diff --git a/package/AUTHORS b/package/AUTHORS index 01b535d69fe..4fcf466fd99 100644 --- a/package/AUTHORS +++ b/package/AUTHORS @@ -209,6 +209,7 @@ Chronological list of authors - Vishal Parmar - Moritz Schaeffler - Xu Hong Chen + - Domenico Marson External code ------------- diff --git a/package/CHANGELOG b/package/CHANGELOG index 66a0fbd4138..1de34d5be7e 100644 --- a/package/CHANGELOG +++ b/package/CHANGELOG @@ -16,10 +16,11 @@ The rules for this file: ??/??/?? IAlibay, pgbarletta, mglagolev, hmacdope, manuel.nuno.melo, chrispfae, ooprathamm, MeetB7, BFedder, v-parmar, MoSchaeffler, jbarnoud, jandom, - xhgchen, jaclark5 + xhgchen, jaclark5, DrDomenicoMarson * 2.5.0 Fixes + * Fix for NetCDF trajectories without `time` variable (Issue #4073) * Allows shape_parameter and asphericity to yield per residue quantities (Issue #3002, PR #3905) * Add tests for "No path data" exception raise in test_psa.py (Issue #4036) diff --git a/package/MDAnalysis/coordinates/TRJ.py b/package/MDAnalysis/coordinates/TRJ.py index 1c342ded68f..2d41ff09207 100644 --- a/package/MDAnalysis/coordinates/TRJ.py +++ b/package/MDAnalysis/coordinates/TRJ.py @@ -528,7 +528,7 @@ def __init__(self, filename, n_atoms=None, mmap=None, **kwargs): # len(dimensions['frame']) == 10: in any case, we need to get # the number of frames from somewhere such as the time variable: if self.n_frames is None: - self.n_frames = self.trjfile.variables['time'].shape[0] + self.n_frames = self.trjfile.variables['coordinates'].shape[0] except KeyError: errmsg = (f"NCDF trajectory {self.filename} does not contain " f"frame information") @@ -544,7 +544,17 @@ def __init__(self, filename, n_atoms=None, mmap=None, **kwargs): # checks for not-implemented features (other units would need to be # hacked into MDAnalysis.units) - self._verify_units(self.trjfile.variables['time'].units, 'picosecond') + try: + self._verify_units(self.trjfile.variables['time'].units, 'picosecond') + self.has_time = True + except KeyError: + self.has_time = False + wmsg = ("NCDF trajectory does not contain `time` information;" + " `time` will be set as an increasing index") + warnings.warn(wmsg) + logger.warning(wmsg) + + self._verify_units(self.trjfile.variables['coordinates'].units, 'angstrom') @@ -640,7 +650,8 @@ def _read_frame(self, frame): self.n_frames)) # note: self.trjfile.variables['coordinates'].shape == (frames, n_atoms, 3) ts._pos[:] = self._get_var_and_scale('coordinates', frame) - ts.time = self._get_var_and_scale('time', frame) + if self.has_time: + ts.time = self._get_var_and_scale('time', frame) if self.has_velocities: ts._velocities[:] = self._get_var_and_scale('velocities', frame) if self.has_forces: @@ -685,7 +696,7 @@ def _get_dt(self): try: t1 = self.trjfile.variables['time'][1] t0 = self.trjfile.variables['time'][0] - except IndexError: + except (IndexError, KeyError): raise AttributeError return t1 - t0 diff --git a/testsuite/MDAnalysisTests/coordinates/test_netcdf.py b/testsuite/MDAnalysisTests/coordinates/test_netcdf.py index 13f656fc0af..c009682421e 100644 --- a/testsuite/MDAnalysisTests/coordinates/test_netcdf.py +++ b/testsuite/MDAnalysisTests/coordinates/test_netcdf.py @@ -35,7 +35,8 @@ from MDAnalysisTests.datafiles import (PFncdf_Top, PFncdf_Trj, GRO, TRR, XYZ_mini, - PRM_NCBOX, TRJ_NCBOX, DLP_CONFIG) + PRM_NCBOX, TRJ_NCBOX, DLP_CONFIG, + CPPTRAJ_TRAJ_TOP, CPPTRAJ_TRAJ) from MDAnalysisTests.coordinates.test_trj import _TRJReaderTest from MDAnalysisTests.coordinates.reference import (RefVGV, RefTZ2) from MDAnalysisTests import make_Universe @@ -299,6 +300,34 @@ def test_box(self, universe, index, expected): assert_almost_equal(self.box_refs[expected], universe.dimensions) +class TestNCDFReader4(object): + """NCDF Trajectory exported by cpptaj, without `time` variable.""" + prec = 3 + + @pytest.fixture(scope='class') + def u(self): + return mda.Universe(CPPTRAJ_TRAJ_TOP, + [CPPTRAJ_TRAJ, CPPTRAJ_TRAJ]) + + def test_chain_times(self, u): + """Check times entries for a chain of trajectories without + a defined time variable""" + ref_times = [0.0, 1.0, 2.0, 3.0, 4.0, 5.0] + time_list = [ts.time for ts in u.trajectory] + assert ref_times == time_list + + def test_dt(self, u): + ref = 1.0 + assert u.trajectory.dt == pytest.approx(ref) + assert u.trajectory.ts.dt == pytest.approx(ref) + + def test_warn_user_no_time_information(self, u): + wmsg = ("NCDF trajectory does not contain `time` information;" + " `time` will be set as an increasing index") + with pytest.warns(UserWarning, match=wmsg): + u2 = mda.Universe(CPPTRAJ_TRAJ_TOP, CPPTRAJ_TRAJ) + + class _NCDFGenerator(object): """A class for generating abitrary ncdf files and exhaustively test edge cases which might not be found in the wild""" diff --git a/testsuite/MDAnalysisTests/data/Amber/cpptraj_traj.nc b/testsuite/MDAnalysisTests/data/Amber/cpptraj_traj.nc new file mode 100644 index 00000000000..d8dc11cc3f7 Binary files /dev/null and b/testsuite/MDAnalysisTests/data/Amber/cpptraj_traj.nc differ diff --git a/testsuite/MDAnalysisTests/data/Amber/cpptraj_traj.prmtop b/testsuite/MDAnalysisTests/data/Amber/cpptraj_traj.prmtop new file mode 100644 index 00000000000..df8f1e30e88 --- /dev/null +++ b/testsuite/MDAnalysisTests/data/Amber/cpptraj_traj.prmtop @@ -0,0 +1,717 @@ +%VERSION VERSION_STAMP = V0001.000 DATE = 03/15/23 21:14:40 +%FLAG TITLE +%FORMAT(20a4) +default_name +%FLAG POINTERS +%FORMAT(10I8) + 84 10 37 48 86 65 166 197 0 0 + 455 5 48 65 197 33 70 86 37 0 + 0 0 0 0 0 0 0 1 24 0 + 0 +%FLAG ATOM_NAME +%FORMAT(20a4) +N H1 H2 H3 CA HA CB HB2 HB3 CG OD1 OD2 C O N H CA HA CB HB2 +HB3 CG OD1 OD2 C O N H CA HA CB HB2 HB3 CG CD1 HD1 NE1 HE1 CE2 CZ2 +HZ2 CH2 HH2 CZ3 HZ3 CE3 HE3 CD2 C O N H CA HA CB HB2 HB3 CG HG2 HG3 +CD OE1 OE2 C O N H CA HA CB HB CG2 HG21HG22HG23CG1 HG12HG13CD1 HD11 +HD12HD13C O +%FLAG CHARGE +%FORMAT(5E16.8) + 1.42498386E+00 4.00890600E+00 4.00890600E+00 4.00890600E+00 5.32091160E-01 + 2.07916443E+00 -4.28224050E-01 -3.07956870E-01 -3.07956870E-01 1.49313526E+01 + -1.47309073E+01 -1.47309073E+01 1.02427548E+01 -1.07311125E+01 -9.40817349E+00 + 5.35006728E+00 