diff --git a/loop/data/backbone_loop_scorer.dat b/loop/data/backbone_loop_scorer.dat
index 8e7f6b7f85c15c48c4fd35417397b0703ff28a80..2d787a1dd00166fcac6b78c1fbcbbc4a95cd7bc4 100644
Binary files a/loop/data/backbone_loop_scorer.dat and b/loop/data/backbone_loop_scorer.dat differ
diff --git a/loop/doc/CMakeLists.txt b/loop/doc/CMakeLists.txt
index aad8160d272b8cb04a9838fd8231222db6761eec..ddd0b2da74420f56ef39b8b55c65c8d5104be4f6 100644
--- a/loop/doc/CMakeLists.txt
+++ b/loop/doc/CMakeLists.txt
@@ -1,14 +1,13 @@
set(LOOP_RST
index.rst
torsion_sampler.rst
-loop_candidate.rst
loop_closing.rst
backbone.rst
backbone_loop_score.rst
monte_carlo.rst
structure_db.rst
load_loop_objects.rst
-
+helper_classes.rst
)
add_doc_source(NAME loop RST ${LOOP_RST})
diff --git a/loop/doc/backbone.rst b/loop/doc/backbone.rst
index 13befcdcbfc4bb2f97cde23c802cd302f872aec1..14508e46ba1c01eb6e02497c8904d5a4f0c50cb9 100644
--- a/loop/doc/backbone.rst
+++ b/loop/doc/backbone.rst
@@ -120,11 +120,18 @@ The Basic Building Blocks
Applies a transformation to the coordinates of the backbone
:param transformation_matrix: The transformation
- :type transformation_matrix: :class:`ost.geom.Mat4`
+ :type transformation_matrix: :class:`ost.geom.Mat4` / :class:`ost.geom.Transform`
+
+ .. method:: GetTransform(target)
+
+ Get transformation performing a minimum RMSD transformation onto
+ *target* considering the positions of the N, CA and C atoms.
+
+ :param target: The target positions
- .. method:: GetTransform()
+ :type target: :class:`Backbone` / :class:`ost.mol.ResidueHandle`
- :returns: The transformation currently applied on the backbone
+ :returns: A 4x4 transformation matrix
:rtype: :class:`ost.geom.Mat4`
@@ -197,24 +204,23 @@ Editing Full Stretches Of Backbone Residues
:return: The amino acid sequence
- .. method:: InsertInto(chain,n_stem,c_stem,[remodel_cterminal_o = True])
+ .. method:: InsertInto(chain,start_resnum,[remodel_cterminal_o = True])
Inserts the backbone list into the **chain**. If the residues corresponding
to the :class:`BackboneList` are already present in the entity, they will
be replaced, otherwise they will be added to the entity.
:param chain: The chain
- :param n_stem: The residue number of the n_stem
- :param c_stem: The residue number of the c_stem
+ :param start_resnum: Residue number defining the start location of
+ insertion
:param remodel_cterminal_o: The position of the cterminal o is dependent
on the residue after the c_stem. If this flag
is set and the residue after the cterminus is
present in **chain**, the according oxygen
position gets recalculated.
- :type entity: :class:`ost.mol.ChainHandle`
- :type n_stem: :class:`int`
- :type c_stem: :class:`int`
- :type remodel_cterminal_o: :class:`bool`
+ :type chain: :class:`ost.mol.ChainHandle`
+ :type start_resnum: :class:`int` / :class:`ost.mol.ResNum`
+ :type remodel_cterminal_o: :class:`bool`
.. method:: ReconstructCBetaPositions()
diff --git a/loop/doc/backbone_loop_score.rst b/loop/doc/backbone_loop_score.rst
index 201939e2f0d73b1eda9162fbf101e3a21ef3124d..55acd78a2b2914f613c3534380a89550d911d3b7 100644
--- a/loop/doc/backbone_loop_score.rst
+++ b/loop/doc/backbone_loop_score.rst
@@ -15,7 +15,6 @@ Some of the available scores are statistical potential based.
When setting up an empty scorer, the parametrization and the score values
of these potentials have to be set manually.
-
The BackboneLoopScorer
--------------------------------------------------------------------------------
@@ -58,6 +57,44 @@ The BackboneLoopScorer
:raises: :class:`RuntimeError` if *cbeta_cutoff* is negative or
*cbeta_bins* is <= 0
+
+ .. method:: SetReducedPotentialParameters(dist_cutoff, dist_bins, angle_bins, dihedral_bins, seq_sep)
+
+ Parametrizes a pairwise statistical potential considering the relative
+ orientation of two residues. Every residue gets represented by its CA
+ position p and a directional component v = norm(ca_pos-n_pos) + norm(ca_pos-c_pos).
+ Assuming an interaction between residues r1 and r2, we can define a line l
+ between p1 and p2. The potential then considers:
+
+ * dist => distance between p1 and p2
+ * alpha => angle between v1 and l
+ * beta => angle between v2 and l
+ * gamma => dihedral between (p1+v1,p1,p2,p2+v2)
+
+ :param dist_cutoff: The maximum distance of two residues to be
+ considered
+
+ :param dist_bins: Number of equally sized bins to describe the
+ distances in a discrete manner
+
+ :param angle_bins: Number of equally sized bins to describe the angle
+ parameters in a discrete manner (range of [0, pi])
+
+ :param dihedral_bins: Number of equally sized bins to describe the dihedral
+ parameter in a discrete manner (range of [-pi,pi])
+
+ :param seq_sep: Minimal separation in sequence two residues must
+ have to be considered
+
+ :type dist_cutoff: :class:`float`
+ :type dist_bins: :class:`int`
+ :type angle_bins: :class:`int`
+ :type dihedral_bins: :class:`int`
+ :type seq_sep: :class:`int`
+
+ :raises: :class:`RuntimeError` if *dist_cutoff* is negative or one
+ of the bin parameters is <= 0
+
.. method:: SetTorsionPotentialParameters(group_definitions, torsion_bins)
Parametrizes a torsion statistical potential, that assigns energies based
@@ -82,7 +119,8 @@ The BackboneLoopScorer
.. method:: SetCBPackingPotentialParameters(cb_packing_cutoff, cb_packing_max_count)
Parametrizes a cb packing statistical potential, that assigns energies
- based on the number of other cbeta atoms in the environment.
+ based on the number of other cbeta atoms in the environment within a certain
+ cutoff distance.
:param cb_packing_cutoff: Radius in which other cbeta atoms are counted
:param cb_packing_max_count: If number of other cbeta atoms exceeds
@@ -145,6 +183,17 @@ The BackboneLoopScorer
or a max parameter is smaller than its min counterpart.
+ .. method:: SetSSAgreementParameters()
+
+ Parametrizes the SSAgreement score. Despite no parameters being given, this
+ function has to be called before you can set any SSAgreement scores since the
+ memory has to be allocated internally. The SSAgreement score itself relates a
+ score to a certain combination of psipred prediction, it's confidence and the
+ actually occuring secondary structure in the model. In every score evaluation,
+ the secondary structure of the loop is estimated by searching for hydrogen bonds
+ leading to a secondary structure as defined by dssp. The hbonds are searched
+ internally in the loop as well as in the environment.
+
.. method:: SetCBetaEnergy(a, b, bin, e)
:param a: Identity of first interaction partner.
@@ -162,6 +211,31 @@ The BackboneLoopScorer
:raises: :class:`RuntimeError` if invalid bin or amino acid is
given
+ .. method:: SetReducedEnergy(a, b, dist_bin, alpha_bin, beta_bin, gamma_bin, e)
+
+ :param a: Identity of first interaction partner.
+ :param b: Identity of second interaction partner.
+ :param dist_bin: Discrete bin describing the interaction distance based
+ on the previously defined *dist_cutoff* and *dist_bins*.
+ :param alpha_bin: Discrete bin describing the alpha angle based
+ on the previously defined *angle_bins*.
+ :param beta_bin: Discrete bin describing the beta angle based
+ on the previously defined *angle_bins*.
+ :param gamma_bin: Discrete bin describing the gamma dihedral based
+ on the previously defined *dihedral_bins*.
+ :param e: Energy to be set
+
+ :type a: :class:`ost.conop.AminoAcid`
+ :type b: :class:`ost.conop.AminoAcid`
+ :type dist_bin: :class:`int`
+ :type alpha_bin: :class:`int`
+ :type beta_bin: :class:`int`
+ :type gamma_bin: :class:`int`
+ :type e: :class:`float`
+
+ :raises: :class:`RuntimeError` if invalid bin or amino acid is
+ given
+
.. method:: SetTorsionEnergy(group_id_idx, phi_bin, psi_bin, e)
:param group_id_idx: Index of group identifier given at setting up the
@@ -217,6 +291,20 @@ The BackboneLoopScorer
:raises: :class:`RuntimeError` if state is not in [0,1,2] or one
of the bins is invalid.
+
+ .. method:: SetSSAgreementScore(psipred_state, int psipred_confidence,
+ dssp_state, score)
+
+ :param psipred_state: must be one of ['H','E','C']
+ :param psipred_confidence: must be in [0,9]
+ :param dssp_state: must be one of ['H','E','C','G','B','S','T','I']
+ :param score: score to be set
+
+ :type psipred_state: :class:`str`
+ :type psipred_confidence: :class:`int`
+ :type dssp_state: :class:`str`
+ :type score: :class:`float`
+
.. method:: Initialize(seqres)
Set up internal scorer with given seqres
@@ -240,6 +328,32 @@ The BackboneLoopScorer
:raises: :class:`RuntimeError` when *seqres_list* contains
element with invalid one letter code
+ .. method:: SetPsipredPrediction(pred)
+
+ Internally sets the psipred prediction, which is necessary to calculate the
+ SSAgreementScore.
+
+ :param pred: The prediction
+ :type pred: :class:`PsipredPrediction`
+
+ :raises: :class:`RuntimeError` If the scorer is not yet initialized,
+ the scorer is initialized for multiple chains or when the
+ the size of the prediction is inconsistent with the internal
+ seqres in the scorer.
+
+ .. method:: SetPsipredPrediction(pred)
+
+ Internally sets the psipred prediction, which is necessary to calculate the
+ SSAgreementScore.
+
+ :param pred: The prediction
+ :type pred: :class:`list` of :class:`PsipredPrediction`
+
+ :raises: :class:`RuntimeError` If the scorer is not yet initialized,
+ the number of predictions is inconsistent with the number of
+ internal chains or when one of the predictions sizes is
+ inconsistent with the according internal seqres
+
.. method:: SetEnvironment(env)
Sets structural environment with which loops to be scored interact.
@@ -276,6 +390,22 @@ The BackboneLoopScorer
when either start_resnum or chain_index point to
invalid positions in the SEQRES.
+ .. method:: ClearEnvironment(start_resnum, num_residues, [chain_index=0])
+
+ Clears a stretch of length *num_residues* in the environment in chain
+ with idx *chain_index* starting from residue number *start_resnum*
+
+ :param start_resnum: Start of stretch to clear
+ :param num_residues: Length of stretch to clear
+ :param chain_index: Chain the stretch belongs to
+
+ :type start_resnum: :class:`int`
+ :type num_residues: :class:`int`
+ :type chain_index: :class:`int`
+
+ :raises: :class:`RuntimeError` when either start_resnum or
+ chain_index point to invalid positions in the SEQRES.
+
.. method:: CalculateClashScore(bb_list, start_resnum, [chain_index=0])
:param bb_list: Loop to calculate the clash score
@@ -313,6 +443,25 @@ The BackboneLoopScorer
according potential or scorer have never been properly
initialized.
+ .. method:: CalculateReducedScore(bb_list, start_resnum, [chain_index=0])
+
+ :param bb_list: Loop to calculate the reduced score
+ :param start_resnum: ResNum defining the position in the SEQRES
+ (first element starts with one!)
+ :param chain_index: Index of the chain the loop belongs to
+
+ :type bb_list: :class:`BackboneList`
+ :type start_resnum: :class:`int`
+ :type chain_index: :class:`int`
+
+ :returns: reduced score
+
+ :raises: :class:`RuntimeError` if size of *bb_list* is smaller
+ than 3, the *chain_index*/*start_resnum* lead to
+ invalid positions in the SEQRES or when the
+ according potential or scorer have never been properly
+ initialized.
+
.. method:: CalculateTorsionScore(bb_list, start_resnum, [chain_index=0])
:param bb_list: Loop to calculate the torsion score
@@ -370,12 +519,10 @@ The BackboneLoopScorer
according potential or scorer have never been properly
initialized.
- .. method:: CalculateDSSPHBondScore(bb_list, start_resnum, [chain_index=0])
- Instead of calculate an hbond score based on a statistical potential,
- an the DSSP hbond energy function gets evaluated in this function.
+ .. method:: CalculateSSAgreementScore(bb_list, start_resnum, [chain_index=0])
- :param bb_list: Loop to calculate the hbond score
+ :param bb_list: Loop to calculate the SSAgreement score
:param start_resnum: ResNum defining the position in the SEQRES
(first element starts with one!)
:param chain_index: Index of the chain the loop belongs to
@@ -384,12 +531,14 @@ The BackboneLoopScorer
:type start_resnum: :class:`int`
:type chain_index: :class:`int`
- :returns: hbond score
+ :returns: SSAgreement score
:raises: :class:`RuntimeError` if size of *bb_list* is smaller
than 3, the *chain_index*/*start_resnum* lead to
- invalid positions in the SEQRES or when the
- scorer has never been properly initialized.
+ invalid positions in the SEQRES or, the
+ scorer have never been properly initialized,
+ or when no :class:`PsipredPrediction` is set to
+ the scorer.
.. method:: TransOmegaTorsions(bb_list, [thresh = 20/180*pi, allow_prepro_cis=True])
diff --git a/loop/doc/helper_classes.rst b/loop/doc/helper_classes.rst
new file mode 100644
index 0000000000000000000000000000000000000000..9c9e87fe2f18e79b12363274f74c5da1aeb46850
--- /dev/null
+++ b/loop/doc/helper_classes.rst
@@ -0,0 +1,552 @@
+Helper Classes
+================================================================================
+
+.. currentmodule:: promod3.loop
+
+This chapter describes helper classes, that are somehow related to the
+functionality in the loop module.
+
+Psipred
+--------------------------------------------------------------------------------
+
+
+
+
+.. class:: PsipredPrediction
+
+ A container for the secondary structure prediction by Psipred.
+
+ .. method:: PsipredPrediction()
+
+ Constructs empty container
+
+ .. method:: PsipredPrediction(prediction, confidence)
+
+ Constructs container with given content
+
+ :param prediction: Secondary structure prediction as element in ['H','E','C']
+ :param confidence: Confidence of prediction as element in [0,9]
+
+ :type prediction: :class:`list`
+ :type confidence: :class:`list`
+
+ :raises: :class:`RuntimeError` if size of **prediction** and
+ **confidence** are inconsistent or if they contain an
+ invalid element
+
+ .. method:: FromHHM(filename)
+
+ Static function to Load a :class:`PsipredPrediction` object from hhm file,
+ as they are provided by the hhsearch suite
+
+ :param filename: Name of file
+ :type filename: :class:`str`
+
+ .. method:: FromHoriz(filename)
+
+ Static function to Load a :class:`PsipredPrediction` object from horiz file,
+ as they are produced by the psipred executable
+
+ :param filename: Name of file
+ :type filename: :class:`str`
+
+ .. method:: Add(prediction, confidence)
+
+ Adds and appends a single residue psipred prediction at the end
+
+ :param prediction: Prediction, must be one in ['H','E','C']
+ :param confidence: Confidence of prediction, must be in [0,9]
+
+ :type prediction: :class:`str`
+ :type confidence: :class:`int`
+
+ :raises: :class:`RuntimeError` if input contains invalid elements
+
+ .. method:: Extract(from, to)
+
+ Extracts content and returns a sub-:class:`PsipredPrediction` with range **from**
+ to **to**, not including **to** itself
+
+ :param from: Idx to start
+ :param to: Idx to end
+
+ :type from: :class:`int`
+ :type to: :class:`int`
+
+ :returns: :class:`PsipredPrediction` with the specified range
+
+ :raises: :class:`RuntimeError` if **from** or **to** are invalid
+
+
+
+ .. method:: GetPrediction(idx)
+
+ :param idx: Index to get prediction from
+ :type idx: :class:`int`
+ :returns: Psipred prediction at pos **idx**
+ :raises: :class:`RuntimeError` if **idx** is invalid
+
+ .. method:: GetConfidence(idx)
+
+ :param idx: Index to get confidence from
+ :type idx: :class:`int`
+ :returns: Psipred confidence at pos **idx**
+ :raises: :class:`RuntimeError` if **idx** is invalid
+
+ .. method:: GetPredictions()
+
+ Get all the predictions in the container
+
+ :returns: :class:`list` containing all the predictions in the container
+
+
+ .. method:: GetConfidences()
+
+ Get all the confidences in the container
+
+ :returns: :class:`list` containing all the confidences in the container
+
+
+ .. method:: __len__()
+
+ :returns: Number of elements in container
+
+
+
+Handling several loops at once
+--------------------------------------------------------------------------------
+
+
+
+.. class:: LoopCandidate(backbone_list)
+
+ Object representing a possible configuration of the backbone of a particular loop being modelled. Apart from the positions, stored in a :class:`BackboneList`, it also has attributes storing different scores associated with the candidate (will be set by calling the corresponding scoring function in :class:`LoopCandidates`) as well as some information on the original structure from which this particular loop configuration was taken (in the case when the configuration was taken from the structural database).
+
+ :param backbone_list: Positions of the backbone atoms
+
+ :type backbone_list: :class:`BackboneList`
+
+ .. method:: CARMSD(other)
+
+ Calculates the C-alpha RMSD between this loop candidate and an *other* loop candidate, after superposition.
+
+ :param other: Other loop
+
+ :type other: :class:`LoopCandidate`
+
+ .. method:: RMSD(other)
+
+ Calculates the RMSD between this loop candidate and an *other* loop candidate, after superposition.
+
+ :param other: Other loop
+
+ :type other: :class:`LoopCandidate`
+
+ .. method:: GetOriginalSequence()
+
+ Returns the sequence of the original loop from the structural database, i.e. the sequence of the piece of structure from which the loop was taken.
+
+ :returns: A sequence
+
+ :rtype: :class:`str`
+
+ .. method:: GetOriginalDSSPState()
+
+ Returns the secondary structure of the original loop from the structural database, i.e. the secondary structure of the piece of structure from which the loop was taken.
