</p>A comma delimited list of global properties, each of which will automatically hold the name of a file in the job's temporary folder, whose name is guaranteed to be unique.<p/>For each global name, an additional global is created (with the suffix <i>_Filename</i>) that hold just the leaf file name of the temporary file.<p/>
<p>A comma delimited list of global properties which will be automatically
exported if this protocol is published as a web service.<p/>Each global property in the list is created with an empty value at the start of the protocol run.</p>
The path to a protocol that will render an HTML user interface for this protocol. This optional parameter is used by Webport to provide a custom user interface for a protocol.
When a recoverable error occurs during processing:
Halt: Terminate the execution of the network
Fail: Continue execution of the network, passing data out the Fail(red) port
Pass: Continue execution of the network, passing data out the Pass(green) port
Halt
Fail
Pass
When an expected data type is not found during processing:
Halt: Terminate the execution of the network
Fail: Continue execution of the network, passing data out the Fail(red) port
Pass: Continue execution of the network, passing data out the Pass(green) port
Halt
Fail
Pass
Component Attributes
ComponentTakesInput
ComponentReturnsPass
ComponentReturnsFail
ComponentRunsLocal
The component this component is based upon.
EmptyProtocol
The user who registered this component.
PaulDobson
The date this component was registered.
Wed Feb 27 16:12:22 2008
Component Comment
A top-level component for building protocols.
Component Usage
The user should customize this description and usage to describe
the functioning of their derived protocol.
Display Name
ChemSpider
Protocol AutoLayout
1
Protocol ShowComment
true
Add Protocol Comment Here
Add Protocol Comment Here
Custom Error Message
Component Icon
ProtocolNode
Component Revision
100
Disabled
0
GUID
{F22608A0-CD91-DF11-7A8E-5C31CA4EA6F3}
Component Point
70 -50
By Ref
0
Fancy Help
100
Search ChemSpider by smiles
Search ChemSpider by Smiles string. Returns the top hit only.
A simple example of soap/wsdl use, using ChemSpider wsdl
http://www.chemspider.com/Search.asmx?WSDL
None
None
None
Runtime Identifier
Protocol Scale
100
Protocol Options
Make Shortcut by Default
Owner Access Only
Protocol Sticky Notes
%VERSION 3%
350 -375 899 520
255 255 0
ChemSpider Structure Search
Returns the top hit from ChemSpider for a SMILES query
Try...
C(C(=O)C(C(C(C(=O)O)O)O)O)O
Uses wsdl...
http://www.chemspider.com/Search.asmx?WSDL
The server version when this component was registered
6.1.1.0
Location of the component in the database
Protocols\DBK\Searches\ChemSpider
The title of the message box that will appear.
Text Prompt
Specifies the message to display, defined as a PilotScript expression.
Text should be quoted, and the expression may also include global property
values.
DisplayWhen
"Sample text prompt for " . @username;
When this expression is evaluated as true, the text prompt is displayed. Any properties used in the expression must be globals. Enter "True" if the text prompt should always be displayed.
True
Property to put any user entered text into. Denote a global property
with a leading @ character.
smiles
Temporary files converted by the network to true temporary filenames
Lists a set of properties (without the @) to be created on the property list for this protocol.
Other properties are created on the global property list
and so are accessible from all protocols.
mText
When the component is executed, whether we process once or until done for each process call
True
False
When an expected data type is not found during processing:
Halt: Terminate the execution of the network
Fail: Continue execution of the network, passing data out the Fail(red) port
Pass: Continue execution of the network, passing data out the Pass(green) port
Halt
Fail
Pass
Component Attributes
ComponentTakesInput
ComponentReturnsPass
ComponentReturnsFail
ComponentRunsLocal
When an recoverable error occurs during processing:
Halt: Terminate the execution of the network
Fail: Continue execution of the network, passing data out the Fail(red) port
Pass: Continue execution of the network, passing data out the Pass(green) port
Halt
Fail
Pass
Protocol Options
Make Shortcut by Default
Cant Replace With Copy
Cant Open
The user who registered this component.
scitegic/core
The date this component was registered.
Wed Sep 20 08:27:19 2006
Component Comment
Displays a dialog box with a message prompt, a type-in box, and OK and Cancel buttons.
Component Usage
Displays a message and allows the users to enter some text in response. The response text can either become a value for a global property or a data property.
Display Name
Text Prompt
Protocol AutoLayout
false
Protocol ShowComment
false
Add Protocol Comment Here
Add Protocol Comment Here
Disabled
0
Custom Error Message
Component Icon
VIEWERNODE
Component Revision
100
The component this component is based upon.
SubProtocol
GUID
{73E1A46F-801B-4469-A7AD-A9592812D1A7}
Protocol Scale
0
Component Point
88 -50
ProtocolCommentSize
1100 500
Fancy Help
100
Displays a dialog box with a message, a text entry field, and OK and Cancel buttons
<p>Provides a method for interactively receiving input while running the protocol. The text entered must be stored as a global property or a new data property, as specified in <i>PropertyForUserText</i>.</p>
<p>Construct the message in <i>MessageText</i> using a PilotScript expression, which can contain static text and global properties.</p>
<p>The protocol is paused until you click OK or Cancel on the message dialog. If you click OK, a single data record is sent out the Pass port. If you click Cancel, or if no text is entered, no data record is generated.</p>
<b>Note:</b>
<ul>
<li>This component is only supported for protocols run from the Pipeline Pilot Professional or Lite client (i.e., does not work in Webport).</li>
</ul>
None
Generic
Empty record or with named text property
None
By Ref
1
The server version when this component was registered
6.0.1.0
Component Sticky Notes
Protocol Sticky Notes
Runtime Identifier
0
Protocol Scale
100
Location of the component in the database
Components\Generic\Viewers\Dialogs\Text Prompt
Subprotocol Made Link Into Copy
0
The name of the property in the data
which holds the SMILES information
KekulizeAromaticBonds
smiles
Turn aromatic bonds into single/double bonds (set to True) or into aromatic query bonds (set to False). Molecules created with aromatic query bonds are more suitable as queries than as specific molecules. They should not be used as input for property calculators such as Molecular Weight, pKa and others, which require the structure to be uniquely defined.
True
False
When an recoverable error occurs during processing:
Halt: Terminate the execution of the network
Fail: Continue execution of the network, passing data out the Fail(red) port
Pass: Continue execution of the network, passing data out the Pass(green) port
Halt
Fail
Pass
When an expected data type is not found during processing:
Halt: Terminate the execution of the network
Fail: Continue execution of the network, passing data out the Fail(red) port
Pass: Continue execution of the network, passing data out the Pass(green) port
Halt
Fail
Pass
Component Attributes
ComponentTakesInput
ComponentReturnsPass
ComponentReturnsFail
ComponentRunsLocal
Comment
Takes a Daylight SMILES string as text on a given property and converts the object into a SciTegic molecule using that information.
The user who registered this component.
scitegic/chemistry
The date this component was registered.
Thu Sep 07 14:22:46 2006
Component Usage
A molecular representation is built for each data record from the SMILES data found in the property list. *Note that if a molecular representation is already present, it will be overwritten by the new molecule.
Input - Data records
Output Pass - Molecular data records
Display Name
Molecule from SMILES
The component this component is based upon.
Molecule from SMILES
Component RunTimeID
1
Custom Error Message
Component Icon
COMPONENTNODE
GUID
{AC8262DA-E648-4D24-9CD1-D731A8F53F9D}
Component Point
363 -50
Disabled
0
Fancy Help
100
Converts a Daylight SMILES text property to a molecule
<p>Builds a molecular representation for each data record from the SMILES string found in the property list. If a molecular representation is already present, it is overwritten by the new molecule. The input SMILES string is preserved.</p>
<p><b>See Also:</b></p>
<ul>
<li>To create a string property containing SMILES data, use <a href="javascript:DoLink('{0C60C40A-5189-42DA-A3C0-4EA44BFF7D15}')">Molecule to SMILES</a> or <a href="javascript:DoLink('{0C60C40A-5189-42DA-A3C0-4EA44BC27D15}')">Canonical Smiles</a>.</li>
<li>To read and write SMILES files, use <a href="javascript:DoLink('{60FC1A04-61FD-4D4F-AC3F-A818AB614C78}')">SMILES Reader</a> and <a href="javascript:DoLink('{72A5A427-651F-4847-9525-54CB438A7166}')">SMILES Writer</a>.</li>
</ul>
Generic
Molecule
Molecular data record created from SMILES string
None
The server version when this component was registered
6.0.0.41
Component Sticky Notes
Location of the component in the database
Components\Chemistry\Converters\Molecule From Text\Molecule from SMILES
<ul>
<li><b>SMILES</b> is a non-canonical representation for the molecule. (This is very fast to calculate compared to Canonical_SMILES.)</li>
<li><b>Canonical_SMILES</b> is the representation that can be compared for identicality.</li>
</ul>
<i>Output</i> properties can be calculated "on demand" by simply using their names within a PilotScript expression or as the parameter value to many parameters that require a property name.
