Syntax summary
This is a summary of the MolScript input file syntax. It is a
simplification of the actual yacc grammar (file molscript.y), which
describes the syntax in a condensed form using a Backus-Naur Form
(BNF) notation. Undocumented features are omitted.
input_file: [title string] plot {plot} ;
plot: {macro_def} plot {header_command} {body_command} end_plot ;
macro_def: macro macro_id commands end_macro ;
header_command: < noframe
| frame < on | off > ';'
| area number number number number ';'
| background colour ';'
| window number ';'
| slab number ';'
| headlight < on | off > ';'
| shadows < on | off > ';'
| fog number ';'
>
body_command: < read mol_id filename ';'
| read mol_id inline-PDB ';'
| copy mol_id atom_selection ';'
| delete mol_id ';'
| comment string ';'
| debug string ';'
| transform atom_selection {by xform} ';'
| store-matrix ';'
| macro_def ';' >
| set parameter_spec {',' parameter_spec} ';'
| ball-and-stick atom_selection [atom_selection] ';'
| bonds atom_selection [atom_selection] ';'
| coil residue_selection ';'
| cylinder residue_selection ';'
| cpk atom_selection ';'
| double-helix residue_selection ';'
| helix residue_selection ';'
| label vector string ';'
| label atom_selection string ';'
| line vector to vector {to vector} ';'
| object filename ';'
| object inline ';'
| strand residue_selection ';'
| turn residue_selection ';'
| viewpoint id origin vector number ';'
| directionallight vector ';'
| directionallight from vector to vector ';'
| pointlight vector ';'
| spotlight vector vector number ';'
| spotlight from vector to vector number ';'
| anchor id [description string] {parameter string}
'{' basic_commands '}' ';'
| level-of-detail
{ number '{' basic_commands '}' }
'{' basic_commands '}' ';'
| viewpoint id from vector to vector [number] ';'
>
atom_selection: < not atom_selection
| require atom_selection {',' atom_selection}
and atom_selection
| either atom_selection {',' atom_selection}
or atom_selection
| atom atom_id
| res-atom residue_name atom_id
| occupancy number number
| b-factor number number
| in residue_selection
| sphere vector number
| close atom_selection number
| peptide
| backbone
| hydrogens
>
residue_selection: < not residue_selection
| require residue_selection {',' residue_selection}
and residue_selection
| either residue_selection {',' residue_selection}
or residue_selection
| molecule mol_id
| model integer
| from residue_name to residue_name
| residue residue_name
| type residue_type
| chain chain_id
| contains atom_selection
| amino-acids
| waters
| nucleotides
| ligands
| segid segment_id
>
Top page