+
+ :returns: The secondary structure code as given in DSSP
+
+ :rtype: :class:`str`
+
+ .. attribute:: bb_list
+
+ The backbone list containing the positions of the backbone atoms
+
+ :type: :class:`BackboneList`
+
+
+ .. attribute:: clash_score
+
+ The clash score of the loop candidate
+
+ :type: :class:`float`
+
+ .. attribute:: cbeta_score
+
+ The C-beta score of the loop candidate
+
+ :type: :class:`float`
+
+ .. attribute:: reduced_score
+
+ The reduced score of the loop candidate
+
+ :type: :class:`float`
+
+ .. attribute:: torsion_score
+
+ The torsion score of the loop candidate
+
+ :type: :class:`float`
+
+ .. attribute:: packing_score
+
+ The packing score of the loop candidate
+
+ :type: :class:`float`
+
+ .. attribute:: hbond_score
+
+ The HBond score of the loop candidate
+
+ :type: :class:`float`
+
+ .. attribute:: ss_agreement
+
+ The SSAgreement score of the loop candidate
+
+ :type: :class:`float`
+
+ .. attribute:: combined_score
+
+ Score value intended to be a placeholder for an arbitrary combination
+ of the other scores
+
+ :type: :class:`float`
+
+
+.. class:: LoopCandidates(seq)
+
+ The *LoopCandidates* is a helper class used as a container for
+ :class:`LoopCandidate` objects enforcing consistent length
+ and sequence among them. It can either be filled manually or
+ generated using static filling functions using the functionality
+ from the :class:`FragDB` or Monte Carlo algorithms. Once it contains
+ candidates you can apply closing, scoring or clustering algorithms on the content.
+ Note, that you have to attach a scorer object before any scoring action.
+
+ :param seq: The sequence being enforced for all candidates
+
+ :type sequence: :class:`str`
+
+
+ .. staticmethod:: FillFromDatabase(n_stem, c_stem, seq, frag_db, \
+ structural_db, extended_search=False)
+
+ Searches for loop candidates matching the length (number of residues in *seq*) and geometry (of *n_stem* and *c_stem*) of the loop to be modelled in a fragment database.
+
+ :param n_stem: The residue at the N-terminal end of the loop
+ :param c_stem: The residue at the C-terminal end of the loop
+ :param seq: The sequence of residues to be added including the
+ *n_stem* and *c_stem*
+ :param frag_db: The fragment database
+ :param structural_db: The according structural database
+ :param extended_search: Whether search should be extended to fragments
+ matching the geometry of the *n_stem* and *c_stem*
+ a bit less precisely.
+
+ :type n_stem: :class:`ost.mol.ResidueHandle`
+ :type c_stem: :class:`ost.mol.ResidueHandle`
+ :type seq: :class:`str`
+ :type frag_db: :class:`FragDB`
+ :type structural_db: :class:`StructureDB`
+ :type extended_search: :class:`bool`
+
+ :returns: A list of loop candidates
+ :rtype: :class:`LoopCandidates`
+
+ .. staticmethod:: FillFromMonteCarloSampler(seq, num_loops, steps, \
+ sampler, closer, scorer, cooler)
+ FillFromMonteCarloSampler(initial_bb, seq, num_loops, steps, \
+ sampler, closer, scorer, cooler)
+
+ Uses Monte Carlo simulated annealing to sample the loop to be modelled.
+ If *initial_bb* is given, every Monte Carlo run starts from that configuration.
+
+ :param initial_bb: Initial configuration used for the sampling
+ :param seq: The sequence of residues to be sampled
+ :param num_loops: Number of loop candidates to return
+ :param steps: Number of MC steps to perform for each loop candidate
+ generated
+ :param sampler: Used to generate a new configuration at each MC step
+ :param closer: Used to close the loop after each MC step
+ :param scorer: Used to score the generated configurations at each MC step
+ :param cooler: Controls the temperature profile of the simulated annealing
+
+ :type initial_bb: :class:`BackboneList`
+ :type seq: :class:`str`
+ :type num_loops: :class:`int`
+ :type steps: :class:`int`
+ :type sampler: :ref:`mc-sampler-object`
+ :type closer: :ref:`mc-closer-object`
+ :type scorer: :ref:`mc-scorer-object`
+ :type cooler: :ref:`mc-cooler-object`
+
+ :returns: The resulting candidates
+ :rtype: :class:`LoopCandidates`
+
+ :raises: A :exc:`RuntimeError`, if *initial_bb* is not given and the Monte
+ Carlo sampler failed to initialize (i.e. stems are too far apart)
+ :raises: A :exc:`RuntimeError`, if *initial_bb* is given and it is
+ inconsistent with *seq*
+
+ .. method:: ClusterCandidates(max_dist, neglect_size_one = true)
+
+ Clusters the loop candidates according to their pairwise CARMSD using a greedy
+ hierarchical clustering algorithm. Every candidate gets assigned a unique cluster.
+ At every clustering step, the two clusters with shortest distance get merged, with
+ the distance definition being the maximal CARMSD between any of the members
+ of the two clusters.
+
+ :param max_dist: Maximal distance two clusters can have to be merged
+ :param neglect_size_one: Whether clusters should be added to the return
+ list if they only contain one :class:`LoopCandidate`
+
+ :type max_dist: :class:`float`
+ :type neglect_size_one: :class:`bool`
+
+
+ :returns: A list of :class:`LoopCandidates`. Each element in the list
+ corresponds to the candidates in one cluster.
+
+ .. method:: ApplyCCD(n_stem, c_stem, max_iterations=1000, \
+ rmsd_cutoff=0.1, keep_non_converged=false, random_seed=0)
+ ApplyCCD(n_stem, c_stem, torsion_sampler, max_iterations=1000, \
+ rmsd_cutoff=0.1, keep_non_converged=false, random_seed=0)
+ ApplyCCD(n_stem, c_stem, torsion_samplers, max_iterations=1000, \
+ rmsd_cutoff=0.1, keep_non_converged=false, random_seed=0)
+
+ Closes all :class:`LoopCandidate` in :class:`LoopCandidates` using the CCD
+ algorithm (i.e. modifies the :class:`LoopCandidate` so that its stem residues
+ match those of *n_stem* and *c_stem*). CCD (cyclic coordinate descent, see
+ :class:`~promod3.loop.CCD`) is an iterative minimization algorithm.
+
+ If *torsion_sampler* or *torsion_samplers* is given, it is used at each step
+ of the closing to calculate the probability of the proposed move, which is
+ then accepted or not depending on a metropolis criterium.
+
+ :param n_stem: Residue defining the n-stem positions every
+ candidate should match
+ :param c_stem: Residue defining the c-stem positions every
+ candidate should match
+ :param torsion_sampler: The torsion sampler
+ :param torsion_samplers: A list containing one torsion sampler for each
+ residue in the loop
+ :param max_iterations: Maximum number of iteration
+ :param rmsd_cutoff: Cutoff in stem residue RMSD used to determine
+ convergence
+ :param keep_non_converged: Whether to keep loop candidates for which the
+ closing did not converged
+ :param random_seed: seed for random number generator used to
+ accept/reject moves in CCD algorithm
+
+ :type n_stem: :class:`ost.mol.ResidueHandle`
+ :type c_stem: :class:`ost.mol.ResidueHandle`
+ :type torsion_sampler: :class:`TorsionSampler`
+ :type torsion_samplers: :class:`list` of :class:`TorsionSampler`
+ :type max_iterations: :class:`int`
+ :type rmsd_cutoff: :class:`float`
+ :type keep_non_converged: :class:`bool`
+ :type random_seed: :class:`int`
+
+
+ .. method:: ApplyKIC(n_stem, c_stem, pivot_one, pivot_two, pivot_three)
+
+ Closes all :class:`LoopCandidate` in :class:`LoopCandidates` (i.e. modifies
+ the :class:`LoopCandidate` so that its stem residues match those of
+ *n_stem* and *c_stem*, which are the stem residues of the loop being
+ modelled), using the KIC algorithm. This algorithm finds analytical
+ solutions for closing the loop by modifying the torsion angles of just
+ three pivot residues. Due to the underlying mathematical formalism in KIC,
+ up to 16 solutions can be found for every candidate. This leads to an
+ increase in number of loops.
+
+ :param n_stem: Residue defining the n-stem positions every candidate
+ should match
+ :param c_stem: Residue defining the c-stem positions every candidate
+ should match
+ :param pivot_one: First pivot residue
+ :param pivot_two: Second pivot residue
+ :param pivot_three: Third pivot residue
+
+ :type n_stem: :class:`ost.mol.ResidueHandle`
+ :type c_stem: :class:`ost.mol.ResidueHandle`
+ :type pivot_one: :class:`int`
+ :type pivot_two: :class:`int`
+ :type pivot_three: :class:`int`
+
+
+ .. method:: Add(loop_candidate)
+
+ Add a loop candidate to the list of candidates
+
+ :param loop_candidate: The loop candidate
+ :type loop_candidate: :class:`LoopCandidate`
+
+ :raises: :class:`RuntimeError` If sequence of *loop_candidate* is not consistent
+ with internal sequence
+
+ .. method:: Add(bb_list)
+
+ Add a loop candidate to the list of candidates from a list of backbone positions
+
+ :param bb_list: The backbone list
+ :type bb_list: :class:`BackboneList`
+
+ :raises: :class:`RuntimeError` If sequence of *bb_list* is not consistent
+ with internal sequence
+
+ .. method:: Remove(index)
+
+ Remove a loop candidate from the list of candidates.