Canonical_Smiles
Smiles
When an recoverable error occurs during processing:
Halt: Terminate the execution of the network
Fail: Continue execution of the network, passing data out the Fail(red) port
Pass: Continue execution of the network, passing data out the Pass(green) port
Halt
Fail
Pass
When an expected data type is not found during processing:
Halt: Terminate the execution of the network
Fail: Continue execution of the network, passing data out the Fail(red) port
Pass: Continue execution of the network, passing data out the Pass(green) port
Halt
Fail
Pass
Component Attributes
ComponentTakesInput
ComponentReturnsPass
ComponentReturnsFail
ComponentRunsLocal
Comment
Calculates a SMILES representation of the molecular information in a molecular data record. SMILES is a text-based representation for molecular information developed by Daylight.
The user who registered this component.
scitegic/chemistry
The date this component was registered.
Wed Jul 21 10:12:26 2004
Component Usage
Select either 'Smiles' or 'Canonical_Smiles" s in the 'Output' pulldown list to generate the required string. The data is augmented with the selected properties.
Input - Molecule data records
Output Pass - Molecule data records augmented with selected properties
Display Name
Canonical Smiles
The component this component is based upon.
Canonical Smiles
Custom Error Message
Component Icon
CALCULATORNODE
GUID
{0C60C40A-5189-42DA-A3C0-4EA44BC27D15}
Component Point
663 -50
Disabled
0
Fancy Help
100
Calculates a SMILES or canonical SMILES representation of the input molecule
<p>SMILES is a terse textual representation of molecular data. Canonical SMILES is a form of SMILES that is independent of how the molecule is drawn and so can be used to compare whether two molecules are identical.</P>
This component can create either or both of two properties:
<ul>
<li><b>SMILES</b> is a non-canonical representation for the molecule. (This is very fast to calculate compared to Canonical_SMILES.)</li>
<li><b>Canonical_SMILES</b> is the representation that can be compared for identicality.</li>
</ul>
<b>Note:</b>
<ul>
<li>The canonicalization algorithm is SciTegic's; while it is derived from the published Daylight algorithm, however, lack of complete documentation of their procedure means that it will not necessarily give identical results. Compare two SMILES for identity only when having both canonicalized by the same method. </li>
</ul>
<b>See Also:</b>
<ul>
<li>You can create a SMILES string as text under any property name using <a href="javascript:DoLink('{0C60C40A-5189-42DA-A3C0-4EA44BFF7D15}')">Molecule to SMILES</a>.</li>
<li>You can convert a SMILES string into a molecule using <a href="javascript:DoLink('{AC8262DA-E648-4D24-9CD1-D731A8F53F9D}')">Molecule from SMILES</a>.</li>
<li>For an alternative way of generating a canonical string representation, see <a href="javascript:DoLink('{EB62CC30-BC6A-4d5f-8618-3EB9AF611C69}')">Molecule to InChI</a>.</li>
</ul>
Molecule
Molecule
Records augmented with a text property containing the canonical SMILES or SMILES
None
The server version when this component was registered
4.1.1.200
Component Sticky Notes
Runtime Identifier
2
Location of the component in the database
Components\Chemistry\Calculators\Canonical Smiles
Molecular Formats
Molecular Formats
The names of properties to remove from each data record entering the component
Structures
When an recoverable error occurs during processing:
Halt: Terminate the execution of the network
Fail: Continue execution of the network, passing data out the Fail(red) port
Pass: Continue execution of the network, passing data out the Pass(green) port
Halt
Fail
Pass
When an expected data type is not found during processing:
Halt: Terminate the execution of the network
Fail: Continue execution of the network, passing data out the Fail(red) port
Pass: Continue execution of the network, passing data out the Pass(green) port
Halt
Fail
Pass
Component Attributes
ComponentTakesInput
ComponentReturnsPass
ComponentReturnsFail
ComponentRunsLocal
the action to perform
Remove
The user who registered this component.
scitegic/core
The date this component was registered.
Fri Sep 15 10:06:31 2006
Component Comment
Removes the specified properties from the property list.
Component Usage
'PropertyList' contains a comma-separated list of the property names that you wish to remove.
Input - Data records
Output Pass - All Data records
Display Name
Remove Properties
Protocol AutoLayout
true
Protocol ShowComment
false
Add Protocol Comment Here
Add Protocol Comment Here
Disabled
0
Custom Error Message
Component Icon
EXPRESSIONNODE
Component Revision
100
The component this component is based upon.
SubProtocol
Protocol Scale
0
Component Point
938 -50
GUID
{C2ED35FF-5397-4877-AADB-10F1A15D60E2}
Fancy Help
100
Removes the specified properties
For each data record that enters the component, the properties specified by <i>PropertyList</i> are removed from the record. To specify more than one property to be removed, use a comma separated list.
<p><b>See Also:</b></p>
<p>To keep only a few properties from a long list, it may be more efficient to instead use <a href="javascript:DoLink('{456195EF-9708-4367-B3DD-21EBF3796604}')">Keep Properties</a>.</p>
Generic
Generic
Data records with the specified properties removed
None
The server version when this component was registered
6.0.0.46
Component Sticky Notes
By Ref
0
Protocol Sticky Notes
Runtime Identifier
3
Location of the component in the database
Components\Generic\Manipulators\Remove Properties
When RunToCompletion is set to True, the subprotocol is re-initialized and executed in its entirety for each record it processes.
True
False
</p>A comma delimited list of global properties, each of which will automatically hold the name of a file in the job's temporary folder, whose name is guaranteed to be unique.<p/>For each global name, an additional global is created (with the suffix <i>_Filename</i>) that hold just the leaf file name of the temporary file.<p/>
<p>Lists a set of properties (without the @) to create on the global property list for this subprotocol. Such properties can only be accessed within the scope of this subprotocol and its descendent subprotocols.<p/>Any global property not declared in this way is created on the top level global property list and is accessible from all protocols, but may collide with another property of the same name.<p/>Scoping global properties to the subprotocol where they are used is highly recommended.</p>
<p><b>Note:</b> This is a prototype feature, which we are making available
because we feel it is a useful technique to improve data throughput speeds in many situations. In particular, it can help to optimize resource use on multi-CPU and multi-core machines and on server clusters.
We welcome your feedback on scenarios where it works well, scenarios where it does not, and any other opinions you have about this utility.
</p><hr/><p>
When set to True, this set of options allow the subprotocol to execute in parallel on one or more independent Pipeline Pilot servers, running local or remote. Additional parameters control the number of data records to send in each process batch, the list of Pipeline Pilot servers to use, the number of protocol processes that can be executed on each server, and whether to preserve the order of the processed data records.
</p><p>
Use this option judiciously, since it will not increase throughput in all circumstances. In general, it will yield improved performance when the parallelization benefits outweigh the data transfer overhead for the specified batch size.
</p><p>
For more information on the parallel subprotocol options, see <a href="javascript:DoLink('scihelpdocs/user/subprots/subprot_parallel_processing.htm')">Parallel Processing Subprotocols</a>.
</p>
Parallel Processing Options Batch Size
Parallel Processing Options Server
Parallel Processing Options Preserve Order
True
False
The number of records to send to the remote server(s) for each subprotocol execution. In general, performance is optimized when the amount of time required to process each batch is at least 10 seconds (note that this can vary depending on the characteristics of the remote server's hardware)
SetDisabledDetails("This parameter is only applicable if 'Parallel Processing Options' is 'True'");
Parameter('Parallel Processing Options');
25
<p>
Comma separated list of Pipeline Pilot servers on which to execute the parallel subprotocol. The server names should be in the same format as the Pipeline Pilot Client's change server dialog (server-name:port-number).
</p><p>
Specifying <b>localhost</b> as a server will cause the subprotocol to use its own Pipeline Pilot server. This can be helpful on multi-CPU/multi-core systems (where the subprotocol jobs are spawned on the same machine) and Pipeline Pilot Linux clusters (where 'localhost' requests spawning the subprotocol jobs on the same cluster).
</p>
Parallel Processing Options Server Processes
SetInvalidDetails('This parameter is required.');
Parameter() ne '';
SetDisabledDetails("This parameter is only applicable if 'Parallel Processing Options' is 'True'");
Parameter('Parallel Processing Options');
Comma separated list of maximum number of batches that can be simultaneously executed on each remote server. The number of entries in this parameter must equal the number of servers. If '*' is specified as the number of processes, then that server will only launch as many batches as the administrator of the remote server has permitted.
/* Server Processes must have the same number of comma separated entries as the Server parameter and must have a value*/
#processes := parameter();
expand(',', #processes);
#servers := parameter('Parallel Processing Options Server');
expand(',', #servers);
if (numvalues(#processes) == 0) then
SetInvalidDetails('This parameter is required.');
else
SetInvalidDetails('The number of server processes (' . numvalues(#processes) . ') must equal the number of servers (' . numvalues(#servers) . ').');
end if;
numvalues(#processes) > 0 and numvalues(#processes) == numvalues(#servers);
SetDisabledDetails("This parameter is only applicable if 'Parallel Processing Options' is 'True'");
Parameter('Parallel Processing Options');
Whether to preserve the order of the data as it enters and leaves the remote subprotocol.
