Blocks
The most basic type of residue description is the BuildingBlock. It contains
information on atom names and their corresponding types, charges and
optionally also their masses. Interactions for all particles can also
be defined even though they are optional, except the bonds giving
information about the connectivity.
You often need to manipulate building blocks or
the residues they refer to in an automated manner. That’s where the
BlockModifiers come in, with the GromacsBlockModifier as a specific
implementation. As a special case there also exist HydrogenConstructors.
The BuildingBlock Class
-
class
BuildingBlock
-
Match (residue[, match_connectivity=True])
Checks, whether the given residue matches the atom names in the
BuildingBlock. The connectivity gets checked optionally.
Parameters: |
- residue (
ResidueHandle ) –
- match_connectivity (
bool ) – If set to true, the function checks the bonds
in the residue with the defined bonds in the
BuildingBlock
|
Returns: | bool
|
-
Connect (residue, editor)
Connects atoms of residue based on the bond definitions of the
BuildingBlock.
Parameters: |
- residue (
ResidueHandle ) – Residue to be connected
- editor (
XCSEditor ) – Editor associated to the residue’s entity
|
Raises: | RuntimeError when required atom can not be found in
residue
|
-
AddAtom (name, type, charge[, mass = None])
Parameters: |
- name (
str ) – Name of atom
- type (
str ) – Its corresponding forcefield type
- charge (
float ) – Its charge
- mass (
float ) – Its mass
|
-
RemoveAtom (name)
Removes atom from BuildingBlock with all its associated values and
interactions
Parameters: | name (str ) – Name of atom to be removed |
-
ReplaceAtom (name, new_name, new_type, new_charge[, new_mass = None])
Replace given atom by resetting name, type, charge and mass. All interactions
containing that atom get adapted as well
Parameters: |
- name (
str ) – Name of atom to be replaced
- new_name (
str ) – New name of atom
- new_type (
str ) – New type of atom
- new_charge (
float ) – New charge of atom
- new_mass (
float ) – New mass of atom
|
-
RemoveInteractionsToPrev ()
Removes all interactions associated to an atom of a previous residues.
This gets indicated in the BuildingBlock by an atom name prefixed by a -
-
RemoveInteractionsToNext ()
Removes all interactions associated to an atom of a next residues.
This gets indicated in the BuildingBlock by an atom name prefixed by a +
-
AddBond (bond[, replace_existing = False])
Parameters: |
- bond (
Interaction ) – Bond to be added
- replace_existing (
bool ) – Whether potentially already existing bond for the
same atoms should be replaced.
|
-
AddAngle (angle[, replace_existing = False])
Parameters: |
- angle (
Interaction ) – Angle to be added
- replace_existing (
bool ) – Whether a potentially already existing angle for the
same atoms should be replaced.
|
-
AddDihedral (dihedral[, replace_existing = False])
Parameters: |
- dihedral (
Interaction ) – Dihedral to be added
- replace_existing (
bool ) – Whether potentially already existing dihedral for the
same atoms should be replaced.
|
-
AddImproper (improper[, replace_existing = False])
Parameters: |
- improper (
Interaction ) – Improper to be added
- replace_existing (
bool ) – Whether potentially already existing improper for the
same atoms should be replaced.
|
-
AddExclusion (exclusion[, replace_existing = False])
Parameters: |
- exclusion (
Interaction ) – Exclusion to be added
- replace_existing (
bool ) – Whether potentially already existing Exclusion for the
same atoms should be replaced.
|
-
AddCMap (cmap[, replace_existing = False])
Parameters: |
- cmap (
Interaction ) – CMap to be added
- replace_existing (
bool ) – Whether potentially already existing cmap for the
same atoms should be replaced.
|
-
AddConstraint (constraint[, replace_existing = False])
Parameters: |
- constraint (
Interaction ) – Constraint to be added
- replace_existing (
bool ) – Whether potentially already existing constraint for the
same atoms should be replaced.
|
-
GetType (name)
Gets forcefield type from atom with given name
Parameters: | name (str ) – Name of atom you want the type from |
Returns: | str |
Raises: | RuntimeError when atom can not be found in
BuildingBlock |
-
GetCharge (name)
Gets charge from atom with given name
Parameters: | name (str ) – Name of atom you want the charge from |
Returns: | float |
Raises: | RuntimeError when atom can not be found in
BuildingBlock |
-
GetMass (name)
Gets mass from atom with given name
Parameters: | name (str ) – Name of atom you want the mass from |
Returns: | float |
Raises: | RuntimeError when atom can not be found in
BuildingBlock |
-
GetAtoms ()
Returns: | list of all atom names |
-
GetTypes ()
Returns: | list of all atom types |
-
GetCharges ()
Returns: | list of all charges |
-
GetMasses ()
Returns: | list of all masses |
-
GetBonds ()
Returns: | list of all bonds |
-
GetAngles ()
Returns: | list of all angles |
-
GetDihedrals ()
Returns: | list of all dihedrals |
-
GetImpropers ()
Returns: | list of all impropers |
-
GetCMaps ()
Returns: | list of all cmaps |
-
GetExclusions ()
Returns: | list of all exlusions |
-
GetConstraints ()
Returns: | list of all constraints |
Block Modifiers
-
class
BlockModifier
Basis class. Block modifiers are used to change building blocks or residues.
