Index to Catalyst Online Help

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Numerics

1D data

correcting errors and property definitions `

indexes for property fields

introduction

preserving when using DELETE_DB

suppressing generation of during database building

updating in databases

2D Attributes

setting Global Preferences

2D Beautify command

description

examples

2D Bond style

changing

double-bond alignment

2D Group Style command

description

2D knurls

on bonds

2D Monochrome command

description

2D selection button

in Toolbox

2D workspaces

graphic

2D3D-Compound command

description

2D/3D database server program

how to determine if catDisk is running

3D constraint appearance

setting Global Preferences

3D Constraint command

description

3D constraint display style

setting Global Preferences

3D Constraints command

how to use

3D Minimize command

description

3D molecule display style

setting Global Preferences

3D selection button

in Toolbox

3D Style

setting Global Preferences for molecules

3D workspaces

graphic

rotating objects in 3D

A

About Catalyst command

description

Activ field

in Generate Hypothesis spreadsheet

Actives and Inactives color fields

Overlay Controls for Workbench Options

Activity

estimating in View Hypothesis workbench

special property

Activity Threshold field

Overlay Controls for Workbench Options

Add Association button

in Exclude/OR QuickTool

Add button

in Function list dialog box

Add Function button

using a template molecule

in Show Function Mapping command

Add to Dictionary command

description

Add to View button

in Show Conformers dialog box

ADD_PROPERTY command

in catDB database utility

Adding

2D and 3D topologies to a database

APPEND in building databases

atoms

bonds

databases

distance constraints

location constraints

properties to property dictionary

substituents

Aliases

displaying in 2D

for defined groups

Aligning

3D molecules to 2D

Alignment

changing for double bonds in 2D

Aliphatic button

in Atom Specification Editor

All Atoms field

Overlay Controls for Workbench Options

All Conformers button

in Export dialog box

in Import Data dialog box

All Elements button

in Atom Specification Editor

AllowNFS option

in catDB database utility

Altering: see Changing Amino acids

building peptides

AND operator

for property data queries

in Edit Hypothesis 1D Properties dialog box

Angle

setting units in Catalyst

Angle and torsion constraints

how they affect Compare

Angle bending function

reference information

Angle constraints

adding in View Hypothesis workbench

Angles

measuring between bonds

measuring

measuring out-of-plane

measuring torsion angles

Append Excluding Entry command

in Exclude/OR QuickTool

APPEND option

in catDB database utility

Append OR Column command

adding more rules with

Append/Replace Database Compounds command

description

how to use

Apply Color To field

Overlay Controls for Workbench Options

Approximately equal function

in Edit Hypothesis 1D Properties dialog box

in property data query

Arithmetic/lexical functions

for property data queries

Aromatic Bond button

in Bond Specification Editor

Aromatic button

in Atom Specification Editor

Aromatize command

description

Association editor

canceling in Exclude/OR QuickTool

Associations

deleting

displaying in Exclude/OR QuickTool

how to set in Exclude/OR QuickTool

in Exclude/OR QuickTool

Atom Labels command

description

displaying atom labels in hypotheses

for displaying function names

Atom Labels display

setting Global Preferences

Atom Specification editor

dialog box in View Hypothesis workbench

expanded dialog box in View Hypothesis workbench

in View Hypothesis Toolbox

Atom specifications

setting in hypotheses

Atoms

adding

changing with keyboard shortcuts

chirality rules

deleting

deprotonating

displaying labels in hypotheses

ionizing

knurls illustration

measuring distance between

moving in 2D

moving in rings

placing in the workspace

protonating

removing charges

selecting

setting specifications in hypotheses

View Atom Labels command

Axial bonds

changing to equatorial

B

Background colors

setting in Global Preferences

Background information

Catalyst database files

crefs in Catalyst databases

for building Catalyst databases

property dictionary for Catalyst databases

Background processes

cancelling

checking status of

cleaning up after

collecting results of

introduction

setting up

viewing conformer generation log files

Backspace key

keyboard shortcut for Erase tool

Ball and Tube command

description

Base Directory

setting Global Preferences

Batch jobs

see Background processes

setting up

Beautifying

2D molecules

Best Fit

method of performing Compare

Best fit plane

adding in View Hypothesis workbench

computing and displaying

Best Flexible Search Databases/Spreadsheets command

description

how to use

BEST option

in catDB database utility

Best Quality conformer generation

description

distribution illustration

successive runs

when to use

Binary field

Overlay Controls for Workbench Options

BioByte command

description

Blue

text and buttons in on-line Help

Bond display style

changing

selecting

Bond Specification editor

dialog box

in View Hypothesis Toolbox

Bond stretching function

reference information

Bond Style tool

in View Compound Toolbox

Bond type

changing

changing with keyboard shortcuts

Bond Type tool

in View Compound Toolbox

Bond types

selecting

specifying in hypotheses

Bonds

adding

changing 2D bond style

changing 2D double bond alignment

changing type

deleting

knurls on

rotating a single bond in 3D

rotating in 3D

selecting

setting specifications in hypotheses

toggling between axial and equatorial

Bonds between hypothesis features

tool in View Hypothesis Toolbox

Boolean button

in Edit Hypothesis 1D Properties dialog box

logic operators for property data queries

BPD command

building and editing a template property dictionary file

in catDB database utility

rules for naming 1D properties

Bridgehead button

in Atom Specification Editor

Bridgeheads

elimination of hydrogens

inverting stereochemistry

Bridges

adding

eliminating hydrogens

Browse Databases/Spreadsheets command

description

how to use

Browsing

databases

databases in batch mode

to combine spreadsheets/databases

Buckingham interactions function

energy reference

Buffer

specifying size for conformers when building databases

Building

a custom database from a StockroomDB with catDB

a database from a subset of another database with catDB

a default database from a StockroomDB in Catalyst

a multiconformer database

a singe-conformer database

databases

hypotheses

molecules

peptides

template property dictionary file

by Object Location

option for Tidy Lab command

option for Tidy Shelf command

by Object Name

option for Tidy Lab command

option for Tidy Shelf command

by Object Type

option for Tidy Lab command

option for Tidy Shelf command

C

Cahn-Ingold-Prelog conventions

use in Catalyst

Cancel QuickTool command

in Exclude/OR QuickTool

in View Compound QuickTool

in View Hypothesis QuickTool

Cancel Running Process button

in Process Information dialog box

Cancelling

background processes

Canonical

display of groups in 2D

.Catalyst file

product.flexfit/excessEnergyPerConf parameter for Best Flexible Search Databases/Spreadsheets command

