Victor
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Implements methods to verify the ligand properties. More...
Public Member Functions | |
void | addAtom (Atom &a) |
virtual void | bindIn (Atom &_this, Bond &c, Atom &_other) |
virtual void | bindIn (SimpleBond &c) |
virtual void | bindOut (Atom &_this, Bond &c, Atom &_other) |
virtual void | bindOut (SimpleBond &c) |
bool | collides (Component &other, double dist=0.0) |
void | copy (const Bond &orig) |
void | copy (const Ligand &orig) |
void | copy (const Group &orig) |
virtual void | copy (const SimpleBond &orig) |
void | copy (const Component &orig) |
virtual const Group & | getInBond (unsigned int n) const |
virtual Group & | getInBond (unsigned int n) |
virtual Atom & | getInBondRef (unsigned int n) |
virtual vgVector3< double > | getLowerBound (double dist=0.0) |
unsigned int | getMaxInBonds () const |
unsigned int | getMaxOutBonds () const |
virtual Atom & | getOpenInBondRef (unsigned int n=0) |
virtual Atom & | getOpenOutBondRef (unsigned int n=0) |
virtual const Group & | getOutBond (unsigned int n) const |
virtual Group & | getOutBond (unsigned int n) |
virtual Atom & | getOutBondRef (unsigned int n) |
virtual string | getType () const |
virtual vgVector3< double > | getUpperBound (double dist=0.0) |
bool | inSync () |
bool | isBond (const SimpleBond &c) const |
bool | isCofactor () |
bool | isInBond (const SimpleBond &c) const |
bool | isIndirectBond (const SimpleBond &c) const |
bool | isIndirectInBond (const SimpleBond &c) const |
bool | isIndirectOutBond (const SimpleBond &c) const |
bool | isMetalCompound () |
bool | isOutBond (const SimpleBond &c) const |
bool | isSimpleMetalIon () |
bool | isTorsionBond (const SimpleBond &c) const |
bool | isWater () |
Ligand & | operator= (const Ligand &orig) |
void | removeAtom (Atom &a) |
void | setMaxInBonds (unsigned int m) |
void | setMaxOutBonds (unsigned int m) |
virtual void | setType (string _name) |
unsigned int | sizeInBonds () const |
unsigned int | sizeOpenInBonds () const |
unsigned int | sizeOpenOutBonds () const |
unsigned int | sizeOutBonds () const |
virtual void | sync () |
virtual void | unbindIn (Bond &c) |
virtual void | unbindIn (SimpleBond &c) |
virtual void | unbindOut (Bond &c) |
virtual void | unbindOut (SimpleBond &c) |
Protected Member Functions | |
Atom * | pGetAtom (const AtomCode &ac) const |
virtual void | pUnbindIn (SimpleBond &c) |
virtual void | pUnbindOut (SimpleBond &c) |
void | resetBoundaries () |
Implements methods to verify the ligand properties.
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inherited |
In-going bond from this to c, from this' atom _this to c's _other atom.
atom | reference, bond reference, atom reference |
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virtualinherited |
Sets and in-bond from this to c.
Reimplemented in Atom.
Out-going bond from this to c, from this' atom _this to c's _other atom.
atom | reference, bond reference, atom reference |
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virtualinherited |
Sets and out-bond from this to c
Reimplemented in Atom.
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inherited |
Is other within dist of this' bounding box?
other | (Component) |
dist | (double) |
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inherited |
Copy operator. Attention: copy() strips orig from its bonds and attaches them to the new bond.
bond | reference |
void copy | ( | const Ligand & | orig | ) |
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inherited |
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virtualinherited |
Copy operator. Attention: copy() strips orig from its bonds and attaches them to the new bond.
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inherited |
Copy the component. Attention: new elements have to be copied also in Monomer::copy() since it does NOT invoke this function (segmentation fault if it does).
orig |
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virtualinherited |
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virtualinherited |
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virtualinherited |
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virtualinherited |
Return the lower bound coordinates.
dist |
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inherited |
Get maximum of in-bonds.
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inherited |
Get maximum of out-bonds.
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virtualinherited |
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virtualinherited |
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virtualinherited |
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virtualinherited |
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virtualinherited |
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virtualinherited |
Is c bonded to this ?
Reimplemented in SideChain.
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virtualinherited |
Return the upper bound coordinates.
dist |
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inherited |
Checks the "Modified" flag in the component.
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inherited |
Is c bonded to this ?
bool isCofactor | ( | ) |
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inherited |
Is c in-bonded to this ?
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inherited |
Checks if this is indirectly bonded to c. (ie. A to C if A bond B and B bond C)
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inherited |
Checks if this is indirectly bonded to c. (ie. A to C if A bond B and B bond C)
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inherited |
Checks if this is indirectly bonded to c. (ie. A to C if A bond B and B bond C)
bool isMetalCompound | ( | ) |
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inherited |
Is c out-bonded to this ?
bool isSimpleMetalIon | ( | ) |
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inherited |
Checks if this is torsion bond to c. (ie. A to D if A indirect bond C and C bond D)
bool isWater | ( | ) |
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protectedinherited |
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protectedvirtualinherited |
Private method to find the matching in-bond from c to this to remove.
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protectedvirtualinherited |
Private method to find the matching out-bond from c to this to remove.
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protectedvirtualinherited |
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inherited |
Sets maximum of in-bonds.
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inherited |
Sets maximum of out-bonds.
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virtualinherited |
Sets type (eg. C atom, GLY amino acid, etc.) of this.
Reimplemented in AminoAcid, Atom, and Nucleotide.
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inherited |
How many in-bonds are there ?
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inherited |
Returns the number of open in-bonds, ie. how many in-bonds can still be added.
void |
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inherited |
Returns the number of open out-bonds, ie. how many out-bonds can still be added.
void |
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inherited |
How many out-bonds are there ?
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virtualinherited |
Synchronizes coords with structure
Reimplemented from Monomer.
Reimplemented in AminoAcid, and Nucleotide.
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virtualinherited |
Remove in-going bond from this to c.
bond | reference |
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virtualinherited |
Removes an in-bond from this to c.
Reimplemented in Atom.
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virtualinherited |
Remove out-going bond from this to c.
bond | reference |
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virtualinherited |
Removes an out-bond from this to c.
Reimplemented in Atom.