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
 Biological Structures at Stanford, funded under the NIH Roadmap for
 Medical Research, grant U54 GM072970. See https://simtk.org.
 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
 Authors: Peter Eastman
 Contributors:
 Contributors:
 
 
@@ -1046,7 +1046,7 @@ class PDBFixer(object):
         self.topology = modeller.topology
         self.topology = modeller.topology
         self.positions = modeller.positions
         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.
         """Add a solvent box surrounding the structure.
 
 
         Parameters
         Parameters
@@ -1063,6 +1063,8 @@ class PDBFixer(object):
             The type of negative ion to add.  Allowed values are 'Cl-', 'Br-', 'F-', and 'I-'.
             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
         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.
             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
         Examples
         --------
         --------
@@ -1080,7 +1082,7 @@ class PDBFixer(object):
 
 
         modeller = app.Modeller(self.topology, self.positions)
         modeller = app.Modeller(self.topology, self.positions)
         forcefield = self._createForceField(self.topology, True)
         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())
         chains = list(modeller.topology.chains())
         if len(chains) == 1:
         if len(chains) == 1:
             chains[0].id = 'A'
             chains[0].id = 'A'