Catalyst

displaying on PCs

introduction

on-line Help system

overview

Catalyst/Hypo

grayed-out menu items

product description

Catalyst/Info

grayed-out menu items

product description

catalyst_ldb.bip

file

catDisk

how to determine if running

catDB commands

for building databases

how to use

introduction to

catSearch commands

-bestFlexible

-browse

-help

-query

batch database searching utility

how to use

Centroids

adding in View Hypothesis workbench

computing and displaying

Changing

2D and 3D topologies while preserving 1D data in a database

database configuration file

database property data

display style of hypotheses

report layout

report layout to display computed property data

size: see Resizing

stereochemistry

topology

values for a property in a variable field

values in a spreadsheet

Charge field

in Atom Specification Editor

Charges

reducing

removing

Chemistry tool

Aromatize command

Oxidize command

Protonate command

Reduce command

Chirality

examples of R and S

rules for designating

viewing

Chirality Labels command

description

Chirality Labels display

setting Global Preferences

Chirality On Non-Carbon Atoms button

setting Global Preferences

CHM files

exporting

importing

Cis

changing to trans

specifying in SMILES files

Clean Process Data button

in Process Information dialog box

Cleaning up

2D molecule display

3D molecule structures

after background processes

background processes

Clear All Report Rows command

description

Clear Current Hypothesis command

description

Clear Display command

description

Clear Elements button

in Atom Specification Editor

Clear Selected Report Rows command

description

removing values from spreadsheets

Clearing

workspace displays

Clicking

in workspace of View Compound workbench

Client-server operation

for databases

Closing

rings

rings in 3D

Clustering hypotheses

Collect Process Data button

in Process Information dialog box

COLLECTED status

in Process Information dialog box

Collecting

results of background process

Color field

in Generate Hypothesis spreadsheet

Colorization

of compounds in quick Compare/Fit

Colorization field

Overlay Controls for Workbench Options

Colors

setting global background colors

setting global constraint colors

setting global highlight colors

setting global label colors

setting global mapped feature colors

setting global object colors

Columns

in Exclude/OR QuickTool

Combine Spreadsheets command

In First AND In Second

In First but NOT In Second option

In First OR Second option

Combining

spreadsheets and databases by browsing

spreadsheets to get compounds in one but not other

spreadsheets to get intersection of compounds in

spreadsheets to get union of compounds in

CoMFA

how to export compounds for

Command line

in UNIX shells

Commands

using

Comments and Suggestions dialog box

how to use

Commit 1D Changes To Database command

changing property data in a database

description - Generate Hypothesis workbench

description - View Database workbench

Compare

how it is different than Fit

introduction to comparing hypotheses and compounds

using tethers with compound and hypothesis

Compare Options

Maximum Omitted Features

Compare/Fit

differences to search mapping

Fast and Best Fit methods

how the fit is measured

illustrated examples

performing Quick Compare/Fit

This Conf and Best Fit Conf methods

Compare/Fit command

differences in database search mapping

introduction

procedure for a hypothesis and a compound

procedure for two compounds

procedure for two hypotheses

Comparing

a compound and a hypothesis

procedure for a hypothesis and a compound

procedure for two compounds

procedure for two hypotheses

two compounds

two hypotheses

Composite OR feature

displaying associations

editing

in constraint definitions

representing set of rules

setting associations for geometric use

steps for setting associations

Compound-All command

description

Compound Name colors

setting Global Preferences

Compound Names command

description

for displaying hypothesis names

for displaying molecule names

Compound to Use field

in Generate Conformers dialog box

CompoundName

special property

Compounds

adding to a database with Append/Replace Database compounds command

adding to a database with catDB

comparing two

comparing with hypotheses

deleting from database with catDB DELETE

deleting from database with catDB SPST_DELETE

finding differences between two spreadsheets

finding intersection of in two spreadsheets

finding union of in two spreadsheets

finding with Find command

object description

see also Molecules

Compound-Table command

description

Compute Property command

description

how to use

Conf Energy

output values in Compare dialog box

ConfBuffer= option

in catDB database utility

CONFIG command

in catDB database utility

Conformational Analysis

see also Conformers

Conformational model

Catalyst database file

how to generate

introduction

viewing

Conformational space

illustration

sampling

Conformer generation

energy range

introduction

Conformers

Best Quality generation

comparison of generation methods

deleting

discard when building databases

displaying single conformers

Fast generation

for relative stereochemistry

for unknown stereochemistry

how to generate

list of tasks

retain when building databases

retrieving from background process

saving

saving after Best Fit with Compare

setting for catDB ConfBuffer= option

setting for catDB MaxConfs= option

settings for catDB ExistingConfs= option

successive generations

viewing

when to use Fast and Best Quality

Constraint colors

setting Global Preferences

Constraint Display

setting Global Preferences for tolerances

Constraint Maximum field

in Constraint Tolerance dialog box

Constraint Minimum field

in Constraint Tolerance dialog box

Constraint Names command

description

for displaying constraint names

Constraint Names display

setting Global Preferences

Constraint Tolerance display

setting Global Preferences

Constraint Tolerances command

for displaying constraint tolerances

Constraints

adding angle constraints

adding excluded volumes

adding torsion constraints

changing display style

changing names of

changing values of

composite OR features in definitions

defining in View Hypothesis

displaying names

displaying tolerances of

displaying values

editing composite OR features in definitions

setting global display style

summary of

using composite OR feature in

Constraints menu

description

Constructing

hypotheses

Convert Molecule to Hypothesis tool

in View Database workbench

Convert Molecules to Cerius2 R-groups

in View Hypothesis Toolbox

Converting

molecules to hypotheses

Coordinates field

in location constraint dialog box

Coordination field

in Atom Specification Editor

Copy command

description

Copying

in non-Catalyst environments

see Duplicating

see Sampling

SMILES out of Catalyst

SMILES strings

SMILES strings into Catalyst

CPD command

in catDB database utility

CPD files

exporting

importing

Crashes

recovering from

CREATE command

in catDB database utility

Create Database command

description

dialog box

how to use

Create Lab command

description

dialog box

Create/Edit Hypothesis 1D Properties command

description

CREATE_1D command

in catDB database utility

Creating

1D hypotheses

a custom database from a StockroomDB with catDB

a database from a subset of another database

a default database from a StockroomDB in Catalyst

a multiconformer database

a singe-conformer database

