</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.
Fri Sep 12 14:57:20 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
M5_ChargeMatching
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
{1BC0173F-8FAE-0F4A-961C-1366BA97C322}
Component Point
70 -50
By Ref
0
Fancy Help
100
Building protocols in Pipeline Pilot.
This is the help window for working with components and protocols in Pipeline Pilot.
To create a protocol, drag items from the Components tab into the workspace. Connect them with pipes, edit their parameters, and then click Run to generate results.
As you select components and protocols, information about using them is displayed in this help window. The parameters are displayed in the adjacent Parameters window.
For more information, go to <a href="javascript:DoLink('scihelpdocs/user/getstart/getstart_intro.htm')">Getting Started with Pipeline Pilot</a>.
None
None
None
Runtime Identifier
Protocol Scale
100
Protocol Options
Make Shortcut by Default
Owner Access Only
Protocol Sticky Notes
%VERSION 3%
975 -350 1257 256
255 218 185
M5 Charge Matching
Supply two SD files and molecule matches at pH 7 will be detected and pairs output
The server version when this component was registered
7.0.1.100
Location of the component in the database
PaulDobson\MergingModels\M5_ChargeMatching
The file or URL source to read
Maximum
SourceTag
Keep Properties
The maximum number of data records to read (all if value is empty)
<p>The type of tag to create to identify the source of data records. A property called <b>SourceTag</b> is created and holds the value indicated.</p>
<ul>
<li><b>None</b>: No SourceTag property is created and any existing ones are removed.</li>
<li><b>Filename</b>: The name of the file read.</li>
<li><b>FilenameAndExtension</b>: The name of the file read with its file extension.</li>
<li><b>FullFilename</b>: The name of the file read, including the directory path.</li>
<li><b>ZipFilename</b>: When reading a compressed zip file, the filename within the compressed archive.</li>
<li><b>Number</b>: When multiple files are read in this component, they are numbered 1,2,3...</li>
<li><b>Letter</b>: When multiple files are read in this component, they are lettered A, B, C...</li>
<li><b>KeepCurrent</b>: Keeps the current value of SourceTag.</li>
</ul>
None
Filename
FilenameAndExtension
FullFilename
ZipFilename
Number
Letter
KeepCurrent
A list of properties the reader should retain for each data record that is output. If a value is not defined, retains all properties. If the parameter contains the value "-" (minus sign), properties are not retained.
Contains less commonly used parameters
ReadProperties
PutNameInProperty
ReadQueryInfo
PutCommentInProperty
SD Format Options
<p>Options available for the SD Reader:</p>
<ul>
<li><b>Properties Can Contain $$$$:</b> By the MDL CTFile standard, a property can contain a '$$$$'-line. Properties or data field values are terminated by a blank line. Only then will the '$$$$'-line terminate the full data block. Setting this option off will terminate the data block upon any read of a '$$$$'-line. This option is available to provide compatibility with some 3rd Party SD files.</li>
<li><b>One-space Lines Terminate Properties:</b> By the MDL CTFile standard, properties or data fields values are terminated by a blank line. Selecting this option will terminate the data block when encountering a line containing a space as the only character in the line. This option is available to provide compatibility with some 3rd Party SD files.</li>
<li><b>Unwrap Long Property Lines:</b> By the MDL CTFile standard, lines in property fields cannot exceed 200 characters. When this option is selected and a property line of exactly 200 characters is found, the newline character will be ignored and property string will continue on the next line.</li>
<li><b>Read Unknown Stereo Parity:</b> When selected, the SD Reader will use the 'Atom Parity' value (parity of '3') to mark unknown stereo centers in 3D mol files. This will leave these atoms marked as 'unknown stereo' and will not calculate the stereo from the coordinates.</li>
</ul>
Properties Can Contain $$$$
One-space Lines Terminate Properties
Unwrap Long Property Lines
Read Unknown Stereo Parity
Select True to read the properties for each molecule (in addition to the structures)
True
False
If properties starting with "QueryInfo" are present, use them to set up query information on the atoms and bonds. (This is how, for example, SMARTS query information can be preserved when writing to an MDL SD format file.) For molecules saved in MDL format, this information only contains information that cannot be written out in MDL SD format.
True
False
What to call the property that holds the name of each molecule
Name
What to call the property that holds the comment associated with each molecule
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
According to the MDL CTfile specifications, the cis/trans character of double bonds with bond stereo set to zero is determined from the coordinates. This parameter controls whether or not to assign unknown bond stereo to double bonds for which the stereo could not be determined from the coordinates, either because there are no coordinates or because of colinearity issues. When the parameter is set to False and the stereo could not be determined, no specific stereo configuration is assigned to the double bond, but it is not marked as unknown stereo.
True
False
Delete the file after the data is read [Be Careful!]
True
False
Comment
Reads MDL MOL (molecule CTAB) files and MDL SD (structured data) files.
The user who registered this component.
scitegic/chemistry
The date this component was registered.
Tue Mar 20 10:03:13 2007
Component Usage
Creates a molecule data record for each molecule represented in the 'Source' data file. Can read zipped (.zip) and url-based files. Any properties contained in the file will be read into the data records created if the user specifies.
Output Pass - Molecule data records
Display Name
SD Reader
Custom Error Message
Component Icon
DOCUMENTNODE
GUID
{CA65B896-4FE6-4E3A-B884-DC16B53B8D26}
The component this component is based upon.
SD Reader
Disabled
0
Component Point
88 -50
Fancy Help
100
Reads MDL MOL (molecule CTAB) files and MDL SD (structured data) files
<p>Creates a molecular data record for each molecule represented in the <i>Source</i> data file. All properties contained in the file are read into the data records.</p>
<p><b>Note:</b><p>
<ul>
<li>This component can also read zipped (.zip) and URL-based files.</li>
</ul>
<p><b>See Also:</b><p>
<ul>
<li>To write files in MDL MOL or SD format, use the <a href="javascript:DoLink('{DC8EE7B0-0620-42FE-944C-B4CD1E79480E}')">SD Writer</a>.</li>
<li>To convert a molecule to and from between text properties in CTAB format, use <a href="javascript:DoLink('{E622FBD9-9FA9-451A-A102-1800B5F28B6D}')">Molecule to CTAB</a> and <a href="javascript:DoLink('{7D354B65-DDD8-4EA4-83A7-21501A8A6852}')">Molecule from CTAB</a>.</li>
<li>Other related MDL format file readers include <a href="javascript:DoLink('{169AB4E5-A470-477B-AA65-50464411036C}')">RG Reader</a>, <a href="javascript:DoLink('{036731AA-0015-4606-9750-7D9D020F21C8}')">RXN Reader</a> and <a href="javascript:DoLink('{55431CCB-06EA-4741-B95B-633C877E3E9B}')">RD Reader</a>.</li>
</ul>
None
Molecule
Data fields in the SD file will be added to the property fields
None
Component Sticky Notes
The server version when this component was registered
6.1.0.11
Runtime Identifier
0
Location of the component in the database
Components\Chemistry\Readers\SD Reader
<p>The name of the property to hold the data record count. If the name begins with "@", this is a global property name and is updated each time a data record is received. Otherwise, it is a local property name and a new property by that name will be created on each data record and given the current value (i.e., the count).</p>
Start Index
Check if Property Already in Use
IndexA
The index (i.e., number) used to start the sequence.
1
Generates an error if the property already exists. This helps prevent overwriting data created by another component. Default is "True".
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
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
Component Attributes
ComponentTakesInput
ComponentReturnsPass
ComponentReturnsFail
ComponentRunsLocal
The user who registered this component.
scitegic/core
The date this component was registered.
Fri Sep 08 07:31:45 2006
GUID
{7BF3D951-BF75-70A2-8B2C-AD8909791909}
Display Name
Add index
Custom Error Message
Component Icon
COMPONENTNODE
The component this component is based upon.
Count and Index Data
Disabled
0
Component Point
363 -50
Fancy Help
100
Counts the number of data records and puts the count in a property
<p>Use this component to create a numerical index of data records and to keep track of the total number of records. The value of <i>Counter Property</i> is incremented each time a data record enters the component.</p>
<p>This component can be used in two modes:</p>
<ul>
<li>If <i>Counter Property</i> is the name of a local property (does not start with "@"), a new property by that name is created on each data record and given the value of the current count.</li>
<li>If <i>Counter Property</i> is the name of a global property (starts with "@"), then each data record that passes through causes this global record count to be incremented, but values are not added to the passing records.</li>
</ul>
Generic
Generic
None
The server version when this component was registered
6.0.0.44
Component Sticky Notes
Runtime Identifier
1
Location of the component in the database
Components\Generic\Calculators\Count and Index Data
</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
Hold original smiles
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
663 -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
2
Location of the component in the database
Components\Generic\Utilities\SubProtocol Utilities\Subprotocol
<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
88 -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
2:0
Location of the component in the database
Components\Chemistry\Calculators\Canonical Smiles
Molecular Formats
Molecular Formats
Property name to change
canonical_smiles
Name of the new property
original_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
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
2:1
GUID
{5A384E06-8AF2-4C10-A9B7-7302DD110A48}
Disabled
0
CustomErrorText
Component Point
363 -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
pH value to use in the calculation of the ionization state.
7
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
Displays the pKa values associated with the pKa sites in the 2D molecular picture.
True
False
Directory with molecular query files defined by the user.
These queries are used to search for pKa sites in the molecule
data\pKa\AcidBaseSites\User\*.sd
Directory with pKa site examples information.
The site examples files are created using the pKa component "Add pKa Data".
The site example information is used in the calculation of pKa values.
This directory contains files created by the user
data\pKa\Data\User\SiteExamples_*.tab
Directory with the molecular query files defined by Scitegic during the
implementation of the pKa components.
These queries are used to search for pKa sites in the molecule
data\pKa\AcidBaseSites\Scitegic\*.sd
Directory with pKa site examples information.
The site examples files are created using the pKa component "Add pKa Data".
The site example information is used in the calculation of pKa values.
This directory contains the original site examples files created by Scitegic
during the implementation of the pKa components.
data\pKa\Data\Scitegic\SiteExamples_*.tab
Directory with pKa Models.
These models are used to calculate pKa values for the molecule.
Several pKa models for different pKa sites developed by Scitegic
are included in this directory
data\pKa\Models\PKAModel_*.txt
Mode
Protonate at pH
The user who registered this component.
scitegic/chemistryadv
The date this component was registered.
