</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>
Names,Values
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 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 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
The component this component is based upon.
EmptyProtocol
The user who registered this component.
Ed
The date this component was registered.
Wed Sep 23 15:38:18 2009
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
Calculate Properties for StarDrop
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
{1169FDD0-72DA-4D89-B4CC-71826B125B3D}
Component Point
88 -50
By Ref
0
Fancy Help
100
Calculate a range of Pipeline Pilot properties (defined to be directly accesible from StarDrop)
This protocol servers as an example of how to contruct protocols that can be used directly from within StarDrop. This protocol takes an array of structures provided by StarDrop and carries out the following steps.
<ul>
<li>Removal of Duplicates
<li>Generation of 3D coordinates/minimisation
<li>Generation of properties
<li>Two webexports are generated: Names (name of each property calculated) and Values (values for each structure submitted)
</ul>
None
None
None
Runtime Identifier
0
Protocol Scale
75
Protocol Options
Make Shortcut by Default
Owner Access Only
Protocol Sticky Notes
%VERSION 3%
75 -400 1174 458
255 255 0
This protocol takes Smiles input from StarDrop and generates a range of descriptors, which it can return directly to StarDrop.
It requires Smiles input, which is defined as @Structure (click on desktop and check Parameters tab below), and exports @Names and @Values as webexports (click desktop then check Implementation tab below).
The server version when this component was registered
6.1.5.0
Location of the component in the database
Protocols\Web Services\StarDrop\Calculate Properties for StarDrop
Expression (or list of expressions separated by semi-colons) to evaluate.
Initial Expression
Final Expression
Keep Calculated Properties
Row := 0;
resize(@Names, 0);
resize(@Values, 0);
Size := NumValues(@Structure);
<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
0
Custom Error Message
Component Icon
EXPRESSIONNODE
Disabled
0
GUID
{0995D675-7EE2-432C-95DF-E91C14052B22}
Component Point
88 -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>
None
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)
Expression (or list of expressions separated by semi-colons) to evaluate.
Initial Expression
Final Expression
Keep Calculated Properties
Row++;
smiles := "";
smiles := @Structure[Row];
<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
1
Custom Error Message
Component Icon
EXPRESSIONNODE
Disabled
0
GUID
{0995D675-7EE2-432C-95DF-E91C14052B22}
Component Point
363 -50
Fancy Help
100
Applies a PilotScript expression to each data record
<p>PilotScript is the native scripting language in Pipeline Pilot. It is based on PL/SQL and allows you to query or alter the properties on data records. For example, the expression:
<blockquote>
<code>A := 10;</code>
</blockquote>
creates a property named "A" and sets the value to "10".</p>
<p>For each incoming data record the PilotScript statements in <i>Expression</i> are evaluated.</p>
<p><b>Notes:</b>
<ul>
<li>To initialize global variables such as counters, use <i>Initial Expression</i>.</li>
<li>To clean up global variables or calculate final results use <i>Final Expression</i>.</li>
<li>Parameters on Custom Manipulators do not become global variables that can be accessed via <i>@ParameterName</i> syntax and can only be accessed by token substitution via <i>$(ParameterName)</i> syntax.</li>
</ul>
<p><b>See Also:</b></p>
<ul>
<li>For more information on PilotScript, see <a href="javascript:DoLink('scihelpdocs/user/pscript/pscript_overview.htm')">PilotScript Overview</a>.</li>
<li>To use PilotScript to filter data records use <a href="javascript:DoLink('{DD58ECD1-516F-48FE-A5DB-8328AED680F2}')">Custom Filter (PilotScript)</a>.</li>
</ul>
Generic
Generic
None
The server version when this component was registered
6.1.0.17
Component Sticky Notes
Location of the component in the database
Components\Generic\Manipulators\Custom Manipulator (PilotScript)
The PilotScript expression used to filter the data.
Initial Expression
Final Expression
Keep Calculated Properties
smiles != ''
<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
663 -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
2
Location of the component in the database
Components\Generic\Filters\Custom Filter (PilotScript)
6.1.0.17
The name of the property in the data
which holds the SMILES information
KekulizeAromaticBonds
smiles
Turn aromatic bonds into single/double bonds (set to True) or into aromatic query bonds (set to False). Molecules created with aromatic query bonds are more suitable as queries than as specific molecules. They should not be used as input for property calculators such as Molecular Weight, pKa and others, which require the structure to be uniquely defined.
True
False
When an recoverable error occurs during processing:
Halt: Terminate the execution of the network
Fail: Continue execution of the network, passing data out the Fail(red) port
Pass: Continue execution of the network, passing data out the Pass(green) port
Halt
Fail
Pass
When an expected data type is not found during processing:
Halt: Terminate the execution of the network
Fail: Continue execution of the network, passing data out the Fail(red) port
Pass: Continue execution of the network, passing data out the Pass(green) port
Halt
Fail
Pass
Component Attributes
ComponentTakesInput
ComponentReturnsPass
ComponentReturnsFail
ComponentRunsLocal
Comment
Takes a Daylight SMILES string as text on a given property and converts the object into a SciTegic molecule using that information.
The user who registered this component.
scitegic/chemistry
The date this component was registered.
Thu Sep 07 14:22:46 2006
Component Usage
A molecular representation is built for each data record from the SMILES data found in the property list. *Note that if a molecular representation is already present, it will be overwritten by the new molecule.
Input - Data records
Output Pass - Molecular data records
Display Name
Molecule from SMILES
The component this component is based upon.
Molecule from SMILES
Component RunTimeID
3
Custom Error Message
Component Icon
COMPONENTNODE
GUID
{AC8262DA-E648-4D24-9CD1-D731A8F53F9D}
Component Point
938 -50
Disabled
0
Fancy Help
100
Converts a Daylight SMILES text property to a molecule
<p>Builds a molecular representation for each data record from the SMILES string found in the property list. If a molecular representation is already present, it is overwritten by the new molecule. The input SMILES string is preserved.</p>
<p><b>See Also:</b></p>
<ul>
<li>To create a string property containing SMILES data, use <a href="javascript:DoLink('{0C60C40A-5189-42DA-A3C0-4EA44BFF7D15}')">Molecule to SMILES</a> or <a href="javascript:DoLink('{0C60C40A-5189-42DA-A3C0-4EA44BC27D15}')">Canonical Smiles</a>.</li>
<li>To read and write SMILES files, use <a href="javascript:DoLink('{60FC1A04-61FD-4D4F-AC3F-A818AB614C78}')">SMILES Reader</a> and <a href="javascript:DoLink('{72A5A427-651F-4847-9525-54CB438A7166}')">SMILES Writer</a>.</li>
</ul>
Generic
Molecule
Molecular data record created from SMILES string
None
The server version when this component was registered
6.0.0.41
Component Sticky Notes
Location of the component in the database
Components\Chemistry\Converters\Molecule From Text\Molecule from SMILES
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 user who registered this component.
scitegic/chemistryadv
The date this component was registered.
