imdclient 0.1.3__py3-none-any.whl → 0.1.4__py3-none-any.whl

imdclient/tests/hpc_testing/namd/alanin.psf

@@ -0,0 +1,206 @@
+PSF 
+
+      11 !NTITLE
+ REMARKS FILENAME="/usr/people/nonella/xplor/benchmark1/ALANIN.PSF"             
+ REMARKS PARAM11.PRO ( from PARAM6A )                                           
+ REMARKS ===========                                                            
+ REMARKS PROTEIN PARAMETERS:                                                    
+ REMARKS PEPTIDE GEOMETRY FROM RAMACHANDRAN ET AL BBA 359:298 (1974)            
+ REMARKS TORSIONS FROM HAGLER ET AL JACS 98:4600 (1976)                         
+ REMARKS LENNARD-JONES NONBONDED PARAMETERS WITH SPECIAL TREATMENT OF 1:4       
+ REMARKS CARBON-CARBON INTERACTIONS: JORGENSON ET. AL.                          
+ REMARKS                           JACS 103:3976-3985 WITH 1-4 RC=1.80/0.1      
+ REMARKS                                                                        
+ REMARKS DATE:16-Feb-89  11:21:29       created by user: nonella                
+
+      66 !NATOM
+       1 MAIN 1    ACE  CA   CH3E   0.000000E+00   15.0350           0
+       2 MAIN 1    ACE  C    C      0.450000       12.0110           0
+       3 MAIN 1    ACE  O    O     -0.450000       15.9994           0
+       4 MAIN 2    ALA  N    NH1   -0.350000       14.0067           0
+       5 MAIN 2    ALA  H    H      0.250000       1.00800           0
+       6 MAIN 2    ALA  CA   CH1E   0.100000       13.0190           0
+       7 MAIN 2    ALA  CB   CH3E   0.000000E+00   15.0350           0
+       8 MAIN 2    ALA  C    C      0.450000       12.0110           0
+       9 MAIN 2    ALA  O    O     -0.450000       15.9994           0
+      10 MAIN 3    ALA  N    NH1   -0.350000       14.0067           0
+      11 MAIN 3    ALA  H    H      0.250000       1.00800           0
+      12 MAIN 3    ALA  CA   CH1E   0.100000       13.0190           0
+      13 MAIN 3    ALA  CB   CH3E   0.000000E+00   15.0350           0
+      14 MAIN 3    ALA  C    C      0.450000       12.0110           0
+      15 MAIN 3    ALA  O    O     -0.450000       15.9994           0
+      16 MAIN 4    ALA  N    NH1   -0.350000       14.0067           0
+      17 MAIN 4    ALA  H    H      0.250000       1.00800           0
+      18 MAIN 4    ALA  CA   CH1E   0.100000       13.0190           0
+      19 MAIN 4    ALA  CB   CH3E   0.000000E+00   15.0350           0
+      20 MAIN 4    ALA  C    C      0.450000       12.0110           0
+      21 MAIN 4    ALA  O    O     -0.450000       15.9994           0
+      22 MAIN 5    ALA  N    NH1   -0.350000       14.0067           0
+      23 MAIN 5    ALA  H    H      0.250000       1.00800           0
+      24 MAIN 5    ALA  CA   CH1E   0.100000       13.0190           0
+      25 MAIN 5    ALA  CB   CH3E   0.000000E+00   15.0350           0
+      26 MAIN 5    ALA  C    C      0.450000       12.0110           0
+      27 MAIN 5    ALA  O    O     -0.450000       15.9994           0
+      28 MAIN 6    ALA  N    NH1   -0.350000       14.0067           0
+      29 MAIN 6    ALA  H    H      0.250000       1.00800           0
+      30 MAIN 6    ALA  CA   CH1E   0.100000       13.0190           0
+      31 MAIN 6    ALA  CB   CH3E   0.000000E+00   15.0350           0
+      32 MAIN 6    ALA  C    C      0.450000       12.0110           0
+      33 MAIN 6    ALA  O    O     -0.450000       15.9994           0
+      34 MAIN 7    ALA  N    NH1   -0.350000       14.0067           0
+      35 MAIN 7    ALA  H    H      0.250000       1.00800           0
+      36 MAIN 7    ALA  CA   CH1E   0.100000       13.0190           0
+      37 MAIN 7    ALA  CB   CH3E   0.000000E+00   15.0350           0
+      38 MAIN 7    ALA  C    C      0.450000       12.0110           0
+      39 MAIN 7    ALA  O    O     -0.450000       15.9994           0
+      40 MAIN 8    ALA  N    NH1   -0.350000       14.0067           0
+      41 MAIN 8    ALA  H    H      0.250000       1.00800           0
+      42 MAIN 8    ALA  CA   CH1E   0.100000       13.0190           0
+      43 MAIN 8    ALA  CB   CH3E   0.000000E+00   15.0350           0
+      44 MAIN 8    ALA  C    C      0.450000       12.0110           0
+      45 MAIN 8    ALA  O    O     -0.450000       15.9994           0
+      46 MAIN 9    ALA  N    NH1   -0.350000       14.0067           0
+      47 MAIN 9    ALA  H    H      0.250000       1.00800           0
+      48 MAIN 9    ALA  CA   CH1E   0.100000       13.0190           0
+      49 MAIN 9    ALA  CB   CH3E   0.000000E+00   15.0350           0
+      50 MAIN 9    ALA  C    C      0.450000       12.0110           0
+      51 MAIN 9    ALA  O    O     -0.450000       15.9994           0
+      52 MAIN 10   ALA  N    NH1   -0.350000       14.0067           0
+      53 MAIN 10   ALA  H    H      0.250000       1.00800           0
+      54 MAIN 10   ALA  CA   CH1E   0.100000       13.0190           0
+      55 MAIN 10   ALA  CB   CH3E   0.000000E+00   15.0350           0
+      56 MAIN 10   ALA  C    C      0.450000       12.0110           0
+      57 MAIN 10   ALA  O    O     -0.450000       15.9994           0
+      58 MAIN 11   ALA  N    NH1   -0.350000       14.0067           0
+      59 MAIN 11   ALA  H    H      0.250000       1.00800           0
+      60 MAIN 11   ALA  CA   CH1E   0.100000       13.0190           0
+      61 MAIN 11   ALA  CB   CH3E   0.000000E+00   15.0350           0
+      62 MAIN 11   ALA  C    C      0.450000       12.0110           0
+      63 MAIN 11   ALA  O    O     -0.450000       15.9994           0
+      64 MAIN 12   CBX  N    NH1   -0.350000       14.0067           0
+      65 MAIN 12   CBX  H    H      0.250000       1.00800           0
+      66 MAIN 12   CBX  CA   CH3E   0.100000       15.0350           0
+
+      65 !NBOND: bonds
+       1       2       2       3       4       6       6       8
+       8       9       4       5       6       7       2       4
+      10      12      12      14      14      15      10      11
+      12      13       8      10      16      18      18      20
+      20      21      16      17      18      19      14      16
+      22      24      24      26      26      27      22      23
+      24      25      20      22      28      30      30      32
+      32      33      28      29      30      31      26      28