6.94269630E-01 1.60356240E+00 -5.52135690E-01 -2.22312060E-01 + -2.22312060E-01 1.45669066E+01 -1.46033512E+01 -1.46033512E+01 9.77808618E+00 + -1.06035564E+01 -7.57501011E+00 4.95464337E+00 -5.01113250E-01 2.04636429E+00 + -9.11115000E-02 6.17735970E-01 6.17735970E-01 -2.57845545E+00 -2.98481274E+00 + 3.75743826E+00 -6.22838214E+00 6.21744876E+00 2.51467740E+00 -4.73962023E+00 + 2.86454556E+00 -2.06640882E+00 2.58209991E+00 -3.59343756E+00 2.63676681E+00 + -4.34966301E+00 3.09779100E+00 2.26503189E+00 1.08841798E+01 -1.03484442E+01 + -9.40817349E+00 5.35006728E+00 7.23425310E-01 2.01356415E+00 1.02044880E+00 + -3.15245790E-01 -3.15245790E-01 2.47823280E-01 -7.74447750E-01 -7.74447750E-01 + 1.46762404E+01 -1.49204192E+01 -1.49204192E+01 9.77808618E+00 -1.06035564E+01 + -7.57501011E+00 4.95464337E+00 -1.08787131E+00 1.58351787E+00 2.37436569E+00 + 3.40757010E-01 -5.83842492E+00 1.60720686E+00 1.60720686E+00 1.60720686E+00 + -7.83558900E-01 4.30046280E-01 4.30046280E-01 -1.20267180E+00 3.38934780E-01 + 3.38934780E-01 3.38934780E-01 1.08841798E+01 -1.03484442E+01 +%FLAG ATOMIC_NUMBER +%FORMAT(10I8) + 7 1 1 1 6 1 6 1 1 6 + 8 8 6 8 7 1 6 1 6 1 + 1 6 8 8 6 8 7 1 6 1 + 6 1 1 6 6 1 7 1 6 6 + 1 6 1 6 1 6 1 6 6 8 + 7 1 6 1 6 1 1 6 1 1 + 6 8 8 6 8 7 1 6 1 6 + 1 6 1 1 1 6 1 1 6 1 + 1 1 6 8 +%FLAG MASS +%FORMAT(5E16.8) + 1.40100000E+01 1.00800000E+00 1.00800000E+00 1.00800000E+00 1.20100000E+01 + 1.00800000E+00 1.20100000E+01 1.00800000E+00 1.00800000E+00 1.20100000E+01 + 1.60000000E+01 1.60000000E+01 1.20100000E+01 1.60000000E+01 1.40100000E+01 + 1.00800000E+00 1.20100000E+01 1.00800000E+00 1.20100000E+01 1.00800000E+00 + 1.00800000E+00 1.20100000E+01 1.60000000E+01 1.60000000E+01 1.20100000E+01 + 1.60000000E+01 1.40100000E+01 1.00800000E+00 1.20100000E+01 1.00800000E+00 + 1.20100000E+01 1.00800000E+00 1.00800000E+00 1.20100000E+01 1.20100000E+01 + 1.00800000E+00 1.40100000E+01 1.00800000E+00 1.20100000E+01 1.20100000E+01 + 1.00800000E+00 1.20100000E+01 1.00800000E+00 1.20100000E+01 1.00800000E+00 + 1.20100000E+01 1.00800000E+00 1.20100000E+01 1.20100000E+01 1.60000000E+01 + 1.40100000E+01 1.00800000E+00 1.20100000E+01 1.00800000E+00 1.20100000E+01 + 1.00800000E+00 1.00800000E+00 1.20100000E+01 1.00800000E+00 1.00800000E+00 + 1.20100000E+01 1.60000000E+01 1.60000000E+01 1.20100000E+01 1.60000000E+01 + 1.40100000E+01 1.00800000E+00 1.20100000E+01 1.00800000E+00 1.20100000E+01 + 1.00800000E+00 1.20100000E+01 1.00800000E+00 1.00800000E+00 1.00800000E+00 + 1.20100000E+01 1.00800000E+00 1.00800000E+00 1.20100000E+01 1.00800000E+00 + 1.00800000E+00 1.00800000E+00 1.20100000E+01 1.60000000E+01 +%FLAG ATOM_TYPE_INDEX +%FORMAT(10I8) + 1 2 2 2 3 4 3 5 5 6 + 7 7 6 7 1 2 3 8 3 5 + 5 6 7 7 6 7 1 2 3 8 + 3 5 5 6 6 9 1 2 6 6 + 10 6 10 6 10 6 10 6 6 7 + 1 2 3 8 3 5 5 3 5 5 + 6 7 7 6 7 1 2 3 8 3 + 5 3 5 5 5 3 5 5 3 5 + 5 5 6 7 +%FLAG NUMBER_EXCLUDED_ATOMS +%FORMAT(10I8) + 12 6 5 4 12 7 8 5 4 3 + 1 1 7 3 10 4 12 7 8 5 + 4 3 1 1 7 3 10 4 12 7 + 12 5 4 11 7 4 7 3 8 7 + 4 6 3 4 3 2 1 1 7 3 + 10 4 13 7 11 6 5 6 4 3 + 2 1 1 7 3 9 4 13 6 14 + 9 8 3 2 1 7 5 4 3 2 + 1 1 1 1 +%FLAG NONBONDED_PARM_INDEX +%FORMAT(10I8) + 1 2 4 7 11 16 22 29 37 46 + 2 3 5 8 12 17 23 30 38 47 + 4 5 6 9 13 18 24 31 39 48 + 7 8 9 10 14 19 25 32 40 49 + 11 12 13 14 15 20 26 33 41 50 + 16 17 18 19 20 21 27 34 42 51 + 22 23 24 25 26 27 28 35 43 52 + 29 30 31 32 33 34 35 36 44 53 + 37 38 39 40 41 42 43 44 45 54 + 46 47 48 49 50 51 52 53 54 55 +%FLAG RESIDUE_LABEL +%FORMAT(20a4) +ASP ASP TRP GLU ILE +%FLAG RESIDUE_POINTER +%FORMAT(10I8) + 1 15 27 51 66 +%FLAG BOND_FORCE_CONSTANT +%FORMAT(5E16.8) + 5.70000000E+02 4.90000000E+02 6.56000000E+02 3.17000000E+02 3.10000000E+02 + 3.17000000E+02 3.67000000E+02 3.37000000E+02 4.69000000E+02 4.69000000E+02 + 4.69000000E+02 4.47000000E+02 4.28000000E+02 4.27000000E+02 5.46000000E+02 + 3.88000000E+02 3.17000000E+02 3.10000000E+02 3.10000000E+02 3.10000000E+02 + 3.10000000E+02 3.10000000E+02 3.10000000E+02 3.40000000E+02 3.40000000E+02 + 4.34000000E+02 3.40000000E+02 4.34000000E+02 3.67000000E+02 4.34000000E+02 + 3.67000000E+02 3.40000000E+02 3.40000000E+02 +%FLAG BOND_EQUIL_VALUE +%FORMAT(5E16.8) + 1.22900000E+00 1.33500000E+00 1.25000000E+00 1.52200000E+00 1.52600000E+00 + 1.52200000E+00 1.47100000E+00 1.44900000E+00 1.40400000E+00 1.40000000E+00 + 1.40000000E+00 1.41900000E+00 1.38000000E+00 1.38100000E+00 1.35200000E+00 + 1.45900000E+00 1.49500000E+00 1.52600000E+00 1.52600000E+00 1.52600000E+00 + 1.52600000E+00 1.52600000E+00 1.52600000E+00 1.09000000E+00 1.09000000E+00 + 1.01000000E+00 1.09000000E+00 1.01000000E+00 1.08000000E+00 1.01000000E+00 + 1.08000000E+00 1.09000000E+00 1.09000000E+00 +%FLAG ANGLE_FORCE_CONSTANT +%FORMAT(5E16.8) + 8.00000000E+01 5.00000000E+01 8.00000000E+01 6.30000000E+01 7.00000000E+01 + 6.30000000E+01 8.00000000E+01 7.00000000E+01 8.00000000E+01 8.00000000E+01 + 8.00000000E+01 6.30000000E+01 6.30000000E+01 6.30000000E+01 6.30000000E+01 + 6.30000000E+01 6.30000000E+01 7.00000000E+01 7.00000000E+01 6.30000000E+01 + 7.00000000E+01 7.00000000E+01 6.30000000E+01 6.30000000E+01 6.30000000E+01 + 7.00000000E+01 7.00000000E+01 6.30000000E+01 8.00000000E+01 6.30000000E+01 + 4.00000000E+01 4.00000000E+01 6.30000000E+01 4.00000000E+01 4.00000000E+01 + 4.00000000E+01 8.00000000E+01 5.00000000E+01 5.00000000E+01 3.50000000E+01 + 5.00000000E+01 5.00000000E+01 5.00000000E+01 5.00000000E+01 3.50000000E+01 + 5.00000000E+01 5.00000000E+01 5.00000000E+01 5.00000000E+01 5.00000000E+01 + 5.00000000E+01 5.00000000E+01 5.00000000E+01 5.00000000E+01 5.00000000E+01 + 5.00000000E+01 5.00000000E+01 5.00000000E+01 3.50000000E+01 5.00000000E+01 + 5.00000000E+01 5.00000000E+01 5.00000000E+01 5.00000000E+01 5.00000000E+01 + 5.00000000E+01 5.00000000E+01 5.00000000E+01 5.00000000E+01 5.00000000E+01 +%FLAG ANGLE_EQUIL_VALUE +%FORMAT(5E16.8) + 2.14501057E+00 2.12755727E+00 2.19911580E+00 1.93906163E+00 2.04203610E+00 + 1.93906163E+00 2.10137732E+00 2.03505478E+00 1.94080696E+00 1.94080696E+00 + 1.91462701E+00 1.92160833E+00 2.09439600E+00 2.09439600E+00 2.14151991E+00 + 2.09439600E+00 2.02807346E+00 2.31779824E+00 