Changeset 0cbad2

Timestamp:

Mar 1, 2011, 1:17:07 PM (14 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, AddingActions_SaveParseParticleParameters, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_ParticleName_to_Atom, Adding_StructOpt_integration_tests, AtomFragments, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, CombiningParticlePotentialParsing, Combining_Subpackages, Debian_Package_split, Debian_package_split_molecuildergui_only, Disabling_MemDebug, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph, EmpiricalPotential_contain_HomologyGraph_documentation, Enable_parallel_make_install, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, FitPartialCharges_GlobalError, Fix_BoundInBox_CenterInBox_MoleculeActions, Fix_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_PopActions, Fix_QtFragmentList_sorted_selection, Fix_Restrictedkeyset_FragmentMolecule, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fix_fitting_potentials, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, FragmentAction_writes_AtomFragments, FragmentMolecule_checks_bonddegrees, GeometryObjects, Gui_Fixes, Gui_displays_atomic_force_velocity, ImplicitCharges, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, MoreRobust_FragmentAutomation, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PdbParser_setsAtomName, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, Rewrite_FitPartialCharges, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, Switchable_LogView, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, TremoloParser_setsAtomName, Ubuntu_1604_changes, stable

Children:

300220

Parents:

3738f0

git-author:

Frederik Heber <heber@…> (02/18/11 23:39:44)

git-committer:

Frederik Heber <heber@…> (03/01/11 13:17:07)

Message:

Moved molecule::CreateAdjacencyListFromDbondFile() over to BondGraph and made more flexible.

• extended molecule::CreateAdjacencyListFromDbondFile() to also parse TREMOLO's dbond files.
• BondFileAction now has two more options: skiplines and offset to control parsing, default values assure behavior as has been.
• same way CreateAdjacencyListFromDbondFile() has these two options added also.
• extended regression test Molecule/BondFile with unconnected PDB and dbond file.

Files:

• src/Actions/MoleculeAction/BondFileAction.cpp (modified) (2 diffs)
• src/Actions/MoleculeAction/BondFileAction.def (modified) (1 diff)
• src/bondgraph.cpp (modified) (1 diff)
• src/bondgraph.hpp (modified) (2 diffs)
• src/molecule.hpp (modified) (1 diff)
• src/molecule_graph.cpp (modified) (1 diff)
• tests/regression/Molecules/BondFile/post/test.pdb (added)
• tests/regression/Molecules/BondFile/pre/silica.dbond.0000 (added)
• tests/regression/Molecules/BondFile/pre/silica.pov1.0000.pdb (added)
• tests/regression/Molecules/BondFile/pre/test.dbond (modified) (1 diff)
• tests/regression/Molecules/BondFile/testsuite-molecules-bond-file.at (modified) (1 diff)

src/Actions/MoleculeAction/BondFileAction.cpp

@@ -20 +20 @@
 #include "CodePatterns/MemDebug.hpp"
 
+#include "bondgraph.hpp"
 #include "CodePatterns/Log.hpp"
 #include "molecule.hpp"
@@ -45 +46 @@
   if(World::getInstance().countSelectedMolecules() == 1) {
     mol = World::getInstance().beginMoleculeSelection()->second;
-    DoLog(0) && (Log() << Verbose(0) << "Parsing bonds from " << params.bondfile << "." << endl);
+    LOG(0, "STATUS: Parsing bonds from " << params.bondfile
+        << ", skipping " << params.skiplines << "lines"
+        << ", adding " << params.id_offset << " to each id.");
     ifstream input(params.bondfile.string().c_str());
-    mol->CreateAdjacencyListFromDbondFile(&input);
+    molecule::atomVector Set = mol->getAtomSet();
+    World::getInstance().getBondGraph()->CreateAdjacencyListFromDbondFile(Set, &input, params.skiplines, params.id_offset);
     input.close();
+    mol->getBondCount();
     return Action::success;
   } else

src/Actions/MoleculeAction/BondFileAction.def

@@ -12 +12 @@
 // ValueStorage by the token "Z" -> first column: int, Z, "Z"
 // "undefine" if no parameters are required, use (NODEFAULT) for each (undefined) default value
-#define paramtypes (boost::filesystem::path)
-#define paramtokens ("bond-file")
-#define paramdescriptions ("name of the bond file")
-#undef paramdefaults
-#define paramreferences (bondfile)
+#define paramtypes (boost::filesystem::path)(int)(int)
+#define paramtokens ("bond-file")("skiplines")("offset")
+#define paramdescriptions ("name of the bond file")("number of header lines to skip")("offset to add to each id")
+#define paramdefaults (NODEFAULT)("1")("0")
+#define paramreferences (bondfile)(skiplines)(id_offset)
 