SetDisabledDetails("This parameter is only applicable if 'Parallel Processing Options' is 'True'");
Parameter('Parallel Processing Options');
True
False
When an recoverable error occurs during processing:
Halt: Terminate the execution of the network
Fail: Continue execution of the network, passing data out the Fail(red) port
Pass: Continue execution of the network, passing data out the Pass(green) port
Halt
Fail
Pass
When an expected data type is not found during processing:
Halt: Terminate the execution of the network
Fail: Continue execution of the network, passing data out the Fail(red) port
Pass: Continue execution of the network, passing data out the Pass(green) port
Halt
Fail
Pass
Component Attributes
ComponentTakesInput
ComponentReturnsPass
ComponentReturnsFail
ComponentRunsLocal
Component Comment
Defines a subprotocol in a pipeline. When you are creating a pipeline that requires a subprotocol as a component, drag this component into the pipeline, open it, and add components to it.
Component Usage
When you are creating a pipeline which requires a subprotocol as
a component, you can drag this SubProtocol component into the
pipeline, open it, and add components into it.
Display Name
Search and Retrieve
Protocol AutoLayout
1
Protocol ShowComment
true
Add Protocol Comment Here
Add Protocol Comment Here
Disabled
0
Custom Error Message
Component Icon
COMPONENTNODE
Component Revision
100
The component this component is based upon.
SubProtocol
GUID
{17001C74-63CE-4B4B-B37C-F0EAA19CE4AA}
Component Point
1238 -50
By Ref
0
Fancy Help
100
Builds subprotocols in Pipeline Pilot.
<p>
Use a subprotocol to collapse one or more components into a single item. Open a subprotocol to view or edit its contents.
</p><p>
To define input and output ports, display icon, and parameter settings, right-click and select Edit. You can save subprotocols and reuse them. For more information, see the User Guide help for <a href="javascript:DoLink('scihelpdocs/user/subprots/subprot_overview.htm')">Subprotocols Overview</a>.
</p><p>
For more information on the parallel subprotocol options, see <a href="javascript:DoLink('scihelpdocs/user/subprots/subprot_parallel_processing.htm')">Parallel Processing Subprotocols</a>.
</p><p>
Tip: Any component can be made into a shortcut, so that the latest version is always used. For more information, see <a href="javascript:DoLink('scihelpdocs/user/subprots/shortcuts.htm')">Creating Shortcuts</a>.
</p>
Generic
Generic
Records passing out of any unconnected pass ports of components inside the subprotocol
Generic
Records passing out of any unconnected fail ports of components inside the subprotocol
The server version when this component was registered
6.1.0.21
Component Sticky Notes
Protocol Sticky Notes
Protocol Scale
100
Protocol Options
Make Shortcut by Default
Owner Access Only
The user who registered this component.
scitegic/core
The date this component was registered.
Tue May 01 14:06:30 2007
Runtime Identifier
4
Location of the component in the database
Components\Generic\Utilities\SubProtocol Utilities\Subprotocol
The WSDL file that descibes the Web service.
Values for the members of the WSDl group are filled with information retrieved from the selected WSDL.
Is IIS
SOAP Port
SOAP Endpoint
Method Namespace
Method Name
SOAP Action
SOAP Messages
http://www.chemspider.com/Search.asmx?WSDL
The URL that points to the SOAP service.
http://www.chemspider.com/Search.asmx
The name of the SOAP method to call.
SimpleSearch2IdList
The SOAP method namespace.
http://www.chemspider.com/
Some SOAP servers require a specific SOAP Action. If this value is not set, then the suggested value "methodnamespace#method" is used.
http://www.chemspider.com/SimpleSearch2IdList
The <wsdl:port> defined for the selected method.
tns:SearchSoap
Message attributes for <wsdl:input> and <wsdl:output> nodes of the selected SOAP method. Attributes are separated by a comma and filled in when a method has more than one overload.
tns:SimpleSearch2IdListSoapIn,tns:SimpleSearch2IdListSoapOut
.NET expects SOAP packets to have a certain style that in some cases is incompatible with Axis.
True
False
SOAP Return Names
Property Return Names
SOAP Parameter Names
Parameter group containing all input parameters for the currently selected SOAP method.
parameters
A comma-separated list of names that the SOAP method returns.
SimpleSearch2IdListResponse
Names of the properties on the data record where the return values of the SOAP method are placed.
SimpleSearch2IdListResponse
Contains less commonly used parameters
Use Keep Alive
HTTP Proxy
Time Out
The hostname and port in URL form of the HTTP proxy.
Example: http://proxy.company.com:8080/
May increase the network speed of HTTP. Some HTTP/SOAP servers handle Keep-Alive poorly, so you may
want to disable this option if you are having problems.
True
False
If a response is not received within the specified number of seconds, raises an error. If set to 0 or no value, it defaults to 300 seconds.
When an recoverable error occurs during processing:
Halt: Terminate the execution of the network
Fail: Continue execution of the network, passing data out the Fail(red) port
Pass: Continue execution of the network, passing data out the Pass(green) port
Halt
Fail
Pass
When an expected data type is not found during processing:
Halt: Terminate the execution of the network
Fail: Continue execution of the network, passing data out the Fail(red) port
Pass: Continue execution of the network, passing data out the Pass(green) port
Halt
Fail
Pass
Component Attributes
ComponentTakesInput
ComponentReturnsPass
ComponentReturnsFail
ComponentRunsLocal
tns:SimpleSearch2IdList
parameters query
Canonical_Smiles
This is only used when the component is in a batch environment.
The user who registered this component.
scitegic/integration
The date this component was registered.
Tue Mar 20 08:30:08 2007
Comment
Enables you to make a SOAP call to a third-party calculator.
Display Name
SOAP Method with WSDL Support
Component Usage
This component can be configured to make a remote SOAP method call over an intranet or the internet. Please read SOAP help documentation for more information.
The component this component is based upon.
SOAP Method
Custom Error Message
Component Icon
COMPONENTNODE
GUID
{03F468D5-DF2E-4D85-8E28-9F2C1291D736}
Component Point
88 -50
Disabled
0
Fancy Help
100
Makes a SOAP call to a third-party calculator
<p>Configure this component to make a remote SOAP method call over an
intranet or the Internet. The target endpoint is the location
of the SOAP server that is programmed to receive calls for the name and parameters
specified by this component. </p>
<p>To simplify the task of entering parameters for a WSDL-supported SOAP component,
use the
WSDL dialog. This dialog is available when you click [...] to edit a WSDL
parameter.</p>
<p><strong>Notes:</strong></p>
<ul>
<li>For a simple service that does not takes input parameters and returns a
single result string, only <em>SOAP Endpoint</em>, <em>Method
Name</em>, and <em>Method Namespace</em> are required. At the completion
of the call, a property named "result" is
added to the current record.</li>
<li>Most services require different types of input sets which may return several
results. These services can take an array as an input parameter or return
an array as output, independent of any batching that occurs.</li>
<li>Parameter mapping is used for services that require multiple inputs, which
can be strings, numbers or arrays. The mapping between <em>SOAP
Parameter Names</em> and <em>Method Parameter Values</em> is used to create the SOAP request envelope. If the call completes successfully,
the result of a SOAP response is parsed from the XML envelope and the results
are mapped into the property names listed in the <em>Property
Return Names</em>.
When an array is returned from a call, the property that is mapped to that
return result contains an array of values.</li>
<li>Any errors returned from the SOAP service are displayed in a dialog. You
can control the processing behavior for when errors occur at the Error Handling
tab for the component.</li>
<li>If the service currently exists as a CORBA service or a UNIX executable,
accessing the service through SOAP is simple and lightweight.</li>
<li>You can return multiple properties in a SOAP call; return two parallel
arrays from your SOAP service. One array includes the descriptor names and
the other includes the descriptor values. For example: </li>
<p><code>string[ ] names = { a , b , c };<br />
int[ ] values = { 1, 2, 3 };</code></p>
<p>In the SOAP component, you have two property names listed for the return
values (for example, "Names" and "Values"). Use these like an other array.</p>
</ul>
<p><strong>See Also: </strong>
<p><a href="javascript:DoLink('sciapps/scitegic/integration/docs/server_side/integration_web_service.pdf')">
Web Services Integration Guide</a></p>
Generic
Generic
None
The server version when this component was registered
6.1.0.11
Component Sticky Notes
Runtime Identifier
4:0
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
Location of the component in the database
Unknown
Property the filter will be applied to
SimpleSearch2IdListResponse.SimpleSearch2IdListResult.int
When an recoverable error occurs during processing:
Halt: Terminate the execution of the network
Fail: Continue execution of the network, passing data out the Fail(red) port
Pass: Continue execution of the network, passing data out the Pass(green) port
Halt
Fail
Pass
When an expected data type is not found during processing:
Halt: Terminate the execution of the network
Fail: Continue execution of the network, passing data out the Fail(red) port
Pass: Continue execution of the network, passing data out the Pass(green) port
Halt
Fail
Pass
Component Attributes
ComponentTakesInput
ComponentReturnsPass
ComponentReturnsFail
ComponentRunsLocal
the action to perform
IsDefined
The user who registered this component.
scitegic/core
The date this component was registered.