+      34      36      36      38      38      39      34      35
+      36      37      32      34      40      42      42      44
+      44      45      40      41      42      43      38      40
+      46      48      48      50      50      51      46      47
+      48      49      44      46      52      54      54      56
+      56      57      52      53      54      55      50      52
+      58      60      60      62      62      63      58      59
+      60      61      56      58      64      66      64      65
+      62      64
+
+      96 !NTHETA: angles
+       1       2       3       4       6       8       6       4       5
+       4       6       7       6       8       9       8       6       7
+       1       2       4       3       2       4       2       4       6
+       2       4       5      10      12      14      12      10      11
+      10      12      13      12      14      15      14      12      13
+       6       8      10       9       8      10       8      10      12
+       8      10      11      16      18      20      18      16      17
+      16      18      19      18      20      21      20      18      19
+      12      14      16      15      14      16      14      16      18
+      14      16      17      22      24      26      24      22      23
+      22      24      25      24      26      27      26      24      25
+      18      20      22      21      20      22      20      22      24
+      20      22      23      28      30      32      30      28      29
+      28      30      31      30      32      33      32      30      31
+      24      26      28      27      26      28      26      28      30
+      26      28      29      34      36      38      36      34      35
+      34      36      37      36      38      39      38      36      37
+      30      32      34      33      32      34      32      34      36
+      32      34      35      40      42      44      42      40      41
+      40      42      43      42      44      45      44      42      43
+      36      38      40      39      38      40      38      40      42
+      38      40      41      46      48      50      48      46      47
+      46      48      49      48      50      51      50      48      49
+      42      44      46      45      44      46      44      46      48
+      44      46      47      52      54      56      54      52      53
+      52      54      55      54      56      57      56      54      55
+      48      50      52      51      50      52      50      52      54
+      50      52      53      58      60      62      60      58      59
+      58      60      61      60      62      63      62      60      61
+      54      56      58      57      56      58      56      58      60
+      56      58      59      66      64      65      60      62      64
+      63      62      64      62      64      66      62      64      65
+
+      31 !NPHI: dihedrals
+       2       4       6       8       1       2       4       6
+       8      10      12      14       4       6       8      10
+       6       8      10      12      14      16      18      20
+      10      12      14      16      12      14      16      18
+      20      22      24      26      16      18      20      22
+      18      20      22      24      26      28      30      32
+      22      24      26      28      24      26      28      30
+      32      34      36      38      28      30      32      34
+      30      32      34      36      38      40      42      44
+      34      36      38      40      36      38      40      42
+      44      46      48      50      40      42      44      46
+      42      44      46      48      50      52      54      56
+      46      48      50      52      48      50      52      54
+      56      58      60      62      52      54      56      58
+      54      56      58      60      58      60      62      64
+      60      62      64      66
+
+      32 !NIMPHI: impropers
+       6       4       8       7       2       1       4       3
+       4       2       6       5      12      10      14      13
+       8       6      10       9      10       8      12      11
+      18      16      20      19      14      12      16      15
+      16      14      18      17      24      22      26      25
+      20      18      22      21      22      20      24      23
+      30      28      32      31      26      24      28      27
+      28      26      30      29      36      34      38      37
+      32      30      34      33      34      32      36      35
+      42      40      44      43      38      36      40      39
+      40      38      42      41      48      46      50      49
+      44      42      46      45      46      44      48      47
+      54      52      56      55      50      48      52      51
+      52      50      54      53      60      58      62      61
+      56      54      58      57      58      56      60      59
+      62      60      64      63      64      62      66      65
+
+      11 !NDON: donors
+       4       5      10      11      16      17      22      23
+      28      29      34      35      40      41      46      47
+      52      53      58      59      64      65
+
+      11 !NACC: acceptors
+       3       2       9       8      15      14      21      20
+      27      26      33      32      39      38      45      44
+      51      50      57      56      63      62
+
+       0 !NNB
+
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0
+
+      33       0 !NGRP
+       0       0       0       1       0       0       3       0       0
+       6       0       0       7       0       0       9       0       0
+      12       0       0      13       0       0      15       0       0
+      18       0       0      19       0       0      21       0       0
+      24       0       0      25       0       0      27       0       0
+      30       0       0      31       0       0      33       0       0
+      36       0       0      37       0       0      39       0       0
+      42       0       0      43       0       0      45       0       0
+      48       0       0      49       0       0      51       0       0
+      54       0       0      55       0       0      57       0       0
+      60       0       0      61       0       0      63       0       0

