Is a container of Polymers (a component of components). Each chain in a PDB (a Protein object) corresponds to a Polymers. Each Polymer corresponds to a Spacer and a LigandSet (if present).
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Is a container of Polymers (a component of components). Each chain in a PDB (a Protein object) corresponds to a Polymers. Each Polymer corresponds to a Spacer and a LigandSet (if present).
In-going bond from this to c, from this' atom _this to c's _other atom.
- Parameters
-
atom | reference, bond reference, atom reference |
- Returns
- void
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.
- Parameters
-
atom | reference, bond reference, atom reference |
- Returns
- void
Sets and out-bond from this to c
Reimplemented in Atom.
- Parameters
-
Reimplemented from Polymer.
bool collides |
( |
Component & |
other, |
|
|
double |
dist = 0.0 |
|
) |
| |
|
inherited |
Is other within dist of this' bounding box?
- Parameters
-
- Returns
- True, if the component collides with "OTHER"
void copy |
( |
const Bond & |
orig | ) |
|
|
inherited |
Copy operator. Attention: copy() strips orig from its bonds and attaches them to the new bond.
- Parameters
-
- Returns
- void
Copy operator. Attention: copy() strips orig from its bonds and attaches them to the new bond.
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).
- Parameters
-
- Parameters
-
Reimplemented from Polymer.
char getChainLetter |
( |
unsigned int |
i | ) |
|
Returns the chainID by index
- Parameters
-
- Returns
- The chainID (char)
unsigned int getChainNum |
( |
char |
c | ) |
|
Returns the chain index by chainID
- Parameters
-
- Returns
- The chainID index in the chains vector
const SimpleBond & getInBond |
( |
unsigned int |
n | ) |
const |
|
virtualinherited |
Atom & getInBondRef |
( |
unsigned int |
n | ) |
|
|
virtualinherited |
Returns reference to the i-th in-bond atom.
- Parameters
-
- Returns
- Atom reference
Return a pointer to the LigandSet with the requested chainID
- Parameters
-
- Returns
- A pointer to the LiganSet
Return a pointer to the LiganSet by an index in the Components vector.
- Parameters
-
n | (unsigned int), the index of the Polymer in the Components vector |
- Returns
- A pointer to the LiganSet
vgVector3< double > getLowerBound |
( |
double |
dist = 0.0 | ) |
|
|
virtualinherited |
Return the lower bound coordinates.
- Parameters
-
- Returns
- The lowerBound vector (vgVector2<double>)
unsigned int getMaxInBonds |
( |
| ) |
const |
|
inherited |
unsigned int getMaxOutBonds |
( |
| ) |
const |
|
inherited |
Get maximum of out-bonds.
Atom & getOpenInBondRef |
( |
unsigned int |
n = 0 | ) |
|
|
virtualinherited |
Returns reference to the i-th open in-bond atom. NB: This is undefined (ie. returns error) for Bond, but is needed for later structures (AminoAcid, etc.).
- Parameters
-
- Returns
- Atom reference
Reimplemented in Spacer, and AminoAcid.
Atom & getOpenOutBondRef |
( |
unsigned int |
n = 0 | ) |
|
|
virtualinherited |
Returns reference to the i-th open out-bond atom. NB: This is undefined (ie. returns error) for Bond, but is needed for later structures (AminoAcid, etc.).
- Parameters
-
- Returns
- atom reference
Reimplemented in Spacer, and AminoAcid.
const SimpleBond & getOutBond |
( |
unsigned int |
n | ) |
const |
|
virtualinherited |
Atom & getOutBondRef |
( |
unsigned int |
n | ) |
|
|
virtualinherited |
Returns reference to the i-th in-bond atom.
- Parameters
-
- Returns
- Atom reference
Polymer & getPolymer |
( |
unsigned int |
n | ) |
|
Return a pointer to the Spacer with the requested chainID
- Parameters
-
- Returns
- A pointer to the Spacer
Spacer * getSpacer |
( |
unsigned int |
n | ) |
|
Return a pointer to the Spacer by an index in the Components vector.
- Parameters
-
n | (unsigned int), the index of the Polymer in the Components vector |
- Returns
- A pointer to the Spacer
Is c bonded to this ?
Reimplemented in SideChain.
vgVector3< double > getUpperBound |
( |
double |
dist = 0.0 | ) |
|
|
virtualinherited |
Return the upper bound coordinates.
- Parameters
-
- Returns
- The upperBound vector (vgVector2<double>)
Checks the "Modified" flag in the component.
- Returns
- True, if the component coordinates have been already syncronized. Checks also for the "superior" class status.
Checks if this is indirectly bonded to c. (ie. A to C if A bond B and B bond C)
bool isIndirectInBond |
( |
const SimpleBond & |
c | ) |
const |
|
inherited |
Checks if this is indirectly bonded to c. (ie. A to C if A bond B and B bond C)
bool isIndirectOutBond |
( |
const SimpleBond & |
c | ) |
const |
|
inherited |
Checks if this is indirectly bonded to c. (ie. A to C if A bond B and B bond C)
Is c out-bonded to this ?
Checks if this is torsion bond to c. (ie. A to D if A indirect bond C and C bond D)
|
protectedvirtualinherited |
Private method to find the matching in-bond from c to this to remove.
|
protectedvirtualinherited |
Private method to find the matching out-bond from c to this to remove.
- Parameters
-
Reimplemented from Polymer.
void removeComponentFromIndex |
( |
unsigned int |
i | ) |
|
|
virtualinherited |
- Parameters
-
Reimplemented in Spacer.
void setMaxInBonds |
( |
unsigned int |
m | ) |
|
|
inherited |
Sets maximum of in-bonds.
void setMaxOutBonds |
( |
unsigned int |
m | ) |
|
|
inherited |
Sets maximum of out-bonds.
void setType |
( |
string |
_name | ) |
|
|
virtualinherited |
unsigned int sizeInBonds |
( |
| ) |
const |
|
inherited |
How many in-bonds are there ?
unsigned int sizeOpenInBonds |
( |
| ) |
const |
|
inherited |
Returns the number of open in-bonds, ie. how many in-bonds can still be added.
- Parameters
-
- Returns
- unsigned int
unsigned int sizeOpenOutBonds |
( |
| ) |
const |
|
inherited |
Returns the number of open out-bonds, ie. how many out-bonds can still be added.
- Parameters
-
- Returns
- unsigned int
unsigned int sizeOutBonds |
( |
| ) |
const |
|
inherited |
How many out-bonds are there ?
void unbindIn |
( |
Bond & |
c | ) |
|
|
virtualinherited |
Remove in-going bond from this to c.
- Parameters
-
- Returns
- void
Removes an in-bond from this to c.
Reimplemented in Atom.
void unbindOut |
( |
Bond & |
c | ) |
|
|
virtualinherited |
Remove out-going bond from this to c.
- Parameters
-
- Returns
- void
Removes an out-bond from this to c.
Reimplemented in Atom.
The documentation for this class was generated from the following files:
- Biopool/Sources/Protein.h
- Biopool/Sources/Protein.cc