willard_chandler.py #332

Zhu-Liu · 2020-04-13T21:40:50Z

From Line 210:

    ngrid, spacing = utilities.compute_compatible_mesh_params(
        self.mesh, box)
    self.spacing, self.ngrid = spacing, ngrid
    #print ("spacing: ", self.spacing)
    #print ("grid: ", self.ngrid)
    #print ("mesh: ", self.mesh)
    grid = utilities.generate_grid_in_box(box, ngrid, order='xyz')
    kernel, _ = utilities.density_map(pos, grid, self.alpha, box)
    #print ("kernel: ", kernel.__dict__)

    #print ("position: ", pos)
    #print ("position shape: ", np.array(pos).shape)

    kernel.pos = pos.copy()
    self.density_field = kernel.evaluate_pbc_fast(grid)

    # Thomas Lewiner, Helio Lopes, Antonio Wilson Vieira and Geovan
    # Tavares. Efficient implementation of Marching Cubes’ cases with
    # topological guarantees. Journal of Graphics Tools 8(2) pp. 1-15
    # (december 2003). DOI: 10.1080/10867651.2003.10487582
    volume = self.density_field.reshape(
        tuple(np.array(ngrid[::-1]).astype(int)))
    #verts, faces, normals, values = marching_cubes(
    #    volume, None, spacing=tuple(spacing))
    volume_cut = volume.max() - 0.9*volume.ptp()
    verts, faces, normals, values = marching_cubes(
        volume, volume_cut, spacing=tuple(spacing))

    # note that len(normals) == len(verts): they are normals
    # at the vertices, and not normals of the faces
    self.triangulated_surface = [verts, faces, normals]
    self.surface_area = measure.mesh_surface_area(verts, faces)
    #verts += spacing[::-1] / 2.

houndci-bot · 2020-04-13T21:40:56Z

pytim/patches.py

 def patchMDTRAJ_ReplacementTables():
    try:
        import mdtraj
-        if not (mdtraj.formats.pdb.PDBTrajectoryFile._atomNameReplacements=={}):
+        if not (mdtraj.formats.pdb.PDBTrajectoryFile._atomNameReplacements == {}):


line too long (82 > 79 characters)

houndci-bot · 2020-04-13T21:40:56Z

pytim/__init__.py

+from .willard_chandler import WillardChandler
+from .chacon_tarazona import ChaconTarazona
+from . import observables, utilities, datafiles
+from .version import __version__


'.version.version' imported but unused

houndci-bot · 2020-04-13T21:40:57Z

pytim/__init__.py

+from .sasa import SASA
+from .willard_chandler import WillardChandler
+from .chacon_tarazona import ChaconTarazona
+from . import observables, utilities, datafiles


'.datafiles' imported but unused
'.observables' imported but unused
'.utilities' imported but unused

houndci-bot · 2020-04-13T21:40:57Z

pytim/__init__.py

+from .gitim import GITIM
+from .sasa import SASA
+from .willard_chandler import WillardChandler
+from .chacon_tarazona import ChaconTarazona


'.chacon_tarazona.ChaconTarazona' imported but unused

houndci-bot · 2020-04-13T21:40:57Z

pytim/__init__.py

+from .itim import ITIM
+from .gitim import GITIM
+from .sasa import SASA
+from .willard_chandler import WillardChandler


'.willard_chandler.WillardChandler' imported but unused

houndci-bot · 2020-04-13T21:40:57Z

pytim/__init__.py

+from .simple_interface import SimpleInterface
+from .itim import ITIM
+from .gitim import GITIM
+from .sasa import SASA


'.sasa.SASA' imported but unused

houndci-bot · 2020-04-13T21:40:58Z

pytim/__init__.py

@@ -2,18 +2,18 @@
 # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
 #from pytim.patches import patchTrajectory, patchOpenMM, patchMDTRAJ

+from .simple_interface import SimpleInterface
+from .itim import ITIM
+from .gitim import GITIM


'.gitim.GITIM' imported but unused

houndci-bot · 2020-04-13T21:40:58Z

pytim/__init__.py

@@ -2,18 +2,18 @@
 # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
 #from pytim.patches import patchTrajectory, patchOpenMM, patchMDTRAJ

+from .simple_interface import SimpleInterface
+from .itim import ITIM


'.itim.ITIM' imported but unused

houndci-bot · 2020-04-13T21:40:58Z

pytim/__init__.py

@@ -2,18 +2,18 @@
 # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
 #from pytim.patches import patchTrajectory, patchOpenMM, patchMDTRAJ

+from .simple_interface import SimpleInterface


'.simple_interface.SimpleInterface' imported but unused

houndci-bot · 2020-04-13T21:40:58Z

docs/source/conf.py

@@ -16,6 +16,7 @@
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
+import sphinx.ext.autodoc


'sphinx.ext.autodoc' imported but unused

Marcello-Sega · 2020-04-25T08:59:29Z

Hi,

I don't understand what you would like to merge. You should branch off the master branch, make your changes and then set up a pull request from your branch into the master branch here.

I went through your branches, could it be what you want to merge is https://github.com/Zhu-Liu/pytim/tree/patch-1 ?

If you have some trouble, you can have a look at https://opensource.com/article/19/7/create-pull-request-github or just contact me back.