Wed Sep 20 17:40:13 2006
Component Comment
Generates 3D coordinates for molecules.
Component Usage
Three-dimensional structural coordinates are calculated for each incoming molecular data record.
Input - Molecular data records
Output Pass - Molecular data records with generated 3D coordinates.
Display Name
3D Coordinates
Custom Error Message
Component Icon
COMPONENTNODE
GUID
{E145CB33-02C3-455E-94CC-F0FA0B88B2AC}
The component this component is based upon.
3D Coords
Disabled
0
Component Point
1238 -50
Fancy Help
100
Generates 3D coordinates for the input molecules.
This component calculates three-dimensional atomic coordinates for each incoming molecule. The calculated coordinates are assigned to the molecule, discarding any existing original coordinates, either 2D or 3D.
<p>
The coordinates are calculated by dividing the molecule into chains and ring systems, generating 3D coordinates for each fragment and putting them together. A few cycles or energy minimization are carried out at the end to clean up the structure and remove any bumps.
<p>
<b>See also:</b>
<li>To optimize the 3D coordinates to minimize the molecular energy, see <a href="javascript:DoLink('{FA683576-279B-429B-A1D1-D6B784A8FF8F}')">Minimize Molecule</a>.</li>
<li>To generate different 3D conformations of the molecule, see <a href="javascript:DoLink('{E88DC05D-6E85-40D2-933C-F49DABE0F3BA}')">3D Conformations</a>.</li>
</ul>
Molecule
Molecule
Molecules with 3D coordinates
None
The server version when this component was registered
6.0.1.0
Component Sticky Notes
Runtime Identifier
4
Location of the component in the database
Components\Chemistry\Manipulators\3D Methods\3D Coords
Identifies the values to store with a molecule:
<ul>
<li><b>Energy</b>: Energy of structure prior to minimization.</li>
<li><b>Minimized_Energy</b>: Energy of minimized structure.</li>
<li><b>Strain_Energy: Difference between the two.</li>
</ul>
MaximumNumberOfSteps
ConvergenceEnergyDifference
Energy
Minimized_Energy
Strain_Energy
The maximim number of minimization steps to perform.
1000
The energy difference between minimization steps required for convergence.
0.0001
Updates the molecular coordinates after minimization is calculated
True
False
Component Attributes
ComponentTakesInput
ComponentReturnsPass
ComponentReturnsFail
ComponentRunsLocal
When an recoverable error occurs during processing:
Halt: Terminate the execution of the network
Fail: Continue execution of the network, passing data out the Fail(red) port
Pass: Continue execution of the network, passing data out the Pass(green) port
Halt
Fail
Pass
When an expected data type is not found during processing:
Halt: Terminate the execution of the network
Fail: Continue execution of the network, passing data out the Fail(red) port
Pass: Continue execution of the network, passing data out the Pass(green) port
Halt
Fail
Pass
The user who registered this component.
scitegic/chemistryadv
The date this component was registered.
Wed Feb 28 13:08:54 2007
GUID
{FA683576-279B-429B-A1D1-D6B784A8FF8F}
Comment
Uses the Clean force-field to generate energy minimized coordinates for the molecules, starting at the current coordinates, if any.
Component Usage
Minimized coordinates and energy values are calculated and added to the property list of a molecule.
Input - Molecular data records
Output Pass - Molecular data records with minimized coordinates.
Display Name
Minimize Molecule
The component this component is based upon.
Minimize
Component RunTimeID
5
Custom Error Message
Component Icon
COMPONENTNODE
Disabled
0
Component Point
1538 -50
Fancy Help
100
Generates energy minimized coordinates for each input molecule
Uses the Clean force-field to generate minimized coordinates for the input molecules. The property <b>Minimized_Energy</b>, with the value of the energy at the end of the minimization, is added to the property list of each molecule.
<p>
<strong>Notes:</strong>
<ul>
<li>Minimization starts from the current 3D coordinates, if there are any present on the input molecule. If the molecule has no 3D coordinates, an initial 3D conformation is generated and minimized.</li>
<li>The Clean force field used in the minimization is described in "Receptor Surface Models. 1. Definition and Construction". Mathew Hahn; <i>J. Med. Chem.</i>; 1995; <b>38(12)</b>; 2080-2090. </li>
</ul>
<p><b>See Also:</b><p>
<ul>
<li>To generate 3D conformations, see <a href="javascript:DoLink('{E88DC05D-6E85-40D2-933C-F49DABE0F3BA}')">3D Conformations</a>. </li>
</ul>
Molecule
Molecule
Minimized molecules with minimized energy values added
None
Component Sticky Notes
The server version when this component was registered
6.1.0.8
Location of the component in the database
Components\Chemistry\Manipulators\3D Methods\Minimize Molecule
Molecular Properties
Molecular Properties
Molecular Properties
pH value to use in the calculation of the ionization state.
7.4
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
1813 -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
6
Location of the component in the database
Components\Chemistry\Manipulators\Ionize Molecule at pH
ALogP molecule-level properties to calculate. Available properties are:
<ul>
<li><b>ALogP</b>: The Ghose and Crippen octanol-water partition coefficient.</li>
<li><b>ALogP_MR</b>: The Ghose and Crippen estimate of molar refractivity.</li>
<li><b>ALogP_Count</b>: An array of 120 numbers that correspond to the 120 Ghose and Crippen atom types. The content of each array element is the number of times that particular atom type was seen in the molecule</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.
