Merge pull request #118 from choderalab/ligands-refactor

Ligand parameterization updates

Author: Bas Rustenburg

devtools/conda-recipe/meta.yaml

@@ -15,6 +15,7 @@ requirements:
     - openmm >=7.2
     - numpy >=1.10
     - scipy >=0.17.0
+    - mdtraj # For extracting trajectory parts
     - openmoltools >=0.7.5
     - openmmtools >=0.9.3
     - ambermini >=15.0.4
@@ -31,12 +32,14 @@ requirements:
     - pandas
     - beautifulsoup4 # for deserialization of html tables
     - saltswap >=0.5.2 # for counterion coupling
+    - networkx # matching protonation state structures
 
   run:
     - python
     - openmm >=7.2
     - numpy >=1.10
     - scipy >=0.17.0
+    - mdtraj # For extracting trajectory parts
     - netcdf4 >=1.2.4
     - hdf4 >4.2.11 # Pinned because of issue with netcdf4
     - openmoltools >=0.7.5
@@ -51,6 +54,7 @@ requirements:
     - pandas
     - saltswap >=0.5.2 # for counterion coupling
     - beautifulsoup4 # for deserialization of html tables
+    - networkx # matching protonation state structures
 
 test:
   requires: