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Merged
merged 249 commits into from
Nov 2, 2023
Merged

Add ability to utilize and manipulate internal coordinates #1053

merged 249 commits into from
Nov 2, 2023

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drroe
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@drroe drroe commented Nov 1, 2023

Version 6.21.0.

Add commands/keywords related to internal coordinates to cpptraj:

  • zmatrix : Apply Z-matrix to a COORDS set or calculate Z-matrix for a molecule/frame in a COORDS set.
  [help zmatrix]
        <COORDS set name> [name <output set name>]
        { zset <input zmatrix set> [parm <top>|parmindex <#>] |
          [molnum <mol#>] [frame <frame#>] [out <zmatrix file>] }
  • sequence : Create a new molecule from a sequence of COORDS sets.
 [help sequence]
        name <output set name> <unit0> <unit1> ...
        [{libset <libsetname>} ...]
  • ic keyword for the graft command: connect source and target without having to RMS-fit.

Also adds the ability to read in units from Amber Prepin and OFF library files as COORDS data sets; the latter can be used directly with the sequence command. Updates the manual and adds new tests. Lots of additional fixes under the hood.

drroe added 30 commits March 4, 2022 14:05
@drroe
Start InternalCoords class
d887aae
@drroe
Add NO_ATOM
0b22ac5
@drroe
Merge branch 'master' into internal.coords
06a57ae
@drroe
Start Zmatrix
c1256f4
@drroe
InternalCoords implementation
b370997
@drroe
Start Zmatrix implementation
eeba724
@drroe
First seed atom
ce57aa5
@drroe
Add comments
ddea7e3
@drroe
Skip building libcpptraj_cluster, not really needed.
2af6f54
@drroe
Merge branch 'master' into internal.coords
a730818
@drroe
Merge remote-tracking branch 'refs/remotes/origin/internal.coords' in…
f27f0c8 
…to internal.coords
@drroe
Add assignment and copy constructor
ccd0c7b
@drroe
Start adding internal to cartesian routine
b50cac6
@drroe
Add files to the build
b4d9f2d
@drroe
Remove xyz coords from InternalCoords
40baa92
@drroe
Update depends
8e0c099
@drroe
Start reading amber prep files
8fcf1dc
@drroe
Start setting up topology and z matrix
dc77a30
@drroe
Add bonds to top
a8df0a1
@drroe
Add ability to add atoms as a seed
a802f2e
@drroe
Do frame setup
35eb86d
@drroe
Find next atom to set
5074294
@drroe
Build the rest of the coordinates
1c34304
@drroe
Do not create separate topology data set. Remove dummy atoms.
ba3e4ea
@drroe
Put prep residue read in separate function, read past section 9
e991c33
@drroe
Separate routines for reading sections. Add bonds from LOOP sections
7acec66
@drroe
Add Test
0b3d096
@drroe
Make exe
43b4346
@drroe
Improve check for STOP
9c81033
@drroe
Hide some debug info. Warn about non-zero bond cutoff
364f086
drroe added 20 commits November 1, 2023 09:47
@drroe
Try to check for SP2 nitrogens with 3 bonds (partial double bond
3c39980 
character)
@drroe
Add test save
8f54647
@drroe
Enable sequence test
36a3baa
@drroe
Test libset keyword
089cbd3
@drroe
Update depends
2cadda1
@drroe
Add stub for arg process function
400eede
@drroe
Make arg processing function virtual
b0d315d
@drroe
Create arg routine for connect associated data
da9c3fa
@drroe
Add help text
5b61646
@drroe
Make const pointer
6141c0f
@drroe
Start connect data set command
080d4b0
@drroe
Start connect data set command
d89eff6
@drroe
Fix printf statement
68d9bcf
@drroe
Test setting head/tail atoms
726974b
@drroe
Add headmask and tailmask keywords to dataset connect. Ensure existing
93e3989 
noe data is overwritten if present.
@drroe
Test using headmask/tailmask
64add9b
@drroe
Add manual entries for sequence and dataset connect
5a57813
@drroe
Add notes about reading prep and lib formats
04442c0
@drroe
Fix up help and manual entry for graft
1624174
@drroe
Version 6.21.0. Minor version bump for the addition of internal
9c92433 
coordinates handling and related commands zmatrix and sequence; also the
reading of Amber prep and lib file formats.
@drroe drroe added enhancement New Command New command for cpptraj New keywords New keywords for existing commands. labels Nov 1, 2023
@drroe drroe self-assigned this Nov 1, 2023
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drroe commented Nov 1, 2023

Sometimes CI runners are no fun. New issue popping up that has never been a problem before - clang/gfortran incompatibility:

Error: Test compile failed: clang++  -Wall  -O3     -std=c++11 -o testp testp.cpp /home/runner/work/cpptraj/cpptraj/lib/liblapack.a /home/runner/work/cpptraj/cpptraj/lib/libblas.a -lgfortran -lpthread    
  Checking built LAPACK/BLAS: 
Error: Check the output below for error messages:
/usr/bin/ld: cannot find -lgfortran: No such file or directory

Not sure how to fix it yet.

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drroe commented Nov 2, 2023

Turns out I had already fixed this transient issue (clang/gfortran) in configure, but only for OSX. I just took that code and made it apply to all OS - seems to have done the trick. 🎉

@drroe drroe merged commit 54ca723 into Amber-MD:master Nov 2, 2023
@drroe drroe deleted the internal.coords branch November 2, 2023 17:46
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