EXIT	To exit the program

OPEN	To open a data file and read selected molecules
Keywords	Value type or value	Notes
FILE	Text string	File to be opened. The format is specified by the extension
MOLECULE	Text string	Molecule(s) to be read (may include wildcards but not a list)
OPTIONS	List of values
	NOHYDROGENS	Do not automatically add hydrogens (useful for search queries)
	HYDROGENS	Force automatic hydrogen addition (not default for PDB)
NAME	Text string	Field containing molecule names (SDF and RDF files only)
CHAIN	Single value from list	Control the creation of molecules for protein chains (PDB files only)
	SEPARATE	Place each protein chain in a separate molecule
	MERGE	Place all protein chains in a single molecule (default)
LOGIC	Single value from list	Combine file and current pharmacophores
	NEW	Replace current profile with that from the file
	ADD	Add file to current profile
	AND	Logical AND of file with current profile
	OR	Logical OR (arithmetic MAXIMUM) of file and current profiles
	EOR	Logical EOR of file and current profiles
	NOT	Retain current pharmacophores NOT in file profile

SAVE	To save selected molecules and/or data in a file
Keywords	Value type or value	Notes
FILE	Text string	File to be created. The format is specified by the extension.
FORMAT	Single value from list	To specify the format (takes precedence over extension)
	CSV	Comma delimited file of SMILES and property values
	SMILES	SMILES file format (.smi)
	SD	MACCS SD file format (.sdf)
	SET	List of molecule names (.set)
	CONFORMERS	MACCS SD file format of conformers (.sdf)
	PHARMS	Pharmacophore file format (.phm)
	PDB	Protein Data Bank file format (.pdb)
	TYPES	Atom type data (.typ)
	LENGTHS	Bond lengths and constants (.bnd)
	ANGLES	Bond angles and constants (.ang)
	RINGCOORD	Ring coordinates (for conformational analysis) (.rng)
	RINGTORS	Ring torsion angles (for conformational analysis) (.tor)
	RD	MACCS RD file format (.rdf)
	PROFILE	Pharmacophore profile file format (.pro)
	KEYS	2D Functional group keys (.key)
	PHCOORDS	Pharmacophore coordinates (in SD format) from a pharmacophore profile
	MAP	Map format (.map)
MOLECULE	Text string	Molecule(s) to be saved (may include wildcards but not a list) (default: All)
OPTIONS	List of values
	NOFIELDS	Omit field data from file
	FILTER	Apply property and substructure filters from learn file (with activity field name)
	HYDROGENS	To include hydrogens in 2D MACCS SD and PDB file formats
	TRANSFORMS	To include hydrogens and write connection types 0-9 to A in SMILES
	MOLECULE	Include molecule name in pharmacophore (PHM) and key (KEY) files
	NOHYDROGENS	Omit hydrogens from 3D MACCS SD file format
	PARENT	Convert to parent ("neutral") molecule (important for pharmacophores)
	NOKEYS	Omit KEYS field from CSV format
R-GROUPS	Text string	List of R-group component files (previously read)
MAP	Text string	Map(s) to be saved (may include wildcards)
QUERY	Text string	Query molecule name (to which an enumerated molecule is fitted)

CLOSE	To close the specified file (deleting the molecules from memory)
Keywords	Value type or value	Notes
FILE	Text string	File to be closed.

LIST	To list various data
Keywords	Value type or value	Notes
INFO	Single value from list	Type of information to be listed
	TYPES	Atom types
	CONNECTIONS	Connections
	2D-COORDS	2D coordinates
	3D-COORDS	3D coordinates
	PROPERTIES	Properties
	MOLECULES	Molecule names
	KEYS	Functional group keys (in hex)
	BOND-ORDERS	Connections with bond orders
	LENGTHS	Bond lengths
	ANGLES	Bond angles
	TORSIONS	Torsion angles
	SYMBOLS	Symbols
	FLEXIBILITY	Rotatable bonds (with type and increments)
	CONFORMERS	Torsion angles for acceptable conformers
	GEOMETRY	Geometry
	PHARMS	Pharmacophores
	CUSTOMISE	Customise settings
	CHIRAL	Chiral centres
	PROFILE	Pharmacophore profile
	SITES	Active sites
	ATOMS	Atoms that match the SELECT criteria
	RESIDUES	Residues that match the SELECT criteria
	MAPS	Maps that match the SELECT criteria
	CHARGES	Partial charges
	DISTANCES	Interatomic distances
OUTPUT	Text string	File for output (default=TTY, spreadsheet=WINDOW, print=PRINTER)
MOLECULE	Text string	Molecules for which data is required
ACTIVITY	Text string	Activity field for Learn filename (see LEARN) for comparison highlights
QUERY	Text string	Query molecule (for RMS property listing)
SELECT	Text string	Restrict output to specified symbols, atoms, residues or maps

