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Add ability to write axes, take user specified base pairs, and report all hydrogen bonds to nastruct #1037

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Merged
drroe merged 39 commits into from
Jul 11, 2023
Merged

Add ability to write axes, take user specified base pairs, and report all hydrogen bonds to nastruct #1037

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3d469f7
Always print a warning when NA residue not recognized. Add some debug
drroe Jul 10, 2023
6f0ca0a
Start the axesout keyword
drroe Jul 10, 2023
980954d
Start initializing base axes traj
drroe Jul 10, 2023
b2a7fc0
Put pseudo traj init into separate function
drroe Jul 10, 2023
b4b894d
Rename function
drroe Jul 10, 2023
e7e7ff3
Set up topology for axes pseudo trajectory
drroe Jul 10, 2023
d4e8efd
Set up the trajectory as well
drroe Jul 10, 2023
9923972
Write psuedo axes frame
drroe Jul 10, 2023
ddfbcd9
Update help and dependencies
drroe Jul 10, 2023
3cec5ab
Actually write the base axes frames
drroe Jul 10, 2023
3ba0b75
Start base pair axes pseudo traj
drroe Jul 10, 2023
aa90a53
Only set up base axes topology once
drroe Jul 11, 2023
03fbb42
Add check that number of bases has not changed
drroe Jul 11, 2023
6ed7a8a
Check for incompatibilities
drroe Jul 11, 2023
985c465
Do base pair axes out
drroe Jul 11, 2023
9a5bcba
Save base pair step axis for output
drroe Jul 11, 2023
a806645
Add base pair step axes write
drroe Jul 11, 2023
23abaab
Fix comments
drroe Jul 11, 2023
3806931
Move the base axes write to before base pair parameters are determined
drroe Jul 11, 2023
1ce4c89
Add some axes write tests
drroe Jul 11, 2023
59fc90d
Add test for step axes coords
drroe Jul 11, 2023
edb7462
Add ability to customize atom axis names
drroe Jul 11, 2023
45e38f1
Update help and fix var names
drroe Jul 11, 2023
8f58999
Remove old code
drroe Jul 11, 2023
8cc4547
Start adding user-specified base pairing
drroe Jul 11, 2023
6b82574
Enable specifiedbp mode
drroe Jul 11, 2023
22e355e
Add test for user-specified base pairing
drroe Jul 11, 2023
56ffce0
Formally deprecate guessbp in favor of specifiedbp
drroe Jul 11, 2023
7f36c6c
Add specifiedbp example to help text
drroe Jul 11, 2023
6eb6de9
Test passing traj args to axes output
drroe Jul 11, 2023
e324c4b
Fix up help, add new keywords.
drroe Jul 11, 2023
6a7b94b
Add wchbonly keyword
drroe Jul 11, 2023
f210d19
Change the keyword to allhb
drroe Jul 11, 2023
bf49913
Document allhb keyword.
drroe Jul 11, 2023
372b50c
6.19.6. Revision bump for adding 'axesout' etc, 'allhb', and 'specifi…
drroe Jul 11, 2023
1583749
Protect tests in parallel
drroe Jul 11, 2023
dbd8aa2
Do proper search for residue # in Bases instead of using user specified
drroe Jul 11, 2023
f23698c
Remove old debug print of axes, superseded by new functionality.
drroe Jul 11, 2023
14ba457
Fix error in printf statement
drroe Jul 11, 2023
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212 changes: 207 additions & 5 deletions doc/cpptraj.lyx
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Original file line number Diff line number Diff line change
Expand Up @@ -33238,7 +33238,7 @@ nastruct
\end_layout

\begin_layout LyX-Code
[bpmode {3dna|babcock}]
[bpmode {3dna|babcock}] [allhb]
\end_layout

\begin_layout LyX-Code
Expand All @@ -33250,15 +33250,33 @@ nastruct
\end_layout

\begin_layout LyX-Code
[{ first | reference | ref <name> | refindex <#> | allframes | guessbp}]
\begin_inset Separator latexpar
\end_inset
[axesout <file> [axesoutarg <arg> ...] [axesparmout <file>]]
\end_layout

\begin_layout LyX-Code
[bpaxesout <file> [bpaxesoutarg <arg> ...] [bpaxesparmout <file>]]
\end_layout

\begin_layout LyX-Code
[stepaxesout <file> [stepaxesoutarg <arg> ...] [stepaxesparmout <file>]]
\end_layout

\begin_layout LyX-Code
[axisnameo <name>] [axisnamex <name>] [axisnamey <name>] [axisnamez
<name>]
\end_layout

\begin_layout LyX-Code
[{ first | reference | ref <name> | refindex <#> |
\end_layout

