Revision: 20972
http://sourceforge.net/p/jmol/code/20972
Author: hansonr
Date: 2016-03-03 22:49:45 +0000 (Thu, 03 Mar 2016)
Log Message:
-----------
Jmol.___JmolVersion="14.4.3_2016.03.03b"
bug fix: CIF reader _atom_site_cartn_x incompatible with _geom_bond
-- this fix now allows Jmol to read very simple CIF files that are equivalent
to unlimited-atom MOL files
-- _ccdc_geom_bond_type is not required, defaulting to S
-- _ccdc_geom_bond_types include S, D, T, Q (quadruple), and A (aromatic)
data_icosahedron
loop_
_atom_site_label
_atom_site_Cartn_x
_atom_site_Cartn_y
_atom_site_Cartn_z
C01 0.0000000000 0.0000000000 9.5105651630
C02 8.5065080835 0.0000000000 4.2532540418
C03 2.6286555606 8.0901699437 4.2532540418
C04 -6.8819096024 5.0000000000 4.2532540418
C05 -6.8819096024 -5.0000000000 4.2532540418
C06 2.6286555606 -8.0901699437 4.2532540418
C07 6.8819096024 5.0000000000 -4.2532540418
C08 -2.6286555606 8.0901699437 -4.2532540418
C09 -8.5065080835 0.0000000000 -4.2532540418
C10 -2.6286555606 -8.0901699437 -4.2532540418
C11 6.8819096024 -5.0000000000 -4.2532540418
C12 0.0000000000 0.0000000000 -9.5105651630
loop_
_geom_bond_atom_site_label_1
_geom_bond_atom_site_label_2
_ccdc_geom_bond_type
C01 C02 S
C01 C03 S
C01 C04 S
C01 C05 S
C01 C06 S
C02 C03 S
C03 C04 S
C04 C05 S
C05 C06 S
...etc...
Modified Paths:
--------------
branches/v14_4/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java
trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java
Modified: branches/v14_4/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java
2016-03-03 03:41:27 UTC (rev 20971)
+++ branches/v14_4/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java
2016-03-03 22:49:45 UTC (rev 20972)
@@ -1572,7 +1572,7 @@
// this 5-model file can be read using one model at a time: load
"c2cc34714h.txt" 3
// but it is far from perfect, and still the best way is load
"c2cc34714h.txt" 3 packed
bondCount++;
- bondTypes.addLast(new Object[] { name1, name2, Float.valueOf(distance),
+ bondTypes.addLast(new Object[] { name1, name2, Float.valueOf(distance),
Float.valueOf(dx), Integer.valueOf(order) });
}
if (bondCount > 0) {
@@ -1626,7 +1626,7 @@
bsSets[ipt] = new BS();
bsSets[ipt].set(i - firstAtom);
}
-
+
// if molecular, we need atom connection lists and radii
if (isMolecular) {
@@ -1661,7 +1661,7 @@
// main loop continues until no new atoms are found
}
- if (isMolecular) {
+ if (isMolecular && iHaveFractionalCoordinates) {
// Set bsAtoms to control which atoms and
// bonds are delivered by the iterators.
