moltric 0.0.2__tar.gz

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  1. moltric-0.0.2/PKG-INFO +130 -0
  2. moltric-0.0.2/README.md +117 -0
  3. moltric-0.0.2/moltric/__init__.py +5 -0
  4. moltric-0.0.2/moltric/arbalign.py +698 -0
  5. moltric-0.0.2/moltric/cli.py +181 -0
  6. moltric-0.0.2/moltric/compare_methods.py +505 -0
  7. moltric-0.0.2/moltric/compare_methods_assume_homonuclear.py +544 -0
  8. moltric-0.0.2/moltric/moltric.py +948 -0
  9. moltric-0.0.2/moltric/otmol_alignment.py +836 -0
  10. moltric-0.0.2/moltric/qapot.py +576 -0
  11. moltric-0.0.2/moltric.egg-info/PKG-INFO +130 -0
  12. moltric-0.0.2/moltric.egg-info/SOURCES.txt +15 -0
  13. moltric-0.0.2/moltric.egg-info/dependency_links.txt +1 -0
  14. moltric-0.0.2/moltric.egg-info/entry_points.txt +2 -0
  15. moltric-0.0.2/moltric.egg-info/top_level.txt +1 -0
  16. moltric-0.0.2/pyproject.toml +36 -0
  17. moltric-0.0.2/setup.cfg +4 -0
moltric-0.0.2/PKG-INFO ADDED
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+ Metadata-Version: 2.4
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+ Name: moltric
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+ Version: 0.0.2
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+ Summary: Moltric Molecular Metric
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+ Keywords: moleculardynamics,initialsampling
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+ Classifier: Development Status :: 5 - Production/Stable
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+ Classifier: Environment :: Console
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+ Classifier: Intended Audience :: Science/Research
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+ Classifier: Operating System :: OS Independent
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+ Classifier: Programming Language :: Python :: 3
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+ Requires-Python: >=3.7
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+ Description-Content-Type: text/markdown
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+
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+
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+ For installation of Moltric, use pip: `pip install moltric`
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+
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+ For questions or suggestions for features to add, contact Kazuumi Fujioka: kazuumi@hawaii.edu
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+
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+
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+
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+ ## How do you best *overlap* two molecules? How do we order the atoms?
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+
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+ <p align="center">
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+ <img width="900" height="400" src="images/permutation1.png">
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+ </p>
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+
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+ ### Finding the best algorithm to do this is a Holy Grail
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+ Many groups have searched for this, but improvements are constantly being made:
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+
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+
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+ - ArbAlign, 2017: [[github](https://github.com/berhane/arbalign)] [[paper](https://doi.org/10.1021/acs.jcim.6b00546)]
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+
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+ - FASTOVERLAP, 2017: [[github](https://github.com/matthewghgriffiths/fastoverlap)] [[paper](https://doi.org/10.1021/acs.jctc.7b00543)]
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+
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+ - MolAlignLib, 2023: [[github](https://github.com/qcuaeh/molalignlib)] [[paper](https://doi.org/10.1021/acs.jcim.2c01187)]
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+
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+ - OTMol, 2025: [[github](https://github.com/weixiaoqimath/otmol)] [[paper](https://doi.org/10.1021/acs.jcim.5c02099)]
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+
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+
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+ <p align="center">
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+ <img width="900" height="400" src="images/rmsdtools1.png">
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+ </p>
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+
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+ # Comparing Software
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+
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+
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+ A few benchmarks will be compared over:
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+ - C10H9 (Bimolecular Reaction of CH + C<sub>9</sub>H<sub>8</sub> and C<sub>2</sub>H<sub>4</sub> + C<sub>8</sub>H<sub>5</sub>)
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+ - H3CS (Bimolecular Reaction of CH + H<sub>2</sub>S)
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+ - H5CBr (Bimolecular Reaction of HBr<sup>+</sup> + CH<sub>4</sub>)
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+ - Ne20 (20-atom Subsets of a Neon<sub>200</sub> Cluster) [[source](https://doi.org/10.1021/acs.jcim.5c02099)]
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+ - Ne180 (180-atom Subsets of a Neon<sub>200</sub> Cluster) [[source](https://doi.org/10.1021/acs.jcim.5c02099)]
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+ - FGG (FGG tripeptide C<sub>13</sub>H<sub>17</sub>N<sub>3</sub>O<sub>4</sub> Conformers) [[source](https://doi.org/10.1021/acs.jcim.5c02099)]
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+ - BsMaWa (Bisulfate-Methylammonium-Water Cluster CH<sub>9</sub>NO<sub>5</sub>S Conformers) [[source](https://doi.org/10.1021/acs.jcim.5c02099)]
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+
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+
