idx int64 0 63k | question stringlengths 53 5.28k | target stringlengths 5 805 |
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59,900 | def pdbe_status_code ( code ) : url = 'http://www.ebi.ac.uk/pdbe/entry-files/download/{0}_1.mmol' . format ( code ) r = requests . head ( url = url ) return r . status_code | Check if a PDB code has structure files on the PDBE site . |
59,901 | def preferred_mmol ( code ) : if code in mmols_numbers . keys ( ) : mmol = mmols_numbers [ code ] [ 1 ] return mmol elif is_obsolete ( code ) : raise ValueError ( 'Obsolete PDB code {0}' . format ( code ) ) else : url_string = "http://www.ebi.ac.uk/pdbe/entry/pdb/{0}/analysis" . format ( code ) r = requests . get ( url... | Get mmol number of preferred biological assembly as listed in the PDBe . |
59,902 | def current_codes_from_pdb ( ) : url = 'http://www.rcsb.org/pdb/rest/getCurrent' r = requests . get ( url ) if r . status_code == 200 : pdb_codes = [ x . lower ( ) for x in r . text . split ( '"' ) if len ( x ) == 4 ] else : print ( 'Request for {0} failed with status code {1}' . format ( url , r . status_code ) ) retu... | Get list of all PDB codes currently listed in the PDB . |
59,903 | def mmols ( self ) : mmols_dict = { } mmol_dir = os . path . join ( self . parent_dir , 'structures' ) if not os . path . exists ( mmol_dir ) : os . makedirs ( mmol_dir ) mmol_file_names = [ '{0}_{1}.mmol' . format ( self . code , i ) for i in range ( 1 , self . number_of_mmols + 1 ) ] mmol_files = [ os . path . join (... | Dict of filepaths for all mmol files associated with code . |
59,904 | def dssps ( self ) : dssps_dict = { } dssp_dir = os . path . join ( self . parent_dir , 'dssp' ) if not os . path . exists ( dssp_dir ) : os . makedirs ( dssp_dir ) for i , mmol_file in self . mmols . items ( ) : dssp_file_name = '{0}.dssp' . format ( os . path . basename ( mmol_file ) ) dssp_file = os . path . join ( ... | Dict of filepaths for all dssp files associated with code . |
59,905 | def fastas ( self , download = False ) : fastas_dict = { } fasta_dir = os . path . join ( self . parent_dir , 'fasta' ) if not os . path . exists ( fasta_dir ) : os . makedirs ( fasta_dir ) for i , mmol_file in self . mmols . items ( ) : mmol_name = os . path . basename ( mmol_file ) fasta_file_name = '{0}.fasta' . for... | Dict of filepaths for all fasta files associated with code . |
59,906 | def mmcif ( self ) : mmcif_dir = os . path . join ( self . parent_dir , 'mmcif' ) if not os . path . exists ( mmcif_dir ) : os . makedirs ( mmcif_dir ) mmcif_file_name = '{0}.cif' . format ( self . code ) mmcif_file = os . path . join ( mmcif_dir , mmcif_file_name ) if not os . path . exists ( mmcif_file ) : get_mmcif ... | Filepath for mmcif file associated with code . |
59,907 | def categories ( self ) : category_dict = { } for ligand in self : if ligand . category in category_dict : category_dict [ ligand . category ] . append ( ligand ) else : category_dict [ ligand . category ] = [ ligand ] return category_dict | Returns the categories of Ligands in LigandGroup . |
59,908 | def category_count ( self ) : category_dict = self . categories count_dict = { category : len ( category_dict [ category ] ) for category in category_dict } return count_dict | Returns the number of categories in categories . |
59,909 | def sequence_molecular_weight ( seq ) : if 'X' in seq : warnings . warn ( _nc_warning_str , NoncanonicalWarning ) return sum ( [ residue_mwt [ aa ] * n for aa , n in Counter ( seq ) . items ( ) ] ) + water_mass | Returns the molecular weight of the polypeptide sequence . |
59,910 | def sequence_molar_extinction_280 ( seq ) : if 'X' in seq : warnings . warn ( _nc_warning_str , NoncanonicalWarning ) return sum ( [ residue_ext_280 [ aa ] * n for aa , n in Counter ( seq ) . items ( ) ] ) | Returns the molar extinction coefficient of the sequence at 280 nm . |
59,911 | def partial_charge ( aa , pH ) : difference = pH - residue_pka [ aa ] if residue_charge [ aa ] > 0 : difference *= - 1 ratio = ( 10 ** difference ) / ( 1 + 10 ** difference ) return ratio | Calculates the partial charge of the amino acid . |
59,912 | def sequence_charge ( seq , pH = 7.4 ) : if 'X' in seq : warnings . warn ( _nc_warning_str , NoncanonicalWarning ) adj_protein_charge = sum ( [ partial_charge ( aa , pH ) * residue_charge [ aa ] * n for aa , n in Counter ( seq ) . items ( ) ] ) adj_protein_charge += ( partial_charge ( 'N-term' , pH ) * residue_charge [... | Calculates the total charge of the input polypeptide sequence . |
