Merge #3252 #3256 #3257

3252: Factor out ParticleList r=jngrad a=fweik Follow up on #3251. Description of changes: - Pulling `ParticleList` out of `particle_data.hpp` to get better header disentanglement. 3256: Remove tutorial 10 and unused LaTeX files r=fweik a=jngrad Closes #3211 Description of changes: - removed tutorial 10 - removed unused LaTeX preambles 3257: Remove PDB parser feature r=fweik a=jngrad The consensus offline at the ICP and online in #1441 is to drop support of the PDB parser feature in favor of the dedicated python package MDAnalysis. Co-authored-by: Florian Weik <[email protected]> Co-authored-by: Jean-Noël Grad <[email protected]>
espressomd · Oct 17, 2019 · a0e4dcd · a0e4dcd
4 parents 34c6bd7 + f28097b + eabc23d + f2fbd3e
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diff --git a/doc/misc/common.tex b/doc/misc/common.tex
diff --git a/doc/sphinx/introduction.rst b/doc/sphinx/introduction.rst
@@ -297,7 +297,6 @@ Currently, the following tutorials are available:
 * :file:`06-active_matter`: Modelling of self-propelling particles.
 * :file:`07-electrokinetics`: Modelling electrokinetics together with hydrodynamic interactions.
 * :file:`08-visualization`: Using the online visualizers of |es|.
-* :file:`10-reaction_ensemble`: Modelling chemical reactions by means of the reaction ensemble.
 * :file:`11-ferrofluid`: Modelling a colloidal suspension of magnetic particles.
 * :file:`12-constant_pH`: Modelling an acid dissociation curve using the constant pH method
 

diff --git a/doc/sphinx/io.rst b/doc/sphinx/io.rst
@@ -369,7 +369,7 @@ Writing various formats using MDAnalysis
 If the MDAnalysis package (https://mdanalysis.org) is installed, it
 is possible to use it to convert frames to any of the supported
 configuration/trajectory formats, including PDB, GROMACS, GROMOS,
-CHARMM/NAMD, AMBER, LAMMPS, ...)
+CHARMM/NAMD, AMBER, LAMMPS, ...
 
 To use MDAnalysis to write in any of these formats, one has first to prepare a stream from
 the |es| particle data using the class :class:`espressomd.MDA_ESP`, and then read from it
@@ -398,9 +398,38 @@ using MDAnalysis. A simple example is the following:
 
 For other examples, see :file:`/samples/MDAnalysisIntegration.py`
 
-.. _Parsing PDB Files:
+.. _Reading various formats using MDAnalysis:
 
-Parsing PDB Files
------------------
+Reading various formats using MDAnalysis
+----------------------------------------
 
-The feature allows the user to parse simple PDB files, a file format introduced by the protein database to encode molecular structures. Together with a topology file (here ) the structure gets interpolated to the grid. For the input you will need to prepare a PDB file with a force field to generate the topology file. Normally the PDB file extension is :file:`.pdb`, the topology file extension is :file:`.itp`. Obviously the PDB file is placed instead of and the topology file instead of .
+MDAnalysis can read various formats, including MD topologies and trajectories.
+To read a PDB file containing a single frame::
+
+    import MDAnalysis
+    import numpy as np
+    import espressomd
+    from espressomd.interactions import HarmonicBond
+
+    # parse protein structure
+    universe = MDAnalysis.Universe("protein.pdb")
+    # extract only the C-alpha atoms of chain A
+    chainA = universe.select_atoms("name CA and segid A")
+    # use the unit cell as box
+    box_l = np.ceil(universe.dimensions[0:3])
+    # setup system
+    system = espressomd.System(box_l=box_l)
+    system.time_step = 0.001
+    system.cell_system.skin = 0.4
+    # configure sphere size sigma and create a harmonic bond
+    system.non_bonded_inter[0, 0].lennard_jones.set_params(
+        epsilon=1, sigma=1.5, cutoff=2, shift="auto")
+    system.bonded_inter[0] = HarmonicBond(k=0.5, r_0=1.5)
+    # create particles and add bonds between them
+    system.part.add(pos=np.array(chainA.positions, dtype=float))
+    for i in range(0, len(chainA) - 1):
+        system.part[i].add_bond((system.bonded_inter[0], system.part[i + 1].id))
+    # visualize protein in 3D
+    from espressomd import visualization
+    visualizer = visualization.openGLLive(system, bond_type_radius=[0.2])
+    visualizer.run(0)
diff --git a/doc/tutorials/06-active_matter/CMakeLists.txt b/doc/tutorials/06-active_matter/CMakeLists.txt
@@ -6,11 +6,10 @@ get_filename_component(BASENAME ${CMAKE_CURRENT_SOURCE_DIR} NAME)
 add_custom_command( 
   OUTPUT ${BASENAME}.pdf
   COMMAND sh ../../latexit.sh
-          ${CMAKE_CURRENT_SOURCE_DIR}:${CMAKE_CURRENT_SOURCE_DIR}/../common
+          ${CMAKE_CURRENT_SOURCE_DIR}
           ${BASENAME}
   DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/${BASENAME}.tex
           ${CMAKE_CURRENT_SOURCE_DIR}
-          ${CMAKE_CURRENT_SOURCE_DIR}/../common
 )
 
 add_custom_target(tutorials_06 DEPENDS ${BASENAME}.pdf)