databases

databases with catDB CREATE

labs

see Adding or

see Building or

see Generating

Crefs

background information

overlapping

reassigning with REPAIR_DB command

selecting starting number when building databases

Current Hypothesis field

in Generate Hypothesis workbench

Currently active element

in Periodic Table

Currently mapped position

for Show Function Mapping command

Custom database

building from a StockroomDB with catDB

Customizing

list of global parameters

setting global preferences

D

Data

1D data in Catalyst

categories of data in Catalyst databases

property data in Catalyst

updating 1D data in databases with spreadsheets

Data fields

in Generate Hypothesis spreadsheet

Data menu

for labs

for workbenches

Data model

for Catalyst databases

Data types

valid characters for

Database access tokens

description

Database Info tokens

description

Database configuration file

background information

creating with the CONFIG command in catDB

Database search

with batch catSearch program

Database server tokens

description

Databases

2D index files

3D index files

adding 2D and 3D topologies while preserving 1D data

adding a 1D property in Catalyst

adding a 1D property with catDB

adding compounds with Append/Replace Database Compounds command

adding compounds with catDB

adding properties to property dictionary

adding to xdbConfigList file

background information for building

batch searching and browsing

best flexible searching

browsing

building

building a custom from a StockroomDB with catDB

building a default from a StockroomDB in Catalyst

building a multiconformer

building a singe-conformer

building and editing a template property dictionary file

building from a subset of another database

client-server operation

conformational model file

correcting 1D data and property definitions

creating

creating a database from Catalyst .cpd files

data model

deleting 1D property data from

deleting a 1D property in Catalyst

deleting a 1D property with catDB

deleting compounds from with catDB DELETE

deleting compounds from with catDB SPST_DELETE

deleting from disk

deleting properties from property dictionary

differences from spreadsheets

disk space requirements

displaying 2D and 3D structures

displaying hits

displaying property definitions

editing property dictionary

editing spreadsheets for updating databases

fast flexible searching

files

how to determine if 2D/3D server program is running

installing

merging

moving location of files

object description

overlapping crefs

problem compounds

problems in building

property data types

property description specification

property dictionary for

recalculating indexes

reference specification

removing

restarting building

rules for naming 1D properties

sampling to workbenches

saving search/browse hits

schema specification

scripts for building a multiconformer database

special properties

stopping building

suppressing 2D indexes

suppressing 3D indexes

suppressing generation of 1D data

updating 1D data

updating 1D data from spreadsheets

updating with Commit 1D Changes to Database

using catDB

validating structures in

writing to database files across NFS-mounted disk partitions

xdbConfigList file

Databases menu

in Stockroom

in View Databases workbench

Date

format for start time for background tasks

Date data type

formats for

valid characters for

Date format

setting global preferences

De-aromatize

rings

Default database

building from a StockroomDB in Catalyst

DEFAULT option

in catDB database utility

Default Host

setting global preferences

Define Constraint command

description

Define R-Group command

description

Defining

groups

Deinstall Database command

description

Deionizing

ions

Delete Association button

in Exclude/OR QuickTool

DELETE command

in catDB database utility

Delete from Dictionary command

description

Delete key

keyboard shortcut for Erase tool

DELETE_DB command

in catDB database utility

DELETE_DB_1D command

in catDB database utility

DELETE_PROPERTY command

in catDB database utility

Deleting

1D property data from a database

compounds from database with catDB DELETE

compounds from database with catDB SPST_DELETE

conformers

databases

hypothesis components

properties from property dictionary

rows from spreadsheets

see also Disposing of

selected objects

Deleting objects

with Dispose from StockroomDB command

with Dispose from Workbench command

Deprotonating

atoms

Deselecting

in View Compound workbench

in View Hypothesis workbench

removing objects from selections

Deselection tool

in Toolbox

Destination

in Print dialog box

Detail option

displaying graphs with

in catDB database utility

Dialog box

for Create Database command

for Export command

for Print

for Process Information

for Save to Shelf As

for setting distance constraints

for Show Conformers command

Dictionary

Feature Dictionary in View Hypothesis workbench

Feature

DIED status

in Process Information dialog box

Dihedral torsion function

reference information

Directory field

in Export dialog box

in Import Data dialog box

Discard

setting for catDB ExistingConfs= option

Disk space requirements

for databases

Displacements

RMS displacements in Compare

Display buttons

in Compare dialog box

in Find dialog box

Displaying

2D and 3D structures in spreadsheets

an object in a new workbench

atom specifications in hypotheses

compound names

computed property data in variable report fields

constraint tolerances

explicit exclusion mappings deriving from symmetry

fragments

function names

graphs of information in databases

hypotheses in different ways

individual conformers

multiple objects

objects in workspaces

property data in variable report fields

results of database search

Displays

clearing

Dispose Conf/Flat button

in Show Conformers dialog box

Dispose from StockroomDB command

description

Dispose from Workbench command

description

Dispose of Workbench command

description

Disposing of

objects

see also Deleting

workbenches

Distance

setting units in Catalyst

Distance constraints

adding

how they affect Compare

introduction

DONE status

in Process Information dialog box

Dots command

description

Double Bond button

2D rendering

in Bond Specification Editor

Dragging and dropping

objects to workbenches

Drawing: see Building

Duplicate command

description

Dynamic Bond Rotations command

description

effect of

use

Dynamic modeling

dynamic bond rotation

introduction

Modeling menu

ring flipping

use of Van der Waals command

E

Edit box

for changing values in a spreadsheet

Edit button

in Generate Hypothesis dialog box

Edit field

in Generate Hypothesis workbench

Edit menu

for labs

for workbenches

Edit Property Dictionary command

description

Edit text box

in Generate Hypothesis workbench

using to change spreadsheet data in Generate Hypothesis workbench

Editing

1D hypothesis

composite OR features

multiline values in spreadsheets

removing rows from spreadsheets

values for a property in a variable field

values in a spreadsheet

Editing topology: see Changing Topology

Elements

changing with keyboard shortcuts

currently active in View Compound workbench

selecting in Periodic Table

Ellipsis points

in menus

Enantiomers

making

Endocyclic button

in Atom Specification Editor

in Bond Specification Editor

Energy

reference information

setting units in Catalyst

Energy Limit

parameter in Compare dialog box

specifying for conformers generated with Best Flexible Search Databases/Spreadsheets command