59,913 | def charge_series ( seq , granularity = 0.1 ) : if 'X' in seq : warnings . warn ( _nc_warning_str , NoncanonicalWarning ) ph_range = numpy . arange ( 1 , 13 , granularity ) charge_at_ph = [ sequence_charge ( seq , ph ) for ph in ph_range ] return ph_range , charge_at_ph | Calculates the charge for pH 1 - 13 . |
59,914 | def sequence_isoelectric_point ( seq , granularity = 0.1 ) : if 'X' in seq : warnings . warn ( _nc_warning_str , NoncanonicalWarning ) ph_range , charge_at_ph = charge_series ( seq , granularity ) abs_charge_at_ph = [ abs ( ch ) for ch in charge_at_ph ] pi_index = min ( enumerate ( abs_charge_at_ph ) , key = lambda x :... | Calculates the isoelectric point of the sequence for ph 1 - 13 . |
59,915 | def measure_sidechain_torsion_angles ( residue , verbose = True ) : chi_angles = [ ] aa = residue . mol_code if aa not in side_chain_dihedrals : if verbose : print ( "Amino acid {} has no known side-chain dihedral" . format ( aa ) ) else : for set_atoms in side_chain_dihedrals [ aa ] : required_for_dihedral = set_atoms... | Calculates sidechain dihedral angles for a residue |
59,916 | def measure_torsion_angles ( residues ) : if len ( residues ) < 2 : torsion_angles = [ ( None , None , None ) ] * len ( residues ) else : torsion_angles = [ ] for i in range ( len ( residues ) ) : if i == 0 : res1 = residues [ i ] res2 = residues [ i + 1 ] omega = None phi = None try : psi = dihedral ( res1 [ 'N' ] . _... | Calculates the dihedral angles for a list of backbone atoms . |
59,917 | def cc_to_local_params ( pitch , radius , oligo ) : rloc = numpy . sin ( numpy . pi / oligo ) * radius alpha = numpy . arctan ( ( 2 * numpy . pi * radius ) / pitch ) alphaloc = numpy . cos ( ( numpy . pi / 2 ) - ( ( numpy . pi ) / oligo ) ) * alpha pitchloc = ( 2 * numpy . pi * rloc ) / numpy . tan ( alphaloc ) return ... | Returns local parameters for an oligomeric assembly . |
59,918 | def residues_per_turn ( p ) : cas = p . get_reference_coords ( ) prim_cas = p . primitive . coordinates dhs = [ abs ( dihedral ( cas [ i ] , prim_cas [ i ] , prim_cas [ i + 1 ] , cas [ i + 1 ] ) ) for i in range ( len ( prim_cas ) - 1 ) ] rpts = [ 360.0 / dh for dh in dhs ] rpts . append ( None ) return rpts | The number of residues per turn at each Monomer in the Polymer . |
59,919 | def polymer_to_reference_axis_distances ( p , reference_axis , tag = True , reference_axis_name = 'ref_axis' ) : if not len ( p ) == len ( reference_axis ) : raise ValueError ( "The reference axis must contain the same number of points " "as the Polymer primitive." ) prim_cas = p . primitive . coordinates ref_points = ... | Returns distances between the primitive of a Polymer and a reference_axis . |
59,920 | def crick_angles ( p , reference_axis , tag = True , reference_axis_name = 'ref_axis' ) : if not len ( p ) == len ( reference_axis ) : raise ValueError ( "The reference axis must contain the same number of points" " as the Polymer primitive." ) prim_cas = p . primitive . coordinates p_cas = p . get_reference_coords ( )... | Returns the Crick angle for each CA atom in the Polymer . |
59,921 | def alpha_angles ( p , reference_axis , tag = True , reference_axis_name = 'ref_axis' ) : if not len ( p ) == len ( reference_axis ) : raise ValueError ( "The reference axis must contain the same number of points " "as the Polymer primitive." ) prim_cas = p . primitive . coordinates ref_points = reference_axis . coordi... | Alpha angle calculated using points on the primitive of helix and axis . |
59,922 | def reference_axis_from_chains ( chains ) : if not len ( set ( [ len ( x ) for x in chains ] ) ) == 1 : raise ValueError ( "All chains must be of the same length" ) coords = [ numpy . array ( chains [ 0 ] . primitive . coordinates ) ] orient_vector = polypeptide_vector ( chains [ 0 ] ) for i , c in enumerate ( chains [... | Average coordinates from a set of primitives calculated from Chains . |
59,923 | def flip_reference_axis_if_antiparallel ( p , reference_axis , start_index = 0 , end_index = - 1 ) : p_vector = polypeptide_vector ( p , start_index = start_index , end_index = end_index ) if is_acute ( p_vector , reference_axis [ end_index ] - reference_axis [ start_index ] ) : reference_axis = numpy . flipud ( refere... | Flips reference axis if direction opposes the direction of the Polymer . |