Zhu-Liu · 2020-05-15T19:18:17Z

[cid:e00e058b-47b6-4ebb-b372-09964471878c] Hi Dr. Sega, I am really sorry that I forgot to answer your email. I attached a code difference comparison, where the right side is the version directly downloaded from your GitHub and left is my slightly modified version. Basically, there are two differences: 1. right Line 225 ---> left Line 323: I put a volume threshold value as the Gaussian density cutoff, which is cutting the Gaussian density around 90%. For this part, you told me in the last emails that Pytim has already included this feature. Thus this may be necessary anymore. 2. right Line 231 ---> left Line 330: I comment out the vertices transfer. This will cause the off of the instantaneous interface location. (At least in all my testing, for example, it will move the willard-chandler interface close to the central water phase.) I also want to mention the x,z coordinates switching, which refers to right Line 213 and the function "generate_grid_in_box" from the "utilities_mesh" module. I have no idea why the "generate_grid_in_box" function is written in that way (line 27--30, see below). In my testing, this will result in the willard-chandler interface from the original xy-plane (along the z-axis) to the yz-plane (along the x-axis). Best, Zhu [cid:83e51ac1-2faf-44f9-9e23-d7f4a2150cd8]

…

-------------------------------------------------------------------------------- Dr. Zhu Liu Postdoctoral Research Associate, Department of Chemistry, Washington State University Tel. +1 509 592-1561 Email: [email protected] https://aclark.chem.wsu.edu/

--------------------------------------------------------------------------------

________________________________ From: Marcello Sega <[email protected]> Sent: Saturday, April 25, 2020 1:59 AM To: Marcello-Sega/pytim <[email protected]> Cc: Liu, Zhu <[email protected]>; Author <[email protected]> Subject: Re: [Marcello-Sega/pytim] willard_chandler.py (#332) Hi, I don't understand what you would like to merge. You should branch off the master branch, make your changes and then set up a pull request from your branch into the master branch here. I went through your branches, could it be what you want to merge is https://github.com/Zhu-Liu/pytim/tree/patch-1<https://urldefense.com/v3/__https://github.com/Zhu-Liu/pytim/tree/patch-1__;!!JmPEgBY0HMszNaDT!4fMwHJS7AM9VGvjgqrs0SoBhXNEbuEf90c3vEC017SpnfWEjs3EQF8k-BdCPi3E$> ? If you have some trouble, you can have a look at https://opensource.com/article/19/7/create-pull-request-github<https://urldefense.com/v3/__https://opensource.com/article/19/7/create-pull-request-github__;!!JmPEgBY0HMszNaDT!4fMwHJS7AM9VGvjgqrs0SoBhXNEbuEf90c3vEC017SpnfWEjs3EQF8k-8lRatns$> or just contact me back. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<https://urldefense.com/v3/__https://github.com/Marcello-Sega/pytim/pull/332*issuecomment-619346518__;Iw!!JmPEgBY0HMszNaDT!4fMwHJS7AM9VGvjgqrs0SoBhXNEbuEf90c3vEC017SpnfWEjs3EQF8k-ekCA3GM$>, or unsubscribe<https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AE5OTV4E3KQBPWKGPQ3NLQ3ROKQ7ZANCNFSM4MHIDOBQ__;!!JmPEgBY0HMszNaDT!4fMwHJS7AM9VGvjgqrs0SoBhXNEbuEf90c3vEC017SpnfWEjs3EQF8k-Qvo0JsM$>.

houndci-bot · 2020-05-19T10:03:44Z

pytim/version.py

@@ -1 +1 @@
-__version__ = '0.8.1'
+__version__ = '0.8.2'


Black would make changes.

houndci-bot · 2020-05-19T10:03:44Z

pytim/interface.py

+                    label_max = np.argmax(counts)
+                    ids_max = np.where(labels == label_max)[0]
+                    self.cluster_group = self.cluster_group[ids_max]
+            except AttributeError: # biggest_cluster_only not set


at least two spaces before inline comment

houndci-bot · 2020-05-19T11:30:13Z

pytim/interface.py

+        <AtomGroup with 2025 atoms>
+
+
+        >>> inter = pytim.SASA( g, alpha=2.5, max_layers=2, cluster_cut=3.5, biggest_cluster_only=True, molecular=True)


line too long (119 > 79 characters)

houndci-bot · 2020-05-19T11:30:13Z

pytim/interface.py

+        >>> u = mda.Universe(ANTAGONISTIC_GRO)
+        >>> g = u.atoms.select_atoms('resname bph4')
+        >>> # Define the interface
+        >>> inter = pytim.SASA( g, alpha=2.5, max_layers=2, cluster_cut=3.5, biggest_cluster_only=False, molecular=True)


line too long (120 > 79 characters)

houndci-bot · 2020-05-19T11:30:13Z

pytim/datafiles/__init__.py

@@ -293,6 +292,9 @@ def _vdwradii_gmx(self, filename):
 ILBENZENE_GRO = resource_filename('pytim', 'data/ilbenzene.gro')
 pytim_data.add('ILBENZENE_GRO', 'conf', 'GRO', 'BMIM PF4 / benzene interface')

+ANTAGONISTIC_GRO = resource_filename('pytim', 'data/antagonistic.gro')
+pytim_data.add('ANTAGONISTIC_GRO', 'conf', 'GRO', '3-Methylpyridine, Sodium Tetraphenylborate and water')


line too long (105 > 79 characters)

houndci-bot · 2020-05-26T12:50:38Z