bend-prot

Releases (1)

• 0.1.0.0 indexed

Definitions (623)

pdb.bend

• def is_conect_line
• def conect_linesCONECT lines anywhere in the file (they follow ENDMDL in practice).
• def pow10Powers of ten for the fractional scale.
• def f32_apply_sign
• def f32_combine
• def parse_f32_frac
• def parse_f32_num
• def parse_f32_int
• def parse_f32_split
• def parse_f32_stripped
• def strip_sign_kept
• def strip_sign_plus
• def strip_sign_if
• def strip_sign_go
• def strip_sign
• def parse_f32Decimal floats: optional sign, digits, optional '.', digits.
• def elem_1Element symbol -> atomic number; unknown -> 0.
• def elem_2
• def elem_no_1
• def elem_no
• def elem_from_name
• def elem_of_go
• def elem_of
• def chain_u32
• def parse_atom_zOne ATOM line -> (chain, seq, atom).
• def parse_atom_y
• def parse_atom_x
• def parse_atom_seq
• def parse_atom_chain
• def parse_atom_serial
• def parse_atom_fields
• def parse_atom_line
• def conect_p4One CONECT line -> [(s0, si)] bonds for each partner present.
• def conect_p3
• def conect_p2
• def conect_p1
• def conect_assemble
• def parse_conect_line
• def collect_extendCollect parsed atoms plus the skipped-line count.
• def collect_finish
• def collect_go
• def collect_atoms
• def append_conect
• def conect_pairs
• def group_res_goPass 1: consecutive equal (chain, seq) merge.
• def group_residues
• def zip_chainsZip the parallel chain/residue lists back into pairs (aligned by construction; extra elements on either side are dropped).
• def group_chain_goPass 2: consecutive equal chains merge into Chain.
• def group_chains_zip
• def group_chains
• def parse_pdb_groupWhole file -> (Complex, skipped lines).
• def parse_pdb_collect
• def parse_pdb
• def complex_of
• def skipped_of
• def first_elem_go
• def first_elem
• def demo_textTwo-line ALA snippet for laws and smoke tests.
• def demo_bad_textA bad serial ("X") so the second line skips.
• def finish_read
• def load_pdb_fileWhole file from disk -> (Complex, skipped lines).
• def pad_left
• def pad_right
• def pad_zero
• def fmt_u32
• def fmt_nat
• def fmt_frac3
• def fmt_abs
• def fmt_f83_sign
• def fmt_f83
• def elem_sym
• def write_atom_line
• def write_atom_pos
• def write_atom
• def write_atoms
• def append_lines
• def write_residue
• def write_residues
• def write_chain
• def write_chains
• def complex_chains
• def write_complex
• def finish_write
• def write_text_file
• def save_pdb_file
• def finish_bonds
• def load_pdb_bondsCONECT bonds from disk.
• def finish_text
• def load_text_fileRaw file text (for template atom collection).

protein.bend

• type Atom
• type Residue
• type Chain
• type Complex
• def Atom.posAtom position (drops serial/elem, keeps pos)
• def Atom.elemAtom element number (drops serial/pos, keeps elem)
• def Atom.serialAtom serial number (drops elem/pos, keeps serial)
• def Atom.dist2
• def Atom.dist
• def count_atoms
• def count_residues