Comments (3)
I think having a tool for 3D structure comparison is sensible. When the number/type of atoms are not the same, however, it is more complicated (but could be done from graph similarity (2D) or fingerprint similarity (1D)). But I think as a Procrustes
tool, only 3D similarity and (maybe) 2D (adjacency matrix) similarity make sense.
It may be that some of the tools are better added as utilities for DiverseSelector.
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We have examples among the existing notebooks for comparing 3D (using Cartesian coordinates loaded by IOData) and 2D structures (based on user-specified adjacency matrices; this can also be provided from RDKit, and we can update the example to show that) using procrustes
functionality; see https://github.com/theochem/procrustes/tree/master/doc/notebooks. @PaulWAyers and @fwmeng88, can you please clarify the scope of this issue?
As we discussed within the context of DiverseSelector, it's best not to add these utilities/wrappers to our various packages. It's best to demonstrate how our packages can be used in conjunction with external libraries (e.g., IOData and RDKit) which are meant to generate structures, fingerprints, etc.
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I'm thinking about a utility function; it may be that it belongs in IOData
or somewhere else. But we need to be able to compare molecules (in bulk, not via a notebook). In this case, I'm not sure that there is need for IOData
or RDKit
; one reads in a list of atomic numbers and their positions and processes directly. Probably we should discuss this now.
For 1D or 2D I don't see the need, right now, for stand-alone Python functions: Notebook-style examples would suffice I think.
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Related Issues (20)
- Can't install from pip HOT 3
- Support of missing values for generalized Procrustes analysis
- L-1 procrustes HOT 10
- Installing with pip according to instructions does not work HOT 5
- Molecular Structure Distance HOT 1
- Non square data in softassign function - cannot reshape array HOT 4
- An alternative way of solving rotational Procrutes problem HOT 4
- Web Site HOT 2
- Would be nice to have the used scaling and translation returned in the answer HOT 9
- translation, scling, weighting for positive semi-definite Procrustes problem HOT 2
- Deprecated `pinv2` function in `scipy.linalg` HOT 2
- Update the summary table when #98 is done
- Failing testing, `test_psdp_woodgate_non_full_rank` HOT 11
- More algorithms on `PSDP` HOT 18
- Another round of code review for GSoC HOT 1
- pinv2 deprecated HOT 12
- Support Weight Matrices
- One-Sided Procrustes for Toeplitz matrices HOT 5
- positive semi-definite Procrustes problem HOT 6
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