ALogP
ALogP_MR
ALogP_Count
These properties are defined for each atom and are stored in the atom property list. <i>Atom Properties Output</i> specifies which atom-level properties to calculate:
<ul>
<li><b>ALogP_AtomClass</b>: Integer with the Ghose and Crippen atom type assigned to the atom, a number from 1 to 120.</li>
<li><b>ALogP_AtomClassName</b>: String describing the Ghose and Crippen atom type assigned to the atom (example: "C in CH2R2").</li>
<li><b>ALogP_AtomScore</b>: atomic contribution to the total value of ALogP.</li>
<li><b>ALogP_AtomMRScore</b>: atomic contribution to the total value of AMR.</li>
</ul>
<p>
The <i>Atom Properties</i> component is available for manipulation of atom properties downstream.
ALogP_AtomClass
ALogP_AtomClassName
ALogP_AtomScore
ALogP_AtomMRScore
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
True
False
The user who registered this component.
scitegic/chemistry
The date this component was registered.
Wed Sep 06 08:53:32 2006
GUID
{F211E9F5-7052-4E5B-9D8D-E234D6EEE41C}
Parameter Help
1989
1989B
1998
Parameter Help
True
False
Whether to identify and ionize molecules with both carboxylic acid and amine groups
True
False
Comment
Calculates the Ghose/Crippen group-contribution estimate for LogP, where P is the relative solubility of a compound in oil (actually, octanol) vs. water.
Component Usage
This component can calculate:
ALogP: the Ghose/Crippen group-contribution estimate for LogP, where P is the relative solubility of a compound in oil (actually, octanol) vs. water.
ALogP_MR: the Ghose/Crippen estimate of molar refractivity, which contains information about molecular volume and polarizability of a compound.
ALogP_Count: returns an array of 120 numbers, which correspond to the 120 Ghose/Crippen atom types. The content of each array element is the number of atoms in the molecule of that particular atom type.
Input - Molecule data records
Output Pass - Molecule data records augmented with selected properties
Display Name
ALogP
The component this component is based upon.
ALogP
Disabled
0
Custom Error Message
Component Icon
CALCULATORNODE
Component Point
2113 -50
Fancy Help
100
Calculates LogP and Molar Refractivity by the Ghose and Crippen method
<p>
This component uses the atom-based method published by Ghose and Crippen to calculate the octanol-water partition coefficient (LogP), and the molar refractivity (MR) for the incoming molecules. LogP provides a measure of the hydrophobicity of the molecule, while MR contains information about molecular volume and polarizability.
</p>
<i>Output</i> specifies which molecule-level properties to calculate and output for each data record:
<ul>
<li><b>ALogP</b>: The Ghose and Crippen octanol-water partition coefficient.</li>
<li><b>ALogP_MR</b>: The Ghose and Crippen estimate of molar refractivity.</li>
<li><b>ALogP_Count</b>: An array of 120 numbers that correspond to the 120 Ghose and Crippen atom types. The content of each array element is the number of times that particular atom type was seen in the molecule</li>
</ul>
<p>
<b>Notes:</b>
<ul>
<li>This component also calculates atom-level properties. These properties are defined for each atom and are stored in the atom property list. <i>Atom Properties Output</i> specifies which atom-level properties to calculate.</li>
<li>For more information on the ALogP method see Ghose, A.K., Viswanadhan V.N., and Wendoloski, J.J., Prediction of Hydrophobic (Lipophilic) Properties of Small Organic Molecules Using Fragment Methods: An Analysis of AlogP and CLogP Methods. J. Phys. Chem. A, 1998, 102, 3762-3772.</li>
</ul>
<p>
<b>See Also:</b>
<li>To manipulate atomic properties see <a href="javascript:DoLink('{B380D0B9-62F9-4b2a-83AE-EEB9465E3F67}')">Atom Properties</a>.</li>
<li>To calculate LogD, the octanol-water partition coefficient calculated taking into account the ionization states of the molecule, see <a href="javascript:DoLink('{DDDB7E61-D653-45e8-9564-39FB67159FD4}')">logD</a>.</li>
</ul>
Molecule
Molecule
Records augmented with the selected property or properties.
None
The server version when this component was registered
6.0.0.44
Component Sticky Notes
Runtime Identifier
7
Location of the component in the database
Components\Chemistry\Calculators\ALogP
AlogP
AlogP
AlogP
Select the E-state properties to output:
<ul>
<li><b>Estate_Keys_Properties</b>: Calculate the E-state sums for all atom types and output them as individual properties.</li>
<li><b>Estate_Counts_Properties</b>: Calculate the E-state counts for all atom types and output them as individual properties.</li>
<li><b>Estate_Keys</b>: Calculate the E-state sums for all atom types and output them in one property as an array of double values.</li>
<li><b>Estate_Counts</b>: Calculate the E-state counts for all atom types and output them in one property as an array of integer values.</li>
<li><b>Estate_NumUnknown</b>: Output the number of atoms that could not be classified into an E-state atom type.</li>
</ul>
OnlyOrganicsAndHalogens
AddEstateValuesToAtoms
Estate_Keys_Properties
Estate_Counts_Properties
Estate_Keys
Estate_Counts
Estate_NumUnknown
Toggles whether to calculate E-state key descriptors only for organic elements (C, N, O, P, S) and halogens (F, Cl, Br, I).
True
False
Toggles the display of the E-state type and value for each atom in the 2D picture of the molecule as the atom label.
True
False
When an recoverable error occurs during processing:
Halt: Terminate the execution of the network
Fail: Continue execution of the network, passing data out the Fail(red) port
Pass: Continue execution of the network, passing data out the Pass(green) port
Halt
Fail
Pass
When an expected data type is not found during processing:
Halt: Terminate the execution of the network
Fail: Continue execution of the network, passing data out the Fail(red) port
Pass: Continue execution of the network, passing data out the Pass(green) port
Halt
Fail
Pass
Component Attributes
ComponentTakesInput
ComponentReturnsPass
ComponentReturnsFail
ComponentRunsLocal
Comment
Calculates the 3D volume for each molecule using the current 3D coordinates. Fails if there are no 3D coordinates for the molecule.
The user who registered this component.
scitegic/chemistry
The date this component was registered.
Wed Jul 21 10:12:26 2004
Component Usage
Calculates the 3D volume for each molecule using the current 3D coordinates and store the total in the property called Molecular_Volume.
Input - Molecule data records
Output Pass - Molecule data records augmented with Molecular_Volume
Display Name
E-state Keys
The component this component is based upon.