Energy range

in conformer generation

parameter for catDB conformer generation

Energy range field

in Generate Conformers dialog box

Energy threshold

setting in Best Conf Compare

Equal button

in Edit Hypothesis 1D Properties dialog box

Equals function

in Edit Hypothesis 1D Properties dialog box

Equatorial bonds

changing to axial

Erase tool

in Toolbox

keyboard shortcuts for

Erasing: see Deleting

errData= option

in catDB database utility

errFile= option

in catDB database utility

Error

special property

Error data file

in catDB operations

Error field

definition

in Generate Hypothesis spreadsheet

Error file

in catDB operations

Errors

correcting 1D data and property definition

ESP files

for catDB CREATE command

Estimate

special property

Estimate Activity command

differences from search mapping

in View Hypothesis workbench

Estimate field

in Generate Hypothesis spreadsheet

Estimated activity

in Score command

Estimating activity

different methods

in different workbenches

Exact button

in Find dialog box

Examples

of Fit operations

Exceptions

narrowing rules with exclusions

steps for specifying exclusions to rules in Exclude/OR QuickTool

Exclude/OR Edit command

for opening Exclude/OR QuickTool

Exclude/OR QuickTool

Add Association button

adding more exclusions

adding OR columns

adding rules

adding valid exclusions

Append Excluding Entry command

associations in

column layout

composite OR feature

Delete Association button

description

diagram

display of associations in

displaying associations

examining exclusion mappings

example of use

exclusion mapping buttons

generalizing hypothesis features

introduction

list of topics

modifying rules

opening

overview

Return from QuickTool command

returning from Association Editor

selecting windows and columns

setting associations in

steps for summarizing rules

steps in specifying exclusions

viewing all exclusions

Excluded volumes

adding in View Hypothesis workbench

how they affect Compare

Exclusion mapping buttons

in Exclude/OR QuickTool

Exclusions

adding valid exclusions in Exclude/OR QuickTool

conceptual diagram of Exclude/OR QuickTool

examining mappings in Exclude/OR QuickTool

explicitly displaying mappings deriving from symmetry

mappings deriving from symmetry

steps in specifying in Exclude/OR QuickTool

viewing all in Exclude/OR QuickTool

Execution Type field

in Generate Conformers dialog box

Exit button

in on-line Help

ExistingConfs= option

in catDB database utility

Exiting

and saving

from Catalyst

from on-line Help system

workbenches: see Iconifying or Disposing of

Exocyclic button

in Atom Specification Editor

in Bond Specification Editor

Expanding

Periodic Table

Export

dialog box

Export command

description

Export Type buttons

in Export dialog box

Export Workbench Alignments command

description

Exporting

chm hypothesis files

compounds as oriented to a hypothesis

cpd mol smi tpl hin mmod compound files

database/spreadsheet browse/search hits

molecules

objects

spreadsheets

spreadsheets for aligned compounds

spst esp spreadsheet files

Extend deselect

description

Extend move function

in Compare

Extend select

description

Extended spreadsheet files

for catDB CREATE command

F

Fast conformer generation

description

when to use

Fast Fit

method of performing Compare

Fast Flexible Search Databases/Spreadsheets command

description

how to use

FAST option

energy range parameter for catDB utility

in catDB database utility

Feature Dictionary

adding user-defined functions and fragments

database file

deleting functions and fragments

graphic

how to use

in View Hypothesis workbench

searching

using fragments and functions from

using in View Hypothesis workbench

Feature name

setting

Feature Selection

portion of Generate Hypothesis dialog box

Features

adding user-defined features to Feature Dictionary

deleting user-defined features from Feature Dictionary

File field

in Print dialog box

File Name field

in Export dialog box

in Import Data dialog box

File Type field

in Export dialog box

in Import Data dialog box

File types

for importing

Files

Catalyst database

database 2D index

database 3D index

database conformational models

database disk space requirements

database feature dictionary

ESP (extended spreadsheet)