@@ -1706,6 +1706,12 @@
bsExclude = null;
}
+ private void fixAtomForBonding(P3 pt, int i) {
+ pt = (pt == null ? atoms[i] : P3.newP(atoms[i]));
+ if (iHaveFractionalCoordinates)
+ symmetry.toCartesian(pt, true);
+ }
+
/**
* Use the site bitset to check for atoms that are within +/-dx Angstroms of
* the specified distances in GEOM_BOND where dx is determined by the
@@ -1737,12 +1743,15 @@
for (int j = bs1.nextSetBit(0); j >= 0; j = bs1.nextSetBit(j + 1))
for (int k = bs2.nextSetBit(0); k >= 0; k = bs2.nextSetBit(k + 1)) {
if ((!isMolecular || !bsConnected[j + firstAtom].get(k))
- && symmetry.checkDistance(atoms[j + firstAtom], atoms[k
- + firstAtom], distance, dx, 0, 0, 0, ptOffset))
+ && checkBondDistance(atoms[j + firstAtom], atoms[k + firstAtom],
distance, dx))
addNewBond(j + firstAtom, k + firstAtom, order);
}
}
+
+ if (!iHaveFractionalCoordinates)
+ return false;
+
// do a quick check for H-X bonds if we have GEOM_BOND
if (bondTypes.size() > 0)
@@ -1754,8 +1763,7 @@
&& atoms[k].elementNumber != 1
&& (!checkAltLoc || atoms[k].altLoc == '\0' || atoms[k].altLoc
== atoms[i].altLoc)) {
if (!bsConnected[i].get(k)
- && symmetry.checkDistance(atoms[i], atoms[k], 1.1f, 0, 0, 0,
- 0, ptOffset))
+ && checkBondDistance(atoms[i], atoms[k], 1.1f, 0))
addNewBond(i, k, 1);
}
}
@@ -1793,16 +1801,14 @@
for (int k = bsBranch.nextSetBit(0); k >= 0; k = bsBranch
.nextSetBit(k + 1)) {
atoms[k].add(ptOffset);
- cart1.setT(atoms[k]);
- symmetry.toCartesian(cart1, true);
+ fixAtomForBonding(cart1, k);
BS bs = bsSets[asc.getAtomIndex(atoms[k].atomName) - firstAtom];
if (bs != null)
for (int ii = bs.nextSetBit(0); ii >= 0; ii = bs
.nextSetBit(ii + 1)) {
if (ii + firstAtom == k)
continue;
- cart2.setT(atoms[ii + firstAtom]);
- symmetry.toCartesian(cart2, true);
+ fixAtomForBonding(cart2, ii + firstAtom);
if (cart2.distance(cart1) < 0.1f) {
bsExclude.set(k);
break;
@@ -1815,6 +1821,13 @@
return false;
}
+ private boolean checkBondDistance(Atom a, Atom b, float distance, float dx) {
+ if (iHaveFractionalCoordinates)
+ return symmetry.checkDistance(a, b, distance, dx, 0, 0, 0, ptOffset);
+ float d = a.distance(b);
+ return (dx > 0 ? Math.abs(d - distance) <= dx : d <= distance && d >
0.1f); // same as in Symmetry
+ }
+
/**
* add the bond and mark it for molecular processing
*
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java 2016-03-03
03:41:27 UTC (rev 20971)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cif/CifReader.java 2016-03-03
22:49:45 UTC (rev 20972)
@@ -1539,11 +1539,20 @@
if (asc.getAtomIndex(name1 = getField(GEOM_BOND_ATOM_SITE_LABEL_1)) < 0
|| asc.getAtomIndex(name2 = getField(GEOM_BOND_ATOM_SITE_LABEL_2)) <
0)
continue;
+ int order = getBondOrder(getField(CCDC_GEOM_BOND_TYPE));
float dx = 0;
String sdist = getField(GEOM_BOND_DISTANCE);
float distance = parseFloatStr(sdist);
- if (distance == 0 || Float.isNaN(distance))
+ if (distance == 0 || Float.isNaN(distance)) {
+ if (!iHaveFractionalCoordinates) {
+ // maybe this is a simple Cartesian file with coordinates and bonds
+ Atom a = asc.getAtomFromName(name1);
+ Atom b = asc.getAtomFromName(name2);
+ if (a != null && b != null)
+ asc.addNewBondWithOrder(a.index, b.index, order);
+ }
continue;
+ }
int pt = sdist.indexOf('(');
if (pt >= 0) {
char[] data = sdist.toCharArray();
@@ -1564,7 +1573,6 @@
} else {
dx = 0.015f;
}
- int order = getBondOrder(getField(CCDC_GEOM_BOND_TYPE));
// This field is from Materials Studio. See supplemental material for
// http://pubs.rsc.org/en/Content/ArticleLanding/2012/CC/c2cc34714h
// http://www.rsc.org/suppdata/cc/c2/c2cc34714h/c2cc34714h.txt
@@ -1661,7 +1669,7 @@
// main loop continues until no new atoms are found
}
- if (isMolecular) {
+ if (isMolecular && iHaveFractionalCoordinates) {
// Set bsAtoms to control which atoms and
// bonds are delivered by the iterators.
