in the creation of the arrays altlocKeys and altlocAtoms, which
+ group alternate location codes and atom sets by atom name:
+
+ {
+ "[8RP]201:A.C1": "D",
+ ...
+ "[MET]23:B.SD" : "CD"
+ }
+
+ and
+
+ {
+ "[8RP]201:A.C1" : ({2093}),
+ ...
+ "[MET]23:B.SD" : ({1039 1040})
+ }
+
+new feature: AMS reader
+ - version extension of ADF reader
+bug fix: patch #40 ADF/AMS output support (Diego Gayaga)
+ - support for ADF output files was not working
+ - for geometry optimizations, only the initial geometry was grabbed
+ without actually being able to visualize the optimized structure.
+ Moreover, vibrational displacements were being applied to this initial structure,
+ which was not consistent.
+ - newer versions of the ADF code are now named Amsterdam Modeling Suite (AMS)
+ instead of ADF; these files were also not properly supported.
+ - bonding energy as a model property is also added.
+
JmolVersion="16.1.37" // (legacy) also 16.1.38 (swingJS)
bug fix: set picking dragAtom does not update measurements
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