Added boxShape option to addSolvent() (#245)

pdbfixer/pdbfixer.py

@@ -6,7 +6,7 @@ Simbios, the NIH National Center for Physics-Based Simulation of
 Biological Structures at Stanford, funded under the NIH Roadmap for
 Medical Research, grant U54 GM072970. See https://simtk.org.
 
-Portions copyright (c) 2013-2021 Stanford University and the Authors.
+Portions copyright (c) 2013-2022 Stanford University and the Authors.
 Authors: Peter Eastman
 Contributors:
 
@@ -1046,7 +1046,7 @@ class PDBFixer(object):
         self.topology = modeller.topology
         self.positions = modeller.positions
 
-    def addSolvent(self, boxSize=None, padding=None, boxVectors=None, positiveIon='Na+', negativeIon='Cl-', ionicStrength=0*unit.molar):
+    def addSolvent(self, boxSize=None, padding=None, boxVectors=None, positiveIon='Na+', negativeIon='Cl-', ionicStrength=0*unit.molar, boxShape='cube'):
         """Add a solvent box surrounding the structure.
 
         Parameters
@@ -1063,6 +1063,8 @@ class PDBFixer(object):
             The type of negative ion to add.  Allowed values are 'Cl-', 'Br-', 'F-', and 'I-'.
         ionicStrength : openmm.unit.Quantity with units compatible with molar, optional, default=0*molar
             The total concentration of ions (both positive and negative) to add.  This does not include ions that are added to neutralize the system.
+        boxShape: str='cube'
+            the box shape to use.  Allowed values are 'cube', 'dodecahedron', and 'octahedron'.  If padding is None, this is ignored.
 
         Examples
         --------
@@ -1080,7 +1082,7 @@ class PDBFixer(object):
 
         modeller = app.Modeller(self.topology, self.positions)
         forcefield = self._createForceField(self.topology, True)
-        modeller.addSolvent(forcefield, padding=padding, boxSize=boxSize, boxVectors=boxVectors, positiveIon=positiveIon, negativeIon=negativeIon, ionicStrength=ionicStrength)
+        modeller.addSolvent(forcefield, padding=padding, boxSize=boxSize, boxVectors=boxVectors, boxShape=boxShape, positiveIon=positiveIon, negativeIon=negativeIon, ionicStrength=ionicStrength)
         chains = list(modeller.topology.chains())
         if len(chains) == 1:
             chains[0].id = 'A'