Solvant Accesible surface area #4025

pegerto · 2023-02-13T10:19:55Z

Changes made in this Pull Request:

Add an implementation of Shrake-Rupley algorithm to calculate SASA per atom.

PR Checklist

Tests?
Docs?
CHANGELOG updated?
Issue raised/referenced?

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Hello there first time contributor! Welcome to the MDAnalysis community! We ask that all contributors abide by our Code of Conduct and that first time contributors introduce themselves on the developer mailing list so we can get to know you. You can learn more about participating here. Please also add yourself to package/AUTHORS as part of this PR.

codecov · 2023-02-13T10:43:16Z

Codecov Report

Base: 93.53% // Head: 93.54% // Increases project coverage by +0.01% 🎉

Coverage data is based on head (b9bef46) compared to base (d27a32a).
Patch coverage: 100.00% of modified lines in pull request are covered.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #4025      +/-   ##
===========================================
+ Coverage    93.53%   93.54%   +0.01%     
===========================================
  Files          191      192       +1     
  Lines        25062    25108      +46     
  Branches      3547     3550       +3     
===========================================
+ Hits         23442    23488      +46     
  Misses        1099     1099              
  Partials       521      521

Impacted Files	Coverage Δ
package/MDAnalysis/analysis/accesibility.py	`100.00% <100.00%> (ø)`

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orbeckst · 2023-02-13T14:12:17Z

Hello @pegerto , thank you for your contribution.

Because this project is listed as a potential GSOC project I have to ask if you intend to apply for Google Summer of Code with MDAnalysis (if MDAnalysis is selected to take part this year).

pegerto · 2023-02-13T14:29:54Z

Google Summer of Code

Hi @orbeckst I saw the documentation of this request listed under GSOC 2021, are you planning to present this project for 2023 as organisation. It was not my intention to do so rather contribute to this analysis module in parallel to my research.

orbeckst · 2023-02-13T14:39:05Z

Ok, good, thank you for letting us know!

RMeli

Hi @pegerto , a few initial comments from skimming through (I haven't looked at the core of the code yet).

I also think it might be better to call the module sasa.py or something similar, accessibility.py is too general IMO (but others might disagree).

RMeli · 2023-02-18T20:43:04Z

package/MDAnalysis/analysis/accesibility.py

+def atomic_radi(e):
+    """van der Waals radii"""
+    DEFAULT_ATOMIC_RADI = 2.0
+    return ATOMIC_RADI[e] if e in ATOMIC_RADI else DEFAULT_ATOMIC_RADI


This looks superfluous. You can use the dictionary's get method with a default argument, or maybe even a defaultdict.

RMeli · 2023-02-18T20:45:48Z

package/MDAnalysis/analysis/accesibility.py

+ATOMIC_RADI = {
+    "H": 1.200,
+    "HE": 1.400,
+    "C": 1.700,
+    "N": 1.550,
+    "O": 1.520,
+    "F": 1.470,
+    "NA": 2.270,
+    "MG": 1.730,
+    "P": 1.800,
+    "S": 1.800,
+    "CL": 1.750,
+    "K": 2.750,
+    "CA": 2.310,
+    "NI": 1.630,
+    "CU": 1.400,
+    "ZN": 1.390,
+    "SE": 1.900,
+    "BR": 1.850,
+    "CD": 1.580,
+    "I": 1.980,
+    "HG": 1.550,
+}


It would be good to add a comment on where you got these numbers from. Even better, you can use the ones already available in MDAnalysis:

mdanalysis/package/MDAnalysis/topology/tables.py

Lines 306 to 314 in d27a32a

TABLE_VDWRADII = r"""

# Van der Waals radii taken from

# [1] Bondi, A. (1964). "Van der Waals Volumes and Radii".

# J. Phys. Chem. 68 (3): 441-451. doi:10.1021/j100785a001.

# [2] Rowland and Taylor (1996). "Intermolecular Nonbonded Contact Distances in Organic Crystal Structures:

# Comparison with Distances Expected from van der Waals Radii".

# J. Phys. Chem., 1996, 100 (18), 7384.7391. doi:10.1021/jp953141+.

# [3] Mantina, et al. (2009). "Consistent van der Waals Radii for the Whole Main Group".

# J. Phys. Chem. A, 2009, 113 (19), 5806-5812. doi:10.1021/jp8111556.

RMeli · 2023-02-18T20:46:09Z

package/MDAnalysis/analysis/accesibility.py

+        n_points: int (optional)
+            Number of points used for the estimation of the atom surface area
+        probe_radius: double ( optional )
+            Radius of the probe atom, by default watter radious


