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Molecule/apply link #241

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Molecule/apply link #241

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4373572
new itp read; featuirng ifdef interpretation
fgrunewald Mar 17, 2020
1022169
small changes
fgrunewald Mar 18, 2020
cd1e1a9
add parser for virtual_sitesn
fgrunewald Mar 19, 2020
1dd5d4c
add natoms of missing interaction for GROMACS
fgrunewald Mar 19, 2020
3d50d6b
new tests for itp reader
fgrunewald Mar 19, 2020
84d8093
Merge branch 'master' into itp-reader
fgrunewald Mar 19, 2020
e414f32
small fixes to the itp-reader
fgrunewald Mar 23, 2020
fc84c12
strip all legecy functionality that originates from ffinput.py
fgrunewald Mar 23, 2020
6cda515
implement index based line interpretation; this also fixes the VS pro…
fgrunewald Mar 23, 2020
747dd07
remove method add_node_from_index and replace by add node in parser
fgrunewald Mar 23, 2020
f7b2648
get rid of cross population of SectionLineParser METH_DICTs
fgrunewald Mar 23, 2020
1694e60
some PEP8 compliance adjustments
fgrunewald Mar 23, 2020
a676850
some PEP8 compliance & code-cov
fgrunewald Mar 24, 2020
017fb3f
inital apply links method
fgrunewald Mar 26, 2020
659e0a4
PEP8 and CodeCov
fgrunewald Mar 27, 2020
dfb7472
fix documentation
fgrunewald Mar 27, 2020
ffde22f
fix test
fgrunewald Mar 27, 2020
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fix documentation
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@fgrunewald
fgrunewald committed Mar 27, 2020
commit dfb7472871066f8bb560de0c70769fef0671154c
4 changes: 1 addition & 3 deletions vermouth/molecule.py
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Expand Up @@ -607,8 +607,6 @@ def find_atoms(self, **attrs):

Parameters
----------
ignore_keys: list
List of keys to ignore from 'template_attributes'.
**attrs: collections.abc.Mapping
The attributes and their desired values

Expand Down Expand Up @@ -925,7 +923,7 @@ def apply_link_between_residues(self, link, resids):

Parameters
----------
link: :class:`vermouth.Molecule.Link`
link: :class:`vermouth.molecule.Link`
A vermouth link definition
resids: list
a list of node attributes used for link matching aside from
Expand Down