1.82212452E+00 1.85703112E+00 + 1.94778828E+00 1.89717371E+00 1.89891904E+00 2.35445017E+00 1.93906163E+00 + 2.18166250E+00 2.24449438E+00 2.01760148E+00 1.91462701E+00 1.93906163E+00 + 1.91113635E+00 1.91113635E+00 1.93906163E+00 1.91113635E+00 1.91113635E+00 + 1.91113635E+00 1.91462701E+00 2.09439600E+00 1.91113635E+00 1.91113635E+00 + 1.91113635E+00 1.91113635E+00 1.91113635E+00 1.91113635E+00 1.91113635E+00 + 1.91113635E+00 1.91113635E+00 1.91113635E+00 2.06018753E+00 1.91113635E+00 + 2.09439600E+00 2.09439600E+00 2.09439600E+00 2.14850123E+00 2.09439600E+00 + 2.09439600E+00 2.09439600E+00 1.91113635E+00 1.91113635E+00 1.91113635E+00 + 1.91113635E+00 1.91113635E+00 1.91113635E+00 1.91113635E+00 1.91113635E+00 + 1.91113635E+00 1.91113635E+00 1.91113635E+00 1.91113635E+00 1.91113635E+00 +%FLAG DIHEDRAL_FORCE_CONSTANT +%FORMAT(5E16.8) + 2.50000000E+00 2.00000000E+00 1.80000000E+00 8.00000000E-01 0.00000000E+00 + 0.00000000E+00 2.70000000E-01 4.20000000E-01 4.24000000E-01 4.59000000E-01 + 5.80000000E-02 1.54000000E-01 0.00000000E+00 2.00000000E-01 2.00000000E-01 + 4.00000000E-01 7.69000000E-01 0.00000000E+00 3.10000000E-02 2.15400000E+00 + 6.47000000E-01 8.90000000E-02 4.50000000E-01 1.58000000E+00 5.50000000E-01 + 3.62500000E+00 3.00000000E+00 3.50000000E+00 6.52500000E+00 1.67500000E+00 + 1.52500000E+00 1.70000000E-02 3.53000000E-01 2.34000000E-01 7.40000000E-02 + 1.50000000E+00 3.65000000E-01 4.08000000E-01 8.19000000E-01 9.50000000E-02 + 7.90000000E-02 3.13000000E-01 3.10000000E-02 4.21000000E-01 3.93000000E-01 + 1.44000000E-01 1.45000000E-01 3.90000000E-01 6.40000000E-02 1.36700000E+00 + 2.22000000E-01 6.08000000E-01 5.60000000E-02 1.00000000E-01 1.84000000E-01 + 7.80000000E-02 1.62000000E-01 7.35000000E-01 1.13000000E-01 1.15000000E-01 + 4.06000000E-01 2.89000000E-01 1.48000000E-01 1.12000000E-01 2.02000000E-01 + 7.70000000E-02 1.07000000E-01 2.24000000E-01 4.47000000E-01 5.30000000E-02 + 2.30000000E-01 3.37000000E-01 2.16000000E-01 1.00000000E-03 3.10000000E-01 + 1.44000000E-01 9.70000000E-02 1.05000000E+01 0.00000000E+00 1.10000000E+00 + 1.55555556E-01 8.00000000E-01 8.00000000E-02 1.50000000E-01 1.60000000E-01 + 1.00000000E+00 +%FLAG DIHEDRAL_PERIODICITY +%FORMAT(5E16.8) + 2.00000000E+00 1.00000000E+00 2.00000000E+00 3.00000000E+00 4.00000000E+00 + 1.00000000E+00 2.00000000E+00 3.00000000E+00 1.00000000E+00 2.00000000E+00 + 3.00000000E+00 4.00000000E+00 2.00000000E+00 1.00000000E+00 2.00000000E+00 + 3.00000000E+00 2.00000000E+00 3.00000000E+00 4.00000000E+00 1.00000000E+00 + 2.00000000E+00 4.00000000E+00 1.00000000E+00 2.00000000E+00 3.00000000E+00 + 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 + 2.00000000E+00 1.00000000E+00 2.00000000E+00 3.00000000E+00 4.00000000E+00 + 2.00000000E+00 1.00000000E+00 2.00000000E+00 3.00000000E+00 4.00000000E+00 + 1.00000000E+00 2.00000000E+00 4.00000000E+00 1.00000000E+00 2.00000000E+00 + 3.00000000E+00 4.00000000E+00 2.00000000E+00 4.00000000E+00 1.00000000E+00 + 2.00000000E+00 3.00000000E+00 4.00000000E+00 1.00000000E+00 2.00000000E+00 + 4.00000000E+00 1.00000000E+00 2.00000000E+00 3.00000000E+00 4.00000000E+00 + 1.00000000E+00 2.00000000E+00 3.00000000E+00 4.00000000E+00 1.00000000E+00 + 2.00000000E+00 3.00000000E+00 4.00000000E+00 1.00000000E+00 2.00000000E+00 + 4.00000000E+00 1.00000000E+00 2.00000000E+00 4.00000000E+00 1.00000000E+00 + 2.00000000E+00 4.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 + 3.00000000E+00 1.00000000E+00 3.00000000E+00 3.00000000E+00 3.00000000E+00 + 2.00000000E+00 +%FLAG DIHEDRAL_PHASE +%FORMAT(5E16.8) + 3.14159400E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 + 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 3.14159400E+00 + 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 + 0.00000000E+00 3.14159400E+00 0.00000000E+00 3.14159400E+00 3.14159400E+00 + 3.14159400E+00 0.00000000E+00 3.14159400E+00 3.14159400E+00 3.14159400E+00 + 3.14159400E+00 3.14159400E+00 3.14159400E+00 3.14159400E+00 3.14159400E+00 + 3.14159400E+00 3.14159400E+00 3.14159400E+00 0.00000000E+00 0.00000000E+00 + 3.14159400E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 3.14159400E+00 + 0.00000000E+00 3.14159400E+00 0.00000000E+00 3.14159400E+00 3.14159400E+00 + 0.00000000E+00 0.00000000E+00 3.14159400E+00 0.00000000E+00 3.14159400E+00 + 3.14159400E+00 3.14159400E+00 3.14159400E+00 3.14159400E+00 3.14159400E+00 + 0.00000000E+00 0.00000000E+00 3.14159400E+00 0.00000000E+00 0.00000000E+00 + 3.14159400E+00 3.14159400E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 + 3.14159400E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 + 0.00000000E+00 0.00000000E+00 3.14159400E+00 3.14159400E+00 0.00000000E+00 + 3.14159400E+00 3.14159400E+00 3.14159400E+00 3.14159400E+00 3.14159400E+00 + 0.00000000E+00 0.00000000E+00 3.14159400E+00 0.00000000E+00 0.00000000E+00 + 3.14159400E+00 +%FLAG SCEE_SCALE_FACTOR +%FORMAT(5E16.8) + 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 + 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 + 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 + 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 + 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 + 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 + 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 + 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 + 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 + 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 + 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 + 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 + 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 + 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 + 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 + 1.20000000E+00 1.20000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 + 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 1.20000000E+00 + 0.00000000E+00 +%FLAG SCNB_SCALE_FACTOR +%FORMAT(5E16.8) + 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 + 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 + 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 + 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 + 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 + 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 + 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 + 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 + 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 + 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 + 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 + 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 + 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 + 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 + 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 + 2.00000000E+00 2.