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// Mutation.h
#ifndef Mutation_H_
#define Mutation_H_
#include "Utils.h"
#include <string>
#include <iostream>
#define FOLDXSEPARATOR ","
using namespace SimTK;
class Mutation : public SingleResidue {
private:
//std::string chain;
// class SingleResidue uses the startResidue variable to hold its one and only ResidueID
//ResidueID startResidue;//residueID;
std::string substitutedResidueType;
std::string wildTypeResidueType;
public:
Mutation() {setChain ( " "); setResidue (ResidueID( -1111, ' '));
//startResidue.setInsertionCode(' ');
setWildTypeResidueType ( "RESIDUE-TYPE-NOT-SET" );
substitutedResidueType = "RESIDUE-TYPE-NOT-SET";
}
// Converts the current Mutation to an AllResiduesWithin, adding a value for the radius member
AllResiduesWithin allResiduesWithin(double radius){AllResiduesWithin myAllResiduesWithin((*this).getChain(), (*this).getResidue(), radius); return myAllResiduesWithin; };
void print(){
std::cout<<__FILE__<<":"<<__LINE__<<" Mutation chain = >"<<getChain()<<"<, residue = >"<< getResidue().outString()<<"<, substitution = >"<<substitutedResidueType<<"<"<<std::endl; }
void setSubstitutedResidueType(std::string myResidueType) {substitutedResidueType = myResidueType;};
std::string getSubstitutedResidueType() {
std::cout<<__FILE__<<":"<<__LINE__<<" About to return substitutedResidueType = "<<std::endl;
std::cout<<__FILE__<<":"<<__LINE__<<" >"<<substitutedResidueType<<"<"<<std::endl;
return substitutedResidueType;
};
int getResidueNumber() {return getResidue().getResidueNumber() ;}
const std::string getInsertionCode() const { std::string myInsertionCode; myInsertionCode = ( getResidue().getInsertionCode()) ; return myInsertionCode;}
std::string getResidueIDAsString() {return getResidue().outString();}
std::string getMutationAsString() {return (getChain() + getResidueIDAsString() + getSubstitutedResidueType());}
std::string getMutationAsFoldxString() {return getWildTypeResidueType() + getChain() + getResidueIDAsString() + getSubstitutedResidueType();}
void validate() {
if (getResidueNumber() < 0) {
std::cout<<__FILE__<<":"<<__LINE__<<" WARNING! The residueNumber is < 0!"<<std::endl;
// Downgraded from error to warning, 24 nov 2019. seems to work fine.
//exit(1);
}
if ((substitutedResidueType.length() == 0) || (substitutedResidueType.length() > 1)) {
std::cout<<__FILE__<<":"<<__LINE__<<" The substitutedResidueType.length() is either 0 or >1."<<std::endl;
exit(1);
}
if ((getInsertionCode().length() == 0) || (getInsertionCode().length() > 1)) {
std::cout<<__FILE__<<":"<<__LINE__<<" getInsertionCode().length() returned either 0 or >1."<<std::endl;
exit(1);
}
std::cout<<__FILE__<<":"<<__LINE__<<" Validated: "<<getMutationAsString()<<std::endl;
}
Mutation(String myChainID, ResidueID myResidueID, String mySubstitutedResidueType ) {
setChain (myChainID);
setResidue(myResidueID);
setSubstitutedResidueType(mySubstitutedResidueType);
validate();}
// This function expects either a breeder formatted (C-NNNI-S) or SKEMPI formatted (WCNNIS) single mutation string. Based on the presence or absence of MUTATIONMINORSEPARATOR (currently '-'), it determines which is being used.
std::string getWildTypeResidueType( ){
std::cout<<__FILE__<<":"<<__LINE__<<" Returning wildTypeResidueType = >"<<wildTypeResidueType<<"< "<<std::endl;
return wildTypeResidueType;}
void setWildTypeResidueType(std::string myWildTypeResidueType ){
wildTypeResidueType = myWildTypeResidueType;
}
void setChainSubstitutionFromSingleMutationString(std::string mySingleMutationString){
std::cout<<__FILE__<<":"<<__LINE__<<" processing : >"<<mySingleMutationString<<"< "<<std::endl;
size_t minorSeparatorPosition1 = mySingleMutationString.find(MUTATIONMINORSEPARATOR);
std::cout<<__FILE__<<":"<<__LINE__<<std::endl;
if (minorSeparatorPosition1 == std::string::npos){ // This is the case the mutation string is in SKEMPI format.
std::cout<<__FILE__<<":"<<__LINE__<<std::endl;
std::string myChain = mySingleMutationString.substr(1,1); // The second character must be the chain ID
std::cout<<__FILE__<<":"<<__LINE__<<std::endl;
setChain (myChain);
std::cout<<__FILE__<<":"<<__LINE__<<std::endl;
std::string myResidueIDString = mySingleMutationString.substr(2,mySingleMutationString.length()-3); // From the third to the penultimate character, must be the residue number and insertion string.
std::cout<<__FILE__<<":"<<__LINE__<<std::endl;
setResidue(ResidueID(myResidueIDString));
std::cout<<__FILE__<<":"<<__LINE__<<" mySingleMutationString.length() = "<<mySingleMutationString.length()<< std::endl;
std::string mySubstitution = mySingleMutationString.substr(mySingleMutationString.length()-1,1); // The last character, must be the substituted residue type.
std::cout<<__FILE__<<":"<<__LINE__<<std::endl;
setSubstitutedResidueType(mySubstitution);
std::cout<<__FILE__<<":"<<__LINE__<<std::endl;
} else { // This is the case the mutation string is in breeder format.
std::cout<<__FILE__<<":"<<__LINE__<<std::endl;
if ((minorSeparatorPosition1 == 0) || (minorSeparatorPosition1 == (mySingleMutationString.length()-1))){
std::cout<<__FILE__<<":"<<__LINE__<<" Invalid minor separator position : "<<minorSeparatorPosition1<<std::endl; exit(1);
}
size_t minorSeparatorPosition2 = mySingleMutationString.find(MUTATIONMINORSEPARATOR, (minorSeparatorPosition1 + 1));
std::cout<<__FILE__<<":"<<__LINE__<<std::endl;
setChain(mySingleMutationString.substr(0,minorSeparatorPosition1));
std::cout<<__FILE__<<":"<<__LINE__<<std::endl;
std::string residueIDString = mySingleMutationString.substr(minorSeparatorPosition1+1,( minorSeparatorPosition2 - minorSeparatorPosition1 - 1));
std::cout<<__FILE__<<":"<<__LINE__<<std::endl;
setResidue(ResidueID(residueIDString));
std::cout<<__FILE__<<":"<<__LINE__<<"..."<<std::endl;
std::string mySubstitution = mySingleMutationString.substr(minorSeparatorPosition2+1,mySingleMutationString.length()-1 ); // The last character, must be the substituted residue type.
if (mySubstitution.length() != 1){
std::cout<<__FILE__<<":"<<__LINE__<<" Invalid substituted residue type : >"<< mySubstitution <<"< " <<std::endl; exit(1);
}
std::cout<<__FILE__<<":"<<__LINE__<<std::endl;
setSubstitutedResidueType(mySubstitution);
}
} // of setChainSubstitutionFromSingleMutationString
};
#endif
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