Tue Oct 31 12:34:50 2006
The component this component is based upon.
PKA
Component Icon
COMPONENTNODE
GUID
{72D1AEC5-EE9E-4a39-A3D6-63637069BF6E}
Comment
Calculates the ionization state of the molecule
Component Usage
Use this component to calculate pKa values.
Input - Molecule data records
Output Pass - Molecule data records augmented with pKa data
Display Name
Ionize Molecule at pH
Custom Error Message
Component Point
938 -50
Disabled
0
Fancy Help
100
Sets the protonation state of the pKa sites according to a given pH
<p>Finds pKa sites and calculates the corresponding pKa values. The molecule is then modified so that the protonation state of those sites is set according to the specified pH.</p>
<p><b>Notes: </b></p>
<ul>
<li>pKa sites are located based on the molecular query files located in "data/pKa/AcidBaseSites/".</li>
<li>Pka values are calculated based on site examples files located in "data/pKa/Data/" and on PLS Models located in "data/pKa/Models".</li>
</ul>
<p><b>See Also: </b></p>
<ul>
<li>For calculation of pKa information for each atom in the molecule, use <a href="javascript:DoLink('{A09482AD-1A24-4a94-B050-43CEF82DE630}')">pKa</a></li>
<li>To calculate the octanol/water partition coefficient utilizing pKa information, use <a href="javascript:DoLink('{DDDB7E61-D653-45e8-9564-39FB67159FD4}')">logD</a>.</li>
<li>To enumerate all the possible ionization states of the molecule based on the pKa values and the pH range, use <a href="javascript:DoLink('{B07C705E-49AC-4d54-887F-E4CE2DABA42D}')">Enumerate Ionization States</a></li>
<li>To add your own data to the pKa model, use <a href="javascript:DoLink('{DF099F9F-CB30-4a20-98BA-2ECAE394AF07}')">Add pKa Data</a>.</li>
<li>To see the number of pkA sites and data points in the existing model, use <a href="javascript:DoLink('{192A4F24-B54B-49ec-834C-C9A6A13C58FC}')">pKa Site Stats Reader</a>.</li>
<li>For other information the calculation of pKa Calculation, see the <a href="javascript:DoLink('sciapps/scitegic/chemistryadv/docs/chemistry_two.pdf')">Advanced Chemistry User Guide</a></li>
</ul>
Generic
Generic
Molecule with ionizable groups in the protonation state corresponding to the specified pH
None
The server version when this component was registered
6.0.1.7
Component Sticky Notes
Runtime Identifier
3
Location of the component in the database
Components\Chemistry\Manipulators\Ionize Molecule at pH
What happens to the values of properties represented in more than one of the records being combined.
<p>
<ul>
<li><b>KeepAll</b>: keeps all property values by appending additional values in an array.</li>
<li><b>KeepFirst</b>: keeps only the properties and values from the first example received. All properties and values from subsequent records for the same molecule are discarded.</li>
<li><b>KeepTogether</b>: keeps all records for the same molecule sequentially together in the ouput (like Sort).</li>
</ul>
KeepAllNullString
WhenMerging
PrefixUsingProperty
KeepAll
KeepFirst
KeepTogether
<p>When merging using KeepAll behavior, provides fine control over how multiple values are treated.</p>
<ul>
<li>OverwriteOrCreate: Copies all properties of each merged record sequentially, overwriting any values that may already exist (instead of generating an array).</li>
<li>OverwriteExisting: Only copies properties that already exist on the first merged record, overwriting those original values (instead of creating an array).</li>
<li>CreateIfNew: Leaves any existing properties alone, and writes only new properties.</li>
<li>AppendOrCreate: Appends (as an array) if a property already exists, otherwise creates it.</li>
<li>AppendExisting: Appends (as an array) only to currently existing properties, and discards other new property values.</li>
</ul>
OverwriteOrCreate
OverwriteExisting
CreateIfNew
AppendOrCreate
AppendExisting
This string is used during append in "KeepAll" to pad out empty values. It keeps the generated arrays of values in sync for multiple samples. The value "None" causes no padding to occur.
None
When multiple values for a property are retained (under KeepAll merge behavior), the original property name is prefixed differently for each original value it must hold. The prefix is constructed from the value of this property, followed by an underscore.
When not specified, a prefix is not used and multiple values are separated as an array (such as property[1], property[2], etc).
Add a property called <b>Frequency</b> that contains the number of individual records included in the resulting merged record
True
False
Temporary files converted by the network to true temporary filenames
Lists a set of properties (without the @) to create on the property list for this protocol. Other properties are created on the global property list and are accessible from all protocols.
When the network runs, processes 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
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
Component Attributes
ComponentTakesInput
ComponentReturnsPass
ComponentReturnsFail
ComponentRunsLocal
The user who registered this component.
scitegic/chemistry
The date this component was registered.
Thu Nov 02 16:47:09 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
Merge Molecules
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
{2E21E16B-6901-46F3-8780-F14D3D7057CE}
Component Point
1238 -50
Protocol Scale
0
By Ref
1
Fancy Help
100
Merges data records containing identical molecules into a single data record
Multiple molecular data records with identical molecules are merged into a single data record. Molecules are identified as identical based on their Canonical_Smiles. If the molecules are already unique, they are passed unchanged through the Pass port.