59,924 | def make_primitive ( cas_coords , window_length = 3 ) : if len ( cas_coords ) >= window_length : primitive = [ ] count = 0 for _ in cas_coords [ : - ( window_length - 1 ) ] : group = cas_coords [ count : count + window_length ] average_x = sum ( [ x [ 0 ] for x in group ] ) / window_length average_y = sum ( [ y [ 1 ] f... | Calculates running average of cas_coords with a fixed averaging window_length . |
59,925 | def make_primitive_smoothed ( cas_coords , smoothing_level = 2 ) : try : s_primitive = make_primitive ( cas_coords ) for x in range ( smoothing_level ) : s_primitive = make_primitive ( s_primitive ) except ValueError : raise ValueError ( 'Smoothing level {0} too high, try reducing the number of rounds' ' or give a long... | Generates smoothed primitive from a list of coordinates . |
59,926 | def make_primitive_extrapolate_ends ( cas_coords , smoothing_level = 2 ) : try : smoothed_primitive = make_primitive_smoothed ( cas_coords , smoothing_level = smoothing_level ) except ValueError : smoothed_primitive = make_primitive_smoothed ( cas_coords , smoothing_level = smoothing_level - 1 ) if len ( smoothed_primi... | Generates smoothed helix primitives and extrapolates lost ends . |
59,927 | def extend ( self , ampal_container ) : if isinstance ( ampal_container , AmpalContainer ) : self . _ampal_objects . extend ( ampal_container ) else : raise TypeError ( 'Only AmpalContainer objects may be merged with ' 'an AmpalContainer.' ) return | Extends an AmpalContainer with another AmpalContainer . |
59,928 | def pdb ( self ) : header_title = '{:<80}\n' . format ( 'HEADER {}' . format ( self . id ) ) data_type = '{:<80}\n' . format ( 'EXPDTA ISAMBARD Model' ) pdb_strs = [ ] for ampal in self : if isinstance ( ampal , Assembly ) : pdb_str = ampal . make_pdb ( header = False , footer = False ) else : pdb_str = ampal . m... | Compiles the PDB strings for each state into a single file . |
59,929 | def sort_by_tag ( self , tag ) : return AmpalContainer ( sorted ( self , key = lambda x : x . tags [ tag ] ) ) | Sorts the AmpalContainer by a tag on the component objects . |
59,930 | def append ( self , item ) : if isinstance ( item , Polymer ) : self . _molecules . append ( item ) else : raise TypeError ( 'Only Polymer objects can be appended to an Assembly.' ) return | Adds a Polymer to the Assembly . |
59,931 | def extend ( self , assembly ) : if isinstance ( assembly , Assembly ) : self . _molecules . extend ( assembly ) else : raise TypeError ( 'Only Assembly objects may be merged with an Assembly.' ) return | Extends the Assembly with the contents of another Assembly . |
59,932 | def get_monomers ( self , ligands = True , pseudo_group = False ) : base_filters = dict ( ligands = ligands , pseudo_group = pseudo_group ) restricted_mol_types = [ x [ 0 ] for x in base_filters . items ( ) if not x [ 1 ] ] in_groups = [ x for x in self . filter_mol_types ( restricted_mol_types ) ] monomers = itertools... | Retrieves all the Monomers from the Assembly object . |
59,933 | def get_ligands ( self , solvent = True ) : if solvent : ligand_list = [ x for x in self . get_monomers ( ) if isinstance ( x , Ligand ) ] else : ligand_list = [ x for x in self . get_monomers ( ) if isinstance ( x , Ligand ) and not x . is_solvent ] return LigandGroup ( monomers = ligand_list ) | Retrieves all ligands from the Assembly . |
59,934 | def get_atoms ( self , ligands = True , pseudo_group = False , inc_alt_states = False ) : atoms = itertools . chain ( * ( list ( m . get_atoms ( inc_alt_states = inc_alt_states ) ) for m in self . get_monomers ( ligands = ligands , pseudo_group = pseudo_group ) ) ) return atoms | Flat list of all the Atoms in the Assembly . |
59,935 | def is_within ( self , cutoff_dist , point , ligands = True ) : return find_atoms_within_distance ( self . get_atoms ( ligands = ligands ) , cutoff_dist , point ) | Returns all atoms in AMPAL object within cut - off distance from the point . |
59,936 | def relabel_polymers ( self , labels = None ) : if labels : if len ( self . _molecules ) == len ( labels ) : for polymer , label in zip ( self . _molecules , labels ) : polymer . id = label else : raise ValueError ( 'Number of polymers ({}) and number of labels ({}) must be equal.' . format ( len ( self . _molecules ) ... | Relabels the component Polymers either in alphabetical order or using a list of labels . |