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+
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+
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+ # Usage:
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+
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+ ## Comparing two sets of molecules:
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+
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+ From a terminal, prepare two xyz files of the two sets of molecules. Then call Moltric, like so:
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+
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+ ```
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+ moltric/moltric.py examples/fromFujioka_CH.indene_19atoms.xyz examples/fromFujioka_CH.indene_19atoms.xyz
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+ ```
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+
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+ this produces:
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+
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+ ```
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+ # Number of points found in 'examples/fromFujioka_CH.indene_19atoms.xyz': 81
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+ # Number of points found in 'examples/fromFujioka_CH.indene_19atoms.xyz': 81
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+ # i j DMD
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+ 0 0 0.0000
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+ 0 1 2.1084
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+ 0 2 3.9254
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+ 0 3 3.9358
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+ 0 4 1.7824
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+ 0 5 2.6834
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+ 0 6 5.1325
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+ 0 7 3.6761
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+ 0 8 6.9604
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+ 0 9 2.2738
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+ .
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+ .
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+ .
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+ ```
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+
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+
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+ ## Benchmarking different molecule alignments for RMSD:
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+
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+ Moltric and other methods can be compared with `compare_methods.py` from the terminal on an example xyz file:
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+
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+ ```
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+ cat examples/fromFujioka_CH.indene_19atoms.xyz | moltric/compare_methods.py 0.00001 output.xyz
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+ ```
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+
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+ this produces:
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+
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+ ```
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+ .
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+ .
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+ .
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+ DMDbound# i j ArbAlign OTMol MolAlign Umeyama FAQ GOATf GOAT minimum (Nf) (N)
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+ Adding index 0 to the training set ... Sparsity 1.0000 = 1/1
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+ 1.5928# 1 0 25.4432 31.6604 19.0167 13.8631 17.9570 21.2356 4.2362 4.2362 (21) (467)
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+ Adding index 1 to the training set ... Sparsity 1.0000 = 2/2
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+ 2.4458# 2 0 39.6316 29.3163 32.7360 11.1385 26.1334 21.7794 5.2278 5.2278 (26) (482)
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+ 1.7212# 2 1 33.6609 12.9877 9.0464 3.5600 3.5600 3.5600 3.5600 3.5600 (18) (389)
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+ Adding index 2 to the training set ... Sparsity 1.0000 = 3/3
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+ 1.8722# 3 0 33.3322 21.9517 28.5810 9.6538 21.7277 21.1000 4.4000 4.4000 (20) (449)
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+ 1.5957# 3 1 24.4360 17.1308 17.4071 3.6724 3.6724 3.6724 3.6724 3.6724 (16) (403)
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+ 0.9671# 3 2 29.2970 22.7893 20.3330 2.0084 2.0084 2.0084 2.0084 2.0084 (18) (474)
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+ Adding index 3 to the training set ... Sparsity 1.0000 = 4/4
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+ 2.8128# 4 0 41.7131 22.6670 23.5538 11.3122 23.8455 22.5683 6.1147 6.1147 (21) (461)
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+ 2.3773# 4 1 34.7580 31.9236 32.2770 4.3386 4.3386 4.3386 4.3386 4.3386 (17) (390)
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+ 0.3376# 4 2 8.8606 6.1540 15.8762 0.7083 0.7083 0.7083 0.7083 0.7083 (18) (385)
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+ 0.7713# 4 3 17.4316 4.9512 8.0874 1.3402 1.3402 1.3402 1.3402 1.3402 (17) (360)
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+ Adding index 4 to the training set ... Sparsity 1.0000 = 5/5
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+ 0.9072# 5 0 19.7347 18.7131 22.0875 2.7445 14.5171 14.5171 2.4299 2.4299 (18) (432)
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+ 0.9114# 5 1 19.6808 3.3077 3.3077 12.6573 3.3077 3.3077 1.8983 1.8983 (16) (366)
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+ 1.9796# 5 2 37.5165 9.5294 11.2601 14.6674 8.1114 6.3697 4.8420 4.8420 (18) (396)
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+ 1.6283# 5 3 23.7955 15.7882 18.5697 9.7445 5.6637 5.6637 4.1777 4.1777 (17) (443)
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+ 2.3768# 5 4 43.0193 24.0932 29.3850 19.2532 6.4887 6.4887 5.0040 5.0040 (17) (396)
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+ .
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+ .
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+ .
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+ ```
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+
moltric-0.0.2/README.md ADDED
@@ -0,0 +1,117 @@
1
+
2
+ For installation of Moltric, use pip: `pip install moltric`
3
+
4
+ For questions or suggestions for features to add, contact Kazuumi Fujioka: kazuumi@hawaii.edu
5
+
6
+
7
+
8
+ ## How do you best *overlap* two molecules? How do we order the atoms?
9
+
10
+ <p align="center">
11
+ <img width="900" height="400" src="images/permutation1.png">
12
+ </p>
13
+
14
+ ### Finding the best algorithm to do this is a Holy Grail
15
+ Many groups have searched for this, but improvements are constantly being made:
16
+
17
+
18
+ - ArbAlign, 2017: [[github](https://github.com/berhane/arbalign)] [[paper](https://doi.org/10.1021/acs.jcim.6b00546)]
19
+
20
+ - FASTOVERLAP, 2017: [[github](https://github.com/matthewghgriffiths/fastoverlap)] [[paper](https://doi.org/10.1021/acs.jctc.7b00543)]
21
+
22
+ - MolAlignLib, 2023: [[github](https://github.com/qcuaeh/molalignlib)] [[paper](https://doi.org/10.1021/acs.jcim.2c01187)]
23
+
24
+ - OTMol, 2025: [[github](https://github.com/weixiaoqimath/otmol)] [[paper](https://doi.org/10.1021/acs.jcim.5c02099)]
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+
26
+
27
+ <p align="center">
28
+ <img width="900" height="400" src="images/rmsdtools1.png">
29
+ </p>
30
+
31
+ # Comparing Software
32
+
33
+
34
+ A few benchmarks will be compared over:
35
+ - C10H9 (Bimolecular Reaction of CH + C<sub>9</sub>H<sub>8</sub> and C<sub>2</sub>H<sub>4</sub> + C<sub>8</sub>H<sub>5</sub>)
36
+ - H3CS (Bimolecular Reaction of CH + H<sub>2</sub>S)
37
+ - H5CBr (Bimolecular Reaction of HBr<sup>+</sup> + CH<sub>4</sub>)
38
+ - Ne20 (20-atom Subsets of a Neon<sub>200</sub> Cluster) [[source](https://doi.org/10.1021/acs.jcim.5c02099)]
39
+ - Ne180 (180-atom Subsets of a Neon<sub>200</sub> Cluster) [[source](https://doi.org/10.1021/acs.jcim.5c02099)]
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+ - FGG (FGG tripeptide C<sub>13</sub>H<sub>17</sub>N<sub>3</sub>O<sub>4</sub> Conformers) [[source](https://doi.org/10.1021/acs.jcim.5c02099)]
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+ - BsMaWa (Bisulfate-Methylammonium-Water Cluster CH<sub>9</sub>NO<sub>5</sub>S Conformers) [[source](https://doi.org/10.1021/acs.jcim.5c02099)]
42
+
43
+
44
+
45
+
46
+ # Usage:
47
+
48
+ ## Comparing two sets of molecules:
49
+
50
+ From a terminal, prepare two xyz files of the two sets of molecules. Then call Moltric, like so:
51
+
52
+ ```
53
+ moltric/moltric.py examples/fromFujioka_CH.indene_19atoms.xyz examples/fromFujioka_CH.indene_19atoms.xyz
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+ ```
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+
56
+ this produces:
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+
58
+ ```
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+ # Number of points found in 'examples/fromFujioka_CH.indene_19atoms.xyz': 81
60
+ # Number of points found in 'examples/fromFujioka_CH.indene_19atoms.xyz': 81
61
+ # i j DMD
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+ 0 0 0.0000
63
+ 0 1 2.1084
64
+ 0 2 3.9254
65
+ 0 3 3.9358
66
+ 0 4 1.7824
67
+ 0 5 2.6834
68
+ 0 6 5.1325
69
+ 0 7 3.6761
70
+ 0 8 6.9604
71
+ 0 9 2.2738
72
+ .