<p>
<i>MergeBehavior</i> specifies how to combine the property values for duplicate molecules.
<p>
<strong>See also:</strong>
<ul>
<li>To merge data records based on the values of a property, see <a href="javascript:DoLink('{1E393621-138C-466E-8A2B-275A3FAB26E3}')">Merge Data</a>.</li>
</ul>
Molecule
Molecule
Single molecule record for all input molecule records with identical molecules
None
The server version when this component was registered
6.0.1.7
Component Sticky Notes
Protocol Sticky Notes
Runtime Identifier
4
Protocol Scale
100
Protocol Options
Make Shortcut by Default
Owner Access Only
Subprotocol Made Link Into Copy
0
Location of the component in the database
Components\Chemistry\Manipulators\Merge Molecules
Subprotocol Modified
0
</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
Process
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
The PilotScript expression used to filter the data.
Initial Expression
Final Expression
Keep Calculated Properties
Frequency > 1
<p>
An expression evaluated only when the component
is first initialized (when the first data record enters).
<p/>
Since there is no data available at initialization time, only expressions referencing global properties are allowed.
</p>
<p>
An expression evaluated only when the
component is finalized (once the last data
record has passed).
<p/>
Since there is no data available at finalization time, only expressions referencing global properties are allowed.
</p>
Allows any properties that were calculated in
"Expression" to be included with the exiting
record.
Otherwise, these properties are removed after
the evaluation is complete.
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
Version of expression parser to use.
2
Comment
Allows you to filter using the result from a PilotScript expression. The expression you specify is evaluated for each incoming data record, and is evaluated to a True or False value. If multiple statements are present, then the value of the last statement is used.
The user who registered this component.
scitegic/core
The date this component was registered.
Mon Apr 23 12:21:34 2007
Component Usage
The 'Expression' is evaluated for each incoming data record. The last statement in the expression evaluates to a boolean value (true/false or nonzero/zero) and determines the fate of the data record: Records which evaluate to 'true' are passed out the Pass port; those which evaluate to 'false' are passed out the 'Fail' port.
Input - Data records
Output Pass - Data records which evaluate 'true'
Output Fail - Data records which evaluate 'false'
Display Name
Custom Filter (PilotScript)
Custom Error Message
Component Icon
FILTERNODE
The component this component is based upon.
Custom Filter (PilotScript)
Disabled
0
GUID
{DD58ECD1-516F-48FE-A5DB-8328AED680F2}
Component Point
88 -50
Fancy Help
100
Passes data records for which a PilotScript expression evaluates to True
<p>For each incoming data record, the PilotScript statements in <i>Expression</i> are evaluated. If the last statement in the expression evaluates to True or non-zero, the record is sent out the Pass port. Otherwise it is sent out the Fail port.</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>
</ul>
Generic
Generic
Data records for which the final expression in the PilotScript evaluates to True or non-zero
Generic
Data records for which the final expression in the PilotScript evaluates to False or zero
Runtime Identifier
5:0
Location of the component in the database
Components\Generic\Filters\Custom Filter (PilotScript)
6.1.0.17
Comma-separated list of property names to keep
RenameList
IndexA, IndexB
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
Property the filter will be applied to
IndexA
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
Property Defined Filter
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
663 -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
5:2
Location of the component in the database
Components\Generic\Filters\Is Property Defined Filter
6.0.0.46
Property the filter will be applied to
IndexB
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
Property Defined Filter
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
938 -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
5:3
Location of the component in the database
Components\Generic\Filters\Is Property Defined Filter
6.0.0.46
Options for the type of standardization you can perform. The default is to standardize the charging and stereochemistry of the molecule. If multiple actions are selected, they are performed in the given order.
Invert Wedge Bond When Changing Direction
StandardizeStereo
StandardizeCharges
CenterMolecule
RemoveSingleAtomFragments
KeepSmallestFragment
KeepLargestFragment
RemoveLargestFragment
MakeNon[H]Atoms[C]Atoms
MakeNon[H]Atoms[A]Atoms
MakeNon[C,H]Atoms[Q]Atoms
MakeAllBondsSingle
ClearCoordinates
ClearMolecule
RemoveMolecule
ClearStereo
ClearUnknownStereo
ClearCisTransBondStereo
SetStereoFromCoordinates
RepositionStereoBonds
FixDirectionOfWedgeBonds
ClearCharges
ClearSgroupData
ClearHighlightColors
ClearQueryInfo
ClearAtomLabels
ClearBondLabels
NeutralizeBondedZwitterions
ClearUnusualValence
This parameter controls whether or not to invert the bond stereo (up or down) when changing the direction of the wedge bond by selecting "FixDirectionOfWedgeBonds" in the <i>Action</i> parameter.
contains(parameter('Action'), 'FixDirectionOfWedgeBonds')
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
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
Componet Attributes
ComponentTakesInput
ComponentReturnsPass
ComponentReturnsFail
ComponentRunsLocal
The user who registered this component.
scitegic/chemistry
The date this component was registered.
Wed Apr 11 14:39:40 2007
Component Comment
Contains a number of actions that are useful for taking molecules from different sources and correcting non-uniform features.
Component Usage
One or more actions can be applied to each molecule to standardize the way molecules are presented to downstream components.