59,937 | def relabel_atoms ( self , start = 1 ) : counter = start for atom in self . get_atoms ( ligands = True ) : atom . id = counter counter += 1 return | Relabels all Atoms in numerical order offset by the start parameter . |
59,938 | def make_pdb ( self , ligands = True , alt_states = False , pseudo_group = False , header = True , footer = True ) : base_filters = dict ( ligands = ligands , pseudo_group = pseudo_group ) restricted_mol_types = [ x [ 0 ] for x in base_filters . items ( ) if not x [ 1 ] ] in_groups = [ x for x in self . filter_mol_type... | Generates a PDB string for the Assembly . |
59,939 | def backbone ( self ) : bb_molecules = [ p . backbone for p in self . _molecules if hasattr ( p , 'backbone' ) ] bb_assembly = Assembly ( bb_molecules , assembly_id = self . id ) return bb_assembly | Generates a new Assembly containing only the backbone atoms . |
59,940 | def primitives ( self ) : prim_molecules = [ p . primitive for p in self . _molecules if hasattr ( p , 'primitive' ) ] prim_assembly = Assembly ( molecules = prim_molecules , assembly_id = self . id ) return prim_assembly | Generates a new Assembly containing the primitives of each Polymer . |
59,941 | def sequences ( self ) : seqs = [ x . sequence for x in self . _molecules if hasattr ( x , 'sequence' ) ] return seqs | Returns the sequence of each Polymer in the Assembly as a list . |
59,942 | def fasta ( self ) : fasta_str = '' max_line_length = 79 for p in self . _molecules : if hasattr ( p , 'sequence' ) : fasta_str += '>{0}:{1}|PDBID|CHAIN|SEQUENCE\n' . format ( self . id . upper ( ) , p . id ) seq = p . sequence split_seq = [ seq [ i : i + max_line_length ] for i in range ( 0 , len ( seq ) , max_line_le... | Generates a FASTA string for the Assembly . |
59,943 | def get_interaction_energy ( self , assign_ff = True , ff = None , mol2 = False , force_ff_assign = False ) : if not ff : ff = global_settings [ 'buff' ] [ 'force_field' ] if assign_ff : for molecule in self . _molecules : if hasattr ( molecule , 'update_ff' ) : molecule . update_ff ( ff , mol2 = mol2 , force_ff_assign... | Calculates the interaction energy of the AMPAL object . |
59,944 | def pack_new_sequences ( self , sequences ) : from ampal . pdb_parser import convert_pdb_to_ampal assembly_bb = self . backbone total_seq_len = sum ( [ len ( x ) for x in sequences ] ) total_aa_len = sum ( [ len ( x ) for x in assembly_bb ] ) if total_seq_len != total_aa_len : raise ValueError ( 'Total sequence length ... | Packs a new sequence onto each Polymer in the Assembly using Scwrl4 . |
59,945 | def repack_all ( self ) : non_na_sequences = [ s for s in self . sequences if ' ' not in s ] self . pack_new_sequences ( non_na_sequences ) return | Repacks the side chains of all Polymers in the Assembly . |
59,946 | def tag_secondary_structure ( self , force = False ) : for polymer in self . _molecules : if polymer . molecule_type == 'protein' : polymer . tag_secondary_structure ( force = force ) return | Tags each Monomer in the Assembly with it s secondary structure . |
59,947 | def tag_dssp_solvent_accessibility ( self , force = False ) : for polymer in self . _molecules : polymer . tag_dssp_solvent_accessibility ( force = force ) return | Tags each Monomer in the Assembly with its solvent accessibility . |
59,948 | def tag_torsion_angles ( self , force = False ) : for polymer in self . _molecules : if polymer . molecule_type == 'protein' : polymer . tag_torsion_angles ( force = force ) return | Tags each Monomer in the Assembly with its torsion angles . |
59,949 | def tag_ca_geometry ( self , force = False , reference_axis = None , reference_axis_name = 'ref_axis' ) : for polymer in self . _molecules : if polymer . molecule_type == 'protein' : polymer . tag_ca_geometry ( force = force , reference_axis = reference_axis , reference_axis_name = reference_axis_name ) return | Tags each Monomer in the Assembly with its helical geometry . |
59,950 | def tag_atoms_unique_ids ( self , force = False ) : tagged = [ 'unique_id' in x . tags . keys ( ) for x in self . get_atoms ( ) ] if ( not all ( tagged ) ) or force : for m in self . get_monomers ( ) : for atom_type , atom in m . atoms . items ( ) : atom . tags [ 'unique_id' ] = ( m . unique_id , atom_type ) return | Tags each Atom in the Assembly with its unique_id . |
59,951 | def convert_pro_to_hyp ( pro ) : with open ( str ( REF_PATH / 'hydroxyproline_ref_1bkv_0_6.pickle' ) , 'rb' ) as inf : hyp_ref = pickle . load ( inf ) align_nab ( hyp_ref , pro ) to_remove = [ 'CB' , 'CG' , 'CD' ] for ( label , atom ) in pro . atoms . items ( ) : if atom . element == 'H' : to_remove . append ( label ) ... | Converts a pro residue to a hydroxypro residue . |