@@ -1706,6 +1714,12 @@
bsExclude = null;
}
+ private void fixAtomForBonding(P3 pt, int i) {
+ pt = (pt == null ? atoms[i] : P3.newP(atoms[i]));
+ if (iHaveFractionalCoordinates)
+ symmetry.toCartesian(pt, true);
+ }
+
/**
* Use the site bitset to check for atoms that are within +/-dx Angstroms of
* the specified distances in GEOM_BOND where dx is determined by the
@@ -1737,12 +1751,15 @@
for (int j = bs1.nextSetBit(0); j >= 0; j = bs1.nextSetBit(j + 1))
for (int k = bs2.nextSetBit(0); k >= 0; k = bs2.nextSetBit(k + 1)) {
if ((!isMolecular || !bsConnected[j + firstAtom].get(k))
- && symmetry.checkDistance(atoms[j + firstAtom], atoms[k
- + firstAtom], distance, dx, 0, 0, 0, ptOffset))
+ && checkBondDistance(atoms[j + firstAtom], atoms[k + firstAtom],
distance, dx))
addNewBond(j + firstAtom, k + firstAtom, order);
}
}
+ if (!iHaveFractionalCoordinates)
+ return false;
+
+
// do a quick check for H-X bonds if we have GEOM_BOND
if (bondTypes.size() > 0)
@@ -1754,8 +1771,7 @@
&& atoms[k].elementNumber != 1
&& (!checkAltLoc || atoms[k].altLoc == '\0' || atoms[k].altLoc
== atoms[i].altLoc)) {
if (!bsConnected[i].get(k)
- && symmetry.checkDistance(atoms[i], atoms[k], 1.1f, 0, 0, 0,
- 0, ptOffset))
+ && checkBondDistance(atoms[i], atoms[k], 1.1f, 0))
addNewBond(i, k, 1);
}
}
@@ -1793,16 +1809,14 @@
for (int k = bsBranch.nextSetBit(0); k >= 0; k = bsBranch
.nextSetBit(k + 1)) {
atoms[k].add(ptOffset);
- cart1.setT(atoms[k]);
- symmetry.toCartesian(cart1, true);
+ fixAtomForBonding(cart1, k);
BS bs = bsSets[asc.getAtomIndex(atoms[k].atomName) - firstAtom];
if (bs != null)
for (int ii = bs.nextSetBit(0); ii >= 0; ii = bs
.nextSetBit(ii + 1)) {
if (ii + firstAtom == k)
continue;
- cart2.setT(atoms[ii + firstAtom]);
- symmetry.toCartesian(cart2, true);
+ fixAtomForBonding(cart2, ii + firstAtom);
if (cart2.distance(cart1) < 0.1f) {
bsExclude.set(k);
break;
@@ -1815,6 +1829,13 @@
return false;
}
+ private boolean checkBondDistance(Atom a, Atom b, float distance, float dx) {
+ if (iHaveFractionalCoordinates)
+ return symmetry.checkDistance(a, b, distance, dx, 0, 0, 0, ptOffset);
+ float d = a.distance(b);
+ return (dx > 0 ? Math.abs(d - distance) <= dx : d <= distance && d >
0.1f); // same as in Symmetry
+ }
+
/**
* add the bond and mark it for molecular processing
*
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