See GromacsBlockModifier for a specific example.
-
class
GromacsBlockModifier
-
ApplyOnBuildingBlock (block)
Applies all defined rules on the given BuildingBlock
-
ApplyOnResidue (residue)
Applies all defined rules on the given ResidueHandle
Parameters: | residue (ResidueHandle ) – Residue to be modified |
-
AddReplaceRule (name, new_name, new_type, new_charge)
Rule, that basically renames an atom and also resets its type and charge
in a BuildingBlock . A simple renaming occurs in a ResidueHandle .
Parameters: |
- name (
str ) – Name of the atom to be changed
- new_name (
str ) – Its new name
- new_type (
str ) – Its new type
- new_charge (
float ) – Its new charge
|
-
AddAddRule (number, method, atom_names, anchors, type, charge)
A rule to add new atoms the Gromacs way, see
Gromacs Manual
for the exact definition of the parameters. A BuildingBlock
gets modified by adding the new atom definitions and also the
corresponding bonds describing the connectivity. In case of
ResidueHandle the new Atoms with connectivity get added with
their positions as defined by the Gromacs adding rule.
Parameters: |
- number (
int ) – Number of atoms to be added
- method (
int ) – Gromacs adding rule
- atom_names (
list ) – Strings containing the new atom names
- anchors (
list ) – Strings containing atom names used as anchor
- type (
str ) – The type the atoms will have
- charge (
float ) – The charge the atoms will have
|
-
AddDeleteAtom (name)
Defines an atom that has to be removed. In case of the
BuildingBlock this removes this particular atom plus all
interactions connected to it, in case of ResidueHandle , the
atom simply gets deleted.
Parameters: | name (str ) – Atom to be deleted |
-
AddBond (bond)
Adds a bond, this only has effect on BuildingBlock , not
on ResidueHandle when the corresponding Apply function gets
called
-
AddAngle (angle)
Adds an angle, this only has effect on BuildingBlock , not
on ResidueHandle when the corresponding Apply function gets
called
-
AddDihedral (dihedral)
Adds a dihedral, this only has effect on BuildingBlock , not
on ResidueHandle when the corresponding Apply function gets
called
Parameters: | dihedral (Interaction ) – Dihedral to be added |
-
AddImproper (improper)
Adds an improper, this only has effect on BuildingBlock , not
on ResidueHandle when the corresponding Apply function gets
called
Parameters: | improper (Interaction ) – Improper to be added |
-
AddCMap (cmap)
Adds a cmap, this only has effect on BuildingBlock , not
on ResidueHandle when the corresponding Apply function gets
called
Hydrogen Constructors
-
class
HydrogenConstructor
Basis class. Hydrogen constructors are used to add hydrogens to residues.
-
class
GromacsHydrogenConstructor
The GromacsHydrogenConstructor is the Gromacs way of adding
hydrogens to a structure.
-
ApplyOnBuildingBlock (block)
Guess what it does: !!ABSOLUTELY NOTHING!! just there for consistency
Parameters: | block (BuildingBlock ) – Block that won’t be changed at all!
Isn’t that awesome? |
-
ApplyOnResidue (residue)
Constructs hydrogens based on the defined hydrogen addition rules
Parameters: | residue (ResidueHandle ) – Residue to be modified |
-
AddHydrogenRule (number, method, hydrogen_names, anchors)
Adds a hydrogen building rule as defined in
Gromacs Manual
Parameters: |
- number (
int ) – Number of hydrogens to be added
- method (
int ) – Gromacs adding rule
- hydrogen_names (
list ) – Strings containing the hydrogen names
- anchors (
list ) – Strings containing atom names used as anchor
|
-
class
HeuristicHydrogenConstructor (block)
As soon as we leave the well defined world of Gromacs residue definitions,
we have to find new ways for constructing hydrogens. The
HeuristicHydrogenConstructor takes a BuildingBlock at
initialization and builds heuristic rules to build hydrogens based on
the connecticity defined in the given block.
Parameters: | block – BuildingBlock from which the connectivity
information for hydrogen construction is extracted |
-
ApplyOnBuildingBlock (block)
Guess what it does: !!ABSOLUTELY NOTHING!! Just there for consistency
Parameters: | block (BlockModifier ) – Block that won’t be changed at all!
Isn’t that awesome? |
-
ApplyOnResidue (residue)
Constructs hydrogen based on heuristic rules
Parameters: | residue (ResidueHandle ) – Residue to be modified |
|
Contents
Search
Enter search terms or a module, class or function name.
Previous topic
Interactions
Next topic
Forcefields
You are here
|