Revision: 20297
http://sourceforge.net/p/jmol/code/20297
Author: hansonr
Date: 2015-02-16 06:27:21 +0000 (Mon, 16 Feb 2015)
Log Message:
-----------
BioModel efficiencies
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/modelset/JmolBioModelSet.java
trunk/Jmol/src/org/jmol/modelset/ModelSet.java
trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java
trunk/Jmol/src/org/jmol/modelsetbio/ProteinStructure.java
trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
trunk/Jmol/src/org/jmol/viewer/PropertyManager.java
trunk/Jmol/src/org/jmol/viewer/StateCreator.java
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: trunk/Jmol/src/org/jmol/modelset/JmolBioModelSet.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/JmolBioModelSet.java 2015-02-15
18:32:52 UTC (rev 20296)
+++ trunk/Jmol/src/org/jmol/modelset/JmolBioModelSet.java 2015-02-16
06:27:21 UTC (rev 20297)
@@ -57,8 +57,7 @@
void getConformations(int modelIndex, int conformationIndex,
boolean doSet, BS bsAtoms, BS bsRet);
- String getFullProteinStructureState(BS bsAtoms, boolean taintedOnly,
- boolean needPhiPsi, int mode);
+ String getFullProteinStructureState(BS bsAtoms, int mode);
BS getIdentifierOrNull(String identifier);
Modified: trunk/Jmol/src/org/jmol/modelset/ModelSet.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2015-02-15 18:32:52 UTC
(rev 20296)
+++ trunk/Jmol/src/org/jmol/modelset/ModelSet.java 2015-02-16 06:27:21 UTC
(rev 20297)
@@ -3823,10 +3823,8 @@
return (haveBioModels ? bioModelset.getGroupsWithinAll(nResidues, bs) :
new BS());
}
- public String getProteinStructureState(BS bsAtoms, boolean taintedOnly,
- boolean needPhiPsi, int mode) {
- return (haveBioModels ? bioModelset.getFullProteinStructureState(bsAtoms,
taintedOnly,
- needPhiPsi, mode) : "");
+ public String getProteinStructureState(BS bsAtoms, int mode) {
+ return (haveBioModels ? bioModelset.getFullProteinStructureState(bsAtoms,
mode) : "");
}
public String calculateStructures(BS bsAtoms, boolean asDSSP,
Modified: trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java 2015-02-15 18:32:52 UTC
(rev 20296)
+++ trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java 2015-02-16 06:27:21 UTC
(rev 20297)
@@ -227,8 +227,7 @@
if (ms.am[i].isBioModel) {
BioModel m = (BioModel) ms.am[i];
if (m.defaultStructure == null)
- m.defaultStructure = getFullProteinStructureState(m.bsAtoms, false,
- false, 0);
+ m.defaultStructure = getFullProteinStructureState(m.bsAtoms,
T.state);
}
}
@@ -377,183 +376,166 @@
((BioModel) ms.am[modelIndex]).recalculateLeadMidpointsAndWingVectors();
}
- @SuppressWarnings("incomplete-switch")
@Override
- public String getFullProteinStructureState(BS bsAtoms2,
- boolean taintedOnly,
- boolean needPhiPsi, int mode) {
- for (int im = 0, mc = ms.mc; im < mc; im++) {
+ public String getFullProteinStructureState(BS bsAtoms, int mode) {
+ boolean taintedOnly = (mode == T.all);
+ if (taintedOnly && !ms.proteinStructureTainted)
+ return "";
+ boolean scriptMode = (mode == T.state || mode == T.all);
+ Atom[] atoms = ms.at;