+
+ :param index: The index of the candidate that will be removed
+ :type index: :class:`int`
+
+ .. method:: AttachScorer(scorer)
+
+ Attaches a scorer to the :class:`LoopCandidates`. The scorer contains the information about the environment of the loop candidates and is mandatory to calculate the different scores for the loop candidates.
+
+ :param scorer: The scorer
+ :type scorer: :class:`BackboneLoopScorer`
+
+
+ .. method:: CalculateClasScores(start_resnum, [chain_index=0])
+
+ Calculates and assigns the clash score for each :class:`LoopCandidate`.
+
+ :param start_resnum: Residue number of the starting residue of the candidates being scored
+ (residue numbers start with one!)
+ :param chain_index: The index of the chain to which the loop belongs (index relative to the entity forming the environment in the :class:`BackboneLoopScorer`)
+
+ :type start_resnum: :class:`int`
+ :type chain_index: :class:`int`
+
+
+ .. method:: CalculateBetaScores(start_resnum, [chain_index=0])
+
+ Calculates and assigns the cbeta score for each :class:`LoopCandidate`.
+
+ :param start_resnum: Residue number of the starting residue of the candidates being scored
+ (residue numbers start with one!)
+ :param chain_index: The index of the chain to which the loop belongs (index relative to the entity forming the environment in the :class:`BackboneLoopScorer`)
+
+ :type start_resnum: :class:`int`
+ :type chain_index: :class:`int`
+
+ .. method:: CalculateReducedScores(start_resnum, [chain_index=0])
+
+ Calculates and assigns the reduced score for each :class:`LoopCandidate`.
+
+ :param start_resnum: Residue number of the starting residue of the candidates being scored
+ (residue numbers start with one!)
+ :param chain_index: The index of the chain to which the loop belongs (index relative to the entity forming the environment in the :class:`BackboneLoopScorer`)
+
+ :type start_resnum: :class:`int`
+ :type chain_index: :class:`int`
+
+
+ .. method:: CalculateTorsionScores(start_resnum, [chain_index=0])
+
+ Calculates and assigns the torsion score for each :class:`LoopCandidate`.
+
+ :param start_resnum: Residue number of the starting residue of the candidates being scored
+ (residue numbers start with one!)
+ :param chain_index: The index of the chain to which the loop belongs (index relative to the entity forming the environment in the :class:`BackboneLoopScorer`)
+
+ :type start_resnum: :class:`int`
+ :type chain_index: :class:`int`
+ .. method:: CalculatePackingScores(start_resnum, [chain_index=0])
+
+ Calculates and assigns the packing score for each :class:`LoopCandidate`.
+
+ :param start_resnum: Residue number of the starting residue of the candidates being scored
+ (residue numbers start with one!)
+ :param chain_index: The index of the chain to which the loop belongs (index relative to the entity forming the environment in the :class:`BackboneLoopScorer`)
+
+ :type start_resnum: :class:`int`
+ :type chain_index: :class:`int`
+
+ .. method:: CalculateHBondcores(start_resnum, [chain_index=0])
+
+ Calculates and assigns the HBond score for each :class:`LoopCandidate`.
+
+ :param start_resnum: Residue number of the starting residue of the candidates being scored
+ (residue numbers start with one!)
+ :param chain_index: The index of the chain to which the loop belongs (index relative to the entity forming the environment in the :class:`BackboneLoopScorer`)
+
+ :type start_resnum: :class:`int`
+ :type chain_index: :class:`int`
+
+ .. method:: CalculateSSAgreementScores(start_resnum, [chain_index=0])
+
+ Calculates and assigns the SSAgreement score for each :class:`LoopCandidate`.
+
+ :param start_resnum: Residue number of the starting residue of the candidates being scored
+ (residue numbers start with one!)
+ :param chain_index: The index of the chain to which the loop belongs (index relative to the entity forming the environment in the :class:`BackboneLoopScorer`)
+
+ :type start_resnum: :class:`int`
+ :type chain_index: :class:`int`
+
+
+ .. method:: CalculateCombinedScores(linear_weights, start_resnum, [chain_index=0])
+
+ Calculates and assigns an arbitrary linear combination of all the available scores for each :class:`LoopCandidate`.
+
+
+ :param linear_weights: Defining the linear weights of the scores as key value pairs. Allowed
+ keys are: ["cbeta","clash","torsion","cb_packing","hbond","ss_agreement", "reduced", "intercept"]
+ For every key, the according function in the attached
+ :class:`BackboneLoopScorer` gets called and the returned score added to
+ the final score with the according weight. If there is an intercept given,
+ the according value also gets added to the final score.
+ :param start_resnum: Residue number of the starting residue of the candidates being scored
+ (residue numbers start with one!)
+ :param chain_index: The index of the chain to which the loop belongs (index relative to the entity forming the environment in the :class:`BackboneLoopScorer`)
+
+ :type linear_weights: :class:`dict`
+ :type start_resnum: :class:`int`
+ :type chain_index: :class:`int`
+
+
+
+ .. method:: GetAVGClashScore()
+
+ :return: The average of the clash scores of all :class:`LoopCandidate`.
+ :rtype: float
+
+ .. method:: GetAVGCBetaScore()
+
+ :return: The average of the cbeta scores of all :class:`LoopCandidate`.
+ :rtype: float
+
+ .. method:: GetAVGReducedScore()
+
+ :return: The average of the reduced scores of all :class:`LoopCandidate`.
+ :rtype: float
+
+ .. method:: GetAVGTorsionScore()
+
+ :return: The average of the torsion scores of all :class:`LoopCandidate`.
+ :rtype: float
+
+ .. method:: GetAVGPackingScore()
+
+ :return: The average of the packing scores of all :class:`LoopCandidate`.
+ :rtype: float
+
+ .. method:: GetAVGHBondscore()
+
+ :return: The average of the HBond scores of all :class:`LoopCandidate`.
+ :rtype: float
+
+ .. method:: GetAVGSSAgreementscore()
+
+ :return: The average of the SSAgreement scores of all :class:`LoopCandidate`.
+ :rtype: float
+
+ .. method:: GetAVGCombinedScore()
+
+ :return: The average of the combined scores of all :class:`LoopCandidate`.
+ :rtype: float
\ No newline at end of file
diff --git a/loop/doc/index.rst b/loop/doc/index.rst
index 4d7e4abf1979161b2b1bba9e59590f11892f5d1c..b74674a2960992ed55bb408b85bcefcb8e242574 100644
--- a/loop/doc/index.rst
+++ b/loop/doc/index.rst
@@ -45,7 +45,7 @@ you a starting point to get an idea of what can be done.
#The candidates usually don't match exactly the required stem coordinates
#CCD (Cyclic Coordinate Descent) is one way to enforce this match.
- loop_candidates.ApplyCCD()
+ loop_candidates.ApplyCCD(n_stem, c_stem)
#now it's time to select one candidate, we load a scorer object to do that
scorer = loop.LoadBackboneLoopScorer()
@@ -57,10 +57,12 @@ you a starting point to get an idea of what can be done.
#the scorer can then be attached to the LoopCandidates object
#to calculate several different scores, we go for a distance dependent
#statistical potential considering the CBeta positions of each residue
- #and a clash score
+ #and a clash score. To calculate the actual score we also have to pass
+ #the location of our loop candidates in the overall structure
+ # => resnum = 24
loop_candidates.AttachScorer(scorer)
- loop_candidates.CalculateCBetaScores()
- loop_candidates.CalculateClashScores()
+ loop_candidates.CalculateCBetaScores(24)
+ loop_candidates.CalculateClashScores(24)
#we simply sum up the previously calculated scores and search for the
#loop with minimal score
@@ -72,10 +74,10 @@ you a starting point to get an idea of what can be done.
min_score = score
min_candidate = i
- #let's insert that loop and save the structure down to disk
- loop_candidates.InsertInto(crambin,min_candidate)
- io.SavePDB(crambin,"remodeled_crambin.pdb")
-
+ #let's insert the found loop into our structure and save it down
+ bb_list = loop_candidates[min_candidate].bb_list
+ bb_list.InsertInto(crambin.chains[0],n_stem.GetNumber())
+ io.SavePDB(crambin,"modified_crambin.pdb")
Contents:
@@ -88,5 +90,5 @@ Contents:
Closing Loops - adapt them to the environment <loop_closing>
Loop Scoring <backbone_loop_score>
Generating Loops DeNovo <monte_carlo>
- Handle several loop candidates at once <loop_candidate>
Loading Precomputed Loop Objects <load_loop_objects>
+ Helper Classes <helper_classes>
diff --git a/loop/doc/load_loop_objects.rst b/loop/doc/load_loop_objects.rst
index 0a5d8bb7e51f973ca739c3a91f849ee934a79051..f14289b9b7a92c14936a626f943ae26b20f01f68 100644
--- a/loop/doc/load_loop_objects.rst
+++ b/loop/doc/load_loop_objects.rst
@@ -65,7 +65,8 @@ Several data objects are used throughout the loop module.
.. method:: LoadFragDB()
- Loads and returns a FragDB with the default StructureDB attached.
+ Loads and returns a FragDB containing fragments up to the length of 14,
+ therefore capable of bridging gaps up to the length of 12.
