From d6a289c071d938399ffe959f15839e5ff6ea43ce Mon Sep 17 00:00:00 2001
From: Michele Ceriotti <michele.ceriott@epfl.ch>
Date: Thu, 6 Aug 2015 18:32:59 +0200
Subject: [PATCH] Used MOLINFO to pass atom names to output files in OUTPUT_PDB
---
src/analysis/OutputPDBFile.cpp | 15 +++++++++++++--
src/analysis/ReadDissimilarityMatrix.cpp | 6 ++++--
src/reference/ReferenceAtoms.cpp | 23 +++++++++++++++++------
src/reference/ReferenceAtoms.h | 2 +-
src/reference/ReferenceConfiguration.cpp | 7 ++++---
src/reference/ReferenceConfiguration.h | 3 ++-
6 files changed, 41 insertions(+), 15 deletions(-)
diff --git a/src/analysis/OutputPDBFile.cpp b/src/analysis/OutputPDBFile.cpp
index 0783b0fc2..073735835 100644
--- a/src/analysis/OutputPDBFile.cpp
+++ b/src/analysis/OutputPDBFile.cpp
@@ -24,7 +24,9 @@
#include "reference/ReferenceArguments.h"
#include "core/ActionRegister.h"
#include "core/PlumedMain.h"
+#include "core/ActionSet.h"
#include "core/Atoms.h"
+#include "core/SetupMolInfo.h"
namespace PLMD {
namespace analysis {
@@ -69,20 +71,29 @@ Action(ao),
AnalysisWithDataCollection(ao),
fmt("%f")
{
+ // Find a moldata object
+ std::vector<SetupMolInfo*> moldat=plumed.getActionSet().select<SetupMolInfo*>();
+ if( moldat.empty() ) warning("PDB output files do not have atom types unless you use MOLDATA");
+
parse("FILE",filename); parse("FMT",fmt);
if( !getRestart() ){ OFile ofile; ofile.link(*this); ofile.setBackupString("analysis"); ofile.backupAllFiles(filename); }
log.printf(" printing data to file named %s \n",filename.c_str() );
}
void OutputPDBFile::performAnalysis(){
+ // Find a moldata object
+ std::vector<SetupMolInfo*> moldat=plumed.getActionSet().select<SetupMolInfo*>();
+ if( moldat.size()>1 ) error("you should only have one MOLINFO action in your input file");
+ SetupMolInfo* mymoldat=NULL; if( moldat.size()==1 ) mymoldat=moldat[0];
+
// Output the embedding in plumed pdb format
OFile afile; afile.link(*this); afile.setBackupString("analysis"); std::size_t psign=fmt.find("%");
afile.open( filename.c_str() ); std::string descr="REMARK WEIGHT=%-" + fmt.substr(psign+1) + " TYPE=" + getMetricName() + "\n";
for(unsigned j=0;j<getNumberOfDataPoints();++j){
afile.printf("DESCRIPTION: analysis data from calculation done at time %f \n",getLabel().c_str(),getTime() );
afile.printf(descr.c_str(),getWeight(j) );
- if( plumed.getAtoms().usingNaturalUnits() ) getReferenceConfiguration(j,false)->print( 1.0, afile, fmt );
- else getReferenceConfiguration(j,false)->print( plumed.getAtoms().getUnits().getLength()/0.1, afile, fmt );
+ if( plumed.getAtoms().usingNaturalUnits() ) getReferenceConfiguration(j,false)->print( 1.0, mymoldat, afile, fmt );
+ else getReferenceConfiguration(j,false)->print( plumed.getAtoms().getUnits().getLength()/0.1, mymoldat, afile, fmt );
}
afile.close();
}
diff --git a/src/analysis/ReadDissimilarityMatrix.cpp b/src/analysis/ReadDissimilarityMatrix.cpp
index 393167fc9..717803ac1 100644
--- a/src/analysis/ReadDissimilarityMatrix.cpp
+++ b/src/analysis/ReadDissimilarityMatrix.cpp
@@ -26,6 +26,7 @@
#include "core/PlumedMain.h"
#include "core/ActionSet.h"
#include "core/ActionRegister.h"
+#include "core/ActionSetup.h"
#include "tools/IFile.h"
//+PLUMEDOC ANALYSIS READ_DISSIMILARITY_MATRIX
@@ -95,8 +96,9 @@ fake_data(NULL)
} else {
fake_data=metricRegister().create<ReferenceConfiguration>( "OPTIMAL" );
}
-
- if( mytraj.length()>0 && plumed.getActionSet().size()!=1 ) error("should only be this action and the READ_ANALYSIS_FRAMES command in the input file");
+
+ std::vector<ActionSetup*> setupActions=plumed.getActionSet().select<ActionSetup*>();
+ if( mytraj.length()>0 && (plumed.getActionSet().size()-setupActions.size())!=1 ) error("should only be this action and the READ_ANALYSIS_FRAMES command in the input file");
if( mytraj.length()==0 && plumed.getActionSet().size()!=0 ) error("read dissimilarity matrix command must be at top of input file");
parse("FILE",fname);
diff --git a/src/reference/ReferenceAtoms.cpp b/src/reference/ReferenceAtoms.cpp
index 48c4fbbad..6a6748222 100644
--- a/src/reference/ReferenceAtoms.cpp
+++ b/src/reference/ReferenceAtoms.cpp
@@ -20,6 +20,7 @@
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
#include "ReferenceAtoms.h"
+#include "core/SetupMolInfo.h"
#include "tools/OFile.h"
#include "tools/PDB.h"
@@ -41,12 +42,22 @@ void ReferenceAtoms::readAtomsFromPDB( const PDB& pdb ){
}
}
-void ReferenceAtoms::printAtoms( const double& lunits, OFile& ofile ) const {
