Revision: 20261
http://sourceforge.net/p/jmol/code/20261
Author: hansonr
Date: 2015-01-30 15:56:30 +0000 (Fri, 30 Jan 2015)
Log Message:
-----------
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/modelset/JmolBioModel.java
trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java
trunk/Jmol/src/org/jmol/modelsetbio/Resolver.java
trunk/Jmol/src/org/jmol/viewer/PropertyManager.java
Modified: trunk/Jmol/src/org/jmol/modelset/JmolBioModel.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/JmolBioModel.java 2015-01-30 15:43:23 UTC
(rev 20260)
+++ trunk/Jmol/src/org/jmol/modelset/JmolBioModel.java 2015-01-30 15:56:30 UTC
(rev 20261)
@@ -60,7 +60,7 @@
public void setAllStructureList(Map<STR, float[]> structureList);
- public void getAllPolymerInfo(BS bs,
+ public void getPolymerInfo(BS bs,
Map<String, Lst<Map<String, Object>>> finalInfo,
Lst<Map<String, Object>> modelVector);
Modified: trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java 2015-01-30 15:43:23 UTC
(rev 20260)
+++ trunk/Jmol/src/org/jmol/modelsetbio/BioModel.java 2015-01-30 15:56:30 UTC
(rev 20261)
@@ -249,7 +249,8 @@
if (ms.am[i].isBioModel) {
BioModel m = (BioModel) ms.am[i];
if (m.nAltLocs > 0)
- m.setConformation(bsAtoms);
+ for (int j = m.bioPolymerCount; --j >= 0;)
+ m.bioPolymers[j].setConformation(bsAtoms);
}
}
@@ -380,20 +381,20 @@
return bs;
}
- private static int selectSeqcodeRange(Group[] groups, int n, int index, int
seqcodeA, int seqcodeB,
+ private static int selectSeqcodeRange(Group[] groups, int groupCount, int
index, int seqcodeA, int seqcodeB,
BS bs) {
int seqcode, indexA, indexB, minDiff;
boolean isInexact = false;
- for (indexA = index; indexA < n
+ for (indexA = index; indexA < groupCount
&& groups[indexA].seqcode != seqcodeA; indexA++) {
}
- if (indexA == n) {
+ if (indexA == groupCount) {
// didn't find A exactly -- go find the nearest that is GREATER than
this value
if (index > 0)
return -1;
isInexact = true;
minDiff = Integer.MAX_VALUE;
- for (int i = n; --i >= 0;)
+ for (int i = groupCount; --i >= 0;)
if ((seqcode = groups[i].seqcode) > seqcodeA
&& (seqcode - seqcodeA) < minDiff) {
indexA = i;
@@ -403,19 +404,19 @@
return -1;
}
if (seqcodeB == Integer.MAX_VALUE) {
- indexB = n - 1;
+ indexB = groupCount - 1;
isInexact = true;
} else {
- for (indexB = indexA; indexB < n
+ for (indexB = indexA; indexB < groupCount
&& groups[indexB].seqcode != seqcodeB; indexB++) {
}
- if (indexB == n) {
+ if (indexB == groupCount) {
// didn't find B exactly -- get the nearest that is LESS than this
value
if (index > 0)
return -1;
isInexact = true;
minDiff = Integer.MAX_VALUE;
- for (int i = indexA; i < n; i++)
+ for (int i = indexA; i < groupCount; i++)
if ((seqcode = groups[i].seqcode) < seqcodeB
&& (seqcodeB - seqcode) < minDiff) {
indexB = i;
@@ -836,7 +837,7 @@
/////////////////////////////////////////////////////////////////////////
-
+
BioModel(ModelSet modelSet, int modelIndex, int trajectoryBaseIndex,
String jmolData, Properties properties, Map<String, Object>
auxiliaryInfo) {
vwr = modelSet.vwr;
@@ -846,7 +847,29 @@
clearBioPolymers();
}
+ private void clearBioPolymers() {
+ bioPolymers = new BioPolymer[8];
+ bioPolymerCount = 0;
+ }
+
@Override
+ public int getBioPolymerCount() {
+ return bioPolymerCount;
+ }
+
+ @Override
+ public void fixIndices(int modelIndex, int nAtomsDeleted, BS bsDeleted) {
+ fixIndicesM(modelIndex, nAtomsDeleted, bsDeleted);
+ recalculateLeadMidpointsAndWingVectors();
+ }
+
+ private void recalculateLeadMidpointsAndWingVectors() {
+ for (int ip = 0; ip < bioPolymerCount; ip++)
+ bioPolymers[ip].recalculateLeadMidpointsAndWingVectors();
+ }
+
+
+ @Override
public boolean freeze() {
freezeM();
bioPolymers = (BioPolymer[])AU.arrayCopyObject(bioPolymers,
bioPolymerCount);
@@ -939,20 +962,11 @@
if (bsConformation.nextSetBit(0) >= 0) {
bsRet.or(bsConformation);
if (doSet)
- setConformation(bsConformation);
+ for (int j = bioPolymerCount; --j >= 0;)
+ bioPolymers[j].setConformation(bsConformation);
}
}
- private void setConformation(BS bsConformation) {
- for (int j = bioPolymerCount; --j >= 0;)
- bioPolymers[j].setConformation(bsConformation);
- }
-
- @Override
- public int getBioPolymerCount() {
- return bioPolymerCount;
- }
-
private void addBioPolymer(BioPolymer polymer) {
if (bioPolymers.length == 0)
clearBioPolymers();
@@ -962,55 +976,7 @@
bioPolymers[bioPolymerCount++] = polymer;
}
- private void clearBioPolymers() {
- bioPolymers = new BioPolymer[8];
- bioPolymerCount = 0;
- }
-
@Override
- public void getDefaultLargePDBRendering(SB sb, int maxAtoms) {
- BS bs = new BS();
- if (getBondCount() == 0)
- bs = bsAtoms;
- // all biopolymer atoms...
