Revision: 20258
http://sourceforge.net/p/jmol/code/20258
Author: hansonr
Date: 2015-01-30 14:43:12 +0000 (Fri, 30 Jan 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.3.12_2015.01.30"
new feature: MUTATE command
-- operates only on last model present if multiple models are loaded
-- replaces one or more amino acids group with others
-- can read from RCSB or from user-specified file
-- examples:
mutate 33 lys // replace resno=33 with lysine
mutate @3 arg // replaces group of atom 3 with arginine
mutate @r gly // replaces groups in variable r with glycine
mutate 22 "myfile.cif" // user-defined replacement
mutate {1-3} ala // replace first three residues with alanine
mutate {1-5} GLVAG // (sequence codes) replace residues 1-5 with
gly-leu-val-ala-gly
mutate {1-3} ~LYS // (force 1-character sequence codes) replace 1-3
with leu-tyr-ser
mutate {1-3} A?L // replace 1 with ala, 3 with leu; skip 2
mutate {within(sequence, "GAT")} GYT // replace locations of GAT with GYT
(needs testing)
mutate 35 @fname // replaces resno=33 with file data (use "==XXX"
for RCSB)
mutate {r} his // same as above; r must be an atom selection
bug fix: code fixes relating to calculate structure in 01.29
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/more/Mol2Reader.java
trunk/Jmol/src/org/jmol/api/JmolBioResolver.java
trunk/Jmol/src/org/jmol/modelset/Model.java
trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java
trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java
trunk/Jmol/src/org/jmol/modelsetbio/Resolver.java
trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
trunk/Jmol/src/org/jmol/scriptext/MathExt.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/adapter/readers/more/Mol2Reader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/more/Mol2Reader.java
2015-01-30 03:05:59 UTC (rev 20257)
+++ trunk/Jmol/src/org/jmol/adapter/readers/more/Mol2Reader.java
2015-01-30 14:43:12 UTC (rev 20258)
@@ -229,7 +229,7 @@
int pt = getPDBGroupLength(atoms[i].group3);
if (pt == 0 || pt > 3)
break;
- if (vwr.getJBR().isKnownPDBGroup(g3.substring(0, pt))) {
+ if (vwr.getJBR().isKnownPDBGroup(g3.substring(0, pt),
Integer.MAX_VALUE)) {
isPDB = this.isPDB = true;
break;
}
Modified: trunk/Jmol/src/org/jmol/api/JmolBioResolver.java
===================================================================
--- trunk/Jmol/src/org/jmol/api/JmolBioResolver.java 2015-01-30 03:05:59 UTC
(rev 20257)
+++ trunk/Jmol/src/org/jmol/api/JmolBioResolver.java 2015-01-30 14:43:12 UTC
(rev 20258)
@@ -41,7 +41,7 @@
public void setGroupLists(int ipt);
- public boolean isKnownPDBGroup(String g3);
+ public boolean isKnownPDBGroup(String g3, int maxID);
public boolean isHetero(String g3);
@@ -56,7 +56,9 @@
public short getGroupID(String g3);
- public boolean mutate(int iatom, String fileName);
+ public boolean mutate(BS bs, String fileName, String[] sequence);
+
+ public String toStdAmino3(String sValue);
}
Modified: trunk/Jmol/src/org/jmol/modelset/Model.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/Model.java 2015-01-30 03:05:59 UTC (rev
20257)
+++ trunk/Jmol/src/org/jmol/modelset/Model.java 2015-01-30 14:43:12 UTC (rev
20258)
@@ -251,6 +251,12 @@
}
protected void freezeM() {
+ for (int i = 0; i < chainCount; i++)
+ if (chains[i].groupCount == 0) {
+ for (int j = i + 1; j < chainCount; j++)
+ chains[j - 1] = chains[j];
+ chainCount--;
+ }
chains = (Chain[]) AU.arrayCopyObject(chains, chainCount);
groupCount = -1;
getGroupCount();
Modified: trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java 2015-01-30 03:05:59 UTC
(rev 20257)
