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Fix potential overflow in string dataset #732

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Merged
drroe merged 5 commits into from
Jun 13, 2019
Merged

Fix potential overflow in string dataset #732

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a4bb779
DRR - Cpptraj: Use actual format width instead of string width when d…
drroe Jun 13, 2019
f593374
DRR - Cpptraj: Revision bump for string dataset overflow fix.
drroe Jun 13, 2019
e480732
DRR - Cpptraj: Make it clear that stfcdiffusion mask2 is needed for l…
drroe Jun 13, 2019
82b9d83
DRR - Cpptraj: Fix manual entry.
drroe Jun 13, 2019
7698a91
DRR - Cpptraj: Update manual.
drroe Jun 13, 2019
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Binary file modified doc/CpptrajManual.pdf
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2 changes: 1 addition & 1 deletion doc/cpptraj.lyx
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Original file line number Diff line number Diff line change
Expand Up @@ -31287,7 +31287,7 @@ stfcdiffusion mask <mask> [out <file>] [time <time per frame>]
\end_layout

\begin_layout LyX-Code
[mask2 <mask>] [lower <distance>] [upper <distance>]
[mask2 <mask> [lower <distance>] [upper <distance>]]
\end_layout

\begin_layout LyX-Code
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8 changes: 7 additions & 1 deletion src/Action_STFC_Diffusion.cpp
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Expand Up @@ -19,7 +19,7 @@ Action_STFC_Diffusion::Action_STFC_Diffusion() :

void Action_STFC_Diffusion::Help() const {
mprintf("\tmask <mask> [out <file>] [time <time per frame>]\n"
"\t[mask2 <mask>] [lower <distance>] [upper <distance>]\n"
"\t[mask2 <mask> [lower <distance>] [upper <distance>]]\n"
"\t[nwout <file>]) [avout <file>] [distances] [com]\n"
"\t[x|y|z|xy|xz|yz|xyz]\n"
" Calculate diffusion of atoms in <mask>\n");
Expand Down Expand Up @@ -95,6 +95,12 @@ Action::RetType Action_STFC_Diffusion::Init(ArgList& actionArgs, ActionInit& ini
calcType_ = DIST;
// See if imaging is to be performed.
image_.InitImaging( !(actionArgs.hasKey("noimage")) );
} else if (actionArgs.Contains("lower")) {
mprinterr("Error: 'lower' requires 'mask2'\n");
return Action::ERR;
} else if (actionArgs.Contains("upper")) {
mprinterr("Error: 'upper' requires 'mask2'\n");
return Action::ERR;
}

if (calcType_ != DEFAULT)
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2 changes: 1 addition & 1 deletion src/DataSet_string.cpp
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Expand Up @@ -38,7 +38,7 @@ void DataSet_string::WriteBuffer(CpptrajFile &cbuffer, SizeArray const& pIn) con
cbuffer.Printf(format_.fmt(), "NoData");
else {
// Protect against CpptrajFile buffer overflow.
if (Data_[pIn[0]].size() >= CpptrajFile::BUF_SIZE) {
if (format_.Width() >= (int)CpptrajFile::BUF_SIZE) {
// FIXME: Data sets should not have to worry about spaces in format strings.
if (format_.fmt()[0] == ' ') cbuffer.Printf(" ");
cbuffer.Write(Data_[pIn[0]].c_str(), Data_[pIn[0]].size());
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2 changes: 1 addition & 1 deletion src/Version.h
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Expand Up @@ -12,7 +12,7 @@
* Whenever a number that precedes <revision> is incremented, all subsequent
* numbers should be reset to 0.
*/
#define CPPTRAJ_INTERNAL_VERSION "V4.14.10"
#define CPPTRAJ_INTERNAL_VERSION "V4.14.11"
/// PYTRAJ relies on this
#define CPPTRAJ_VERSION_STRING CPPTRAJ_INTERNAL_VERSION
#endif