Proteax function listing

The following functions are callable via the Web API. As the API presents a very generic interface to Proteax all parameters must be passed as p1, p2, p3..., not as named parameters.

To see examples of the API usage, please visit the help page.

as_fasta

Protein entry converted to FASTA format. Note that this strips all chemical annotations.

Parameter	Description
(p1) protein_text	Protein entry in UniProt, PLN, GPMAW or FASTA format.

as_gpmaw

Protein entry converted to GPMAW format.

Parameter	Description
(p1) protein_text	Protein entry in UniProt, PLN, GPMAW or FASTA format.

as_molfile

The chemical 2D structure that the supplied protein entry represents. The structure is represented in MDL molfile format (V2000 or V3000 depending on molecule size).

Parameter	Description
(p1) protein_text	Protein entry in UniProt, PLN, GPMAW or FASTA format.

as_molfile_cond

The condensed chemical representation of as_molfile(). Non-modified amino acid residues are represented as single atoms to produce a compact representation.

Parameter	Description
(p1) protein_text	Protein entry in UniProt, PLN, GPMAW or FASTA format.

as_pln

Protein entry converted to PLN (Protein Line Notation) format.

Parameter	Description
(p1) protein_text	Protein entry in UniProt, PLN, GPMAW or FASTA format.

as_uniprot

Protein entry converted to UniProt format.

Parameter	Description
(p1) protein_text	Protein entry in UniProt, PLN, GPMAW or FASTA format.

dernot_applied

Returns a protein derivative produced by applying the DerNot expression to the reference protein.

Parameter	Description
(p1) dernot_expression	DerNot text adhering to the Biochemfusion DerNot specification.
(p2) ref_protein_text	Reference protein entry in UniProt, PLN, GPMAW or FASTA format.

dernot_diff

Calculates the DerNot expression that will produce the given protein when applied to the reference protein.

Parameter	Description
(p1) protein_text	Protein entry in UniProt, PLN, GPMAW or FASTA format.
(p2) ref_protein_text	Reference protein entry in UniProt, PLN, GPMAW or FASTA format.
(p3) diff_format	DerNot formatting, 1-3 characters: "*" for anonymous expressions, "L" to force chain locants, "D" to display deleted residues in des- parts.

formula

The sum formula of the chemical structure represented by the supplied protein entry.

Parameter	Description
(p1) protein_text	Protein entry in UniProt, PLN, GPMAW or FASTA format.

formula_add

Adds two sum formulas.

Parameter	Description
(p1) formula1	Sum formula in normal or GPMAW format.
(p2) formula2	Sum formula in normal or GPMAW format.
(p3) result_format	Output format: 'N' for Normal (default) or 'G' for GPMAW format.

formula_element_count

Extracts the number of atoms of a given element within a sum formula.

Parameter	Description
(p1) formula	Sum formula in normal or GPMAW format.
(p2) element_symbol	Atom symbol of the element whose count you want.

formula_mass_avg

Average molecular weight of the supplied sum formula.

Parameter	Description
(p1) formula	Sum formula in normal or GPMAW format.

formula_mass_mono

Mono-isotopic molecular weight of the supplied sum formula.

Parameter	Description
(p1) formula	Sum formula in normal or GPMAW format.

formula_mult

Multiplies a sum formula by an integer number. This means that all element counts will be multiplied by the integer number.

Parameter	Description
(p1) formula	Sum formula in normal or GPMAW format.
(p2) multiplier	Integer multiplier.
(p3) result_format	Output format: 'N' for Normal (default) or 'G' for GPMAW format.

formula_sub

Subtracts the second sum formula from the first.

Parameter	Description
(p1) formula1	Sum formula in normal or GPMAW format.
(p2) formula2	Sum formula in normal or GPMAW format.
(p3) result_format	Output format: 'N' for Normal (default) or 'G' for GPMAW format.

full_sequence

The full plain sequence of the supplied protein entry, including non-expressed sequence parts.

Parameter	Description
(p1) protein_text	Protein entry in UniProt, PLN, GPMAW or FASTA format.

full_sequence_mw

The simple average molecular weight of the protein entry sequence. Calculation follows the algorithm as given at http://www.expasy.ch/tools/pi_tool-doc.html.

Parameter	Description
(p1) protein_text	Protein entry in UniProt, PLN, GPMAW or FASTA format.

id

The ID, if any defined, of the supplied protein entry.

Parameter	Description
(p1) protein_text	Protein entry in UniProt, PLN, GPMAW or FASTA format.

mol_render_info

Produces condensed or full-structure molecule rendering info for the supplied protein entry. Will also accept V2000 MDL molfile input if the molfile is a plain connection table with atom and bond blocks only.

Parameter	Description
(p1) protein_text	Protein entry in UniProt, PLN, GPMAW or FASTA format.

mw_avg

Average molecular weight of the chemical structure represented by the supplied protein entry. Proteax uses the IUPAC 2007 atomic masses at http://www.chem.qmul.ac.uk/iupac/AtWt/index.html.

Parameter	Description
(p1) protein_text	Protein entry in UniProt, PLN, GPMAW or FASTA format.

mw_mono

Mono-isotopic molecular weight of the chemical structure represented by the supplied protein entry. Proteax uses the UniMod masses found at http://www.unimod.org/masses.html.

Parameter	Description
(p1) protein_text	Protein entry in UniProt, PLN, GPMAW or FASTA format.

name

The name, if any defined, of the supplied protein entry.

Parameter	Description
(p1) protein_text	Protein entry in UniProt, PLN, GPMAW or FASTA format.

norm_protein

The ordered expressed chains of the supplied protein entry. This is similar to norm_sequence(), except that modified residues, terminals and full-cyclic chains are annotated in a PLN-like notation. The structural features thus enable structural comparisons.

Parameter	Description
(p1) protein_text	Protein entry in UniProt, PLN, GPMAW or FASTA format.

norm_protein_chksum

The MD5 checksum of the output from norm_protein().

Parameter	Description
(p1) protein_text	Protein entry in UniProt, PLN, GPMAW or FASTA format.

norm_sequence

The ordered expressed plain-sequence chains of the supplied protein entry. Chains are separated by periods. Cyclic chains are normalized to ensure identical sort order regardless of in-chain rotation.

Parameter	Description
(p1) protein_text	Protein entry in UniProt, PLN, GPMAW or FASTA format.

norm_sequence_chksum

The MD5 checksum of the output from norm_sequence().

Parameter	Description
(p1) protein_text	Protein entry in UniProt, PLN, GPMAW or FASTA format.

render_info

Produces sequence rendering info for the supplied protein entry.

Parameter	Description
(p1) protein_text	Protein entry in UniProt, PLN, GPMAW or FASTA format.
(p2) residues_per_line	Integer number of residues to display per line.

sequence

The expressed chains of the supplied protein entry. Chains are separated by periods.

Parameter	Description
(p1) protein_text	Protein entry in UniProt, PLN, GPMAW or FASTA format.

version

Returns the Proteax version string.