8000 Implement standard XYZ format by drroe · Pull Request #927 · Amber-MD/cpptraj · GitHub
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Implement standard XYZ format #927

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Merged
merged 15 commits into from
Dec 17, 2021
Merged

Implement standard XYZ format #927

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79920cc
Start revamping XYZ detection
drroe Dec 17, 2021
760e23d
Recognized the regular XYZ format
drroe Dec 17, 2021
c4e02ec
Add parsing of box information
drroe Dec 17, 2021
5778724
Add files for reading box coords test
drroe Dec 17, 2021
51dc4e2
Add test for reading box coords from comments
drroe Dec 17, 2021
4931dda
Add namexyz format write
drroe Dec 17, 2021
77600cb
Ensure box coords are written in comment
drroe Dec 17, 2021
8d16f04
Add standard format write for xyz
drroe Dec 17, 2021
9158b7a
Bsae box write on what coord info states, not what frame has
drroe Dec 17, 2021
d90924c
Specify the type
drroe Dec 17, 2021
21933b0
namexyz (standard xyz) now the default
drroe Dec 17, 2021
4479154
Minor version bump to 6.1.0. Support for standard XYZ format; now the
drroe Dec 17, 2021
1ea0c66
Update XYZ output format options
drroe Dec 17, 2021
9dc6ee5
Add case for UNKNOWN (likely trajout)
drroe Dec 17, 2021
254c61a
Fix clean rule
drroe Dec 17, 2021
8000
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19 changes: 17 additions & 2 deletions doc/cpptraj.lyx
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Original file line number Diff line number Diff line change
Expand Up @@ -17014,7 +17014,8 @@ Options for XYZ format:
\end_layout

\begin_layout LyX-Code
ftype {atomxyz|xyz} titletype {none|single|perframe} width <#> prec <#>
[ftype {namexyz|atomxyz|xyz}] [titletype {none|single|perframe}] [width
<#>] [prec <#>]
\end_layout

\begin_deeper
Expand All @@ -17023,7 +17024,16 @@ ftype
\begin_inset space ~
\end_inset

{atomxyz|xyz} Choose either 'ATOM X Y Z' (default) or 'X Y Z' output format.
{atomxyz|xyz} Choose either 'NAME X Y Z' (default), 'ATOM X Y Z', or 'X
Y Z' output format.

\series bold
'namexyz'
\series default
format is the standard XYZ format, where each frame is preceded by the
number of atoms and a comment.
The comment written by CPPTRAJ will include the set number and box information
(if present).
\end_layout

\begin_layout Description
Expand All @@ -17033,6 +17043,11 @@ titletype

{none|single|perframe} No title, one title (default), or title before every
frame.
Only applies if not
\series bold
'namexyz'
\series default
.
\end_layout

\begin_layout Description
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