Coordinate interval update

gamd/config.py

@@ -235,6 +235,7 @@ def serialize(self, root):
         assign_tag(xml_energy_tags, "interval", self.energy_interval)
         xml_coordinates_tags = ET.SubElement(root, "coordinates")
         assign_tag(xml_coordinates_tags, "file-type", self.coordinates_file_type)
+        assign_tag(xml_coordinates_tags, "interval", self.coordinates_interval)
         xml_statistics_tags = ET.SubElement(root, "statistics")
         assign_tag(xml_statistics_tags, "interval", self.statistics_interval)
         return

gamd/gamdSimulation.py

@@ -8,6 +8,7 @@
 """
 import os
 
+import mdtraj
 import parmed
 import openmm as openmm
 import openmm.app as openmm_app
@@ -25,7 +26,10 @@
 
 
 def load_pdb_positions_and_box_vectors(pdb_coords_filename, need_box):
-    positions = openmm_app.PDBFile(pdb_coords_filename)
+    try:
+        positions = openmm_app.PDBxFile(pdb_coords_filename) # More consistency with large systems
+    except:
+        positions = openmm_app.PDBFile(pdb_coords_filename)
     pdb_parmed = parmed.load_file(pdb_coords_filename)
     if need_box:
         assert pdb_parmed.box_vectors is not None, "No box vectors "\
@@ -265,7 +269,8 @@ def createGamdSimulation(self, config, platform_name, device_index):
 
         elif config.outputs.reporting.coordinates_file_type == "pdb":
             gamdSimulation.traj_reporter = openmm_app.PDBReporter
-
+        elif config.outputs.reporting.coordinates_file_type == "h5":
+            gamdSimulation.traj_reporter = mdtraj.reporters.HDF5Reporter
         else:
             raise Exception("Reporter type not found:",
                             config.outputs.reporting.coordinates_file_type)

gamd/parser.py

@@ -318,6 +318,9 @@ def parse_outputs_tag(tag):
                         if coordinates_tag.tag == "file-type":
                             outputs_config.reporting.coordinates_file_type \
                                 = assign_tag(coordinates_tag, str).lower()
+                        elif coordinates_tag.tag == "interval":
+                            outputs_config.reporting.coordinates_interval \
+                                = assign_tag(coordinates_tag, int)
                         else:
                             print("Warning: parameter in XML not found in "
                                   "coordinates tag. Spelling error?", 

gamd/runners.py

@@ -6,6 +6,7 @@
 import subprocess
 import sys
 
+import mdtraj
 import openmm.unit as unit
 import openmm.app as openmm_app
 
@@ -250,6 +251,9 @@ def register_trajectory_reporter(self, restart):
         elif traj_reporter == openmm_app.PDBReporter:
             simulation.reporters.append(traj_reporter(
                 traj_name, self.config.outputs.reporting.coordinates_interval))
+        elif traj_reporter == mdtraj.reporters.HDF5Reporter:
+            simulation.reporters.append(traj_reporter(
+                traj_name, self.config.outputs.reporting.coordinates_interval))
 
     def register_state_data_reporter(self, restart):
         if self.state_data_reporter_enabled:

setup.py

@@ -52,7 +52,7 @@
 
     # Additional entries you may want simply uncomment the lines you want and fill in the data
     # url='http://www.my_package.com',  # Website
-    install_requires=["numpy", "parmed", "pytest", "matplotlib"], 
+    install_requires=["numpy", "parmed", "pytest", "matplotlib", "mdtraj"], 
     # Required packages, pulls from pip if needed; do not use for Conda deployment
     # platforms=['Linux',
     #            'Mac OS-X',