Input - Molecular data records
Output Pass - Molecular data records with standardization changes
Description of StandardizeStereo option:
Atoms that are perceived as true stereo atoms but which have no stereochemical markings (UnknownAtomStereo, EvenAtomStereo, or OddAtomStereo) are set to UnknownAtomStereo. Atoms that have stereochemical markings but which are not true stereoatoms are set to NoAtomStereo. 2D or 3D coordinates are not used in this process.
Similarly, bonds that are perceived as true stereo double bonds but
which have no stereochemical markings (UnknownBondStereo, CisBondStereo, or TransBondStereo) are set to UnknownBondStereo. Bonds that have stereochemical markings but which are not true stereo bonds are set to NoBondStereo. Again, 2D or 3D coordinates are not used in this process.
Display Name
Standardize Molecule
Custom Error Message
Component Icon
COMPONENTNODE
The component this component is based upon.
Standardize Charges
Disabled
0
GUID
{EFEA1A46-A6DB-4DB9-A5A9-C7F3D2ADFDE2}
Component Point
1238 -50
Fancy Help
100
Applies selected predefined actions to the input molecules
<p>One or more actions can be applied to each molecule to standardize the way molecules are presented to downstream components.
<p>
Standardization is important when comparing molecular libraries from different sources. If different rules were used for structural representation when creating these libraries, a straight comparison would yield incorrect results. This component allows you to apply a consistent set of rules to structures before comparing them.
<p>
Available actions:
<ul>
<li><strong>StandardizeStereo: </strong>
Atoms that are perceived as true stereo atoms but which have no stereochemical
markings (UnknownAtomStereo, EvenAtomStereo, or OddAtomStereo) are set to UnknownAtomStereo.
Atoms that have stereochemical markings but which are not true stereoatoms are
set to NoAtomStereo. 2D or 3D coordinates are not used in this process. <br />
Similarly, bonds that are perceived as true stereo double bonds, but which have
no stereochemical markings (UnknownBondStereo, CisBondStereo, or TransBondStereo)
are set to UnknownBondStereo. Bonds that have stereochemical markings but which
are not true stereo bonds are set to NoBondStereo. Again, 2D or 3D coordinates
are not used in this process.</li>
<li><strong>StandardizeCharges:</strong>
Sets standard formal charges for common functional groups: Quaternary Nitrogen:
+1 <br />
Nitro groups: N+(=O)O- <br>
Diazonium N: +1 <br>
Oxygen with three attachments: +1 <br>
X=O-C Oxygen: +1 <br>
Sulfur with three attachments: +1 <br>
S=O-C Sulfur: +1 <br>
F, Cl, Br, I with no attachments: -1 <br>
Note that halogen acids with explicit hydrogens (H-X) are not modified. </li>
<li><strong>CenterMolecule:</strong>
Translates the molecule to the center of geometry. </li>
<li><strong>RemoveSingleAtomFragments:</strong>
Removes all unattached atoms from the molecule. </li>
<li><strong>KeepSmallestFragment:</strong>
Keeps only the fragment with fewer atoms in the case of multifragment molecules. </li>
<li><strong>MakeNon[H]Atoms[C]Atoms:</strong>
Converts all the atoms in the molecule to Carbon. </li>
<li><strong>MakeNon[C,H]Atoms[Q]Atoms: </strong>
Converts all non-carbon, non-hydrogen atoms in the molecule to the Q query atom type. </li>
<li><strong>MakeNon[H]Atoms[A]Atoms: </strong>
Converts all non-hydrogen atoms in the molecule to the A query atom type. </li>
<li><strong>MakeAllBondsSingle: </strong>
Converts all the bonds in the molecule to Single bonds. </li>
<li><strong>ClearCoordinates:</strong>
Sets all x, y, z coordinates to zero. </li>
<li><strong>ClearMolecule:</strong>
Deletes all atoms and bonds in the molecule, keeping the molecule object in the data record. </li>
<li><strong>RemoveMolecule:</strong>
Deletes the molecule object from the data record. </li>
<li><strong>ClearStereo: </strong>
Sets all atoms and bonds to NoStereo. </li>
<li><strong>ClearUnknownStereo:</strong>
Sets all atoms and bonds that are marked UnknownStereo to NoStereo. </li>
<li><strong>ClearCisTransBondStereo:</strong>
Sets all bonds that are marked CisStereo or TransStereo to UnknownStereo. </li>
<li><strong>ClearCharges: </strong>
Sets all formal charges to zero. </li>
<li><strong>SetStereoFromCoordinates: </strong>
This option uses the 2D coordinates and up/down bond markings, or the
3D coordinates, to assign the stereochemistry of the atoms or bonds. Typically,
this is done by the readers or the molecules from text components. Occasionally,
components may create molecules that need to have their stereo reperceived. </li>
<li><strong>RepositionStereoBonds: </strong>
This option repositions the stereo bond markings, trying to find the best bond to mark as a wedge bond for each stereo atom. </li>
<li><strong>FixDirectionOfWedgeBonds: </strong>
This option checks the wedge bonds in the molecule to make sure that the wedge is drawn with the stereo atom at the narrow end of the wedge. Any wedge bond for which there is a stereo atom at the wide end and no stereo atom at the narrow end is reversed to point in the other direction. A separate option, <i>Invert Wedge Bond When Changing Direction</i>, controls whether or not to invert the bond stereo (up or down) when changing the direction of the wedge bond. </li>
<li><strong>ClearQueryInfo: </strong>
Deletes all query information from atoms and bonds. </li>
<li><strong>NeutralizeBondedZwitterions:</strong>
Converts directly bonded zwitterions (positively charged atom bonded to negatively charged atom, A+B-) to the neutral representation (A=B). </li>
<li><strong>ClearSGroupData:</strong>
Clears any SGroup information from the molecule. </li>
<li><strong>ClearHighlightColors:</strong>
Clears any highlight colors from atoms and bonds. </li>
<li><strong>ClearAtomLabels:</strong>
Clears any labels assigned to the atoms. </li>
<li><strong>ClearBondLabels:</strong>
Clears any labels assigned to the bonds. </li>
<li><strong>NeutralizeBondedZwitterions:</strong>
Converts directly bonded zwitterions (positively charged atom bonded to negatively charged atom, A+B-) to the neutral representation (A=B)</li>
<li><strong>ClearUnusualValence:</strong>
Clears any atom valence query features and resets all implicit hydrogen counts to their standard values.</li>
</ul>
Molecule
Generic
Transformed molecules
None
Component Sticky Notes
The server version when this component was registered
6.1.0.16
Runtime Identifier
5:4
Location of the component in the database
Components\Chemistry\Manipulators\Standardize Molecule
Name of the new property to create
Type
Value to give to the new property
Charge
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
the action to perform
Create
The user who registered this component.
