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Added conformers interface to plams #319

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cdac92e
Added conformers interface to plams
Sep 12, 2025
6381798
black formatting
Sep 12, 2025
d42bd8c
generate_example.sh updated some commands to uv
Sep 15, 2025
3126997
run generate_example.sh
Sep 15, 2025
a6fb675
converted to absolute imports
Sep 15, 2025
957940a
added type hints and better errors
Sep 15, 2025
6355f3d
Fix path sanitisation in generate_examples script
dormrod Sep 16, 2025
d572a57
remove awk dependence in generate_example.sh
mhellstr Sep 16, 2025
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1 change: 1 addition & 0 deletions CONTRIBUTING.md
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Expand Up @@ -22,6 +22,7 @@ top of things.
* Make commits of logical units
* Make sure your commit messages are informative
* Make sure you have added the necessary tests for your changes
* Add examples: take a look at the corresponding [README.md](./examples/README.md)
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@dormrod dormrod Sep 16, 2025

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Also update CHANGELOG (here and for your change!)

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@GiulioIlBen GiulioIlBen Sep 17, 2025

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should I mention that I changed the CONTRIBUTING.md file in the CHANGELOG?


## Submitting Changes

Expand Down
34 changes: 17 additions & 17 deletions doc/source/examples/COSMORSConformers/cosmors_conformers.ipynb.rst
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Expand Up @@ -8,14 +8,14 @@ Initial imports

from scm.plams.recipes.adfcosmorsconformers import ADFCOSMORSConfJob, ADFCOSMORSConfFilter
from scm.plams import Molecule, from_smiles, Settings, init, config, JobRunner
from scm.conformers import ConformersJob
from scm.plams import ConformersJob

# this line is not required in AMS2025+
init();

::

PLAMS working folder: /path/plams/examples/COSMORSConformers/plams_workdir
PLAMS working folder: /path/plams/examples/COSMORSConformers/plams_workdir.002

.. code:: ipython3

Expand Down Expand Up @@ -80,21 +80,21 @@ Finally, we give this information to the ``ADFCOSMORSConfJob`` class. We also sp

::

[19.03|15:33:37] JOB plamsjob STARTED
[19.03|15:33:37] Waiting for job plamsjob to finish
[19.03|15:33:37] JOB plamsjob/conformers_uff STARTED
[19.03|15:33:37] JOB plamsjob/additional_1 STARTED
[19.03|15:33:37] JOB plamsjob/adf_conformers STARTED
[19.03|15:33:37] JOB plamsjob/adf_filter STARTED
[19.03|15:33:37] Waiting for job conformers_uff to finish
[19.03|15:33:37] Waiting for job adf_filter to finish
[19.03|15:33:37] Waiting for job additional_1 to finish
[19.03|15:33:37] Waiting for job adf_conformers to finish
[19.03|15:33:44] JOB plamsjob/conformers_uff SUCCESSFUL
[19.03|15:33:45] JOB plamsjob/additional_1 SUCCESSFUL
[19.03|15:43:18] JOB plamsjob/adf_conformers SUCCESSFUL
[19.03|15:43:19] JOB plamsjob/adf_filter SUCCESSFUL
[19.03|15:43:19] JOB plamsjob/replay STARTED
[12.09|16:17:48] JOB plamsjob STARTED
[12.09|16:17:48] Waiting for job plamsjob to finish
[12.09|16:17:48] JOB plamsjob/conformers_uff STARTED
[12.09|16:17:48] JOB plamsjob/additional_1 STARTED
[12.09|16:17:48] JOB plamsjob/adf_conformers STARTED
[12.09|16:17:48] JOB plamsjob/adf_filter STARTED
[12.09|16:17:48] Waiting for job adf_filter to finish
[12.09|16:17:48] Waiting for job conformers_uff to finish
[12.09|16:17:48] Waiting for job additional_1 to finish
[12.09|16:17:48] Waiting for job adf_conformers to finish
[12.09|16:17:52] JOB plamsjob/conformers_uff SUCCESSFUL
[12.09|16:17:54] JOB plamsjob/additional_1 SUCCESSFUL
[12.09|16:24:45] JOB plamsjob/adf_conformers SUCCESSFUL
[12.09|16:24:45] JOB plamsjob/adf_filter SUCCESSFUL
[12.09|16:24:45] JOB plamsjob/replay STARTED
... (PLAMS log lines truncated) ...