\begin_layout LyX-Code
[bptype {anti | para} ...]
allframes |
\end_layout

\begin_layout LyX-Code
specifiedbp pairs <b1>-<b2>,...
}]
\end_layout

\begin_deeper
Expand Down Expand Up @@ -33367,6 +33385,11 @@ literal "true"
parallel.
\end_layout

\begin_layout Description
[allhb] Report the total number of hydrogen bonds detected instead of just
the number of Watson-Crick-Franklin hydrogen bonds.
\end_layout

\begin_layout Description
[hbcut
\begin_inset space ~
Expand Down Expand Up @@ -33445,6 +33468,123 @@ literal "true"
\end_layout

\end_deeper
\begin_layout Description
[axesout
\begin_inset space ~
\end_inset

<file>] Trajectory file to write base axes to.
\end_layout

\begin_deeper
\begin_layout Description
[axesoutarg
\begin_inset space ~
\end_inset

<arg>] Trajectory argument to pass to base axes trajectory file (can specify
more than once).
\end_layout

\begin_layout Description
[axesparmout
\begin_inset space ~
\end_inset

<file>] Topology file to write base axes pseudo topology to.
\end_layout

\end_deeper
\begin_layout Description
[bpaxesout
\begin_inset space ~
\end_inset

<file>] Trajectory file to write base pair axes to.
\end_layout

\begin_deeper
\begin_layout Description
[bpaxesoutarg
\begin_inset space ~
\end_inset

<arg>] Trajectory argument to pass to base pair axes trajectory file (can
specify more than once).
\end_layout

\begin_layout Description
[bpaxesparmout
\begin_inset space ~
\end_inset

<file>] Topology file to write base pair axes pseudo topology to.
\end_layout

\end_deeper
\begin_layout Description
[stepaxesout
\begin_inset space ~
\end_inset

<file>] Trajectory file to write base pair step axes to.
\end_layout

\begin_deeper
\begin_layout Description
[stepaxesoutarg
\begin_inset space ~
\end_inset

<arg>] Trajectory argument to pass to base pair step axes trajectory file
(can specify more than once).
\end_layout

\begin_layout Description
[stepaxesparmout
\begin_inset space ~
\end_inset

<file>] Topology file to write base pair step axes pseudo topology to.
\end_layout

\end_deeper
\begin_layout Description
[axisnameo
\begin_inset space ~
\end_inset

<name>] Change name of axis origin pseudo atom (default 'Orig').
\end_layout

\begin_layout Description
[axisnamex
\begin_inset space ~
\end_inset

<name>] Change name of axis origin pseudo atom (default 'X').
\end_layout

\begin_layout Description
[axisnamey
\begin_inset space ~
\end_inset

<name>] Change name of axis origin pseudo atom (default 'Y').
\end_layout

\begin_layout Description
[axisnamez
\begin_inset space ~
\end_inset

<name>] Change name of axis origin pseudo atom (default 'Z').
\end_layout

\begin_layout Standard
How to determine base pairing:
\end_layout

\begin_layout Description
[first] Use first frame to determine base pairing (default).
\end_layout
Expand Down Expand Up @@ -33481,6 +33621,23 @@ ref
[allframes] If specified determine base pairing each frame.
\end_layout

\begin_layout Description
[specifiedbp
\begin_inset space ~
\end_inset

pairs
\begin_inset space ~
\end_inset

<b1>-<b2>,...] User specified base pairing.
Base pairs are specified in a comma-separated list after the 'pairs' keyword
as <b1>-<b2>, where <b1> and <b2> are the residue numbers of bases in the
base pair, e.g.
'pairs 1-16,2-15,3-14,4-13'.
Can specify 'pairs' multiple times.
\end_layout

\begin_layout Standard
DataSets Created:
\end_layout
Expand Down Expand Up @@ -33687,6 +33844,15 @@ Base pairs are determined either once from the first frame or from a reference
allframes
\series default
is specified.
Base pairing can also be specified via the
\series bold
specifiedbp
\series default
and
\series bold
pairs
\series default
keywords.
Base pairing is determined first by base reference axis origin distance,
then by stagger, then by angle between base Z axes, then finally by hydrogen
bonding (at least one hydrogen bond must be present).
Expand Down Expand Up @@ -33784,6 +33950,42 @@ sscalc
.
\end_layout

\begin_layout Standard
Base axes, base pair axes, and base pair step axes can be written to trajectory
files using the
\series bold
axesout
\series default
,
\series bold
bpaxesout
\series default
, and
\series bold
stepaxesout
\series default
and related keywords.
The axes are written using 4 points: an origin, and X Y and Z which are
bonded to the origin.
The names of these pseudo atoms can be changed using the
\series bold
axisnameo
\series default
,
\series bold
axisnamex
\series default
,
\series bold
axisnamey
\series default
, and
\series bold
axisnamez
\series default
keywords.
\end_layout

\begin_layout Subsubsection*
Custom Nucleic Acid Base References
\end_layout
Expand Down
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