journal

moving location of database

scripts for building a multiconformer database

SMILES files

TPL format

writing to database across NFS-mounted disk partitions

Find Best Conf

method of performing Compare

Find button

in Find dialog box

Find command

how to use

Find dialog box

display buttons

Exact button

Find button

Find item text box

Open Lab button

Sample to Shelf button

Save to Shelf button

Show button

Substring button

Find item text box

in Find dialog box

First Conformer button

in Export dialog box

in Import dialog box

Fit

how it is different from Compare

Fit objects

in workspace

Fit operations

differences from search mapping

illustrated examples

Fit to Window tool

in Toolbox

Fit value

how it is computed in Compare

Fitting

objects with Compare/Fit command

Flip 2D command

description

Flipping

molecules in 2D

rings in 3D

topology in 2D

Floating view tokens

description

Force field

references for

Forces

Van der Waals Forces command

description

Four-per-page command

description

Fragment constraints

how they affect Compare

Fragments

adding from Feature Dictionary

changing style of

description

how they are displayed

Fragments & Functions mode

in Feature Dictionary

Fragments Only mode

in Feature Dictionary

Full screen toggle

in all workbenches

Function keys

on Macintosh computers

on PCs

Function Mapping

dialog box

displaying in View Hypothesis workbench

Function Mapping dialog box

for Show Function Mapping command

Functional areas

of workbenches

Functions

adding from Feature Dictionary

adding location constraints to

description

description of Catalyst's chemical functions

deselecting

displaying labels

example of placing with template molecules

how they affect Compare

how to merge

in Feature Dictionary

placing with template molecules

selecting for hypothesis generation

summary of Feature Dictionary functions

Functions Only mode

in Feature Dictionary

G

Generalizing hypothesis features

by adding rules to

with Exclude/OR QuickTool

Generate Conformational Model command

how to generate conformers

how to use

Generate Hypothesis command

how to use

summary

Generate Hypothesis dialog box

MappingCoeff parameter

MinPoints parameter

MinSubsetPoints parameter

More Hypothesis Options button

Spacing parameter

Total Features fields

WeightVariation parameter

Generate Hypothesis workbench

features of

overview

overview of hypothesis generation

topics

Generate Standard 3D command

description

examples

Generating conformational models

Generate Conformational Model

how to

Generating conformers

Best Quality mode

comparison of generation methods

distribution illustration

energy range

Fast mode

how to

setting up background process

when to use Fast and Best Quality generation

Generating hypotheses

how to

overview of

preparing for

setting up spreadsheet for

Generation Type mode

in Generate Conformers dialog box

Geometric object colors

setting global preferences

Geometric Object display style

setting global preferences

Geometric Object Names command

description

for displaying geometric object names

Geometric Object Names display

setting global preferences

Geometric objects

best fit plane

centroids

defining

hydrogen bond acceptor vectors

hydrogen bond donor vectors

introduction

vectors

Geometric Objects command

description

how to use

Global Preferences command

description

list of parameters

Graphic2D

special property

Graphic3D

special property

Graphics

generic workbench

Stockroom

View Compound workbench

View Database workbench

Graphs

of information in databases

Gray data fields

in Generate Hypothesis spreadsheet

Grayed-out menu items

In Catalyst/Hypo

Greater than function

in Edit Hypothesis 1D Properties dialog box

Greater than or equal function

in Edit Hypothesis 1D Properties dialog box

in property data query

Group command

description

Grouping

property data searching criteria

Groups

2D Group Style command

canonical display

Define R-Group command

defining

displaying as alias

Group command

Select Group command

selecting

symbolic display

Ungroup command

ungrouping

using

Groups menu

description

H

Halogens button

in Atom Specification Editor

HB ACCEPTOR function

in Feature Dictionary

HB ACCEPTOR lipid function

in Feature Dictionary

HB DONOR function

in Feature Dictionary

Help

on-line documentation

Help buttons

in on-line Help

HELP command

in catDB database utility

HELP menu

for all workbenches

Highlight colors

setting in Global Preferences

HIN files

exporting

importing

History Window

description

Hits

controlling with Min Fit for Search

description

displaying

saving as individual compound

Hydrogen bond acceptor vector

adding in View Hypothesis workbench

Hydrogen bond acceptors

ways of creating

Hydrogen bond donor vector

adding in View Hypothesis workbench

Hydrogen bond donors

ways of creating

Hydrogen count

resetting in hypotheses

Hydrogen Count field

in Atom Attribute Editor

Hydrogens

deleting

important

replacing with another element

viewing

Hydrogens command

description

Hydrogens Visible

setting global preferences

HYDROPHOBIC function

algorithm for

in Feature Dictionary

Hypertext links

in on-line Help

Hypotheses

adding distance constraints

adding fragments

adding functions

adding items from Feature Dictionary

adding location constraints

AND operator for 1D data searches

approximately equal function in 1D data searches

arithmetic/lexical functions for 1D data searches

bringing into workbenches

changing display style

comparing to compounds

comparing two

converting molecules to

deleting components

deselecting

displaying atom specifications

displaying in workspaces

displaying names of

editing 1D

equals function in 1D data searches

examples

exporting

features of

finding with Find command

for searching databases

fragments in

functions in

generating regression for estimating activities

greater than function in 1D data searches

greater than or equal function in 1D data searches

how to generate

how to use Score Hypothesis command

illustrated Fit examples

importing multiple

importing one at a time

introduction

less than function in 1D data searches

less than or equal function in 1D data searches

logic operators for 1D data searches

matching compounds in a database search

Max field in property data searching criteria

merging

methods for building

Min field in property data searching criteria

Min Fit for Search value for 1D data searches

modifying

not equal function in 1D data searches

NOT operator for 1D data searches

OR operator for 1D data searches

parentheses in property data searching criteria

placing functions with template molecules

preparing for generation of

Hypothesis generation

cost analysis of hypotheses

selecting functions for

Hypothesis name colors

setting global preferences

Hypothesis tokens

description

I

Icon display

changing with View As command

Iconify Lab command

description

Iconify Workbench command

description

Iconifying

Catalyst

labs

workbenches

Iconifying Catalyst

button in Stockroom

Icons

dragging and dropping

moving

rearranging with Tidy Lab

viewing styles

Import All button

in Import List dialog box

Import command

description

Import Data dialog box

how to use

Import List Dialog box

how to use

Important hydrogens

description

Importing

chm hypothesis files

cpd mol smi tpl hin mmod compound files

dialog box

file types

hypotheses one at a time

Import command description

molecules one at a time

multiple hypotheses

multiple molecules

multiple objects

multiple spreadsheets

objects one at a time

.sd file as a shape query

spreadsheets one at a time

spst and esp spreadsheet files

types of file formats

types of objects

In First AND In Second option

for Combine Spreadsheets command

In First but NOT In Second option

for Combine Spreadsheets command

In First OR In Second option

for Combine Spreadsheets command

Indexes

effect on performance

for 1D data fields

recalculating for databases

suppressing 2D

suppressing 3D

INFO command

in catDB database utility

Info highlight colors

setting global preferences

Input data

preparing spreadsheets for hypothesis generation

Install Database command

description

Installing

training data set

Integer data type

valid characters for

Introduction

catDB commands

Catalyst

Generate Hypothesis workbench

generating a conformational model

generating conformers

hypotheses

Periodic Table

Stockroom and labs

to StockroomDB