Molecular Volume
Custom Error Message
Component Icon
CALCULATORNODE
GUID
{BA0A633D-6BD0-474B-B50B-24BA38735FA6}
Component Point
2388 -50
Disabled
0
Fancy Help
100
Calculates the Electrotopological State keys for the molecule
<p>Calculates the sums of the Electrotopological State (E-state) values and/or the counts of each atom type. The output can be as a number of
individual properties, one for each atom type, or as a single property with an array of values. The type of output is controlled
by <i>What to Output</i>:</p>
<ul>
<li><b>Estate_Keys_Properties</b>: Calculate the E-state sums for all atom types and output them as individual properties.</li>
<li><b>Estate_Counts_Properties</b>: Calculate the E-state counts for all atom types and output them as individual properties.</li>
<li><b>Estate_Keys</b>: Calculate the E-state sums for all atom types and output them in one property as an array of double values.</li>
<li><b>Estate_Counts</b>: Calculate the E-state counts for all atom types and output them in one property as an array of integer values.</li>
<li><b>Estate_NumUnknown</b>: Output the number of atoms that could not be classified into an E-state atom type.</li>
</ul>
<p>E-state keys are calculated for organic elements (C, N, O, P, S), halogens (F, Cl, Br, and I) and for Li, Be, B, Si, Ge, As, Se, Sn, and Pb.</p>
<b>See Also:</b>
<ul>
<li>The Electrotopological State (E-State) descriptors calculated by this component are defined by Kier and Hall:
<ul>
<li>Hall L., Mohney B., Kier L., <i>J. Chem. Inf. Comput. Sci.</i>, 1991, <b>31</b>, 76-82.</li>
<li>Hall L., Kier L., <i>J. Chem. Inf. Comput. Sci.</i>, 2000, <b>40</b>, 784-791).</li>
</ul>
</li>
</ul>
Molecule
Molecule
Records augmented with the E-State properties
None
Component Sticky Notes
The server version when this component was registered
4.1.1.200
Runtime Identifier
8
Location of the component in the database
Components\Chemistry\Calculators\E-state Keys
Select the property or properties to create. The element type is the first part of the name, followed by the string "_Count".
<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.
H_Count
He_Count
Li_Count
Be_Count
B_Count
C_Count
N_Count
O_Count
F_Count
Ne_Count
Na_Count
Mg_Count
Al_Count
Si_Count
P_Count
S_Count
Cl_Count
Ar_Count
K_Count
Ca_Count
Sc_Count
Ti_Count
V_Count
Cr_Count
Mn_Count
Fe_Count
Co_Count
Ni_Count
Cu_Count
Zn_Count
Ga_Count
Ge_Count
As_Count
Se_Count
Br_Count
Kr_Count
Rb_Count
Sr_Count
Y_Count
Zr_Count
Nb_Count
Mo_Count
Tc_Count
Ru_Count
Rh_Count
Pd_Count
Ag_Count
Cd_Count
In_Count
Sn_Count
Sb_Count
Te_Count
I_Count
Xe_Count
Cs_Count
Ba_Count
La_Count
Ce_Count
Pr_Count
Nd_Count
Pm_Count
Sm_Count
Eu_Count
Gd_Count
Tb_Count
Dy_Count
Ho_Count
Er_Count
Tm_Count
Yb_Count
Lu_Count
Hf_Count
Ta_Count
W_Count
Re_Count
Os_Count
Ir_Count
Pt_Count
Au_Count
Hg_Count
Tl_Count
Pb_Count
Bi_Count
Po_Count
At_Count
Rn_Count
Fr_Count
Ra_Count
Ac_Count
Th_Count
Pa_Count
U_Count
Np_Count
Pu_Count
Am_Count
Cm_Count
Bk_Count
Cf_Count
Es_Count
Fm_Count
Md_Count
No_Count
Lr_Count
Z_Count
R_Count
X_Count
Q_Count
A_Count
AA_Count
NN_Count
*_Count
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
Comment
Counts the atoms of each of the selected element types. (Note: Use advanced parameters to return the total number of atoms using a list of element types.)
The user who registered this component.
scitegic/chemistry
The date this component was registered.
Wed Jul 21 10:12:26 2004
Component Usage
The user selects the element count type from a pulldown list. The number
of atoms with those atom types are then calculated and returned. (For a count of all atoms, use Molecule Property Counts to calculate Num_Atoms).
Input - Molecule data records
Output Pass - Molecule data records augmented with selected properties
ADVANCED PROPERTIES
'Elements' is a list of element names, and is an alternate way of specifying the list of outputs.
'Total' is the name of a property into which the total of all elements in the list is put. It turns off the output of the individual atoms in the Elements list.
'NotList' specifies whether the Elements list is the list for the total, or is the list of elements *not* to count. For example, inorganic count may give an element list of C,N,O,F,S,P,Cl,Br,I, and set NotList to True, and set Total to Inorganic_Count.
Display Name
Element Count
The component this component is based upon.
Atom Count
Custom Error Message
Component Icon
CALCULATORNODE
Disabled
0
GUID
{2F7D3B2D-981B-4BE7-8571-2E40024480E2}
Component Point
2688 -50
Fancy Help
100
Calculates the number of atoms of specified element types
<p>Each count is created as a separate property. The format of each property name is <b>xx_Count</b>, where the "xx" is replaced by the one- or two-character element type string.</p>
<b>See Also:</b>
<ul>
<li>To create properties containing counts of more than one element type, see <a href="javascript:DoLink('{2F7D3B2D-981B-DDDF-8571-2E40024480E2}')">Element Count (Advanced)</a>.</li>
</ul>
Molecule
Any molecular data
Molecule
Records augmented with properties for the requested atom counts
None
The server version when this component was registered
4.1.1.200
Component Sticky Notes
Runtime Identifier
9
Location of the component in the database
Components\Chemistry\Calculators\Element Count
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Element Counts
Outputs the logD
pH
logD
pH value(s) for the calculation of logD.
Input can be a single pH value or a comma-separated set of values. The output for a single pH value is named 'LogD#pH', except when the pH is equal to the default value of 7.4, in which case the name is 'LogD'.
The output for multiple pH values is an array of logD values, with the pH values indicated in the name: 'LogD#pH1,pH2,pH3,pH4,...'