.. code:: ipython3
Expand Down
148 changes: 56 additions & 92 deletions doc/source/examples/ConformersGeneration/conformers.ipynb.rst
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Expand Up @@ -12,15 +12,15 @@ Initial imports
import matplotlib.pyplot as plt
import numpy as np

from scm.conformers import ConformersJob
from scm.plams import ConformersJob
from scm.plams import *

# this line is not required in AMS2025+
init();

::

PLAMS working folder: /path/plams/examples/ConformersGeneration/plams_workdir
PLAMS working folder: /path/plams/examples/ConformersGeneration/plams_workdir.002

Initial structure
~~~~~~~~~~~~~~~~~
Expand Down Expand Up @@ -83,10 +83,10 @@ Run conformer generation

::

[04.02|15:07:47] JOB generate STARTED
[04.02|15:07:47] JOB generate RUNNING
[04.02|15:08:56] JOB generate FINISHED
[04.02|15:08:56] JOB generate SUCCESSFUL
[12.09|16:10:47] JOB generate STARTED
[12.09|16:10:47] JOB generate RUNNING
[12.09|16:10:51] JOB generate FINISHED
[12.09|16:10:51] JOB generate SUCCESSFUL

Conformer generation results
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Expand Down Expand Up @@ -115,33 +115,6 @@ Some helper functions
def get_conformers(job: ConformersJob):
return job.results.get_conformers()


def plot_conformers(job: ConformersJob, indices=None, temperature=298, unit="kcal/mol", lowest=True):
molecules = get_conformers(job)
energies = get_energies(job, unit)
populations = get_populations(job, temperature)

if isinstance(indices, int):
N_plot = min(indices, len(energies))
if lowest:
indices = list(range(N_plot))
else:
indices = np.linspace(0, len(energies) - 1, N_plot, dtype=np.int32)
if indices is None:
indices = list(range(min(3, len(energies))))

fig, axes = plt.subplots(1, len(indices), figsize=(12, 3))
if len(indices) == 1:
axes = [axes]

for ax, i in zip(axes, indices):
mol = molecules[i]
E = energies[i]
population = populations[i]

plot_molecule(mol, ax=ax)
ax.set_title(f"#{i+1}\nΔE = {E:.2f} kcal/mol\nPop.: {population:.3f} (T = {temperature} K)")

.. code:: ipython3

try:
Expand Down Expand Up @@ -203,27 +176,27 @@ You can also see the **relative populations** of these conformers at the specifi
============ ============= ================
Conformer Id ΔE [kcal/mol] Pop. (T = 298 K)
============ ============= ================
1 0.00 0.557
2 0.57 0.214
3 1.00 0.102
4 1.18 0.076
5 2.12 0.015
6 2.22 0.013
7 2.40 0.010
8 2.50 0.008
9 3.44 0.002
10 3.53 0.001
11 3.76 0.001
12 5.50 0.000
13 6.78 0.000
14 12.85 0.000
15 15.70 0.000
16 18.79 0.000
1 0.00 0.503
2 0.30 0.302
3 0.67 0.162
4 2.11 0.014
5 2.12 0.014
6 2.89 0.004
7 3.84 0.001
8 6.71 0.000
9 13.42 0.000
10 14.07 0.000
11 15.25 0.000
12 15.79 0.000
13 15.83 0.000
14 17.77 0.000
15 18.79 0.000
16 23.98 0.000
============ ============= ================

.. code:: ipython3

plot_conformers(generate_job, 4, temperature=temperature, unit=unit, lowest=True)
generate_job.results.plot_conformers(4, temperature=temperature, unit=unit, lowest=True);

.. figure:: conformers_files/conformers_18_0.png

Expand All @@ -249,7 +222,7 @@ Below, the most stable conformers (within 8 kcal/mol of the most stable conforme

::

InputConformersSet /path/plams/examples/ConformersGeneration/plams_workdir.006/generate/conformers.rkf
InputConformersSet /path/plams/examples/ConformersGeneration/plams_workdir.002/generate/conformers.rkf

InputMaxEnergy 8.0

Expand All @@ -265,10 +238,10 @@ Below, the most stable conformers (within 8 kcal/mol of the most stable conforme