:returns: The Fragment database
:rtype: :class:`FragDB`
diff --git a/loop/doc/loop_candidate.rst b/loop/doc/loop_candidate.rst
deleted file mode 100644
index d5cdd9b6c52b5524a6e7ca3488bc4d1d79a64cc6..0000000000000000000000000000000000000000
--- a/loop/doc/loop_candidate.rst
+++ /dev/null
@@ -1,388 +0,0 @@
-Loop Candidates
-================================================================================
-
-.. currentmodule:: promod3.loop
-
-.. class:: LoopCandidate(backbone_list)
-
- Object representing a possible configuration of the backbone of a particular loop being modelled. Apart from the positions, stored in a :class:`BackboneList`, it also has attributes storing different scores associated with the candidate (will be set by calling the corresponding scoring function in :class:`LoopCandidates`) as well as some information on the original structure from which this particular loop configuration was taken (in the case when the configuration was taken from the structural database).
-
- :param backbone_list: Positions of the backbone atoms
-
- :type backbone_list: :class:`BackboneList`
-
- .. method:: CARMSD(other)
-
- Calculates the C-alpha RMSD between this loop candidate and an *other* loop candidate, after superposition.
-
- :param other: Other loop
-
- :type other: :class:`LoopCandidate`
-
- .. method:: RMSD(other)
-
- Calculates the RMSD between this loop candidate and an *other* loop candidate, after superposition.
-
- :param other: Other loop
-
- :type other: :class:`LoopCandidate`
-
- .. method:: GetoriginalSequence()
-
- Returns the sequence of the original loop from the structural database, i.e. the sequence of the piece of structure from which the loop was taken.
-
- :returns: A sequence
-
- :rtype: :class:`str`
-
- .. method:: GetoriginalDSSPState()
-
- Returns the secondary structure of the original loop from the structural database, i.e. the secondary structure of the piece of structure from which the loop was taken.
-
- :returns: The secondary structure code as given in DSSP
-
- :rtype: :class:`str`
-
- .. attribute:: bb_list
-
- The backbone list containing the positions of the backbone atoms
-
- :type: :class:`BackboneList`
-
- .. attribute:: stem_rmsd
-
- The backbone RMSD of the two stem residues of the loop candidate relative to the stem residues for which the loop is being modelled. This is a measure of how well the loop candidate fits in the structure where it is being added.
-
- :type: :class:`float`
-
- .. attribute:: clash_score
-
- The clash score of the loop candidate
-
- :type: :class:`float`
-
- .. attribute:: cbeta_score
-
- The C-beta score of the loop candidate
-
- :type: :class:`float`
-
- .. attribute:: torsion_score
-
- The torsion score of the loop candidate
-
- :type: :class:`float`
-
- .. attribute:: packing_score
-
- The packing score of the loop candidate
-
- :type: :class:`float`
-
- .. attribute:: hbond_score
-
- The H-bond score of the loop candidate
-
- :type: :class:`float`
-
- .. attribute:: dssp_hbond_score
-
- The DSSP H-bond of the loop candidate
-
- :type: :class:`float`
-
-
-.. class:: LoopCandidates(n_stem,c_stem,seq)
-
- The *LoopCandidates* is the basic object used for loop modelling.
- It contains the positions of the two anchor residues, the *n_stem* and *c_stem*
- residues, and the sequence of the residues to be modelled in between these
- anchor residues.
- It also contains a list of :class:`LoopCandidate`, which are possible
- conformations of the backbone between the stem residues.
-
-
- :param n_stem: The residue at the N-terminal end of the loop
- :param c_stem: The residue at the C-terminal end of the loop
- :param seq: The sequence of residues to be added between the
- *n_stem* and *c_stem*
-
- :type n_stem: :class:`ost.mol.ResidueHandle`
- :type c_stem: :class:`ost.mol.ResidueHandle`
- :type sequence: :class:`str`
-
-
- .. staticmethod:: FillFromDatabase(n_stem, c_stem, seq, frag_db, \
- structural_db, extended_search=False)
-
- Searches for loop candidates matching the length (number of residues in *seq*) and geometry (of *n_stem* and *c_stem*) of the loop to be modelled in a fragment database.
-
- :param n_stem: The residue at the N-terminal end of the loop
- :param c_stem: The residue at the C-terminal end of the loop
- :param seq: The sequence of residues to be added between the
- *n_stem* and *c_stem*
- :param frag_db: The fragment database
- :param structural_db: The according structural database
- :param extended_search: Whether search should be extended to fragments
- matching the geometry of the *n_stem* and *c_stem*
- a bit less precisely.
-
- :type n_stem: :class:`ost.mol.ResidueHandle`
- :type c_stem: :class:`ost.mol.ResidueHandle`
- :type seq: :class:`str`
- :type frag_db: :class:`FragDB`
- :type structural_db: :class:`StructureDB`
- :type extended_search: :class:`bool`
-
- :returns: A list of loop candidates
- :rtype: :class:`LoopCandidates`
-
- .. staticmethod::
- FillFromMonteCarloSampler(n_stem, c_stem, seq, num_loops, \
- steps, sampler, closer, scorer, cooler)
- FillFromMonteCarloSampler(n_stem, c_stem, initial_bb, seq, num_loops, \
- steps, sampler, closer, scorer, cooler)
-
- Uses Monte Carlo simulated annealing to sample the loop to be modelled.
-
- :param n_stem: The residue at the N-terminal end of the loop
- :param c_stem: The residue at the C-terminal end of the loop
- :param initial_bb: Initial configuration used for the sampling (optional)
- :param seq: The sequence of residues to be added between the
- *n_stem* and *c_stem*
- :param num_loops: Number of loop candidates to return
- :param steps: Number of MC steps to perform for each loop candidate
- generated
- :param sampler: Used to generate a new configuration at each MC step
- :param closer: Used to close the loop (make it match the *n_stem*
- and *c_stem* geometry) after each MC step
- :param scorer: Used to score the generated configurations at each
- MC step
- :param cooler: Controls the temperature profile of the simulated annealing
-
- :type n_stem: :class:`ost.mol.ResidueHandle`
- :type c_stem: :class:`ost.mol.ResidueHandle`
- :type initial_bb: :class:`BackboneList`
- :type seq: :class:`str`
- :type num_loops: :class:`int`
- :type steps: :class:`int`
- :type sampler: :ref:`mc-sampler-object`
- :type closer: :ref:`mc-closer-object`
- :type scorer: :ref:`mc-scorer-object`
- :type cooler: :ref:`mc-cooler-object`
-
- :returns: A list of loop candidates
- :rtype: :class:`LoopCandidates`
-
- :raises: A :exc:`RuntimeError`, if *initial_bb* is not given and the Monte
- Carlo sampler failed to initialize (i.e. stems are too far apart)
- :raises: A :exc:`RuntimeError`, if *initial_bb* is given and it is
- inconsistent with *seq*
-
- .. method:: ClusterCandidates()
-
- Clusters the loop candidates according to their pairwise CA-RMSD using a
- FLAME (fuzzy clustering by local approximation fo memberships) clustering
- algorithm.
-
- :returns: A list of :class:`LoopCandidates`. Each element in the list
- corresponds to the candidates in one cluster.
-
- .. method:: ApplyCCD(max_iterations=1000, rmsd_cutoff=0.1, \
- keep_non_converged=false, random_seed=0, step_size=1.0)
- ApplyCCD(torsion_sampler, max_iterations=1000, rmsd_cutoff=0.1, \
- keep_non_converged=false, random_seed=0, step_size=1.0)
- ApplyCCD(torsion_samplers, max_iterations=1000, rmsd_cutoff=0.1, \
- keep_non_converged=false, random_seed=0, step_size=1.0)
-
- Closes all :class:`LoopCandidate` in :class:`LoopCandidates` using the CCD
- algorithm (i.e. modifies the :class:`LoopCandidate` so that its stem residues
- match those of the :class:`LoopCandidates`, which are the stem residues of the
- loop being modelled).
- CCD (cyclic coordinate descent, see :class:`~promod3.loop.CCD`) is an
- iterative minimization algorithm.
-
- If *torsion_sampler* or *torsion_samplers* is given, it is used at each step
- of the closing to calculate the probability of the proposed move, which is
- then accepted (or not) depending on a metropolis criterium.
-
- :param torsion_sampler: the torsion sampler
- :param torsion_samplers: a list containing one torsion sampler for each
- residue in the loop.
- :param max_iterations: maximum number of iteration
- :param rmsd_cutoff: cutoff in stem residue RMSD used to determine
- convergence
- :param keep_non_converged: whether to keep loop candidates for which the
- closing did not converge. If this is False, it
- erases loop candidates which didn't converge!
- :param random_seed: seed for random number generator
- :param step_size: size of the steps taken during loop closing.
-
- :type torsion_sampler: :class:`TorsionSampler`
- :type torsion_samplers: :class:`list` of :class:`TorsionSampler`
- :type max_iterations: :class:`int`
- :type rmsd_cutoff: :class:`float`
- :type keep_non_converged: :class:`bool`
- :type random_seed: :class:`int`
- :type step_size: :class:`float`
-
- .. method:: ApplyKIC(pivot_one,pivot_two,pivot_three)
-
- Closes all :class:`LoopCandidate` in :class:`LoopCandidates` (i.e. modifies the :class:`LoopCandidate` so that its stem residues match those of the :class:`LoopCandidates`, which are the stem residues of the loop being modelled), using the KIC algorithm. This algorithm finds analytical solutions for closing the loop by modifying the torsion angles of just three pivot residues. Due to the underlying mathematical formalism in KIC, up to 16 solutions can be found for every candidate. This leads to an increase in number of loops.
