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All Atom Scorers
AllAtomOverallScorer class
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class
promod3.scoring. AllAtomOverallScorer
Container that allows for the storage of multiple scorers identified by a key
(str ) and the computation of combined scores.
Scorers need to be individually set or loaded by
LoadDefaultAllAtomOverallScorer()
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Contains (key)
Returns: | True, if a scorer object for this key was already added. |
Return type: | bool |
Parameters: | key (str ) – Key for desired scorer. |
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Get (key)
Returns: | Scorer with the given key (read-only access). |
Return type: | AllAtomScorer |
Parameters: | key (str ) – Key for desired scorer. |
Raises: | RuntimeError if there is no scorer with that
key. |
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AttachEnvironment (env)
Parameters: | env (AllAtomEnv ) – Link all scorers to this score environment. |
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CalculateLinearCombination (linear_weights, start_resnum, num_residues, chain_idx)
Calculate linear combination of scores for the desired loop(s) (extracted
from environment) against the set environment (see
AllAtomScorer.CalculateScore() ).
Parameters: |
- linear_weights (
dict (keys: str ,
values: float )) – Weights for each desired scorer. You can add a
constant value to each score by defining a weight
with key “intercept”.
- start_resnum (
int / list of int ) – Res. number(s) defining the position(s) in the SEQRES
(see AllAtomEnv for indexing)
- num_residues (
int / list of int ) – Length of loop(s).
- chain_idx (
int / list of int ) – Index of chain the loop(s) belongs to
(see AllAtomEnv for indexing)
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Returns: | Score for the given set of atoms.
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Return type: | float
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Raises: | RuntimeError if linear_weights has a key for
which no scorer exists or anything raised in
AllAtomScorer.CalculateScore() for any of the used scorers.
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__getitem__ (key)
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__setitem__ (key)
Allow read/write access (with [key]) to scorer object with given key.
Parameters: | key (str ) – Key for desired scorer. |
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promod3.scoring. LoadDefaultAllAtomOverallScorer ()
Returns: | Loads or creates the default scorers accessible through
following keys:
“aa_interaction”, “aa_packing”, “aa_clash” |
Return type: | AllAtomOverallScorer |
AllAtomScorer base class
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class
promod3.scoring. AllAtomScorer
Base class for all the all atom scorers listed below.
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AttachEnvironment (env)
Parameters: | env (AllAtomEnv ) – Link scorer to this score environment. |
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CalculateScore (start_resnum, num_residues, chain_idx)
Calculates score for the desired loop(s) (extracted from environment) against
the set environment. Unless otherwise noted in the scorer, a lower “score”
is better!
Parameters: |
- start_resnum (
int / list of int ) – Res. number(s) defining the position(s) in the SEQRES
(see AllAtomEnv for indexing)
- num_residues (
int / list of int ) – Length of loop(s).
- chain_idx (
int / list of int ) – Index of chain the loop(s) belongs to
(see AllAtomEnv for indexing)
|
Returns: | Score for the given set of atoms.
|
Return type: | float
|
Raises: | (for most scorers) RuntimeError if scorer was
never attached to a score environment, if scorer has never been
properly initialized or if chain_index / start_resnum lead to
invalid positions.
|
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CalculateScoreProfile (start_resnum, num_residues, chain_idx=0)
Calculates per residue scores for the desired loop(s) (extracted from
environment) against the set environment.
Parameters: |
- start_resnum (
int / list of int ) – Res. number(s) defining the position(s) in the SEQRES
(see AllAtomEnv for indexing)
- num_residues (
int ) – Length of loop(s).
- chain_idx (
int / list of int ) – Index of chain the loop(s) belongs to
(see AllAtomEnv for indexing)
|
Returns: | Scores for the given loop(s), one for each residue.
|
Return type: | list of float / list of list
of float
|
Raises: | same RuntimeError as CalculateScore() .
|
AllAtomInteractionScorer class
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class
promod3.scoring. AllAtomInteractionScorer (cutoff, bins, seq_sep)
Inherits all functionality of AllAtomScorer . Evaluates a pairwise
pseudo interaction energy between all atoms which are located within a
cutoff and which are at least seq_sep residues apart. An energy is
assigned to each distance using equally sized bins and distinguishing all
possible pairs of atoms (usually the energy only differs for chemically
distinguishable heavy atoms).
By default, the scorer calculates the scores by
including everything, the stuff set in the environment and the coordinates
in the input loops. You can change this behaviour with the according
functions.
The scorer needs to be initialized either by loading a predefined scorer (e.g.
LoadAllAtomInteractionScorer() ) or by setting all energies (see SetEnergy() ).
Parameters: |
- cutoff (
float ) – Radius in which other atoms are counted.
- bins (
int ) – Number of equally sized bins to discretize distances (range
of [0,*cutoff*]).
- seq_sep (
int ) – Minimal separation in sequence two residues must have to
be considered.
|
Raises: | RuntimeError if cutoff < 0, bins < 1 or
seq_sep < 1.
|
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static
Load (filename)
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static
LoadPortable (filename)
Loads raw binary file generated with Save() (optimized for fast
reading) / portable file generated with SavePortable() (slower but
less machine-dependent).
