Contents
Schrödinger Software Release 2015-2
xviii
Appendix B:
Atom Types
............................................................................................... 423
Appendix C:
Substructure Notation
....................................................................... 431
C.1
Atom and Bond Types
........................................................................................ 431
C.2
Ring closure
.......................................................................................................... 433
C.3
Chain branching
................................................................................................... 433
C.4
Optional atoms
..................................................................................................... 434
C.5
Special Cases
....................................................................................................... 434
C.6
Examples
............................................................................................................... 435
C.7
Formal Charge Extensions
................................................................................ 436
C.8
Atom Type Equivalence Labels
......................................................................... 437
C.9
Differences between mmsubs and bmin notations
....................................... 438
C.10
Related Files
....................................................................................................... 438
Appendix D:
Project Utilities
........................................................................................ 439
D.1
project_convert
................................................................................................... 439
D.2
project_create
....................................................................................................... 439
D.3
project_append
.................................................................................................... 439
D.4
project_extract
..................................................................................................... 440
D.5
project_version
.................................................................................................... 440
Appendix E:
Property Names
.................................................................................... 441
Glossary
.................................................................................................................................... 443
Index
............................................................................................................................................ 447
Maestro 10.2 User Manual
xix
Document Conventions
In addition to the use of italics for names of documents, the font conventions that are used in
this document are summarized in the table below.
Links to other locations in the current document or to other PDF documents are colored like
this:
Document Conventions
.
In descriptions of command syntax, the following UNIX conventions are used: braces { }
enclose a choice of required items, square brackets [ ] enclose optional items, and the bar
symbol | separates items in a list from which one item must be chosen. Lines of command
syntax that wrap should be interpreted as a single command.
File name, path, and environment variable syntax is generally given with the UNIX conven-
tions. To obtain the Windows conventions, replace the forward slash / with the backslash \ in
path or directory names, and replace the $ at the beginning of an environment variable with a %
at each end. For example, $SCHRODINGER/maestro becomes %SCHRODINGER%\maestro.
Keyboard references are given in the Windows convention by default, with Mac equivalents in
parentheses, for example
CTRL+H (
H
). Where Mac equivalents are not given,
COMMAND
should be read in place of
CTRL
. The convention
CTRL-H
is not used.
In this document, to
type text means to type the required text in the specified location, and to
enter text means
to type the required text, then press the
ENTER
key.
References to literature sources are given in square brackets, like this: [10].
Font
Example
Use
Sans serif
Project Table
Names of GUI features, such as panels, menus,
menu items, buttons, and labels
Monospace
$SCHRODINGER/maestro
File
names,
directory names, commands, envi-
ronment variables, command input and output
Italic
filename
Text that the user must replace with a value
Sans serif
uppercase
CTRL+H Keyboard
keys