59,952 | def align_nab ( tar , ref ) : rot_trans_1 = find_transformations ( tar [ 'N' ] . array , tar [ 'CA' ] . array , ref [ 'N' ] . array , ref [ 'CA' ] . array ) apply_trans_rot ( tar , * rot_trans_1 ) rot_ang_ca_cb = dihedral ( tar [ 'CB' ] , ref [ 'CA' ] , ref [ 'N' ] , ref [ 'CB' ] ) tar . rotate ( rot_ang_ca_cb , ref [ ... | Aligns the N - CA and CA - CB vector of the target monomer . |
59,953 | def apply_trans_rot ( ampal , translation , angle , axis , point , radians = False ) : if not numpy . isclose ( angle , 0.0 ) : ampal . rotate ( angle = angle , axis = axis , point = point , radians = radians ) ampal . translate ( vector = translation ) return | Applies a translation and rotation to an AMPAL object . |
59,954 | def find_ss_regions_polymer ( polymer , ss ) : if isinstance ( ss , str ) : ss = [ ss [ : ] ] tag_key = 'secondary_structure' monomers = [ x for x in polymer if tag_key in x . tags . keys ( ) ] if len ( monomers ) == 0 : return Assembly ( ) if ( len ( ss ) == 1 ) and ( all ( [ m . tags [ tag_key ] == ss [ 0 ] for m in ... | Returns an Assembly of regions tagged as secondary structure . |
59,955 | def flat_list_to_polymer ( atom_list , atom_group_s = 4 ) : atom_labels = [ 'N' , 'CA' , 'C' , 'O' , 'CB' ] atom_elements = [ 'N' , 'C' , 'C' , 'O' , 'C' ] atoms_coords = [ atom_list [ x : x + atom_group_s ] for x in range ( 0 , len ( atom_list ) , atom_group_s ) ] atoms = [ [ Atom ( x [ 0 ] , x [ 1 ] ) for x in zip ( ... | Takes a flat list of atomic coordinates and converts it to a Polymer . |
59,956 | def backbone ( self ) : bb_poly = Polypeptide ( [ x . backbone for x in self . _monomers ] , self . id ) return bb_poly | Returns a new Polymer containing only the backbone atoms . |
59,957 | def pack_new_sequence ( self , sequence ) : from ampal . pdb_parser import convert_pdb_to_ampal polymer_bb = self . backbone if len ( sequence ) != len ( polymer_bb ) : raise ValueError ( 'Sequence length ({}) does not match Polymer length ({}).' . format ( len ( sequence ) , len ( polymer_bb ) ) ) scwrl_out = pack_sid... | Packs a new sequence onto the polymer using Scwrl4 . |
59,958 | def sequence ( self ) : seq = [ x . mol_letter for x in self . _monomers ] return '' . join ( seq ) | Returns the sequence of the Polymer as a string . |
59,959 | def backbone_bond_lengths ( self ) : bond_lengths = dict ( n_ca = [ distance ( r [ 'N' ] , r [ 'CA' ] ) for r in self . get_monomers ( ligands = False ) ] , ca_c = [ distance ( r [ 'CA' ] , r [ 'C' ] ) for r in self . get_monomers ( ligands = False ) ] , c_o = [ distance ( r [ 'C' ] , r [ 'O' ] ) for r in self . get_mo... | Dictionary containing backbone bond lengths as lists of floats . |
59,960 | def backbone_bond_angles ( self ) : bond_angles = dict ( n_ca_c = [ angle_between_vectors ( r [ 'N' ] - r [ 'CA' ] , r [ 'C' ] - r [ 'CA' ] ) for r in self . get_monomers ( ligands = False ) ] , ca_c_o = [ angle_between_vectors ( r [ 'CA' ] - r [ 'C' ] , r [ 'O' ] - r [ 'C' ] ) for r in self . get_monomers ( ligands = ... | Dictionary containing backbone bond angles as lists of floats . |
59,961 | def tag_secondary_structure ( self , force = False ) : tagged = [ 'secondary_structure' in x . tags . keys ( ) for x in self . _monomers ] if ( not all ( tagged ) ) or force : dssp_out = run_dssp ( self . pdb , path = False ) if dssp_out is None : return dssp_ss_list = extract_all_ss_dssp ( dssp_out , path = False ) fo... | Tags each Residue of the Polypeptide with secondary structure . |
59,962 | def tag_residue_solvent_accessibility ( self , tag_type = False , tag_total = False , force = False , include_hetatms = False ) : if tag_type : tag_type = tag_type else : tag_type = 'residue_solvent_accessibility' tagged = [ tag_type in x . tags . keys ( ) for x in self . _monomers ] if ( not all ( tagged ) ) or force ... | Tags Residues wirh relative residue solvent accessibility . |
59,963 | def tag_dssp_solvent_accessibility ( self , force = False ) : tagged = [ 'dssp_acc' in x . tags . keys ( ) for x in self . _monomers ] if ( not all ( tagged ) ) or force : dssp_out = run_dssp ( self . pdb , path = False ) if dssp_out is None : return dssp_acc_list = extract_solvent_accessibility_dssp ( dssp_out , path ... | Tags each Residues Polymer with its solvent accessibility . |