View Compound Toolbox

View Compound workbench

View Hypothesis Toolbox

Inverting stereochemistry

at bridgeheads

Ionizing

atoms

Ions

creating ammonium and phosphonium

creating negative ions

removing charges

J

Job Options

list in Generate Hypothesis dialog box

Job Options dialog box

in Generate Hypothesis workbench

Joining

hypotheses

Journals

files

introduction to

journal.in file

journal_catalyst.current

journal_catalyst-1

journal_catalyst-2

object description

using the Run Journal command

viewing Catalyst journal files

K

Keyboard shortcuts

for changing bond type

for elements in Periodic Table

for Erase tool

for writing SMILES

Keys

on Macintosh computers

on PCs

Known stereochemistry

changing to unknown

Knurls

flipping topology in 2D

on atoms

on bonds

Knurls on bonds

illustration

L

Lab icon display style

setting Global Preferences

Lab menu

description

Label colors

setting Global Preferences

Labels

atoms

compound names

constraints

functions in hypotheses

geometric objects

stereochemistry

Labs

Create Lab command

example lab hierarchy

finding with Find command

Iconify Lab command

introduction

moving objects between

object description

opening

saving a spreadsheet into

tasks list for

Large Editor button

how to use

Lasso selection

Layout

changing workspace layout

for workbenches

setting for workbench

Leaving

see Quitting

Lennard Jones interactions function

energy reference

Less than function

in Edit Hypothesis 1D Properties dialog box

Less than or equal function

in Edit Hypothesis 1D Properties dialog box

in property data query

Licensing system

Catalyst tokens

database tokens

Linear deformation function

reference information

Linking

hypotheses

Loading

databases

Local Directory field

in Job Options dialog in Generate Hypothesis

in Setup Background Process dialog box

Local objects

description

operations creating them

Save As command

Location constraints

adding

description

for vector features

how they affect Compare

introduction

limit in generated hypotheses

Log files

viewing for conformer generation

Logic operators

for property data queries

Lone Pair Count field

in Atom Specification Editor

M

Macintosh computers

displaying Catalyst on

Magnifying

molecules and hypotheses

Mapped Features colors

setting Global Preferences

Mapping

functions on template molecules

MappingCoeff parameter

in Generate Hypothesis dialog box

Mappings

combinations from symmetry

differences between search and fit

exporting compounds as oriented to a hypothesis

multiple combinations in Compare

number reported

showing in Generate Hypothesis workbench

viewing between hypothesis and compound

viewing conformers containing

Mappings-Confs button

in Compare dialog box

Mass Number field

in Atom Specification Editor

Matching

in a database search

Max Field

in Edit Hypothesis 1D Properties dialog box

Max Find Hits

setting Global Preferences

Max Search/Browse Hits

specifying for databases/spreadsheets

MaxConfs= option

in catDB database utility

Maximum Number of Conformers field

in Generate Conformers dialog box

Maximum Omitted Features

in Global Preferences dialog box

Measure tool

in View Compound Toolbox

in View Hypothesis Toolbox

Measuring

distance between atoms

interatomic distance and angles

out-of-plane angles

torsion angles

Memory requirements

disk space for databases

Menu bar

description

graphic

Menus

Constraints

Data (for workbenches)

Data menu for labs

Databases

Edit (for workbenches)

Edit menu for labs

Groups

Help

Lab

Modeling

Preferences

ReportStyle (View Database workbench)

Style

Tools (Generate Hypothesis workbench)

Tools (View Compound workbench)

Tools (View Database workbench)

Tools (View Hypothesis workbench)

View

Windows

Workbench

MERGE command

in catDB database utility

Merge Features tool

in View Hypothesis Toolbox

Merging

hypotheses

hypotheses features

Merging functions

how to do

Mesh command

description

Metals button

in Atom Specification Editor

Min Field

in Edit Hypothesis 1D Properties dialog box

Min Fit for Search

field in Edit Hypothesis 1D Properties dialog box

Minimizing

3D Minimize command

MinPoints parameter

in Generate Hypothesis dialog box

MinSubsetPoints parameter

in Generate Hypothesis dialog box

Mistakes

correcting

MMOD files

exporting

importing

Modeling

dynamic

Modeling menu

description

Modifying

see changing

MOL command

in catDB database utility

MOL files

building databases from

exporting

importing

Mol Formula field

in Generate Hypothesis spreadsheet

Mol Wt field

in Generate Hypothesis spreadsheet

Molecule display style

setting Global Preferences

Molecules

adding to a database with Append/Replace Database Compounds command

adding to a database with catDB

bringing into workbenches

building

conformers: see Conformers

converting to hypotheses

copying as SMILES

deleting from database with catDB DELETE

deleting from database with catDB SPST_DELETE

displaying in workspaces

exporting

importing multiple

importing one at a time

matching hypotheses in a database search

sampling to workbenches

saving

saving to shelf

selecting parts of

summary of rules for selecting components

viewing names of

MolFormula

special property

MolWt

special property

Monochrome display in 2D

setting Global Preferences

More Hypothesis Options

button in Generate Hypothesis dialog box

Morse potential

energy reference

Moving

an object in a workspace

atoms and bonds in 2D

icons

location of database files

objects

objects to labs

objects to workbenches

workbenches and windows

Multiconformer database

building

scripts for building

Multiline values

editing in spreadsheets

N

Name field

in Generate Hypothesis spreadsheet

Names

displaying constraint names

displaying function names

displaying hypothesis names

displaying molecule names

see also Labels

viewing style for icons

Navigating

on-line Help system

Navigation keys

for moving among cells in spreadsheet

NEG CHARGE function

in Feature Dictionary

NEG IONIZABLE function

in Feature Dictionary

NFS-mounted disk partitions

writing across to database files

No Atoms field

Overlay Controls for Workbench Options

No1D option

example of usage in script

in catDB database utility

No2DIndex option

in catDB database utility

No3DIndex option

in catDB database utility

Not equal function

in Edit Hypothesis 1D Properties dialog box

NOT operator

in Edit Hypothesis 1D Properties dialog box

NOT_SAVED

schema in .bpd file

Now

as start time

NULL

special type specification for 1D property

O

Object Name field

in Duplicate Object Name dialog box

Objects

bringing into workbenches

changing size

displaying in workspaces

dragging and dropping

importing multiple

importing one at a time

introduction

local objects

magnifying or shrinking

moving

moving in workspaces

operations creating local objects

rotating

sampling to workbenches

saving to disk

selecting entire object

selecting

types of Catalyst objects

On-line Help system

additional buttons

how to use

leaving

navigating

universal Help buttons

One-Line Help area

description for Stockroom and labs

showing contents of objects

Only Non-Heteroatoms field

Overlay Controls for Workbench Options

Open command

description

in Data menu

Open Lab button

in Find dialog box

Opening

a new workbench to display an object

Exclude/OR QuickTool

labs

Open command

Opening workbenches

alternative methods

Options

for setting workspace layout

Selection Options command

setting for workbenches

OR columns

adding in Exclude/OR QuickTool

OR feature

composite representing set of rules

OR operator

in Edit Hypothesis 1D Properties dialog box

Orient 3D to 2D command

description

examples

Orienting

3D molecules to 2D

Original objects

difference from sample objects

Out of plane deformation function

reference information

Out-of-plane angles

measuring

Output Hypothesis field

in Generate Hypothesis dialog box

OutputDB= option

in catDB database utility

Overlay Controls

in Workbench Options dialog

OverlayColor

special property

Overlays

exporting compounds as oriented to a hypothesis

Overview

of Catalyst

Oxidize command

description

P

Panels

resizing

Parallel processing

for database searches

Parameters

MappingCoeff for hypothesis generation

MinPoints for hypothesis generation

MinSubsetPoints for hypothesis generation

product/confAnalysis.catDB.maxEnergySpread

product.flexfit/excessEnergyPerConf for Best Flexible Search Databases/Spreadsheets command