scitegic/core
The date this component was registered.
Fri Sep 15 10:04:44 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
Type
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
{EDF965C5-6B38-4DB7-A9EB-FD885343B2CC}
Component Point
1538 -50
Protocol Scale
0
By Ref
0
Fancy Help
100
Creates a new property with a specified value
For every data record that enters the component, a new property with name given by <i>NewProperty</i> is created with the value specified in <i>DefaultValue</i>.
For example, to create a new property with today's date for each record, enter "Date" in <i>NewProperty</i>
and today's date in <i>DefaultValue</i>.
Generic
Generic
None
The server version when this component was registered
6.0.0.46
Component Sticky Notes
Protocol Sticky Notes
Runtime Identifier
5:5
Location of the component in the database
Components\Generic\Manipulators\Create New Property
Expression (or list of expressions separated by semi-colons) to evaluate.
Initial Expression
Final Expression
Keep Calculated Properties
FOR #i IN 1 .. numvalues(IndexA) LOOP
keyA := IndexA[#i];
FOR #j IN 1 .. numvalues(IndexB) LOOP
key := keyA." ".IndexB[#j];
APPEND(pairs, key);
END LOOP;
END LOOP;
<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 Pairs
The component this component is based upon.
Custom Manipulator (PilotScript)
Component RunTimeID
5:6
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)
<p>The names of the one or more properties to separate and return as separate data records. If no property names are given, then all properties with
multiple values will be unmerged. If multiple properties are unmerged, the number of unmerged records is the number of values of a property with the maximum number of values.
Pairs
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
Separates data records containing multiple values into multiple duplicate records each containing only one of the values.
The user who registered this component.
scitegic/core
The date this component was registered.
Fri Sep 08 07:32:06 2006
Component Usage
Each incoming data record with more than one value in the specified property is duplicated for each of the multiple values. For example, a data object with three values would generate three data objects, each with only one of the three values (but otherwise identical).
If no property names are given, then all properties with multiple values are unmerged.
If multiple properties are unmerged, they must contain the same number of values.
Input - Data records
Output Pass - Data records (containing the separated values)
Display Name
Unmerge Data
Unmerge Data
Component RunTimeID
5:7
Custom Error Message
Component Icon
GENERATORNODE
Disabled
0
Unmerge Data
{5E28C170-2FEC-4A3C-90A6-2DCEAA330E9D}
Component Point
2113 -50
Fancy Help
100
Separates data records containing array properties into individual records with one array value per record
<p>Each incoming data record with more than one value for the property or properties specified by <i>PropertyNames</i> is duplicated for each of the values. For example, a input data record with three values will generate three output data records. Each output record will contain one of the values for the <i>PropertyNames</i> property, and all other properties will be identical.</p>
<b>Notes:</b>
<ul>
<li>If no property names are given, then all properties with multiple values are unmerged. In this case, unexpected occurrences of arrays in a property will cause unintentional unmerge operations. Try to specify a value for <i>PropertyNames</i> if possible.</li>
<li>If multiple unmerge properties are specified, the number of data records that result from unmerging a given incoming data record is equal to the number of values of the unmerge property that has the most values. That is, if two unmerge properties, "A" and "B" are specified where A has 5 values and B has 7 values, then 7 data records will result. The first 5 records will contain, in order, the 5 values of A. For the last two records, A will be undefined. All other properties will be duplicated on each record.</li>
</ul>
Generic
Generic
Data records containing the separated values for the property or properties specified.
None
Location of the component in the database
Components\Generic\Manipulators\Unmerge Data
6.0.0.44
Expression (or list of expressions separated by semi-colons) to evaluate.
