Added possibility to retrieve more info from MOLINFO

src/core/SetupMolInfo.cpp

@@ -151,4 +151,17 @@ void SetupMolInfo::getBackbone( std::vector<std::string>& restrings, const std::
   }
 }
 
+
+std::string SetupMolInfo::getAtomName(AtomNumber a)const{
+  return pdb.getAtomName(a);
+}
+
+unsigned SetupMolInfo::getResidueNumber(AtomNumber a)const{
+  return pdb.getResidueNumber(a);
+}
+
+std::string SetupMolInfo::getResidueName(AtomNumber a)const{
+  return pdb.getResidueName(a);
+}
+
 }

src/core/SetupMolInfo.h

@@ -41,6 +41,9 @@ public:
   static void registerKeywords( Keywords& keys );
   SetupMolInfo(const ActionOptions&ao);
   void getBackbone( std::vector<std::string>& resstrings, const std::vector<std::string>& atnames, std::vector< std::vector<AtomNumber> >& backbone );
+  std::string getAtomName(AtomNumber a)const;
+  unsigned getResidueNumber(AtomNumber a)const;
+  std::string getResidueName(AtomNumber a)const;
 };
 
 }

src/tools/PDB.cpp

@@ -48,6 +48,27 @@ const std::vector<AtomNumber> & PDB::getAtomNumbers()const{
   return numbers;
 }
 
+std::string PDB::getAtomName(AtomNumber a)const{
+  std::map<AtomNumber,unsigned>::const_iterator p;
+  p=number2index.find(a);
+  if(p==number2index.end()) return "";
+  else return atomsymb[p->second];
+}
+
+unsigned PDB::getResidueNumber(AtomNumber a)const{
+  std::map<AtomNumber,unsigned>::const_iterator p;
+  p=number2index.find(a);
+  if(p==number2index.end()) return 0;
+  else return residue[p->second];
+}
+
+std::string PDB::getResidueName(AtomNumber a) const{
+  std::map<AtomNumber,unsigned>::const_iterator p;
+  p=number2index.find(a);
+  if(p==number2index.end()) return "";
+  else return residuenames[p->second];
+}
+
 unsigned PDB::size()const{
   return positions.size();
 }
@@ -65,6 +86,7 @@ bool PDB::readFromFilepointer(FILE *fp,bool naturalUnits,double scale){
     string record=line.substr(0,6);
     string serial=line.substr(6,5);
     string atomname=line.substr(12,4);
+    string residuename=line.substr(17,3);
     string chainID=line.substr(21,1);
     string resnum=line.substr(22,4);
     string x=line.substr(30,8);
@@ -94,6 +116,7 @@ bool PDB::readFromFilepointer(FILE *fp,bool naturalUnits,double scale){
       // scale into nm
       p*=scale;
       numbers.push_back(a);
+      number2index[a]=positions.size();
       std::size_t startpos=atomname.find_first_not_of(" \t");
       std::size_t endpos=atomname.find_last_not_of(" \t");
       atomsymb.push_back( atomname.substr(startpos, endpos-startpos+1) );
@@ -102,6 +125,7 @@ bool PDB::readFromFilepointer(FILE *fp,bool naturalUnits,double scale){
       occupancy.push_back(o);
       beta.push_back(b);
       positions.push_back(p);
+      residuenames.push_back(residuename);
     }
   }
   return file_is_alive;

src/tools/PDB.h

@@ -27,6 +27,7 @@
 #include <vector>
 #include <string>
 #include "Log.h"
+#include <map>
 
 
 namespace PLMD{
@@ -42,6 +43,8 @@ class PDB{
   std::vector<double> beta;
   std::vector<std::string> remark;
   std::vector<AtomNumber> numbers;
+  std::map<AtomNumber,unsigned> number2index;
+  std::vector<std::string> residuenames;
 public:
 /// Read the pdb from a file, scaling positions by a factor scale
   bool read(const std::string&file,bool naturalUnits,double scale);
@@ -73,6 +76,12 @@ public:
   void renameAtoms( const std::string& old_name, const std::string& new_name );
 ///use the log to dump information  
   friend Log& operator<<(Log& ostr, const PDB& pdb);
+/// return the name of a specific atom
+  std::string getAtomName(AtomNumber a) const;
+/// return the residue number for a specific atom
+  unsigned getResidueNumber(AtomNumber a) const;
+/// return the residue name for a specific atom
+  std::string getResidueName(AtomNumber a) const;
 };
 
 }