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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... |
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.
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4-letter words..
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3-letter words: residue abbreviations.
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2-letter words: element symbols.
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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 |
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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.
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protein secondary structure element types.
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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(). |
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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(). |
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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(). |
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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(). |
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atom_dist(At1, At2): returns the distance between two Atom_ entries.
Referenced by Pdbentry_::Conno(). |
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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(). |
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alloc_pdbentry(): creates and returns a clean Pdbentry_ or NULL if allocation failed.
Referenced by Pdbentry_::Conno(). |
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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(). |