Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2021-2023 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             : 
      23             : #include "Tree.h"
      24             : #include "Tools.h"
      25             : #include "Vector.h"
      26             : #include "AtomNumber.h"
      27             : #include "core/GenericMolInfo.h"
      28             : #include <vector>
      29             : #include <limits>
      30             : 
      31             : namespace PLMD {
      32             : 
      33           0 : Tree::Tree(GenericMolInfo* moldat) {
      34             : // initialize class
      35           0 :   moldat_ = moldat;
      36             : // check if molinfo present
      37           0 :   if(!moldat_) plumed_merror("MOLINFO DATA not found");
      38             : // check if reference structure is whole
      39           0 :   if(!moldat_->isWhole()) plumed_merror("Check that reference structure in PDB file is not broken by pbc and set WHOLE in MOLINFO line");
      40           0 : }
      41             : 
      42           0 : std::vector<AtomNumber> Tree::getTree(std::vector<AtomNumber> atoms)
      43             : {
      44             :   // Implementation inspired from:
      45             :   // https://mayanknatani.wordpress.com/2013/05/31/euclidean-minimummaximum-spanning-tree-emst/
      46             :   //
      47             :   // list of AtomNumbers ordered by proximity in PDB file
      48             :   std::vector<AtomNumber> tree;
      49             :   // clear root_ vector
      50           0 :   root_.clear();
      51             : 
      52             :   // remove atoms not in PDB file
      53             :   std::vector<AtomNumber> addtotree, addtoroot;
      54             :   std::vector<AtomNumber> newatoms;
      55           0 :   newatoms.reserve(atoms.size());
      56           0 :   if(!moldat_->checkForAtom(atoms[0])) plumed_merror("The first atom in the list should be present in the PDB file");
      57             :   // store first atom
      58           0 :   newatoms.push_back(atoms[0]);
      59           0 :   for(unsigned i=1; i<atoms.size(); ++i) {
      60           0 :     if(!moldat_->checkForAtom(atoms[i])) {
      61             :       // store this atom for later
      62           0 :       addtotree.push_back(atoms[i]);
      63             :       // along with its root (the previous atom)
      64           0 :       addtoroot.push_back(atoms[i-1]);
      65             :     } else {
      66           0 :       newatoms.push_back(atoms[i]);
      67             :     }
      68             :   }
      69             :   // reassign atoms
      70           0 :   atoms=newatoms;
      71             :   // start EMST
      72           0 :   std::vector<bool> intree(atoms.size(), false);
      73           0 :   std::vector<double> mindist(atoms.size(), std::numeric_limits<double>::max());
      74             :   // initialize tree with first atom
      75           0 :   mindist[0] = 0.0;
      76             :   // loops
      77           0 :   for(unsigned i=0; i<atoms.size(); ++i) {
      78             :     int selected_vertex = -1;
      79           0 :     for(unsigned j=0; j<atoms.size(); ++j) {
      80           0 :       if( !intree[j] && (selected_vertex==-1 || mindist[j] < mindist[selected_vertex]) )
      81           0 :         selected_vertex = j;
      82             :     }
      83             :     // add to tree
      84           0 :     plumed_assert(selected_vertex>=0);
      85           0 :     tree.push_back(atoms[selected_vertex]);
      86             :     intree[selected_vertex] = true;
      87             :     // update distances
      88             :     double minroot = std::numeric_limits<double>::max();
      89             :     int iroot = -1;
      90           0 :     for(unsigned j=0; j<atoms.size(); ++j) {
      91           0 :       double dist = delta(moldat_->getPosition(atoms[selected_vertex]), moldat_->getPosition(atoms[j])).modulo2();
      92           0 :       if(dist < mindist[j]) mindist[j] = dist;
      93           0 :       if(dist < minroot && intree[j] && dist>0.0) {
      94             :         minroot = dist;
      95           0 :         iroot = j;
      96             :       }
      97             :     }
      98             :     // add to root vector
      99           0 :     if(iroot>=0) root_.push_back(atoms[iroot]);
     100             :   }
     101             : 
     102             :   // now re-add atoms not present in the PDB
     103           0 :   for(unsigned i=0; i<addtotree.size(); ++i) {
     104           0 :     tree.push_back(addtotree[i]);
     105           0 :     root_.push_back(addtoroot[i]);
     106             :   }
     107             : 
     108             :   // return
     109           0 :   return tree;
     110             : }
     111             : 
     112           0 : std::vector<AtomNumber> Tree::getRoot() const
     113             : {
     114           0 :   return root_;
     115             : }
     116             : 
     117             : }