Arrestin system

bgmol/data/termini.yaml

@@ -0,0 +1,31 @@
+ACE:
+  #- ["H1", "CH3", "C", "N"]
+  #- ["CH3", "C", "N", "CA"]
+  - ["C", "CH3", "H1", "H2"]
+  - ["H3", "CH3", "C", "H1"] 
+  #- ["C", "N", "CA", "C"]
+  #- ["O", "C", "N", "CA"]
+
+NME:
+  #- ["N", "C", "CA", "N"] 
+  #- ["H", "N", "O", "C"]
+  #- ["C", "N", "C", "CA"]
+  #- ["H1", "C", "N", "C"] 
+  - ["C", "N", "H1", "H2"] 
+  - ["H3", "C", "N", "H1"] 
+
+
+HSE:
+  - ["HN", "N", "CA", "C"]
+  - ["O", "C", "CA", "N"]
+  - ["HA", "CA", "N", "C"]
+
+HSD:
+  - ["HN", "N", "CA", "C"]
+  - ["O", "C", "CA", "N"]
+  - ["HA", "CA", "N", "C"]
+
+HSP:
+  - ["HN", "N", "CA", "C"]
+  - ["O", "C", "CA", "N"]
+  - ["HA", "CA", "N", "C"]

bgmol/datasets/__init__.py

@@ -3,3 +3,4 @@
 from .ala2 import *
 from .minipeptides import *
 from .chignolin import *
+from .arrestin import *

bgmol/datasets/arrestin.py

@@ -0,0 +1,73 @@
+import os
+import numpy as np
+from bgmol.datasets.base import DataSet
+from bgmol.api import system_by_name
+from mdtraj import load_dcd
+
+
+__all__ = ["ArrestinActive"]
+
+
+class ArrestinActive(DataSet):
+    """ArrestinActive at 310 K.
+    1 ms Langevin dynamics with 1/ps friction coefficient and 2fs time step,
+    output spaced in 10 ps intervals.
+    """
+    #url = "http://ftp.mi.fu-berlin.de/pub/cmb-data/bgmol/datasets/ala2/Ala2Implicit300.tgz"
+    #md5 = "ce9d6f6aa214f3eb773d52255aeaeacb"
+    #num_frames = 99999
+    #size = 49692000 # in bytes
+    selection = "all"
+    openmm_version = "7.4.1"
+    date = "2021/8/15"
+
+    def __init__(self, root=os.getcwd()):
+        super(ArrestinActive, self).__init__(root=root)
+        self._system = system_by_name("ArrestinActive")
+        self._temperature = 310
+#        name = 'arr2-active_coordinates'
+#        with open(name + '.pkl', 'rb') as f:
+#            coords = pickle.load(f)
+#            self._xyz = coords
+
+    @property
+    def trajectory_file(self):
+        return os.path.join(self.root, "openmm-arrestin/arr2-active_output.dcd")
+
+    def read(self):
+        self.trajectory = load_dcd(self.trajectory_file, top=self._system.mdtraj_topology)
+        #energy_logfile = 'arr2-active_log.txt'
+        #self._energies = np.loadtxt(energy_logfile, delimiter=',')[:,1]
+#        self._forces = np.loadtxt(force_logfile, delimiter=',')[:,1]
+
+
+
+
+class ArrestinInactive(DataSet):
+    """ArrestinInactive at 310 K.
+    1 ms Langevin dynamics with 1/ps friction coefficient and 2fs time step,
+    output spaced in 10 ps intervals.
+    """
+    #url = "http://ftp.mi.fu-berlin.de/pub/cmb-data/bgmol/datasets/ala2/Ala2Implicit1000.tgz"
+    #md5 = "9a90965254dac7440976d0d62687caed"
+    #num_frames = 100000
+    #size = 51071715 # in bytes
+    selection = "all"
+    openmm_version = "7.4.1"
+    date = "2021/08/15"
+
+    def __init__(self, root=os.getcwd(), download: bool = False, read: bool = False):
+        super(ArrestinInactive, self).__init__(root=root, download=download, read=read)
+        self._system = system_by_name("ArrestinInactive")
+        self._temperature = 310
+        name = 'arr2-inactive_coordinates'
+        with open(name + '.pkl', 'rb') as f:
+            coords = pickle.load(f)
+            self._xyz = coords
+
+    def read(self):
+#        self.trajectory = load_dcd(self.trajectory_file)
+        energy_logfile = 'arr2-inactive_log.txt'
+        self._energies = np.loadtxt(energy_logfile, delimiter=',')[:,1]
+#        self._forces = np.loadtxt(force_logfile, delimiter=',')[:,1]
+

bgmol/systems/__init__.py

@@ -6,3 +6,4 @@
 from .minipeptides import *
 from .chignolin import *
 from .fastfolders import *
+from .arrestin import *

bgmol/systems/arrestin.py

@@ -0,0 +1,44 @@
+import os
+import tempfile
+from ..systems.base import OpenMMSystem
+from torchvision.datasets.utils import download_url
+
+from ..util.importing import import_openmm
+mm, unit, app = import_openmm()
+
+
+__all__ = ["ArrestinActive"]
+
+
+class ArrestinActive(OpenMMSystem):
+    """
+    """
+    url = "http://ftp.mi.fu-berlin.de/pub/cmb-data/bgmol/systems/arrestin/"
+
+    def __init__(self,  root=tempfile.gettempdir(), download=True):
+        super(ArrestinActive, self).__init__()
+
+        if download:
+            filename = self._download(root)
+        assert os.path.isfile(filename)
+
+        pdb = app.PDBFile(filename)
+        forcefield = app.ForceField("amber99sbildn.xml", "amber96_obc.xml")
+
+        self._system = forcefield.createSystem(
+            pdb.topology,
+            nonbondedMethod=app.PME,
+            nonbondedCutoff=1 * unit.nanometer,
+            constraints=app.HBonds
+        )
+
+        self._positions = pdb.getPositions(asNumpy=True).value_in_unit(unit.nanometer)
+        self._topology = pdb.getTopology()
+
+    def _download(self, root):
+        md5 = "c428fe87c0e888bc19e444eef05a9b3d"
+        filename = "arr2-active_start.pdb"
+        download_url(self.url+filename, root, filename, md5)
+        local_file = os.path.join(root, filename)
+        return local_file
+

bgmol/tests/systems/test_arrestin.py

@@ -0,0 +1,6 @@
+
+from bgmol.systems import ArrestinActive
+
+
+def test_arrestin_system():
+    arrestin = ArrestinActive()