59,964 | def tag_sidechain_dihedrals ( self , force = False ) : tagged = [ 'chi_angles' in x . tags . keys ( ) for x in self . _monomers ] if ( not all ( tagged ) ) or force : for monomer in self . _monomers : chi_angles = measure_sidechain_torsion_angles ( monomer , verbose = False ) monomer . tags [ 'chi_angles' ] = chi_angle... | Tags each monomer with side - chain dihedral angles |
59,965 | def tag_torsion_angles ( self , force = False ) : tagged = [ 'omega' in x . tags . keys ( ) for x in self . _monomers ] if ( not all ( tagged ) ) or force : tas = measure_torsion_angles ( self . _monomers ) for monomer , ( omega , phi , psi ) in zip ( self . _monomers , tas ) : monomer . tags [ 'omega' ] = omega monome... | Tags each Monomer of the Polymer with its omega phi and psi torsion angle . |
59,966 | def tag_ca_geometry ( self , force = False , reference_axis = None , reference_axis_name = 'ref_axis' ) : tagged = [ 'rise_per_residue' in x . tags . keys ( ) for x in self . _monomers ] if ( not all ( tagged ) ) or force : if len ( self ) < 7 : rprs = [ None ] * len ( self ) rocs = [ None ] * len ( self ) rpts = [ Non... | Tags each Residue with rise_per_residue radius_of_curvature and residues_per_turn . |
59,967 | def valid_backbone_bond_lengths ( self , atol = 0.1 ) : bond_lengths = self . backbone_bond_lengths a1 = numpy . allclose ( bond_lengths [ 'n_ca' ] , [ ideal_backbone_bond_lengths [ 'n_ca' ] ] * len ( self ) , atol = atol ) a2 = numpy . allclose ( bond_lengths [ 'ca_c' ] , [ ideal_backbone_bond_lengths [ 'ca_c' ] ] * l... | True if all backbone bonds are within atol Angstroms of the expected distance . |
59,968 | def valid_backbone_bond_angles ( self , atol = 20 ) : bond_angles = self . backbone_bond_angles omegas = [ x [ 0 ] for x in measure_torsion_angles ( self ) ] trans = [ 'trans' if ( omega is None ) or ( abs ( omega ) >= 90 ) else 'cis' for omega in omegas ] ideal_n_ca_c = [ ideal_backbone_bond_angles [ x ] [ 'n_ca_c' ] ... | True if all backbone bond angles are within atol degrees of their expected values . |
59,969 | def backbone ( self ) : try : backbone = OrderedDict ( [ ( 'N' , self . atoms [ 'N' ] ) , ( 'CA' , self . atoms [ 'CA' ] ) , ( 'C' , self . atoms [ 'C' ] ) , ( 'O' , self . atoms [ 'O' ] ) ] ) except KeyError : missing_atoms = filter ( lambda x : x not in self . atoms . keys ( ) , ( 'N' , 'CA' , 'C' , 'O' ) ) raise Key... | Returns a new Residue containing only the backbone atoms . |
59,970 | def unique_id ( self ) : if self . is_hetero : if self . mol_code == 'HOH' : hetero_flag = 'W' else : hetero_flag = 'H_{0}' . format ( self . mol_code ) else : hetero_flag = ' ' return self . ampal_parent . id , ( hetero_flag , self . id , self . insertion_code ) | Generates a tuple that uniquely identifies a Monomer in an Assembly . |
59,971 | def side_chain_environment ( self , cutoff = 4 , include_neighbours = True , inter_chain = True , include_ligands = False , include_solvent = False ) : if self . mol_code == 'GLY' : return [ self ] side_chain_dict = { x : { y : self . states [ x ] [ y ] for y in self . states [ x ] if self . states [ x ] [ y ] in self ... | Finds Residues with any atom within the cutoff distance of side - chain . |
59,972 | def load_global_settings ( ) : with open ( settings_path , 'r' ) as settings_f : global global_settings settings_json = json . loads ( settings_f . read ( ) ) if global_settings is None : global_settings = settings_json global_settings [ u'package_path' ] = package_dir else : for k , v in settings_json . items ( ) : if... | Loads settings file containing paths to dependencies and other optional configuration elements . |
59,973 | def build ( self ) : for i in range ( 2 ) : self . _molecules . append ( self . make_helix ( self . aas [ i ] , self . axis_distances [ i ] , self . z_shifts [ i ] , self . phis [ i ] , self . splays [ i ] , self . off_plane [ i ] ) ) return | Builds a HelixPair using the defined attributes . |
59,974 | def make_helix ( aa , axis_distance , z_shift , phi , splay , off_plane ) : start = numpy . array ( [ axis_distance , 0 + z_shift , 0 ] ) end = numpy . array ( [ axis_distance , ( aa * 1.52 ) + z_shift , 0 ] ) mid = ( start + end ) / 2 helix = Helix . from_start_and_end ( start , end , aa = aa ) helix . rotate ( splay ... | Builds a helix for a given set of parameters . |
