Revision: 21190
http://sourceforge.net/p/jmol/code/21190
Author: hansonr
Date: 2016-08-09 22:07:19 +0000 (Tue, 09 Aug 2016)
Log Message:
-----------
mmtf alt-loc working
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/cif/MMCifReader.java
trunk/Jmol/src/org/jmol/adapter/readers/cif/MMTFReader.java
trunk/Jmol/src/org/jmol/adapter/smarter/XtalSymmetry.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cif/MMCifReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cif/MMCifReader.java
2016-08-09 16:53:29 UTC (rev 21189)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cif/MMCifReader.java
2016-08-09 22:07:19 UTC (rev 21190)
@@ -1197,6 +1197,8 @@
private String modelStrings = "";
+ protected boolean done;
+
@Override
protected int checkPDBModelField(int modelField, int currentModelNo) throws
Exception {
// the model field value is only used if
@@ -1223,9 +1225,12 @@
}
}
if (iHaveDesiredModel && asc.atomSetCount > 0 && !isAssembly) {
- parser.skipLoop(false);
- // but only this atom loop
- skipping = false;
+ done = true;
+ if (parser != null) {
+ parser.skipLoop(false);
+ // but only this atom loop
+ skipping = false;
+ }
continuing = true;
return Integer.MIN_VALUE;
}
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cif/MMTFReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cif/MMTFReader.java 2016-08-09
16:53:29 UTC (rev 21189)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cif/MMTFReader.java 2016-08-09
22:07:19 UTC (rev 21190)
@@ -79,6 +79,9 @@
public class MMTFReader extends MMCifReader {
+ private boolean haveStructure;
+
+
@Override
protected void addHeader() {
// no header for this type
@@ -129,14 +132,22 @@
id = "?";
fileAtomCount = ((Integer) map.get("numAtoms")).intValue();
int nBonds = ((Integer) map.get("numBonds")).intValue();
- Logger.info("id atoms bonds " + id + " " + fileAtomCount + " " + nBonds);
+
+ groupCount = ((Integer) map.get("numGroups")).intValue();
+ groupModels = new int[groupCount]; // group model (file-based)
+ groupDSSP = new int[groupCount]; // group structure type (Jmol-based)
+ groupMap = new int[groupCount]; // file->jmol group index map
+
+ int modelCount = ((Integer) map.get("numModels")).intValue();
+ appendLoadNote("id=" + id + " numAtoms=" + fileAtomCount + " numBonds="
+ + nBonds + " numGroups=" + groupCount + " numModels=" + modelCount);
getMMTFAtoms(doDoubleBonds);
if (!isCourseGrained) {
- int[] bo = (int[]) decode("bondOrderList");
+ int[] bo = (int[]) decode("bondOrderList");
int[] bi = (int[]) decode("bondAtomList");
addMMTFBonds(bo, bi, 0, doDoubleBonds, true);
if (isDSSP1 || mmtfImplementsDSSP2)
- getStructure((int[]) decode("secStructList"));
+ getStructure();
}
setMMTFSymmetry();
getMMTFBioAssembly();
@@ -145,15 +156,27 @@
Logger.info(SV.getVariable(map).asString());
}
+ @Override
+ public void applySymmetryAndSetTrajectory() throws Exception {
+ ac0 = ac;
+ super.applySymmetryAndSetTrajectory();
+ if (haveStructure)
+ addStructureSymmetry();
+ }
+
//////////////////////////////// MMTF-Specific /////////////////////////
private Map<String, Object> map; // input JSON-like map from MessagePack
binary file
private int fileAtomCount;
private int opCount = 0;
- private int[] groupModels;
+ private int[] groupModels, groupMap, groupDSSP, atomGroup;
private String[] labelAsymList; // created in getAtoms; used in
getBioAssembly
private Atom[] atomMap; // necessary because some atoms may be deleted.
