MOLE API 0.5.4

MOLE API

version 0.5.4 build 082222

MOLE API is a service for programmatic access to the MOLE 2.5 channel analysis software.

Biomacromolecular channels and pores play significant biological roles, e.g., in molecular recognition and enzyme substrate specificity. We present a RESTful web service providing a programatic access to the advanced software tool entitled MOLE 2.5, which has been designed to analyze molecular channels and pores. Benchmark tests against other available software tools showed that MOLE 2.5 is by comparison quicker, more robust and more versatile. As a new feature, MOLE 2.5 provides an automatic mode for transmembrane channel identification.

How to read the documentation: Individual parameters are marked with '<' and '>' symbols (e.g. <computationId>). In case these parameters are optional, a question mark is introduced (e.g. ?<Pores>). Parameters are appended to the source URL using '?' symbol and multiple parameters are appended to the URL using & symbol.

Support: Technical questions: webchemistryhelp@gmail.com; General questions: mole@upol.cz or webchemistryhelp@gmail.com

Initialize /Init/?<Pores>/<pdbId>?<optional parameters>
Initialize a new MOLE computation with a user structure or a PDB Id.

Http Request	Name	Description
GET	Pores	Initialize computation for transmembrane pore identification (assumed biological unit is downloaded).
GET	assemblyId	Optional assembly Id of a PDB entry in a string format (e.g. 1,2, PAU...).
POST	file	User file to be processed by /Init. Presently, PDB (.pdb, .pdb1, ...) and mmCIF (.cif) file formats are supported. Optionally, they can be gzipped (.gz)

Submit /Submit/<Mode>/<computationId>
Submit a new computation as long as the server is not under heavy load and previous computation has been finished.

Examples

URL Parameters

Http Request	Mode	Description
POST	Mole	Submit a new MOLE computation with a parameters provided in the POST body. List of the allowed parameters is provided below.
POST	Pores	Submits a new pore computation

Pores Post Attributes

Input Attributes

Name	Type	Description
InMembrane	Bool	Compute pore only in the transmembrane region.
IsBetaBarel	Bool	Determine if submitted structure is formed by β-sheets in its transmembrane part.
Chains	String	One or more characters that specify which chains should participate in the computation. If empty or not present, all chains are loaded. Case sensitive!
InteriorThreshold	Double?	Minimum radius of void inside the protein structure. Approximation of minimal channel radius.
ProbeRadius	Double?	Regulates level of detail of the molecular surface. Approximation of maximal channel radius.

MOLE Post Attributes

Input Attributes

Name	Type	Description
SpecificChains	String	One or more characters that specify which chains should participate in the computation. If empty or not present, all chains are loaded. Case sensitive!
ReadAllModels	Bool	Determines whether to read all models from the PDB file. All models are read automatically for PDB assemblies (*.pdb0).

Cavity Attributes

Name	Type	Description
IgnoreHETAtoms	Bool	Allows to exclude the HET atoms from the computation.
IgnoreHydrogens	Bool	Allows to exclude the hydrogen atoms from the computation.
InteriorThreshold	Double	Minimum radius of void inside the protein structure. Approximation of minimal channel radius.
ProbeRadius	Double	Regulates level of detail of the molecular surface. Approximation of maximal channel radius.
NonActiveResidues	Residue[]	List of residues to be excluded from the computation.
QueryFilter	String	Select atoms/residues to be discarded prior to the channel computation using PatternQuery expressions.

Tunnel Attributes

Name	Type	Description
WeightFunction	String	One of VoronoiScale, LengthAndRadius, Length, Constant.
BottleneckRadius	Double	Determines weight function used to compute channels. For most of the globular proteins VoronoiScale works the best, while pores are typically identified with Length.
BottleneckTolerance	Double	Maximum length of a valid channel for which the radius is less than BottleneckRadius.
MaxTunnelSimilarity	Double	Maximum degree of similarity between two tunnels before the longer channel is discarded.
OriginRadius	Double	If the user defined a channel start point, expand the search for channel start points to a sphere of given radius.
SurfaceCoverRadius	Double	Regulates the density of exit points tested at eeach outer boudary. Higher SurfaceCoverRadius produces a lower density of exit points.
UseCustomExitsOnly	Bool	Only user defined exits are used for the channel computation.

Origin Attributes

Name	Type	Description
Origins	Origin[]	Origin - Start point of a channel identification. Single origin can be formed of by Point3D, ResidueOrigin or QueryOrigin.
CustomExits	Origin[]	Custom channel end points. These can be used for automatic identification of channels from Origin, or pairwise detection of pores. The format of input is the same as with Origin Point3D, ResidueOrigin or QueryOrigin.
QueryOrigin	String	Origin is composed out of individual selections made by PatternQuery expression.

Point3D

Property	Type	Description
X	Double	X-coordinate
Y	Double	Y-coordinate
Z	Double	Z-coordinate

ResidueOrigin

Property	Type	Description
SequenceNumber	Int	Residue identifier, corresponds to the '_atom_site.auth_seq_id' field.
Chain	String	Chain identifier, corresponds to the '_atom_site.auth_asym_id' field.

Check computation status /Status/<computationId>?<submitId>
Check status of the computation with given computation Id. Just a single running computation is allowed per computation Id.

Examples

/Status/jZrfNQsEEyVmBnHivNq8A
/Status/jZrfNQsEEyVmBnHivNq8A?submitId=5

URL Parameters

Name	Type	Description
computationId	String	Computation Id retrieved from the /Init query.
submitId	String	Submit Id of the given computation.

