Mtb

[MTLehner]

Description

Adding python class for mtb files

[lgtm-com[bot]]

This pull request introduces 1 alert and fixes 7 when merging e86d53558b97f6e5101e7f0ff01cc9171fa2bbe5 into af7b15b41d1823733a0ee6bc85b49ce0ed4dcdd5 - view on LGTM.com

new alerts:

• 1 for Unreachable code

fixed alerts:

• 7 for Unused local variable

[lgtm-com[bot]]

This pull request introduces 1 alert and fixes 7 when merging 5edc4f447189f0e9b8392f4cdd130b7cf5a310d8 into af7b15b41d1823733a0ee6bc85b49ce0ed4dcdd5 - view on LGTM.com

new alerts:

• 1 for Unreachable code

fixed alerts:

• 7 for Unused local variable

[lgtm-com[bot]]

This pull request introduces 1 alert and fixes 7 when merging 33e37a675c3d1c469de40014a387bb741c557ced into af7b15b41d1823733a0ee6bc85b49ce0ed4dcdd5 - view on LGTM.com

new alerts:

• 1 for Unreachable code

fixed alerts:

• 7 for Unused local variable

[lgtm-com[bot]]

This pull request introduces 4 alerts and fixes 10 when merging e6ac8cfd67fc57ffac8c0fb9b2594cfb93715e31 into af7b15b41d1823733a0ee6bc85b49ce0ed4dcdd5 - view on LGTM.com

new alerts:

• 3 for Unused import
• 1 for Unreachable code

fixed alerts:

• 7 for Unused local variable
• 3 for 'import *' may pollute namespace

[MTLehner]

@pultar @SchroederB The mtb structure diverges significantly from the usual block structure. The solution I used was to create a list of mtb blocks. these can then be used like normal gromos blocks. This PR only takes care of the MTB python representation as a class. Further tools like smile->mtb->top will follow in a different PR

[lgtm-com[bot]]

This pull request introduces 4 alerts and fixes 10 when merging 7dc2a623d7e2c1c422ebc3e7decc684224cd83b4 into af7b15b41d1823733a0ee6bc85b49ce0ed4dcdd5 - view on LGTM.com

new alerts:

• 3 for Unused import
• 1 for Unreachable code

fixed alerts:

• 7 for Unused local variable
• 3 for 'import *' may pollute namespace

[codecov[bot]]

Codecov Report

Merging #229 (29ec280) into release3 (f72f057) will increase coverage by 2.56%. The diff coverage is 87.25%.

@@             Coverage Diff              @@
##           release3     #229      +/-   ##
============================================
+ Coverage     52.14%   54.71%   +2.56%     
============================================
  Files            94       94              
  Lines         13051    13864     +813     
============================================
+ Hits           6806     7585     +779     
- Misses         6245     6279      +34     

Flag	Coverage Δ
unittests	54.71% <87.25%> (+2.56%)	:arrow_up:

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
pygromos/files/blocks/mtb_blocks.py	86.84% <86.61%> (+57.95%)	:arrow_up:
pygromos/files/blocks/_all_blocks.py	100.00% <100.00%> (ø)
pygromos/files/blocks/topology_blocks.py	78.81% <100.00%> (+0.05%)	:arrow_up:
pygromos/files/topology/mtb.py	100.00% <100.00%> (+100.00%)	:arrow_up:
pygromos/files/coord/cnf.py	45.29% <0.00%> (-0.11%)	:arrow_down:

---

Continue to review full report at Codecov.

Legend - Click here to learn more Δ = absolute <relative> (impact), ø = not affected, ? = missing data Powered by Codecov. Last update f72f057...29ec280. Read the comment docs.

[lgtm-com[bot]]

This pull request introduces 6 alerts and fixes 10 when merging 00f293eb9cdc696070ba1765d05f47e8fe5f3917 into af7b15b41d1823733a0ee6bc85b49ce0ed4dcdd5 - view on LGTM.com

new alerts:

• 3 for Unused import
• 2 for `__eq__` not overridden when adding attributes
• 1 for Unreachable code

fixed alerts:

• 7 for Unused local variable
• 3 for 'import *' may pollute namespace

[lgtm-com[bot]]

This pull request introduces 6 alerts and fixes 10 when merging f72872a1703589f24167bfe11cc0b29f2df6f16f into af7b15b41d1823733a0ee6bc85b49ce0ed4dcdd5 - view on LGTM.com

new alerts:

• 3 for Unused import
• 2 for `__eq__` not overridden when adding attributes
• 1 for Unreachable code

fixed alerts:

• 7 for Unused local variable
• 3 for 'import *' may pollute namespace

[lgtm-com[bot]]