- for(unsigned i=0;i<reference_atoms.size();++i){
- ofile.printf("ATOM %4d X RES %4u %8.3f %8.3f %8.3f %6.2f %6.2f\n",
- indices[i].serial(), i,
- lunits*reference_atoms[i][0], lunits*reference_atoms[i][1], lunits*reference_atoms[i][2],
- align[i], displace[i] );
+void ReferenceAtoms::printAtoms( const double& lunits, SetupMolInfo* mymoldat, OFile& ofile ) const {
+ if( !mymoldat ){
+ for(unsigned i=0;i<reference_atoms.size();++i){
+ ofile.printf("ATOM %4d X RES %4u %8.3f %8.3f %8.3f %6.2f %6.2f\n",
+ indices[i].serial(), i,
+ lunits*reference_atoms[i][0], lunits*reference_atoms[i][1], lunits*reference_atoms[i][2],
+ align[i], displace[i] );
+ }
+ } else {
+ for(unsigned i=0;i<reference_atoms.size();++i){
+ ofile.printf("ATOM %5d %-4s %3s %4d %8.3f%8.3f%8.3f%6.2f%6.2f\n",
+ indices[i].serial(), mymoldat->getAtomName(indices[i]).c_str(),
+ mymoldat->getResidueName(indices[i]).c_str(), mymoldat->getResidueNumber(indices[i]),
+ lunits*reference_atoms[i][0], lunits*reference_atoms[i][1], lunits*reference_atoms[i][2],
+ align[i], displace[i] );
+ }
}
}
diff --git a/src/reference/ReferenceAtoms.h b/src/reference/ReferenceAtoms.h
index 6fc17ced1..a3dde109a 100644
--- a/src/reference/ReferenceAtoms.h
+++ b/src/reference/ReferenceAtoms.h
@@ -88,7 +88,7 @@ public:
/// Set the positions of the reference atoms
virtual void setReferenceAtoms( const std::vector<Vector>& conf, const std::vector<double>& align_in, const std::vector<double>& displace_in )=0;
/// Print the atomic positions
- void printAtoms( const double& lunits, OFile& ofile ) const ;
+ void printAtoms( const double& lunits, SetupMolInfo* mymoldat, OFile& ofile ) const ;
/// Return all atom indexes
const std::vector<AtomNumber>& getAbsoluteIndexes();
/// This returns how many atoms there should be
diff --git a/src/reference/ReferenceConfiguration.cpp b/src/reference/ReferenceConfiguration.cpp
index 288aafe15..496580e76 100644
--- a/src/reference/ReferenceConfiguration.cpp
+++ b/src/reference/ReferenceConfiguration.cpp
@@ -25,6 +25,7 @@
#include "core/Value.h"
#include "tools/OFile.h"
#include "tools/PDB.h"
+#include "core/SetupMolInfo.h"
namespace PLMD{
@@ -101,10 +102,10 @@ double ReferenceConfiguration::calculate( const std::vector<Vector>& pos, const
void ReferenceConfiguration::print( const double& lunits, OFile& ofile, const double& time, const double& weight, const double& old_norm ){
ofile.printf("REMARK TIME=%f LOG_WEIGHT=%f OLD_NORM=%f\n",time, weight, old_norm );
- print( lunits, ofile, "%f" ); // HARD CODED FORMAT HERE AS THIS IS FOR CHECKPOINT FILE
+ print( lunits, NULL, ofile, "%f" ); // HARD CODED FORMAT HERE AS THIS IS FOR CHECKPOINT FILE
}
-void ReferenceConfiguration::print( const double& lunits, OFile& ofile, const std::string& fmt ){
+void ReferenceConfiguration::print( const double& lunits, SetupMolInfo* mymoldat, OFile& ofile, const std::string& fmt ){
ReferenceArguments* args=dynamic_cast<ReferenceArguments*>(this);
if( property_names.size()>0 ){
ofile.printf("REMARK PROPERTIES=%s", property_names[0].c_str() );
@@ -123,7 +124,7 @@ void ReferenceConfiguration::print( const double& lunits, OFile& ofile, const st
}
if(args) args->printArguments( ofile, fmt );
ReferenceAtoms* atoms=dynamic_cast<ReferenceAtoms*>(this);
- if(atoms) atoms->printAtoms( lunits, ofile );
+ if(atoms) atoms->printAtoms( lunits, mymoldat, ofile );
ofile.printf("END\n");
}
diff --git a/src/reference/ReferenceConfiguration.h b/src/reference/ReferenceConfiguration.h
index 081d38e94..d122f3e64 100644
--- a/src/reference/ReferenceConfiguration.h
+++ b/src/reference/ReferenceConfiguration.h
@@ -37,6 +37,7 @@ class Value;
class Pbc;
class OFile;
class PDB;
+class SetupMolInfo;
/// \ingroup TOOLBOX
/// Abstract base class for calculating the distance from a reference configuration.
@@ -120,7 +121,7 @@ public:
void copyDerivatives( const ReferenceConfiguration* );
/// Print a pdb file containing the reference configuration
void print( const double& lunits, OFile& ofile, const double& time, const double& weight, const double& old_norm );
- void print( const double& lunits, OFile& ofile, const std::string& fmt );
+ void print( const double& lunits, SetupMolInfo* mymoldat, OFile& ofile, const std::string& fmt );
/// Get one of the referene arguments
virtual double getReferenceArgument( const unsigned& i ) const { plumed_error(); return 0.0; }
/// These are overwritten in ReferenceArguments and ReferenceAtoms but are required here
--
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