SEARCH	To search a data file
Keywords	Value type or value	Notes
QUERY	Text string	Query molecule name
FILE	Text string	File to be searched (format indicated by extension)
OUTPUT	Text string	Output file of hits (format indicated by extension)
MODE	Single value from list
	EXACT	Exact matches (default)
	SUBSTRUCTURE	Substructure matches
	SIMILARITY	Similarity matches
	3D	3D matches
	SITE	Active Site matches
	R-GROUP	R-group component matches (for Combinatorial Chemistry)
	PROFILE	To search using pharmacophore queries from the current profile
OPTIONS	List of values
	ORDER	Match bond orders
	TYPES	Match atom types
	REACTION	Match group numbers and serial numbers for reaction
	PARENT	Convert to parent ("neutral") molecule (useful for 3D search)
	FILTER	Apply property and substructure filters from learn file (with activity field name)
	ALL-CONFORMERS	To save all conformers rather than just the best conformer in 3D and SITE searches
	SIDE-CHAINS	Allow side-chains to move in a SITE search (also uses protein extended radii or hydrogen atoms)
	RMS	Compute RMS for 3D query with Exact and 2D searches
CUTOFF	Integer value	Minimum cutoff for similarity search or score for Site search
SITE	Text string	Protein receptor site molecule (for SITE search) or R-group atom (for reagent search)

KEY	To generate functional group keys
Keywords	Value type or value	Notes
OPTIONS	List of values
	REPORT	List keys to screen
	NOREPORT	Don't list keys to screen
FILE	Text string	File to be processed
MOLECULE	Text string	Molecule(s) in memory to be processed

DISPLAY	To display molecule(s) or data
Keywords	Value type or value	Notes
MODE	Single value from list	Display mode (required)
	2D	2D display of molecule(s)
	3D	3D display of molecule(s)
	PANEL	25 panels of plots for different no of centres (0-24)
	KEYS	Plot of keys vs molecules
	HISTOGRAM	Histogram of keys for specified molecules
	CONFORMERS	3D display of conformers
	TILE	Tile display of molecules
	CUBE	3D plot of molecular volume, lipophilicity and centres
MOLECULE	Text string	Molecule(s) to be displayed
QUERY	Text string	Query molecule (superimposed)
ACTIVITY	Text string	Activity field for colour coding
SIGNIFICANCE	Integer value	Significance factor for activity classification and colour coding
OPTIONS	List of values
	TYPE	Atom labels to include atom type
	SERIAL	Atom labels to include serial number
	GROUP	Atom labels to include group number
	NAME	Atom labels to include name (element+serial)
	RESIDUE	Atom labels to include residue name
	SEQUENCE	Atom labels to include sequence number, insertion and chain codes
	CONTACTS	Display CPK/VdW atom contacts
	MAPPING	Display query-molecule atom fitting correspondence
	INTERACTIONS	Display query-molecule pharmacophore interactions
	PANEL	Include the display panel to control colour, visibility etc
STYLE	Single value from list
	LINE	Line drawing
	STICK	Bonds cylinder sticks
	BALL-AND-STICK	Balls for atoms and cylinder sticks for bonds
	CPK	Balls for atoms at 0.6 of VdW radii
	VDW	Balls for atoms at VdW radii
MAP	Text string	Map to be displayed