7.4
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
True
False
True
False
0.85
True
False
4
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
Predict pKas
Comment
Calculates pKa values for the molecule.
The user who registered this component.
scitegic/chemistryadv
The date this component was registered.
Wed Nov 01 15:27:24 2006
Component Usage
Use this component to calculate pKa values.
Input - Molecule data records
Output Pass - Molecule data records augmented with pKa data
Display Name
logD
The component this component is based upon.
PKA
Custom Error Message
Component Icon
CALCULATORNODE
GUID
{DDDB7E61-D653-45e8-9564-39FB67159FD4}
Component Point
2963 -50
Disabled
0
Fancy Help
100
Calculates logD for the input molecules
This component calculates the value of logD, the octanol-water partition coefficient calculated taking into account the ionization states of the molecule.
<p>
The name of the output property depends on the value specified for the <i>pH</i> parameter. For pH equals to the default value of 7.4, logD is output as <b>logD</b>. For pH set to any other single value, logD is output as <b>logD#pH</b>, where 'pH' is the pH value. For pH set as a comma-delimited list of values, logD consists of an array of values, one for each pH, and the name of the property is set to <b>logD#pH1,pH2,pH3...</b>, where 'pH1,pH2,pH3' are the pH values.
<p>
<strong>Notes: </strong></p>
<ul>
<li>The logD calculation utilizes pKa information for each atom in the molecule. Pka sites are located based on the molecular query files located in "data/pKa/AcidBaseSites/". Pka values are calculated based on site examples files located in "data/pKa/Data/" and on PLS Models located in "data/pKa/Models".</li>
<li>The AlogP method is used to calculate the logP of each specie.</li>
</ul>
<p>
<strong>See Also: </strong></p>
<ul>
<li>
<a href="javascript:DoLink('{A09482AD-1A24-4a94-B050-43CEF82DE630}')">pKa</a> for calculation of pKa information for each atom in the molecule</li>
<li>
<a href="javascript:DoLink('{72D1AEC5-EE9E-4a39-A3D6-63637069BF6E}')">Ionize Molecule at pH</a> to transform the molecule according to the calculated pKa values</li>
<li>
<a href="javascript:DoLink('{B07C705E-49AC-4d54-887F-E4CE2DABA42D}')">Enumerate Ionization States</a> to enumerate all the possible ionization states of the molecule based on the pKa values and the pH range</li>
<li>For details on the pKa and logD calculations, see
<a href="javascript:DoLink('sciapps/scitegic/chemistryadv/docs/chemistry_two.pdf')">pKa Calculation User Guide</a>
</li>
</ul>
Molecule
Input molecules
Molecule
Molecules augmented with logD data
None
The server version when this component was registered
6.0.1.7
Component Sticky Notes
Runtime Identifier
10
Location of the component in the database
Components\Chemistry\Calculators\logD
Molecular Properties
<ul>
<li><b>Energy</b>: Gives the energy of the molecule's current 3D conformation.</li>
<li><b>Minimized_Energy</b>: Gives the energy after a fast minimization procedure.</li>
<li><b>Strain_Energy</b>: Gives the point strain energy. Strain_Energy is the difference between Energy and Minimized_Energy</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.
Energy
Minimized_Energy
Strain_Energy
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 the energy of a molecule, either in its current configuration or after a rapid minimization procedure. Uses a variant of the published clean force-field.
The user who registered this component.
scitegic/chemistry
The date this component was registered.
Thu Sep 07 14:22:17 2006
Component Usage
Select the desired property or properties from the list. 'Energy' gives the energy of the molecule's current 3D conformation. 'Minimized_Energy' gives the energy after a fast minimization procedure. 'Strain_Energy' gives the point strain energy.
Input - Molecule data records
Output Pass - Molecule data records augmented with selected properties
Display Name
Molecular Energy
The component this component is based upon.
Molecular Energy
Custom Error Message
Component Icon
CALCULATORNODE
GUID
{F88508BA-C363-4032-B52C-0A2299BCE130}
Component Point
3263 -50
Disabled
0
Fancy Help
100
Calculates the energy of the input molecules
<p>The molecular energy is based on the input coordinates or the coordinates resulting from a rapid minimization that uses a variant of the published Clean force-field. The input molecules require 3D coordinates.
<p>
Three properties may be output:</p>
<ul>
<li><b>Energy</b>: Gives the energy of the molecule's current 3D conformation.</li>
<li><b>Minimized_Energy</b>: Gives the energy after a fast minimization procedure.</li>
<li><b>Strain_Energy</b>: Gives the point strain energy. Strain_Energy is the difference between Energy and Minimized_Energy</li>
</ul>
<p><b>Note: </b></p>
<ul>
<li>Details of the Clean force field can be found in "Receptor Surface Models. 1. Definition and Construction", Mathew Hahn; <i>J. Med. Chem.</i>; 1995; <b>38(12)</b>; 2080-2090.</li>
</ul>
<p><b>See Also:</b></p>
<ul>
<li>To minimize structures using the Clean force-field use <a href="javascript:DoLink('{FA683576-279B-429B-A1D1-D6B784A8FF8F}')">Minimize Molecule</a>.</li>
</ul>
Molecule
Molecule
Molecular data records augmented with the selected properties.
None
The server version when this component was registered
6.0.0.41
Component Sticky Notes
Runtime Identifier
11
Location of the component in the database
Components\Chemistry\Calculators\Molecular Energy
Molecular Properties
Molecular Properties
Molecular Properties
Selects which property(-ies) to calculate
FormalCharge
CoordDimension
IsChiral
BondDistance_Table
AverageBondLength
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
Contains a number of whole-molecule properties so you do not have to work with numerous separate components.
The user who registered this component.
scitegic/chemistry
The date this component was registered.
Wed Nov 01 10:13:50 2006
Component Usage
Select any of the counts in the 'Output' pulldown list for calculation. The data is augmented with these properties.
Input - Molecule data records
Output Pass - Molecule data records augmented with selected properties
Display Name
Molecular Properties
The component this component is based upon.
