schrodinger.sitemap module¶
SiteMap C++ wrappers
- class schrodinger.sitemap.Config¶
- schrodinger::sitemap::Config
SiteMap configuration settings. For documentation of each member variable, see the $SCHRODINGER/sitemap help message.
- __init__(*args, **kwargs)¶
- addphil¶
- addphob¶
- addsp¶
- border¶
- compact_mode_threshold¶
- cutoff¶
- d2thresh¶
- dthresh¶
- dvscale¶
- dvscbig¶
- dvscnorm¶
- enclosure¶
FKA sitecut
- evalfile¶
- extend¶
- ffield¶
- grid¶
FKA griddel
- jobname¶
- kmax¶
- kmax2¶
- mapdist¶
- margin¶
FKA gridmargin
- maxdist¶
FKA imaxsite
- maxeval¶
FKA maxrep
- maxvdw¶
FKA sitescmin
- mingroup¶
- modbalance¶
- modcharges¶
FKA modchg
- modphobic¶
FKA modphob
- modrad¶
- nearres¶
- nthresh¶
- r2thresh¶
- receptortype¶
- reportsize¶
FKA repsize
- rthresh¶
- siteasl¶
- sitebox¶
- sitefile¶
- siteref¶
- surf_only¶
- usebox¶
- verbosity¶
- writegrids¶
FXA gridfiles
- writevis¶
FKA visfiles
- xcent¶
- xrange¶
- ycent¶
- yrange¶
- zcent¶
- zrange¶
- class schrodinger.sitemap.Site¶
schrodinger::sitemap::Site A Site bundles together the structure representation of a SiteMap site with its associated surface and volume data. Note: this class is non-copyable because it manages the mmvol/mmsurf handles and deletes them on destruction.
- __init__(*args, **kwargs)¶
- getSiteScore(self) double¶
Return the value of the SiteScore function for the site.
- getStructure(self) schrodinger::Structure¶
Get a Structure object where the site points are represented as dummy atoms, and with the SiteScore and other results stored as structure properties (e.g.,
r_sitemap_SiteScore).
- getTitle(self) std::string¶
Get the title of the underlying Structure object.
- setTitle(self, new_title)¶
Set the title and entry name of the underlying Structure object, as well as the title used in the ASL expressions stored with the surfaces.
- writeVisFiles(self) std::vector< std::string,std::allocator< std::string > >¶
Write the .vis files associated with the Site. Returns the names of the files written. (Does nothing if the job had WRITEVIS disabled.)
- schrodinger.sitemap.checkin_license()¶
Check in the SITEMAP_MAIN license, if the number of calls to checkin_license() matches the number of calls to checkout_license().
- schrodinger.sitemap.checkout_license()¶
Check out the SITEMAP_MAIN license, if it is not already checked out. Calling this function is not required for run_sitemap() to work, but preemptively checking out the license prevents repeated checkout/checkin each time run_sitemap() is called.
- schrodinger.sitemap.get_surf_surf(recep, lig, resolution=0.7) MMvol¶
Generate volume data for the SiteMap “surf” surface. The caller is responsible for ensuring that the mmvol library is initialized, because otherwise the return value would become invalid.
- Parameters:
recep: – receptor structure
lig: – ligand structure
resolution: – grid resolution in Angstroms
- Return type:
int
- Returns:
: mmvol handle. Caller is responsible for deleting it.
- Raises:
: runtime_error
- schrodinger.sitemap.run_sitemap(config, recep, lig) _SiteList¶
- schrodinger.sitemap.run_sitemap(config, recep) _SiteList
- schrodinger.sitemap.run_sitemap(recep, lig) std::vector< schrodinger::Structure,std::allocator< schrodinger::Structure > >
- schrodinger.sitemap.run_sitemap(recep) std::vector< schrodinger::Structure,std::allocator< schrodinger::Structure > >
Overload 1:
Run the full SiteMap workflow (finding, mapping, and evaluating sites). Requires SITEMAP license.
- Parameters:
config: – job settings
recep: – receptor structure to evaluate
lig (schrodinger::Structure) – ligand structure used to constrain the search volume
- Return type:
std::vector< std::shared_ptr< schrodinger::sitemap::Site >,std::allocator< std::shared_ptr< schrodinger::sitemap::Site > > >
- Returns:
: list of SiteMap Site objects
- Raises:
: runtime_error
Overload 2:
Run the full SiteMap workflow (finding, mapping, and evaluating sites). This overload searches the entire receptor unless the config specifies a a box.
Requires SITEMAP license.
- Parameters:
config: – job settings
recep: – receptor structure to evaluate
- Return type:
std::vector< std::shared_ptr< schrodinger::sitemap::Site >,std::allocator< std::shared_ptr< schrodinger::sitemap::Site > > >
- Returns:
: list of SiteMap Site objects
- Raises:
: runtime_error
- Overload 3:
Deprecated: run the SiteMap calculation using global settings set by calling set_keyword().
- Overload 4:
Deprecated: run the SiteMap calculation using global settings set by calling set_keyword().
- schrodinger.sitemap.set_defaults()¶
The set_defaults(), set_keyword(), and the run_sitemap() overloads that do not take a Config operate on global state, which can easily result in bugs if the global state does not get set correctly between calls to run_sitemap().
Deprecated: reset all global SiteMap keywords to their default values.
- schrodinger.sitemap.set_keyword(keyword, val)¶
- schrodinger.sitemap.set_keyword(keyword, val) None
- schrodinger.sitemap.set_keyword(keyword, val) None
- schrodinger.sitemap.set_keyword(keyword, val) None
Overload 1: Deprecated: set the value of a global SiteMap keyword.
Overload 2: Deprecated: set the value of a global SiteMap keyword.
Overload 3: Deprecated: set the value of a global SiteMap keyword.
Overload 4: Deprecated: set the value of a global SiteMap keyword.
- schrodinger.sitemap.write_surf_surf(ivol, jobname)¶
Write <jobname>.vis using the SiteMap “surf” surface style.