Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Molecule/apply link #241

Closed
wants to merge 17 commits into from
Closed

Molecule/apply link #241

Changes from 1 commit
Commits
Show all changes
17 commits
Select commit Hold shift + click to select a range
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
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Prev Previous commit
Next Next commit
add natoms of missing interaction for GROMACS
  • Loading branch information
@fgrunewald
fgrunewald committed Mar 19, 2020
commit 1dd5d4c368101442ddf8f9738a4f92d802380886
11 changes: 10 additions & 1 deletion vermouth/gmx/itp_read.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -59,8 +59,16 @@ class ITPDirector(SectionLineParser):
'impropers': 4,
'constraints': 2,
'virtual_sites2': 3,
'virtual_sites3': 4,
'virtual_sites4': 5,
'pairs': 2,
'position_restraints':1
'pairs_nb':2,
'position_restraints':1,
'distance_restraints':2,
'dihedral_restraints':4,
'orientation_restraints':2,
'angle_restraints':4,
'angle_restraints_z':2
}

def __init__(self, force_field):
Expand Down Expand Up @@ -475,6 +483,7 @@ def _base_parser(tokens, context, context_type, section, current_meta, natoms=No
parameters = _parse_interaction_parameters(tokens)

apply_to_all_interactions = context._apply_to_all_interactions[section]

if current_meta:
meta = {current_meta['condition']:current_meta['tag']}
else:
Expand Down