59,975 | def build ( self ) : self . _molecules = [ ] if self . handedness == 'l' : handedness = - 1 else : handedness = 1 rot_ang = self . rot_ang * handedness for i in range ( self . num_of_repeats ) : dup_unit = copy . deepcopy ( self . repeat_unit ) z = ( self . rise * i ) * numpy . array ( [ 0 , 0 , 1 ] ) dup_unit . transl... | Builds a Solenoid using the defined attributes . |
59,976 | def from_start_and_end ( cls , start , end , sequence , helix_type = 'b_dna' , phos_3_prime = False ) : start = numpy . array ( start ) end = numpy . array ( end ) instance = cls ( sequence , helix_type = helix_type , phos_3_prime = phos_3_prime ) instance . move_to ( start = start , end = end ) return instance | Generates a helical Polynucleotide that is built along an axis . |
59,977 | def move_to ( self , start , end ) : start = numpy . array ( start ) end = numpy . array ( end ) if numpy . allclose ( start , end ) : raise ValueError ( 'start and end must NOT be identical' ) translation , angle , axis , point = find_transformations ( self . helix_start , self . helix_end , start , end ) if not numpy... | Moves the Polynucleotide to lie on the start and end vector . |
59,978 | def fit_heptad_register ( crangles ) : crangles = [ x if x > 0 else 360 + x for x in crangles ] hept_p = [ x * ( 360.0 / 7.0 ) + ( ( 360.0 / 7.0 ) / 2.0 ) for x in range ( 7 ) ] ideal_crangs = [ hept_p [ 0 ] , hept_p [ 2 ] , hept_p [ 4 ] , hept_p [ 6 ] , hept_p [ 1 ] , hept_p [ 3 ] , hept_p [ 5 ] ] full_hept = len ( cr... | Attempts to fit a heptad repeat to a set of Crick angles . |
59,979 | def gather_layer_info ( self ) : for i in range ( len ( self . cc [ 0 ] ) ) : layer_radii = [ x [ i ] . tags [ 'distance_to_ref_axis' ] for x in self . cc ] self . radii_layers . append ( layer_radii ) layer_alpha = [ x [ i ] . tags [ 'alpha_angle_ref_axis' ] for x in self . cc ] self . alpha_layers . append ( layer_al... | Extracts the tagged coiled - coil parameters for each layer . |
59,980 | def calc_average_parameters ( parameter_layers ) : mean_layers = [ numpy . mean ( x ) if x [ 0 ] else 0 for x in parameter_layers ] overall_mean = numpy . mean ( [ x for x in mean_layers if x ] ) return mean_layers , overall_mean | Takes a group of equal length lists and averages them across each index . |
59,981 | def heptad_register ( self ) : base_reg = 'abcdefg' exp_base = base_reg * ( self . cc_len // 7 + 2 ) ave_ca_layers = self . calc_average_parameters ( self . ca_layers ) [ 0 ] [ : - 1 ] reg_fit = fit_heptad_register ( ave_ca_layers ) hep_pos = reg_fit [ 0 ] [ 0 ] return exp_base [ hep_pos : hep_pos + self . cc_len ] , r... | Returns the calculated register of the coiled coil and the fit quality . |
59,982 | def generate_report ( self ) : lines = [ 'Register Assignment\n-------------------' ] register , fit = self . heptad_register ( ) lines . append ( '{}\n{}\n' . format ( register , '\n' . join ( self . cc . sequences ) ) ) lines . append ( 'Fit Quality - Mean Angular Discrepancy = {:3.2f} (Std Dev = {:3.2f})\n' . format... | Generates a report on the coiled coil parameters . |
59,983 | def buff_interaction_eval ( cls , specification , sequences , parameters , ** kwargs ) : instance = cls ( specification , sequences , parameters , build_fn = default_build , eval_fn = buff_interaction_eval , ** kwargs ) return instance | Creates optimizer with default build and BUFF interaction eval . |
59,984 | def rmsd_eval ( cls , specification , sequences , parameters , reference_ampal , ** kwargs ) : eval_fn = make_rmsd_eval ( reference_ampal ) instance = cls ( specification , sequences , parameters , build_fn = default_build , eval_fn = eval_fn , mp_disabled = True , ** kwargs ) return instance | Creates optimizer with default build and RMSD eval . |
59,985 | def parse_individual ( self , individual ) : scaled_ind = [ ] for i in range ( len ( self . value_means ) ) : scaled_ind . append ( self . value_means [ i ] + ( individual [ i ] * self . value_ranges [ i ] ) ) fullpars = list ( self . arrangement ) for k in range ( len ( self . variable_parameters ) ) : for j in range ... | Converts a deap individual into a full list of parameters . |
59,986 | def run_opt ( self , pop_size , generations , cores = 1 , plot = False , log = False , log_path = None , run_id = None , store_params = True , ** kwargs ) : self . _cores = cores self . _store_params = store_params self . parameter_log = [ ] self . _model_count = 0 self . halloffame = tools . HallOfFame ( 1 ) self . st... | Runs the optimizer . |