This pull request introduces 10 alerts and fixes 10 when merging f7a10c42eed999da8b977b4cf5d7a887a09e7422 into af7b15b41d1823733a0ee6bc85b49ce0ed4dcdd5 - view on LGTM.com

new alerts:

• 4 for Unused import
• 3 for `__eq__` not overridden when adding attributes
• 3 for Unreachable code

fixed alerts:

• 7 for Unused local variable
• 3 for 'import *' may pollute namespace

[lgtm-com[bot]]

This pull request introduces 10 alerts and fixes 10 when merging 0472ec6dff4de696802bc83dcf8ff4a805a07929 into f72f057858b9381fea7cc6f3083174bdcde5f02a - view on LGTM.com

new alerts:

• 4 for Unused import
• 3 for `__eq__` not overridden when adding attributes
• 3 for Unreachable code

fixed alerts:

• 7 for Unused local variable
• 3 for 'import *' may pollute namespace

[MTLehner]

All numbers seem to be parsed correctly, but there seems to be a specific format required

[lgtm-com[bot]]

This pull request introduces 7 alerts and fixes 10 when merging ac7f8bc13ff5a3e44f33ab2fe9bd1a1f9c63066b into f72f057858b9381fea7cc6f3083174bdcde5f02a - view on LGTM.com

new alerts:

• 4 for Unused import
• 3 for Unreachable code

fixed alerts:

• 7 for Unused local variable
• 3 for 'import *' may pollute namespace

[MTLehner]

All numbers seem to be parsed correctly, but there seems to be a specific format required

This is fixed after commit https://github.com/rinikerlab/PyGromosTools/pull/229/commits/ac7f8bc13ff5a3e44f33ab2fe9bd1a1f9c63066b Apparently make_top does not like tabs and need spaces for proper formatting. Simple example like the creation of a CHE topology work now with a mtb file which has been read in and written out with pygromos

@pultar

[lgtm-com[bot]]

This pull request introduces 3 alerts and fixes 16 when merging 8bbef9710fea190093823cf750ea5698f1e168d8 into f72f057858b9381fea7cc6f3083174bdcde5f02a - view on LGTM.com

new alerts:

• 3 for Unused import

fixed alerts:

• 7 for Unused local variable
• 6 for Unused import
• 3 for 'import *' may pollute namespace

[pultar]

Looks like lots of great work! Maybe I have overseen it but should we add a notebook / section in another notebook to demonstrate the usage of the new class?

[pultar]

Parsed files look a bit wild for me after being processed by the new class. How about we use ljust and rjust instead to have alignment look nicer, like demonstrated here: https://github.com/rinikerlab/PyGromosTools/blob/f72f057858b9381fea7cc6f3083174bdcde5f02a/pygromos/files/blocks/qmmm_blocks.py#L38

[lgtm-com[bot]]

This pull request introduces 3 alerts and fixes 16 when merging 720bab3051390da155094cbea3fc4ccd0f483780 into f72f057858b9381fea7cc6f3083174bdcde5f02a - view on LGTM.com

new alerts:

• 3 for Unused import

fixed alerts:

• 7 for Unused local variable
• 6 for Unused import
• 3 for 'import *' may pollute namespace

[lgtm-com[bot]]

This pull request introduces 3 alerts and fixes 16 when merging 865dc35ac2976cabfdefcd48d11a39540ce53067 into f72f057858b9381fea7cc6f3083174bdcde5f02a - view on LGTM.com

new alerts:

• 3 for Unused import

fixed alerts:

• 7 for Unused local variable
• 6 for Unused import
• 3 for 'import *' may pollute namespace

[RiesBen]

I like the branch and think after discussing the dict suggestions, we can merge it.

my suggestion is basically this:

which would make searching for residues easier, and it could be included in the Constructor. we could then consider making the lists _ private

[lgtm-com[bot]]

This pull request introduces 3 alerts and fixes 16 when merging 97ebb6e0fcc4d66ecc4870f2f70cd4c26b8c4311 into e4d1c5a3ac952472e67f77e38c102dec60ca8621 - view on LGTM.com

new alerts:

• 3 for Unused import

fixed alerts:

• 7 for Unused local variable
• 6 for Unused import
• 3 for 'import *' may pollute namespace

[lgtm-com[bot]]

This pull request introduces 3 alerts and fixes 16 when merging 29ec280efa59ae2083d369d8c0ae165b698b3ea7 into e4d1c5a3ac952472e67f77e38c102dec60ca8621 - view on LGTM.com

new alerts:

• 3 for Unused import

fixed alerts:

• 7 for Unused local variable
• 6 for Unused import
• 3 for 'import *' may pollute namespace