Spacing

WeightVariation for hypothesis generation

Paste command

description

Pasting

SMILES into Catalyst

SMILES strings out of Catalyst

PC computer

displaying Catalyst on

Peptides

building

Percent sign

wildcard character for string property data searches

Periodic Table

abbreviated form

expanded form

introduction

selecting elements

selecting substituents

Placing

atoms in the workspace

functions with template molecules

substituents in the workspace

Placing functions

with Add Function button

POS CHARGE function

in Feature Dictionary

POS IONIZABLE function

in Feature Dictionary

PostScript printing

description

Potential energy functions

reference information

Preferences

setting for workbenches

setting global

Preferences menu

in Stockroom and Labs

Preparing for

hypothesis generation

Print command

description

dialog box for

how to use

Print from field

in Print dialog box

Print Scene As field

in Print dialog box

Printer button

in Print dialog box

Printing

database search results

PostScript

Print command

reports

screen image

workspaces

Priority

in Job Options dialog in Generate Hypothesis

Problem compounds

encountered during database building

Problems

in building databases

Process Information command

description

dialog box for

how to use

Process Information dialog box

COLLECTED

DIED status

DONE status

QUEUED status

REGISTERED status

RUNNING status

WAIT status

Process Name field

in Job Options dialog box in Generate Hypothesis workbench

in Setup Background Process dialog box

Product description

Catalyst

Catalyst/Hypo

Catalyst/Info

product/confAnalysis.catDB.maxEnergySpread

energy range parameter

product.flexfit/excessEnergyPerConf

parameter for Best Flexible Search Databases/Spreadsheets command

PropDict= option

in catDB database utility

Property

attributes

field in Edit Hypothesis 1D Properties dialog box

sorting spreadsheet entries by

Property constraints

how they affect Compare

Property data

access tokens

correcting errors and property definitions

introduction

specifying description in .bpd file

specifying reference in .bpd file

specifying schema in .bpd file

specifying type in .bpd file

updating in databases

Property Dictionary

adding a 1D property with catDB

adding a property in Catalyst

adding or deleting properties

building and editing a template file for

data types in .bpd file

deleting a 1D property in Catalyst

deleting a property with catDB

description for Catalyst databases

description in .bpd file

editing

reference in .bpd file

schema in .bpd file

special properties

specifying with PropDict= option

Property name

rules for naming 1D

reserved words for 1D

Proteins

building

Protonate command

description

Protonating

how to

Pseudochirality

description

Q

Queue After field

in Job Options dialog box in Generate Hypothesis workbench

Queue After list

in Setup Background Process dialog box

QUEUED status

in Process Information dialog box

Quick Compare/Fit

description

QUICK_REF

reference in .bpd file

QuickTool area

description

graphic

QuickTool menu

in View Compound QuickTool

in View Hypothesis QuickTool

QuickTools

introduction to

summary of

View Compound QuickTool

View Hypothesis QuickTool

Quitting

and saving

from Catalyst

from on-line Help system

workbenches: see Iconifying or Disposing of

R

R Stereochemistry

(r) pseudochirality

example

R-groups

for input to Cerius²

Raster printing

description

Real data type

valid characters for

Reassigning crefs

procedure for

RECALC command

in catDB database utility

RECONFIG command

in catDB database utility

Recover button

in Catalyst recovery dialog box

Recovering

from system crashes

Reduce command

description

Region select

description

toggle

Register Confs button

in Show Conformers dialog box

REGISTERED status

in Process Information dialog box

Regress Hypothesis command

description

Relative stereochemistry

conformational analysis

specifying

Remote Directory field

in Setup Background Process dialog box

Remote Host field

in Generate Hypothesis dialog box

in Setup Background Process dialog box

Remove

button in Generate Hypothesis dialog box

Remove Entry button

in Import List dialog box

Removing: see Deleting

REPAIR_DB command

example of usage

in catDB database utility

procedure for using

Replacing

hydrogen with another element

see also Adding

see also Changing

Reports

displaying computed property data in variable fields

displaying property data in variable fields

printing

ReportStyle menu

in View Database workbench

Reserved words

for 1D property names

specified by NOT_SAVED schema

Reset Hydrogen Count command

in View Hypothesis workbench

Resizing

fitting all objects in workspace

objects in workspaces

panels in workbenches

workbenches with border adjustment

workbenches with full screen toggle

Restarting

database building

Return button

in Association Editor

Return from QuickTool command

in Exclude/OR QuickTool

in View Compound QuickTool

in View Hypothesis QuickTool

RING AROMATIC function

in Feature Dictionary

Rings

Aromatize command

closing

closing in 3D

flipping in 3D

RMS Displacements

how it is computed in Compare

output value in Compare dialog

Rotating

bonds in 3D

objects in 3D

objects in one plane

Row field

in Generate Hypothesis spreadsheet

Rubber band

from atoms

Rules

adding in Exclude/OR QuickTool

conceptual diagram of Exclude/OR QuickTool

displaying associations in composite OR feature

modifying in Exclude/OR QuickTool

steps for summarizing with associations

summarizing in composite OR feature

Run As Background Process

in Generate Conformers dialog box

Run Journal command

description

how to use

Run Locally

button in Generate Hypothesis dialog box

Run Locally field

in Setup Background Process dialog box

Run Remotely field

in Setup Background Process dialog box

Run Remotely on

button in Generate Hypothesis dialog box

Run Within Catalyst button

in Generate Conformers dialog box

RUNNING

status in Process Information dialog box

Running

journals

S

S Stereochemistry

(s) pseudochirality

example

Sample objects

difference from original objects

Sample to Shelf button

in Find dialog box

Sampling

conformational space

databases to workbenches

hypotheses to workbenches

molecules to workbenches

objects to workbenches

spreadsheets to workbenches

Save and Exit button

how to use

Save As Local Object command

description

Save Confs function

in Compare

Save Report To Lab As Spreadsheet command

description

how to use

Save StockroomDB command

description

how to use

Save to Lab As command

description

dialog box

Save to Shelf button

in Find dialog box

Saving

1D hypothesis

all objects to disk

conformers

hit compounds as a spreadsheet

hit compounds from searching or browsing

hypotheses

individual hit compounds

molecules

objects

objects to the shelf

spreadsheet into lab

spreadsheets

StockroomDB

Saving to shelf

1D hypothesis

hypotheses

molecules

spreadsheets

Schema

specifying in .bpd file

Score Hypothesis command

description

how to use

value in Status Area

Scoring

spreadsheets

Scripts

for building a multiconformer database

Scrolling all objects

in workspaces

SD command

in catDB database utility

SD files

building databases from

Search String field

in Feature Dictionary

Searching

databases: see Searching databases

Feature Dictionary

for compounds, hypotheses, spreadsheets, or labs

Searching databases

AND operator for property data queries

approximately equal function for property data

arithmetic/lexical functions for property data queries

batch mode with catSearch

best flexible

defining 1D data searching criteria

differences between fast and best

differences from Fit operations

displaying results

equals function for property data

fast flexible

for names of molecules

for string property data

for substructures

for values of 1D properties

greater than function for property data

greater than or equal function for property data

grouping property data searching criteria

how to

in background with catSearch

indexing for efficient performance

introduction

less than function for property data

less than or equal function for property data

logic operators for property data queries

not equal function for property data

NOT operator for property data queries

OR operator for property data queries

printing results

saving property data queries

setting lower boundary for property data query

setting upper boundary for property data query

specifying Min Fit for Search value

specifying properties for 1D data query

when do compounds match hypotheses?