-
- :param pivot_one: Maximum number of iteration
- :param pivot_two: Cutoff in stem residue RMSD used
- :param pivot_three: Wether to keep loop candidates for
-
- :type max_iterations: :class:`int`
- :type rmsd_cutoff: :class:`float`
- :type keep_non_converged: :class:`bool`
- :type random_seed: :class:`int`
- :type step_size: :class:`float`
-
- .. method:: ToEntity(index)
-
- Transforms the loop candidate with index *index* in the list of candidates into an :class:`ost.mol.EntityHandle`.
-
- :param index: The index of the :class:`LoopCandidate` that will be transformed into an class:`ost.mol.EntityHandle`
- :type index: :class:`int`
-
- :returns: An class:`ost.mol.EntityHandle`
-
- .. method:: InsertInto(entity,index)
-
- Inserts the loop candidate with index *index* in the list of candidates into the *entity*.
-
- :param index: The index of the :class:`LoopCandidate`
- :param entity: The entity
-
- :type index: :class:`int`
- :type entity: class:`ost.mol.EntityHandle`
-
- .. method:: CalculateClasScores([chain_index=0])
-
- Calculates and assigns the clash score for each :class:`LoopCandidate`. Scores include interactions within the loop and between the loop and the environment (set in the scorer).
-
- :param chain_index: The index of the chain to which the loop belongs (index relative to the entity forming the environment in the :class:`BackboneScorer`)
- :type chain_index: :class:`int`
-
-
- .. method:: CalculateBetaScores([chain_index=0])
-
- Calculates and assigns the C-beta score for each :class:`LoopCandidate`. Scores include interactions within the loop and between the loop and the environment (set in the scorer).
- This score is a pairwise statistical potential based only on C-beta positions.
-
- :param chain_index: The index of the chain to which the loop belongs (index relative to the entity forming the environment in the :class:`BackboneScorer`)
- :type chain_index: :class:`int`
-
- .. method:: CalculateTorsionScores([chain_index=0])
-
- Calculates and assigns the torsion score for each :class:`LoopCandidate`. This score only includes contributions from the torsion angles of the :class:`LoopCandidate`.
-
- This score is a statistical potential based only on backbone dihedral angles specific for triplet of residues (torsion potential depends on the identity of the residue and its two neighbors).
-
- :param chain_index: The index of the chain to which the loop belongs (index relative to the entity forming the environment in the :class:`BackboneScorer`)
- :type chain_index: :class:`int`
-
- .. method:: CalculatePackingScores([chain_index=0])
-
- Calculates and assigns the packing score for each :class:`LoopCandidate`. Scores include interactions within the loop and between the loop and the environment (set in the scorer).
- This score is a statistical potential measuring and scoring the solvent exposure of the residues.
-
- :param chain_index: The index of the chain to which the loop belongs (index relative to the entity forming the environment in the :class:`BackboneScorer`)
- :type chain_index: :class:`int`
-
- .. method:: CalculateHBondcores([chain_index=0])
-
- Calculates and assigns the HBond score for each :class:`LoopCandidate`. Scores include interactions within the loop and between the loop and the environment (set in the scorer).
- This score measures the energy of H-bonds.
-
- :param chain_index: The index of the chain to which the loop belongs (index relative to the entity forming the environment in the :class:`BackboneScorer`)
- :type chain_index: :class:`int`
-
- .. method:: CalculateDSSPHBondScores([chain_index=0])
-
- Calculates and assigns the C-beta score for each :class:`LoopCandidate`. Scores include interactions within the loop and between the loop and the environment (set in the scorer).
- This score measures the energy of H-bonds as defined by DSSP.
-
- :param chain_index: The index of the chain to which the loop belongs (index relative to the entity forming the environment in the :class:`BackboneScorer`)
- :type chain_index: :class:`int`
-
- .. method:: CalculateStemRMSD()
-
- Calculates and assigns the stem RMSD (i.e. the RMSD between the stem residues of the loop candidate and the stem residues of the loop being modelled) for each :class:`LoopCandidate`.
-
- .. method:: GetAVGClasScore()
-
- :return: The average of the clash scores of all :class:`LoopCandidate`.
- :rtype: float
-
- .. method:: GetAVGCBetaScore()
-
- :return: The average of the C-beta scores of all :class:`LoopCandidate`.
- :rtype: float
-
- .. method:: GetAVGTorsionScore()
-
- :return: The average of the torsion scores of all :class:`LoopCandidate`.
- :rtype: float
-
- .. method:: GetAVGPackingScore()
-
- :return: The average of the packing scores of all :class:`LoopCandidate`.
- :rtype: float
-
- .. method:: GetAVGHBondcore()
-
- :return: The average of the H-bond scores of all :class:`LoopCandidate`.
- :rtype: float
-
- .. method:: GetAVGDSSPHBondScore()
-
- :return: The average of the DSSP H-bond scores of all :class:`LoopCandidate`.
- :rtype: float
-
- .. method:: GetAVGStemRMSD()
-
- :return: The average of the stem RMSDs of all :class:`LoopCandidate`.
- :rtype: float
-
- .. method:: GetNStem()
-
- :return: The N-stem of loop being modelled
- :rtype: :class:`ost.mol.EntityHandle`
-
- .. method:: GetCStem()
-
- :return: The C-stem of loop being modelled
- :rtype: :class:`ost.mol.EntityHandle`
-
- .. method:: Add(loop_candidate)
-
- Add a loop candidate to the list of candidates
-
- :param loop_candidate: The loop candidate
- :type loop_candidate: :class:`LoopCandidate`
-
- .. method:: Add(bb_list)
-
- Add a loop candidate to the list of candidates from a list of backbone positions
-
- :param bb_list: The backbone list
- :type bb_list: :class:`BackboneList`
-
- .. method:: Remove(index)
-
- Remove a loop candidate from the list of candidates.
-
- :param index: The index of the candidate that will be removed
- :type index: :class:`int`
-
- .. method:: AttachScorer(scorer)
-
- Attaches a scorer to the :class:`LoopCandidates`. The scorer contains the information about the environment of the loop candidates and is mandatory to calculate the different scores for the loop candidates.
-
- :param scorer: The scorer
- :type scorer: :class:`BackboneLoopScorer`
-
-
diff --git a/loop/doc/structure_db.rst b/loop/doc/structure_db.rst
index 0f792588a93a6c6198fa4b9a22d4faad8a08c8d2..5841a3c225c1ef26472d2ff2567591ddd723cab1 100644
--- a/loop/doc/structure_db.rst
+++ b/loop/doc/structure_db.rst
@@ -572,8 +572,8 @@ ultra fast.
:param frag_size: The length of the fragment
:param extended_search: Whether an extended search should be performed, which will include fragments from bins surrounding the bin describing the **n_stem** and **c_stem** geometry.