::

[04.02|15:08:56] JOB reoptimize STARTED
[04.02|15:08:56] JOB reoptimize RUNNING
[04.02|15:09:01] JOB reoptimize FINISHED
[04.02|15:09:01] JOB reoptimize SUCCESSFUL
[12.09|16:11:00] JOB reoptimize STARTED
[12.09|16:11:00] JOB reoptimize RUNNING
[12.09|16:11:02] JOB reoptimize FINISHED
[12.09|16:11:02] JOB reoptimize SUCCESSFUL

.. code:: ipython3

Expand All @@ -277,22 +250,18 @@ Below, the most stable conformers (within 8 kcal/mol of the most stable conforme
============ ============= ================
Conformer Id ΔE [kcal/mol] Pop. (T = 298 K)
============ ============= ================
1 0.00 0.270
2 0.11 0.225
3 0.41 0.134
4 0.63 0.093
5 0.91 0.058
6 0.97 0.052
7 1.02 0.048
8 1.14 0.039
9 1.19 0.036
10 1.41 0.025
11 1.57 0.019
1 0.00 0.540
2 0.64 0.184
3 0.84 0.131
4 1.09 0.086
5 1.82 0.025
6 1.90 0.022
7 2.25 0.012
============ ============= ================

.. code:: ipython3

plot_conformers(reoptimize_job, 4, temperature=temperature, unit=unit, lowest=True)
reoptimize_job.results.plot_conformers(4, temperature=temperature, unit=unit, lowest=True);

.. figure:: conformers_files/conformers_23_0.png

Expand All @@ -318,10 +287,10 @@ The **Score** task runs **SinglePoint** jobs on the conformers in a set. This le

::

[04.02|15:09:02] JOB score STARTED
[04.02|15:09:02] JOB score RUNNING
[04.02|15:09:05] JOB score FINISHED
[04.02|15:09:05] JOB score SUCCESSFUL
[12.09|16:11:09] JOB score STARTED
[12.09|16:11:09] JOB score RUNNING
[12.09|16:11:10] JOB score FINISHED
[12.09|16:11:10] JOB score SUCCESSFUL

.. code:: ipython3

Expand All @@ -330,22 +299,18 @@ The **Score** task runs **SinglePoint** jobs on the conformers in a set. This le
============ ============= ================
Conformer Id ΔE [kcal/mol] Pop. (T = 298 K)
============ ============= ================
1 0.00 0.373
2 0.34 0.209
3 0.40 0.188
4 0.70 0.114
5 1.06 0.063
6 1.85 0.016
7 1.89 0.015
8 2.41 0.006
9 2.48 0.006
10 2.59 0.005
11 2.73 0.004
1 0.00 0.654
2 0.89 0.146
3 0.93 0.136
4 1.70 0.037
5 2.12 0.018
6 2.60 0.008
7 4.01 0.001
============ ============= ================

.. code:: ipython3

plot_conformers(score_job, 4, temperature=temperature, unit=unit, lowest=True)
score_job.results.plot_conformers(4, temperature=temperature, unit=unit, lowest=True);

.. figure:: conformers_files/conformers_27_0.png

Expand All @@ -372,10 +337,10 @@ Below, we filter the conformers set to only the conformers within 1 kcal/mol of

::

[04.02|15:09:05] JOB filter STARTED
[04.02|15:09:05] JOB filter RUNNING
[04.02|15:09:06] JOB filter FINISHED
[04.02|15:09:06] JOB filter SUCCESSFUL
[12.09|16:11:15] JOB filter STARTED
[12.09|16:11:15] JOB filter RUNNING
[12.09|16:11:15] JOB filter FINISHED
[12.09|16:11:15] JOB filter SUCCESSFUL

.. code:: ipython3

Expand All @@ -384,15 +349,14 @@ Below, we filter the conformers set to only the conformers within 1 kcal/mol of
============ ============= ================
Conformer Id ΔE [kcal/mol] Pop. (T = 298 K)
============ ============= ================
1 0.00 0.421
2 0.34 0.236
3 0.40 0.213
4 0.70 0.129
1 0.00 0.699
2 0.89 0.156
3 0.93 0.145
============ ============= ================

.. code:: ipython3

plot_conformers(filter_job, 4, temperature=temperature, unit=unit, lowest=True)
filter_job.results.plot_conformers(4, temperature=temperature, unit=unit, lowest=True);

.. figure:: conformers_files/conformers_32_0.png

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