+ int at0 = (bsAtoms == null ? 0 : bsAtoms.nextSetBit(0));
+ if (at0 < 0)
+ return "";
+ if (bsAtoms != null && mode == T.ramachandran) {
+ bsAtoms = BSUtil.copy(bsAtoms);
+ for (int i = ms.ac; --i >= 0;)
+ if (Float.isNaN(atoms[i].group.getGroupParameter(T.phi))
+ || Float.isNaN(atoms[i].group.getGroupParameter(T.psi)))
+ bsAtoms.clear(i);
+ }
+ int at1 = (bsAtoms == null ? ms.ac : bsAtoms.length()) - 1;
+ int im0 = atoms[at0].mi;
+ int im1 = atoms[at1].mi;
+ Lst<ProteinStructure> lstStr = new Lst<ProteinStructure>();
+ Map<ProteinStructure, Boolean> map = new Hashtable<ProteinStructure,
Boolean>();
+ SB cmd = new SB();
+ for (int im = im0; im <= im1; im++) {
if (!ms.am[im].isBioModel)
continue;
BioModel m = (BioModel) ms.am[im];
- boolean showMode = (mode == 3);
- boolean pdbFileMode = (mode == 1);
- boolean scriptMode = (mode == 0);
- BS bs = null;
- SB cmd = new SB();
- SB sbTurn = new SB();
- SB sbHelix = new SB();
- SB sbSheet = new SB();
- STR type = STR.NONE;
- STR subtype = STR.NONE;
- int id = 0;
- int iLastAtom = 0;
- int iLastModel = -1;
- int lastId = -1;
- int res1 = 0;
- int res2 = 0;
- String sid = "";
- String group1 = "";
- String group2 = "";
- String chain1 = "";
- String chain2 = "";
- int n = 0;
- int nHelix = 0;
- int nTurn = 0;
- int nSheet = 0;
- BS bsTainted = null;
- Model[] models = ms.am;
- Atom[] atoms = ms.at;
- int ac = ms.ac;
-
- if (taintedOnly) {
- if (!ms.proteinStructureTainted)
- return "";
- bsTainted = new BS();
- for (int i = m.firstAtomIndex; i < ac; i++)
- if (models[atoms[i].mi].structureTainted)
- bsTainted.set(i);
- bsTainted.set(ac);
+ if (taintedOnly && !m.structureTainted)
+ continue;
+ BS bsA = new BS();
+ bsA.or(m.bsAtoms);
+ bsA.andNot(m.bsAtomsDeleted);
+ int i0 = bsA.nextSetBit(0);
+ if (i0 < 0)
+ continue;
+ if (scriptMode) {
+ cmd.append(" structure none ")
+ .append(
+ Escape.eBS(ms.getModelAtomBitSetIncludingDeleted(im, false)))
+ .append(" \t# model=" + ms.getModelNumberDotted(im))
+ .append(";\n");
}
- for (int i = 0; i <= ac; i++)
- if (i == ac || bsAtoms == null || bsAtoms.get(i)) {
- if (taintedOnly && !bsTainted.get(i))
- continue;
- id = 0;
- if (i == ac || (id = atoms[i].group.getStrucNo()) != lastId) {
- if (bs != null) {
- switch (type) {
- case HELIX:
- case TURN:
- case SHEET:
- n++;
- if (scriptMode) {
- int iModel = atoms[iLastAtom].mi;
- String comment = " \t# model="
- + ms.getModelNumberDotted(iModel);
- if (iLastModel != iModel) {
- iLastModel = iModel;
- cmd.append(" structure none ")
- .append(
- Escape.eBS(ms.getModelAtomBitSetIncludingDeleted(
- iModel, false))).append(comment).append(";\n");
- }
- comment += " & (" + res1 + " - " + res2 + ")";
- String stype = subtype.getBioStructureTypeName(false);
- cmd.append(" structure ").append(stype).append(" ")
- .append(Escape.eBS(bs)).append(comment).append(";\n");
- } else {
- String str;
- int nx;
- SB sb;
- // NNN III GGG C RRRR GGG C RRRR
- // HELIX 99 99 LYS F 281 LEU F 293 1
- // NNN III 2 GGG CRRRR GGG CRRRR
- // SHEET 1 A 8 ILE A 43 ASP A 45 0
- // NNN III GGG CRRRR GGG CRRRR
- // TURN 1 T1 PRO A 41 TYR A 44