Fri Sep 15 09:45:05 2006
Component Comment
Defines a subprotocol in a pipeline. When you are creating a pipeline that requires a subprotocol as a component, drag this component into the pipeline, open it, and add components to it.
Component Usage
When you are creating a pipeline which requires a subprotocol as
a component, you can drag this SubProtocol component into the
pipeline, open it, and add components into it.
Display Name
Check
Protocol AutoLayout
1
Protocol ShowComment
true
Add Protocol Comment Here
Add Protocol Comment Here
Disabled
0
Custom Error Message
Component Icon
FILTERNODE
Component Revision
100
The component this component is based upon.
SubProtocol
GUID
{74CB089F-EAA6-4FC4-A247-08453D1ADED4}
Component Point
363 -50
Protocol Scale
0
By Ref
0
Fancy Help
100
Passes data records for which a specified property is defined
<p>For each incoming data record, the value of the property specified by <i>KeyProperty</i> is checked. If the value is defined, the record is sent out the Pass port. Otherwise it is sent out the Fail port.</p>
Generic
Generic
Data records for which the property is defined
Generic
Data records for which the property is NOT defined
Runtime Identifier
4:1
Location of the component in the database
Components\Generic\Filters\Is Property Defined Filter
6.0.0.46
Property name to change
SimpleSearch2IdListResponse.SimpleSearch2IdListResult.int
Name of the new property
id
When an recoverable error occurs during processing:
Halt: Terminate the execution of the network
Fail: Continue execution of the network, passing data out the Fail(red) port
Pass: Continue execution of the network, passing data out the Pass(green) port
Halt
Fail
Pass
When an expected data type is not found during processing:
Halt: Terminate the execution of the network
Fail: Continue execution of the network, passing data out the Fail(red) port
Pass: Continue execution of the network, passing data out the Pass(green) port
Halt
Fail
Pass
When a General or DataType error occurs during processing:
LeaveData: The data is passed unalterd
ClearData: The data is cleared before being passed (an empty data item)
DeleteData: The data is deleted and not passed
LeaveData
ClearData
DeleteData
Component Attributes
ComponentTakesInput
ComponentReturnsPass
ComponentReturnsFail
ComponentRunsLocal
the action to perform
Rename
Sets the Components Icon
EXPRESSIONNODE
Comment
Renames a single property.
The user who registered this component.
scitegic/core
The date this component was registered.
Fri Sep 15 10:07:49 2006
Component Usage
The component works for single properties as well as property arrays.
Input - Data records
Output Pass - All Data records
Display Name
Rename Property
The component this component is based upon.
Evaluate Expression
Component RunTimeID
4:2
GUID
{5A384E06-8AF2-4C10-A9B7-7302DD110A48}
Disabled
0
CustomErrorText
Component Point
663 -50
Fancy Help
100
Renames a property
For each data record entering the component, the property with name specified by <i>Property</i> is renamed to the name specified by <i>NewProperty</i>.
Generic
Generic
None
The server version when this component was registered
6.0.0.46
Component Sticky Notes
Location of the component in the database
Components\Generic\Manipulators\Rename Property
Expression (or list of expressions separated by semi-colons) to evaluate.
Initial Expression
Final Expression
Keep Calculated Properties
id := id[1];
<p>
This expression is executed only the first time data passes into the component.
<p/>
Since there is no data available at initialization time, only expressions referencing global properties are allowed.
</p>
<p>
This expression is executed only at finalization (after the last data passes out of the component).
<p/>
Since there is no data available at finalization time, only expressions referencing global properties are allowed.
</p>
Adds any properties calculated in this component to a data record's property list.
True
False
When an recoverable error occurs during processing:
Halt: Terminate the execution of the network
Fail: Continue execution of the network, passing data out the Fail(red) port
Pass: Continue execution of the network, passing data out the Pass(green) port
Halt
Fail
Pass
When an expected data type is not found during processing:
Halt: Terminate the execution of the network
Fail: Continue execution of the network, passing data out the Fail(red) port
Pass: Continue execution of the network, passing data out the Pass(green) port
Halt
Fail
Pass
Component Attributes
ComponentTakesInput
ComponentReturnsPass
ComponentReturnsFail
ComponentRunsLocal
When TRUE, controls which exit port is used for
each data record by evaluating the final expression
(or only one) listed in the "Expression" parameter.
-Pass (green) port when expression true
-Fail (red) port when expression false
True
False
Version of expression parser to use.
2
Comment
Processes commands expressed in PilotScript syntax to apply rapid
manipulations to data record properties. In this way, the component may be
customized to build a new, specialized data manipulation component.
The user who registered this component.
scitegic/core
The date this component was registered.
Mon Apr 23 12:20:45 2007
Component Usage
The 'Expression' is evaluated for each data record, and may alter and manipulate the properties of the data objects. The 'Initial expression' is evaluated the first time data passes into the component and is typically used for initializing global variables. See the online documentation for full details of PilotScript expression syntax.
Input - Data records
Output Pass - All Data records
Display Name
Get id
The component this component is based upon.
Custom Manipulator (PilotScript)
Component RunTimeID
4:3
Custom Error Message
Component Icon
EXPRESSIONNODE
Disabled
0
GUID
{0995D675-7EE2-432C-95DF-E91C14052B22}
Component Point
938 -50
Fancy Help
100
Applies a PilotScript expression to each data record
<p>PilotScript is the native scripting language in Pipeline Pilot. It is based on PL/SQL and allows you to query or alter the properties on data records. For example, the expression:
<blockquote>
<code>A := 10;</code>
</blockquote>
creates a property named "A" and sets the value to "10".</p>
<p>For each incoming data record the PilotScript statements in <i>Expression</i> are evaluated.</p>
<p><b>Notes:</b>
<ul>
<li>To initialize global variables such as counters, use <i>Initial Expression</i>.</li>
<li>To clean up global variables or calculate final results use <i>Final Expression</i>.</li>
<li>Parameters on Custom Manipulators do not become global variables that can be accessed via <i>@ParameterName</i> syntax and can only be accessed by token substitution via <i>$(ParameterName)</i> syntax.</li>
</ul>
<p><b>See Also:</b></p>
<ul>
<li>For more information on PilotScript, see <a href="javascript:DoLink('scihelpdocs/user/pscript/pscript_overview.htm')">PilotScript Overview</a>.</li>
<li>To use PilotScript to filter data records use <a href="javascript:DoLink('{DD58ECD1-516F-48FE-A5DB-8328AED680F2}')">Custom Filter (PilotScript)</a>.</li>
</ul>
Generic
Generic
None
The server version when this component was registered
6.1.0.17
Component Sticky Notes
Location of the component in the database
Components\Generic\Manipulators\Custom Manipulator (PilotScript)
The WSDL file that descibes the Web service.
Values for the members of the WSDl group are filled with information retrieved from the selected WSDL.
Is IIS
SOAP Port
SOAP Endpoint
Method Namespace
Method Name
SOAP Action
SOAP Messages
http://www.chemspider.com/Search.asmx?WSDL
The URL that points to the SOAP service.
http://www.chemspider.com/Search.asmx
The name of the SOAP method to call.
GetRecordDetails
The SOAP method namespace.
http://www.chemspider.com/
Some SOAP servers require a specific SOAP Action. If this value is not set, then the suggested value "methodnamespace#method" is used.
http://www.chemspider.com/GetRecordDetails
The <wsdl:port> defined for the selected method.
tns:SearchSoap
Message attributes for <wsdl:input> and <wsdl:output> nodes of the selected SOAP method. Attributes are separated by a comma and filled in when a method has more than one overload.
tns:GetRecordDetailsSoapIn,tns:GetRecordDetailsSoapOut
.NET expects SOAP packets to have a certain style that in some cases is incompatible with Axis.
True
False
SOAP Return Names
Property Return Names
SOAP Parameter Names
Parameter group containing all input parameters for the currently selected SOAP method.
parameters
A comma-separated list of names that the SOAP method returns.
GetRecordDetailsResponse
Names of the properties on the data record where the return values of the SOAP method are placed.
GetRecordDetailsResponse
Contains less commonly used parameters
Use Keep Alive
HTTP Proxy
Time Out
The hostname and port in URL form of the HTTP proxy.
Example: http://proxy.company.com:8080/
May increase the network speed of HTTP. Some HTTP/SOAP servers handle Keep-Alive poorly, so you may
want to disable this option if you are having problems.