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 + 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 2.00000000E+00 + 0.00000000E+00 +%FLAG SOLTY +%FORMAT(5E16.8) + 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 + 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 + 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 + 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 + 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 + 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 + 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 + 0.00000000E+00 0.00000000E+00 +%FLAG LENNARD_JONES_ACOEF +%FORMAT(5E16.8) + 9.44293233E+05 2.12601181E+03 1.39982777E-01 9.95480466E+05 2.56678134E+03 + 1.04308023E+06 2.01791425E+04 9.14716912E+00 2.27401052E+04 2.01823541E+02 + 8.96776989E+04 1.07193646E+02 9.71708117E+04 1.41077189E+03 7.51607703E+03 + 8.82619071E+05 2.27577561E+03 9.24822270E+05 2.01619733E+04 8.61541883E+04 + 8.19971662E+05 6.06829342E+05 1.02595236E+03 6.47841731E+05 1.12780457E+04 + 5.44261042E+04 5.74393458E+05 3.79876399E+05 6.20665997E+04 5.94667300E+01 + 6.78771368E+04 8.79040886E+02 4.98586848E+03 6.01816484E+04 3.69471530E+04 + 3.25969625E+03 6.58473870E+04 6.63368273E+01 7.18621074E+04 9.55000044E+02 + 5.34045360E+03 6.37148278E+04 3.93690817E+04 3.50301067E+03 3.76169105E+03 + 7.91627154E+04 8.90987508E+01 8.59947003E+04 1.21014911E+03 6.55825601E+03 + 7.62451550E+04 4.77908183E+04 4.33325458E+03 4.64559155E+03 5.71629601E+03 +%FLAG LENNARD_JONES_BCOEF +%FORMAT(5E16.8) + 8.01323529E+02 2.09604198E+01 9.37598976E-02 7.36907417E+02 2.06278363E+01 + 6.75612247E+02 6.45756063E+01 7.57919667E-01 6.13981767E+01 3.56012899E+00 + 1.36131731E+02 2.59456373E+00 1.26919150E+02 9.41257003E+00 2.17257828E+01 + 6.53361429E+02 1.82891803E+01 5.99015525E+02 5.44372326E+01 1.12529845E+02 + 5.31102864E+02 6.77220874E+02 1.53505284E+01 6.26720080E+02 5.08951803E+01 + 1.11805549E+02 5.55666448E+02 5.64885984E+02 1.13252061E+02 1.93248820E+00 + 1.06076943E+02 7.42992380E+00 1.76949863E+01 9.40505980E+01 9.21192136E+01 + 1.43076527E+01 1.15327881E+02 2.01792524E+00 1.07908863E+02 7.65648470E+00 + 1.81057616E+01 9.56748258E+01 9.40124296E+01 1.46638650E+01 1.50233639E+01 + 1.26451907E+02 2.33864085E+00 1.18043746E+02 8.61880722E+00 2.00642027E+01 + 1.04660679E+02 1.03580945E+02 1.63092814E+01 1.66953734E+01 1.85196588E+01 +%FLAG BONDS_INC_HYDROGEN +%FORMAT(10I8) + 18 21 24 18 24 24 12 15 25 0 + 3 26 0 6 26 0 9 26 54 57 + 24 54 60 24 48 51 27 42 45 28 + 135 138 29 129 132 29 123 126 29 117 + 120 29 108 111 30 102 105 31 90 93 + 32 90 96 32 84 87 27 78 81 28 + 171 174 24 171 177 24 162 165 24 162 + 168 24 156 159 27 150 153 28 234 237 + 32 234 240 32 234 243 32 225 228 24 + 225 231 24 213 216 32 213 219 32 213 + 222 32 207 210 33 201 204 27 195 198 + 28 +%FLAG BONDS_WITHOUT_HYDROGEN +%FORMAT(10I8) + 36 39 1 36 42 2 27 30 3 27 + 33 3 18 27 4 12 18 5 12 36 + 6 0 12 7 72 75 1 72 78 2 + 63 66 3 63 69 3 54 63 4 48 + 54 5 48 72 6 42 48 8 144 147 + 1 144 150 2 135 141 9 129 135 10 + 123 129 10 117 123 10 114 117 11 114 + 141 12 108 114 13 102 108 14 99 102 + 15 99 141 16 90 99 17 84 90 18 + 84 144 6 78 84 8 189 192 1 189 + 195 2 180 183 3 180 186 3 171 180 + 4 162 171 19 156 162 5 156 189 6 + 150 156 8 246 249 1 225 234 20 207 + 213 21 207 225 22 201 207 23 201 246 + 6 195 201 8 +%FLAG ANGLES_INC_HYDROGEN +%FORMAT(10I8) + 36 42 45 38 24 18 27 39 21 18 + 24 40 21 18 27 39 15 12 18 41 + 15 12 36 42 12 18 21 43 12 18 + 24 43 9 0 12 44 6 0 9 45 + 6 0 12 44 3 0 6 45 3 0 + 9 45 3 0 12 44 0 12 15 46 + 72 78 81 38 60 54 63 39 57 54 + 60 40 57 54 63 39 51 48 54 47 + 51 48 72 48 48 54 57 43 48 54 + 60 43 45 42 48 49 42 48 51 50 + 144 150 153 38 138 135 141 51 132 129 + 135 52 129 135 138 52 126 123 129 52 + 123 129 132 52 120 117 123 52 117 123 + 126 52 114 117 120 53 111 108 114 54 + 105 102 108 55 102 108 111 56 99 102 + 105 57 96 90 99 58 93 90 96 59 + 93 90 99 58 87 84 90 60 87 84 + 144 48 84 90 93 61 84 90 96 61 + 81 78 84 49 78 84 87 50 189 195 + 198 38 177 171 180 39 174 171 177 40 + 174 171 180 39 168 162 171 62 165 162 + 168 40 165 162 171 62 162 171 174 62 + 162 171 177 62 159 156 162 47 159 156 + 189 48 156 162 165 43 156 162 168 43 + 153 150 156 49 150 156 159 50 240 234 + 243 59 237 234 240 59 237 234 243 59 + 231 225 234 63 228 225 231 40 228 225 + 234 63 225 234 237 64 225 234 240 64 + 225 234 243 64 219 213 222 59 216 213 + 219 59 216 213 222 59 210 207 213 65 + 210 207 225 66 207 213 216 67 207 213 + 219 67 207 213 222 67 207 225 228 68 + 207 225 231 68 204 201 207 69 204 201 + 246 48 201 207 210 70 198 195 201 49 + 195 201 204 50 +%FLAG ANGLES_WITHOUT_HYDROGEN +%FORMAT(10I8) + 39 36 42 1 36 42 48 2 30 27 + 33 3 18 12 36 4 18 27 30 5 + 18 27 33 5 12 18 27 6 12 36 + 39 7 12 36 42 8 0 12 18 9 + 0 12 36 10 75 72 78 1 72 78 + 84 2 66 63 69 3 54 48 72 4 + 54 63 66 5 54 63 69 5 48 54 + 63 6 48 72 75 7 48 72 78 8 + 42 48 54 11 42 48 72 12 147 144 + 150 1 144 150 156 2 129 135 141 13 + 123 129 135 14 117 114 141 15 117 123 + 129 14 114 117 123 16 114 141 135 17 + 108 114 117 18 108 114 141 19 102 99 + 141 20 102 108 114 21 99 102 108 22 + 99 141 114 23 99 141 135 24 90 84 + 144 25 90 99 102 26 90 99 141 27 + 84 90 99 28 84 144 147 7 84 144 + 150 8 78 84 90 29 78 84 144 12 + 192 189 195 1 189 195 201 2 183 180 + 186 3 171 180 183 5 171 180 186 5 + 162 156 189 4 162 171 