Suggested change

Radius of the probe atom, by default watter radious

Radius of the probe atom, by default water radious

RMeli · 2023-02-18T20:46:20Z

package/MDAnalysis/analysis/accesibility.py

+            Atom group used for the calculation.
+        n_points: int (optional)
+            Number of points used for the estimation of the atom surface area
+        probe_radius: double ( optional )


Suggested change

probe_radius: double ( optional )

probe_radius: double (optional)

RMeli · 2023-02-18T20:49:34Z

package/MDAnalysis/analysis/accesibility.py

+    DEFAULT_ATOMIC_RADI = 2.0
+    return ATOMIC_RADI[e] if e in ATOMIC_RADI else DEFAULT_ATOMIC_RADI
+
+


Can you please add the DOI(s) of the relevant publication(s)/source(s) on which this analysis class is based? People need such references to double check the method and see where the default values come from.

You can find an example of how to do that here:

mdanalysis/package/MDAnalysis/analysis/msd.py

Lines 256 to 263 in d27a32a

due.cite(Doi("10.21105/joss.00877"),

description="Mean Squared Displacements with tidynamics",

path="MDAnalysis.analysis.msd",

cite_module=True)

due.cite(Doi("10.1051/sfn/201112010"),

description="FCA fast correlation algorithm",

path="MDAnalysis.analysis.msd",

cite_module=True)

RMeli · 2023-02-18T20:51:31Z

testsuite/MDAnalysisTests/analysis/test_accesibility.py

+from MDAnalysis.analysis.accesibility import SASA
+
+
+class TestSASA(object):


Are there simple cases for which an analytical result is available?

RMeli · 2023-02-18T20:55:42Z

package/MDAnalysis/analysis/accesibility.py

+        self._atom_neighbours = KDTree(ag.positions, 10)
+        self._n_points = n_points
+        self._sphere = self._compute_sphere()
+        self._twice_max_radi = (max(list(ATOMIC_RADI.values())) + probe_radius) * 2


Is there a better name for this variable, since it is not twice the maximum radius?

RMeli · 2023-02-18T20:58:46Z

package/MDAnalysis/analysis/accesibility.py

+
+        for atom in self._ag.atoms:
+            r_w = atomic_radi(atom.type)
+            raddi = r_w + self._probe_radius


Suggested change

raddi = r_w + self._probe_radius

radii = r_w + self._probe_radius

But maybe radius (singular) is more pertinent here? See also the other occurrences.

IAlibay

Thanks for this @pegerto

I however have two concerns:

The _compute and _compute_sphere methods are very reminiscent of the way classes are defined in Biopython. I haven't had a chance to do a direct comparison of the class content here, so please forgive me rudely asking - how much, if any, of this code comes from Biopython?
The AnalysisBase class methods aren't being used properly, I would suggest having a look at the docs for how to create such a child class: https://userguide.mdanalysis.org/stable/examples/analysis/custom_trajectory_analysis.html

IAlibay · 2023-02-20T15:32:56Z

package/MDAnalysis/analysis/accesibility.py

+    return ATOMIC_RADI[e] if e in ATOMIC_RADI else DEFAULT_ATOMIC_RADI
+
+
+class SASA(AnalysisBase):


I'm not seeing anything being defined for _prepare, _single_frame, or _conclude, and so it looks like you're not using the AnalysisBase class properly to allow it to iterate over a trajectory.

pegerto · 2023-02-20T18:23:42Z

The _compute and _compute_sphere methods are very reminiscent of the way classes are defined in Biopython. I haven't had a chance to do a direct comparison of the class content here, so please forgive me rudely asking - how much, if any, of this code comes from Biopython?

Hey @IAlibay not problem at all I definitely looked at the biopython implementation, the idea of precompute the sphere points and then stretch it and translate centroid of the atoms comes from this implementations.

Thanks for the feedback

orbeckst · 2023-02-20T18:32:08Z

Do you have an sense of relative performance compared to eg freesasa?

We have an active PR open for SASA. MDAnalysis/mdanalysis#4025

orbeckst · 2023-02-22T00:28:49Z

@pegerto if your code is based on biopython's Bio.PDB.SASA, wouldn't it be easier to just import the code and work on moving data between MDA and Biopython? How much of a cost does one incur doing so?