Initial Expression
Final Expression
Keep Calculated Properties
array := RSPLIT(Pairs, " ");
IndexA := array[1];
IndexB := array[2];
<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
5:8
Custom Error Message
Component Icon
EXPRESSIONNODE
Disabled
0
GUID
{0995D675-7EE2-432C-95DF-E91C14052B22}
Component Point
2388 -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)
Comma-separated list of property names to keep
RenameList
IndexA, IndexB, Type
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
2688 -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
5:9
Location of the component in the database
Components\Generic\Manipulators\Keep Properties
Specifies the maximum number of table rows in the HTML page
2000
The number of rows displayed on each page
25
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
When the network is run, 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
The optional title of the HTML document
Protocol Options
Make Shortcut by Default
Cant Replace With Copy
Cant Open
The user who registered this component.
scitegic/generic
The date this component was registered.
Wed Sep 20 14:45:58 2006
Component Comment
Generates and displays an HTML table page of molecules and their properties.
Component Usage
This component will generate and display an HTML page in Internet Explorer of molecules and their associated properties as a table with a single molecule per row.
See also the 'HTML Grouped Viewer' and 'HTML Cluster Viewer' for alternative displays of multiple molecules
Display Name
HTML 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
ProtocolCommentSize
1100 500
The component this component is based upon.
SubProtocol
GUID
{F6A20C96-BC1C-48f3-82E9-4D8F023F82EE}
Protocol Scale
0
By Ref
1
Fancy Help
100
Displays data records as HTML in Internet Explorer
<p>Generates and displays an HTML table page of data records, with one record per row. Each property becomes a column in the table and each value a cell.
<p>
<b>Notes:</b>
<ul>
<li>Molecules will be displayed if present.</li>
<li>For hierarchical data records, only top level properties are displayed.</li>
<li>Any grouped data is displayed in nested tables.</li>
</ul>
<b>See Also:</b>
<ul>
<li>If you prefer not to view the grouped data, use <a href="javascript:DoLink('{ACCDEEEF-FEED-4B27-B263-BA531EABFC9C}')">Delete Children</a>.</li>
<li>For more control over the display of molecules, use <a href="javascript:DoLink('{485D30CD-737C-4AD3-89C9-F81CB20E47AE}')">HTML Molecular Table Viewer</a>.</li>
</ul>
None
None
None
The server version when this component was registered
6.0.1.0
Component Sticky Notes
Protocol Sticky Notes
Runtime Identifier
6
Protocol Scale
100
Subprotocol Made Link Into Copy
0
Location of the component in the database
Components\Generic\Viewers\HTML Table Viewer
The file or URL source to read
Maximum
SourceTag
Keep Properties
The maximum number of data records to read (all if value is empty)
<p>The type of tag to create to identify the source of data records. A property called <b>SourceTag</b> is created and holds the value indicated.</p>
<ul>
<li><b>None</b>: No SourceTag property is created and any existing ones are removed.</li>
<li><b>Filename</b>: The name of the file read.</li>
<li><b>FilenameAndExtension</b>: The name of the file read with its file extension.</li>
<li><b>FullFilename</b>: The name of the file read, including the directory path.</li>
<li><b>ZipFilename</b>: When reading a compressed zip file, the filename within the compressed archive.</li>
<li><b>Number</b>: When multiple files are read in this component, they are numbered 1,2,3...</li>
<li><b>Letter</b>: When multiple files are read in this component, they are lettered A, B, C...</li>
<li><b>KeepCurrent</b>: Keeps the current value of SourceTag.</li>
</ul>
None
Filename
FilenameAndExtension
FullFilename
ZipFilename
Number
Letter
KeepCurrent
A list of properties the reader should retain for each data record that is output. If a value is not defined, retains all properties. If the parameter contains the value "-" (minus sign), properties are not retained.
Contains less commonly used parameters
ReadProperties
PutNameInProperty
ReadQueryInfo
PutCommentInProperty
SD Format Options
<p>Options available for the SD Reader:</p>
<ul>
<li><b>Properties Can Contain $$$$:</b> By the MDL CTFile standard, a property can contain a '$$$$'-line. Properties or data field values are terminated by a blank line. Only then will the '$$$$'-line terminate the full data block. Setting this option off will terminate the data block upon any read of a '$$$$'-line. This option is available to provide compatibility with some 3rd Party SD files.</li>
<li><b>One-space Lines Terminate Properties:</b> By the MDL CTFile standard, properties or data fields values are terminated by a blank line. Selecting this option will terminate the data block when encountering a line containing a space as the only character in the line. This option is available to provide compatibility with some 3rd Party SD files.</li>
<li><b>Unwrap Long Property Lines:</b> By the MDL CTFile standard, lines in property fields cannot exceed 200 characters. When this option is selected and a property line of exactly 200 characters is found, the newline character will be ignored and property string will continue on the next line.</li>
<li><b>Read Unknown Stereo Parity:</b> When selected, the SD Reader will use the 'Atom Parity' value (parity of '3') to mark unknown stereo centers in 3D mol files. This will leave these atoms marked as 'unknown stereo' and will not calculate the stereo from the coordinates.</li>
</ul>
Properties Can Contain $$$$
One-space Lines Terminate Properties
Unwrap Long Property Lines
Read Unknown Stereo Parity
Select True to read the properties for each molecule (in addition to the structures)
True
False
If properties starting with "QueryInfo" are present, use them to set up query information on the atoms and bonds. (This is how, for example, SMARTS query information can be preserved when writing to an MDL SD format file.) For molecules saved in MDL format, this information only contains information that cannot be written out in MDL SD format.
