Chem-Structure-Parser
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h('structure_info'); # by name
h(*res_type); # by name, unquoted
h(\&aa3to1); # by reference
h(); # the list of documented functions
perl -MChem::Structure::Parser -e 'h(*structure_info)' # straight from the shell
Note that `h(res_type)`, with no quotes and no sigil, cannot be made to work:
every function here is exported, so Perl parses the bareword as a call to
`res_type()` before `h` is ever reached. Use one of the three forms above.
# Functions/Subroutines
## structure_info
my $info = structure_info($file, %options);
Reads `$file` and returns a hash reference. The format is worked out from the
file name — `.pdb`, `.ent`, `.cif`, `.mmcif`, `.pdbx` — and from the first
records in the file when the name gives nothing away. `.gz` files are read as
they are, without unpacking to a temporary file.
### What comes back
Laid out the way `tree` lays out a directory, this is `1a22.ent.pdb` — a real
file, real values, the long lists cut short:
$info
├── file '1a22.ent.pdb' the path it was read from
├── format 'pdb' or 'mmcif'
├── id '1A22' from HEADER, or from the file name
├── title 'HUMAN GROWTH HORMONE BOUND TO SINGLE RECEPTOR'
├── header
│ ├── classification 'COMPLEX (HORMONE/RECEPTOR)'
│ ├── deposit_date '15-JAN-98'
│ └── id_code '1A22'
├── experiment [ 'X-RAY DIFFRACTION' ]
├── resolution 2.6 REMARK 2
├── r_work 0.187 REMARK 3
├── r_free undef this entry does not report one
├── temperature 287 REMARK 200
├── ph 6.5
├── keywords [ 'COMPLEX (HORMONE-RECEPTOR)', 'PITUITARY HORMONE', ... ]
├── authors [ 'A.M.DE VOS', 'M.ULTSCH' ]
├── journal
│ ├── auth [ 'T.CLACKSON', 'M.H.ULTSCH', 'J.A.WELLS', 'A.M.DE VOS' ]
│ ├── titl 'STRUCTURAL AND FUNCTIONAL ANALYSIS OF THE 1:1 GROWTH...'
│ ├── ref 'J.MOL.BIOL. V. 277 1111 1998'
│ ├── refn 'ISSN 0022-2836'
│ ├── pmid '9571026'
│ └── doi '10.1006/JMBI.1998.1669'
├── compound COMPND, by MOL_ID
│ ├── 1
│ │ ├── mol_id '1'
│ │ ├── molecule 'GROWTH HORMONE'
│ │ ├── chain [ 'A' ]
│ │ ├── engineered 'YES'
│ │ └── mutation 'YES'
│ └── 2 { molecule 'GROWTH HORMONE RECEPTOR', chain [ 'B' ],
│ fragment 'EXTRACELLULAR DOMAIN', engineered 'YES' }
├── source SOURCE, by MOL_ID
│ └── 1 { organism_scientific 'HOMO SAPIENS', organism_common
│ 'HUMAN', organism_taxid '9606', mol_id '1',
│ expression_system 'ESCHERICHIA COLI',
│ expression_system_taxid '562' }
├── entity_of_chain COMPND and SOURCE, by chain
│ ├── A { mol_id '1', molecule 'GROWTH HORMONE', fragment undef,
│ │ ec undef, organism 'HOMO SAPIENS', taxid '9606',
│ │ expressed_in 'ESCHERICHIA COLI' }
│ └── B { ..., fragment 'EXTRACELLULAR DOMAIN' }
├── seqres what SEQRES says was in the crystal
│ ├── A
│ │ ├── sequence 'FPTIPLSRLFDNAMLRAHRLHQLAFDTYQEFEEAYIPKEQKYSFLQ...'
│ │ ├── residues [ 'PHE', 'PRO', 'THR', 'ILE', ... ] 191 of them
│ │ └── length 191
│ └── B { sequence, residues, length 238 }
├── dbref
│ └── A [ { database 'UNP', accession 'P01241',
│ db_id 'SOMA_HUMAN', seq_begin '1', seq_end '191',
│ db_begin '27', db_end '217', chain 'A' } ]
├── seqadv [ { chain 'A', resseq '120', resname 'ARG',
│ db_res 'GLY', db_seq '146', comment 'ENGINEERED' } ]
├── modres { } no MSE-style residues here
├── het
│ └── HOH { het_id 'HOH', formula '69(H2 O)', water 1 }
├── hetnam { }
├── formul { }
├── helix [ { id '1', class '1', length '29',
│ init_chain 'A', init_resname 'SER', init_resseq '7',
│ end_chain 'A', end_resname 'TYR', end_resseq '35' },
│ ... ] 12 of them
├── sheet [ ... ] 12
├── ssbond [ { chain1 'A', resseq1 '53',
│ chain2 'A', resseq2 '165', length '2.02' }, ... ] 5
├── link [ ]
├── cispep [ ]
├── site [ ]
├── cryst1 { a '67.7', b '67.7', c '228',
│ alpha '90', beta '90', gamma '90',
│ sgroup 'P 43 21 2', z '8' }
├── biological_assembly [ 32 lines of REMARK 350, verbatim ]
├── revdat [ { num '3', date '18-APR-18', id '1A22',
│ type '1', what 'REMARK' }, ... ]
├── remarks every REMARK, by number
│ ├── 2 [ '', 'RESOLUTION. 2.60 ANGSTROMS.' ]
│ ├── 350 [ ... ] 32 lines
│ └── ... 1, 3, 4, 100, 200, 280, 290, 300, 465, 470, 500
├── conect [ [ 448, 1255 ], ... ] 10
├── records every record type, counted
│ ├── REMARK 365
│ ├── SEQRES 34
│ ├── HELIX 12
│ └── ... AUTHOR, COMPND, CONECT, CRYST1, DBREF, SOURCE, SSBOND, ...
