Allow manual translation or rotation.

Adds a settings widget to the manipulate tool.
This allows manual translation or rotation
around the origin or the center of geometry.
Also supports undo of manipulations.

Change-Id: I45a9e02dc6251dfc6f2f0f55d79ed6039ce88697
Modify the setOBMol method to fill crystal cells.

The existing code will import only the asymmetric
unit cell, which is surprising for most inorganic
crystals. (It works fine for molecular crystals.)
This patch adds a heuristic to fill the unit cell
when presented with a crystal < 4 carbon atoms.

This also removes similar code from the insert
crystal extension.

Change-Id: I07f613cebaa72bb6b51c7c6714f1e2d8533ab792
Add a DNA/RNA builder.

Uses Open Babel's FASTA format support.
In OB 2.3.1, this enables single/double strand
DNA and modifying the # of bp per turn.

Change-Id: I82e13b1ac9bd66eea18adadbd94dc7fc9c0793ff
Fix crash reported when crystal files not present.

Simply disables the entire interface.
Uses qWarning() to spit out a warning to console.
Fixes bug report PR#3530795.

Change-Id: Ifbbf1b6a3c1b99fdfedb9158862d889eebd856af
Prevent a quick double-insert.

With the "grow by fragment" feature, accidentally
double-clicking "insert" could give you much more
than you intended. Adds a 2-second delay to ensure
you actually want to grow the selected insert.

Change-Id: Ib9fb77b067a6470dd7d2672d8ba9e3b7e3738ca4
Fix for crash when using "cut" on a selection.

The code now checks if a unit cell exists
before copying it. Fixes a crash found when
testing.

Change-Id: Id5ac034beca06e2f93a66685be19feb374e55674
Fix residue and atom code assignment.

Any time the selection was updated, residue codes would be killed.
(No need to call Primitive::update())
Also, be conservative about changing elements when copying atoms
for the same reason. Finally, avoid calling OBChainsParser unless
*absolutely* necessary, because of bugs like PR#3102300.
Fully fixes this bug.

Change-Id: If990ce1903d668f596fe67208e34094edb70cfc7
Fix dereference of NULL pointer errors from clang.

Clang static analyzer found a number of logic errors,
most notably some NULL dereference pathways in swig.cpp.
This adds defensive checks which solve the bug.

Change-Id: I3d63efa5083c6404628abae92f3a005447343e60
simple lammps input generator for water

This input generator along with the OpenBabel lmpdat format can be used
to create input files for MD simulations.

The SPC and SPC/E water models are programmed.

J. Phys. Chem. A, 2001, 105 (43), pp 9954–9960
DOI: 10.1021/jp003020w

Change-Id: Icf27536174cfa7a720ec3e625849310e71ff1bfd
Add three example WFN files.

Gives test files for QTAIM analysis,
including diborane (B2H6), C4H4, and
HCO2. These files will be used for a tutorial.

Change-Id: I0489ea1b23ea4683596069bd219ef8cb3c9874d1
Add ChemSpider name index to the NIH resolver.

The "fetch by name" through the NIH resolver can use
the ChemSpider index if requested specifically. Add this
(since it's a fall-back option, e.g., for "rapamycin").

Also adds a "requester" parameter so the NIH can track usage.

Change-Id: I09ce0b77b0e094983cd8b398993466c15dd52a46
Automated update of translation templates (POT) using latest strings.

Change-Id: I78e782a10e39b7d3488d5e5cc5a984682fbf3a1d
Merge topic 'ENH_add_wfn_testfile' into master

2ffee8c4 Add three example WFN files.
Automated update of translation templates (POT) using latest strings.

Change-Id: If7e7bded33c09da90fcf9ec974dbe51a747e95e7
Hide the option to pick the text render in releases.

In Release builds, the textRendering combo
(which selects between QPainter and built-in code)
is hidden, along with its label.

This patch is intentionally conservative for 1.1.0.

Change-Id: Ic27285a636126a0f03dac362503702f5a52355f6
Merge topic 'FIX_hide-label-render-code' into master

85d2f5c9 Hide the option to pick the text render in releases.
Merge topic 'FIX-crash-on-cut' into master

65452b16 Fix for crash when using "cut" on a selection.
Fix crash with dipole moment after optimization.

Fixes PR#3521044. Request new instance of force
field object for calculating dipole moment.
Otherwise, multi-threaded usage causes crashing.

Change-Id: Iaebf31c13677d29e7acec95b91a17f9e06a17aa4
Merge topic 'FIX_use-make-new-instance' into master

d540d144 Fix crash with dipole moment after optimization.
Merge topic 'FIX_residue_atom_labels' into master

5c31094e Fix residue and atom code assignment.