True
False
If a response is not received within the specified number of seconds, raises an error. If set to 0 or no value, it defaults to 300 seconds.
When an recoverable error occurs during processing:
Halt: Terminate the execution of the network
Fail: Continue execution of the network, passing data out the Fail(red) port
Pass: Continue execution of the network, passing data out the Pass(green) port
Halt
Fail
Pass
When an expected data type is not found during processing:
Halt: Terminate the execution of the network
Fail: Continue execution of the network, passing data out the Fail(red) port
Pass: Continue execution of the network, passing data out the Pass(green) port
Halt
Fail
Pass
Component Attributes
ComponentTakesInput
ComponentReturnsPass
ComponentReturnsFail
ComponentRunsLocal
tns:GetRecordDetails
parameters id
id
This is only used when the component is in a batch environment.
The user who registered this component.
scitegic/integration
The date this component was registered.
Tue Mar 20 08:30:08 2007
Comment
Enables you to make a SOAP call to a third-party calculator.
Display Name
SOAP Method with WSDL Support
Component Usage
This component can be configured to make a remote SOAP method call over an intranet or the internet. Please read SOAP help documentation for more information.
The component this component is based upon.
SOAP Method
Custom Error Message
Component Icon
COMPONENTNODE
GUID
{03F468D5-DF2E-4D85-8E28-9F2C1291D736}
Component Point
1238 -50
Disabled
0
Fancy Help
100
Makes a SOAP call to a third-party calculator
<p>Configure this component to make a remote SOAP method call over an
intranet or the Internet. The target endpoint is the location
of the SOAP server that is programmed to receive calls for the name and parameters
specified by this component. </p>
<p>To simplify the task of entering parameters for a WSDL-supported SOAP component,
use the
WSDL dialog. This dialog is available when you click [...] to edit a WSDL
parameter.</p>
<p><strong>Notes:</strong></p>
<ul>
<li>For a simple service that does not takes input parameters and returns a
single result string, only <em>SOAP Endpoint</em>, <em>Method
Name</em>, and <em>Method Namespace</em> are required. At the completion
of the call, a property named "result" is
added to the current record.</li>
<li>Most services require different types of input sets which may return several
results. These services can take an array as an input parameter or return
an array as output, independent of any batching that occurs.</li>
<li>Parameter mapping is used for services that require multiple inputs, which
can be strings, numbers or arrays. The mapping between <em>SOAP
Parameter Names</em> and <em>Method Parameter Values</em> is used to create the SOAP request envelope. If the call completes successfully,
the result of a SOAP response is parsed from the XML envelope and the results
are mapped into the property names listed in the <em>Property
Return Names</em>.
When an array is returned from a call, the property that is mapped to that
return result contains an array of values.</li>
<li>Any errors returned from the SOAP service are displayed in a dialog. You
can control the processing behavior for when errors occur at the Error Handling
tab for the component.</li>
<li>If the service currently exists as a CORBA service or a UNIX executable,
accessing the service through SOAP is simple and lightweight.</li>
<li>You can return multiple properties in a SOAP call; return two parallel
arrays from your SOAP service. One array includes the descriptor names and
the other includes the descriptor values. For example: </li>
<p><code>string[ ] names = { a , b , c };<br />
int[ ] values = { 1, 2, 3 };</code></p>
<p>In the SOAP component, you have two property names listed for the return
values (for example, "Names" and "Values"). Use these like an other array.</p>
</ul>
<p><strong>See Also: </strong>
<p><a href="javascript:DoLink('sciapps/scitegic/integration/docs/server_side/integration_web_service.pdf')">
Web Services Integration Guide</a></p>
Generic
Generic
None
The server version when this component was registered
6.1.0.11
Component Sticky Notes
Runtime Identifier
4:4
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
Location of the component in the database
Unknown
Property name to change
GetRecordDetailsResponse.GetRecordDetailsResult.anyType
Name of the new property
array
When an recoverable error occurs during processing:
Halt: Terminate the execution of the network
Fail: Continue execution of the network, passing data out the Fail(red) port
Pass: Continue execution of the network, passing data out the Pass(green) port
Halt
Fail
Pass
When an expected data type is not found during processing:
Halt: Terminate the execution of the network
Fail: Continue execution of the network, passing data out the Fail(red) port
Pass: Continue execution of the network, passing data out the Pass(green) port
Halt
Fail
Pass
When a General or DataType error occurs during processing:
LeaveData: The data is passed unalterd
ClearData: The data is cleared before being passed (an empty data item)
DeleteData: The data is deleted and not passed
LeaveData
ClearData
DeleteData
Component Attributes
ComponentTakesInput
ComponentReturnsPass
ComponentReturnsFail
ComponentRunsLocal
the action to perform
Rename
Sets the Components Icon
EXPRESSIONNODE
Comment
Renames a single property.
The user who registered this component.
scitegic/core
The date this component was registered.
Fri Sep 15 10:07:49 2006
Component Usage
The component works for single properties as well as property arrays.
Input - Data records
Output Pass - All Data records
Display Name
Rename Property
The component this component is based upon.
Evaluate Expression
Component RunTimeID
4:5
GUID
{5A384E06-8AF2-4C10-A9B7-7302DD110A48}
Disabled
0
CustomErrorText
Component Point
1538 -50
Fancy Help
100
Renames a property
For each data record entering the component, the property with name specified by <i>Property</i> is renamed to the name specified by <i>NewProperty</i>.
Generic
Generic
None
The server version when this component was registered
6.0.0.46
Component Sticky Notes
Location of the component in the database
Components\Generic\Manipulators\Rename Property
Expression (or list of expressions separated by semi-colons) to evaluate.
Initial Expression
Final Expression
Keep Calculated Properties
id := array[1];
smiles := array[4];
<p>
This expression is executed only the first time data passes into the component.
<p/>
Since there is no data available at initialization time, only expressions referencing global properties are allowed.
</p>
<p>
This expression is executed only at finalization (after the last data passes out of the component).
<p/>
Since there is no data available at finalization time, only expressions referencing global properties are allowed.
</p>
Adds any properties calculated in this component to a data record's property list.
True
False
When an recoverable error occurs during processing:
Halt: Terminate the execution of the network
Fail: Continue execution of the network, passing data out the Fail(red) port
Pass: Continue execution of the network, passing data out the Pass(green) port
Halt
Fail
Pass
When an expected data type is not found during processing:
Halt: Terminate the execution of the network
Fail: Continue execution of the network, passing data out the Fail(red) port
Pass: Continue execution of the network, passing data out the Pass(green) port
Halt
Fail
Pass
Component Attributes
ComponentTakesInput
ComponentReturnsPass
ComponentReturnsFail
ComponentRunsLocal
When TRUE, controls which exit port is used for
each data record by evaluating the final expression
(or only one) listed in the "Expression" parameter.
-Pass (green) port when expression true
-Fail (red) port when expression false
True
False
Version of expression parser to use.
2
Comment
Processes commands expressed in PilotScript syntax to apply rapid
manipulations to data record properties. In this way, the component may be
customized to build a new, specialized data manipulation component.
The user who registered this component.
scitegic/core
The date this component was registered.
Mon Apr 23 12:20:45 2007
Component Usage
The 'Expression' is evaluated for each data record, and may alter and manipulate the properties of the data objects. The 'Initial expression' is evaluated the first time data passes into the component and is typically used for initializing global variables. See the online documentation for full details of PilotScript expression syntax.
Input - Data records
Output Pass - All Data records
Display Name
Custom Manipulator (PilotScript)
The component this component is based upon.
Custom Manipulator (PilotScript)
Component RunTimeID
4:6
Custom Error Message
Component Icon
EXPRESSIONNODE
Disabled
0
GUID
{0995D675-7EE2-432C-95DF-E91C14052B22}
Component Point
1813 -50
Fancy Help
100
Applies a PilotScript expression to each data record
<p>PilotScript is the native scripting language in Pipeline Pilot. It is based on PL/SQL and allows you to query or alter the properties on data records. For example, the expression:
<blockquote>
<code>A := 10;</code>
</blockquote>
creates a property named "A" and sets the value to "10".</p>
<p>For each incoming data record the PilotScript statements in <i>Expression</i> are evaluated.</p>
<p><b>Notes:</b>
<ul>
<li>To initialize global variables such as counters, use <i>Initial Expression</i>.</li>
<li>To clean up global variables or calculate final results use <i>Final Expression</i>.</li>
<li>Parameters on Custom Manipulators do not become global variables that can be accessed via <i>@ParameterName</i> syntax and can only be accessed by token substitution via <i>$(ParameterName)</i> syntax.</li>
</ul>
<p><b>See Also:</b></p>
<ul>
<li>For more information on PilotScript, see <a href="javascript:DoLink('scihelpdocs/user/pscript/pscript_overview.htm')">PilotScript Overview</a>.</li>
<li>To use PilotScript to filter data records use <a href="javascript:DoLink('{DD58ECD1-516F-48FE-A5DB-8328AED680F2}')">Custom Filter (PilotScript)</a>.</li>
</ul>
Generic
Generic
None
The server version when this component was registered
6.1.0.17
Component Sticky Notes
Location of the component in the database
Components\Generic\Manipulators\Custom Manipulator (PilotScript)
The names of properties to remove from each data record entering the component
array
When an recoverable error occurs during processing:
Halt: Terminate the execution of the network
Fail: Continue execution of the network, passing data out the Fail(red) port
Pass: Continue execution of the network, passing data out the Pass(green) port
Halt
Fail
Pass
When an expected data type is not found during processing:
Halt: Terminate the execution of the network
Fail: Continue execution of the network, passing data out the Fail(red) port
Pass: Continue execution of the network, passing data out the Pass(green) port
Halt
Fail
Pass
Component Attributes
ComponentTakesInput
ComponentReturnsPass
ComponentReturnsFail
ComponentRunsLocal
the action to perform
Remove
The user who registered this component.
scitegic/core
The date this component was registered.