- if (bs != bsAtoms)
- for (int i = 0; i < bioPolymerCount; i++)
- bioPolymers[i].getRange(bs, isMutated);
- if (bs.nextSetBit(0) < 0)
- return;
- // ...and not connected to backbone:
- BS bs2 = new BS();
- if (bs == bsAtoms) {
- bs2 = bs;
- } else {
- for (int i = 0; i < bioPolymerCount; i++)
- if (bioPolymers[i].getType() == BioPolymer.TYPE_NOBONDING)
- bioPolymers[i].getRange(bs2, isMutated);
- }
- if (bs2.nextSetBit(0) >= 0)
- sb.append("select ").append(Escape.eBS(bs2)).append(";backbone only;");
- if (ac <= maxAtoms)
- return;
- // ...and it's a large model, to wireframe:
- sb.append("select ").append(Escape.eBS(bs)).append(" & connected;
wireframe only;");
- // ... and all non-biopolymer and not connected to stars...
- if (bs != bsAtoms) {
- bs2.clearAll();
- bs2.or(bsAtoms);
- bs2.andNot(bs);
- if (bs2.nextSetBit(0) >= 0)
- sb.append("select " + Escape.eBS(bs2) + " & !connected;stars
0.5;spacefill off;");
- }
- }
-
- @Override
- public void fixIndices(int modelIndex, int nAtomsDeleted, BS bsDeleted) {
- fixIndicesM(modelIndex, nAtomsDeleted, bsDeleted);
- for (int i = 0; i < bioPolymerCount; i++)
- bioPolymers[i].recalculateLeadMidpointsAndWingVectors();
- }
-
- @Override
public Lst<BS> getBioBranches(Lst<BS> biobranches) {
// scan through biopolymers quickly --
BS bsBranch;
@@ -1028,7 +994,7 @@
}
@Override
- public void getAllPolymerInfo(
+ public void getPolymerInfo(
BS bs,
Map<String, Lst<Map<String, Object>>>
finalInfo,
Lst<Map<String, Object>> modelVector) {
@@ -1114,12 +1080,6 @@
pdbCONECT, bsWritten, ptTemp);
}
- private void recalculateLeadMidpointsAndWingVectors() {
- for (int ip = 0; ip < bioPolymerCount; ip++)
- bioPolymers[ip].recalculateLeadMidpointsAndWingVectors();
- }
-
-
/**
* from ModelSet.setAtomPositions
*
@@ -1144,5 +1104,41 @@
getRasmolHydrogenBonds(bs, bs, null, false, Integer.MAX_VALUE, false,
null);
}
+ @Override
+ public void getDefaultLargePDBRendering(SB sb, int maxAtoms) {
+ BS bs = new BS();
+ if (getBondCount() == 0)
+ bs = bsAtoms;
+ // all biopolymer atoms...
+ if (bs != bsAtoms)
+ for (int i = 0; i < bioPolymerCount; i++)
+ bioPolymers[i].getRange(bs, isMutated);
+ if (bs.nextSetBit(0) < 0)
+ return;
+ // ...and not connected to backbone:
+ BS bs2 = new BS();
+ if (bs == bsAtoms) {
+ bs2 = bs;
+ } else {
+ for (int i = 0; i < bioPolymerCount; i++)
+ if (bioPolymers[i].getType() == BioPolymer.TYPE_NOBONDING)
+ bioPolymers[i].getRange(bs2, isMutated);
+ }
+ if (bs2.nextSetBit(0) >= 0)
+ sb.append("select ").append(Escape.eBS(bs2)).append(";backbone only;");
+ if (ac <= maxAtoms)
+ return;
+ // ...and it's a large model, to wireframe:
+ sb.append("select ").append(Escape.eBS(bs)).append(" & connected;
wireframe only;");
+ // ... and all non-biopolymer and not connected to stars...
+ if (bs != bsAtoms) {
+ bs2.clearAll();
+ bs2.or(bsAtoms);
+ bs2.andNot(bs);
+ if (bs2.nextSetBit(0) >= 0)
+ sb.append("select " + Escape.eBS(bs2) + " & !connected;stars
0.5;spacefill off;");
+ }
+ }
+
}
Modified: trunk/Jmol/src/org/jmol/modelsetbio/Resolver.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/Resolver.java 2015-01-30 15:43:23 UTC
(rev 20260)
+++ trunk/Jmol/src/org/jmol/modelsetbio/Resolver.java 2015-01-30 15:56:30 UTC
(rev 20261)
@@ -1826,7 +1826,7 @@
+ " 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)}){"
+ + " if ({r1 & within(group, r0)}){\n"
+ " var haveHs = ({_H and connected(res0)} != 0)\n"
+ " if (!haveHs) {delete _H and res1}\n"
+ " var sm = '[*.N][*.CA][*.C][*.O]'\n"
Modified: trunk/Jmol/src/org/jmol/viewer/PropertyManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/PropertyManager.java 2015-01-30 15:43:23 UTC
(rev 20260)
+++ trunk/Jmol/src/org/jmol/viewer/PropertyManager.java 2015-01-30 15:56:30 UTC
(rev 20261)
@@ -1491,7 +1491,7 @@
Model[] models = vwr.ms.am;
for (int i = 0; i < modelCount; ++i)
if (models[i].isBioModel)
- ((JmolBioModel) models[i]).getAllPolymerInfo(bs, finalInfo,
modelVector);
+ ((JmolBioModel) models[i]).getPolymerInfo(bs, finalInfo, modelVector);
finalInfo.put("models", modelVector);
return finalInfo;
}
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