# replication attempt D and E

+ complete deinstallation of DW from the computer
+ new installation of DW with installer about DW 5.5.0 for Linux downloaded by
  2022-05-18.  By check of the md5sum of the installer with a download of the
  installer for Linux today, the installer did not change since then.
+ test run `10mol.dwar` to yield conformers, `10mol_conformersD.dwar`.  The new
  set considers all 10 IDs, there is no variation in column `Stereo Isomer`, and
  there is no flip of R/S, E/Z, nor P/M.  The result matches the anticipation.
+ test `Random_Molecules.dwar` to yield file `Random_Molecules_conformersD.dwar` 
  where all 12 IDs are considered and variation of stereochemistry does occur.
  The result is wrong; but Thomas' reply announces an adjustment by the updates
+ as a check point of comparison, the `datawarrior.jar` used:

```shell
norwid@debian:/opt/datawarrior$ md5sum ./datawarrior.jar 
f71c136cc853d6d2b904fbfff002bd59  ./datawarrior.jar
```

+ now application of the update as fetched today, 2023-06-09 / packaged by
  2023-06-08 in reply to the observation,

```shell
  $ md5sum 2023-06-09_dw550x.zip 
8a2da97698d3e3737f3c9db6a5c1d55f  2023-06-09_dw550x.zip
```

  for the archive, and for its content

```shell
~/Desktop/2023-06-09_dw550x$ md5sum *
d21420e72c77d7fd9791d5fc7aeb945a  datawarrior.jar
0263213f071f3f009068c4d57e9f3539  jniinchi.jar
97e5d5ef686ab87a421b0379c079bb32  mmtf.jar
9d1da1c59a4ee48761b2f9f9e543fd27  opsin.jar
```

  A check that these .jar are now in place:

```shell
/opt/datawarrior$ md5sum ./datawarrior.jar jniinchi.jar mmtf.jar opsin.jar 
d21420e72c77d7fd9791d5fc7aeb945a  ./datawarrior.jar
0263213f071f3f009068c4d57e9f3539  jniinchi.jar
97e5d5ef686ab87a421b0379c079bb32  mmtf.jar
9d1da1c59a4ee48761b2f9f9e543fd27  opsin.jar
```

  which -- by the checksums -- they are.

+ test with `10mol.dwar` to yield `10mol_conformersE.dwar`.  In the new set,
  there is no variation of stereochemistry. However, equally in the new set,
  IDs 2, 4, 6, 7, 9, and 10 are absent.  In `10mol.dwar`, the sketcher confirmed
  IDs 2, 4, 6 and 10 with "this enantiomer"; 7 only contains one explicit (Z)
  double bond, while ID 9 is without anything about CIP.
+ test with `Random_Molecules.dwar` to yield `Random_Molecules_conformersE.dwar`
  which is an empty set.  However the original IDs 2, 5, 8, or 11 do not include
  a motif to be eventually described with either (R/S), (E/Z), nor (P/M).
+ test with `RM_edited.dwar` (entry 1 of `Random_Molecules.dwar` was edited, now
  with an explicit (E) double bond, and an explict (R) centre -- DW sketcher
  confirms "this enantiomer"), to yield results in `RM_edited_conformersE.dwar`.
  The results are reported to equally be an empty set; no ID 1.

# test system

Observations refer to an installation of DataWarrior 5.5.0 in Linux Debian 12 /
bookworm running the Linux installation of DW.  Generation of the sets of random
molecules only by or with DataWarrior.

# archive content:

```shell
.
├── 10mol_conformersE.dwar
├── 10mol.dwar
├── clip_report.txt
├── Random_Molecules_conformersE.dwar
├── Random_Molecules.dwar
├── RM_edit.dwar
├── RM_edited_conformersE.dwar
├── Screenshot_2023-06-09_10-53-21.png
└── Screenshot_2023-06-09_10-56-57.png

1 directory, 9 files
```