Fri Sep 15 10:06:31 2006
Component Comment
Removes the specified properties from the property list.
Component Usage
'PropertyList' contains a comma-separated list of the property names that you wish to remove.
Input - Data records
Output Pass - All Data records
Display Name
Remove Properties
Protocol AutoLayout
true
Protocol ShowComment
false
Add Protocol Comment Here
Add Protocol Comment Here
Disabled
0
Custom Error Message
Component Icon
EXPRESSIONNODE
Component Revision
100
The component this component is based upon.
SubProtocol
Protocol Scale
0
Component Point
2113 -50
GUID
{C2ED35FF-5397-4877-AADB-10F1A15D60E2}
Fancy Help
100
Removes the specified properties
For each data record that enters the component, the properties specified by <i>PropertyList</i> are removed from the record. To specify more than one property to be removed, use a comma separated list.
<p><b>See Also:</b></p>
<p>To keep only a few properties from a long list, it may be more efficient to instead use <a href="javascript:DoLink('{456195EF-9708-4367-B3DD-21EBF3796604}')">Keep Properties</a>.</p>
Generic
Generic
Data records with the specified properties removed
None
The server version when this component was registered
6.0.0.46
Component Sticky Notes
By Ref
0
Protocol Sticky Notes
Runtime Identifier
4:7
Location of the component in the database
Components\Generic\Manipulators\Remove Properties
The name of the property in the data
which holds the SMILES information
KekulizeAromaticBonds
smiles
Turn aromatic bonds into single/double bonds (set to True) or into aromatic query bonds (set to False). Molecules created with aromatic query bonds are more suitable as queries than as specific molecules. They should not be used as input for property calculators such as Molecular Weight, pKa and others, which require the structure to be uniquely defined.
True
False
When an recoverable error occurs during processing:
Halt: Terminate the execution of the network
Fail: Continue execution of the network, passing data out the Fail(red) port
Pass: Continue execution of the network, passing data out the Pass(green) port
Halt
Fail
Pass
When an expected data type is not found during processing:
Halt: Terminate the execution of the network
Fail: Continue execution of the network, passing data out the Fail(red) port
Pass: Continue execution of the network, passing data out the Pass(green) port
Halt
Fail
Pass
Component Attributes
ComponentTakesInput
ComponentReturnsPass
ComponentReturnsFail
ComponentRunsLocal
Comment
Takes a Daylight SMILES string as text on a given property and converts the object into a SciTegic molecule using that information.
The user who registered this component.
scitegic/chemistry
The date this component was registered.
Thu Sep 07 14:22:46 2006
Component Usage
A molecular representation is built for each data record from the SMILES data found in the property list. *Note that if a molecular representation is already present, it will be overwritten by the new molecule.
Input - Data records
Output Pass - Molecular data records
Display Name
Molecule from SMILES
The component this component is based upon.
Molecule from SMILES
Component RunTimeID
4:8
Custom Error Message
Component Icon
COMPONENTNODE
GUID
{AC8262DA-E648-4D24-9CD1-D731A8F53F9D}
Component Point
2388 -50
Disabled
0
Fancy Help
100
Converts a Daylight SMILES text property to a molecule
<p>Builds a molecular representation for each data record from the SMILES string found in the property list. If a molecular representation is already present, it is overwritten by the new molecule. The input SMILES string is preserved.</p>
<p><b>See Also:</b></p>
<ul>
<li>To create a string property containing SMILES data, use <a href="javascript:DoLink('{0C60C40A-5189-42DA-A3C0-4EA44BFF7D15}')">Molecule to SMILES</a> or <a href="javascript:DoLink('{0C60C40A-5189-42DA-A3C0-4EA44BC27D15}')">Canonical Smiles</a>.</li>
<li>To read and write SMILES files, use <a href="javascript:DoLink('{60FC1A04-61FD-4D4F-AC3F-A818AB614C78}')">SMILES Reader</a> and <a href="javascript:DoLink('{72A5A427-651F-4847-9525-54CB438A7166}')">SMILES Writer</a>.</li>
</ul>
Generic
Molecule
Molecular data record created from SMILES string
None
The server version when this component was registered
6.0.0.41
Component Sticky Notes
Location of the component in the database
Components\Chemistry\Converters\Molecule From Text\Molecule from SMILES
</p>A comma delimited list of global properties, each of which will automatically hold the name of a file in the job's temporary folder, whose name is guaranteed to be unique.<p/>For each global name, an additional global is created (with the suffix <i>_Filename</i>) that hold just the leaf file name of the temporary file.<p/>
<p>Lists a set of properties (without the @) to create on the global property list for this subprotocol. Such properties can only be accessed within the scope of this subprotocol and its descendent subprotocols.<p/>Any global property not declared in this way is created on the top level global property list and is accessible from all protocols, but may collide with another property of the same name.<p/>Scoping global properties to the subprotocol where they are used is highly recommended.</p>
When RunToCompletion is set to True, the subprotocol is re-initialized and executed in its entirety for each record it processes.
True
False
<p><b>Note:</b> This is a prototype feature, which we are making available
because we feel it is a useful technique to improve data throughput speeds in many situations. In particular, it can help to optimize resource use on multi-CPU and multi-core machines and on server clusters.
We welcome your feedback on scenarios where it works well, scenarios where it does not, and any other opinions you have about this utility.
</p><hr/><p>
When set to True, this set of options allow the subprotocol to execute in parallel on one or more independent Pipeline Pilot servers, running local or remote. Additional parameters control the number of data records to send in each process batch, the list of Pipeline Pilot servers to use, the number of protocol processes that can be executed on each server, and whether to preserve the order of the processed data records.
</p><p>
Use this option judiciously, since it will not increase throughput in all circumstances. In general, it will yield improved performance when the parallelization benefits outweigh the data transfer overhead for the specified batch size.
</p><p>
For more information on the parallel subprotocol options, see <a href="javascript:DoLink('scihelpdocs/user/subprots/subprot_parallel_processing.htm')">Parallel Processing Subprotocols</a>.
</p>
Parallel Processing Options Batch Size
Parallel Processing Options Server
Parallel Processing Options Preserve Order
True
False
The number of records to send to the remote server(s) for each subprotocol execution. In general, performance is optimized when the amount of time required to process each batch is at least 10 seconds (note that this can vary depending on the characteristics of the remote server's hardware)
SetDisabledDetails("This parameter is only applicable if 'Parallel Processing Options' is 'True'");
Parameter('Parallel Processing Options');
25
<p>
Comma separated list of Pipeline Pilot servers on which to execute the parallel subprotocol. The server names should be in the same format as the Pipeline Pilot Client's change server dialog (server-name:port-number).
</p><p>
Specifying <b>localhost</b> as a server will cause the subprotocol to use its own Pipeline Pilot server. This can be helpful on multi-CPU/multi-core systems (where the subprotocol jobs are spawned on the same machine) and Pipeline Pilot Linux clusters (where 'localhost' requests spawning the subprotocol jobs on the same cluster).
</p>
Parallel Processing Options Server Processes
SetInvalidDetails('This parameter is required.');
Parameter() ne '';
SetDisabledDetails("This parameter is only applicable if 'Parallel Processing Options' is 'True'");
Parameter('Parallel Processing Options');
Comma separated list of maximum number of batches that can be simultaneously executed on each remote server. The number of entries in this parameter must equal the number of servers. If '*' is specified as the number of processes, then that server will only launch as many batches as the administrator of the remote server has permitted.
/* Server Processes must have the same number of comma separated entries as the Server parameter and must have a value*/
#processes := parameter();
expand(',', #processes);
#servers := parameter('Parallel Processing Options Server');
expand(',', #servers);
if (numvalues(#processes) == 0) then
SetInvalidDetails('This parameter is required.');
else
SetInvalidDetails('The number of server processes (' . numvalues(#processes) . ') must equal the number of servers (' . numvalues(#servers) . ').');
end if;
numvalues(#processes) > 0 and numvalues(#processes) == numvalues(#servers);
SetDisabledDetails("This parameter is only applicable if 'Parallel Processing Options' is 'True'");
Parameter('Parallel Processing Options');
Whether to preserve the order of the data as it enters and leaves the remote subprotocol.
