Serialized Form

Package PIP.Collections

Class PIP.Collections.MultiMap extends AbstractMap<K,V extends java.util.Collection> implements Serializable

Serialized Fields

backing

java.util.Map<K,V> backing

factory

org.apache.commons.collections.Factory factory

Class PIP.Collections.Piecewise extends AbstractList<T> implements Serializable

Serialized Fields

ranges

java.util.List<E> ranges

Class PIP.Collections.Range extends AbstractList<E> implements Serializable

serialVersionUID: 944563220162252424L

Serialized Fields

viewed

java.util.List<E> viewed

start

int start

end

int end

Package PIP.Collections.Persistent

Class PIP.Collections.Persistent.SArrayList extends AbstractList<T> implements Serializable

Serialized Fields

list

java.util.ArrayList<E> list

Class PIP.Collections.Persistent.SHashMap extends AbstractMap<K,V> implements Serializable

Serialized Fields

map

java.util.HashMap<K,V> map

Package PIP.Core

Class PIP.Core.Assembly extends java.lang.Object implements Serializable

serialVersionUID: 862034269047613535L

Serialized Fields

crystalPacking

boolean crystalPacking

Kim Henrick decided to include assemblies which are due to crystal packing according to PQS but may have interesting properties. Most of the time only use assemblies where crystalPacking is false otherwise you will be using non valid assemblies.

msdid

int msdid

The msdid is the id of the Assembly within the MSD. It can be used to link back to the MSD

entry

Entry entry

The entry is the PDB entry from where this Assembly is observed

chains

java.util.List<E> chains

The chains, domain and interactions are just lists of all of the chains, domain and domain interactions seen in the Assembly

domains

java.util.List<E> domains

interactions

java.util.List<E> interactions

Class PIP.Core.Atom extends java.lang.Object implements Serializable

serialVersionUID: 947832201522528654L

Serialized Fields

msdid

int msdid

msdid - The id of the Atom within the MSD. It can be used to link back to the MSD

residue

Residue residue

residue - A link back to the residue that the atom belongs to.

element

byte element

element - The standard one or two character symbol of the chemical element of the atom

atomName

java.lang.String atomName

atomName - The standard PDB name of the atom in the molecule that correspond with the definition of the ligand in the chemical dictionary. This might be different from the name in the PDB entry either due to inconsistent naming, or because this is a totally different ligand.

alternative

char alternative

alternative - The ALT code of the atom as defined in the PDB

point

float[] point

point - The co-ordinates of the atom (XYZ)

Class PIP.Core.Chain extends java.lang.Object implements Serializable

serialVersionUID: 81118151882939012L

Serialized Fields

msdid

int msdid

assembly

Assembly assembly

nonAssValid

boolean nonAssValid

chainCodeMSD

java.lang.String chainCodeMSD

chainCodeOneLetter

char chainCodeOneLetter

residues

java.util.List<E> residues

authorChainCode

java.lang.String authorChainCode

type

char type

swissprotId

java.lang.String swissprotId

swissprotAcc

java.lang.String swissprotAcc

goTerms

java.util.List<E> goTerms

interproTerms

java.util.List<E> interproTerms

ASA

double ASA

Class PIP.Core.Element extends java.lang.Object implements Serializable

serialVersionUID: 8797878654L

Serialized Fields

element

java.lang.String element

Class PIP.Core.Elements extends java.lang.Object implements Serializable

serialVersionUID: 947891522528654L

Serialized Fields

stringMap

java.util.Map<K,V> stringMap

elements

java.util.List<E> elements

Class PIP.Core.Entry extends java.lang.Object implements Serializable

serialVersionUID: 2176715737651643674L

Serialized Fields

msdid

int msdid

assemblies

java.util.List<E> assemblies

resolution

float resolution

et

byte et

entryCode

java.lang.String entryCode

Class PIP.Core.ExperimentType extends java.lang.Object implements Serializable

serialVersionUID: 2528654L

Serialized Fields

ex

java.lang.String ex

Class PIP.Core.ExperimentTypes extends java.lang.Object implements Serializable

serialVersionUID: 947832201527854L

Serialized Fields

stringMap

java.util.Map<K,V> stringMap

ex

java.util.List<E> ex

Class PIP.Core.Residue extends java.lang.Object implements Serializable

serialVersionUID: 280247219205433591L

Serialized Fields

msdid

int msdid

msdid - The id of the Residue within the MSD. It can be used to link back to the MSD

atoms

java.util.List<E> atoms

WBR

char WBR

The type of the component R:residue, B:bound molecule, W:water. This normally has to correspond with the type of the chain where there residue belongs

secStruct

char secStruct

A symbol for the secondary structure as derived by DSSP B:bulge, C:coil, E:strand, G:3-10-helix, H:alpha-helix, S:bend, I:inverse-turn, T:beta-turn

code

char code

One code letter for the ligand (aminoacid, nucleic acid) in order to construct sequences

pos

float[] pos

the coordinates for the average position of all of the atoms in the residue

resName

short resName

This attribute provides a code from the chem comp dictionary for standard residues. This attribute must be the same for small molecules that represent our variations on topology/chemistry for a polymer component e.g. All ALA's should have a code_3_letter of ALA. All adenosine nucleotides should have a 3 letter code of A, except for those that have a topology of 'free'.

chain

Chain chain

Link to the chain to which the residue belongs

resPosition

int resPosition

res position in the chain as per the MSD - starting at 1 - do not use for domains...

SPSerial

int SPSerial

the position of the residue in the chain according to swissprot

PDBOriginalCode

java.lang.String PDBOriginalCode

The 3 letter residue code as seen in the original PDB file.

PDBSeq

int PDBSeq

The seq of the residue in the original PDB file

Class PIP.Core.ResidueName extends java.lang.Object implements Serializable

serialVersionUID: 94783276922528654L

Serialized Fields

name

java.lang.String name

Class PIP.Core.ResidueNames extends java.lang.Object implements Serializable

serialVersionUID: 94783220152754L

Serialized Fields

stringMap

java.util.Map<K,V> stringMap

resName

java.util.List<E> resName

Package PIP.Domains

Class PIP.Domains.Domain extends Piecewise<Residue> implements Serializable

serialVersionUID: 4546999511671930746L

Serialized Fields

id

java.lang.String id

family

Family family

uniqueID

java.lang.String uniqueID

Package PIP.Domains.Family

Class PIP.Domains.Family.Cath extends HierarchicalFamily implements Serializable

serialVersionUID: 14783220542328654L

Serialized Fields

levels

int[] levels

Class PIP.Domains.Family.HierarchicalFamily extends java.lang.Object implements Serializable

Class PIP.Domains.Family.Pfam extends java.lang.Object implements Serializable

serialVersionUID: 94783220152253454L

Serialized Fields

id

java.lang.String id

Class PIP.Domains.Family.Scop extends HierarchicalFamily implements Serializable

serialVersionUID: 543832265522528654L

Serialized Fields

cls

java.lang.String cls

levels

int[] levels

Class PIP.Domains.Family.Subfamily extends HierarchicalFamily implements Serializable

serialVersionUID: 3554620804269045L

Serialized Fields

family

HierarchicalFamily family

levels

int levels