True
False
What to call the property that holds the name of each molecule
Name
What to call the property that holds the comment associated with each molecule
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
According to the MDL CTfile specifications, the cis/trans character of double bonds with bond stereo set to zero is determined from the coordinates. This parameter controls whether or not to assign unknown bond stereo to double bonds for which the stereo could not be determined from the coordinates, either because there are no coordinates or because of colinearity issues. When the parameter is set to False and the stereo could not be determined, no specific stereo configuration is assigned to the double bond, but it is not marked as unknown stereo.
True
False
Delete the file after the data is read [Be Careful!]
True
False
Comment
Reads MDL MOL (molecule CTAB) files and MDL SD (structured data) files.
The user who registered this component.
scitegic/chemistry
The date this component was registered.
Tue Mar 20 10:03:13 2007
Component Usage
Creates a molecule data record for each molecule represented in the 'Source' data file. Can read zipped (.zip) and url-based files. Any properties contained in the file will be read into the data records created if the user specifies.
Output Pass - Molecule data records
Display Name
SD Reader
Custom Error Message
Component Icon
DOCUMENTNODE
GUID
{CA65B896-4FE6-4E3A-B884-DC16B53B8D26}
The component this component is based upon.
SD Reader
Disabled
0
Component Point
88 -350
Fancy Help
100
Reads MDL MOL (molecule CTAB) files and MDL SD (structured data) files
<p>Creates a molecular data record for each molecule represented in the <i>Source</i> data file. All properties contained in the file are read into the data records.</p>
<p><b>Note:</b><p>
<ul>
<li>This component can also read zipped (.zip) and URL-based files.</li>
</ul>
<p><b>See Also:</b><p>
<ul>
<li>To write files in MDL MOL or SD format, use the <a href="javascript:DoLink('{DC8EE7B0-0620-42FE-944C-B4CD1E79480E}')">SD Writer</a>.</li>
<li>To convert a molecule to and from between text properties in CTAB format, use <a href="javascript:DoLink('{E622FBD9-9FA9-451A-A102-1800B5F28B6D}')">Molecule to CTAB</a> and <a href="javascript:DoLink('{7D354B65-DDD8-4EA4-83A7-21501A8A6852}')">Molecule from CTAB</a>.</li>
<li>Other related MDL format file readers include <a href="javascript:DoLink('{169AB4E5-A470-477B-AA65-50464411036C}')">RG Reader</a>, <a href="javascript:DoLink('{036731AA-0015-4606-9750-7D9D020F21C8}')">RXN Reader</a> and <a href="javascript:DoLink('{55431CCB-06EA-4741-B95B-633C877E3E9B}')">RD Reader</a>.</li>
</ul>
None
Molecule
Data fields in the SD file will be added to the property fields
None
Component Sticky Notes
The server version when this component was registered
6.1.0.11
Runtime Identifier
7
Location of the component in the database
Components\Chemistry\Readers\SD Reader
<p>The name of the property to hold the data record count. If the name begins with "@", this is a global property name and is updated each time a data record is received. Otherwise, it is a local property name and a new property by that name will be created on each data record and given the current value (i.e., the count).</p>
Start Index
Check if Property Already in Use
IndexB
The index (i.e., number) used to start the sequence.
1
Generates an error if the property already exists. This helps prevent overwriting data created by another component. Default is "True".
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
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
Component Attributes
ComponentTakesInput
ComponentReturnsPass
ComponentReturnsFail
ComponentRunsLocal
The user who registered this component.
scitegic/core
The date this component was registered.
Fri Sep 08 07:31:45 2006
GUID
{7BF3D951-BF75-70A2-8B2C-AD8909791909}
Display Name
Add index
Custom Error Message
Component Icon
COMPONENTNODE
The component this component is based upon.
Count and Index Data
Disabled
0
Component Point
363 -350
Fancy Help
100
Counts the number of data records and puts the count in a property
<p>Use this component to create a numerical index of data records and to keep track of the total number of records. The value of <i>Counter Property</i> is incremented each time a data record enters the component.</p>
<p>This component can be used in two modes:</p>
<ul>
<li>If <i>Counter Property</i> is the name of a local property (does not start with "@"), a new property by that name is created on each data record and given the value of the current count.</li>
<li>If <i>Counter Property</i> is the name of a global property (starts with "@"), then each data record that passes through causes this global record count to be incremented, but values are not added to the passing records.</li>
</ul>
Generic
Generic
None
The server version when this component was registered
6.0.0.44
Component Sticky Notes
Runtime Identifier
8
Location of the component in the database
Components\Generic\Calculators\Count and Index Data
</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
Hold original smiles
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
663 -350
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
9
Location of the component in the database
Components\Generic\Utilities\SubProtocol Utilities\Subprotocol
<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
88 -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
0:0
Location of the component in the database
Components\Chemistry\Calculators\Canonical Smiles
Molecular Formats
Molecular Formats
Property name to change
canonical_smiles
Name of the new property
original_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
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
0:1
GUID
{5A384E06-8AF2-4C10-A9B7-7302DD110A48}
Disabled
0
CustomErrorText
Component Point
363 -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