- :type n_stem: :class:`ost.mol.ResidueHandle`
- :type c_stem: :class:`ost.mol.ResidueHandle`
+ :type n_stem: :class:`ost.mol.ResidueHandle` / :class:`Backbone`
+ :type c_stem: :class:`ost.mol.ResidueHandle` / :class:`Backbone`
:type frag_size: :class:`float`
:type extended_search: :class:`bool`
@@ -707,19 +707,15 @@ arbitrary linear combination of following components:
:type w: :class:`float`
:type subst: :class:`ost.seq.SubstWeightMatrix`
- .. method:: AddSSAgreeParameters(w, psipred_prediction, psipred_confidence)
+ .. method:: AddSSAgreeParameters(w, psipred_prediction)
Add SSAgree score component with linear weight **w**
:param w: linear weight
- :param psipred_prediction: Secondary structure state ('H','E','C') as predicted
- by PSIPRED for every item in the Fraggers target sequence
- :param psipred_confidence: Confidence for secondary structure state ([0,9]) as predicted
- by PSIPRED for every item in the Fraggers target sequence
+ :param psipred_prediction: Psipred prediction for fraggers target_sequence
:type w: :class:`str`
- :type psipred_prediction: :class:`list`
- :type psipred_confidence: :class:`list`
+ :type psipred_prediction: :class:`PsipredPrediction`
.. method:: AddSequenceProfileParameters(w, hmm)
diff --git a/loop/pymod/CMakeLists.txt b/loop/pymod/CMakeLists.txt
index 3e10528de5ddc0fa7197710759a18c56f8905789..aa24d300115eb879c8fc6cc0b9043ca4661c6e63 100644
--- a/loop/pymod/CMakeLists.txt
+++ b/loop/pymod/CMakeLists.txt
@@ -9,6 +9,7 @@ export_loop_object_loader.cc
export_loop_score.cc
export_loop_closure.cc
export_fragger.cc
+export_psipred_prediction.cc
wrap_loop.cc
)
diff --git a/loop/pymod/__init__.py b/loop/pymod/__init__.py
index 13572b1bc16d5462fc17a512e64b986d71dfc1e4..9725f9223db22a93595dc31fa64ef9055911ba70 100644
--- a/loop/pymod/__init__.py
+++ b/loop/pymod/__init__.py
@@ -1,3 +1,169 @@
'''__init__.py of the loop module
'''
from _loop import *
+
+# TODO: extract this into some _....py file and import here (like in modelling)
+from ost.conop import OneLetterCodeToResidueName
+
+def _AssembleTorsionSamplers(psipred_pred,
+ torsion_sampler_coil,
+ torsion_sampler_helix,
+ torsion_sampler_extended):
+
+ samplers = [torsion_sampler_coil]*len(psipred_pred)
+ for i in range(len(psipred_pred)):
+ if psipred_pred.GetPrediction(i) == 'H' and psipred_pred.GetConfidence(i) >= 6:
+ samplers[i] = torsion_sampler_helix
+ if psipred_pred.GetPrediction(i) == 'E' and psipred_pred.GetConfidence(i) >= 6:
+ samplers[i] = torsion_sampler_extended
+ return samplers
+
+def _GenerateFragger(hmm,psipred_pred,
+ num_fragments,
+ rmsd_thresh,
+ ss_agreement_weight,
+ sequence_profile_weight,
+ structure_profile_weight,
+ torsion_weight,
+ aa_before,
+ aa_after,
+ structure_db,
+ torsion_sampler_coil,
+ torsion_sampler_helix,
+ torsion_sampler_extended):
+
+ torsion_samplers = _AssembleTorsionSamplers(psipred_pred,
+ torsion_sampler_coil,
+ torsion_sampler_helix,
+ torsion_sampler_extended)
+
+ fragger = Fragger(hmm.sequence)
+ fragger.AddSSAgreeParameters(ss_agreement_weight,psipred_pred)
+ fragger.AddSequenceProfileParameters(sequence_profile_weight,hmm)
+ fragger.AddStructureProfileParameters(structure_profile_weight,hmm)
+ fragger.AddTorsionProbabilityParameters(torsion_weight,torsion_samplers,
+ aa_before,aa_after)
+
+ fragger.Fill(structure_db,rmsd_thresh,num_fragments)
+
+ return fragger
+
+
+def GenerateFragger(hmm, psipred_pred,
+ num_fragments = 100,
+ rmsd_thresh = 0.0,
+ ss_agreement_weight = 1.0,
+ sequence_profile_weight = 0.8,
+ structure_profile_weight = 2.0,
+ torsion_weight = 13.0,
+ aa_before = "ALA",
+ aa_after = "ALA",
+ structure_db = None,
+ torsion_sampler_coil = None,
+ torsion_sampler_helix = None,
+ torsion_sampler_extended = None):
+
+ if len(hmm) != len(psipred_pred):
+ raise ValueError("Length of HMM must be consistent with Psipred!")
+
+ if structure_db == None:
+ structure_db = LoadStructureDB()
+
+ if torsion_sampler_coil == None:
+ torsion_sampler_coil = LoadTorsionSamplerCoil()
+
+ if torsion_sampler_helix == None:
+ torsion_sampler_helix = LoadTorsionSamplerHelical()
+
+ if torsion_sampler_extended == None:
+ torsion_sampler_extended = LoadTorsionSamplerExtended()
+
+ if len(aa_before) == 1:
+ #seems to be a one_letter_code, let's try our best
+ aa_before = OneLetterCodeToResidueName(aa_before)
+
+ if len(aa_after) == 1:
+ #seems to be a one_letter_code, let's try our best
+ aa_after = OneLetterCodeToResidueName(aa_after)
+
+ return _GenerateFragger(hmm, psipred_pred,
+ num_fragments,
+ rmsd_thresh,
+ ss_agreement_weight,
+ sequence_profile_weight,
+ structure_profile_weight,
+ torsion_weight,
+ aa_before,
+ aa_after,
+ structure_db,
+ torsion_sampler_coil,
+ torsion_sampler_helix,
+ torsion_sampler_extended)
+
+
+def GenerateFraggerList(hmm, psipred_pred,
+ fragment_length = 9,
+ fragments_per_position = 100,
+ rmsd_thresh = 0.0,
+ ss_agreement_weight = 1.0,
+ sequence_profile_weight = 0.8,
+ structure_profile_weight = 2.0,
+ torsion_weight = 13.0,
+ structure_db = None,
+ torsion_sampler_coil = None,
+ torsion_sampler_helix = None,
+ torsion_sampler_extended = None):
+
+
+ if len(hmm) != len(psipred_pred):
+ raise ValueError("Length of HMM must be consistent with Psipred!")
+
+ if structure_db == None:
+ structure_db = LoadStructureDB()
+
+ if torsion_sampler_coil == None:
+ torsion_sampler_coil = LoadTorsionSamplerCoil()
+
+ if torsion_sampler_helix == None:
+ torsion_sampler_helix = LoadTorsionSamplerHelical()
+
+ if torsion_sampler_extended == None:
+ torsion_sampler_extended = LoadTorsionSamplerExtended()
+
+ sequence = hmm.sequence
+ num_positions = len(sequence) - fragment_length + 1
+
+ fragger_list = list()
+
+ for i in range(num_positions):
+
+ aa_before = "ALA"
+ aa_after = "ALA"
+
+ if i > 0:
+ aa_before = OneLetterCodeToResidueName(sequence[i-1])
+
+ if i + fragment_length < len(sequence):
+ aa_after = OneLetterCodeToResidueName(sequence[i+fragment_length])
+
+ sub_hmm = hmm.Extract(i,i+fragment_length)
+ sub_psipred_pred = psipred_pred.Extract(i,i+fragment_length)
+
+ fragger = _GenerateFragger(sub_hmm, sub_psipred_pred,
+ fragments_per_position,
+ rmsd_thresh,
+ ss_agreement_weight,
+ sequence_profile_weight,
+ structure_profile_weight,
+ torsion_weight,
+ aa_before,
+ aa_before,
+ structure_db,
+ torsion_sampler_coil,
+ torsion_sampler_helix,
+ torsion_sampler_extended)
+
+ fragger_list.append(fragger)
+
+ return fragger_list
+
diff --git a/loop/pymod/export_backbone.cc b/loop/pymod/export_backbone.cc
index b4d36455d30f9c402bde7e6ce38200c33461b485..6b4edb7e3bf5ec6fe47641d844de3e9affc2e673 100644
--- a/loop/pymod/export_backbone.cc
+++ b/loop/pymod/export_backbone.cc
@@ -86,6 +86,22 @@ void ApplyTransformMat4(BackboneListPtr p, const geom::Mat4& t){ p->ApplyTransfo
void ApplyTransformTransform(BackboneListPtr p, const geom::Transform& t) { p->ApplyTransform(t); }
void ApplyTransformSingle(BackbonePtr p, const geom::Mat4& t){ p->ApplyTransform(t); }
+
+void InsertInto_int(BackboneListPtr p, ost::mol::ChainHandle& chain, uint start_resnum,
+ bool remodel_cterminal_o){
+ p->InsertInto(chain,start_resnum,remodel_cterminal_o);
+}
+
+void InsertInto_resnum(BackboneListPtr p, ost::mol::ChainHandle& chain,
+ const ost::mol::ResNum start_resnum,
+ bool remodel_cterminal_o){
+ p->InsertInto(chain,start_resnum,remodel_cterminal_o);
+}
+
+
+
+
+
}//ns
void export_Backbone(){
@@ -118,7 +134,8 @@ void export_Backbone(){
.def("__init__", make_constructor(&FullInitWrapperRHList))
.def("ToEntity",&BackboneList::ToEntity)
.def("GetSequence",&BackboneList::GetSequence)
- .def("InsertInto",&BackboneList::InsertInto,(arg("chain"),arg("n_stem"),arg("c_stem"),arg("remodel_cterminal_o")=true))
+ .def("InsertInto",&InsertInto_int,(arg("chain"),arg("start_resnum"),arg("remodel_cterminal_o")=true))
+ .def("InsertInto",&InsertInto_resnum,(arg("chain"),arg("start_resnum"),arg("remodel_cterminal_o")=true))
.def("ReconstructCBetaPositions",&BackboneList::ReconstructCBetaPositions)
.def("ReconstructOxygenPositions",&BackboneList::ReconstructOxygenPositions,(arg("last_psi")=-0.78540))
