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Appendix D:

Project Utilities

Schrödinger software is distributed with a number of utility programs and scripts that can be

used in conjunction with any of the computational programs. These UNIX utility programs are

installed in $SCHRODINGER/utilities (with one exception). A complete list of utilities is

given in the 

Schrödinger Utilities

 quick reference. The general-purpose utilities are described

in the 

General Utilities

 reference. This appendix lists utilities for Maestro project management.

UNIX conventions are used for the command syntax—see 

page xix

 for more information. 

D.1

project_convert 

This utility converts a project to the current version. This utility is run automatically from

Maestro, under Job Control, when you open a project from a previous release. The syntax is: 

project_convert [

options] input_project output_project 

If the input and output project names are the same, the input project is overwritten. For a

description of the options, run the command with the -h option.

D.2

project_create

This utility creates a project using specified structure files. The syntax is:

$SCHRODINGER/run project_create 

structure-file [-t type] project.prj 

$SCHRODINGER/run project_create -f 

file-list [-t type] project.prj

$SCHRODINGER/run project_create -d 

dir [-l type] project.prj

The project name must include the .prj extension. For a description of the options, run the

command with the -h option.

D.3

project_append

This utility appends the structures in the specified structure files to a project. The syntax is:

$SCHRODINGER/run project_append 

structure-file [-t type] project.prj 

$SCHRODINGER/run project_append -f 

file-list [-t type] project.prj

$SCHRODINGER/run project_append -d 

dir [-l type] project.prj

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The project name must include the .prj extension. For a description of the options, run the

command with the -h option.

D.4

project_extract

This utility extracts usable data from a corrupted Maestro project. The syntax is:

project_extract -i 

corrupted-project.prj  -o new-project.prj 

[-e 

data-types]

where -i and -o specify the path to the corrupted project and the path to the new project. If -e

is not used, the utility only attempts to extract the entry data (including properties). If -e is

used, it must be followed by a quoted, comma-separated string listing the data types to attempt

to extract, from the following types:

D.5

project_version

This utility lists the Maestro version and release that could have produced a project. The syntax

is:

project_version 

project1 [project2 ...]

Each project is listed with the Maestro version and the release name in parentheses. If the

project has ben converted from one format to another, the version for the latest format is

reported. 

all

 

Attempt to extract all data types

auxiliarydata

 

Auxiliary data for entries. Includes things like trajectories, vibrations,

surfaces, Phase hypotheses, etc.

jobsdata

 

Job-related information for applications you have run

plotxy

 

XY plots of Project Table entry properties

primex

 PrimeX 

data

psp

 Prime 

data

phase

 Phase 

data

strike

 Strike 

data

userdata

 User 

data

vcs

 CombiGlide 

data

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Appendix E

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Appendix E:

Property Names

Properties of entries have two names: an internal name and a display name, or visible name.

The display name is the name that is shown in the headings of the Project Table columns. Prop-

erties also belong to a “family”, and the family name is shown in menus used for property

selection.

The internal name is the name used by Maestro to identify the property, and is the name that is

written to and read from Maestro files. The internal name has the format type_author_label.

The type is a single character, which identifies the variable as an integer (i), a real number (r),

a string (s), or a Boolean (b). The author identifies the program that generated the property, or

more generally the source of the property. Finally, the label gives information about the prop-

erty itself. For example, s_m_title is the internal name of a string property generated by the

author m, which stands for Maestro, that is the title of the entry. 

When the internal name is parsed by Maestro, it is split into the three pieces. The type is used

to assign a variable internally to store the property value. The author is mapped to the “family”

name, and the label is mapped to the display name. Maestro has a table of mappings of the

author to the family names and of the label to the display names. If there is no entry for label

in the map, then the display name is constructed by replacing any underscores in label with

spaces: thus, if the label is My_property, the display name is 

My property

. Likewise, author is

displayed as is for the family name if it has no entry in the map. A list of authors and their

mappings is given in 

Table E.1

. The list of property names is much larger, and is not given

here. The display names are stored as part of the project. 

The display name and the internal name can both be changed within a Maestro session—see

Section 9.11.9 on page 237

. The display name is used only in the project. It is the internal

name that is exported when you export structures. If you want to export a property with a new

name (for example to an SD file), you can create a new property, and copy the desired property

to the new property for export. The author for the new property in this case is user, by default.

You can change the author, but since the author and type are stripped out when exporting to an

SD file, the author is not relevant in this case.

For SD properties, you can protect the underscore characters so that they are displayed in the

Project Table by preceding them with backslash characters. 

Atom properties also have an internal name and a display name. The internal name has the

same format as the entry properties, and the display name is derived in the same way as for

entry properties that do not have a mapping, i.e. the type and the author are stripped off, and

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