Skip to content

Fixes and improvements for SPAM and volmap, 3d grids #838

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
drroe merged 7 commits into from
Aug 22, 2020
Merged

Fixes and improvements for SPAM and volmap, 3d grids #838

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
7 commits
Select commit Hold shift + click to select a range
52a9455
Start importing changes from the fixspam branch. Improved formatting …
drroe Aug 21, 2020
4e1b965
Update dependencies.
drroe Aug 21, 2020
5bf3abf
Changes from fixspam. Peaks are stored in a data set now. Allow volma…
drroe Aug 21, 2020
b89c3bd
Clean up the volmap and spam manual entries.
drroe Aug 21, 2020
7274169
Add type keyword to OpenDX read help and manual entry
drroe Aug 21, 2020
d10bb6b
Add description of the sets created by SPAM.
drroe Aug 21, 2020
0b1bb01
Increment revision for SPAM/volmap improvements.
drroe Aug 21, 2020
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
566 changes: 407 additions & 159 deletions doc/cpptraj.lyx
View file
Open in desktop

Large diffs are not rendered by default.

192 changes: 111 additions & 81 deletions src/Action_Spam.cpp
View file
Open in desktop

Large diffs are not rendered by default.

6 changes: 5 additions & 1 deletion src/Action_Spam.h
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,8 @@
#include "Vec3.h"
#include "Timer.h"
#include "PairList.h"
// Forward declares
class DataSet_Vector_Scalar;
/**
SPAM is a water profiling technique developed by Guanglei Cui at
GlaxoSmithKline (GSK). The original implementation involved a set of specialized
Expand Down Expand Up @@ -52,6 +54,7 @@ class Action_Spam: public Action {
Action::RetType DoPureWater(int, Frame const&);
Action::RetType DoSPAM(int, Frame&);

int GetPeaks(std::string const&, DataSetList const&);
typedef bool (Action_Spam::*FxnType)(Vec3, Vec3, double) const;
bool inside_box(Vec3, Vec3, double) const;
bool inside_sphere(Vec3, Vec3, double) const;
Expand Down Expand Up @@ -86,11 +89,12 @@ class Action_Spam: public Action {
DataSet* ds_ds_; ///< Hold final -T*S values for each peak
Parray peakFrameData_; ///< A list of all omitted frames for each peak
DSarray myDSL_; ///< Hold energy data sets
Varray peaks_; ///< List of each peak location
Varray comlist_; ///< For given frame, each residue C.O.M. coords.
Rarray solvent_residues_; ///< List of each solvent residue
int Nframes_; ///< Total number of frames
bool overflow_; ///< True if cutoff overflowed our box coordinates
DataSetList peaksdsl_; ///< Will allocate DataSet for peaks data if loading from a file.
DataSet_Vector_Scalar* peaksData_; ///< Hold peaks DataSet
// Timers
Timer t_action_;
Timer t_resCom_;
Expand Down
Loading