180 30 156 162 + 171 31 156 189 192 7 156 189 195 8 + 150 156 162 11 150 156 189 12 213 207 + 225 32 207 201 246 33 207 225 234 34 + 201 207 213 35 201 207 225 36 201 246 + 249 7 195 201 207 37 195 201 246 12 +%FLAG DIHEDRALS_INC_HYDROGEN +%FORMAT(10I8) + 39 36 42 45 2 39 36 -42 45 1 + 36 42 48 51 13 24 18 12 36 81 + 24 18 27 30 13 24 18 27 33 13 + 21 18 12 36 81 21 18 27 30 13 + 21 18 27 33 13 15 12 18 21 81 + 15 12 18 24 81 15 12 18 27 81 + 15 12 36 39 13 15 12 36 42 13 + 12 36 42 45 1 9 0 12 15 81 + 9 0 12 18 81 9 0 12 36 81 + 6 0 12 15 81 6 0 12 18 81 + 6 0 12 36 81 3 0 12 15 81 + 3 0 12 18 81 3 0 12 36 81 + 0 12 18 21 81 0 12 18 24 81 + 75 72 78 81 2 75 72 -78 81 1 + 72 78 84 87 13 60 54 48 72 81 + 60 54 63 66 13 60 54 63 69 13 + 57 54 48 72 81 57 54 63 66 13 + 57 54 63 69 13 51 48 54 57 81 + 51 48 54 60 81 51 48 54 63 81 + 51 48 72 75 82 51 48 -72 75 13 + 51 48 -72 75 83 51 48 72 78 13 + 48 72 78 81 1 45 42 48 51 13 + 45 42 48 54 13 45 42 48 72 13 + 42 48 54 57 81 42 48 54 60 81 + 147 144 150 153 2 147 144 -150 153 1 + 144 150 156 159 13 132 129 135 138 26 + 132 129 135 141 26 126 123 129 132 26 + 126 123 129 135 26 123 129 135 138 26 + 120 117 114 141 26 120 117 123 126 26 + 120 117 123 129 26 117 123 129 132 26 + 114 117 123 126 26 114 141 135 138 28 + 111 108 114 117 31 111 108 114 141 31 + 108 114 117 120 26 105 102 99 141 29 + 105 102 108 111 36 105 102 108 114 36 + 99 102 108 111 36 99 141 135 138 28 + 96 90 84 144 81 96 90 99 102 13 + 96 90 99 141 13 93 90 84 144 81 + 93 90 99 102 13 93 90 99 141 13 + 90 99 102 105 29 87 84 90 93 81 + 87 84 90 96 81 87 84 90 99 81 + 87 84 144 147 82 87 84 -144 147 13 + 87 84 -144 147 83 87 84 144 150 13 + 84 144 150 153 1 81 78 84 87 13 + 81 78 84 90 13 81 78 84 144 13 + 78 84 90 93 81 78 84 90 96 81 + 192 189 195 198 2 192 189 -195 198 1 + 189 195 201 204 13 177 171 180 183 13 + 177 171 180 186 13 174 171 180 183 13 + 174 171 180 186 13 168 162 156 189 81 + 168 162 171 174 84 168 162 171 177 84 + 168 162 171 180 81 165 162 156 189 81 + 165 162 171 174 84 165 162 171 177 84 + 165 162 171 180 81 159 156 162 165 81 + 159 156 162 168 81 159 156 162 171 81 + 159 156 189 192 82 159 156 -189 192 13 + 159 156 -189 192 83 159 156 189 195 13 + 156 162 171 174 85 156 162 171 177 85 + 156 189 195 198 1 153 150 156 159 13 + 153 150 156 162 13 153 150 156 189 13 + 150 156 162 165 81 150 156 162 168 81 + 231 225 234 237 84 231 225 234 240 84 + 231 225 234 243 84 228 225 234 237 84 + 228 225 234 240 84 228 225 234 243 84 + 222 213 207 225 85 219 213 207 225 85 + 216 213 207 225 85 213 207 225 228 85 + 213 207 225 231 85 210 207 201 246 81 + 210 207 213 216 84 210 207 213 219 84 + 210 207 213 222 84 210 207 225 228 84 + 210 207 225 231 84 210 207 225 234 85 + 207 225 234 237 85 207 225 234 240 85 + 207 225 234 243 85 204 201 207 210 81 + 204 201 207 213 81 204 201 207 225 81 + 204 201 246 249 82 204 201 -246 249 13 + 204 201 -246 249 83 201 207 213 216 85 + 201 207 213 219 85 201 207 213 222 85 + 201 207 225 228 85 201 207 225 231 85 + 198 195 201 204 13 198 195 201 207 13 + 198 195 201 246 13 195 201 207 210 81 + 36 48 -42 -45 80 129 141 -135 -138 80 + 123 135 -129 -132 80 117 129 -123 -126 80 + 114 123 -117 -120 80 102 114 -108 -111 86 + 99 108 -102 -105 80 72 84 -78 -81 80 + 144 156 -150 -153 80 189 201 -195 -198 80 +%FLAG DIHEDRALS_WITHOUT_HYDROGEN +%FORMAT(10I8) + 39 36 42 48 1 36 42 48 54 2 + 36 42 -48 54 3 36 42 -48 54 4 + 36 42 -48 54 5 36 42 48 72 6 + 36 42 -48 72 7 36 42 -48 72 8 + 36 42 -48 72 5 27 18 12 36 9 + 27 18 -12 36 10 27 18 -12 36 11 + 27 18 -12 36 12 18 12 36 39 13 + 18 12 36 42 14 18 12 -36 42 15 + 18 12 -36 42 16 18 12 -36 42 5 + 12 18 27 30 6 12 18 -27 30 17 + 12 18 -27 30 18 12 18 -27 30 19 + 12 18 27 33 6 12 18 -27 33 17 + 12 18 -27 33 18 12 18 -27 33 19 + 12 36 42 48 1 0 12 18 27 20 + 0 12 -18 27 21 0 12 -18 27 11 + 0 12 -18 27 22 0 12 36 39 13 + 0 12 36 42 13 75 72 78 84 1 + 72 78 84 90 2 72 78 -84 90 3 + 72 78 -84 90 4 72 78 -84 90 5 + 72 78 84 144 6 72 78 -84 144 7 + 72 78 -84 144 8 72 78 -84 144 5 + 63 54 48 72 9 63 54 -48 72 10 + 63 54 -48 72 11 63 54 -48 72 12 + 54 48 72 75 13 54 48 72 78 14 + 54 48 -72 78 15 54 48 -72 78 16 + 54 48 -72 78 5 48 54 63 66 6 + 48 54 -63 66 17 48 54 -63 66 18 + 48 54 -63 66 19 48 54 63 69 6 + 48 54 -63 69 17 48 54 -63 69 18 + 48 54 -63 69 19 48 72 78 84 1 + 42 48 54 63 20 42 48 -54 63 21 + 42 48 -54 63 11 42 48 -54 63 22 + 42 48 72 75 13 42 48 72 78 23 + 42 48 -72 78 24 42 48 -72 78 25 + 42 48 -72 78 5 147 144 150 156 1 + 144 150 156 162 2 144 150 -156 162 3 + 144 150 -156 162 4 144 150 -156 162 5 + 144 150 156 189 6 144 150 -156 189 7 + 144 150 -156 189 8 144 150 -156 189 5 + 123 117 114 141 26 123 129 -135 141 26 + 117 114 141 135 27 117 123 -129 135 26 + 114 117 123 129 26 114 141 -135 129 28 + 108 102 -99 141 29 108 114 117 123 26 + 108 114 141 135 27 102 99 -141 114 30 + 102 99 141 135 30 102 108 114 117 31 + 102 108 -114 141 31 99 90 84 144 32 + 99 90 -84 144 33 99 90 -84 144 34 + 99 90 -84 144 35 99 102 -108 114 36 + 99 141 -114 108 27 99 141 114 117 27 + 99 141 135 129 28 90 84 144 147 13 + 90 84 144 150 14 90 84 -144 150 15 + 90 84 -144 150 16 90 84 -144 150 5 + 90 99 102 108 29 90 99 141 114 30 + 90 99 141 135 30 84 90 99 102 6 + 84 90 -99 102 13 84 90 -99 102 18 + 84 90 -99 102 5 84 90 99 141 37 + 84 90 -99 141 38 84 90 -99 141 39 + 84 90 -99 141 40 84 144 150 156 1 + 78 84 90 99 41 78 84 -90 99 42 + 78 84 -90 99 34 78 84 -90 99 43 + 78 84 144 147 13 78 84 144 150 23 + 78 84 -144 150 24 78 84 -144 150 25 + 78 84 -144 150 5 192 189 195 201 1 + 189 195 201 207 2 189 195 -201 207 3 + 189 195 -201 207 4 189 195 -201 207 5 + 189 195 201 246 6 189 195 -201 246 7 + 189 195 -201 246 8 189 195 -201 246 5 + 171 162 156 189 44 171 162 -156 189 45 + 171 162 -156 189 46 171 162 -156 189 47 + 162 156 189 192 13 162 156 189 195 14 + 162 156 -189 195 15 162 156 -189 195 16 + 162 156 -189 195 5 162 171 180 183 48 + 162 171 -180 183 49 162 171 180 186 48 + 162 171 -180 186 49 156 162 171 180 50 + 156 162 -171 180 51 156 162 -171 180 52 + 156 162 -171 180 53 156 189 195 201 1 + 150 156 