imdclient 0.1.0__py3-none-any.whl

imdclient/data/namd/md/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/data/namd/md/namd_v3.namd

@@ -0,0 +1,47 @@
+# 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
+
+dcdfile	alanin.dcd
+dcdfreq	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/results.py

@@ -0,0 +1,332 @@
+# Copy of MDAnalysis.analysis.results from 2.8.0
+
+"""Analysis results and their aggregation --- :mod:`MDAnalysis.analysis.results`
+================================================================================
+
+Module introduces two classes, :class:`Results` and :class:`ResultsGroup`,
+used for storing and aggregating data in
+:meth:`MDAnalysis.analysis.base.AnalysisBase.run()`, respectively.
+
+
+Classes
+-------
+
+The :class:`Results` class is an extension of a built-in dictionary
+type, that holds all assigned attributes in :attr:`self.data` and 
+allows for access either via dict-like syntax, or via class-like syntax:
+
+.. code-block:: python
+
+    from MDAnalysis.analysis.results import Results
+    r = Results()
+    r.array = [1, 2, 3, 4]
+    assert r['array'] == r.array == [1, 2, 3, 4]
+
+
+The :class:`ResultsGroup` can merge multiple :class:`Results` objects.
+It is mainly used by :class:`MDAnalysis.analysis.base.AnalysisBase` class, 
+that uses :meth:`ResultsGroup.merge()` method to aggregate results from
+multiple workers, initialized during a parallel run:
+
+.. code-block:: python
+
+    from MDAnalysis.analysis.results import Results, ResultsGroup
+    import numpy as np
+    
+    r1, r2 = Results(), Results()
+    r1.masses = [1, 2, 3, 4, 5]
+    r2.masses = [0, 0, 0, 0]
+    r1.vectors = np.arange(10).reshape(5, 2)
+    r2.vectors = np.arange(8).reshape(4, 2)
+
+    group = ResultsGroup(
+        lookup = {
+            'masses': ResultsGroup.flatten_sequence,
+            'vectors': ResultsGroup.ndarray_vstack
+            }
+        )
+
+    r = group.merge([r1, r2])
+    assert r.masses == list((*r1.masses, *r2.masses))
+    assert (r.vectors == np.vstack([r1.vectors, r2.vectors])).all()
+"""
+
+from collections import UserDict
+import numpy as np
+from typing import Callable, Sequence
+
+
+class Results(UserDict):
+    r"""Container object for storing results.
+
+    :class:`Results` are dictionaries that provide two ways by which values
+    can be accessed: by dictionary key ``results["value_key"]`` or by object
+    attribute, ``results.value_key``. :class:`Results` stores all results
+    obtained from an analysis after calling :meth:`~AnalysisBase.run()`.
+
+    The implementation is similar to the :class:`sklearn.utils.Bunch`
+    class in `scikit-learn`_.
+
+    .. _`scikit-learn`: https://scikit-learn.org/
+    .. _`sklearn.utils.Bunch`: https://scikit-learn.org/stable/modules/generated/sklearn.utils.Bunch.html
+
+    Raises
+    ------
+    AttributeError
+        If an assigned attribute has the same name as a default attribute.
+
+    ValueError
+        If a key is not of type ``str`` and therefore is not able to be
+        accessed by attribute.
+
+    Examples
+    --------
+    >>> from MDAnalysis.analysis.base import Results
+    >>> results = Results(a=1, b=2)
+    >>> results['b']
+    2
+    >>> results.b
+    2
+    >>> results.a = 3
+    >>> results['a']
+    3
+    >>> results.c = [1, 2, 3, 4]
+    >>> results['c']
+    [1, 2, 3, 4]
+
+
+    .. versionadded:: 2.0.0
+
+    .. versionchanged:: 2.8.0
+        Moved :class:`Results` to :mod:`MDAnalysis.analysis.results`
+    """
+
+    def _validate_key(self, key):
+        if key in dir(self):
+            raise AttributeError(
+                f"'{key}' is a protected dictionary attribute"
+            )
+        elif isinstance(key, str) and not key.isidentifier():
+            raise ValueError(f"'{key}' is not a valid attribute")
+
+    def __init__(self, *args, **kwargs):
+        kwargs = dict(*args, **kwargs)
+        if "data" in kwargs.keys():
+            raise AttributeError(f"'data' is a protected dictionary attribute")
+        self.__dict__["data"] = {}
+        self.update(kwargs)
+
+    def __setitem__(self, key, item):
+        self._validate_key(key)
+        super().__setitem__(key, item)
+
+    def __setattr__(self, attr, val):
+        if attr == "data":
+            super().__setattr__(attr, val)
+        else:
+            self.__setitem__(attr, val)
+
+    def __getattr__(self, attr):
+        try:
+            return self[attr]
+        except KeyError as err:
+            raise AttributeError(
+                f"'Results' object has no attribute '{attr}'"
+            ) from err
+
+    def __delattr__(self, attr):
+        try:
+            del self[attr]
+        except KeyError as err:
+            raise AttributeError(
+                f"'Results' object has no attribute '{attr}'"
+            ) from err
+
+    def __getstate__(self):
+        return self.data
+
+    def __setstate__(self, state):
+        self.data = state
+
+
+class ResultsGroup:
+    """
+    Management and aggregation of results stored in :class:`Results` instances.
+
+    A :class:`ResultsGroup` is an optional description for :class:`Result` "dictionaries"
+    that are used in analysis classes based on :class:`AnalysisBase`. For each *key* in a
