Merge branch 'master' of github.com:SimTk/openmm

platforms/reference/src/ReferenceKernels.cpp

@@ -2026,6 +2026,7 @@ void ReferenceIntegrateCustomStepKernel::initialize(const System& system, const
     // Create the computation objects.
 
     dynamics = new ReferenceCustomDynamics(system.getNumParticles(), integrator);
+    SimTKOpenMMUtilities::setRandomNumberSeed((unsigned int) integrator.getRandomNumberSeed());
     vector<ReferenceCCMAAlgorithm::AngleInfo> angles;
     findAnglesForCCMA(system, angles);
     constraints = new ReferenceCCMAAlgorithm(system.getNumParticles(), numConstraints, constraintIndices, constraintDistances, masses, angles, (RealOpenMM)integrator.getConstraintTolerance());

wrappers/python/simtk/openmm/app/internal/pdbstructure.py

@@ -8,7 +8,7 @@ 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) 2012 Stanford University and the Authors.
+Portions copyright (c) 2012-2013 Stanford University and the Authors.
 Authors: Christopher M. Bruns
 Contributors: Peter Eastman
 
@@ -139,6 +139,7 @@ class PdbStructure(object):
         self.models_by_number = {}
         self._unit_cell_dimensions = None
         self.sequences = []
+        self.modified_residues = []
         # read file
         self._load(input_stream)
 
@@ -178,6 +179,8 @@ class PdbStructure(object):
                 if len(self.sequences) == 0 or chain_id != self.sequences[-1].chain_id:
                     self.sequences.append(Sequence(chain_id))
                 self.sequences[-1].residues.extend(pdb_line[19:].split())
+            elif (pdb_line.find("MODRES") == 0):
+                self.modified_residues.append(ModifiedResidue(pdb_line[16], int(pdb_line[18:22]), pdb_line[12:15].strip(), pdb_line[24:27].strip()))
         self._finalize()
 
     def write(self, output_stream=sys.stdout):
@@ -278,6 +281,14 @@ class Sequence(object):
         self.chain_id = chain_id
         self.residues = []
 
+class ModifiedResidue(object):
+    """ModifiedResidue holds information about a modified residue, as specified by a MODRES record."""
+    def __init__(self, chain_id, number, residue_name, standard_name):
+        self.chain_id = chain_id
+        self.number = number
+        self.residue_name = residue_name
+        self.standard_name = standard_name
+
 
 class Model(object):
     """Model holds one model of a PDB structure.

wrappers/python/simtk/openmm/app/pdbfile.py

@@ -36,7 +36,8 @@ import sys
 import math
 import xml.etree.ElementTree as etree
 from copy import copy
-from simtk.openmm import Vec3
+from datetime import date
+from simtk.openmm import Vec3, Platform
 from simtk.openmm.app.internal.pdbstructure import PdbStructure
 from simtk.openmm.app import Topology
 from simtk.unit import nanometers, angstroms, is_quantity, norm, Quantity
@@ -242,6 +243,7 @@ class PDBFile(object):
          - topology (Topology) The Topology defining the molecular system being written
          - file (file=stdout) A file to write the file to
         """
+        print >>file, "REMARK   1 CREATED WITH OPENMM %s, %s" % (Platform.getOpenMMVersion(), str(date.today()))
         boxSize = topology.getUnitCellDimensions()
         if boxSize is not None:
             size = boxSize.value_in_unit(angstroms)