UMol.PDBReader Class Reference

Creates a UnityMolStructure object from a local or remote PDB file More...

Inheritance diagram for UMol.PDBReader:

Public Member Functions
	PDBReader (string fileName="", string PDBServer="")
IEnumerator	Fetch (string entryCode, System.Action< UnityMolStructure > result, bool readHet=true, bool readWater=true)
UnityMolStructure	Fetch (string EntryCode, bool readHet=true, bool readWater=true)
Public Member Functions inherited from UMol.Reader
	Reader ()
	Reader (string fileName)
void	updateFileNames ()
UnityMolStructure	Read (bool readHet=true, bool readWater=true)
	Reads a file from local HDD and parses the data More...

Static Public Member Functions
static UnityMolStructure	ParseFromString (string pdbContent)
static string	Write (UnityMolStructure structure)
	PDB writer Uses a structure and outputs a string containing all the models Ignores secondary structure information More...
static string	Write (UnityMolSelection select, bool writeModel=false, bool writeHET=true, bool forceHetAsAtom=false, Vector3[] overridedPos=null)
	PDB writer Uses a selection Ignores secondary structure information More...
static bool	isLigand (string resName)
static string	GuessElementFromAtomName (string atomName, string resName, bool isHET)
	Guess atom element from atom name By default, if the element cannot be guessed, returns X. More...
static void	AddToStructure (string lines, UnityMolStructure structure)
	Add atoms to a structure using pdb lines Atoms are only added to the current model of the structure More...
Static Public Member Functions inherited from UMol.Reader
static void	identifyStructureMolecularType (UnityMolStructure s)
	Fills the structureType field in the UnityMolStructure class based on atom names More...
static Reader	GuessReaderFrom (string filename, string format="")

Static Public Attributes
static string []	PDBextensions = {"pdb", "pdb.gz", "ent", "pqr"}
Static Public Attributes inherited from UMol.Reader
static int	limitBigMolecule = 5000

Protected Member Functions
override UnityMolStructure	ReadData (StreamReader sr, bool readHET, bool readWater, bool ignoreStructureM=false)
	Parses a PDB file to a UnityMolStructure object ignoreStructureM flag is used to avoid adding the structure into managers and just returns a UnityMolStructure More...

Additional Inherited Members
Static Protected Member Functions inherited from UMol.Reader
static void	FillSecondaryStructure (UnityMolStructure structure, List< secStruct > secStructsList)
static void	CreateColliders (UnityMolSelection sel)
	Creates sphere collider for each atom of the current model of the structure More...
static bool	QuickStartWith (string full, string comp)
	Check if the string full contains at the begining, the string comp More...
static string	findNewAtomName (HashSet< string > residueAtoms, string name)
Protected Attributes inherited from UMol.Reader
string	fileName
string	fileNameWithoutExtension

Detailed Description

Creates a UnityMolStructure object from a local or remote PDB file

Constructor & Destructor Documentation

PDBReader()

UMol.PDBReader.PDBReader	(	string	fileName = "",
		string	PDBServer = ""
	)

Member Function Documentation

AddToStructure()

static void UMol.PDBReader.AddToStructure ( string  lines, UnityMolStructure  structure  )

static

Add atoms to a structure using pdb lines Atoms are only added to the current model of the structure

Fetch() [1/2]

IEnumerator UMol.PDBReader.Fetch	(	string	entryCode,
		System.Action< UnityMolStructure >	result,
		bool	readHet = true,
		bool	readWater = true
	)

Fetch() [2/2]

UnityMolStructure UMol.PDBReader.Fetch	(	string	EntryCode,
		bool	readHet = true,
		bool	readWater = true
	)

GuessElementFromAtomName()

static string UMol.PDBReader.GuessElementFromAtomName ( string  atomName, string  resName, bool  isHET  )

static

Guess atom element from atom name By default, if the element cannot be guessed, returns X.

isLigand()

static bool UMol.PDBReader.isLigand ( string  resName )

static

ParseFromString()

static UnityMolStructure UMol.PDBReader.ParseFromString ( string  pdbContent )

static

ReadData()

override UnityMolStructure UMol.PDBReader.ReadData ( StreamReader  sr, bool  readHET, bool  readWater, bool  ignoreStructureM = false  )

protectedvirtual

Parses a PDB file to a UnityMolStructure object ignoreStructureM flag is used to avoid adding the structure into managers and just returns a UnityMolStructure

Implements UMol.Reader.

Write() [1/2]

static string UMol.PDBReader.Write ( UnityMolStructure  structure )

static

PDB writer Uses a structure and outputs a string containing all the models Ignores secondary structure information

Write() [2/2]

static string UMol.PDBReader.Write ( UnityMolSelection  select, bool  writeModel = false, bool  writeHET = true, bool  forceHetAsAtom = false, Vector3 []  overridedPos = null  )

static

PDB writer Uses a selection Ignores secondary structure information

Member Data Documentation

PDBextensions

string [] UMol.PDBReader.PDBextensions = {"pdb", "pdb.gz", "ent", "pqr"}

static

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The documentation for this class was generated from the following file:

• C:/Users/Xavier/Dev/UnityMolX/Assets/Scripts/ParseData/PDBReader.cs