SetDisabledDetails("This parameter is only applicable if 'Parallel Processing Options' is 'True'");
Parameter('Parallel Processing Options');
True
False
When an recoverable error occurs during processing:
Halt: Terminate the execution of the network
Fail: Continue execution of the network, passing data out the Fail(red) port
Pass: Continue execution of the network, passing data out the Pass(green) port
Halt
Fail
Pass
When an expected data type is not found during processing:
Halt: Terminate the execution of the network
Fail: Continue execution of the network, passing data out the Fail(red) port
Pass: Continue execution of the network, passing data out the Pass(green) port
Halt
Fail
Pass
Component Attributes
ComponentTakesInput
ComponentReturnsPass
ComponentReturnsFail
ComponentRunsLocal
Component Comment
Defines a subprotocol in a pipeline. When you are creating a pipeline that requires a subprotocol as a component, drag this component into the pipeline, open it, and add components to it.
Component Usage
When you are creating a pipeline which requires a subprotocol as
a component, you can drag this SubProtocol component into the
pipeline, open it, and add components into it.
Display Name
Tidy up
Protocol AutoLayout
1
Protocol ShowComment
true
Add Protocol Comment Here
Add Protocol Comment Here
Disabled
0
Custom Error Message
Component Icon
EXPRESSIONNODE
Component Revision
100
The component this component is based upon.
SubProtocol
GUID
{17001C74-63CE-4B4B-B37C-F0EAA19CE4AA}
Component Point
1538 -50
By Ref
0
Fancy Help
100
Builds subprotocols in Pipeline Pilot.
<p>
Use a subprotocol to collapse one or more components into a single item. Open a subprotocol to view or edit its contents.
</p><p>
To define input and output ports, display icon, and parameter settings, right-click and select Edit. You can save subprotocols and reuse them. For more information, see the User Guide help for <a href="javascript:DoLink('scihelpdocs/user/subprots/subprot_overview.htm')">Subprotocols Overview</a>.
</p><p>
For more information on the parallel subprotocol options, see <a href="javascript:DoLink('scihelpdocs/user/subprots/subprot_parallel_processing.htm')">Parallel Processing Subprotocols</a>.
</p><p>
Tip: Any component can be made into a shortcut, so that the latest version is always used. For more information, see <a href="javascript:DoLink('scihelpdocs/user/subprots/shortcuts.htm')">Creating Shortcuts</a>.
</p>
Generic
Generic
Records passing out of any unconnected pass ports of components inside the subprotocol
None
Records passing out of any unconnected fail ports of components inside the subprotocol
The server version when this component was registered
6.1.0.21
Component Sticky Notes
Protocol Sticky Notes
Protocol Scale
100
Protocol Options
Make Shortcut by Default
Owner Access Only
The user who registered this component.
scitegic/core
The date this component was registered.
Tue May 01 14:06:30 2007
Runtime Identifier
5
Location of the component in the database
Components\Generic\Utilities\SubProtocol Utilities\Subprotocol
Property name to change
id
Name of the new property
ChemSpider
When an recoverable error occurs during processing:
Halt: Terminate the execution of the network
Fail: Continue execution of the network, passing data out the Fail(red) port
Pass: Continue execution of the network, passing data out the Pass(green) port
Halt
Fail
Pass
When an expected data type is not found during processing:
Halt: Terminate the execution of the network
Fail: Continue execution of the network, passing data out the Fail(red) port
Pass: Continue execution of the network, passing data out the Pass(green) port
Halt
Fail
Pass
When a General or DataType error occurs during processing:
LeaveData: The data is passed unalterd
ClearData: The data is cleared before being passed (an empty data item)
DeleteData: The data is deleted and not passed
LeaveData
ClearData
DeleteData
Component Attributes
ComponentTakesInput
ComponentReturnsPass
ComponentReturnsFail
ComponentRunsLocal
the action to perform
Rename
Sets the Components Icon
EXPRESSIONNODE
Comment
Renames a single property.
The user who registered this component.
scitegic/core
The date this component was registered.
Fri Sep 15 10:07:49 2006
Component Usage
The component works for single properties as well as property arrays.
Input - Data records
Output Pass - All Data records
Display Name
Rename Property
The component this component is based upon.
Evaluate Expression
Component RunTimeID
5:0
GUID
{5A384E06-8AF2-4C10-A9B7-7302DD110A48}
Disabled
0
CustomErrorText
Component Point
88 -50
Fancy Help
100
Renames a property
For each data record entering the component, the property with name specified by <i>Property</i> is renamed to the name specified by <i>NewProperty</i>.
Generic
Generic
None
The server version when this component was registered
6.0.0.46
Component Sticky Notes
Location of the component in the database
Components\Generic\Manipulators\Rename Property
Comma-separated list of property names to keep
RenameList
Canonical_Smiles, ChemSpider
If provided, it causes the properties given in PropertyList to be
renamed to the corresponding name in this list. If not provided, then no properties are renamed.
When an recoverable error occurs during processing:
Halt: Terminate the execution of the network
Fail: Continue execution of the network, passing data out the Fail(red) port
Pass: Continue execution of the network, passing data out the Pass(green) port
Halt
Fail
Pass
When an expected data type is not found during processing:
Halt: Terminate the execution of the network
Fail: Continue execution of the network, passing data out the Fail(red) port
Pass: Continue execution of the network, passing data out the Pass(green) port
Halt
Fail
Pass
Component Attributes
ComponentTakesInput
ComponentReturnsPass
ComponentReturnsFail
ComponentRunsLocal
the action to perform
Keep
The user who registered this component.
scitegic/core
The date this component was registered.
Tue Oct 17 16:03:31 2006
Component Comment
Removes all but the specified properties from the property list.
Component Usage
'PropertyList' contains a comma-separated list of the property names that you wish to keep. All other properties will be removed.
Input - Data records
Output Pass - All Data records
Display Name
Keep Properties
Protocol AutoLayout
true
Protocol ShowComment
false
Add Protocol Comment Here
Add Protocol Comment Here
Disabled
0
Custom Error Message
Component Icon
EXPRESSIONNODE
Component Revision
100
The component this component is based upon.
SubProtocol
Protocol Scale
0
Component Point
363 -50
GUID
{456195EF-9708-4367-B3DD-21EBF3796604}
Fancy Help
100
Keeps only the specified properties
For each incoming data record, retains only the properties found in the list of property names specified by <i>PropertyList</i>. All other properties are removed.
<p><b>Note:</b>
<ul>
<li>Use <i>RenameList</i> if you wish to change the names of the retained properties.
</ul>
<p><b>See Also:</b></p>
<ul>
<li>To remove specified properties from each data record, use
<a href="javascript:DoLink('{C2ED35FF-5397-4877-AADB-10F1A15D60E2}')">Remove Properties</a>.
</ul>
Generic
Generic
With only the specified properties remaining
None
The server version when this component was registered
6.0.1.4
Component Sticky Notes
By Ref
0
Protocol Sticky Notes
Runtime Identifier
5:1
Location of the component in the database
Components\Generic\Manipulators\Keep Properties
Maximum number of table rows in the HTML page
2000
The number of rows displayed on each page
25
General (non-chemistry) options pertaining to how the molecular image is generated.
ImageSize
Caption Property
WidthToHeightRatio
The square molecule image size to generate (in pixels).
256
The ratio of the width to the height. When not equal to 1.0, the image height is given by <i>ImageSize</i> and the image width is scaled to fit the given <i>WidthToHeightRatio</i>.
A larger <i>WidthToHeightRatio</i> is often desired for viewing Reactions due to the presence of multiple molecules lined up horizontally.
1.0
The property to use to display a picture caption. If this parameter is
not set, a caption is not displayed.
Chemistry options pertaining to how the molecular image is generated.
DrawImplicitHydrogens
DrawAromaticRings
DrawUnknownDoubleBonds
DrawFunctionalGroups
FunctionalGroupsQueries
AtomAttributeProperty
AtomLabelsScaleFactor
DisplayHighlightedAtomsAs
ShowAtomAndBondPropertiesTables
UseColor
Defines which implicit Hydrogen atoms to draw:
<ul>
<li><b>AllHydrogens:</b> Displays all implicit Hydrogen atoms (this option overrides the other options).</li>
<li><b>HeteroHydrogens:</b> Displays implicit Hydrogen atoms on heteroatoms.</li>
<li><b>TerminalCarbonHydrogens:</b> Displays implicit Hydrogen atoms on terminal Carbon atoms.</li>
</ul>
AllHydrogens
HeteroHydrogens
TerminalCarbonHydrogens
How to draw aromatic rings.