* GSoC 2023 blog post draft * Apply suggestions from code review * add gsoc list to config * remove SASA project We have an active PR open for SASA. MDAnalysis/mdanalysis#4025 * embed MDAnalysis 2021 trailer * post updates - fix project numbering (now same as in https://github.com/MDAnalysis/mdanalysis/wiki/GSoC-2023-Project-Ideas) - fix broken link constructs to GSoC list - add final remarks subheading for better showing difference between requirements and comments - add Discord as contact to last paragraph - close with a friendly sign off - use GitHub and Discord team handles in signature * fixed Discord gsoc-mentor handle * removed unavailable mentors --------- Co-authored-by: Rocco Meli <[email protected]> Co-authored-by: Lily Wang <[email protected]>

IAlibay · 2023-07-11T19:37:35Z

@pegerto is this still something you are interested in contributing?

IAlibay · 2023-07-31T10:53:01Z

I'm going to close this PR as stale, please do go ahead and re-open if you still wish to contribute this @pegerto, it is still a very much needed feature.

basic sasa implementation

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basic doc

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pegerto changed the title ~~basic sasa implementation~~ Solvant Accesible surface area Feb 13, 2023

pegerto mentioned this pull request Feb 13, 2023

Molecular volume and (solvent-accessible) surface area #2439

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pegerto-ck added 3 commits February 13, 2023 10:49

lint fixes

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lint fixes

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lint fixes

4761f5a

lint fix

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pegerto force-pushed the sasa branch 2 times, most recently from 001ae79 to 58d9cfc Compare February 18, 2023 11:35

add basic test

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pegerto force-pushed the sasa branch from 58d9cfc to 01e1e39 Compare February 18, 2023 11:51

pegerto-ck added 2 commits February 18, 2023 11:53

include name in AUTHORS

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add header

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pegerto force-pushed the sasa branch from ca4a893 to 9084fe7 Compare February 18, 2023 11:57

pegerto and others added 3 commits February 18, 2023 11:59

Merge branch 'develop' into sasa

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add doc

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add changelog

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pegerto marked this pull request as ready for review February 18, 2023 19:55

fix doc

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RMeli reviewed Feb 18, 2023

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IAlibay requested changes Feb 20, 2023

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orbeckst added a commit to MDAnalysis/MDAnalysis.github.io that referenced this pull request Feb 22, 2023

remove SASA project

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We have an active PR open for SASA. MDAnalysis/mdanalysis#4025

IAlibay closed this Jul 31, 2023

JureCerar mentioned this pull request Jan 8, 2024

Accessible Surface Area calculations #4417

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Solvant Accesible surface area #4025

Solvant Accesible surface area #4025

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	TABLE_VDWRADII = r"""
	# Van der Waals radii taken from
	# [1] Bondi, A. (1964). "Van der Waals Volumes and Radii".
	# J. Phys. Chem. 68 (3): 441-451. doi:10.1021/j100785a001.
	# [2] Rowland and Taylor (1996). "Intermolecular Nonbonded Contact Distances in Organic Crystal Structures:
	# Comparison with Distances Expected from van der Waals Radii".
	# J. Phys. Chem., 1996, 100 (18), 7384.7391. doi:10.1021/jp953141+.
	# [3] Mantina, et al. (2009). "Consistent van der Waals Radii for the Whole Main Group".
	# J. Phys. Chem. A, 2009, 113 (19), 5806-5812. doi:10.1021/jp8111556.

	Radius of the probe atom, by default watter radious
	Radius of the probe atom, by default water radious

	probe_radius: double ( optional )
	probe_radius: double (optional)

		DEFAULT_ATOMIC_RADI = 2.0
		return ATOMIC_RADI[e] if e in ATOMIC_RADI else DEFAULT_ATOMIC_RADI

	due.cite(Doi("10.21105/joss.00877"),
	description="Mean Squared Displacements with tidynamics",
	path="MDAnalysis.analysis.msd",
	cite_module=True)
	due.cite(Doi("10.1051/sfn/201112010"),
	description="FCA fast correlation algorithm",
	path="MDAnalysis.analysis.msd",
	cite_module=True)

		from MDAnalysis.analysis.accesibility import SASA


		class TestSASA(object):

	raddi = r_w + self._probe_radius
	radii = r_w + self._probe_radius

		return ATOMIC_RADI[e] if e in ATOMIC_RADI else DEFAULT_ATOMIC_RADI


		class SASA(AnalysisBase):

Solvant Accesible surface area #4025

Solvant Accesible surface area #4025

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