cpdb

Pdb file parser library written in C

What is Pdb file format ?

Pdb file format was created in 1970's and had been using for keeping 3D crystal structure of biological molecules. Besides there are newer generation formats Pdb format is still the commonly used one, since it the oldest and most humanly readable text based format.

What is cpdb ?

cpdb is a library for parsing pdb files which is written in C language ( not C++ ). Although there are good and reliable parsers in languages as C++, Python, Ruby etc, there are limited alternative to pure C language. This is the reason why cpdb born.

Not a parser !

Since a good parser should parse all file without losing any information, cpdb is just focused on parsing atoms in pdb file. This is because me and most of other scientist are just dealing with topological studies.

## Usage

### Quick Start cpdb usage is stupidly easy with 4 steps.

1. include header into your own project #include "cpdb.h"
2. create a pdb type pointer and init pdb *P = initPDB()
3. parse pdb file from a path parsePDB("foo/foo.pdb", P , "")
4. release the pdb after your job is done freePDB(P)

Basic Parsing Functions

pdb* initPDB()

for initialise pdb structure type. To work with cpdb all data is stored into one pdb structure type.

int parsePDB (char *pdbFilePath, pdb *P , char *options);

parsing pdb file from pdbFilePath path to P pdb type pointer. options is used for changing parser function behaviour.

options

by default parsePDB function do not parse duplicated atoms and hydrogen atoms. This is common behaviour for many scientist. To parse these atoms

• pass h for hydrogen
• pass l for alternate locations
• pass a for parsing all

int writePDB (const char *filename, const pdb *P);

write pdb type to filepath given as filename with using pdb format.

int writeFilePDB (FILE *F, const pdb *P);

write pdb type to file pointer given F For whom who needs to handle file opening by himself.

int printPDB (pdb *P);

prints pdb type as pdb format to screen

void freePDB (pdb *P);

free allocated pdb type

Additional Creating functions

Here are some function for creating pdb type without existing file. For whom may want to use same structure without pdb file format.

void appendChaintoPdb (pdb *P, chain newChain); void appendResiduetoChain (chain *C, residue newResidue); void appendAtomtoResidue (residue *R, atom newAtom);

Utils Functions

atom* getAtom (residue *resA, char *atomType);

returns desited atomType from residue type getAtom ( *Res, "CA" )

float distanceAtom (atom A, atomB);

calculate distance between two atoms

Structure

This library has 5 types of custom structure. pdb, chain, residue, atom, v3. Here is these structure details.

struct pdb {
    chain *chains;
    int size; // number of chains in pdb
    char name[32];
};

struct chain {
    char id;
    residue *residues;
    int size; // number of residues in chain
};
struct residue {
    int id;
    int idx;
    char type[5];
    atom *atoms;
    int size; // number of atoms in residue
    residue *next, *prev;
};

struct atom {
    int id;
    int idx;
    char type[5];
    char element[3];
    v3 coor;
    float tfactor, occupancy;
    atom *next, *prev;
    residue *res;
};

struct v3 {
    float x,y,z;
};

TODO

Checking pdb format

Sometimes, pdb format has some defects or there may be some missing residues or missing atoms in the crystal structure. Checking these defects should be added for both warning and correction level.

Mutation Pdb

Add functions for delete and replace residues and atoms

### Parse Secondary structure Add parsing secondary structure info

parse multiple model

add parsing multiple model for nmr

Warning

This library is still under development. It means that didn't passed my hardcore testing for scientific research yet.