 #undef statetypes

src/bondgraph.cpp

@@ -206 +206 @@
     LOG(1, "I detected " << BondCount << " bonds in the molecule.");
 }
+

src/bondgraph.hpp

@@ -30 +30 @@
 #include "IPointCloud.hpp"
 #include "PointCloudAdaptor.hpp"
+#include "WorldTime.hpp"
 
 /****************************************** forward declarations *****************************/
@@ -151 +152 @@
       LOG(1, "REJECT: AtomCount is " << counter << ", thus no bonds, no connections.");
     }
+  }
+
+  /** Creates an adjacency list of the given \a Set of atoms.
+   *
+   * Note that the input stream is required to refer to the same number of
+   * atoms also contained in \a Set.
+   *
+   * \param &Set container with atoms
+   * \param *input input stream to parse
+ * \param skiplines how many header lines to skip
+ * \param id_offset is base id compared to World startin at 0
+   */
+  template <class container_type,
+            class iterator_type,
+            class const_iterator_type>
+  void CreateAdjacencyListFromDbondFile(
+      AtomSetMixin<container_type,iterator_type,const_iterator_type> &Set,
+      ifstream *input,
+      unsigned int skiplines,
+      int id_offset) const
+  {
+    char line[MAXSTRINGSIZE];
+
+    // check input stream
+    if (input->fail()) {
+      ELOG(0, "Opening of bond file failed \n");
+      return;
+    };
+    // skip headers
+    unsigned int bondcount = 0;
+    for (unsigned int i=0;i<skiplines;i++)
+      input->getline(line,MAXSTRINGSIZE);
+
+    // create lookup map
+    LOG(1, "STATUS: Creating lookup map.");
+    std::map< unsigned int, atom *> AtomLookup;
+    unsigned int counter = id_offset; // if ids do not start at 0
+    for (iterator_type iter = Set.begin(); iter != Set.end(); ++iter) {
+      AtomLookup.insert( make_pair( counter++, *iter) );
+    }
+    LOG(2, "INFO: There are " << counter << " atoms in the given set.");
+
+    LOG(1, "STATUS: Scanning file.");
+    unsigned int atom1, atom2;
+    unsigned int bondcounter = 0;
+    while (!input->eof()) // Check whether we read everything already
+    {
+      input->getline(line,MAXSTRINGSIZE);
+      stringstream zeile(line);
+      if (zeile.str().empty())
+        continue;
+      zeile >> atom1;
+      zeile >> atom2;
+
+      LOG(4, "INFO: Looking for atoms " << atom1 << " and " << atom2 << ".");
+      if (atom2 < atom1) //Sort indices of atoms in order
+        std::swap(atom1, atom2);
+      ASSERT(atom2 < counter,
+          "BondGraph::CreateAdjacencyListFromDbondFile() - ID "
+          +toString(atom2)+" exceeds number of present atoms "+toString(counter)+".");
+      ASSERT(AtomLookup.count(atom1),
+          "BondGraph::CreateAdjacencyListFromDbondFile() - Could not find an atom with the ID given in dbond file");
+      ASSERT(AtomLookup.count(atom2),
+          "BondGraph::CreateAdjacencyListFromDbondFile() - Could not find an atom with the ID given in dbond file");
+      atom * const Walker = AtomLookup[atom1];
+      atom * const OtherWalker = AtomLookup[atom2];
+
+      LOG(3, "INFO: Creating bond between atoms " << atom1 << " and " << atom2 << ".");
+      bond * const Binder = new bond(Walker, OtherWalker, 1, -1);
+      Walker->RegisterBond(WorldTime::getTime(), Binder);
+      OtherWalker->RegisterBond(WorldTime::getTime(), Binder);
+      bondcounter++;
+    }
+    LOG(1, "STATUS: "<< bondcounter << " bonds have been parsed.");
   }
 

