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modeller.hh
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1 //------------------------------------------------------------------------------
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3 //
4 // Copyright (C) 2008-2015 by the OpenStructure authors
5 //
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18 //------------------------------------------------------------------------------
19 
20 #ifndef OST_MM_MODELLER_HH
21 #define OST_MM_MODELLER_HH
22 
23 
24 #include <vector>
25 #include <set>
26 
27 #include <ost/platform.hh>
28 #include <ost/io/mol/pdb_reader.hh>
29 #include <ost/mol/entity_handle.hh>
31 #include <ost/mol/atom_handle.hh>
32 #include <ost/geom/vec3.hh>
33 #include <ost/geom/composite.hh>
34 #include <ost/geom/transform.hh>
35 #include <ost/mol/xcs_editor.hh>
36 #include <ost/mol/bond_handle.hh>
37 #include <ost/message.hh>
38 #include <ost/mol/bounding_box.hh>
40 #include <ost/mol/mm/forcefield.hh>
41 #include <ost/mol/mm/settings.hh>
42 #include <ost/mol/mm/index.hh>
43 #include <ost/mol/mm/topology.hh>
44 #include <ost/conop/heuristic.hh>
46 
47 
48 namespace ost { namespace mol{ namespace mm{
49 
50 class Modeller{
51 public:
52 
53  static void GenerateDisulfidBonds(ost::mol::EntityHandle& handle);
54 
55  //may sound pretty stupid...
56  //But this is necessary if we want to compare our energies with
57  //the energies calculated by gromacs. When ost writes and entity
58  //down to disk, it uses 3 digits precision.
59  //If we feed this into gromacs, it also produces a topology
60  //with three digits precision. The problem is, that gromacs
61  //uses nm, therefore the precision gets lowered tenfold.
62  //To take care of that it is necessary to lower our precision...
63  static void LowerPrecision(ost::mol::EntityHandle& handle);
64 
65  static void AssignPDBNaming(ost::mol::EntityHandle& handle);
66 
67  static void AssignGromacsNaming(ost::mol::EntityHandle& handle);
68 };
69 
70 
71 }}}
72 
73 #endif
static void AssignPDBNaming(ost::mol::EntityHandle &handle)
static void AssignGromacsNaming(ost::mol::EntityHandle &handle)
Protein or molecule.
static void GenerateDisulfidBonds(ost::mol::EntityHandle &handle)
static void LowerPrecision(ost::mol::EntityHandle &handle)