162 171 54 150 156 -162 171 55 + 150 156 -162 171 46 150 156 -162 171 56 + 150 156 189 192 13 150 156 189 195 23 + 150 156 -189 195 24 150 156 -189 195 25 + 150 156 -189 195 5 225 207 201 246 57 + 225 207 -201 246 58 225 207 -201 246 59 + 225 207 -201 246 60 213 207 201 246 61 + 213 207 -201 246 62 213 207 -201 246 63 + 213 207 -201 246 64 213 207 225 234 65 + 213 207 -225 234 66 213 207 -225 234 67 + 213 207 -225 234 68 207 201 246 249 13 + 201 207 225 234 69 201 207 -225 234 70 + 201 207 -225 234 67 201 207 -225 234 71 + 195 201 207 213 72 195 201 -207 213 73 + 195 201 -207 213 63 195 201 -207 213 74 + 195 201 207 225 75 195 201 -207 225 76 + 195 201 -207 225 59 195 201 -207 225 77 + 195 201 246 249 13 12 42 -36 -39 78 + 18 30 -27 -33 78 48 78 -72 -75 78 + 54 66 -63 -69 78 84 150 -144 -147 78 + 99 114 -141 -135 79 108 117 -114 -141 79 + 141 90 -99 -102 80 156 195 -189 -192 78 + 171 183 -180 -186 78 +%FLAG EXCLUDED_ATOMS_LIST +%FORMAT(10I8) + 2 3 4 5 6 7 8 9 10 13 + 14 15 3 4 5 6 7 13 4 5 + 6 7 13 5 6 7 13 6 7 8 + 9 10 11 12 13 14 15 16 17 7 + 8 9 10 13 14 15 8 9 10 11 + 12 13 14 15 9 10 11 12 13 10 + 11 12 13 11 12 13 12 0 14 15 + 16 17 18 19 25 15 16 17 16 17 + 18 19 20 21 22 25 26 27 17 18 + 19 25 18 19 20 21 22 23 24 25 + 26 27 28 29 19 20 21 22 25 26 + 27 20 21 22 23 24 25 26 27 21 + 22 23 24 25 22 23 24 25 23 24 + 25 24 0 26 27 28 29 30 31 49 + 27 28 29 28 29 30 31 32 33 34 + 49 50 51 29 30 31 49 30 31 32 + 33 34 35 48 49 50 51 52 53 31 + 32 33 34 49 50 51 32 33 34 35 + 36 37 39 46 48 49 50 51 33 34 + 35 48 49 34 35 48 49 35 36 37 + 38 39 40 44 46 47 48 49 36 37 + 38 39 40 46 48 37 38 39 48 38 + 39 40 41 42 46 48 39 40 48 40 + 41 42 43 44 46 47 48 41 42 43 + 44 45 46 48 42 43 44 48 43 44 + 45 46 47 48 44 45 46 45 46 47 + 48 46 47 48 47 48 48 0 50 51 + 52 53 54 55 64 51 52 53 52 53 + 54 55 56 57 58 64 65 66 53 54 + 55 64 54 55 56 57 58 59 60 61 + 64 65 66 67 68 55 56 57 58 64 + 65 66 56 57 58 59 60 61 62 63 + 64 65 66 57 58 59 60 61 64 58 + 59 60 61 64 59 60 61 62 63 64 + 60 61 62 63 61 62 63 62 63 63 + 0 65 66 67 68 69 70 83 66 67 + 68 67 68 69 70 71 72 76 83 84 + 68 69 70 83 69 70 71 72 73 74 + 75 76 77 78 79 83 84 70 71 72 + 76 83 84 71 72 73 74 75 76 77 + 78 79 80 81 82 83 84 72 73 74 + 75 76 77 78 79 83 73 74 75 76 + 77 78 79 83 74 75 76 75 76 76 + 77 78 79 80 81 82 83 78 79 80 + 81 82 79 80 81 82 80 81 82 81 + 82 82 0 84 0 +%FLAG HBOND_ACOEF +%FORMAT(5E16.8) + +%FLAG HBOND_BCOEF +%FORMAT(5E16.8) + +%FLAG HBCUT +%FORMAT(5E16.8) + +%FLAG AMBER_ATOM_TYPE +%FORMAT(20a4) +N3 H H H CX HP 2C HC HC CO O2 O2 C O N H CX H1 2C HC +HC CO O2 O2 C O N H CX H1 CT HC HC C* CW H4 NA H CN CA +HA CA HA CA HA CA HA CB C O N H CX H1 2C HC HC 2C HC HC +CO O2 O2 C O N H CX H1 3C HC CT HC HC HC 2C HC HC CT HC +HC HC C O +%FLAG TREE_CHAIN_CLASSIFICATION +%FORMAT(20a4) +BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA M E M E 3 E +E B E E M E M E M E 3 E E B B E B E S B +E B E B E S E E M E M E M E 3 E E 3 E E +B E E M E M E M E 3 E 3 E E E 3 E E 3 E +E E M E +%FLAG JOIN_ARRAY +%FORMAT(10I8) + 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 0 0 0 0 + 0 0 0 0 0 0 0 0 0 0 + 0 0 0 0 +%FLAG IROTAT +%FORMAT(10I8) + 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 0 0 0 0 + 0 0 0 0 0 0 0 0 0 0 + 0 0 0 0 +%FLAG SOLVENT_POINTERS +%FORMAT(3I8) + 5 1 2 +%FLAG ATOMS_PER_MOLECULE +%FORMAT(10I8) + 84 +%FLAG BOX_DIMENSIONS +%FORMAT(5E16.8) + 9.00000000E+01 7.26144463E+01 7.71983807E+01 7.99681950E+01 +%FLAG RADIUS_SET +%FORMAT(1a80) +modified Bondi radii (mbondi) +%FLAG RADII +%FORMAT(5E16.8) + 1.55000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00 1.70000000E+00 + 1.30000000E+00 1.70000000E+00 1.30000000E+00 1.30000000E+00 1.70000000E+00 + 1.50000000E+00 1.50000000E+00 1.70000000E+00 1.50000000E+00 1.55000000E+00 + 1.30000000E+00 1.70000000E+00 1.30000000E+00 1.70000000E+00 1.30000000E+00 + 1.30000000E+00 1.70000000E+00 1.50000000E+00 1.50000000E+00 1.70000000E+00 + 1.50000000E+00 1.55000000E+00 1.30000000E+00 1.70000000E+00 1.30000000E+00 + 1.70000000E+00 1.30000000E+00 1.30000000E+00 1.70000000E+00 1.70000000E+00 + 1.30000000E+00 1.55000000E+00 1.30000000E+00 1.70000000E+00 1.70000000E+00 + 1.30000000E+00 1.70000000E+00 1.30000000E+00 1.70000000E+00 1.30000000E+00 + 1.70000000E+00 1.30000000E+00 1.70000000E+00 1.70000000E+00 1.50000000E+00 + 1.55000000E+00 1.30000000E+00 1.70000000E+00 1.30000000E+00 1.70000000E+00 + 1.30000000E+00 1.30000000E+00 1.70000000E+00 1.30000000E+00 1.30000000E+00 + 1.70000000E+00 1.50000000E+00 1.50000000E+00 1.70000000E+00 1.50000000E+00 + 1.55000000E+00 1.30000000E+00 1.70000000E+00 1.30000000E+00 1.70000000E+00 + 1.30000000E+00 1.70000000E+00 1.30000000E+00 1.30000000E+00 1.30000000E+00 + 1.70000000E+00 1.30000000E+00 1.30000000E+00 1.70000000E+00 1.30000000E+00 + 1.30000000E+00 1.30000000E+00 1.70000000E+00 1.50000000E+00 +%FLAG SCREEN +%FORMAT(5E16.8) + 7.90000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01 + 8.50000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01 + 8.50000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 7.90000000E-01 + 8.50000000E-01 7.20000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 + 8.50000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01 + 8.50000000E-01 7.90000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 + 7.20000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01 7.20000000E-01 + 8.50000000E-01 7.90000000E-01 8.50000000E-01 7.20000000E-01 7.20000000E-01 + 8.50000000E-01 7.20000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 + 7.20000000E-01 8.50000000E-01 7.20000000E-01 7.20000000E-01 8.50000000E-01 + 7.90000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 7.20000000E-01 + 8.50000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01 + 7.20000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 + 7.90000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 7.20000000E-01 + 8.50000000E-01 7.20000000E-01 8.50000000E-01 8.50000000E-01 8.50000000E-01 + 7.20000000E-01 8.50000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 + 8.50000000E-01 8.50000000E-01 