Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2013-2019 The plumed team
3 : (see the PEOPLE file at the root of the distribution for a list of names)
4 :
5 : See http://www.plumed.org for more information.
6 :
7 : This file is part of plumed, version 2.
8 :
9 : plumed is free software: you can redistribute it and/or modify
10 : it under the terms of the GNU Lesser General Public License as published by
11 : the Free Software Foundation, either version 3 of the License, or
12 : (at your option) any later version.
13 :
14 : plumed is distributed in the hope that it will be useful,
15 : but WITHOUT ANY WARRANTY; without even the implied warranty of
16 : MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17 : GNU Lesser General Public License for more details.
18 :
19 : You should have received a copy of the GNU Lesser General Public License
20 : along with plumed. If not, see <http://www.gnu.org/licenses/>.
21 : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
22 : #include "PathBase.h"
23 : #include "core/ActionRegister.h"
24 :
25 : //+PLUMEDOC COLVAR GPROPERTYMAP
26 : /*
27 : Property maps but with a more flexible framework for the distance metric being used.
28 :
29 : This colvar calculates a property map using the formalism developed by Spiwok \cite Spiwok:2011ce.
30 : In essence if you have the value of some property, \f$X_i\f$, that it takes at a set of high-dimensional
31 : positions then you calculate the value of the property at some arbitrary point in the high-dimensional space
32 : using:
33 :
34 : \f[
35 : X=\frac{\sum_i X_i*\exp(-\lambda D_i(x))}{\sum_i \exp(-\lambda D_i(x))}
36 : \f]
37 :
38 : Within PLUMED there are multiple ways to define the distance from a high-dimensional configuration, \f$D_i\f$. You could calculate
39 : the RMSD distance or you could calculate the ammount by which a set of collective variables change. As such this implementation
40 : of the propertymap allows one to use all the different distance metric that are discussed in \ref dists. This is as opposed to
41 : the alternative implementation \ref PROPERTYMAP which is a bit faster but which only allows one to use the RMSD distance.
42 :
43 : \par Examples
44 :
45 : The input shown below can be used to calculate the interpolated values of two properties called X and Y based on the values
46 : that these properties take at a set of reference configurations and using the formula above. For this input the distances
47 : between the reference configurations and the instantaneous configurations are calculated using the OPTIMAL metric that is
48 : discussed at length in the manual pages on \ref RMSD.
49 :
50 : \plumedfile
51 : p2: GPROPERTYMAP REFERENCE=allv.pdb PROPERTY=X,Y LAMBDA=69087
52 : PRINT ARG=p2.X,p2.Y,p2.zpath STRIDE=1 FILE=colvar
53 : \endplumedfile
54 :
55 : The additional input file for this calculation, which contains the reference frames and the values of X and Y at these reference
56 : points has the following format.
57 :
58 : \verbatim
59 : REMARK X=1 Y=2
60 : ATOM 1 CL ALA 1 -3.171 0.295 2.045 1.00 1.00
61 : ATOM 5 CLP ALA 1 -1.819 -0.143 1.679 1.00 1.00
62 : ATOM 6 OL ALA 1 -1.177 -0.889 2.401 1.00 1.00
63 : ATOM 7 NL ALA 1 -1.313 0.341 0.529 1.00 1.00
64 : ATOM 8 HL ALA 1 -1.845 0.961 -0.011 1.00 1.00
65 : ATOM 9 CA ALA 1 -0.003 -0.019 0.021 1.00 1.00
66 : ATOM 10 HA ALA 1 0.205 -1.051 0.259 1.00 1.00
67 : ATOM 11 CB ALA 1 0.009 0.135 -1.509 1.00 1.00
68 : ATOM 15 CRP ALA 1 1.121 0.799 0.663 1.00 1.00
69 : ATOM 16 OR ALA 1 1.723 1.669 0.043 1.00 1.00
70 : ATOM 17 NR ALA 1 1.423 0.519 1.941 1.00 1.00
71 : ATOM 18 HR ALA 1 0.873 -0.161 2.413 1.00 1.00
72 : ATOM 19 CR ALA 1 2.477 1.187 2.675 1.00 1.00
73 : END
74 : FIXED
75 : REMARK X=2 Y=3
76 : ATOM 1 CL ALA 1 -3.175 0.365 2.024 1.00 1.00
77 : ATOM 5 CLP ALA 1 -1.814 -0.106 1.685 1.00 1.00
78 : ATOM 6 OL ALA 1 -1.201 -0.849 2.425 1.00 1.00
79 : ATOM 7 NL ALA 1 -1.296 0.337 0.534 1.00 1.00
80 : ATOM 8 HL ALA 1 -1.807 0.951 -0.044 1.00 1.00
81 : ATOM 9 CA ALA 1 0.009 -0.067 0.033 1.00 1.00
82 : ATOM 10 HA ALA 1 0.175 -1.105 0.283 1.00 1.00
83 : ATOM 11 CB ALA 1 0.027 0.046 -1.501 1.00 1.00
84 : ATOM 15 CRP ALA 1 1.149 0.725 0.654 1.00 1.00
85 : ATOM 16 OR ALA 1 1.835 1.491 -0.011 1.00 1.00
86 : ATOM 17 NR ALA 1 1.380 0.537 1.968 1.00 1.00
87 : ATOM 18 HR ALA 1 0.764 -0.060 2.461 1.00 1.00
88 : ATOM 19 CR ALA 1 2.431 1.195 2.683 1.00 1.00
89 : END
90 : \endverbatim
91 :
92 : */
93 : //+ENDPLUMEDOC
94 :
95 : namespace PLMD {
96 : namespace mapping {
97 :
98 6 : class PropertyMap : public PathBase {
99 : public:
100 : static void registerKeywords( Keywords& keys );
101 : explicit PropertyMap(const ActionOptions&);
102 : };
103 :
104 6455 : PLUMED_REGISTER_ACTION(PropertyMap,"GPROPERTYMAP")
105 :
106 4 : void PropertyMap::registerKeywords( Keywords& keys ) {
107 4 : PathBase::registerKeywords( keys );
108 4 : ActionWithValue::useCustomisableComponents( keys );
109 12 : keys.addFlag("NOMAPPING",false,"do not calculate the position on the manifold");
110 4 : }
111 :
112 3 : PropertyMap::PropertyMap(const ActionOptions& ao):
113 : Action(ao),
114 3 : PathBase(ao)
115 : {
116 6 : bool nos; parseFlag("NOMAPPING",nos);
117 :
118 : std::string empty;
119 3 : if(!nos) {
120 18 : for(unsigned i=0; i<getNumberOfProperties(); ++i) {
121 18 : empty="LABEL="+getPropertyName(i);
122 12 : addVessel( "SPATH", empty, 0 );
123 : }
124 : }
125 3 : readVesselKeywords();
126 3 : checkRead();
127 3 : }
128 :
129 : }
130 4839 : }
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