Molecular Property Counts
Custom Error Message
Component Icon
CALCULATORNODE
GUID
{3BE0BDC7-53C5-421d-892A-B02A82410FD5}
Component Point
3538 -50
Disabled
0
Fancy Help
100
Calculates whole-molecule properties that are not explicitly "counts"
This component calculates the following molecular properties:
<ul>
<li><b>FormalCharge</b>: The total formal charge of the molecule.</li>
<li><b>CoordDimension</b>: Flag that indicates the type of X,Y,Z coordinates present in the molecule. Possible values are 0 (all coordinates are zero), 2 (2D structure, only X and Y coordinates are defined), and 3 (3D structure, X, Y and Z coordinates are defined).</li>
<li><b>IsChiral</b>: Flag to indicate whether the molecule exists only in the represented absolute stereo configuration (value equals 1) or as a pair of enantiomers (value equals 0). This flag mirrors the Chiral flag in the MDL CTAB format.</li>
<li><b>BondDistance_Table</b>: Calculates the number of bonds in the shortest path between each pairs of atoms in the molecule. The results are output as an array of strings representing the atom-atom distance matrix.</li>
<li><b>AverageBondLength</b>: Calculates the average bond length for the molecule based on the atomic coordinates.</li>
</ul>
<p>
<b>See also:</b>
<ul>
<li>To calculate molecular properties that can be defined as "counts", see <a href="javascript:DoLink('{74147AAA-1C18-4308-9899-EB7896C88DBE}')">Molecular Property Counts</a>.</li>
</ul>
Molecule
Input molecules
Molecule
Records augmented with the specified property or properties
None
The server version when this component was registered
6.0.1.7
Component Sticky Notes
Runtime Identifier
12
Location of the component in the database
Components\Chemistry\Calculators\Molecular Properties
Molecular Properties
Molecular Properties
Molecular Properties
Molecular Properties
Molecular Properties
<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.
Num_Atoms
Num_Bonds
Num_Hydrogens
Num_ExplicitHydrogens
Num_PositiveAtoms
Num_NegativeAtoms
Num_RingBonds
Num_RotatableBonds
Num_AromaticBonds
Num_BridgeBonds
Num_Rings
Num_AromaticRings
Num_RingAssemblies
Num_Rings3
Num_Rings4
Num_Rings5
Num_Rings6
Num_Rings7
Num_Rings8
Num_Rings9Plus
Num_Chains
Num_ChainAssemblies
Num_Fragments
Num_StereoAtoms
Num_StereoBonds
Num_UnknownStereoAtoms
Num_UnknownStereoBonds
Num_TrueStereoAtoms
Num_UnknownTrueStereoAtoms
Num_AtomClasses
Num_Macro_Chains
Num_Macro_Residues
Num_TerminalRotomers
Num_SpiroAtoms
Num_BridgeHeadAtoms
Num_MetalAtoms
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
Contains a number of whole-molecule properties so you do not have to work with numerous separate components.
The user who registered this component.
scitegic/chemistry
The date this component was registered.
Thu Sep 07 14:22:22 2006
Component Usage
Select any of the counts in the 'Output' pulldown list for calculation. The data is augmented with these properties.
Input - Molecule data records
Output Pass - Molecule data records augmented with selected properties
Display Name
Molecular Property Counts
The component this component is based upon.
Molecular Property Counts
Custom Error Message
Component Icon
CALCULATORNODE
GUID
{74147AAA-1C18-4308-9899-EB7896C88DBE}
Component Point
3838 -50
Disabled
0
Fancy Help
100
Calculates counts of molecular features
<p></i>Output</i> specifies which molecular features are counted. Each selection creates a property on the output data record. This component is more efficient than using a consecutive series of individual property calculators.</p>
<p><b>See Also:</b></p>
<ul>
<li>For information on which molecular features can be counted, see the User Guide help topic for <a href="javascript:DoLink('sciapps/scitegic/chemistry/docs/chemistry_one.pdf')">Molecular Property Counts</a>.</li>
</ul>
Molecule
Molecule
Records augmented with the required property or properties
None
The server version when this component was registered
6.0.0.41
Component Sticky Notes
Runtime Identifier
13
Location of the component in the database
Components\Chemistry\Calculators\Molecular Property Counts
Molecular Property Counts
Molecular Property Counts
Molecular Property Counts
Molecular Property Counts
Molecular Property Counts
Molecular Property Counts
Molecular Property Counts
Molecular Property Counts
Molecular Property Counts
Molecular Property Counts
Molecular Property Counts
Molecular Property Counts
Molecular Property Counts
Molecular Property Counts
Molecular Property Counts
Molecular Property Counts
Molecular Property Counts
Molecular Property Counts
Molecular Property Counts
Molecular Property Counts
Molecular Property Counts
Molecular Property Counts
Molecular Property Counts
Molecular Property Counts
Molecular Property Counts
Molecular Property Counts
Molecular Property Counts
Molecular Property Counts
Molecular Property Counts
Molecular Property Counts
Molecular Property Counts
Molecular Property Counts
Molecular Property Counts
Molecular Property Counts
Molecular Property Counts
Molecular Property Counts
The following properties are available for calculation:
<ul>
<li><b>Molecular_Weight</b>: The sum of the atomic masses with the isotope average used for each atomic mass.</li>
<li><b>Molecular_Mass</b>: The sum of the atomic masses with the most common isotope is used for each atomic mass.</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.
Molecular_Weight
Molecular_Mass
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 the molecular weight of the atomic weights of the individual atoms in the molecule and the molecular mass of the sum of the atomic weights, using the most common isotope.
The user who registered this component.
scitegic/chemistry
The date this component was registered.
Tue Oct 31 08:18:26 2006
Component Usage
Calculates the molecular weight for each molecule and store it in the property called Molecular_Weight.
Input - Molecule data records
Output Pass - Molecule data records augmented with Molecular_Weight
Display Name
Molecular Weight
The component this component is based upon.
Molecular Weight
Custom Error Message
Component Icon
CALCULATORNODE
GUID
{4706C7A2-77DA-4BBF-AEFA-E0D6F4269688}
Component Point
4113 -50
Disabled
0
Fancy Help
100
Calculates the molecular weight and/or molecular mass
The following <i>Output</i> properties are available for calculation:
<ul>
<li><b>Molecular_Weight</b>: The sum of the atomic masses with the isotope average used for each atomic mass.</li>
<li><b>Molecular_Mass</b>: The sum of the atomic masses with the most common isotope is used for each atomic mass.</li>
</ul>
Molecule
Molecule
Records augmented with the calculated properties
None
Runtime Identifier
14
Location of the component in the database
Components\Chemistry\Calculators\Molecular Weight
6.0.1.7
Molecular Properties
Molecular Properties
Selects Hydrogen bond acceptors and/or donors
<p>
<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.
