Framework bonds #118

ahyork · 2019-09-17T22:42:56Z

No description provided.

…nd add bonds to framework docs.

…arges, everything else is keyword arg

…ion error

…write_cif

… the future. add function for wrapping positions to unit cell

…p the apply symmetry rules

…ow takes place after it has been read in and uses the apply_symmetry_rules function

…to add new file type later

…ds to the inferred bonds

… once for every atom

…ation to the docs site.

…'t work on replicated structures

…l Not making it keyword so that it doesn't break other uses, and it will be common to use own bonding rules

coveralls · 2019-09-17T23:25:38Z

Pull Request Test Coverage Report for Build 580

108 of 125 (86.4%) changed or added relevant lines in 1 file are covered.
No unchanged relevant lines lost coverage.
Overall coverage decreased (-0.2%) to 80.955%

Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
src/Crystal.jl	108	125	86.4%

Totals
Change from base Build 544:	-0.2%
Covered Lines:	1288
Relevant Lines:	1591

💛 - Coveralls

ahyork added 30 commits August 26, 2019 16:08

start bond branch, create infer_bonds function, BondingRule struct, a…

e8fd725

…nd add bonds to framework docs.

update base framework constructor to require name, box, atoms, and ch…

622348e

…arges, everything else is keyword arg

fix infer_bonds to include wildcards, add test for replication assert…

9a97e65

…ion error

add function for removing bonds from a framework

c855ee2

fix tests add new testing info for removing bonds

e2aec85

fix tests

8c032ce

add bond comparison function, add writing bond info functionality to …

acb60d4

…write_cif

restructure cif readder to make it easier to add new read in types in…

9bbc435

… the future. add function for wrapping positions to unit cell

fix issue with henry tests

e6f063e

working on bond reader

b7b9a2f

able to read in bond info from cif files

e0c965d

added tests for checking the bond info from the write_cif function

2d3072d

read_bonds_from_file defaults to false now.

bb35d9a

add testing file for reading in bonds

387a180

start pdb reader, adjust write cif to change formatting

7a1c4cf

add CRYST1 tag interpreter to pdb reader, start working on cleaning u…

4cade0b

…p the apply symmetry rules

remove artifacts of old converter within the cif reader. conversion n…

6bb275b

…ow takes place after it has been read in and uses the apply_symmetry_rules function

moved symmetry application to outside the cif reader, make it easier …

3f9262e

…to add new file type later

pre-allocate space for symmetry rules

5b19669

did the rebase

608632d

fix bond comparison function, works correctly

d4caaba

add more headers in framework constructor, add test comparing pdb bon…

f2df73e

…ds to the inferred bonds

add testing files for new crystal tests

af260c3

fix bond comparison

c15a430

add bond writer, fix infer_bonds for speed and TODOs

0140679

generate symmetry rules once when they are used as a group instead of…

28699c6

… once for every atom

add documentation for function headers, add demo of using bond inform…

7a89f70

…ation to the docs site.

add missing end statement to warning in the bond_information writer

2a9d348

Add assertion for P1 symmetry to replicate because symmetry rules don…

f50ae8b

…'t work on replicated structures

add bonding to the addition section

5667875

ahyork and others added 2 commits September 17, 2019 15:42

make the bonding rules an optional argument for infer_bonds./uninstal…

94b7207

…l Not making it keyword so that it doesn't break other uses, and it will be common to use own bonding rules

Merge branch 'symmetry_reader' into framework_bonds

5dd7860

ahyork merged commit 6c3ce20 into symmetry_reader Sep 17, 2019

ahyork deleted the framework_bonds branch September 17, 2019 23:41

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Framework bonds #118

Framework bonds #118

ahyork commented Sep 17, 2019

coveralls commented Sep 17, 2019 •

edited

Framework bonds #118

Framework bonds #118

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ahyork commented Sep 17, 2019

coveralls commented Sep 17, 2019 • edited

Pull Request Test Coverage Report for Build 580

💛 - Coveralls

coveralls commented Sep 17, 2019 •

edited