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pdbread.h File Reference

Protein Data Bank I/O routines. More...

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Compounds

struct  Residue_
 a residue or hetgroup. More...

struct  Atom_
 an atom or heteroatom. More...

struct  Connect_
 a connection. More...

struct  Secstr_
 a protein secondary structure element. More...

struct  Ssbond_
 a protein disulfide bridge. More...

struct  Chain_
 a biopolymer chain. More...

struct  Hetgroup_
 a HET group. More...

struct  Hetnamformul_
 a HETNAM or FORMUL. More...

struct  Seqinfo_
 "theoretical" sequence information. More...

struct  Site_
 a site. More...

struct  Pdbentry_
 a PDB record. More...


Typedefs

typedef char Str4_ [5]
 4-letter words..

typedef char Str3_ [4]
 3-letter words: residue abbreviations.

typedef char Str2_ [3]
 2-letter words: element symbols.


Enumerations

enum  Typeflags_ {
  PDB_UNKNOWN = 0, PDB_PROTEIN = 1, PDB_RNA = 2, PDB_DNA = 4,
  PDB_NACID = 6, PDB_SACCH = 8, PDB_BIOPOLY = 15, PDB_HETERO = 16
}
 Flags to indicate macromolecule types: can be ORed together to describe chains which contain different things. More...

enum  Solvtype_ { PDB_NOSOLVENT = 0, PDB_WATER = 1, PDB_SOLVENT = 2 }
 These are possible values for the Hetgroup_.Solvent field: PDB_WATER indicates water molecules for which no HET record is provided, PDB_SOLVENT is for other solvents which have a '*' at pos.19 in their FORMUL record and are represented by a HET group (but perhaps with incorrect atom count), PDB_NOSOLVENT is for all other hetgroups. More...

enum  Sectype_ { PDB_HELIX, PDB_SHEET, PDB_TURN }
 protein secondary structure element types. More...


Functions

char aa_code31 (const char *Aa3)
 aa_code31(Aa3): converts 3-letter all-uppercase amino acid abbreviations into 1-char codes. More...

char* aa_code13 (char Aa1)
 aa_code13(Aa1): converts the 1-letter codes to 3-letter standards. More...

char nu_code31 (const char *Nu3)
 nu_code31(Nu3): converts the "3-letter" nucleotide specifications (right-justified space+letter strings like " A" or " +I") into their 1-letter equivalent. More...

Pdbentry_read_pdb (const char *Pdbfn)
 read_pdb(Pdbfn): reads a PDB file called Pdbfn and puts the result in a Pdbentry_ which is created inside and returned. More...

float atom_dist (const Atom_ *At1, const Atom_ *At2)
 atom_dist(At1, At2): returns the distance between two Atom_ entries.

void write_pdb (const char *Pdbfn, Pdbentry_ *Entry, char *Remarks[], int Remno)
 write_pdb(Pdbfn, Entry, Remarks, Remno): writes the atomic coordinate information in Entry to the file Pdbfn in PDB format. More...

Pdbentry_alloc_pdbentry ()
 alloc_pdbentry(): creates and returns a clean Pdbentry_ or NULL if allocation failed.

void free_pdb (Pdbentry_ *Entry)
 free_pdb(Entry): frees up memory allocated to Entry and its arrays. More...


Detailed Description

Protein Data Bank I/O routines.

Can read and write PDB files that correspond to the PDB 2.1 format specification. Not all PDB cards are implemented.

Definition in file pdbread.h.


Typedef Documentation

typedef char Str4_
 

4-letter words..

Definition at line 70 of file pdbread.h.

typedef char Str3_
 

3-letter words: residue abbreviations.

Definition at line 71 of file pdbread.h.

typedef char Str2_
 

2-letter words: element symbols.

Definition at line 72 of file pdbread.h.


Enumeration Type Documentation

enum Typeflags_
 

Flags to indicate macromolecule types: can be ORed together to describe chains which contain different things.

PDB_NACID==PDB_RNA|PDB_DNA PDB_BIOPOLY==PDB_PROTEIN|PDB_NACID|PDB_SACCH

Enumeration values:
PDB_UNKNOWN  
PDB_PROTEIN  
PDB_RNA  
PDB_DNA  
PDB_NACID  
PDB_SACCH  
PDB_BIOPOLY  
PDB_HETERO  

Definition at line 80 of file pdbread.h.

enum Solvtype_
 

These are possible values for the Hetgroup_.Solvent field: PDB_WATER indicates water molecules for which no HET record is provided, PDB_SOLVENT is for other solvents which have a '*' at pos.19 in their FORMUL record and are represented by a HET group (but perhaps with incorrect atom count), PDB_NOSOLVENT is for all other hetgroups.

Enumeration values:
PDB_NOSOLVENT  
PDB_WATER  
PDB_SOLVENT  

Definition at line 91 of file pdbread.h.

enum Sectype_
 

protein secondary structure element types.

Enumeration values:
PDB_HELIX  
PDB_SHEET  
PDB_TURN  

Definition at line 128 of file pdbread.h.


Function Documentation

char aa_code31 ( const char * Aa3 )
 

aa_code31(Aa3): converts 3-letter all-uppercase amino acid abbreviations into 1-char codes.

Returns 'X' if it cannot translate Aa3. In addition to the 20 standard AA-s, the following translations are accepted: ALB -> 'A' (beta-alanine) CYH, CSH, CSS, CYX -> 'C' (cysteine and cystine) HYP, PR0, PRZ -> 'P' (hydroxyproline and various Pro synonyms) ILU -> 'I' (isoleucine) TRY-> 'W' (tryptophan) UNK -> 'U' (unknown) any other code is translated to X.

Referenced by Pdbentry_::Conno().

char * aa_code13 ( char Aa1 )
 

aa_code13(Aa1): converts the 1-letter codes to 3-letter standards.

Almost the inverse of aa_code31(). Non-standard translations: J->JJJ, O->OOO, U->UNK, X->XXX

Referenced by Pdbentry_::Conno().

char nu_code31 ( const char * Nu3 )
 

nu_code31(Nu3): converts the "3-letter" nucleotide specifications (right-justified space+letter strings like " A" or " +I") into their 1-letter equivalent.

Returns 'X' if it did not work.

Referenced by Pdbentry_::Conno().

Pdbentry_ * read_pdb ( const char * Pdbfn )
 

read_pdb(Pdbfn): reads a PDB file called Pdbfn and puts the result in a Pdbentry_ which is created inside and returned.

If something went wrong then NULL is returned.

Referenced by Pdbentry_::Conno().

float atom_dist ( const Atom_ * At1,
const Atom_ * At2 )
 

atom_dist(At1, At2): returns the distance between two Atom_ entries.

Referenced by Pdbentry_::Conno().

void write_pdb ( const char * Pdbfn,
Pdbentry_ * Entry,
char * Remarks[],
int Remno )
 

write_pdb(Pdbfn, Entry, Remarks, Remno): writes the atomic coordinate information in Entry to the file Pdbfn in PDB format.

Remno remarks are supplied in a char array Remarks[].

Referenced by Pdbentry_::Conno().

Pdbentry_ * alloc_pdbentry ( )
 

alloc_pdbentry(): creates and returns a clean Pdbentry_ or NULL if allocation failed.

Referenced by Pdbentry_::Conno().

void free_pdb ( Pdbentry_ * Entry )
 

free_pdb(Entry): frees up memory allocated to Entry and its arrays.

Does not set Entry to NULL. (Destructor in C++)

Referenced by Pdbentry_::Conno().


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