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           2 : Tree::Tree(GenericMolInfo* moldat) {
      34             : // initialize class
      35           2 :   moldat_ = moldat;
      36             : // check if molinfo present
      37           2 :   if(!moldat_) {
      38           0 :     plumed_merror("MOLINFO DATA not found");
      39             :   }
      40             : // check if reference structure is whole
      41           2 :   if(!moldat_->isWhole()) {
      42           0 :     plumed_merror("Check that reference structure in PDB file is not broken by pbc and set WHOLE in MOLINFO line");
      43             :   }
      44           2 : }
      45             : 
      46           2 : std::vector<AtomNumber> Tree::getTree(std::vector<AtomNumber> atoms) {
      47             :   // Implementation inspired from:
      48             :   // https://mayanknatani.wordpress.com/2013/05/31/euclidean-minimummaximum-spanning-tree-emst/
      49             :   //
      50             :   // list of AtomNumbers ordered by proximity in PDB file
      51             :   std::vector<AtomNumber> tree;
      52             :   // clear root_ vector
      53           2 :   root_.clear();
      54             : 
      55             :   std::vector<Vector> positions;
      56             : 
      57             :   // remove atoms not in PDB file
      58             :   std::vector<AtomNumber> addtotree, addtoroot;
      59             :   std::vector<AtomNumber> newatoms;
      60           2 :   newatoms.reserve(atoms.size());
      61           2 :   positions.reserve(atoms.size());
      62           2 :   tree.reserve(atoms.size());
      63           2 :   root_.reserve(atoms.size());
      64           2 :   if(!moldat_->checkForAtom(atoms[0])) {
      65           0 :     plumed_merror("The first atom in the list should be present in the PDB file");
      66             :   }
      67             :   // store first atom
      68           2 :   newatoms.push_back(atoms[0]);
      69           2 :   positions.push_back(moldat_->getPosition(atoms[0]));
      70         245 :   for(unsigned i=1; i<atoms.size(); ++i) {
      71         243 :     if(!moldat_->checkForAtom(atoms[i])) {
      72             :       // store this atom for later
      73          61 :       addtotree.push_back(atoms[i]);
      74             :       // along with its root (the previous atom)
      75          61 :       addtoroot.push_back(atoms[i-1]);
      76             :     } else {
      77         182 :       newatoms.push_back(atoms[i]);
      78         364 :       positions.push_back(moldat_->getPosition(atoms[i]));
      79             :     }
      80             :   }
      81             :   // reassign atoms
      82           2 :   atoms=newatoms;
      83             :   // start EMST
      84           2 :   std::vector<bool> intree(atoms.size(), false);
      85           2 :   std::vector<double> mindist(atoms.size(), std::numeric_limits<double>::max());
      86             :   // initialize tree with first atom
      87           2 :   mindist[0] = 0.0;
      88             :   // loops
      89         186 :   for(unsigned i=0; i<atoms.size(); ++i) {
      90             :     int selected_vertex = -1;
      91       19034 :     for(unsigned j=0; j<atoms.size(); ++j) {
      92       18850 :       if( !intree[j] && (selected_vertex==-1 || mindist[j] < mindist[selected_vertex]) ) {
      93        1078 :         selected_vertex = j;
      94             :       }
      95             :     }
      96             :     // add to tree
      97         184 :     plumed_assert(selected_vertex>=0);
      98         184 :     tree.push_back(atoms[selected_vertex]);
      99             :     intree[selected_vertex] = true;
     100             :     // update distances
     101             :     double minroot = std::numeric_limits<double>::max();
     102             :     int iroot = -1;
     103       19034 :     for(unsigned j=0; j<atoms.size(); ++j) {
     104       18850 :       double dist = delta(positions[selected_vertex], positions[j]).modulo2();
     105       18850 :       if(dist < mindist[j]) {
     106        4312 :         mindist[j] = dist;
     107             :       }
     108       22401 :       if(dist < minroot && intree[j] && dist>0.0) {
     109             :         minroot = dist;
     110        2822 :         iroot = j;
     111             :       }
     112             :     }
     113             :     // add to root vector
     114         184 :     if(iroot>=0) {
     115         182 :       root_.push_back(atoms[iroot]);
     116             :     }
     117             :   }
     118             : 
     119             :   // now re-add atoms not present in the PDB
     120          63 :   for(unsigned i=0; i<addtotree.size(); ++i) {
     121          61 :     tree.push_back(addtotree[i]);
     122          61 :     root_.push_back(addtoroot[i]);
     123             :   }
     124             : 
     125             :   // return
     126           2 :   return tree;
     127             : }
     128             : 
     129           2 : std::vector<AtomNumber> Tree::getRoot() const {
     130           2 :   return root_;
     131             : }
     132             : 
     133             : }