From: Michael T H. <mic...@us...> - 2003-11-18 21:41:58
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Update of /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/script In directory sc8-pr-cvs1:/tmp/cvs-serv11384/src/org/openscience/jmol/viewer/script Modified Files: Token.java Log Message: corrected predefined set definitions Index: Token.java =================================================================== RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/script/Token.java,v retrieving revision 1.14 retrieving revision 1.15 diff -u -r1.14 -r1.15 --- Token.java 16 Nov 2003 22:49:21 -0000 1.14 +++ Token.java 18 Nov 2003 21:41:55 -0000 1.15 @@ -504,21 +504,21 @@ static String[] predefinitions = { "@at a,t", - "@acidic d,e", - "@acyclic a,r,n,d,c,e,q,g,i,l,k,m,s,t,v", - "@aliphatic a,g,i,l,v", + "@acidic asp,glu", + "@acyclic amino&!cyclic", + "@aliphatic ala,gly,ile,leu,val", "@alpha _atomid=1", // rasmol doc says "approximately *.CA" - whatever? "@amino _resid<=22", - "@aromatic h,f,w,y", + "@aromatic his,phe,trp,tyr", // "@backbone amino & _atomid<=3,nucleic & _atomid>=4 & _atomid<=15", - "@backbone amino & _atomid<=3", + "@backbone amino&_atomid<=3", "@mainchain backbone", - "@basic r,h,k", + "@basic arg,his,lys", "@bonded _bondedcount>0", - "@buried a,c,i,l,m,f,w,v", + "@buried ala,cys,ile,leu,met,phe,trp,val", "@cg c,g", "@charged acidic,basic", - "@cyclic h,f,p,w,y", + "@cyclic his,phe,pro,trp,tyr", // "@cystine", "@helix _structure=3", // "@hetero", handled specially @@ -526,17 +526,17 @@ // text description of hydrophobic says this // "@hydrophobic ala,leu,val,ile,pro,phe,met,trp", // table says this - "@hydrophobic a,g,i,l,m,f,p,w,y,v", + "@hydrophobic ala,gly,ile,leu,met,phe,pro,trp,tyr,val", "@ions _resid=29,_resid=30", - "@large r,e,q,h,i,l,k,m,f,w,y", + "@large arg,glu,gln,his,ile,leu,lys,met,phe,trp,tyr", "@ligand hetero & !solvent", - "@medium n,d,c,p,t,v", + "@medium asn,asp,cys,pro,thr,val", // doc is inconsistent // is h basic or neutral "@negative acidic", - "@neutral a,n,c,q,g,h,i,l,m,f,p,s,t,w,y,v", + "@neutral amino&!(acidic,basic)", "@nucleic a,c,g,t", - "@polar !hydrophobic", + "@polar amino&!hydrophobic", "@positive basic", "@protein amino", // + common post-translational modifications ?? "@purine a,g", @@ -544,11 +544,17 @@ // selected - special and is handled at runtime "@sheet _structure=2", "@sidechain (protein or nucleic) and !backbone", // doc & code inconsistent - "@small a,g,s", + "@small ala,gly,ser", "@solvent _resid>=27 & _resid<=30", // water or ions "@surface !buried", "@turn _structure=1", - "@water _resid=27,_resid=28", "@hoh water", + "@water _resid=27,_resid=28", + "@hoh water", + + "@a _resid=23", + "@c _resid=24", + "@g _resid=25", + "@t _resid=26", /* eliminated because some of these conflict with nucleic acids |