Parameters: | filename (str ) – Path to the file from which to load. |
Returns: | The loaded scorer |
Return type: | AllAtomInteractionScorer |
Raises: | RuntimeError if file cannot be opened or if
file cannot be parsed (see here for details). |
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Save (filename)
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SavePortable (filename)
Saves a raw / portable binary representation. Use portable files for
distribution and convert locally to raw files. See here
for details.
Parameters: | filename (str ) – Path to the file where it will be saved. |
Raises: | RuntimeError if file cannot be opened. |
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SetEnergy (aaa1, aaa2, bin, energy)
Setup one energy value. Unless a predefined scorer is loaded, this must be
called for every pair of heavy atom types and for every bin < bins.
Internal symmetry is enforced => Calling SetEnergy(aaa1, aaa2, bin, energy) is
equivalent to calling SetEnergy(aaa1, aaa2, bin, energy) AND
SetEnergy(aaa2, aaa1, bin, energy).
Parameters: |
- aaa1 (
AminoAcidAtom ) – Heavy atom type for first interaction partner.
- aaa2 (
AminoAcidAtom ) – Heavy atom type for second interaction partner.
- bin (
int ) – Discrete bin describing the interaction distance.
- energy (
float ) – Energy to set for those parameters.
|
Raises: | RuntimeError if inputs are invalid
|
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DoInternalScores (do_it)
Parameters: | do_it (bool ) – Whether to include pairwise interactions within the
loop. True by default. |
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DoExternalScores (do_it)
Parameters: | do_it (bool ) – Whether to include pairwise interactions towards the
environment. True by default. |
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DoNormalize (do_it)
Parameters: | do_it (bool ) – Whether to normalize the calculated scores by the number
of residues in the input loop. True by default. |
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promod3.scoring. LoadAllAtomInteractionScorer ()
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AllAtomPackingScorer class
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class
promod3.scoring. AllAtomPackingScorer (cutoff, max_count)
Inherits all functionality of AllAtomScorer . Evaluates pseudo
energies by counting surrounding atoms within a certain cutoff radius around
all heavy atoms not belonging to the assessed residue itself.
The scorer needs to be initialized either by loading a predefined scorer (e.g.
LoadAllAtomPackingScorer() ) or by setting all energies (see
SetEnergy() ).
Parameters: |
- cutoff (
float ) – Radius in which other atoms are counted.
- max_count (
int ) – If number of other atoms exceeds max_count, it will
be set to this number.
|
Raises: | RuntimeError if cutoff < 0, max_count < 1.
|
-
static
Load (filename)
-
static
LoadPortable (filename)
Loads raw binary file generated with Save() (optimized for fast
reading) / portable file generated with SavePortable() (slower but
less machine-dependent).
Parameters: | filename (str ) – Path to the file from which to load. |
Returns: | The loaded scorer |
Return type: | AllAtomPackingScorer |
Raises: | RuntimeError if file cannot be opened or if
file cannot be parsed (see here for details). |
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Save (filename)
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SavePortable (filename)
Saves a raw / portable binary representation. Use portable files for
distribution and convert locally to raw files. See here
for details.
Parameters: | filename (str ) – Path to the file where it will be saved. |
Raises: | RuntimeError if file cannot be opened. |
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SetEnergy (aaa, count, energy)
Setup one energy value. Unless a predefined scorer is loaded, this must be
called for every heavy atom type and for every count <= max_count.
Parameters: |
- aaa (
AminoAcidAtom ) – Heavy atom type for which to set energy.
- count (
int ) – Number of surrounding atoms for which to set energy.
- energy (
float ) – Energy to set for those parameters.
|
Raises: | RuntimeError if inputs are invalid
|
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DoNormalize (do_it)
Parameters: | do_it (bool ) – Whether to normalize the calculated scores by the number
of residues in the input loop. True by default. |
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promod3.scoring. LoadAllAtomPackingScorer ()
Returns: | The default predefined AllAtomPackingScorer (loaded from disk) |
Return type: | AllAtomPackingScorer |
AllAtomClashScorer class
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class
promod3.scoring. AllAtomClashScorer
Inherits all functionality of AllAtomScorer . Calculates a simple
clash score of all atoms against the environment. There is no need to define
any parameters here as all interaction energies are fixed (see Eq. (11) in
[canutescu2003b]). By default, the scorer calculates the scores by
including everything, the stuff set in the environment and the coordinates
in the input loops. You can change this behaviour with the according
functions.
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DoInternalScores (do_it)
Parameters: | do_it (bool ) – Whether to include pairwise interactions within the
loop. True by default. |
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DoExternalScores (do_it)
Parameters: | do_it (bool ) – Whether to include pairwise interactions towards the
environment. True by default. |
-
DoNormalize (do_it)
Parameters: | do_it (bool ) – Whether to normalize the calculated scores by the number
of residues in the input loop. True by default. |
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