- switch (type) {
- case HELIX:
- nx = ++nHelix;
- if (sid == null || pdbFileMode)
- sid = PT.formatStringI("%3N %3N", "N", nx);
- str = "HELIX %ID %3GROUPA %1CA %4RESA %3GROUPB %1CB
%4RESB";
- sb = sbHelix;
- String stype = null;
- switch (subtype) {
- case HELIX:
- case HELIXALPHA:
- stype = " 1";
- break;
- case HELIX310:
- stype = " 5";
- break;
- case HELIXPI:
- stype = " 3";
- break;
- }
- if (stype != null)
- str += stype;
- break;
- case SHEET:
- nx = ++nSheet;
- if (sid == null || pdbFileMode) {
- sid = PT.formatStringI("%3N %3A 0", "N", nx);
- sid = PT.formatStringS(sid, "A", "S" + nx);
- }
- str = "SHEET %ID %3GROUPA %1CA%4RESA %3GROUPB
%1CB%4RESB";
- sb = sbSheet;
- break;
- case TURN:
- default:
- nx = ++nTurn;
- if (sid == null || pdbFileMode)
- sid = PT.formatStringI("%3N %3N", "N", nx);
- str = "TURN %ID %3GROUPA %1CA%4RESA %3GROUPB
%1CB%4RESB";
- sb = sbTurn;
- break;
- }
- str = PT.formatStringS(str, "ID", sid);
- str = PT.formatStringS(str, "GROUPA", group1);
- str = PT.formatStringS(str, "CA", chain1);
- str = PT.formatStringI(str, "RESA", res1);
- str = PT.formatStringS(str, "GROUPB", group2);
- str = PT.formatStringS(str, "CB", chain2);
- str = PT.formatStringI(str, "RESB", res2);
- sb.append(str);
- if (showMode)
- sb.append(" strucno= ").appendI(lastId);
- sb.append("\n");
+ ProteinStructure ps;
+ for (int i = i0; i >= 0; i = bsA.nextSetBit(i + 1)) {
+ Atom a = atoms[i];
+ if (!(a.group instanceof AlphaMonomer)
+ || (ps = ((AlphaMonomer) a.group).proteinStructure) == null
+ || map.containsKey(ps))
+ continue;
+ lstStr.addLast(ps);
+ map.put(ps, Boolean.TRUE);
+ }
+ }
+ getStructureLines(bsAtoms, cmd, lstStr, STR.HELIX, scriptMode, mode);
+ getStructureLines(bsAtoms, cmd, lstStr, STR.SHEET, scriptMode, mode);
+ getStructureLines(bsAtoms, cmd, lstStr, STR.TURN, scriptMode, mode);
+ return cmd.toString();
+ }
- /*
- * HELIX 1 H1 ILE 7 PRO 19 1 3/10 CONFORMATION RES 17,19
1CRN 55
- * HELIX 2 H2 GLU 23 THR 30 1 DISTORTED 3/10 AT RES 30 1CRN
56
- * SHEET 1 S1 2 THR 1 CYS 4 0 1CRNA 4 SHEET 2 S1 2 CYS 32
ILE 35
- */
- }
- }
- bs = null;
+ @SuppressWarnings("incomplete-switch")
+ private int getStructureLines(BS bsAtoms, SB cmd, Lst<ProteinStructure>
lstStr, STR type,
+ boolean scriptMode, int mode) {
+ //boolean pdbFileMode = (mode == T.pdb || mode == T.ramachandran);
+ boolean showMode = (mode == T.show);
+ int nHelix = 0, nSheet = 0, nTurn = 0;
+ String sid = null;
+ BS bs = new BS();
+ int n = 0;
+ for (int i = 0, ns = lstStr.size(); i < ns; i++) {
+ ProteinStructure ps = lstStr.get(i);
+ if (ps.type != type)
+ continue;
+ bs.clearAll();
+ // could be a subset of atoms, not just the ends
+ Monomer m1 = ps.findMonomer(bsAtoms, true);
+ Monomer m2 = ps.findMonomer(bsAtoms, false);
+ if (m1 == null || m2 == null)
+ continue;
+ int iModel = ps.apolymer.model.modelIndex;
+ String comment = (scriptMode ? " \t# model="
+ + ms.getModelNumberDotted(iModel) : null);
+ int res1 = m1.getResno();
+ int res2 = m2.getResno();
+ STR subtype = ps.subtype;
+ switch (type) {
+ case HELIX:
+ case TURN:
+ case SHEET:
+ n++;
+ if (scriptMode) {
+ String stype = subtype.getBioStructureTypeName(false);
+ cmd.append(" structure ").append(stype).append(" ")
+ .append(Escape.eBS(ps.getAtoms(bs))).append(comment)
+ .append(" & (" + res1 + " - " + res2 + ")").append(";\n");
+ } else {
+ String str;
+ int nx;
+ // NNN III GGG C RRRR GGG C RRRR
+ // HELIX 99 99 LYS F 281 LEU F 293 1
+ // NNN III 2 GGG CRRRR GGG CRRRR
+ // SHEET 1 A 8 ILE A 43 ASP A 45 0
+ // NNN III GGG CRRRR GGG CRRRR
+ // TURN 1 T1 PRO A 41 TYR A 44
+ switch (type) {
+ case HELIX:
+ nx = ++nHelix;
+ sid = PT.formatStringI("%3N %3N", "N", nx);
+ str = "HELIX %ID %3GROUPA %1CA %4RESA %3GROUPB %1CB %4RESB";
+ String stype = null;
+ switch (subtype) {
+ case HELIX:
+ case HELIXALPHA:
+ stype = " 1";
+ break;
+ case HELIX310:
+ stype = " 5";
+ break;
+ case HELIXPI:
+ stype = " 3";
+ break;
}
- if (id == 0
- || bsAtoms != null
- && needPhiPsi
- && (Float.isNaN(atoms[i].group.getGroupParameter(T.phi)) ||
Float
- .isNaN(atoms[i].group.getGroupParameter(T.psi))))
- continue;
+ if (stype != null)
+ str += stype;
+ break;
+ case SHEET:
+ nx = ++nSheet;
+ sid = PT.formatStringI("%3N %3A 0", "N", nx);
+ sid = PT.formatStringS(sid, "A", "S" + nx);
+ str = "SHEET %ID %3GROUPA %1CA%4RESA %3GROUPB %1CB%4RESB";
+ break;
+ case TURN:
+ default:
+ nx = ++nTurn;
+ sid = PT.formatStringI("%3N %3N", "N", nx);
+ str = "TURN %ID %3GROUPA %1CA%4RESA %3GROUPB %1CB%4RESB";
+ break;
}
- String ch = atoms[i].getChainIDStr();
- if (bs == null) {
- bs = new BS();
- res1 = atoms[i].getResno();
- group1 = atoms[i].getGroup3(false);
- chain1 = ch;
- }
- type = atoms[i].group.getProteinStructureType();
- subtype = atoms[i].group.getProteinStructureSubType();
- sid = atoms[i].group.getProteinStructureTag();
- bs.set(i);
- lastId = id;
- res2 = atoms[i].getResno();
- group2 = atoms[i].getGroup3(false);
- chain2 = ch;
- iLastAtom = i;
+ str = PT.formatStringS(str, "ID", sid);
+ str = PT.formatStringS(str, "GROUPA", m1.getGroup3());
+ str = PT.formatStringS(str, "CA", m1.getLeadAtom().getChainIDStr());
+ str = PT.formatStringI(str, "RESA", res1);
+ str = PT.formatStringS(str, "GROUPB", m2.getGroup3());
+ str = PT.formatStringS(str, "CB", m2.getLeadAtom().getChainIDStr());
+ str = PT.formatStringI(str, "RESB", res2);
+ cmd.append(str);
+ if (showMode)
+ cmd.append(" strucno= ").appendI(ps.strucNo);
+ cmd.append("\n");
+
+ /*
+ * HELIX 1 1 ILE 7 PRO 19 1 3/10 CONFORMATION RES 17,19 1CRN 55
+ * HELIX 2 2 GLU 23 THR 30 1 DISTORTED 3/10 AT RES 30 1CRN 56
+ * SHEET 1 S1 2 THR 1 CYS 4 0 1CRNA 4 SHEET 2 S1 2 CYS 32 ILE 35
+ */
}
- if (n > 0)
- cmd.append("\n");
- return (scriptMode ? cmd.toString() : sbHelix.appendSB(sbSheet)
- .appendSB(sbTurn).appendSB(cmd).toString());
+ }
}
- return "";
+ if (n > 0)
+ cmd.append("\n");
+ return n;
}
@Override
Modified: trunk/Jmol/src/org/jmol/modelsetbio/ProteinStructure.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/ProteinStructure.java 2015-02-15
18:32:52 UTC (rev 20296)
+++ trunk/Jmol/src/org/jmol/modelsetbio/ProteinStructure.java 2015-02-16