59,987 | def _make_parameters ( self ) : self . value_means = [ ] self . value_ranges = [ ] self . arrangement = [ ] self . variable_parameters = [ ] current_var = 0 for parameter in self . parameters : if parameter . type == ParameterType . DYNAMIC : self . value_means . append ( parameter . value [ 0 ] ) if parameter . value ... | Converts a list of Parameters into DEAP format . |
59,988 | def assign_fitnesses ( self , targets ) : self . _evals = len ( targets ) px_parameters = zip ( [ self . specification ] * len ( targets ) , [ self . sequences ] * len ( targets ) , [ self . parse_individual ( x ) for x in targets ] ) if ( self . _cores == 1 ) or ( self . mp_disabled ) : models = map ( self . build_fn ... | Assigns fitnesses to parameters . |
59,989 | def dynamic ( cls , label , val_mean , val_range ) : return cls ( label , ParameterType . DYNAMIC , ( val_mean , val_range ) ) | Creates a static parameter . |
59,990 | def run_scwrl ( pdb , sequence , path = True ) : if path : with open ( pdb , 'r' ) as inf : pdb = inf . read ( ) pdb = pdb . encode ( ) sequence = sequence . encode ( ) try : with tempfile . NamedTemporaryFile ( delete = False ) as scwrl_tmp , tempfile . NamedTemporaryFile ( delete = False ) as scwrl_seq , tempfile . N... | Runs SCWRL on input PDB strong or path to PDB and a sequence string . |
59,991 | def parse_scwrl_out ( scwrl_std_out , scwrl_pdb ) : score = re . findall ( r'Total minimal energy of the graph = ([-0-9.]+)' , scwrl_std_out ) [ 0 ] split_scwrl = scwrl_pdb . splitlines ( ) fixed_scwrl = [ ] for line in split_scwrl : if len ( line ) < 80 : line += ' ' * ( 80 - len ( line ) ) if re . search ( r'H?E?T?AT... | Parses SCWRL output and returns PDB and SCWRL score . |
59,992 | def pack_sidechains ( pdb , sequence , path = False ) : scwrl_std_out , scwrl_pdb = run_scwrl ( pdb , sequence , path = path ) return parse_scwrl_out ( scwrl_std_out , scwrl_pdb ) | Packs sidechains onto a given PDB file or string . |
59,993 | def parse_pdb_file ( self ) : self . pdb_parse_tree = { 'info' : { } , 'data' : { self . state : { } } } try : for line in self . pdb_lines : self . current_line = line record_name = line [ : 6 ] . strip ( ) if record_name in self . proc_functions : self . proc_functions [ record_name ] ( ) else : if record_name not in... | Runs the PDB parser . |
59,994 | def proc_atom ( self ) : atom_data = self . proc_line_coordinate ( self . current_line ) ( at_type , at_ser , at_name , alt_loc , res_name , chain_id , res_seq , i_code , x , y , z , occupancy , temp_factor , element , charge ) = atom_data a_state = self . pdb_parse_tree [ 'data' ] [ self . state ] res_id = ( res_seq ,... | Processes an ATOM or HETATM record . |
59,995 | def make_ampal ( self ) : data = self . pdb_parse_tree [ 'data' ] if len ( data ) > 1 : ac = AmpalContainer ( id = self . id ) for state , chains in sorted ( data . items ( ) ) : if chains : ac . append ( self . proc_state ( chains , self . id + '_state_{}' . format ( state + 1 ) ) ) return ac elif len ( data ) == 1 : ... | Generates an AMPAL object from the parse tree . |
59,996 | def proc_state ( self , state_data , state_id ) : assembly = Assembly ( assembly_id = state_id ) for k , chain in sorted ( state_data . items ( ) ) : assembly . _molecules . append ( self . proc_chain ( chain , assembly ) ) return assembly | Processes a state into an Assembly . |
59,997 | def proc_chain ( self , chain_info , parent ) : hetatom_filters = { 'nc_aas' : self . check_for_non_canonical } polymer = False chain_labels , chain_data = chain_info chain_label = list ( chain_labels ) [ 0 ] monomer_types = { x [ 2 ] for x in chain_labels if x [ 2 ] } if ( 'P' in monomer_types ) and ( 'N' in monomer_t... | Converts a chain into a Polymer type object . |
59,998 | def proc_monomer ( self , monomer_info , parent , mon_cls = False ) : monomer_labels , monomer_data = monomer_info if len ( monomer_labels ) > 1 : raise ValueError ( 'Malformed PDB, single monomer id with ' 'multiple labels. {}' . format ( monomer_labels ) ) else : monomer_label = list ( monomer_labels ) [ 0 ] if mon_c... | Processes a records into a Monomer . |
59,999 | def generate_antisense_sequence ( sequence ) : dna_antisense = { 'A' : 'T' , 'T' : 'A' , 'C' : 'G' , 'G' : 'C' } antisense = [ dna_antisense [ x ] for x in sequence [ : : - 1 ] ] return '' . join ( antisense ) | Creates the antisense sequence of a DNA strand . |
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