73
+ .
74
+ .
75
+ ```
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+
77
+
78
+ ## Benchmarking different molecule alignments for RMSD:
79
+
80
+ Moltric and other methods can be compared with `compare_methods.py` from the terminal on an example xyz file:
81
+
82
+ ```
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+ cat examples/fromFujioka_CH.indene_19atoms.xyz | moltric/compare_methods.py 0.00001 output.xyz
84
+ ```
85
+
86
+ this produces:
87
+
88
+ ```
89
+ .
90
+ .
91
+ .
92
+ DMDbound# i j ArbAlign OTMol MolAlign Umeyama FAQ GOATf GOAT minimum (Nf) (N)
93
+ Adding index 0 to the training set ... Sparsity 1.0000 = 1/1
94
+ 1.5928# 1 0 25.4432 31.6604 19.0167 13.8631 17.9570 21.2356 4.2362 4.2362 (21) (467)
95
+ Adding index 1 to the training set ... Sparsity 1.0000 = 2/2
96
+ 2.4458# 2 0 39.6316 29.3163 32.7360 11.1385 26.1334 21.7794 5.2278 5.2278 (26) (482)
97
+ 1.7212# 2 1 33.6609 12.9877 9.0464 3.5600 3.5600 3.5600 3.5600 3.5600 (18) (389)
98
+ Adding index 2 to the training set ... Sparsity 1.0000 = 3/3
99
+ 1.8722# 3 0 33.3322 21.9517 28.5810 9.6538 21.7277 21.1000 4.4000 4.4000 (20) (449)
100
+ 1.5957# 3 1 24.4360 17.1308 17.4071 3.6724 3.6724 3.6724 3.6724 3.6724 (16) (403)
101
+ 0.9671# 3 2 29.2970 22.7893 20.3330 2.0084 2.0084 2.0084 2.0084 2.0084 (18) (474)
102
+ Adding index 3 to the training set ... Sparsity 1.0000 = 4/4
103
+ 2.8128# 4 0 41.7131 22.6670 23.5538 11.3122 23.8455 22.5683 6.1147 6.1147 (21) (461)
104
+ 2.3773# 4 1 34.7580 31.9236 32.2770 4.3386 4.3386 4.3386 4.3386 4.3386 (17) (390)
105
+ 0.3376# 4 2 8.8606 6.1540 15.8762 0.7083 0.7083 0.7083 0.7083 0.7083 (18) (385)
106
+ 0.7713# 4 3 17.4316 4.9512 8.0874 1.3402 1.3402 1.3402 1.3402 1.3402 (17) (360)
107
+ Adding index 4 to the training set ... Sparsity 1.0000 = 5/5
108
+ 0.9072# 5 0 19.7347 18.7131 22.0875 2.7445 14.5171 14.5171 2.4299 2.4299 (18) (432)
109
+ 0.9114# 5 1 19.6808 3.3077 3.3077 12.6573 3.3077 3.3077 1.8983 1.8983 (16) (366)
110
+ 1.9796# 5 2 37.5165 9.5294 11.2601 14.6674 8.1114 6.3697 4.8420 4.8420 (18) (396)
111
+ 1.6283# 5 3 23.7955 15.7882 18.5697 9.7445 5.6637 5.6637 4.1777 4.1777 (17) (443)
112
+ 2.3768# 5 4 43.0193 24.0932 29.3850 19.2532 6.4887 6.4887 5.0040 5.0040 (17) (396)
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+ .
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+ .
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+ .
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+ ```
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+
moltric-0.0.2/moltric/__init__.py ADDED
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+ from .moltric import *
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+ from .arbalign import arbalign # Kazuumi's python3 translation for ArbAlign
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+ from .otmol_alignment import otmol_alignment # Copy of OTMol for benchmarking
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+
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+ __version__ = "0.0.2"