4.13. MOL2 file format — MDAnalysis.coordinates.MOL2
¶
Classes to read Tripos molecule structure format (MOL2) coordinate and topology files. Used by the DOCK docking code.
4.13.1. Classes¶
-
class
MDAnalysis.topology.MOL2Parser.
MOL2Parser
(filename, universe=None, guess_bonds_mode=False, **kwargs)[source]¶ Read topology from a Tripos MOL2 file.
Changed in version 0.9: Now subclasses TopologyReader
Standard arguments for a TopologyReader:
Arguments: - filename
name of the topology file
Keywords: - universe
Supply a Universe to the Parser. This then passes it to the atom instances that are created within parsers.
- guess_bonds_mode
True
: attempt to derive bonds from a distance search if no connectivity information is available or parsedFalse
: only load a list of atoms (and possibly identify residues and segments)- default:
False
- kwargs
Other keyword arguments that can vary with the specific format. These are stored as self.kwargs
-
close
()¶ Close the trajectory file.
-
close_trajectory
()¶ Specific implementation of trajectory closing.
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convert_forces_from_native
(force, inplace=True)¶ In-place conversion of forces array force from native units to base units.
By default, the input force is modified in place and also returned.
New in version 0.7.7.
-
convert_forces_to_native
(force, inplace=True)¶ In-place conversion of force array force from base units to native units.
By default, the input force is modified in place and also returned.
New in version 0.7.7.
-
convert_pos_from_native
(x, inplace=True)¶ In-place conversion of coordinate array x from native units to base units.
By default, the input x is modified in place and also returned.
Changed in version 0.7.5: Keyword inplace can be set to
False
so that a modified copy is returned unless no conversion takes place, in which case the reference to the unmodified x is returned.
-
convert_pos_to_native
(x, inplace=True)¶ Conversion of coordinate array x from base units to native units.
By default, the input x is modified in place and also returned.
Changed in version 0.7.5: Keyword inplace can be set to
False
so that a modified copy is returned unless no conversion takes place, in which case the reference to the unmodified x is returned.
-
convert_time_from_native
(t, inplace=True)¶ Convert time t from native units to base units.
By default, the input t is modified in place and also returned (although note that scalar values t are passed by value in Python and hence an in-place modification has no effect on the caller.)
Changed in version 0.7.5: Keyword inplace can be set to
False
so that a modified copy is returned unless no conversion takes place, in which case the reference to the unmodified x is returned.
-
convert_time_to_native
(t, inplace=True)¶ Convert time t from base units to native units.
By default, the input t is modified in place and also returned. (Also note that scalar values t are passed by value in Python and hence an in-place modification has no effect on the caller.)
Changed in version 0.7.5: Keyword inplace can be set to
False
so that a modified copy is returned unless no conversion takes place, in which case the reference to the unmodified x is returned.
-
convert_velocities_from_native
(v, inplace=True)¶ In-place conversion of velocities array v from native units to base units.
By default, the input v is modified in place and also returned.
New in version 0.7.5.
-
convert_velocities_to_native
(v, inplace=True)¶ In-place conversion of coordinate array v from base units to native units.
By default, the input v is modified in place and also returned.
New in version 0.7.5.
-
parse
(filename=None)[source]¶ Parse MOL2 file filename and return the dict structure.
Only reads the list of atoms.
Returns: MDAnalysis internal structure dict See also
The structure dict is defined in
MDAnalysis.topology.PSFParser.PSFParser()
.