+++ trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java 2015-01-30 14:43:12 UTC
(rev 20258)
@@ -81,6 +81,7 @@
private int bioPolymerCount = 0;
public BioPolymer[] bioPolymers;
+ boolean isMutated;
private String defaultStructure;
private Viewer vwr;
@@ -298,6 +299,10 @@
@Override
public void calculateAllPolymers(Group[] groups, int groupCount,
int baseGroupIndex, BS modelsExcluded) {
+ boolean checkConnections = !vwr.getBoolean(T.pdbsequential);
+ if (groupCount < 0)
+ groupCount = groups.length;
+
if (modelsExcluded != null)
for (int j = 0; j < groupCount; ++j) {
Group group = groups[j];
@@ -309,8 +314,22 @@
}
for (int i = 0, mc = ms.mc; i < mc; i++)
if ((modelsExcluded == null || !modelsExcluded.get(i))
- && ms.am[i].isBioModel)
- calculateAllPolymers2(groups, groupCount, baseGroupIndex);
+ && ms.am[i].isBioModel) {
+ for (int j = baseGroupIndex; j < groupCount; ++j) {
+ Group g = groups[j];
+ Model model = g.getModel();
+ if (!model.isBioModel || !(g instanceof Monomer))
+ continue;
+ boolean doCheck = checkConnections
+ && !ms.isJmolDataFrameForModel(ms.at[g.firstAtomIndex].mi);
+ BioPolymer bp = (((Monomer) g).bioPolymer == null ? Resolver
+ .allocateBioPolymer(groups, j, doCheck) : null);
+ if (bp == null || bp.monomerCount == 0)
+ continue;
+ ((BioModel) model).addBioPolymer(bp);
+ j += bp.monomerCount - 1;
+ }
+ }
}
@Override
@@ -318,30 +337,9 @@
for (int i = 0; i < ms.mc; i++)
if (ms.am[i].isBioModel && !bsModelsExcluded.get(i))
((BioModel) ms.am[i]).clearBioPolymers();
- calculateAllPolymers2(groups, -1, 0);
+ calculateAllPolymers(groups, -1, 0, bsModelsExcluded);
}
- private void calculateAllPolymers2(Group[] groups,
- int groupCount, int baseGroupIndex) {
- boolean checkConnections = !vwr.getBoolean(T.pdbsequential);
- if (groupCount < 0)
- groupCount = groups.length;
- for (int j = baseGroupIndex; j < groupCount; ++j) {
- Group g = groups[j];
- Model model = g.getModel();
- if (!model.isBioModel || !(g instanceof Monomer))
- continue;
- boolean doCheck = checkConnections
- && !ms.isJmolDataFrameForModel(ms.at[g.firstAtomIndex].mi);
- BioPolymer bp = (((Monomer) g).bioPolymer == null ? Resolver
- .allocateBioPolymer(groups, j, doCheck) : null);
- if (bp == null || bp.monomerCount == 0)
- continue;
- ((BioModel) model).addBioPolymer(bp);
- j += bp.monomerCount - 1;
- }
- }
-
@Override
public BS getGroupsWithinAll(int nResidues, BS bs) {
BS bsResult = new BS();
@@ -976,7 +974,7 @@
// all biopolymer atoms...
if (bs != bsAtoms)
for (int i = 0; i < bioPolymerCount; i++)
- bioPolymers[i].getRange(bs);
+ bioPolymers[i].getRange(bs, isMutated);
if (bs.nextSetBit(0) < 0)
return;
// ...and not connected to backbone:
@@ -986,7 +984,7 @@
} else {
for (int i = 0; i < bioPolymerCount; i++)
if (bioPolymers[i].getType() == BioPolymer.TYPE_NOBONDING)
- bioPolymers[i].getRange(bs2);
+ bioPolymers[i].getRange(bs2, isMutated);
}
if (bs2.nextSetBit(0) >= 0)
sb.append("select ").append(Escape.eBS(bs2)).append(";backbone only;");
@@ -1017,7 +1015,7 @@
BS bsBranch;
for (int j = 0; j < bioPolymerCount; j++) {
bsBranch = new BS();
- bioPolymers[j].getRange(bsBranch);
+ bioPolymers[j].getRange(bsBranch, isMutated);
int iAtom = bsBranch.nextSetBit(0);
if (iAtom >= 0) {
if (biobranches == null)
Modified: trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java 2015-01-30 03:05:59 UTC
(rev 20257)
+++ trunk/Jmol/src/org/jmol/modelsetbio/BioPolymer.java 2015-01-30 14:43:12 UTC
(rev 20258)
@@ -103,13 +103,18 @@
monomers[i].setBioPolymer(this, i);
model = monomers[0].getModel();
}
-
- public void getRange(BS bs) {
+
