# Read proteins from PDB files
#!/usr/bin/python

from Bio.PDB import *
import numpy as np

def getStructure(fileName):
    # create a protein structure parser
    parser = PDBParser();

    # read the protein structure with the parser
    try:
    	structure = parser.get_structure('5szs', fileName);
    	return structure;
    except Exception, err:
	    print err

def getModels(structure):
    for model in structure.get_models():
        yield model;

def getChains(model):
    for chain in model.get_chains():
        yield chain;

def getResidues(chain):
    for residue in chain.get_residues():
        yield residue;

def getAtoms(residue):
    for atom in residue.get_atoms():
	yield atom;

def getAtomInfo(atom):
	print atom.get_name(), atom.get_id(), atom.get_full_id(), atom.get_coord(), atom.get_bfactor(), atom.get_occupancy(), atom.get_fullname(), atom.get_altloc(), atom.get_vector(), atom.get_vector().get_array(), atom.get_parent().get_id()
		

# Walk through protein with iteration
def getStructure(fileName):
    # create a protein structure parser
    parser = PDBParser();

    # read the protein structure with the parser
    try:
    	structure = parser.get_structure('5szs', fileName);
    	return structure;
    except Exception, err:
	    print err

def main():
    structure = getStructure('4mv2.pdb');

    for model in structure:
	for chain in model:
	    for residue in chain:
		print residue.get_resname()
		

# Read proteins from cif files
def getStructure(fileName):
    # create a protein structure parser
    parser = MMCIFParser();

    # read the protein structure with the parser
    try:
    	structure = parser.get_structure('5szs', fileName);
    	return structure;
    except Exception, err:
	    print err
		

# Output a structure to a pdb file
def getStructure(fileName):
    # create a protein structure parser
    parser = PDBParser();

    # read the protein structure with the parser
    try:
    	structure = parser.get_structure('5szs', fileName);
    	return structure;
    except Exception, err:
	    print err

def main():
    ''' Generate dihedral angles for a specific residue 
    
        Args:
            residueName (string), target residue
    '''
    structure = getStructure('5szs.pdb');

    # Dice
    Dice.extract(structure, 'A', 1, 100, 'temp2.pdb');

    # PDBIO
    io = PDBIO();
    sel = Dice.ChainSelector('A', 1, 100);

    io.set_structure(structure);
    io.save('temp.pdb', sel);
		

def getStructure(fileName):
    pdbl = PDBList();
    pdbl.retrieve_pdb_file(fileName, file_format = 'mmCif');

def main():
    ''' Generate dihedral angles for a specific residue 
    
        Args:
            residueName (string), target residue
    '''
    structure = getStructure('1FAT');
		

# Read header information from a pdb or cif file
def getStructure(fileName):
    # create a protein structure parser
    parser = PDBParser();

    # read the protein structure with the parser
    try:
    	structure = parser.get_structure('5szs', fileName);
    	return structure;
    except Exception, err:
	    print err

def main():
    ''' Generate dihedral angles for a specific residue 
    
        Args:
            residueName (string), target residue
    '''
    structure = getStructure('5szs.pdb');
    print structure.header;
		

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