CALCULATE	To calculate various molecular properties
Keywords	Value type or value	Notes
OPTIONS	List of values
	REPORT	List value(s) to screen
	NOREPORT	Don't list value(s) to screen
	FILTER	Apply property and substructure filters from learn file (with activity field name)
PROPERTIES	List of values	(default 2D+3D properties)
	2D	2D Properties
	3D	3D Properties
	PHARMACOPHORES	Pharmacophore profile
MOLECULE	Text string	Molecule(s) to be processed
FILE	Text string	File of molecules to be processed (format indicated by extension)
ACTIVITY	Text string	Activity field for Learn filename (see LEARN) for comparison
QUERY	Text string	Query molecule (for RMS properties)
MAP	Text string	Name of the map to be calculated
TYPE	Single value from list
	VDW	VdW volume
	POTENTIAL	Electrostatic potential
	LIGAND	Volume occupied by fitted ligands
	CAVITY	Cavity map of protein
	RESULT	Resultant map from combining other maps of the same type
RANGE	Text string	Map range (min_x,max_x,min_y,max_y,min_z,max_z)
GRID	Integer value	Separation of grid points (default 0.5 Angstroms)
ATOMS	Text string	Atoms to be processed (used in conjunction with MOLECULE)
BEST	Integer value	Number of ligand maps to be kept
FROM	Text string	Maps defining separated by & (and), ! (not), | (eor) and , (or)

SUGGEST	To generate novel molecules
Keywords	Value type or value	Notes
MOLECULE	Text string	Starting molecule name (usually an active molecule)
OUTPUT	Text string	Output file for molecules (format indicated by extension)
TRANSFORMS	Text string	File name for transformations
OPTIONS	List of values
	ADD	Add to existing property diversity
GROUP	Integer value	Group number for part of molecule to be modified
MAXIMUM	Integer value	Maximum no of molecules to be generated
TIME	Integer value	Maximum no of attempts to build molecules (default no limit)
REJECT	Text string	File name for rejection substructures
DISPLAY	List of values	Display properties or resulting molecules
	PANEL	25 panels of plots for different no of centres (1-25)
	CUBE	3D plot of molecular volume, lipophilicity and centres
LIMIT	Integer value	Limit property diversity cell occupancy
SITE	Text string	Specify 3D to preserve the code or protein name or map name
CURB	Integer value	Curb the number of non-H inserted atoms when this exceeds the curb value by progressively scaling do

DELETE	To delete molecules from memory
Keywords	Value type or value	Notes
MOLECULE	Text string	Remove the specified molecule(s) from memory
MAP	Text string	Remove the specified map(s) from memory

LEARN	To generate a learn file of discriminating property limits and substructures
Keywords	Value type or value	Notes
PROPERTIES	Text string	Comma separated list of field names, keys and/or pharms for consideration (default all+keys)
OPTIONS	List of values
	ADD	Add to existing property diversity
	CLEAR	Clear existing property diversity