imdclient/tests/hpc_testing/namd/namd_v3_nst_1.namd

@@ -0,0 +1,59 @@
+# This is a test namd configuration file
+
+timestep	0.5
+numsteps	10
+structure	alanin.psf
+parameters	alanin.params
+coordinates	alanin.pdb
+exclude		scaled1-4
+1-4scaling	0.4
+outputname 	output[myReplica]
+margin		1.0
+stepspercycle   3
+temperature	0
+
+switching 	on
+switchdist	7.0
+cutoff		8.0
+pairlistdist 	9.0
+
+# Add box dimensions 
+cellBasisVector1  32.76  0.0   0.0
+cellBasisVector2   0.0  31.66  0.0
+cellBasisVector3   0.0   0.0  32.89
+
+DCDfile	alanin.dcd
+DCDfreq	1
+DCDUnitCell    yes
+velDcdFile	alanin.vel.dcd
+velDcdFreq	1
+forceDcdFile	alanin.force.dcd
+forceDcdFreq	1
+XSTFile     alanin.xst
+xstFreq		1
+
+#restartname	alanin.restart
+#restartfreq	10
+
+#langevin	on
+#langevinTemp	300.0
+#langevincol	O
+
+#constraints	on
+
+#fma		on
+
+seed		12345
+
+IMDon		yes
+IMDport		8888
+IMDfreq		1
+IMDwait		on
+IMDversion     3
+IMDsendPositions        yes
+IMDsendEnergies     yes
+IMDsendTime        yes
+IMDsendBoxDimensions       yes
+IMDsendVelocities       yes
+IMDsendForces      yes
+IMDwrapPositions       yes

