Existing traj integration

adaptivemd/analysis/pyemma/_remote.py

@@ -26,7 +26,6 @@
 
 def remote_analysis(
         trajectories,
-        traj_name='output.dcd',
         selection=None,
         features=None,
         topfile='input.pdb',
@@ -40,10 +39,7 @@ def remote_analysis(
 
     Parameters
     ----------
-    trajectories : Sized of `Trajectory`
-        a list of `Trajectory` objects
-    traj_name : str
-        name of the trajectory file with the trajectory directory given
+    trajectories : Trajectory file paths
     selection : str
         an atom subset selection string as used in mdtraj .select
     features : dict or list or None
@@ -122,8 +118,7 @@ def apply_feat_part(featurizer, parts):
 
     print '#trajectories :', len(trajectories)
 
-    files = [os.path.join(t, traj_name) for t in trajectories]
-    inp = pyemma.coordinates.source(files, feat)
+    inp = pyemma.coordinates.source(trajectories, feat)
 
     tica_obj = pyemma.coordinates.tica(
         inp, lag=tica_lag, dim=tica_dim, kinetic_map=False)

adaptivemd/analysis/pyemma/emma.py

@@ -170,12 +170,23 @@ def execute(
                 # ups, one of the trajectories does not have the required type!
                 return
 
+        if len(set(traj.types[outtype].stride for traj in trajs)) > 1:
+            # using different strides in trajectories
+            return
+
+        if len(set(traj.types[outtype].selection for traj in trajs)) > 1:
+            # different selection strings among trajectories
+            return
+
         ty = trajs[0].types[outtype]
 
+        traj_paths = []
+        for traj in trajs:
+            traj_paths.append(traj.file(traj.types[outtype].filename).path)
+
         t.call(
             remote_analysis,
-            trajectories=trajs,
-            traj_name=ty.filename,  # we need the filename in the traj folder
+            trajectories=traj_paths,
             selection=ty.selection,  # tell pyemma the subsets of atoms
             features=features,
             topfile=input_pdb,

docs/examples.rst

@@ -10,3 +10,4 @@ Examples Notebooks
    examples/example4
    examples/example5
    examples/example6
+   examples/example7

docs/examples/example7.rst

@@ -0,0 +1,6 @@
+.. _example7:
+
+Example 7 - Miscellaneous
+=========================
+
+.. notebook:: examples/tutorial/7_example_misc.ipynb