with estimated activities

with wildcard characters for property data

Select All command

for labs

for workbenches

Select Group command

description

Selected Function Definitions

list in Generate Hypothesis dialog box

Selecting

atoms

bond display style

bond type

bonds

deselecting in View Compound workbench

deselecting in View Hypothesis workbench

elements from Periodic Table

entire object

extend select

groups

items inside an area

methods of

objects

parts of molecules

region select

region selection toggle

removing objects from selections

Select All command for labs

Select All command for workbenches

substituents from Periodic Table

values in a spreadsheet

windows and columns in Exclude/OR QuickTool

Selection Options command

description

Selections

in molecules

Send Comments command

description

Separating conformers

in Compare

Serious internal error

recovering from

Set Activity button

in Generate Hypothesis workbench

Set Activity field

in Generate Hypothesis workbench

Set Bond between Features tool

in View Hypothesis Toolbox

Set Constraint Tolerance tool

in View Hypothesis Toolbox

Set Current Hypothesis command

description

Set Feature Name command

in View Hypothesis workbench

Set Feature Weight command

description

Setting: see Specifying

Setup Background Process button

in Generate Conformers dialog box

Shape integration

Shelf

description

dragging and dropping icons on

graphic

Save to Lab As command

Tidy Shelf command

Shortcuts

using keyboard shortcuts

Show button

in Find dialog box

Show Conformational Model command

description

dialog box for

Show Exclusion Column command

in Exclude/OR QuickTool

Show Function Mapping command

description

how to use

Show Process Log button

in Process Information dialog box

Show Selected Compounds/Mappings command

for displaying hit compounds

Generate Hypothesis workbench

View Database workbench

Shrinking

Periodic Table

Single Bond button

in Bond Specification Editor

Single-conformer database

building

Six-per-page command

description

Sizing: see Resizing

Sketching

molecules

SLOW_REF

reference in .bpd file

Small Icons

viewing style

SMILES

copying and pasting

copying into Catalyst

copying out of Catalyst

writing with keyboard shortcuts

SMILES command

in catDB database utility

SMILES files

Catalyst's stereochemically extended SMILES language

building databases from

examples of standard SMILES

exporting

importing

rules for writing

specifying chiral centers

specifying cis/trans

specifying ring substituent stereochemistry

specifying tetrahedral centers

stereochemical extensions

Sort by Property command

description

View Database workbench

Spacefilling command

description

Spacing parameter

in Generate Hypothesis dialog box

Special field

in .bpd file

SPECIFIC

schema in .bpd file

Specifications

displaying for atoms

for bonds in hypotheses

Specifying

approximately equal function arguments in 1D queries

arithmetic/lexical function arguments in 1D queries

bond types in hypotheses

equals function arguments in 1D queries

greater than function arguments in 1D queries

greater than or equal function arguments in 1D queries

less than function arguments in 1D queries

less than or equal arguments in 1D queries

logic operator arguments in 1D queries

maximum search/browse hits for databases/spreadsheets

Min Fit for Search value

not equal function arguments in 1D queries

property dictionary for a database

relative stereochemistry

searching criteria for values of 1D properties

unknown stereochemistry

values for Property field for 1D data searches

wildcard characters in 1D queries

Spectrum field

Overlay Controls for Workbench Options

Sphere and Rod command

description

Spreadsheets

bringing into workbenches

combining to get compounds in one but not other

combining to get intersection of compounds in

combining two to get union of compounds in

description in Generate Hypothesis workbench

differences from databases

displaying 2D structures

editing multiline values in

editing values for a property in a variable field in

editing values in

exporting

finding with Find command

gray data fields in Generate Hypothesis workbench

importing multiple

importing one at a time

introduction in Generate Hypothesis workbench

object description

preparing for hypothesis generation

preparing tabular reports in Generate Hypothesis workbench

printing search results

sampling to workbenches

Save Spreadsheet command

saving

saving to shelf

selecting values in

updating 1D data in databases with

SPST_CREATE command

in catDB database utility

SPST_DELETE command

in catDB database utility

SPST_UPDATE command

in catDB database utility

Standard 3D structures

generating

Start Time field

in Job Options dialog in Generate Hypothesis

in Setup Background Process dialog box

StartAfter= option

example of usage in script

in catDB database utility

StartCref= option

example of usage in script

in catDB database utility

Status Area

value for Score Hypothesis

Statuses

in Process Information dialog box

Stereochemistry

changing between R and S

changing

examples of R and S

generating conformers for relative stereochemistry

generating conformers for unknown stereochemistry

inverting at bridgeheads

making enantiomers

pseudochirality

relative

rules for designating chirality

setting R or S

specifying

specifying relative stereocenters

stereochemical extensions to SMILES format

toggling between axial and equatorial bonds

toggling between cis and trans

toggling R and S

unknown

unknown/known toggle

viewing labels

Stereochemistry tool

in View Compound Toolbox

Stockroom

example lab hierarchy

graphic

introduction

overview

tasks list

topics

StockroomDB

files

introduction

Save StockroomDB command

saving

StockroomDB.bdb

file

Stop button

in Compare dialog

StopAfter= option

example of usage in script

in catDB database utility

Stopping

database building

String data type

valid characters for

Structure-Activity-24 command

description

Structure-Activity-9 command

description

Structure-Activity-View command

description

Structure-View-12

description

Structures

validating in databases

Style

Ball and Tube command

changing 2D bond display

Dots command

Mesh command

of constraints

of displaying fragments

of hypothesis appearance

Spacefilling command

Sphere and Rod command

Tube command

Wireframe command

Style menu

description

Substituents

adding

currently active

placing in the workspace

selecting from Periodic Table

Substring button

in Find dialog box

Substructures

copying as SMILES

searching databases for

Summarizing rules

defining associations in Exclude/OR QuickTool

displaying associations

steps for setting associations

Symbolic

display of groups in 2D

Symmetry

exclusion mappings deriving from

explicitly displaying exclusion mappings deriving from

System crash

recovering from