From: <ha...@us...> - 2010-06-16 20:31:54
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Revision: 13405 http://jmol.svn.sourceforge.net/jmol/?rev=13405&view=rev Author: hansonr Date: 2010-06-16 20:31:48 +0000 (Wed, 16 Jun 2010) Log Message: ----------- 12.0.RC19 VERSION # bug fix: QChem reader MO fix # bug fix: MO using cartesian instead of spherical D orbitals. # bug fix: modelKitMode replacing atoms with H # bug fix: bioSMARTS X:Y problem # bug fix: set logLevel (with no arguments)/show logLevel # bug fix: alas, MEP mapping has been in Bohr, not Angstroms. Values are actually 1.89x prev. calculation # default range set to -0.1 to 0.1 for MEP and MLP. # new feature: atomic lipophilicity mapping (MLP) and generalized MEP: # isosurface sasurface map MLP|MEP [function type (integer 0 to 3)] [resource fileName] # isosurface sasurface map MLP|MEP [function type (integer 0 to 3)] [property_xxxx] # isosurface sasurface map MLP|MEP [function type (integer 0 to 3)] [property propertyName] # The defaults are: # isosurface sasurface map MEP 0 property partialCharge # isosurface sasurface map MLP 3 "http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol/src/org/jmol/quantum/atomicLipophilicity.txt" # Implemented here is a flexible way of mapping atomic potential data onto # a surface. Given a set of atoms, we assign numbers to the atoms from: # # a) a resource in this package and based on atom names, or # b) a table of data read from a file and based on atom names, or # c) an array of properties assigned to the atoms. # # In addition, once those potentials are assigned, we can apply a variety # of functions of distance: # # (0) Coulomb's law distance function (same as rasmol potential distance function) # (1) f * e^(-d/2) # Gaillard, P., Carrupt, P.A., Testa, B. and Boudon, A., J.Comput.Aided Mol.Des. 8, 83-96 (1994) # (2) f/(1 + d) # Audry, E.; Dubost, J. P.; Colleter, J. C.; Dallet, P. A new approach to structure-activity relations: the "molecular lipophilicity potential". Eur. J. Med. Chem. 1986, 21, 71-72. # (3) f * e^(-d) # Fauchere, J. L.; Quarendon, P.; Kaetterer, L. Estimating and representing hydrophobicity potential. J. Mol. Graphics 1988, 6, 203-206. # from http://www.life.illinois.edu/crofts/bc1_in_chime/chime_talk/chimescript2.html # The difference between MEP and MLP is simply the defaults for resource and function: # # a) the default resource is property partialCharge for MEP and atomicLipophilicity.txt for MLP # b) the default function is Coulomb for MEP and Fauchere for MLP # bug fix: make WebExport Widgets compatible with IE6 through 8 # bug fix: isosurface vdw map ... not working # new feature: preliminary molecular lipophilic potential. # isosurface vdw map MLP # new feature: bioSMARTS indicates all cross-linking for carbohydrates # bug fix: name conflicts in WebExport Widgets js files. # bug fix: table now wide enough for colorpicker popup in WebExport. # bug fix: angstroms measurement unit not showing up as proper A symbol. # new feature: measure search("Ocnc") # or measure search "Ocnc" # - operates on previously selected atoms # bug fix: application -- set modelkitmode does not feedback to buttons # SMILES/SMARTS options summary: # # examples: # # selecting atoms using SMARTS: # # select search("CC") // selects ALL matching atoms using SMARTS notation # select search("CC", 1.1) // same as above, but within model 1.1 # # assigning variables based on SMARTS: # # x = {1.1}.find("CC") // assigns a single bitset to all matching atoms # x = {1.1}.find("CC", true) // same as above, but returns an array of pattern matches # n = {1.1}.find("CC", true).length // counts the number of matches # # SMILES string comparison and searching: # # x = "CC(C)CC".find("smiles","CCC(C)C") // smiles matching -- returns an array of length=1 # x = "CC(C)CC".find("smarts","CCCC") // returns a bitset containing all atoms # x = "CC(C)CC".find("smarts","CCCC", true) // returns an array of bitsets containing the pattern # # generating SMILES and bioSMILES strings: # # x = {1.1}.find("SMILES") // get the SMILES string for the model 1.1 # x = {1.1}.find("SMILES", true) // get the bioSMILES string for the model 1.1 # - use select search(...) to do SMARTS substructure searching # - use the find function to assign variables. # - use TRUE with the find function to retrieve and count matches # - use find(..).length to count the number of matches # - use find to get the SMILES or bioSMILES string for a structure // deprecated/unnecessary: # select substructure("..") // same as select smarts(... # select within(smarts...) // same as select smarts(... # select within(smiles...) // same as select smiles(..., but not recommended # x = within("smarts", "CC") // same as {*}.find("CC") # x = within("smiles", "CC") // same as {*}.find("smiles", "CC") # bug fix: SMILES errors should be reported but not cause script failure # bug fix: select within("smarts","Cn",all,atomno=19) does not properly # restrict set to only those patterns that include atomno=19 # bug fix: select substructure(...) now synonymous with select SMARTS(), not select SMILES() # as would be expected for substructure searches. # bug fix: modelkit connection doesn't modify bonds automatically # new feature: assign CONNECT {a} {b} # -- does a simple connection, but then, # like assign atom and assign bond, fixes hydrogens 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 2010-06-16 20:28:36 UTC (rev 13404) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2010-06-16 20:31:48 UTC (rev 13405) @@ -1,7 +1,7 @@ # Developers: to add a description of changes you have made, # add it on a line starting with # below the "version=..." line -version=12.0.RC19_dev +version=12.0.RC19 # bug fix: QChem reader MO fix # bug fix: MO using cartesian instead of spherical D orbitals. 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