imdclient/tests/hpc_testing/namd/validate_namd.sh

@@ -0,0 +1,71 @@
+#!/bin/bash
+
+NAMD_BINARY="namd3"
+CONFIG_FILE="namd_v3_nst_1.namd"
+OUTPUT_FILE="namd_output.log"
+TOPOL_PATH="alanin.pdb"
+TRAJ_PATH="alanin.dcd"
+VEL_PATH="alanin.vel.dcd"
+FORCE_PATH="alanin.force.dcd"
+
+# Parse args
+while [[ $# -gt 0 ]]; do
+    case $1 in
+        --namd_binary)
+            NAMD_BINARY="$2"
+            shift 2
+            ;;
+        --config_file)
+            CONFIG_FILE="$2"
+            shift 2
+            ;;
+        --topol_path)
+            TOPOL_PATH="$2"
+            shift 2
+            ;;
+        --traj_path)
+            TRAJ_PATH="$2"
+            shift 2
+            ;;
+        --vel_path)
+            VEL_PATH="$2"
+            shift 2
+            ;;
+        --force_path)
+            FORCE_PATH="$2"
+            shift 2
+            ;;
+        *)
+            echo "Unknown argument: $1"
+            exit 1
+            ;;
+    esac
+done
+
+# Start the simulation
+$NAMD_BINARY $CONFIG_FILE &> "$OUTPUT_FILE" &
+
+# Wait for the simulation to be ready
+await_namd_imd() {
+    grep -q "INTERACTIVE MD AWAITING CONNECTION" $OUTPUT_FILE
+}
+
+while ! await_namd_imd; do
+    echo "Waiting for NAMD IMD readiness in $OUTPUT_FILE..."
+    sleep 5
+done
+
+# Run the test
+
+echo "Running test with the following parameters:"
+echo "  Topology file: $TOPOL_PATH"
+echo "  Trajectory file: $TRAJ_PATH"
+echo "  Velocity file: $VEL_PATH"
+echo "  Force file: $FORCE_PATH"
+
+python ../../test_manual.py \
+    --topol_path "$TOPOL_PATH" \
+    --traj_path "$TRAJ_PATH" \
+    --vel_path "$VEL_PATH" \
+    --force_path "$FORCE_PATH" \
+    --first_frame 0

imdclient/tests/server.py

@@ -93,7 +93,7 @@ class InThreadIMDServer:
             positions,
             wrapped_coords,
             velocities,
-            forces
+            forces,
         )
         logger.debug(f"InThreadIMDServer: Sending session info")
         self.conn.sendall(sinfo)
@@ -101,14 +101,6 @@ class InThreadIMDServer:
     def join_accept_thread(self):
         self.accept_thread.join()
 
-    def _expect_go(self):
-        logger.debug(f"InThreadIMDServer: Waiting for go")
-        head_buf = bytearray(IMDHEADERSIZE)
-        read_into_buf(self.conn, head_buf)
-        header = IMDHeader(head_buf)
-        if header.type != IMDHeaderType.IMD_GO:
-            raise ValueError("Expected IMD_GO packet, got something else")
-
     def send_frames(self, start, end):
         for i in range(start, end):
             self.send_frame(i)
@@ -126,7 +118,7 @@ class InThreadIMDServer:
             )
 
             self.conn.sendall(time_header + time)
-        
+
         if self.imdsinfo.energies:
             energy_header = create_header_bytes(IMDHeaderType.IMD_ENERGIES, 1)
             energies = create_energy_bytes(
@@ -183,7 +175,6 @@ class InThreadIMDServer:
 
             self.conn.sendall(force_header + force)
 