private Object[] entities;
+ private int groupCount;
+ private int ac0;
+ private BS[] bsStructures;
+ private int lastGroup;
// TODO - also consider mapping group indices
@@ -177,23 +200,17 @@
// groups
int[] groupTypeList = (int[]) decode("groupTypeList");
- int groupCount = groupTypeList.length;
- groupModels = new int[groupCount];
int[] groupIdList = (int[]) decode("groupIdList");
Object[] groupList = (Object[]) map.get("groupList");
char[] insCodes = (char[]) decode("insCodeList");
-
- int[] atomId = (int[]) decode("atomIdList");
+ int[] atomId = (int[]) decode("atomIdList");
boolean haveSerial = (atomId != null);
-
char[] altloc = (char[]) decode("altLocList"); // rldecode32
float[] occ = (float[]) decode("occupancyList");
-
float[] x = (float[]) decode("xCoordList");//getFloatsSplit("xCoord",
1000f);
float[] y = (float[]) decode("yCoordList");
float[] z = (float[]) decode("zCoordList");
float[] bf = (float[]) decode("bFactorList");
- int iatom = 0;
String[] nameList = (useAuthorChainID ? authAsymList : labelAsymList);
int iModel = -1;
int iChain = 0;
@@ -202,15 +219,13 @@
int nGroup = 0;
int chainpt = 0;
int seqNo = 0;
+ int iatom = 0;
String chainID = "";
String authAsym = "", labelAsym = "";
char insCode = '\0';
atomMap = new Atom[fileAtomCount];
- for (int j = 0; j < groupCount; j++) {
- int a0 = iatom;
- if (insCodes != null)
- insCode = insCodes[j];
- seqNo = groupIdList[j];
+ atomGroup = new int[fileAtomCount];
+ for (int j = 0, thisGroup = -1; j < groupCount; j++) {
if (++iGroup >= nGroup) {
chainID = nameList[chainpt];
authAsym = authAsymList[chainpt];
@@ -224,11 +239,24 @@
setModelPDB(true);
incrementModel(iModel + 1);
nAtoms0 = asc.ac;
+ if (done)
+ return;
}
}
Map<String, Object> g = (Map<String, Object>)
groupList[groupTypeList[j]];
+ String[] atomNameList = (String[]) g.get("atomNameList");
+ int len = atomNameList.length;
+ if (skipping) {
+ iatom += len;
+ continue;
+ }
+ int a0 = iatom;
+ if (insCodes != null)
+ insCode = insCodes[j];
+ seqNo = groupIdList[j];
String group3 = (String) g.get("groupName");
- if (vwr.getJBR().isHetero(group3)) {
+ boolean isHetero = vwr.getJBR().isHetero(group3);
+ if (isHetero) {
// looking for CHEM_COMP_NAME here... "IRON/SULFUR CLUSTER" for SF4 in
1blu
String hetName = "" + g.get("chemCompType");
if (htHetero == null || !htHetero.containsKey(group3)) {
@@ -250,11 +278,11 @@
addHetero(group3, hetName, false, true);
}
}
- String[] atomNameList = (String[]) g.get("atomNameList");
String[] elementList = (String[]) g.get("elementList");
- int len = atomNameList.length;
+ boolean haveAtom = false;
for (int ia = 0, pt = 0; ia < len; ia++, iatom++) {
Atom a = new Atom();
+ a.isHetero = isHetero;
if (insCode != 0)
a.insertionCode = insCode;
setAtomCoordXYZ(a, x[iatom], y[iatom], z[iatom]);
@@ -274,13 +302,20 @@
a.atomSerial = atomId[iatom];
if (!filterAtom(a, -1) || !processSubclassAtom(a, labelAsym, authAsym))
continue;
+
+ if (!haveAtom) {
+ thisGroup++;
+ haveAtom = true;
+ }
if (haveSerial) {
asc.addAtomWithMappedSerialNumber(a);
} else {
asc.addAtom(a);
}
atomMap[iatom] = a;
- ++ac;
+ atomGroup[ac] = j;
+ groupMap[j] = lastGroup = thisGroup;
+ ac++;
}
if (!isCourseGrained) {
int[] bo = (int[]) g.get("bondOrderList");
@@ -301,7 +336,7 @@
Bond bond = new Bond(a1.index, a2.index, doMulti ? bo[bj] : 1);
asc.addBond(bond);
if (Logger.debugging && isInter) {
- Logger.info("inter-group bond " + a1.group3 + a1.sequenceNumber +
"." + a1.atomName
+ Logger.info("inter-group (" + (a1.atomSetIndex + 1) + "." + a1.index
+ "/" + (a2.atomSetIndex + 1) + "." + a2.index + ") bond " + a1.group3 +