examples/tutorial/7_example_misc.ipynb

@@ -0,0 +1,305 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "deletable": true,
+    "editable": true
+   },
+   "source": [
+    "## Importing existing trajectory data"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "deletable": true,
+    "editable": true
+   },
+   "source": [
+    "In many cases, some trajectory data already exists before running an adaptive simulation. It is thus most efficiently to import this data into the framework. This works in principle by creating `Trajectory` objects and adding them to the `Project`. Since all of the trajectory-related data however is stored in the `Engine` object that generated it, this needs to be created as well."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "deletable": true,
+    "editable": true
+   },
+   "source": [
+    "### Imports"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": true,
+    "deletable": true,
+    "editable": true
+   },
+   "outputs": [],
+   "source": [
+    "import sys, os"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": false,
+    "deletable": true,
+    "editable": true
+   },
+   "outputs": [],
+   "source": [
+    "from adaptivemd import Project"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "deletable": true,
+    "editable": true
+   },
+   "source": [
+    "Let's open our `test` project by its name. If you completed the previous example this should all work out of the box."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": false,
+    "deletable": true,
+    "editable": true
+   },
+   "outputs": [],
+   "source": [
+    "project = Project('tutorial')"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "deletable": true,
+    "editable": true
+   },
+   "source": [
+    "Open all connections to the `MongoDB` and `Session` so we can get started."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "deletable": true,
+    "editable": true
+   },
+   "source": [
+    "### Create an import `Engine`"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": true,
+    "deletable": true,
+    "editable": true
+   },
+   "outputs": [],
+   "source": [
+    "from adaptivemd import Trajectory\n",
+    "import time"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": true,
+    "deletable": true,
+    "editable": true
+   },
+   "outputs": [],
+   "source": [
+    "pdb_file = File('file://init.pdb').named('initial_pdb').load()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "deletable": true,
+    "editable": true
+   },
+   "source": [
+    "Since it is not desired to expand the trajectories at this point, system and integrator files are not given. In principle, if compatible restart files are available, one could create a complete engine and expand existing trajectories."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": true,
+    "deletable": true,
+    "editable": true
+   },
+   "outputs": [],
+   "source": [
+    "import_engine = OpenMMEngine(pdb_file=pdb_file,\n",
+    "                             system_file=None,\n",
+    "                             integrator_file=None,\n",
+    "                             args=None\n",
+    "                             ).named('openmm-import')"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "deletable": true,
+    "editable": true
+   },
+   "source": [
+    "Now, to use the same `Modeller` as for the trajectories generated with `AdaptiveMD`, we build compatible output types. This means, they should contain the original file names with the respective strides and be named accordly. "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": true,
+    "deletable": true,
+    "editable": true
+   },
+   "outputs": [],
+   "source": [
+    "import_engine.add_output_type('master', 'old-file-name-full.dcd', \n",
+    "                              stride=stride_full)\n",
+    "import_engine.add_output_type('protein', 'old-file-name-protein.dcd', \n",
+    "                              stride=stride_prot, \n",
+    "                              selection='protein')"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "deletable": true,
+    "editable": true
+   },
+   "source": [
+    "## Initialize `Trajectory` objects\n",
+    "To add the actual file paths, `Trajectory` objects have to be initialized. \n",
+    "- `Trajectory` locations are folders, not files, and end with '/'.\n",
+    "- `frame` can be None if the initial frame is not known.\n",
+    "- `length` as defined by the engine time step, not by the output/save rate of an output type.\n",
+    "- `engine`: import engine defined above.\n",
+    "\n",
+    "The example below uses a list of trajectory folders to import, `existing_trajectory_paths`. Note that when adding this path with the `shared://` prefix, it must be a relative path in the root shared cluster file system. For absolute paths, use `worker://` instead. The trajectory lengths are known and stored in `existing_trajectory_lengths`.\n",
+    "\n",
+    "The `created` variable has to be set a creation time in order to let the database know the trajectory already exists. In the example below, the (arbitrary) import time is used."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": true,
+    "deletable": true,
+    "editable": true
+   },
+   "outputs": [],
+   "source": [
+    "trajs = []\n",
+    "for traj_path, traj_length in zip(existing_trajectory_paths, \n",
+    "                                  existing_trajectory_lengths):\n",
+    "    traj = Trajectory('shared://' + traj_path,\n",
+    "                      frame=None,\n",
+    "                      length=traj_length,\n",
+    "                      engine=import_engine)\n",
+    "    traj.created = time.time()\n",
+    "    trajs.append(traj)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "deletable": true,
+    "editable": true
+   },
+   "source": [
+    "#### Add the trajectories to the project"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": true,
+    "deletable": true,
+    "editable": true
+   },
+   "outputs": [],
+   "source": [
+    "map(project.files.add, trajs)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "deletable": true,
+    "editable": true
+   },
+   "source": [
+    "Let's check if the trajectories have been added:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": true,
+    "deletable": true,
+    "editable": true
+   },
+   "outputs": [],
+   "source": [
+    "len(project.trajectories)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": true,
+    "deletable": true,
+    "editable": true
+   },
+   "outputs": [],
+   "source": [
+    "project.close()"
+   ]
+  }
+ ],
+ "metadata": {
+  "anaconda-cloud": {},
+  "kernelspec": {
+   "display_name": "py27_mar17",
+   "language": "python",
+   "name": "py27_mar17"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 2
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython2",
+   "version": "2.7.13"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 1
+}