06:27:21 UTC (rev 20297)
@@ -30,6 +30,7 @@
import javajs.util.V3;
import org.jmol.c.STR;
+import org.jmol.java.BS;
import org.jmol.util.Logger;
public abstract class ProteinStructure {
@@ -49,7 +50,7 @@
protected V3 vectorProjection;
private static int globalStrucNo = 1000;
- private int monomerIndexLast;
+ int monomerIndexLast;
private P3[] segments;
/**
@@ -198,4 +199,25 @@
axisA = null;
segments = null;
}
+
+ BS getAtoms(BS bs) {
+ Monomer[] ms = apolymer.monomers;
+ for (int i = monomerIndexFirst; i <= monomerIndexLast; i++)
+ ms[i].setAtomBits(bs);
+ return bs;
+ }
+
+ public Monomer findMonomer(BS bsAtoms, boolean isFirst) {
+ Monomer[] ms = apolymer.monomers;
+ if (isFirst) {
+ for (int i = monomerIndexFirst; i <= monomerIndexLast; i++)
+ if (bsAtoms == null || bsAtoms.get(ms[i].leadAtomIndex))
+ return ms[i];
+ } else {
+ for (int i = monomerIndexLast; i >= monomerIndexFirst; --i)
+ if (bsAtoms == null || bsAtoms.get(ms[i].leadAtomIndex))
+ return ms[i];
+ }
+ return null;
+ }
}
Modified: trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2015-02-15 18:32:52 UTC
(rev 20296)
+++ trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2015-02-16 06:27:21 UTC
(rev 20297)
@@ -3905,7 +3905,7 @@
case T.structure:
if ((len = slen) == 2) {
if (!chk)
- msg = vwr.getProteinStructureState();
+ msg = vwr.ms.getProteinStructureState(vwr.bsA(), T.show);
break;
}
String shape = paramAsStr(2);
Modified: trunk/Jmol/src/org/jmol/viewer/PropertyManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/PropertyManager.java 2015-02-15 18:32:52 UTC
(rev 20296)
+++ trunk/Jmol/src/org/jmol/viewer/PropertyManager.java 2015-02-16 06:27:21 UTC
(rev 20297)
@@ -2018,7 +2018,7 @@
bsSelected.and(bsAtoms);
if (isPDB && addStructure)
out.append("\n\n"
- + vwr.ms.getProteinStructureState(bsWritten, false, ctype == 'R',
1));
+ + vwr.ms.getProteinStructureState(bsWritten, ctype == 'R' ?
T.ramachandran : T.pdb));
return out.toString();
}
Modified: trunk/Jmol/src/org/jmol/viewer/StateCreator.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/StateCreator.java 2015-02-15 18:32:52 UTC
(rev 20296)
+++ trunk/Jmol/src/org/jmol/viewer/StateCreator.java 2015-02-16 06:27:21 UTC
(rev 20297)
@@ -305,7 +305,7 @@
// unnecessary. Removed in 11.5.35 -- oops!
if (withProteinStructure)
- commands.append(ms.getProteinStructureState(null, isAll, false, 0));
+ commands.append(ms.getProteinStructureState(null, isAll ? T.all :
T.state));
getShapeState(commands, isAll, Integer.MAX_VALUE);
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2015-02-15 18:32:52 UTC (rev
20296)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2015-02-16 06:27:21 UTC (rev
20297)
@@ -2838,10 +2838,6 @@
return getStateCreator().getModelState(null, false, true);
}
- public String getProteinStructureState() {
- return ms.getProteinStructureState(bsA(), false, false, 3);
- }
-
public String getCoordinateState(BS bsSelected) {
return getStateCreator().getAtomicPropertyState(AtomCollection.TAINT_COORD,
bsSelected);
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