Num_H_Acceptors
Num_H_Donors
Num_H_Acceptors_Lipinski
Num_H_Donors_Lipinski
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
Provides a very fast, approximate estimate of the number of hydrogen acceptors and donors. A hydrogen-bond acceptor is an oxygen or nitrogen with a lone pair of electrons. A hydrogen-bond donor is an oxygen or nitrogen with a hydrogen on it.
The user who registered this component.
scitegic/chemistry
The date this component was registered.
Mon Mar 19 12:17:07 2007
Component Usage
Select either of the counts in the 'Output' pulldown list for calculation. The data is augmented with these properties, which are a rapid calculation
of the number of hydrogen bond acceptors or donors.
Input - Molecule data records
Output Pass - Molecule data records augmented with selected properties
Display Name
Num H Acceptor Donors
The component this component is based upon.
Num H AcceptorDonors
Custom Error Message
Component Icon
CALCULATORNODE
GUID
{875D442D-7C3B-4E94-9E40-DA4C84BB7FB9}
Component Point
4413 -50
Disabled
0
Fancy Help
100
Calculates the number of hydrogen acceptors and/or donors.
Calculates and outputs the counts of hydrogen bond donors and acceptors in the input molecules. Two properties can be calculated:
<ul>
<li><b>Num_H_Acceptors</b>: number of heteroatoms (Oxygen, Nitrogen, Sulfur, or Phosphorus) with one or more lone pairs, excluding atoms with positive formal charges, amide and pyrrole-type Nitrogens, and aromatic Oxygen and Sulfur atoms in heterocyclic rings.</li>
<li><b>Num_H_Donors</b>: number of heteroatoms (Oxygen, Nitrogen, Sulfur, or Phosphorus) with one or more attached Hydrogen atoms.</li>
<li><b>Num_H_Acceptors_Lipinski</b>: number of acceptors using Lipinski's simpler convention of counting all Oxygen and Nitrogen atoms as acceptors.</li>
<li><b>Num_H_Donors_Lipinski</b>: the number of OH and NH bonds. Note that primary amines count as two donors.</li>
</ul>
<p>
<b>Note:</b>
<ul>
<li>The calculable properties <i>HBA_Count</i> and <i>HBD_Count</i>, available for use in PilotScript expressions, are defined differently that the properties calculated by this component. They are calculated using substructure queries to count the number of times the queries match structural features in the molecule. The substructure queries used to calculate these properties are present in the data/Queries folder:
<ul>
<li><i>Acceptors</i>: HBA-Nitrogen.mol, HBA-Carboxylate.mol, HBA-Ester.mol, HBA-Ether.mol, HBA-Carbonyl.mol, HBA-Phenol.mol</li>
<li><i>Donors</i>: HBD-PrimaryAlcohol.mol, HBD-PrimaryAmine.mol, HBD-SecondaryAlcohol.mol, HBD-SecondaryAmine.mol, HBD-TertiaryAmine.mol</li>
</ul>
Users can change the way hydrogen bond donors and acceptors are counted by adding their own definitions. The only constraint is that the file names should start with the prefix HBA- or HBD-
</li>
</ul>
Molecule
Molecule
Records augmented with the calculated properties.
None
The server version when this component was registered
6.1.0.11
Component Sticky Notes
Runtime Identifier
15
Location of the component in the database
Components\Chemistry\Calculators\Num H AcceptorDonors
Molecular Property Counts
Molecular Property Counts
Molecular Property Counts
Molecular Property Counts
<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.
Molecular_Solubility
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 the aqueous Solubility, expressed as logS, where S is the solubility in mol/L.
The user who registered this component.
scitegic/chemistry
The date this component was registered.
Thu Sep 07 14:22:26 2006
Component Usage
Calculates the aqueous Solubility, expressed as logS, where S is the solubility in mol/L, and stores the value in the property called Solubility.
Input - Molecule data records
Output Pass - Molecule data records augmented with Solubility
Display Name
Solubility
The component this component is based upon.
Solubility
Custom Error Message
Component Icon
CALCULATORNODE
GUID
{A6B26860-8671-44BD-B1DA-24AF02A0458A}
Component Point
4688 -50
Disabled
0
Fancy Help
100
Calculates aqueous solubility
<p>Outputs <b>Molecular_Solubility</b> expressed as logS, where S is the solubility in mol/L.</p>
<b>Note:</b>
<ul>
<li>The method used to estimate the solubility is the published multiple linear regression model: "Estimation of Aqueous Solubility of Chemical Compounds Using E-State Indices" by Tetko <i>et al.</i>, <i>J Chem Inf. Comput. Sci</i>, 2001, <b>41</b>, 1488-1493.</li>
</ul>
Molecule
Molecule
None
The server version when this component was registered
6.0.0.41
Component Sticky Notes
Runtime Identifier
16
Location of the component in the database
Components\Chemistry\Calculators\Solubility
Molecular Properties
<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.
PolarAtoms
Molecular_SurfaceArea
Molecular_PolarSurfaceArea
Molecular_FractionalPolarSurfaceArea
Molecular_SASA
Molecular_PolarSASA
Molecular_FractionalPolarSASA
Molecular_Volume
Molecular_SAVol
Select the atoms to be considered polar in the calculation of Molecular_PolarSurfaceArea and Molecular_PolarSASA.
The default setting is to select N, O, P, and S as polar. If a different setting is selected, the selected polar atoms will be appended to the property name. For example, the property name when selecting only N and O as polar atoms will be Molecular_PolarSurfaceArea#NO and Molecular_PolarSASA#NO.
N
O
P
S
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 surface area and volume properties for each molecule
The user who registered this component.
scitegic/chemistry
The date this component was registered.
Mon Oct 30 13:29:22 2006
Component Usage
Calculates surface area and volume properties for each molecule
Input - Molecule data records
Output Pass - Molecule data records augmented with Molecular_SurfaceArea and Molecular_PolarSurfaceArea
Display Name
Surface Area and Volume
The component this component is based upon.
Molecular Volume
Custom Error Message
Component Icon
CALCULATORNODE
GUID
{5D1413B8-2FAB-4C85-AB2E-240CC4AAA1CC}
Component Point
4988 -50
Disabled
0
Fancy Help
100
Calculates surface area, polar surface area (PSA) and volume properties for each molecule.