+ public void getRange(BS bs, boolean isMutated) {
// this is OK -- doesn't relate to added hydrogens
if (monomerCount == 0)
return;
- bs.setBits(monomers[0].firstAtomIndex,
- monomers[monomerCount - 1].lastAtomIndex + 1);
+ if (isMutated) {
+ for (int i = monomerCount; --i >= 0;)
+ monomers[i].setAtomBits(bs);
+ } else {
+ bs.setBits(monomers[0].firstAtomIndex,
+ monomers[monomerCount - 1].lastAtomIndex + 1);
+ }
}
public void clearStructures() {
Modified: trunk/Jmol/src/org/jmol/modelsetbio/Resolver.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/Resolver.java 2015-01-30 03:05:59 UTC
(rev 20257)
+++ trunk/Jmol/src/org/jmol/modelsetbio/Resolver.java 2015-01-30 14:43:12 UTC
(rev 20258)
@@ -871,11 +871,15 @@
}
}
+ /**
+ * @param g3
+ * @param max max ID (e.g. 20); can be Integer.MAX_VALUE to allow
carbohydrate
+ * @return true if found
+ */
@Override
- public boolean isKnownPDBGroup(String g3) {
- // mol2 reader only
- return knownGroupID(g3) >= 0
- || checkCarbohydrate(g3);
+ public boolean isKnownPDBGroup(String g3, int max) {
+ int pt = knownGroupID(g3);
+ return (pt > 0 ? pt < max : max == Integer.MAX_VALUE &&
checkCarbohydrate(g3));
}
@Override
@@ -1149,6 +1153,7 @@
int pt = Group.standardGroupList.indexOf(group3);
return (pt < 0 || pt / 6 + 1 >= JC.GROUPID_WATER);
}
+
public static short group3NameCount;
private final static String[] predefinedGroup3Names = {
// taken from PDB spec
@@ -1215,8 +1220,35 @@
"SO4", // 47 sulphate ions
"UNL", // 48 unknown ligand
+ };
- };
+ /*
+ * Convert "AVG" to "ALA VAL GLY"; unknowns to UNK
+ *
+ */
+ @Override
+ public String toStdAmino3(String g1) {
+ if (g1.length() == 0)
+ return "";
+ SB s = new SB();
+ int pt = knownGroupID("==A");
+ if (pt < 0) {
+ // just the amino acids
+ for (int i = 1; i <= 20; i++) {
+ pt = knownGroupID(predefinedGroup3Names[i]);
+ htGroup.put("==" + predefinedGroup1Names[i], Short.valueOf((short)
pt));
+ }
+ }
+ for (int i = 0, n = g1.length(); i < n; i++) {
+ char ch = g1.charAt(i);
+ pt = knownGroupID("==" + ch);
+ if (pt < 0)
+ pt = 23;
+ s.append(" ").append(predefinedGroup3Names[pt]);
+ }
+ return s.toString().substring(1);
+ }
+
private static int getStandardPdbHydrogenCount(String group3) {
int pt = knownGroupID(group3);
return (pt < 0 || pt >= pdbHydrogenCount.length ? -1 :
pdbHydrogenCount[pt]);
@@ -1737,9 +1769,36 @@
}
@Override
- public boolean mutate(int iatom, String fileName) {
+ public boolean mutate(BS bs, String group, String[] sequence) {
+
+ int i0 = bs.nextSetBit(0);
+ if (sequence == null)
+ return mutateAtom(i0, group);
+ boolean isFile = (group == null);
+ if (isFile)
+ group = sequence[0];
+ Group lastGroup = null;
+ boolean isOK = true;
+ for (int i = i0, pt = 0; i >= 0; i = bs.nextSetBit(i + 1)) {
+ Group g = vwr.ms.at[i].group;
+ if (g == lastGroup)
+ continue;
+ lastGroup = g;
+ if (!isFile) {
+ group = sequence[pt++ % sequence.length];
+ if (group.equals("UNK"))
+ continue;
+ group = "==" + group;
+ }
+ mutateAtom(i, group);
+ }
+ return isOK;
+ }
+
+ private boolean mutateAtom(int iatom, String fileName) {
// no mutating a trajectory. What would that mean???
- if (vwr.ms.isTrajectory(vwr.ms.at[iatom].mi))
+ int iModel = vwr.ms.at[iatom].mi;
+ if (vwr.ms.isTrajectory(iModel))
return false;
String[] info = vwr.fm.getFileInfo();
@@ -1749,6 +1808,7 @@
// get the initial group -- protein for now
if (!(g instanceof AminoMonomer))
return false;
+ ((BioModel) vwr.ms.am[iModel]).isMutated = true;
AminoMonomer res0 = (AminoMonomer) g;
int ac = vwr.ms.ac;
BS bsRes0 = new BS();
@@ -1757,34 +1817,41 @@
// just use a script -- it is much easier!