src/molecule.hpp

@@ -210 +210 @@
 
   /// Initialising routines in fragmentation
-  void CreateAdjacencyListFromDbondFile(ifstream *output);
+  void CreateAdjacencyListFromDbondFile(ifstream *output,unsigned int skiplines,int id_offset);
   void OutputBondsList() const;
   void CyclicBondAnalysis() const;

src/molecule_graph.cpp

@@ -72 +72 @@
 
 /************************************* Functions for class molecule *********************************/
-
-/** Creates an adjacency list of the molecule.
- * We obtain an outside file with the indices of atoms which are bondmembers.
- */
-void molecule::CreateAdjacencyListFromDbondFile(ifstream *input)
-{
-  Info FunctionInfo(__func__);
-  // 1 We will parse bonds out of the dbond file created by tremolo.
-  int atom1, atom2;
-  atom *Walker, *OtherWalker;
-  char line[MAXSTRINGSIZE];
-
-  if (input->fail()) {
-    DoeLog(0) && (eLog() << Verbose(0) << "Opening of bond file failed \n");
-    performCriticalExit();
-  };
-  doCountAtoms();
-
-  // skip header
-  input->getline(line,MAXSTRINGSIZE);
-  DoLog(1) && (Log() << Verbose(1) << "Scanning file ... \n");
-  while (!input->eof()) // Check whether we read everything already
-  {
-    input->getline(line,MAXSTRINGSIZE);
-    stringstream zeile(line);
-    zeile >> atom1;
-    zeile >> atom2;
-
-    DoLog(2) && (Log() << Verbose(2) << "Looking for atoms " << atom1 << " and " << atom2 << "." << endl);
-    if (atom2 < atom1) //Sort indices of atoms in order
-      std::swap(atom1, atom2);
-    Walker = FindAtom(atom1);
-    ASSERT(Walker,"Could not find an atom with the ID given in dbond file");
-    OtherWalker = FindAtom(atom2);
-    ASSERT(OtherWalker,"Could not find an atom with the ID given in dbond file");
-    AddBond(Walker, OtherWalker); //Add the bond between the two atoms with respective indices.
-  }
-}
 
 /** Checks for presence of bonds within atom list.

tests/regression/Molecules/BondFile/pre/test.dbond

@@ -1 @@
-m       n
-0       1
-0       3
-0       4
-0       5
-1       2
-1       6
-1       7
-2       8
-2       9
-2       10
+m n
+0 1
+0 3
+0 4
+0 5
+1 2
+1 6
+1 7
+2 8
+2 9
+2 10

tests/regression/Molecules/BondFile/testsuite-molecules-bond-file.at

@@ -1 +1 @@
 ### Bonds from file
 
-AT_SETUP([Molecules - Bonds from file])
+AT_SETUP([Molecules - Fragmentation bonds file])
 AT_KEYWORDS([Molecules])
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/BondFile/pre/test.* .], 0)
-AT_CHECK([../../molecuilder -i test.conf  -v 4 --select-molecule-by-id 0 -A test.dbond], 0, [stdout], [stderr])
-AT_CHECK([fgrep "Looking for atoms 2 and 9." stdout], 0, [ignore], [ignore])
+AT_CHECK([../../molecuilder -i test.conf -o pdb -v 4 --select-molecule-by-id 0 -A test.dbond --skiplines 1 --offset 0], 0, [stdout], [stderr])
+AT_CHECK([file=test.pdb; diff -I '.*reated by molecuilder.*' $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/BondFile/post/$file], 0, [ignore], [ignore])
 AT_CLEANUP
+
+AT_SETUP([Molecules - TREMOLO dbond file])
+AT_KEYWORDS([Molecules])
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/BondFile/pre/silica.* .], 0)
+AT_CHECK([../../molecuilder -i silica.pov1.0000.pdb -v 4 --select-molecule-by-id 0 -A silica.dbond.0000 --skiplines 2 --offset 1], 0, [stdout], [stderr])
+AT_CHECK([fgrep -c "CONECT 7153 6098 5949 5922" silica.pov1.0000.pdb], 0, [1
+], [ignore])
+AT_CLEANUP