CUSTOMISE	To set various parameters
Keywords	Value type or value	Notes
BACKGROUND	Text string	Background colour for display
FOREGROUND	Text string	Foreground colour for display of plots and 2D molecules
ACTIVE	Text string	Colour for coding active molecules
INACTIVE	Text string	Colour for coding inactive molecules
CONTACTS	Single value from list
	CPK	Use CPK contacts in conformational analysis
	VDW	Use VdW contacts in conformational analysis
	IGNORE	Do not check contacts in conformational analysis
FILES	Integer value	No of files which may be nested in script
SAMPLE	Integer value	No of conformers to be sampled
CONFORMERS	Single value from list
	SYSTEMATIC	Systematic search (default)
	RANDOM	Random sample conformers
	SAMPLE	Representative sample conformers
SINGLE	Integer value	No of increments for single bonds (0=disable)
ALPHA	Integer value	No of increments for alpha bonds (sp3-sp2) (0=disable)
CONJUGATED	Integer value	No of increments for conjugated bonds (0=disable)
CROWDED	Integer value	No of increments for crowded bonds (0=disable)
AMIDE	Integer value	No of increments for amide bonds (0=disable)
RING	Integer value	No of increments for ring bonds (0=disable)
CPK	Integer value	Ratio (default 0.6) to VdW radius for CPK contacts check
CENTRES	Integer value	Number of centres in pharmacophore (3 or 4)
BINS	Text string	Pharmacophore bin definitions
TYPES	Text string	Pharmacophore centre types: Enter *, short (D,A,C,B,R,L,N,P,M,X,W,Z) or long names
DONOR	Single value from list
	HYDROGEN	H-bond donors must have an attached hydrogen (default)
	NOHYDROGEN	H-bond donors do not require an attached hydrogen
COUNT	Single value from list
	CONFORMER	Count pharmacophores for conformers
	MOLECULE	Count unique pharmacophores for molecules (maximum for any conformer)
	POPULATION	Boltzman percentage population of pharmacophores for molecules
	FRACTION	Percentage of pharmacophores for molecules (100*count/no of conformers)
ACTIVITY	Text string	Field containing activity data
ATTRIBUTES	List of values
	LOW	Low activity value is desirable
	HIGH	High activity value is desirable
	LOG	Take log of activity values
	NOLOG	Do not take log of activity values (default)
	ABSOLUTE	Significance specified as absolute value(s)
	FACTOR	Significance specified as fraction of activity value range (default)
SIGNIFICANCE	Text string	Factor or absolute value(s) (a_min,a_max) for identifying active and inactive sets of molecules
VOLUME	Integer value	Minimum volume (per non-H atom) for 4 centre pharmacophores (default 0.25)
AREA	Integer value	Minimum area (per non-H atom) for 3 centre pharmacophores (default 0.25)
ANGLE	Integer value	Minimum accessibility angle for 3 and 4 centre pharmacophores (default 30)
TIMEOUT	Integer value	Maximum time (minutes) for conformational generation (default 60)
TOLERANCE	Integer value	Maximum distance tolerance for 3D and SITE searches (default 0.5)
RESIDUES	Single value from list
	ANY	Pharmacophores can be defined by any residues (default)
	DIFFERENT	Pharmacophores must be defined by different residues (search only)
WARP	Integer value	To set the warp speed (>=0 <100) for SITE searches (default 10)
TILE	Integer value	To set the tile size (typically 100-300).
NAME	Text string	To use the specified name as the molecule name field in a MACCS file.
FIELD	Text string	To create a field with specified name.
RADIUS	Single value from list
	TOLERANCE	Use atom radius tolerance in 3D/SITE searches when > normal tolerance.
	NOTOLERANCE	Ignore atom radius in 3D/SITE searches (default).
VDW	Text string	Contour level and colour for VdW maps (level,colour)
POTENTIAL	Text string	Contour levels and colours for potential maps (level1,colour1,level2,colour2,etc)
LIGAND	Text string	Contour level and colour for ligand maps (level,colour)
PHARMACOPHORES	Integer value	Set the maximum number of pharmacophores to be processed. 0=No limit (default)
EMPTY	Integer value	To set the pharmacophore bin occupancy (>=0 <100) below which the pharmacophore is ignored
SCORE	Single value from list
	CS2.1	Use an enhanced ChemScore for ligand-protein interactions
	TS1.0	Use THINKscore for ligand-protein interactions
TWIST	Integer value	The maximum number of bonds for systematic conformer generation before switching to sample
GENERATE	Integer value	The maximum number of conformers generated by a systematic search before switching to sample
PRIORITY	Single value from list
	LOW	To lower the process priority for THINK
	NORMAL	To restore the process priority for THINK to normal
REJECT	Text string	Default file name for rejections in SMILES format (THINK_EXEC:reject.smi).
LEARN	Text string	Default file name for learn file (THINK_EXEC:default.lrn).
EXTENT	Integer value	Minimum extent (per non-H atom) for 2 centre pharmacophores (default 0.25)

CHECK	To check the property values for molecules
Keywords	Value type or value	Notes
ACTIVITY	Text string	Activity field for Learn filename
REPORT	List of values
	SUMMARY	Summary information to be listed to the screen
	FULL	Ful l property listing with comparison highlights
REJECT	Text string	File of rejection substructures
MOLECULE	Text string	Molecules in memory to be checked
OUTPUT	Text string	Output file

SELECT	To select molecules from a file using property or pharmacophore diversity (not both).
Keywords	Value type or value	Notes
FILE	Text string	File of molecules to be processed (format indicated by extension)
OUTPUT	Text string	Output file of molecules (format indicated by extension)
MODE	List of values
	ADD	To select molecules which add to existing property or pharmacophore diversity
	AND	To select molecules with pharmacophores which overlap with the existing diversity
DISPLAY	List of values
	PANEL	25 panels of plots for different no of centres (1-25)
	CUBE	3D plot of molecular volume, lipophilicity and centres
LIMIT	Integer value	Limit to the property diversity cell occupancy
PHARMACOPHORES	Integer value	Minimum number of new pharmacophores for molecule to be selected

ROTATE	To rotate all the molecules in memory
Keywords	Value type or value	Notes
ABOUT	Text string	Axis for rotation (X, Y, Z or atom1-atom2 for bond; atom1 moves)
ANGLE	Integer value	Angle for rotation
TOBOND	Text string	Pair of atoms for vector to be aligned to Z axis
TOPLANE	Text string	List of atoms for plane to be oriented in X,Y plane
TOFIT	Text string	Pairs (>3) of atoms to be fitted (first move)
TOMAP	Text string	Name of map to be oriented in X,Y plane.