7.20000000E-01 8.50000000E-01 diff --git a/testsuite/MDAnalysisTests/datafiles.py b/testsuite/MDAnalysisTests/datafiles.py index 68417b9e560..0db51954b04 100644 --- a/testsuite/MDAnalysisTests/datafiles.py +++ b/testsuite/MDAnalysisTests/datafiles.py @@ -38,13 +38,13 @@ __all__ = [ "PSF", "DCD", "CRD", # CHARMM (AdK example, DIMS trajectory from JMB 2009 paper) - "DCD2", # CHARMM (AdK example, DIMS trajectory from PLOS Comput Biol paper) + "DCD2", # CHARMM (AdK example, DIMS trajectory from PLOS Comput Biol paper) "PSF_notop", "PSF_BAD", # Same as PSF but no bonds etc, malformed version of previous "DCD_empty", "PSF_TRICLINIC", "DCD_TRICLINIC", # CHARMM c36 new unitcell, NPT 125 TIP3P (box vectors, see Issue 187 for details) "PSF_NAMD", "PDB_NAMD", # NAMD - "PSF_NAMD_TRICLINIC", "DCD_NAMD_TRICLINIC", # NAMD, triclinic unitcell (Issue 187) - "PSF_NAMD_GBIS", "DCD_NAMD_GBIS", # NAMD, implicit solvent, 100 steps, #1819 + "PSF_NAMD_TRICLINIC", "DCD_NAMD_TRICLINIC", # NAMD, triclinic unitcell (Issue 187) + "PSF_NAMD_GBIS", "DCD_NAMD_GBIS", # NAMD, implicit solvent, 100 steps, #1819 "PSF_nosegid", # psf without a segid, Issue 121 "PSF_cmap", # ala3 PSF from ParmEd test files with cmap "PDB_small", # PDB @@ -64,15 +64,15 @@ "PDB_cm", "PDB_cm_bz2", "PDB_cm_gz", "PDB_mc", "PDB_mc_bz2", "PDB_mc_gz", "PDB_chainidnewres", # Issue 1110 - "PDB_sameresid_diffresname", #Case where two residues share the same resid + "PDB_sameresid_diffresname", #Case where two residues share the same resid "PDB_chainidrepeat", # Issue #1107 "PDB", "GRO", "XTC", "TRR", "TPR", "GRO_velocity", # Gromacs (AdK) "GRO_incomplete_vels", "COORDINATES_GRO_BZ2", - "GRO_large", #atom number truncation at > 100,000 particles, Issue 550 + "GRO_large", #atom number truncation at > 100,000 particles, Issue 550 "GRO_residwrap", # resids wrapping because of 5 digit field (Issue #728) "GRO_residwrap_0base", # corner case of #728 with resid=0 for first atom - "GRO_sameresid_diffresname", # Case where two residues share the same resid + "GRO_sameresid_diffresname", # Case where two residues share the same resid "PDB_xvf", "TPR_xvf", "TRR_xvf", # Gromacs coords/veloc/forces (cobrotoxin, OPLS-AA, Gromacs 4.5.5 tpr) "H5MD_xvf", # TPR_xvf + TRR_xvf converted to h5md format "XVG_BZ2", # Compressed xvg file about cobrotoxin @@ -93,7 +93,7 @@ "TRR_sub_sol", "XTC_sub_sol", "XYZ", "XYZ_psf", "XYZ_bz2", - "XYZ_mini", "XYZ_five", # 3 and 5 atoms xyzs for an easy topology + "XYZ_mini", "XYZ_five", # 3 and 5 atoms xyzs for an easy topology "TXYZ", "ARC", "ARC_PBC", # Tinker files "PRM", "TRJ", "TRJ_bz2", # Amber (no periodic box) "INPCRD", @@ -101,15 +101,16 @@ "PRM7", "NCDFtruncoct", # Amber (cpptrj test trajectory, see Issue 488) "PRM12", "TRJ12_bz2", # Amber (v12 format, Issue 100) "PRMncdf", "TRJncdf", "NCDF", # Amber (netcdf) - "PFncdf_Top", "PFncdf_Trj", # Amber ncdf with Positions and Forces - "PRMcs", # Amber (format, Issue 1331) - "PRMNCRST", # Amber ncrst with positions/forces/velocities - "PRM_NCBOX", "TRJ_NCBOX", # Amber parm7 + nc w/ pos/forces/vels/box - "PRMNEGATIVE", # Amber negative ATOMIC_NUMBER (Issue 2306) - "PRMErr1", "PRMErr2", "PRMErr3", # Amber TOP files to check raised errors - "PRM_UreyBradley", # prmtop from ParmEd test files with Urey-Bradley angles + "PFncdf_Top", "PFncdf_Trj", # Amber ncdf with Positions and Forces + "CPPTRAJ_TRAJ_TOP", "CPPTRAJ_TRAJ", # Amber ncdf extracted from CPPTRAJ without time variable + "PRMcs", # Amber (format, Issue 1331) + "PRMNCRST", # Amber ncrst with positions/forces/velocities + "PRM_NCBOX", "TRJ_NCBOX", # Amber parm7 + nc w/ pos/forces/vels/box + "PRMNEGATIVE", # Amber negative ATOMIC_NUMBER (Issue 2306) + "PRMErr1", "PRMErr2", "PRMErr3", # Amber TOP files to check raised errors + "PRM_UreyBradley", # prmtop from ParmEd test files with Urey-Bradley angles "PRM7_ala2", "RST7_ala2", # prmtop and rst files from ParmEd example files - "PRM19SBOPC", # prmtop w/ ff19SB CMAP terms and OPC water (Issue #2449) + "PRM19SBOPC", # prmtop w/ ff19SB CMAP terms and OPC water (Issue #2449) "PQR", # PQR v1 "PQR_icodes", # PQR v2 with icodes "PDBQT_input", # PDBQT @@ -117,9 +118,9 @@ "PDB_multipole", "FASTA", # sequence alignment, Issue 112 + 113 "HELANAL_BENDING_MATRIX", # HELANAL test (from PSF+DCD (AdK) helix 8) - "HELANAL_BENDING_MATRIX_SUBSET", # As above, slice of frames 10 to 79 + "HELANAL_BENDING_MATRIX_SUBSET", # As above, slice of frames 10 to 79 "PDB_HOLE", # gramicidin A - "MULTIPDB_HOLE", # gramicidin A, normal mode 7 from ElNemo + "MULTIPDB_HOLE", # gramicidin A, normal mode 7 from ElNemo "DMS", "DMS_DOMAINS", # ADK closed with multiple segids "DMS_NO_SEGID", # ADK closed with no segids or chains @@ -143,25 +144,25 @@ "LAMMPScnt", "LAMMPScnt2", # triclinic box "LAMMPShyd", "LAMMPShyd2", "LAMMPSdata_deletedatoms", # with deleted atoms - "LAMMPSdata_triclinic", # lammpsdata file to test triclinic dimension parsing, albite with most atoms deleted + "LAMMPSdata_triclinic", # lammpsdata file to test triclinic dimension parsing, albite with most atoms deleted "LAMMPSdata_PairIJ", # lammps datafile with a PairIJ Coeffs section "LAMMPSDUMP", "LAMMPSDUMP_long", # lammpsdump file with a few zeros sprinkled in the first column first frame "LAMMPSDUMP_allcoords", # lammpsdump file with all coordinate conventions (x,xs,xu,xsu) present, from LAMMPS rdf example "LAMMPSDUMP_nocoords", # lammpsdump file with no coordinates - "LAMMPSDUMP_triclinic", # lammpsdump file to test triclinic dimension parsing, albite with most atoms deleted - "LAMMPSDUMP_image_vf", # Lammps dump file with image flags, velocities, and forces. - "LAMMPS_image_vf", # Lammps data file to go with LAMMPSDUMP_image_vf + "LAMMPSDUMP_triclinic", # lammpsdump file to test triclinic dimension parsing, albite with most atoms deleted + "LAMMPSDUMP_image_vf", # Lammps dump file with image flags, velocities, and forces. + "LAMMPS_image_vf", # Lammps data file to go with LAMMPSDUMP_image_vf "unordered_res", # pdb file with resids non sequential "GMS_ASYMOPT", # GAMESS C1 optimization "GMS_SYMOPT", # GAMESS D4h optimization - "GMS_ASYMSURF", # GAMESS C1 surface + "GMS_ASYMSURF", # GAMESS C1 surface "two_water_gro", "two_water_gro_nonames", # for bond guessing, 2 water molecules, one with weird names "two_water_gro_multiframe", "two_water_gro_widebox", # Issue #548 "DLP_CONFIG", "DLP_CONFIG_order", "DLP_CONFIG_minimal", # dl_poly 4 config file "DLP_HISTORY", "DLP_HISTORY_order", "DLP_HISTORY_minimal", # dl_poly 4 history file - "DLP_HISTORY_minimal_cell", # dl_poly 4 history file with cell parameters + "DLP_HISTORY_minimal_cell", # dl_poly 4 history file with cell parameters "DLP_HISTORY_classic", # dl_poly classic history file "waterPSF","waterDCD","rmsfArray", "HoomdXMLdata", @@ -172,7 +173,7 @@ "COORDINATES_XYZ_BZ2", "COORDINATES_GRO", "COORDINATES_GRO_INCOMPLETE_VELOCITY", - "Martini_membrane_gro", # for testing the leaflet finder + "Martini_membrane_gro", # for testing the leaflet finder "COORDINATES_XTC", "COORDINATES_TRR", "COORDINATES_TNG", @@ -180,11 +181,11 @@ "COORDINATES_DCD", "COORDINATES_TOPOLOGY", "NUCLsel", - "GRO_empty_atom", "GRO_missing_atomname", # for testing GROParser exception raise - "ENT", #for testing ENT file extension + "GRO_empty_atom", "GRO_missing_atomname", # for testing GROParser exception raise + "ENT", #for testing ENT file extension "RANDOM_WALK", - "RANDOM_WALK_TOPO", # garbage topology to go along with XTC positions above - "AUX_XVG", "XVG_BAD_NCOL", #for testing .xvg auxiliary reader + "RANDOM_WALK_TOPO", # garbage topology to go along with XTC positions above + "AUX_XVG", "XVG_BAD_NCOL", #for testing .xvg auxiliary reader "AUX_XVG_LOWF", "AUX_XVG_HIGHF", "AUX_EDR", "AUX_EDR_TPR", "AUX_EDR_XTC", "AUX_EDR_RAW", @@ -192,36 +193,36 @@ "MMTF", "MMTF_gz", 'MMTF_skinny', # skinny - some optional fields stripped out "MMTF_skinny2", "ALIGN_BOUND", # two component bound system - "ALIGN_UNBOUND", # two component unbound system - "legacy_DCD_ADK_coords", # frames 5 and 29 read in for adk_dims.dcd using legacy DCD reader - "legacy_DCD_NAMD_coords", # frame 0 read in for SiN_tric_namd.dcd using legacy DCD reader - "legacy_DCD_c36_coords", # frames 1 and 4 read in for tip125_tric_C36.dcd using legacy DCD reader + "ALIGN_UNBOUND", # two component unbound system + "legacy_DCD_ADK_coords", # frames 5 and 29 read in for adk_dims.dcd using legacy DCD reader + "legacy_DCD_NAMD_coords", # frame 0 read in for SiN_tric_namd.dcd using legacy DCD reader + "legacy_DCD_c36_coords", # frames 1 and 4 read in for tip125_tric_C36.dcd using legacy DCD reader "GSD", "GSD_bonds", "GSD_long", - "GRO_MEMPROT", "XTC_MEMPROT", # YiiP transporter in POPE:POPG lipids with Na+, Cl-, Zn2+ dummy model without water - "DihedralArray", "DihedralsArray", # time series of single dihedral - "RamaArray", "GLYRamaArray", # time series of phi/psi angles - "JaninArray", "LYSJaninArray", # time series of chi1/chi2 angles - "PDB_rama", "PDB_janin", # for testing failures of Ramachandran and Janin classes - "BATArray", # time series of bond-angle-torsion coordinates array from Molecule_comments_header.mol2 + "GRO_MEMPROT", "XTC_MEMPROT", # YiiP transporter in POPE:POPG lipids with Na+, Cl-, Zn2+ dummy model without water + "DihedralArray", "DihedralsArray", # time series of single dihedral + "RamaArray", "GLYRamaArray", # time series of phi/psi angles + "JaninArray", "LYSJaninArray", # time series of chi1/chi2 angles + "PDB_rama", "PDB_janin", # for testing failures of Ramachandran and Janin classes + "BATArray", # time series of bond-angle-torsion coordinates array from Molecule_comments_header.mol2 # DOS line endings "WIN_PDB_multiframe", "WIN_DLP_HISTORY", "WIN_TRJ", "WIN_LAMMPSDUMP", "WIN_ARC", - "GRO_huge_box", # for testing gro parser with hige box sizes - "ITP", # for GROMACS generated itps - "ITP_nomass", # for ATB generated itps + "GRO_huge_box", # for testing gro parser with hige box sizes + "ITP", # for GROMACS generated itps + "ITP_nomass", # for ATB generated itps "ITP_atomtypes", # atom definitions to check atomtyes section parsing - "ITP_charges", # atom definitions to test custom particle charge parsing. - "NAMDBIN", # for NAMD generated binary file - "ITP_edited", # to check different directives are read properly - "ITP_tip5p", # tip5p water from opls-aa, edited with additional keywords - "ITP_spce", # spce water from gromos54a7, edited with additional keywords, - "GMX_TOP", # 2 ala10 chains + 3 spc water - "GMX_DIR", # GROMACS directory - "GMX_TOP_BAD", # file with an #include that doesn't exist - "ITP_no_endif", # file missing an #endif - "PDB_CRYOEM_BOX", # Issue 2599, Issue #2679, PR #2685 - "PDB_CHECK_RIGHTHAND_PA", # for testing right handedness of principal_axes - "MMTF_NOCRYST", # File with meaningless CRYST1 record (Issue #2679, PR #2685) - "FHIAIMS", # to test FHIAIMS coordinate files + "ITP_charges", # atom definitions to test custom particle charge parsing. + "NAMDBIN", # for NAMD generated binary file + "ITP_edited", # to check different directives are read properly + "ITP_tip5p", # tip5p water from opls-aa, edited with additional keywords + "ITP_spce", # spce water from gromos54a7, edited with additional keywords, + "GMX_TOP", # 2 ala10 chains + 3 spc water + "GMX_DIR", # GROMACS directory + "GMX_TOP_BAD", # file with an #include that doesn't exist + "ITP_no_endif", # file missing an #endif + "PDB_CRYOEM_BOX", # Issue 2599, Issue #2679, PR #2685 + "PDB_CHECK_RIGHTHAND_PA", # for testing right handedness of principal_axes + "MMTF_NOCRYST", # File with meaningless CRYST1 record (Issue #2679, PR #2685) + "FHIAIMS", # to test FHIAIMS coordinate files "SDF_molecule", # MDL SDFile for rdkit "PDBX", # PDBxfile "PDB_elements", # PDB file with elements @@ -429,6 +430,9 @@ PFncdf_Top = resource_filename(__name__, 'data/Amber/posfor.top') PFncdf_Trj = resource_filename(__name__, 'data/Amber/posfor.ncdf') +CPPTRAJ_TRAJ_TOP = resource_filename(__name__, 'data/Amber/cpptraj_traj.prmtop') +CPPTRAJ_TRAJ = resource_filename(__name__, 'data/Amber/cpptraj_traj.nc') + PRMpbc = resource_filename(__name__, 'data/Amber/capped-ala.prmtop') TRJpbc_bz2 = resource_filename(__name__, 'data/Amber/capped-ala.mdcrd.bz2')