a1.sequenceNumber + "." + a1.atomName
+ " - " + a2.group3 + a2.sequenceNumber + "." + a2.atomName + " "
+ bond.order);
}
@@ -385,33 +420,69 @@
/**
* Get and translate the DSSP string from digit format
*
- * @param a
* input data
*/
- private void getStructure(int[] a) {
- BS[] bsStructures = new BS[] { new BS(), null, new BS(), new BS(),
- new BS(), null, new BS() };
+ private void getStructure() {
+ int[] a = (int[]) decode("secStructList");
if (Logger.debugging)
Logger.info(PT.toJSON("secStructList", a));
+ bsStructures = new BS[] { new BS(), null, new BS(), new BS(),
+ new BS(), null, new BS() };
int lastGroup = -1;
- for (int i = 0; i < a.length; i++) {
- int type = a[i];
+ for (int j = 0; j < a.length; j++) {
+ int type = a[j];
switch (type) {
case 0: // PI
case 2: // alpha
case 3: // sheet
case 4: // 3-10
case 6: // turn
- bsStructures[type].set(i);
- lastGroup = i;
+ int igroup = groupMap[j];
+ bsStructures[type].set(igroup);
+ groupDSSP[igroup] = type + 1;
+ lastGroup = j;
}
}
int n = (isDSSP1 ? asc.iSet : groupModels[lastGroup]);
- if (lastGroup >= 0)
+ if (lastGroup >= 0) {
+ // a single structure takes care of everything
+ haveStructure = true;
asc.addStructure(new Structure(n, null, null, null, 0, 0, bsStructures));
+ }
}
+ /**
+ * We must add groups to the proper bsStructure element
+ *
+ */
+ private void addStructureSymmetry() {
+ if (asc.ac == 0)
+ return;
+ Atom[] atoms = asc.atoms;
+ BS bsAtoms = asc.bsAtoms;
+
+ // must point to groups here.
+
+ int ptGroup = lastGroup;
+ int mygroup = -1;
+ for (int i = ac0, n = asc.ac; i < n; i++) {
+ if (bsAtoms == null || bsAtoms.get(i)) {
+ Atom a = atoms[i];
+ int igroup = atomGroup[a.atomSite];
+ if (igroup != mygroup) {
+ mygroup = igroup;
+ ptGroup++;
+ }
+ int dssp = groupDSSP[igroup];
+ if (dssp > 0) {
+ bsStructures[dssp - 1].set(ptGroup);
+ }
+ }
+ }
+ }
+
+
/////////////// MessagePack decoding ///////////////
private Object decode(String key) {
@@ -446,8 +517,10 @@
case 14: // two-byte
case 15: // one-byte
return unpack(b, 16 - type, n);
+ default:
+ Logger.error("MMTF type " + type + " not found!");
+ return null;
}
- return null;
}
/**
@@ -558,7 +631,7 @@
return null;
char[] ret = new char[n];
for (int i = 0, pt = 3; i < n;) {
- char val = (char) b[(pt++) << 2];
+ char val = (char) b[((pt++) << 2) + 3];
for (int j = BC.bytesToInt(b, (pt++) << 2, true); --j >= 0;)
ret[i++] = val;
}
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/XtalSymmetry.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/XtalSymmetry.java 2016-08-09
16:53:29 UTC (rev 21189)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/XtalSymmetry.java 2016-08-09
22:07:19 UTC (rev 21190)
@@ -155,7 +155,7 @@
private void setUnitCell(float[] info, M3 matUnitCellOrientation,
P3 unitCellOffset) {
unitCellParams = new float[info.length];
- this.unitCellOffset = unitCellOffset;
+ //this.unitCellOffset = unitCellOffset;
for (int i = 0; i < info.length; i++)
unitCellParams[i] = info[i];
asc.haveUnitCell = true;
@@ -493,7 +493,7 @@
private final P3 ptOffset = new P3();
- private P3 unitCellOffset;
+ //private P3 unitCellOffset;
private P3i minXYZ, maxXYZ;
private P3 minXYZ0, maxXYZ0;
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2016-08-09 16:53:29 UTC
(rev 21189)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2016-08-09 22:07:19 UTC
(rev 21190)
@@ -49,7 +49,7 @@
Jmol.___JmolVersion="14.7.1_2016.08.09"
-
+sycnronized with Jmol 14.6.1
bug fix: upgrade of RCSB mmtf format reading to version 0.2 specs
load =2tbv.mmtf {1 1 1} filter "biomolecule 1;*.ca"
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