- String script = "try{var atoms0 = {*}\n"
- + "var res0 = " + BS.escape(bsRes0,'(',')') + "\n"
- + "set appendNew false\n"
- + "load append \""+fileName+"\"\n"
- + "set appendNew " + b + "\n"
- + "var res1 = {!atoms0};var r1 = res1[1];var r0 = res1[0]\n"
- + "if ({r1 & within(group, r0)}){"
- + "var haveHs = ({_H and connected(res0)} != 0)\n"
- + "if (!haveHs) {delete _H and res1}\n"
- + "var sm = '[*.N][*.CA][*.C][*.O]'\n"
- + "var keyatoms = res1.find(sm)\n"
- + "var x = compare(res1,res0,sm,'BONDS')\n"
- + "if(x){\n"
- + "rotate branch @x 1\n"
- + "compare res1 res0 SMARTS @sm rotate translate 0\n"
- + "var N2 = {*.N and !res0 && connected(res0)}\n"
- + "var C0 = {*.C and !res0 && connected(res0)}\n"
- + "delete res0\n"
- + "if (N2) {\n"
- + "delete *.OXT and res1\n"
- + "connect {N2} {res1 & *.C}\n"
- + "}\n"
- + "if (C0) {\n"
- + "connect {C0} {res1 & *.N}\n"
- + "}\n"
- + "}\n"
- + "}}catch(e){print e}\n";
+ fileName = PT.esc(fileName);
+ String script = "" +
+ "try{\n"
+ + " var atoms0 = {*}\n"
+ + " var res0 = " + BS.escape(bsRes0,'(',')') + "\n"
+ + " set appendNew false\n"
+ + " load append "+fileName+"\n"
+ + " set appendNew " + b + "\n"
+ + " var res1 = {!atoms0};var r1 = res1[1];var r0 = res1[0]\n"
+ + " if ({r1 & within(group, r0)}){"
+ + " var haveHs = ({_H and connected(res0)} != 0)\n"
+ + " if (!haveHs) {delete _H and res1}\n"
+ + " var sm = '[*.N][*.CA][*.C][*.O]'\n"
+ + " var keyatoms = res1.find(sm)\n"
+ + " var x = compare(res1,res0,sm,'BONDS')\n"
+ + " if(x){\n"
+ + " print 'mutating ' + res0[1].label('%n%r') + ' to ' +
"+fileName+".trim('=')\n"
+ + " rotate branch @x\n"
+ + " compare res1 res0 SMARTS @sm rotate translate 0\n"
+ + " var N2 = {*.N and !res0 && connected(res0)}\n"
+ + " var C0 = {*.C and !res0 && connected(res0)}\n"
+ + " delete res0\n"
+ + " if (N2) {\n"
+ + " delete *.OXT and res1\n"
+ + " connect {N2} {res1 & *.C}\n"
+ + " }\n"
+ + " if (C0) {\n"
+ + " connect {C0} {res1 & *.N}\n"
+ + " }\n"
+ + " }\n"
+ + " }\n"
+ + "}catch(e){print e}\n";
try {
+ if (Logger.debugging)
+ Logger.debug(script);
vwr.eval.runScript(script);
} catch (ScriptException e) {
// TODO
@@ -1815,6 +1882,7 @@
BS bsExclude = BSUtil.newBitSet2(0, vwr.ms.mc);
bsExclude.clear(res1.chain.model.modelIndex);
res1.chain.model.groupCount = -1;
+ res1.chain.model.freeze();
vwr.ms.recalculatePolymers(bsExclude);
//} catch (Exception e) {
// System.out.println("" + e);
Modified: trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2015-01-30 03:05:59 UTC
(rev 20257)
+++ trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2015-01-30 14:43:12 UTC
(rev 20258)
@@ -2188,20 +2188,49 @@
private void mutate() throws ScriptException {
// mutate {resno} "LYS" or "file identifier"
- if (tokAt(1) == T.integer)
- st[1] =T.o(T.string, "" + st[1].value); // allows @x
- int iatom = atomExpressionAt(1).length() - 1;
-
+ // mutate {1-3} ~GGGL
+ BS bs;
+ int i;
+ switch (tokAt(1)) {
+ case T.integer:
+ st[1] = T.o(T.string, "" + st[1].value); // allows @x and "*"
+ //$FALL-THROUGH$
+ default:
+ bs = atomExpressionAt(1);
+ i = ++e.iToken;
+ break;
+ case T.times:
+ bs = vwr.getAllAtoms();
+ i = 2;
+ break;
+ }
+
// check for last model
- if (iatom < 0 || vwr.ms.mc != vwr.ms.at[iatom].mi + 1)
+ bs.and(vwr.getModelUndeletedAtomsBitSet(vwr.ms.mc - 1));
+ int iatom = bs.length() - 1;
+ if (iatom < 0 || vwr.ms.at[iatom].mi + 1 != vwr.ms.mc
+ || vwr.ms.isTrajectory(vwr.ms.at[iatom].mi))
return;
- int i = ++e.iToken;
- String group = e.optParameterAsString(e.checkLast(i));
+ String group = e.optParameterAsString(i);
+ e.checkLast(i);
if (chk)
return;
- if (tokAt(i) != T.string)
