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obrms is not computing RMSDs for all conformations in a multimol2 file #2671

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isabellaguedes opened this issue Feb 9, 2024 · 3 comments

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@isabellaguedes
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Environment Information

Open Babel version: Open Babel 3.1.1 -- Dec 12 2023 -- 11:30:06
Operating system and version:

Expected Behavior

obrms should output the RMSD for all conformations in the reference file (output generated with the 3.1.1 version installed on Apr 14 2023):

RMSD 1dmp_ligand_rnum_run_11.pdb:1dmp_ligand_rnum.pdb 0.464196
RMSD 1dmp_ligand_rnum_run_2.pdb:1dmp_ligand_rnum.pdb 0.368087
RMSD 1dmp_ligand_rnum_run_3.pdb:1dmp_ligand_rnum.pdb 5.14613
RMSD 1dmp_ligand_rnum_run_14.pdb:1dmp_ligand_rnum.pdb 1.90711
RMSD 1dmp_ligand_rnum_run_9.pdb:1dmp_ligand_rnum.pdb 5.15166

Actual Behavior

When using a multi-conformer input as reference file, obrms only calculate the RMSD for the first conformation (3.1.1 version installed on Dec 12 2023):

RMSD 1dmp_ligand_rnum_run_11.pdb:1dmp_ligand_rnum.pdb 0.464196

Steps to Reproduce

obrms 1dmp_leaders.mol2 1dmp_ligand_rnum.pdb

result-dmp.zip

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welcome bot commented Feb 9, 2024

Thanks for opening your first issue here! Be sure to follow the issue template!

@dkoes
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dkoes commented Feb 9, 2024

I'm pretty sure this is fixed in git - can you please verify?

@isabellaguedes
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isabellaguedes commented Feb 21, 2024

I've cloned again today, but it is still not working.

My master branch is in the following commit:

*   commit 32cf131444c1555c749b356dab44fb9fe275271f (HEAD -> master, origin/master, origin/HEAD)
|\  Merge: f67d6bc3e c39cf723c
| | Author: Geoff Hutchison <geoff.hutchison@gmail.com>
| | Date:   Wed Dec 6 09:59:04 2023 -0500
| | 
| |     Merge pull request #2654 from ghutchis/more-cjson
| |     
| |     Add more cjson features, including conformer energies

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