PDB Reader

Options

Settings

Read from

Select a file system which stores the data you want to read. There are four default file system options to choose from:

• Local File System: Allows you to select a file/folder from your local system.
• Mountpoint: Allows you to read from a mountpoint. When selected, a new drop-down menu appears to choose the mountpoint. Unconnected mountpoints are greyed out but can still be selected (note that browsing is disabled in this case). Go to the KNIME Explorer and connect to the mountpoint to enable browsing. A mountpoint is displayed in red if it was previously selected but is no longer available. You won't be able to save the dialog as long as you don't select a valid i.e. known mountpoint.
• Relative to: Allows you to choose whether to resolve the path relative to the current mountpoint, current workflow or the current workflow's data area. When selected a new drop-down menu appears to choose which of the three options to use.
• Custom/KNIME URL: Allows to specify a URL (e.g. file://, http:// or knime:// protocol). When selected, a spinner appears that allows you to specify the desired connection and read timeout in milliseconds. In case it takes longer to connect to the host / read the file, the node fails to execute. Browsing is disabled for this option.

To read from other file systems, click on ... in the bottom left corner of the node icon followed by Add File System Connection port . Afterwards, connect the desired file system connector node to the newly added input port. The file system connection will then be shown in the drop-down menu. It is greyed out if the file system is not connected in which case you have to (re)execute the connector node first. Note: The default file systems listed above can't be selected if a file system is provided via the input port.

Mode

Select whether you want to read a single file or multiple files in a folder. When reading files in a folder, you can set filters to specify which files and subfolders to include (see below).

Filter options

Only displayed if the mode Files in folder is selected. Allows to specify which files should be included according to their file extension and/or name. It is also possible to include hidden files. The folder filter options enable you to specify which folders should be included based on their name and hidden status. Note that the folders themselves will not be included, only the files they contain.

Include subfolders

If this option is checked, the node will include all files from subfolders that satisfy the specified filter options. If left unchecked, only the files in the selected folder will be included and all files from subfolders are ignored.

File, Folder or URL

Enter a URL when reading from Custom/KNIME URL, otherwise enter a path to a file or folder. The required syntax of a path depends on the chosen file system, such as "C:\path\to\file" (Local File System on Windows) or "/path/to/file" (Local File System on Linux/MacOS and Mountpoint). For file systems connected via input port, the node description of the respective connector node describes the required path format. You can also choose a previously selected file/folder from the drop-down list, or select a location from the "Browse..." dialog. Note that browsing is disabled in some cases:

• Custom/KNIME URL: Browsing is always disabled.
• Mountpoint: Browsing is disabled if the selected mountpoint isn't connected. Go to the KNIME Explorer and connect to the mountpoint to enable browsing.
• File systems provided via input port: Browsing is disabled if the connector node hasn't been executed since the workflow has been opened. (Re)execute the connector node to enable browsing.

The location can be exposed as or automatically set via a path flow variable.

Ignore SEQRES records

If Integrate SEQRES Records is on, then all residues in the SEQRES records will be created, including those without corresponding entries in the ATOM records.

Ignore CONECT records

If Ignore CONECT Records is on, then CONECT records will not be used when creating bonds.

Enable AutoConnect

If Enable Auto-connect is on, automatic bonding of atoms [Labute 2005] is performed after CONECT records are applied. Automatic bonding is always done on atoms of amino acid residues.

Ignore Waters

If Waters is on, then all waters in the PDB file will be ignored.

Ignore Hetero

If Hetero is on, then all hetero residues in the PDB file will be ignored.

Automatic Chain tags

If Auto-tag is on, then any chain with an empty tag will receive the name of the PDB file as its tag. This ensures that chains which originate from a single file are grouped together by their tags even in the case where no tag is specified in the file.

Symmetries

Crystallographic will read the MTRIXn records, Biomolecule will apply the BIOMT transforms if any.

All models

Read all models if applicable

Views

This node has no views

Workflows

• MOE 02 - Fragment Based DesignKNIME Hub
• MOE 04 - Protein-Protein-InteractionsKNIME Hub

Links

• No links available

Developers