Status

Name	Description
Initializing	Parameters were succesfully passed. Attempting to gather requested data.
Initialized	Input structure has been succesfully downloaded/uploaded. Ready to start computation.
FailedInitialization	Something went wrong during fetching structure. Check error message. Possibly incorect PDB Id or assembly Id.
Running	Computation has been succesfully started and is running.
Finished	Computation has finished. Results are made available for download.
Error	Something went wrong during execution of the computation. Check error message.
Deleted	The computation has been deleted on user request. Nothing to download.
Aborted	Computation has been killed on user request.

Download results /Data/<computationId>?<submitId>?<format>
Download results of the computation in various formats as well as the input structure. If no additional parameters are provided json results of the last computation are retrieved.

Examples

/Data/OaUmDZj0Kk2ZBgJLLxVUA
/Data/OaUmDZj0Kk2ZBgJLLxVUA?submitId=1&format=pymol

URL Parameters

Http Request	Name	Type	Description
GET	computationId	String	Computation Id retrieved from the /Init query.
GET	submitId	String	Submit Id retrieved from the /Submit query.
GET	format	Enum	Download results in a numerous formats.

Format parameters

Name	Description
molecule	Download input structure used for channel computation.
pymol	Download channels as a PyMol script.
vmd	Download channels as a VMD script.
pdb	Download channels in the plain old Protein Data Bank format in a *.zip archive.
chimera	Download channels as a Chimera script.
report	Download all results in a *.zip archive.
membrane	Download membrane information [Pores mode only].

Initialize /Init/?<Pores>/<pdbId>?<optional parameters>
Initialize a new MOLE computation with a user structure or a PDB Id.

Examples

URL Parameters

Submit /Submit/<Mode>/<computationId>
Submit a new computation as long as the server is not under heavy load and previous computation has been finished.

Examples

URL Parameters

Pores Post Attributes

Input Attributes

MOLE Post Attributes

Input Attributes

Cavity Attributes

Tunnel Attributes

Origin Attributes

Point3D

ResidueOrigin

Check computation status /Status/<computationId>?<submitId>
Check status of the computation with given computation Id. Just a single running computation is allowed per computation Id.

Examples

URL Parameters

Status

Download results /Data/<computationId>?<submitId>?<format>
Download results of the computation in various formats as well as the input structure. If no additional parameters are provided json results of the last computation are retrieved.

Examples

URL Parameters

Format parameters

Retrieve parameters /CompInfo/<computationId>
Retrieves parameters of all submissions.

Examples

URL Parameters

CSA active site /CSA/<computationId>
Retrieves active sites annotated in the CSA database for this structure.

Examples

URL Parameters

EBI calls /EBI/<pdbId>?<ignoreHet>
Endpoint for backward compatibility with EBI environment.

Examples

URL Parameters

Delete computation /Delete/<computationId>
Delete entire computation folder from our server.

Examples

URL Parameters

Kill submission /Kill/<computationId>
Kill presently running submission.

Examples

URL Parameters

Version info /Version
Get version information about employed services

Examples

Initialize /Init/?<Pores>/<pdbId>?<optional parameters> Initialize a new MOLE computation with a user structure or a PDB Id.

Examples

URL Parameters

Submit /Submit/<Mode>/<computationId> Submit a new computation as long as the server is not under heavy load and previous computation has been finished.

Examples

URL Parameters

Pores Post Attributes

Input Attributes

MOLE Post Attributes

Input Attributes

Cavity Attributes

Tunnel Attributes

Origin Attributes

Point3D

ResidueOrigin

Check computation status /Status/<computationId>?<submitId> Check status of the computation with given computation Id. Just a single running computation is allowed per computation Id.

Examples

URL Parameters

Status

Download results /Data/<computationId>?<submitId>?<format> Download results of the computation in various formats as well as the input structure. If no additional parameters are provided json results of the last computation are retrieved.

Examples

URL Parameters

Format parameters

Retrieve parameters /CompInfo/<computationId> Retrieves parameters of all submissions.

Examples

URL Parameters

CSA active site /CSA/<computationId> Retrieves active sites annotated in the CSA database for this structure.

Examples

URL Parameters

EBI calls /EBI/<pdbId>?<ignoreHet> Endpoint for backward compatibility with EBI environment.

Examples

URL Parameters

Delete computation /Delete/<computationId> Delete entire computation folder from our server.

Examples

URL Parameters

Kill submission /Kill/<computationId> Kill presently running submission.

Examples

URL Parameters

Version info /Version Get version information about employed services

Examples

Initialize /Init/?<Pores>/<pdbId>?<optional parameters>
Initialize a new MOLE computation with a user structure or a PDB Id.

Submit /Submit/<Mode>/<computationId>
Submit a new computation as long as the server is not under heavy load and previous computation has been finished.

Check computation status /Status/<computationId>?<submitId>
Check status of the computation with given computation Id. Just a single running computation is allowed per computation Id.

Download results /Data/<computationId>?<submitId>?<format>
Download results of the computation in various formats as well as the input structure. If no additional parameters are provided json results of the last computation are retrieved.

Retrieve parameters /CompInfo/<computationId>
Retrieves parameters of all submissions.

CSA active site /CSA/<computationId>
Retrieves active sites annotated in the CSA database for this structure.

EBI calls /EBI/<pdbId>?<ignoreHet>
Endpoint for backward compatibility with EBI environment.

Delete computation /Delete/<computationId>
Delete entire computation folder from our server.

Kill submission /Kill/<computationId>
Kill presently running submission.

Version info /Version
Get version information about employed services