- group = "==" + group;
- vwr.getJBR().mutate(iatom, group);
+ boolean isFile = (tokAt(i) == T.string);
+ String[] list = null;
+ if (isFile) {
+ list = new String[] { group };
+ group = null;
+ } else {
+ group = PT.replaceAllCharacters(group, ",; \t\n", " ").trim()
+ .toUpperCase();
+ if (group.startsWith("~") || group.length() != 3
+ || !vwr.getJBR().isKnownPDBGroup(group, 20))
+ group = vwr.getJBR().toStdAmino3(group);
+ }
+ list = PT.getTokens(group);
+ if (list.length == 0)
+ return;
+ vwr.getJBR().mutate(bs, group, list);
}
private void navigate() throws ScriptException {
Modified: trunk/Jmol/src/org/jmol/scriptext/MathExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/MathExt.java 2015-01-30 03:05:59 UTC
(rev 20257)
+++ trunk/Jmol/src/org/jmol/scriptext/MathExt.java 2015-01-30 14:43:12 UTC
(rev 20258)
@@ -884,7 +884,8 @@
// {*}.find("CF",true|false)
// {*}.find("MF")
// {*}.find("MF", "C2H4")
- // {*}.find("SEQENCE")
+ // {*}.find("SEQUENCE")
+ // "AVA".find("SEQUENCE")
// {*}.find("SMARTS", "CCCC")
// "CCCC".find("SMARTS", "CC")
// "CCCC".find("SMILES", "MF")
@@ -1016,6 +1017,9 @@
}
return mp.addXAS(listNew);
}
+ if (isSequence) {
+ return mp.addXStr(vwr.getJBR().toStdAmino3(SV.sValue(x1)));
+ }
return mp.addXInt(SV.sValue(x1).indexOf(sFind) + 1);
}
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-01-30 03:05:59 UTC
(rev 20257)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-01-30 14:43:12 UTC
(rev 20258)
@@ -15,6 +15,28 @@
TODO: remove HTML5 dependency on synchronous file loading (check SCRIPT
command for problems)
TODO: add 2D graphics panel for Ramachandran and NBO-style 2D graphics -- send
to browser as data uri?
+Jmol.___JmolVersion="14.3.12_2015.01.30"
+
+new feature: MUTATE command
+ -- operates only on last model present if multiple models are loaded
+ -- replaces one or more amino acids group with others
+ -- can read from RCSB or from user-specified file
+ -- examples:
+ mutate 33 lys // replace resno=33 with lysine
+ mutate @3 arg // replaces group of atom 3 with arginine
+ mutate @r gly // replaces groups in variable r with glycine
+ mutate 22 "myfile.cif" // user-defined replacement
+ mutate {1-3} ala // replace first three residues with alanine
+ mutate {1-5} GLVAG // (sequence codes) replace residues 1-5 with
gly-leu-val-ala-gly
+ mutate {1-3} ~LYS // (force 1-character sequence codes) replace 1-3
with leu-tyr-ser
+ mutate {1-3} A?L // replace 1 with ala, 3 with leu; skip 2
+ mutate {within(sequence, "GAT")} GYT // replace locations of GAT with
GYT (needs testing)
+ mutate 35 @fname // replaces resno=33 with file data (use "==XXX"
for RCSB)
+ mutate {r} his // same as above; r must be an atom selection
+
+
+bug fix: code fixes relating to calculate structure in 01.29
+
Jmol.___JmolVersion="14.3.12_2015.01.29"
bug fix: 01.28 version does not write correct PDB CONECT records
@@ -24,17 +46,6 @@
JmolVersion="14.3.12_2015.01.28"
-new feature: MUTATE command
- -- operates only on last model present if multiple models are loaded
- -- replaces one amino acid group with another
- -- can read from RCSB or from user-specified file
- -- examples:
- mutate 33 lys // uses last occurrence of resno=33
- mutate @@3 arg // replaces group of atom 3 in current model
- mutate @r @fname // replaces resno in variable r with file data
(use "==XXX" for RCSB)
- mutate {r} his // same as above; r must be an atom selection
- mutate 22 "myfile.cif" // user-defined replacement
-
bug fix: write "t.pdb" now correctly sequences groups and atoms, even after
mutation
new feature: resno is user settable
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