PLOT	To display molecule(s) or data to the printer or plotter
Keywords	Value type or value	Notes
MODE	Single value from list	Display mode
	2D	2D display of molecule(s)
	3D	3D display of molecule(s)
	PANEL	25 panels of plots for different no of centres (0-24)
	KEYS	Plot of keys vs molecules
	HISTOGRAM	Histogram of keys for specified molecules
	CONFORMERS	3D display of conformers
	TILE	Tile display of molecules
	CUBE	3D plot of molecular volume, lipophilicity and centres
MOLECULE	Text string	Molecule(s) to be displayed
QUERY	Text string	Query molecule (superimposed)
ACTIVITY	Text string	Activity field for colour coding
SIGNIFICANCE	Integer value	Significance factor for activity classification and colour coding
OPTIONS	List of values
	TYPE	Atom labels to include atom type
	SERIAL	Atom labels to include serial number
	GROUP	Atom labels to include group number
	NAME	Atom labels to include name (element+serial)
	RESIDUE	Atom labels to include residue name
	SEQUENCE	Atom labels to include sequence number, insertion and chain codes
	CONTACTS	Display CPK/VdW atom contacts
	MAPPING	Display query-molecule atom fitting correspondence
	INTERACTIONS	Display query-molecule pharmacophore interactions
STYLE	Single value from list
	LINE	Line drawing
	STICK	Bonds cylinder sticks
	BALL-AND-STICK	Balls for atoms and cylinder sticks for bonds
	CPK	Balls for atoms at 0.6 of VdW radii
	VDW	Balls for atoms at VdW radii

MODIFY	To modify the molecules or create complementary centres
Keywords	Value type or value	Notes
MOLECULE	Text string	Specify the molecule to be modified
LIGAND	Text string	Specify the ligand molecule (optional for INTERACT)
RATIO	Integer value	Specify the ratio of the contact radius to VdW radius
DELETE	Text string	Specify the atoms to be deleted (from one molecule)
MAKE-BOND	Text string	Specify the atoms to be bonded (in same molecule)
BREAK-BOND	Text string	Specify the bond to be broken
REBUILD	Single value from list
	2D	Rebuild 2D coordinates
	3D	Rebuild 3D coordinates
	CONNECTIONS	Rebuild connectivity from 3D coordinates
	BOND-ORDERS	Rebuild bond-orders from 3D coordinates
	OPTIMISE	Use Molecular Mechanics to optimise 3D coordinates
INTERACTIONS	Text string	Create complementary centres for molecule
CHANGE	Text string	Specify atoms to be changed
INSERT	Text string	Specify new atom for molecule
TO	Text string	Specify new name for molecule
NAME	Text string	Specify new name for changed atom
TYPE	Text string	Specify new type for changed atom
SERIAL	Text string	Specify new serial number for changed atom
GROUP	Text string	Specify new group number for changed atom
SITE	Text string	Find the binding site for the specified protein molecule

CLUSTER	To cluster the molecules according to their functional group keys
Keywords	Value type or value	Notes
SIZE	Integer value	Maximum number of clusters (0=defined by similarity)
SIMILARITY	Integer value	Minimum similarity between molecules for same cluster

HELP	To list this help text

CALL	Take commands from the file specified
RETURN	Close script file and return to previous file or keyboard
GOTO	Jump to specified label in current file
LABEL	Specify label (for GOTOs)
LET	Assign symbol to value or result of expression
WHILE	Loop while condition is true
END	End of loop
IF	Conditional execution of following statements
ELSE	Alternative execution of following statements
ELSEIF	Conditional execution of following statements
ENDIF	End of conditional/alternative execution
READ	Read text from a file (first parameter) into a symbol (second parameter)
WRITE	Write text to a file (first parameter) from a symbol (second parameter)