<ul>
<li><b>UsingSingleDoubleBonds:</b> A kekule representation using alternating single and double bonds.</li>
<li><b>AsSolidCircles:</b> A solid circle is drawn inside the aromatic ring.</li>
</ul>
UsingSingleDoubleBonds
AsSolidCircles
How to draw double bonds with unknown stereochemistry (such as in molecules read from SMILES);
either <b>AsStandardDoubleBond</b> or <b>AsCrossedLines</b>.
AsStandardDoubleBond
AsCrossedLines
If set to true, the molecular image will be colored according to atom types. If false, the image will be black and white only.
H
C
N
O
P
S
Halogen
Other
True
False
Color to use to draw explicit Hydrogen atoms.
<br>
Default is Black (0,0,0)
<br>
The color can be defined as a string with three comma-separated integers between 0 and 255 representing the RGB numbers (example: 200,0,0) or as one of the predefined color names (Red, Green, Blue, Yellow, Cyan, Magenta, Black).
parameter("UseColor") = "True"
0,0,0
Color to use to draw Carbon atoms.
<br>
Default is Black (0,0,0)
<br>
The color can be defined as a string with three comma-separated integers between 0 and 255 representing the RGB numbers (example: 200,0,0) or as one of the predefined color names (Red, Green, Blue, Yellow, Cyan, Magenta, Black).
parameter("UseColor") = "True"
0,0,0
Color to use to draw Nitrogen atoms.
<br>
Default is Blue (0,0,200)
<br>
The color can be defined as a string with three comma-separated integers between 0 and 255 representing the RGB numbers (example: 200,0,0) or as one of the predefined color names (Red, Green, Blue, Yellow, Cyan, Magenta, Black).
parameter("UseColor") = "True"
0,0,200
Color to use to draw Oxygen atoms.
<br>
Default is Red (200,0,0)
<br>
The color can be defined as a string with three comma-separated integers between 0 and 255 representing the RGB numbers (example: 200,0,0) or as one of the predefined color names (Red, Green, Blue, Yellow, Cyan, Magenta, Black).
parameter("UseColor") = "True"
200,0,0
Color to use to draw Phosphorus atoms.
<br>
Default is Magenta (0,200,200)
<br>
The color can be defined as a string with three comma-separated integers between 0 and 255 representing the RGB numbers (example: 200,0,0) or as one of the predefined color names (Red, Green, Blue, Yellow, Cyan, Magenta, Black).
parameter("UseColor") = "True"
0,200,200
Color to use to draw Sulfur atoms.
<br>
Default is dark yellow (200,200,0)
<br>
The color can be defined as a string with three comma-separated integers between 0 and 255 representing the RGB numbers (example: 200,0,0) or as one of the predefined color names (Red, Green, Blue, Yellow, Cyan, Magenta, Black).
parameter("UseColor") = "True"
200,200,0
Color to use to draw halogen atoms (F, Cl, Br,I).
<br>
Default is Green (0,200,0)
<br>
The color can be defined as a string with three comma-separated integers between 0 and 255 representing the RGB numbers (example: 200,0,0) or as one of the predefined color names (Red, Green, Blue, Yellow, Cyan, Magenta, Black).
parameter("UseColor") = "True"
0,200,0
Color to use to draw atoms other than H, C, N, O, P, S, and halogens.
<br>
Default is Black (0,0,0)
<br>
The color can be defined as a string with three comma-separated integers between 0 and 255 representing the RGB numbers (example: 200,0,0) or as one of the predefined color names (Red, Green, Blue, Yellow, Cyan, Magenta, Black).
parameter("UseColor") = "True"
0,0,0
<p>Draw specific functional groups as text instead of the actual atoms and bonds.</p>
<ul>
<li>The functional groups to draw are defined using substructure searching with queries contained in the directory specified by <i>FunctionalGroupsQueries</i>. The default location of the functional group queries is /data/Queries/FunctionalGroups.</li>
<li>Each functional group query mol file must define the text to be drawn, the text color, and the core atom that connects the functional group to the rest of the molecule. Only functional groups with a single core atom are allowed.</li>
</ul>
True
False
Location of the functional group queries.
data\Queries\FunctionalGroups\*.mol
The name of the atom attribute that contains a value for display
Label
<p>Factor to scale the size of the atom labels (atom type, atom number, valence, value, charge).</p>
<p>Set this factor to the default value of 1.0 to use the font size determined internally by PipelinePilot. Values greater than 1.0 will increase the font size. Values smaller than 1.0 will decrease the font size.</p>
1.0
Select how to highlight selected atoms.
<ul>
<li><b>ColoredBlocks:</b> Display a colored block superimposed on all the selected atoms.</li>
<li><b>ColoredLabels:</b> Color all the selected atom labels with the same highlight color.</li>
</ul>
ColoredBlocks
ColoredLabels
Toggles display of the <b>Atom Properties</b> and <b>Bond Properties</b> table columns. When this parameter is active, the molecule for each row is scanned for atom and bond properties. If any are found, tables of atom and/or bond properties are displayed.
True
False
Lists the set of temporary files which will be converted by the network to true temporary file names
temphtml
Lists a set of properties (without the @) to be created on the property list for this protocol.
Other properties are created on the global property list
and so are accessible from all protocols.
HTML Filename,newViewer
When the network is run, whether we process once or until done for each process call
True
False
Component Attributes
ComponentTakesInput
ComponentReturnsPass
ComponentReturnsFail
ComponentRunsLocal
When an recoverable error occurs during processing:
Halt: Terminate the execution of the network
Fail: Continue execution of the network, passing data out the Fail(red) port
Pass: Continue execution of the network, passing data out the Pass(green) port
Halt
Fail
Pass
When an expected data type is not found during processing:
Halt: Terminate the execution of the network
Fail: Continue execution of the network, passing data out the Fail(red) port
Pass: Continue execution of the network, passing data out the Pass(green) port
Halt
Fail
Pass
Protocol Options
Make Shortcut by Default
Cant Replace With Copy
Cant Open
Component Comment
Generates and displays an HTML table page of molecules and properties.
Component Usage
This component will generate an HTML table of molecules and their associated properties and display it in Internet Explorer.
Display Name
HTML Molecular Table Viewer
Protocol AutoLayout
true
Protocol ShowComment
false
Add Protocol Comment Here
Add Protocol Comment Here
Component Point
1813 -50
Disabled
0
Custom Error Message
Component Icon
VIEWERNODE
Component Revision
100
The component this component is based upon.
SubProtocol
Protocol Scale
0
By Ref
1
Fancy Help
100
Generates and displays an HTML table page of molecules and properties
<p>Each row of the table corresponds to one molecule record, with columns for the structure and each property.</p>
<p>The first column of the resulting table contains an image of the molecule. The input coordinates are used to create the image. If no input coordinates are present (e.g. molecules imported from SMILES), then two dimensional coordinates will be internally generated using the <i>2D Coords</i> component.</p>
<p>The output table is a "paged table". That is, only <i>Rows Per Page</i> records are displayed on each HTML page. A number of links (e.g. "Next", "Previous") are present on each page to let the user navigate between different ranges of the output.</p>
<p>For molecules which have atom and/or bond properties, a table of that molecule's atom and bond properties can be displayed inside each row in the <b>Atom Properties</b> and <b>Bond Properties</b> columns. The <i>ShowAtomAndBondPropertiesTable</i> parameter toggles the generation and display of these tables.</p>
<p><b>Note:</b></p>
<ul>
<li>Any grouped data is displayed in nested tables. If you prefer not to view the grouped data, use the <a href="javascript:DoLink('{ACCDEEEF-FEED-4B27-B263-BA531EABFC9C}')">Delete Children</a> component with a blank <i>PackId Property</i> parameter to remove it.</li>
</ul>
<p><b>See Also:</b></p>
<ul>
<li>To write the HTML to a file, use the <a href="javascript:DoLink('{AE1CFEA1-7CD1-408a-B7BB-58A55B6130C7}')">HTML Molecular Table Writer</a></li>
<li>To view an HTML page of molecules grouped by property or cluster, use <a href="javascript:DoLink('{6049A843-46A8-4738-9DE5-C71AB92B3215}')">HTML Molecular Grouped Viewer</a> or <a href="javascript:DoLink('{583E555F-8343-42B5-B87D-77C6D21F9043}')">HTML Molecular Cluster Viewer</a>.</li>
</ul>
Molecule
None
None
Component Sticky Notes
Protocol Sticky Notes
The server version when this component was registered
6.1.0.22
Runtime Identifier
6
Protocol Scale
100
The property name of a property containing a list of atom IDs to highlight in
the image.
The property name of a property containing a list of bond IDs to highlight in
the image.
The highlight color for selected atoms or bonds
Red
Green
Blue
Yellow
Cyan
Magenta
Black
The user who registered this component.
scitegic/chemistry
The date this component was registered.
Tue May 08 12:31:25 2007
GUID
{485D30CD-737C-4AD3-89C9-F81CB20E47AE}
Subprotocol Made Link Into Copy
0
Location of the component in the database
Components\Chemistry\Viewers\HTML Molecular Table Viewer