<p>Calculates one or more of the following:</p>
<ul>
<li><b>Molecular_SurfaceArea</b>: Calculates the total surface area for each molecule using a 2D approximation.</li>
<li><b>Molecular_PolarSurfaceArea</b>: Calculates the polar surface area for each molecule using a 2D approximation.</li>
<li><b>Molecular_FractionalPolarSurfaceArea</b>: The ratio of the polar surface area divided by the total surface area.</li>
<li><b>Molecular_Volume</b>: Calculates the 3D volume for each molecule using the current 3D coordinates. The component will fail if there are no 3D coordinates for the molecule. The <i>3D Coords</i> and/or <i>Minimize Molecule</i> components can be used prior to the molecular volume calculation if no 3D coordinates are present for the molecules on the input stream. </li>
<li><b>Molecular_SASA</b>: Calculates the total solvent accessible surface area for each molecule using a 2D approximation.</li>
<li><b>Molecular_PolarSASA</b>: Calculates the polar solvent accessible surface area for each molecule using a 2D approximation. The polar solvent accessible surface area is defined as the sum of the solvent accessible surface area of all the selected polar elements, which can include N, O, P, and S.</li>
<li><b>Molecular_FractionalPolarSASA</b>: The ratio of the polar solvent accessible surface area divided by the total solvent accessible surface area.</li>
<li><b>Molecular_SAVol</b>: Calculates the solvent accessible volume for each molecule using a 2D approximation.</li>
</ul>
<p><b>Notes: </b></p>
<ul>
<li>Solvent accessible surface area and solvent accessible volume are calculated assuming a solvent probe radius of 1.4 Angstroms.</li>
<li>The Molecular_SurfaceArea and Molecular_PolarSurfaceArea descriptors are calculated using a method based on the published method: "Fast calculation of molecular polar surface area as a sum of fragment based contributions and its application to the prediction of drug transport properties", Ertl, P., Rohde, B., Selzer, P., <i>J. Med. Chem.</i> 2000, <b>43</b>, 3714-3717.</li>
<li>The solvent-accessible surface area descriptors measure the surface area exposed to a solvent probe. It is based on a 2D approximation which uses models parameterized to reproduce the results obtained with a full 3D calculation using a dot-based method similar to the one originally described in: "Environment and exposure to solvent of protein atoms, lysozyme and insulin", Shrake, A. and Rupley, J.A., <i>J. Mol. Biol.</i>, <b>79</b>, 351-371, 1973. </li>
</ul>
<p><b>See Also:</b></p>
<ul>
<li>To quickly generate 3D coordinates for a molecule, use the <a href="javascript:DoLink('{E145CB33-02C3-455E-94CC-F0FA0B88B2AC}')">3D Coords</a> or <a href="javascript:DoLink('{E88DC05D-6E85-40D2-933C-F49DABE0F3BA}')">3D Conformations</a> components.</li>
<li>To generate 3D coordinates using the Clean force-field, use the <a href="javascript:DoLink('{FA683576-279B-429B-A1D1-D6B784A8FF8F}')">Minimize Molecule</a> component.
<li>For more details see the User Guide Help topic <a href="javascript:DoLink('sciapps/scitegic/chemistry/docs/chemistry_one.pdf')">Molecular Surface Area</a>.
</li>
</ul>
Molecule
Molecule
Data records augmented with the calculated properties
None
Component Sticky Notes
The server version when this component was registered
6.0.1.6
Runtime Identifier
17
Location of the component in the database
Components\Chemistry\Calculators\Surface Area and Volume
Surface Area and Volume
Surface Area and Volume
Surface Area and Volume
Surface Area and Volume
Surface Area and Volume
Surface Area and Volume
Surface Area and Volume
Surface Area and Volume
Expression (or list of expressions separated by semi-colons) to evaluate.
Initial Expression
Final Expression
Keep Calculated Properties
remove('text');
<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
18
Custom Error Message
Component Icon
EXPRESSIONNODE
Disabled
0
GUID
{0995D675-7EE2-432C-95DF-E91C14052B22}
Component Point
5263 -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)
Select the type of output required: Smiles or Canonical Smiles
<p>
<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 Sep 20 11:20:58 2006
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
Molecule to SMILES
Molecule to SMILES
The component this component is based upon.
Canonical Smiles
Custom Error Message
Component Icon
CALCULATORNODE
GUID
{0C60C40A-5189-42DA-A3C0-4EA44BFF7D15}
Component Point
5563 -50
Disabled
0
Fancy Help
100
Creates a text property containing a SMILES representation of the 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 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
Molecular data records augmented with text properties containing either the SMILES and/or the canonical SMILES of the molecule
None
The server version when this component was registered
6.0.1.0
Component Sticky Notes
Runtime Identifier
19
Location of the component in the database
Components\Chemistry\Converters\Molecule To Text\Molecule to SMILES
Molecular Formats
Molecular Formats
Expression (or list of expressions separated by semi-colons) to evaluate.
Initial Expression
Final Expression
Keep Calculated Properties
remove('duplicate','counter','originalsmiles','id', 'smiles', 'Canonical_Smiles');
/*rename('Canonical_Smiles','Structure');*/
if Row EQ 1 THEN
resize(@Names, 0);
for #i in 3 .. numproperties()
loop
append(@Names, ITHPROPERTYNAME(#i));
end loop;
end if;
for #j in 3 .. numproperties()
loop
append(@Values, ithproperty(#j));
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
Custom Manipulator (PilotScript)
The component this component is based upon.
Custom Manipulator (PilotScript)
Component RunTimeID
20
Custom Error Message
Component Icon
EXPRESSIONNODE
Disabled
0
GUID
{0995D675-7EE2-432C-95DF-E91C14052B22}
Component Point
5838 -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 Data
None
The server version when this component was registered
6.1.0.17
Component Sticky Notes
Location of the component in the database
Components\Generic\Manipulators\Custom Manipulator (PilotScript)
The PilotScript expression used to filter the data.
Initial Expression
Final Expression
Keep Calculated Properties
Row = Size
<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
6138 -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
None
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
21
Location of the component in the database
Components\Generic\Filters\Custom Filter (PilotScript)
6.1.0.17