Mol2Atom

This is a general class to hold an atom as it appears in a Mol2 file.

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Class Summary

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KEYWORD

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AUTHORS

copyright: SAMBA Group , Tel-Aviv Univ. Israel, 2003.

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CHANGES LOG

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GOALS

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USAGE

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Mol2Atom();

An empty constructor that gives the atom members null values

  Mol2Atom();

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Mol2Atom(const Vector3& p, const unsigned short aid, const string atom_name, const string atom_type, const ELEMENT element_, const unsigned int subst_id, const string subst_name, const float partialCharge_);

An explicit constructor

  Mol2Atom(const Vector3& p, const unsigned short aid, 
	     const string atom_name, const string atom_type, 
	     const ELEMENT element_, const unsigned int subst_id, 
	     const string subst_name, const float partialCharge_);

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explicit Mol2Atom(const char* const mol2rec);

A constructor that intiates an atom type from a line of a Mol2 record

  explicit Mol2Atom(const char* const mol2rec);

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unsigned short getAtomId() const ;

returns the atom id in the mol2 file

  unsigned short getAtomId() const                   
;

Function is currently defined inline.

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string getAtomName() const ;

returns atom name

  string getAtomName() const                     
;

Function is currently defined inline.

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string getAtomType() const ;

returns atom Sybyl type

  string getAtomType() const                     
;

Function is currently defined inline.

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unsigned int getSubstId() const ;

returns substructure id

  unsigned int getSubstId() const                    
;

Function is currently defined inline.

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string getSubstName() const ;

returns substructure name

  string getSubstName() const                      
;

Function is currently defined inline.

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float getPartialCharge() const ;

  float getPartialCharge() const                          
;

Function is currently defined inline.

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float getRadius() const;

  float getRadius() const;

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bool isHetero() const ;

  bool isHetero() const                                                                                                                                                                                                                                             ;

Function is currently defined inline.

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ELEMENT getElement() const ;

  ELEMENT getElement() const                    
;

Function is currently defined inline.

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ELEMENT getElement(const string atomName, const string sybylAtomType);

Determines the periodic table element according to the given SYBYL atom type

  static ELEMENT getElement(const string atomName, const string sybylAtomType);

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void setPartialCharge(float charge) ;

  void setPartialCharge(float charge)                          
;

Function is currently defined inline.

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void dumpInfo(ostream& output) const;

  void dumpInfo(ostream& output) const;

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friend ostream& operator<<(ostream& s, const Mol2Atom& at);

Writing back the mol2 line - without the endline

  friend ostream& operator<<(ostream& s, const Mol2Atom& at);

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ostream& output2PDB(ostream& s, unsigned int atomOffset ) const;

Writing back in PDB format

  ostream& output2PDB(ostream& s, unsigned int atomOffset = 0) const;

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void buildAtomType2ElementMap();

This method builds a static hash that maps sybyl atom type in upper case to the appropriate atom element.

  static void buildAtomType2ElementMap();

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void buildElement2RadiusMap();

builds mapping between element type and radius

  static void buildElement2RadiusMap();

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unsigned short atomId;

  unsigned short atomId;      // atom index

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string atomName;

  string atomName;            // atom name

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string atomType;

  string atomType;            // Sybyl atom type

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ELEMENT element;

  ELEMENT element;            // The periodic table element

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unsigned int substId;

  unsigned int substId;       // id of the substructure (not in use now, may cause problems with more than one substr)

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string substName;

  string substName;           // name of the substructure (not in use now, may cause problems with more than one substr)

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float partialCharge;

  float partialCharge;        // atom partialCharge  

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All Members

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Ancestors

• Vector3

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Descendants

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