integrating ambertools pipeline

[SalomeRonja]

integrate amber2gromos and ambertools pipeline to parameterize a molecule and create a gromos_system

includes a small example jupyter notebook

[codecov[bot]]

Codecov Report

Merging #230 (6c605dd) into release3 (af7b15b) will decrease coverage by 0.45%. The diff coverage is 17.85%.

@@             Coverage Diff              @@
##           release3     #230      +/-   ##
============================================
- Coverage     52.60%   52.14%   -0.46%     
============================================
  Files            93       94       +1     
  Lines         12885    13051     +166     
============================================
+ Hits           6778     6806      +28     
- Misses         6107     6245     +138     

Flag	Coverage Δ
unittests	52.14% <17.85%> (-0.46%)	:arrow_down:

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

Impacted Files	Coverage Δ
...gromos/files/gromos_system/ff/forcefield_system.py	58.97% <14.28%> (-16.47%)	:arrow_down:
pygromos/gromos/gromosPP.py	17.82% <14.28%> (-0.11%)	:arrow_down:
pygromos/files/gromos_system/ff/amber2gromos.py	16.66% <16.66%> (ø)
pygromos/files/gromos_system/gromos_system.py	65.67% <38.46%> (-0.61%)	:arrow_down:

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[lgtm-com[bot]]

This pull request introduces 5 alerts when merging cb06dcedb7ecbe7f2c598199e2fca55f6b7d98cc into af7b15b41d1823733a0ee6bc85b49ce0ed4dcdd5 - view on LGTM.com

new alerts:

• 2 for Testing equality to None
• 2 for Unused local variable
• 1 for Unused import

[lgtm-com[bot]]

This pull request introduces 5 alerts when merging 6c605ddb17632515295e49b9ec9d135dfb1a3b2e into af7b15b41d1823733a0ee6bc85b49ce0ed4dcdd5 - view on LGTM.com

new alerts:

• 2 for Testing equality to None
• 2 for Unused local variable
• 1 for Unused import

[SalomeRonja]

Very nice!

thanks for merging :)