+    :class:`Result` it describes how multiple pieces of the data held under the key are
+    to be aggregated. This approach is necessary when parts of a trajectory are analyzed
+    independently (e.g., in parallel) and then need to me merged (with :meth:`merge`) to
+    obtain a complete data set.
+
+    Parameters
+    ----------
+    lookup : dict[str, Callable], optional
+        aggregation functions lookup dict, by default None
+
+    Examples
+    --------
+
+    .. code-block:: python
+
+        from MDAnalysis.analysis.results import ResultsGroup, Results
+        group = ResultsGroup(lookup={'mass': ResultsGroup.float_mean})
+        obj1 = Results(mass=1)
+        obj2 = Results(mass=3)
+        assert {'mass': 2.0} == group.merge([obj1, obj2])
+
+
+    .. code-block:: python
+
+        # you can also set `None` for those attributes that you want to skip
+        lookup = {'mass': ResultsGroup.float_mean, 'trajectory': None}
+        group = ResultsGroup(lookup)
+        objects = [Results(mass=1, skip=None), Results(mass=3, skip=object)]
+        assert group.merge(objects, require_all_aggregators=False) == {'mass': 2.0}
+
+    .. versionadded:: 2.8.0
+    """
+
+    def __init__(self, lookup: dict[str, Callable] = None):
+        self._lookup = lookup
+
+    def merge(
+        self, objects: Sequence[Results], require_all_aggregators: bool = True
+    ) -> Results:
+        """Merge multiple Results into a single Results instance.
+
+        Merge multiple :class:`Results` instances into a single one, using the
+        `lookup` dictionary to determine the appropriate aggregator functions for
+        each named results attribute. If the resulting object only contains a single
+        element, it just returns it without using any aggregators.
+
+        Parameters
+        ----------
+        objects : Sequence[Results]
+            Multiple :class:`Results` instances with the same data attributes.
+        require_all_aggregators : bool, optional
+            if True, raise an exception when no aggregation function for a
+            particular argument is found. Allows to skip aggregation for the
+            parameters that aren't needed in the final object --
+            see :class:`ResultsGroup`.
+
+        Returns
+        -------
+        Results
+            merged :class:`Results`
+
+        Raises
+        ------
+        ValueError
+            if no aggregation function for a key is found and ``require_all_aggregators=True``
+        """
+        if len(objects) == 1:
+            merged_results = objects[0]
+            return merged_results
+
+        merged_results = Results()
+        for key in objects[0].keys():
+            agg_function = self._lookup.get(key, None)
+            if agg_function is not None:
+                results_of_t = [obj[key] for obj in objects]
+                merged_results[key] = agg_function(results_of_t)
+            elif require_all_aggregators:
+                raise ValueError(f"No aggregation function for {key=}")
+        return merged_results
+
+    @staticmethod
+    def flatten_sequence(arrs: list[list]):
+        """Flatten a list of lists into a list
+
+        Parameters
+        ----------
+        arrs : list[list]
+            list of lists
+
+        Returns
+        -------
+        list
+            flattened list
+        """
+        return [item for sublist in arrs for item in sublist]
+
+    @staticmethod
+    def ndarray_sum(arrs: list[np.ndarray]):
+        """sums an ndarray along ``axis=0``
+
+        Parameters
+        ----------
+        arrs : list[np.ndarray]
+            list of input arrays. Must have the same shape.
+
+        Returns
+        -------
+        np.ndarray
+            sum of input arrays
+        """
+        return np.array(arrs).sum(axis=0)
+
+    @staticmethod
+    def ndarray_mean(arrs: list[np.ndarray]):
+        """calculates mean of input ndarrays along ``axis=0``
+
+        Parameters
+        ----------
+        arrs : list[np.ndarray]
+            list of input arrays. Must have the same shape.
+
+        Returns
+        -------
+        np.ndarray
+            mean of input arrays
+        """
+        return np.array(arrs).mean(axis=0)
+
+    @staticmethod
+    def float_mean(floats: list[float]):
+        """calculates mean of input float values
+
+        Parameters
+        ----------
+        floats : list[float]
+            list of float values
+
+        Returns
+        -------
+        float
+            mean value
+        """
+        return np.array(floats).mean()
+
+    @staticmethod
+    def ndarray_hstack(arrs: list[np.ndarray]):
+        """Performs horizontal stack of input arrays
+
+        Parameters
+        ----------
+        arrs : list[np.ndarray]
+            input numpy arrays
+
+        Returns
+        -------
+        np.ndarray
+            result of stacking
+        """
+        return np.hstack(arrs)
+
+    @staticmethod
+    def ndarray_vstack(arrs: list[np.ndarray]):
+        """Performs vertical stack of input arrays
+
+        Parameters
+        ----------
+        arrs : list[np.ndarray]
+            input numpy arrays
+
+        Returns
+        -------
+        np.ndarray
+            result of stacking
+        """
+        return np.vstack(arrs)