-        
     def expect_packet(self, packet_type, expected_length=None):
         head_buf = bytearray(IMDHEADERSIZE)
         read_into_buf(self.conn, head_buf)

imdclient/tests/test_imdclient.py

@@ -69,6 +69,7 @@ class TestIMDClientV3:
             buffer_size=imdframe_memsize(universe.trajectory.n_atoms, imdsinfo)
             * 2,
         )
+        server.join_accept_thread()
         yield server, client
         client.stop()
         server.cleanup()
@@ -84,6 +85,7 @@ class TestIMDClientV3:
             port,
             universe.trajectory.n_atoms,
         )
+        server.join_accept_thread()
         yield server, client
         client.stop()
         server.cleanup()
@@ -149,6 +151,22 @@ class TestIMDClientV3:
         # server should receive disconnect from client (though it doesn't have to do anything)
         server.expect_packet(IMDHeaderType.IMD_DISCONNECT)
 
+    @pytest.mark.parametrize("cont", [True, False])
+    def test_continue_after_disconnect(self, universe, imdsinfo, port, cont):
+        server = InThreadIMDServer(universe.trajectory)
+        server.set_imdsessioninfo(imdsinfo)
+        server.handshake_sequence("localhost", port, first_frame=False)
+        client = IMDClient(
+            f"localhost",
+            port,
+            universe.trajectory.n_atoms,
+            continue_after_disconnect=cont,
+        )
+        server.join_accept_thread()
+        server.expect_packet(
+            IMDHeaderType.IMD_WAIT, expected_length=(int)(not cont)
+        )
+
 
 class TestIMDClientV3ContextManager:
     @pytest.fixture

imdclient/tests/test_imdreader.py

@@ -171,7 +171,9 @@ class TestIMDReaderBaseAPI(MultiframeReaderTest):
             decimal=ref.prec,
         )
 
-    @pytest.mark.skip(reason="Stream-based reader can only be read iteratively")
+    @pytest.mark.skip(
+        reason="Stream-based reader can only be read iteratively"
+    )
     def test_changing_dimensions(self, ref, reader):
         if ref.changing_dimensions:
             reader.rewind()
@@ -656,3 +658,60 @@ def test_n_atoms_mismatch():
             f"imd://localhost:{port}",
             n_atoms=universe.trajectory.n_atoms + 1,
         )
+
+# raise errors for incompatible methods
+class TestIMDReaderBaseAPIExceptions():
+
+    @pytest.fixture
+    def reader(self):
+        universe = mda.Universe(COORDINATES_TOPOLOGY, COORDINATES_H5MD)
+        imdsinfo = create_default_imdsinfo_v3()
+        port = get_free_port()
+        server = InThreadIMDServer(universe.trajectory)
+        server.set_imdsessioninfo(imdsinfo)
+        server.handshake_sequence("localhost", port, first_frame=True)
+
+        reader = IMDReader(
+            f"imd://localhost:{port}", n_atoms=universe.trajectory.n_atoms
+        )
+        server.send_frames(1, 5)
+        yield reader
+        server.cleanup()
+
+    # test copy method
+    def test_copy_raises_notimplemented_error(self, reader):
+        with pytest.raises(NotImplementedError):
+            reader.copy()
+
+    # test _reopen method
+    def test_reopen_raises_runtime_error_on_second_call(self, reader):
+        # First call should be fine
+        reader._reopen()
+        # Second call should raise RuntimeError
+        with pytest.raises(RuntimeError):
+            reader._reopen()
+    
+    # test n_frames
+    def test_n_frames_raises_runtime_error(self, reader):
+        with pytest.raises(RuntimeError):
+            reader.n_frames()
+
+    # test __len__
+    def test_len_raises_runtime_error(self, reader):
+        with pytest.raises(RuntimeError):
+            reader.__len__()
+    
+    # test rewind method
+    def test_rewind_raises_error(self, reader):
+        with pytest.raises(RuntimeError):
+            reader.rewind()
+
+    # Test __getstate__ method
+    def test_getstate_raises_notimplemented_error(self, reader):
+        with pytest.raises(NotImplementedError):
+            reader.__getstate__()
+
+    # Test __setstate__ method
+    def test_setstate_raises_notimplemented_error(self, reader):
+        with pytest.raises(NotImplementedError):
+            reader.__setstate__(None)