├── n_models 1 how many MODEL records the file has
├── model 1 which one the chains below are
├── models there only with model => 'all'
├── stats
│ ├── n_atoms 3113 atoms kept: this model, less what was filtered
│ ├── total_atoms 3113 atoms the file has, every model, unfiltered
│ ├── n_hetatm 69 of n_atoms, the ones written as HETATM
│ ├── n_hydrogens 0
│ ├── n_water_atoms 69
│ ├── n_lines 3605
│ ├── n_atom_records 3044 ATOM lines seen, whether kept or not
│ ├── n_hetatm_records 69 HETATM lines, likewise
│ ├── n_anisou 0
│ ├── n_skipped 0 coordinate lines the options threw away
│ ├── elements { C 1946, O 643, N 507, S 17 }
│ │ every element in the file, keyed by its IUPAC
│ │ symbol; the counts add up to n_atoms
│ ├── bfactor { min '2.7', max '85.39', mean 30.83, n 3113 }
│ ├── bbox { xmin '12.142', xmax '80.34', ymin '2.011', ... }
│ └── center [ '46.241', '29.135', '134.559' ]
├── chain_order [ 'A', 'B' ] the order the file has them in
└── chains
├── A
│ ├── id 'A'
│ ├── type 'protein' protein dna rna water hetero unknown
│ ├── sequence 'FPTIPLSRLFDNAMLRAHRLHQLAFDTYQEFEEAYIPKEQ...'
│ │ single-letter, what has coordinates
│ ├── seqres 'FPTIPLSRLFDNAMLRAHRLHQLAFDTYQEFEEAYIPKEQ...'
│ ├── seqres_length 191
│ ├── n_residues 206
│ ├── n_polymer 180
│ ├── n_water 26
│ ├── n_ligand 0
│ ├── n_atoms 1492
│ ├── n_hetatm 26
│ ├── elements { C 938, O 301, N 246, S 7 }
│ │ the same tally for this chain alone;
│ │ adds up to the chain's n_atoms
│ ├── n_missing 11 SEQRES less what was modelled
│ ├── gaps [ { after 129, before 136, missing 6 },
│ │ { after 148, before 154, missing 5 } ]
│ ├── n_gaps 2
│ ├── missing_residues
│ │ [ 130, 131, 132, 133, 134, 135,
│ │ 149, 150, 151, 152, 153 ]
│ ├── first 1 the first and last polymer residue keys
│ ├── last 191
│ ├── residue_types { amino_acid 180, water 26 }
│ ├── molecule 'GROWTH HORMONE' from COMPND
│ ├── organism 'HOMO SAPIENS' from SOURCE
│ ├── mol_id '1'
│ ├── dbref [ { ... } ] as in the top-level dbref
│ │ ec and fragment are here too, in a
│ │ chain whose file gives them
│ ├── residue_order [ '1', '2', '3', ... '574' ] file order, 206
│ └── residues keyed number + insertion code
│ ├── 54
│ │ ├── resname 'PHE'
│ │ ├── number 54
│ │ ├── icode ''
│ │ ├── key '54'
│ │ ├── chain 'A'
│ │ ├── one 'F' '' when there is no letter for it
│ │ ├── type 'amino_acid'
│ │ │ nucleotide water ligand ion
│ │ ├── standard 1 one of the twenty, or a standard base
│ │ ├── modified 0 1 for MSE, still an M in the sequence
│ │ ├── hetero 0 1 when it was written as HETATM
│ │ ├── free not here; 1 for a free amino acid
│ │ │ bound in a site (see below)
│ │ ├── n_atoms 11
│ │ ├── b_mean 22.55
│ │ ├── center [ 65.311, 17.127, 140.515 ]
│ │ ├── atom_order [ 'N', 'CA', 'C', 'O', 'CB', ... ]
│ │ └── atoms
│ │ ├── CA
│ │ │ ├── name 'CA'
│ │ │ ├── serial 450
│ │ │ ├── element 'C'
│ │ │ ├── charge ''
│ │ │ ├── x '66.446'
│ │ │ ├── y '18.25'
│ │ │ ├── z '141.982'
│ │ │ ├── occupancy '1'
│ │ │ ├── bfactor '24.53'
│ │ │ ├── altloc ''
│ │ │ ├── hetero 0
│ │ │ └── altlocs [ { altloc, x, y, z, occupancy,
│ │ │ bfactor }, ... ]
│ │ │ present only when the atom has
│ │ │ alternate conformers; every conformer
│ │ │ is listed, the chosen one included,
│ │ │ and one of them having no letter at
│ │ │ all does not take it off the list
│ │ └── ... N, C, O, CB, CG, CD1, CD2, CE1, CE2, CZ
│ └── ... 1 .. 191, then the waters at 512 .. 574
└── B the same again: 235 residues, 1621 atoms
A record that is not in the file reads as `undef`, and a list that is not in
the file reads as an empty arrayref — `title` being `undef` means there was no
TITLE, which is a different thing from a TITLE that was blank.
Everything the module does not take apart is still in `remarks` and in the
raw record counts, so nothing in the file is lost.
### The two sequences
`sequence` and `seqres` are the two different questions people mean by "the
sequence": what was modelled, and what was in the crystal. They differ
wherever a terminus or a loop went unmodelled, which is what `gaps` counts and
`n_missing` totals — eleven residues of chain A above, in two stretches.
`missing_residues` is the same eleven one number at a time, in ascending
order, for asking whether a particular residue was modelled without walking
( run in 1.032 second using v1.01-cache-2.11-cpan-364913b4093 )