The purpose of this issue is for me to keep track of the refactored functions. A list of currently implemented functions is below:
All ticked methods contain docstrings, were modified and only require final checks.
def backbone(inpath=None, outpath=None):def calpha_only(inpdb, outpdb):def check_pdb_directory(directory,single=True,allsame=True,sequence=None):def check_pdbs(models,single=True,allsame=True,sequence=None):def extract_chain(inpdb, outpdb, chainID=None, newChainID=None, cAlphaOnly=False, renumber=True ):def extract_model(inpdb, outpdb, modelID ):def keep_matching(refpdb=None, targetpdb=None, outpdb=None, resSeqMap=None ):def _keep_matching(refpdb=None, targetpdb=None, outpdb=None, resSeqMap=None ):def get_info(inpath):def match_resseq(targetPdb=None, outPdb=None, resMap=None, sourcePdb=None ):def merge(pdb1=None, pdb2=None, pdbout=None ):def molecular_weight(pdbin):def most_prob(hierarchy, always_keep_one_conformer=True):def num_atoms_and_residues(pdbin,first=False):def _parse_modres(modres_text):def prepare_nmr_model(nmr_model_in,models_dir):def reliable_sidechains(inpath=None, outpath=None ):def rename_chains(inpdb=None, outpdb=None, fromChain=None, toChain=None ):def resseq(pdbin):def _resseq(hierarchy):def renumber_residues(pdbin, pdbout, start=1):def _renumber(hierarchy, start):def renumber_residues_gaps(pdbin, pdbout, gaps, start=1):def _rog_side_chain_treatment(hierarchy, scores, del_orange):def rog_side_chain_treatment(pdbin, pdbout, rog_data, del_orange=False):def select_residues(pdbin, pdbout, chain_id=None, delete=None, tokeep=None, delete_idx=None, tokeep_idx=None, raw=False):def sequence(pdbin):def _sequence(hierarchy):def _sequence1(hierarchy):def sequence_data(pdbin):def _sequence_data(hierarchy):def split_pdb(pdbin, directory=None):def split_into_chains(pdbin, chain=None, directory=None):def standardise(pdbin, pdbout, chain=None, del_hetatm=False):def std_residues_cctbx(pdbin, pdbout, del_hetatm=False):def std_residues(pdbin, pdbout, del_hetatm=False):def strip(pdbin, pdbout, hetatm=False, hydrogen=False, atom_types=[]):def _strip(hierachy, hetatm=False, hydrogen=False, atom_types=[]):def to_single_chain(inpath, outpath):def translate(inpdb=None, outpdb=None, ftranslate=None):
Deleted functions
def extract_header_pdb_code(pdb_input):def extract_header_title(pdb_input):def _parse_rwcontents(logfile):def _run_rwcontents(pdbin, logfile):def reliable_sidechains_cctbx(pdbin=None, pdbout=None ):def Xselect_residues(inpath=None, outpath=None, residues=None):def Xsplit(pdbin):def Xstd_residues(pdbin, pdbout ):def xyz_coordinates(pdbin):def _xyz_coordinates(hierarchy):def xyz_cb_coordinates(pdbin):def _xyz_cb_coordinates(hierarchy):def _xyz_atom_coords(atom_group): 
The purpose of this issue is for me to keep track of the refactored functions. A list of currently implemented functions is below:
All ticked methods contain docstrings, were modified and only require final checks.
def backbone(inpath=None, outpath=None):def calpha_only(inpdb, outpdb):def check_pdb_directory(directory,single=True,allsame=True,sequence=None):def check_pdbs(models,single=True,allsame=True,sequence=None):def extract_chain(inpdb, outpdb, chainID=None, newChainID=None, cAlphaOnly=False, renumber=True ):def extract_model(inpdb, outpdb, modelID ):def keep_matching(refpdb=None, targetpdb=None, outpdb=None, resSeqMap=None ):def _keep_matching(refpdb=None, targetpdb=None, outpdb=None, resSeqMap=None ):def get_info(inpath):def match_resseq(targetPdb=None, outPdb=None, resMap=None, sourcePdb=None ):def merge(pdb1=None, pdb2=None, pdbout=None ):def molecular_weight(pdbin):def most_prob(hierarchy, always_keep_one_conformer=True):def num_atoms_and_residues(pdbin,first=False):def _parse_modres(modres_text):def prepare_nmr_model(nmr_model_in,models_dir):def reliable_sidechains(inpath=None, outpath=None ):def rename_chains(inpdb=None, outpdb=None, fromChain=None, toChain=None ):def resseq(pdbin):def _resseq(hierarchy):def renumber_residues(pdbin, pdbout, start=1):def _renumber(hierarchy, start):def renumber_residues_gaps(pdbin, pdbout, gaps, start=1):def _rog_side_chain_treatment(hierarchy, scores, del_orange):def rog_side_chain_treatment(pdbin, pdbout, rog_data, del_orange=False):def select_residues(pdbin, pdbout, chain_id=None, delete=None, tokeep=None, delete_idx=None, tokeep_idx=None, raw=False):def sequence(pdbin):def _sequence(hierarchy):def _sequence1(hierarchy):def sequence_data(pdbin):def _sequence_data(hierarchy):def split_pdb(pdbin, directory=None):def split_into_chains(pdbin, chain=None, directory=None):def standardise(pdbin, pdbout, chain=None, del_hetatm=False):def std_residues_cctbx(pdbin, pdbout, del_hetatm=False):def std_residues(pdbin, pdbout, del_hetatm=False):def strip(pdbin, pdbout, hetatm=False, hydrogen=False, atom_types=[]):def _strip(hierachy, hetatm=False, hydrogen=False, atom_types=[]):def to_single_chain(inpath, outpath):def translate(inpdb=None, outpdb=None, ftranslate=None):Deleted functions
def extract_header_pdb_code(pdb_input):def extract_header_title(pdb_input):def _parse_rwcontents(logfile):def _run_rwcontents(pdbin, logfile):def reliable_sidechains_cctbx(pdbin=None, pdbout=None ):def Xselect_residues(inpath=None, outpath=None, residues=None):def Xsplit(pdbin):def Xstd_residues(pdbin, pdbout ):def xyz_coordinates(pdbin):def _xyz_coordinates(hierarchy):def xyz_cb_coordinates(pdbin):def _xyz_cb_coordinates(hierarchy):def _xyz_atom_coords(atom_group):