mosdef-hub / foyer / 396
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Jobs 4
Files 9
Run time 4min
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Checks for correct topology parameterization (#155)

* Added checks for correct topology parameterization

`Forcefield.apply` will now check to make sure parameters are found
for all angles, proper dihedrals, and improper dihedrals. By
default, if parameters are not found for all angles and proper
dihedrals, the script will exit with an error. A warning will be
raised if parameters are not found for all impropers. However, the
behavior (error/warning) for each of these topology objects can be
toggled by the user.

Unit tests have been added to test this behavior.

* Reduced duplicate code

* Add _system_data attribute to Forcefield

* Store system info in Forcefield._SystemData

* Clean up tests for missing topo params

* Cleaner modification of self._SystemData

* Add test forcefield XML files

* Separate structure.dihedrals into propers and impropers

* Ignore unparameterized dihedrals in test using partial FF

* Rewrite _SystemData each time `createSystem` is called

* Added classes for alkyne atomtypes

* Added classes for pyridine atomtypes

* Added classes for pyrimidine atomtypes

* Added class for acetal ether atomtype

* Added classes for acetal atomtypes

* Updated list of molecules correctly parametrized by OPLS

* Updated list of implemented TraPPE molecules

* Warn user that all RB torsions are processed as propers

* Appveyor debugging - replace `conda build` with `conda-build`

* Add conda-forge channel to YAML files

* Appveyor debugging

* Appveyor debugging

* Appveyor debugging

* Appveyor debugging

* Appveyor debugging

* Appveyor debugging

* Appveyor debugging

* Appveyor fix

* Appveyor debugging

* Reverting appveyor changes

* Add conda forge channel to appveyor.yml

701 of 796 relevant lines covered (88.07%)

3.52 hits per line

Jobs
ID Job ID Ran Files Coverage
1 396.1 (PYTHON_VERSION=2.7) 0
87.81
 Travis Job 396.1
2 396.2 (PYTHON_VERSION=3.5) 0
88.07
 Travis Job 396.2
3 396.3 (PYTHON_VERSION=2.7) 0
87.81
 Travis Job 396.3
4 396.4 (PYTHON_VERSION=3.5) 0
88.07
 Travis Job 396.4
Source Files on build 396
Detailed source file information is not available for this build.