.def("ApplyTransform",&ApplyTransformMat4,(arg("transformation_matrix")))
diff --git a/loop/pymod/export_frag_db.cc b/loop/pymod/export_frag_db.cc
index 789b7fe4f561325104a8a3d4d8119696c3e4d418..2ed493fc131cde2f88e6fe226478303f0746c0a0 100644
--- a/loop/pymod/export_frag_db.cc
+++ b/loop/pymod/export_frag_db.cc
@@ -13,11 +13,30 @@ namespace{
return FragDBPtr(new FragDB(dist_bin_s,ang_bin_s,false));
}
- boost::python::list WrapSearchDB(FragDBPtr p,
- const ost::mol::ResidueHandle& n_stem,
- const ost::mol::ResidueHandle& c_stem,
- uint frag_size,
- bool extended_search){
+ boost::python::list WrapSearchDBResidueHandle(FragDBPtr p,
+ const ost::mol::ResidueHandle& n_stem,
+ const ost::mol::ResidueHandle& c_stem,
+ uint frag_size,
+ bool extended_search){
+ std::vector<FragmentInfo> fragments;
+
+ p->SearchDB(n_stem,c_stem,frag_size,fragments,extended_search);
+
+ boost::python::list return_list;
+
+ for(std::vector<FragmentInfo>::iterator i = fragments.begin();
+ i != fragments.end(); ++i){
+ return_list.append(*i);
+ }
+
+ return return_list;
+ }
+
+ boost::python::list WrapSearchDBBackbone(FragDBPtr p,
+ const Backbone& n_stem,
+ const Backbone& c_stem,
+ uint frag_size,
+ bool extended_search){
std::vector<FragmentInfo> fragments;
p->SearchDB(n_stem,c_stem,frag_size,fragments,extended_search);
@@ -37,8 +56,6 @@ namespace{
int GetNumFragments(FragDBPtr p){ return p->GetNumFragments(); }
int GetNumFragmentsGivenLength(FragDBPtr p, uint length) {return p->GetNumFragments(length); }
-
-
}
void export_FragDB(){
@@ -55,7 +72,8 @@ void export_FragDB(){
.def("GetNumStemPairs",&GetNumStemPairsGivenLength,(arg("loop_length")))
.def("GetNumFragments",&GetNumFragments)
.def("GetNumFragments",&GetNumFragmentsGivenLength,(arg("loop_length")))
- .def("SearchDB",&WrapSearchDB,(arg("n_stem"),arg("c_stem"),arg("frag_size"),arg("extended_search")=false))
+ .def("SearchDB",&WrapSearchDBResidueHandle,(arg("n_stem"),arg("c_stem"),arg("frag_size"),arg("extended_search")=false))
+ .def("SearchDB",&WrapSearchDBBackbone,(arg("n_stem"),arg("c_stem"),arg("frag_size"),arg("extended_search")=false))
;
register_ptr_to_python<FragDBPtr>();
diff --git a/loop/pymod/export_fragger.cc b/loop/pymod/export_fragger.cc
index 928c6cfd03d43ffd3691815717e6d0349c94dbb0..835f54e3d143b3bf25f16a1c34a677ee4f3d44fc 100644
--- a/loop/pymod/export_fragger.cc
+++ b/loop/pymod/export_fragger.cc
@@ -43,23 +43,6 @@ namespace{
return fragger.GetScore(parameter_index,index);
}
- void WrapSSAgreeParameters(Fragger& fragger, Real w,
- const boost::python::list& p_p,
- const boost::python::list& p_c){
- std::vector<char> v_p_p;
- std::vector<int> v_p_c;
-
- for(uint i = 0; i < boost::python::len(p_p); ++i){
- v_p_p.push_back(boost::python::extract<char>(p_p[i]));
- }
-
- for(uint i = 0; i < boost::python::len(p_c); ++i){
- v_p_c.push_back(boost::python::extract<int>(p_c[i]));
- }
-
- fragger.AddSSAgreeParameters(w,v_p_p,v_p_c);
- }
-
void WrapTorsionSingle(Fragger& fragger, Real w,
TorsionSamplerPtr t_s, const String& before,
const String& after){
@@ -83,7 +66,7 @@ void export_Fragger(){
class_<Fragger> ("Fragger", init<String>())
.def("AddSeqIDParameters",&Fragger::AddSeqIDParameters,(arg("weight")))
.def("AddSeqSimParameters",&Fragger::AddSeqSimParameters,(arg("weight"),arg("subst_matrix")))
- .def("AddSSAgreeParameters",&WrapSSAgreeParameters,(arg("weight"),arg("psipred_prediction"),arg("psipred_confidence")))
+ .def("AddSSAgreeParameters",&Fragger::AddSSAgreeParameters,(arg("weight"),arg("psipred_prediction")))
.def("AddTorsionProbabilityParameters",&WrapTorsionSingle,(arg("weight"),arg("torsion_sampler"),arg("aa_before")="ALA",arg("aa_after")="ALA"))
.def("AddTorsionProbabilityParameters",&WrapTorsionList,(arg("weight"),arg("torsion_sampler_list"),arg("aa_before")="ALA",arg("aa_after")="ALA"))
.def("AddSequenceProfileParameters",&Fragger::AddSequenceProfileParameters,(arg("weight"),arg("hmm")))
diff --git a/loop/pymod/export_loop_candidate.cc b/loop/pymod/export_loop_candidate.cc
index 86983412eb3994c7b7ff538c8f46751609608409..77b954a3cb048b09cf5ea48fbcc0e2b9ba7ce582 100644
--- a/loop/pymod/export_loop_candidate.cc
+++ b/loop/pymod/export_loop_candidate.cc
@@ -18,20 +18,35 @@ namespace{
return (*lcs)[i];
}
- void ApplyCCDWithAllSamplers(LoopCandidatesPtr p, boost::python::list l, int max_iterations, Real rmsd_cutoff, bool keep_non_converged, int random_seed){
+ void ApplyCCDWithAllSamplers(LoopCandidatesPtr p,
+ const ost::mol::ResidueHandle& n_stem,
+ const ost::mol::ResidueHandle& c_stem,
+ boost::python::list l,
+ int max_iterations, Real rmsd_cutoff,
+ bool keep_non_converged, int random_seed){
std::vector<TorsionSamplerPtr> v;
for(uint i = 0; i < boost::python::len(l); ++i){
v.push_back(boost::python::extract<TorsionSamplerPtr>(l[i]));
}
- p->ApplyCCD(v,max_iterations,rmsd_cutoff,keep_non_converged,random_seed);
+ p->ApplyCCD(n_stem,c_stem,v,max_iterations,rmsd_cutoff,keep_non_converged,random_seed);
}
- void ApplyCCDWithSampler(LoopCandidatesPtr p, TorsionSamplerPtr torsion_sampler, int max_iterations, Real rmsd_cutoff, bool keep_non_converged, int random_seed){
- p->ApplyCCD(torsion_sampler, max_iterations,rmsd_cutoff, keep_non_converged, random_seed);
+ void ApplyCCDWithSampler(LoopCandidatesPtr p,
+ const ost::mol::ResidueHandle& n_stem,
+ const ost::mol::ResidueHandle& c_stem,
+ TorsionSamplerPtr torsion_sampler,
+ int max_iterations, Real rmsd_cutoff,
+ bool keep_non_converged, int random_seed){
+ p->ApplyCCD(n_stem,c_stem,torsion_sampler,
+ max_iterations,rmsd_cutoff, keep_non_converged, random_seed);
}
- void ApplyCCDWithoutSampler(LoopCandidatesPtr p, int max_iterations, Real rmsd_cutoff, bool keep_non_converged, int random_seed){
- p->ApplyCCD(max_iterations, rmsd_cutoff, keep_non_converged, random_seed);
+ void ApplyCCDWithoutSampler(LoopCandidatesPtr p,
+ const ost::mol::ResidueHandle& n_stem,
+ const ost::mol::ResidueHandle& c_stem,
+ int max_iterations,
+ Real rmsd_cutoff, bool keep_non_converged){
+ p->ApplyCCD(n_stem,c_stem,max_iterations, rmsd_cutoff, keep_non_converged);
}
void AddLoopCandidate(LoopCandidatesPtr p, LoopCandidate& candidate){
@@ -42,31 +57,46 @@ namespace{
p->Add(bb);
}
- LoopCandidatesPtr FillFromMC(const ost::mol::ResidueHandle& n_stem,
- const ost::mol::ResidueHandle& c_stem,
- const String& seq,
+ LoopCandidatesPtr FillFromMC(const String& seq,
uint num_loops, uint steps,
MonteCarloSamplerPtr sampler,
MonteCarloCloserPtr closer,
MonteCarloScorerPtr scorer,
MonteCarloCoolerPtr cooler){
- return LoopCandidates::FillFromMonteCarloSampler(n_stem,c_stem,seq,num_loops,steps,
+ return LoopCandidates::FillFromMonteCarloSampler(seq,num_loops,steps,
sampler,closer,scorer,cooler);
}
- LoopCandidatesPtr FillFromMCInit(const ost::mol::ResidueHandle& n_stem,
- const ost::mol::ResidueHandle& c_stem,
- const BackboneList& initial_bb,
+ LoopCandidatesPtr FillFromMCInit(const BackboneList& initial_bb,
const String& seq,
uint num_loops, uint steps,
MonteCarloSamplerPtr sampler,
MonteCarloCloserPtr closer,
MonteCarloScorerPtr scorer,
MonteCarloCoolerPtr cooler){
- return LoopCandidates::FillFromMonteCarloSampler(n_stem,c_stem,initial_bb,seq,num_loops,steps,
+ return LoopCandidates::FillFromMonteCarloSampler(initial_bb,seq,num_loops,steps,
sampler,closer,scorer,cooler);
}
-}
+
+ void WrapCombinedScores(LoopCandidatesPtr p,
+ const boost::python::dict& weights,
+ uint start_resnum, uint chain_index){
+
+ String key;
+ Real value;
+ std::map<String,Real> m_weights;
+ boost::python::list keys = weights.keys();
+
+ for(int i = 0; i < boost::python::len(keys); ++i){
+ key = boost::python::extract<String>(keys[i]);
+ value = boost::python::extract<Real>(weights[keys[i]]);
+ m_weights[key] = value;
+ }
+
+ p->CalculateCombinedScores(m_weights, start_resnum, chain_index);
+ }
+
+} //ns
void export_loop_candidate()
@@ -83,41 +113,40 @@ void export_loop_candidate()
.def("GetOriginalDSSPState",&LoopCandidate::GetOriginalDSSPState)
.def_readwrite("clash_score", &LoopCandidate::clash_score)
.def_readwrite("cbeta_score", &LoopCandidate::cbeta_score)
+ .def_readwrite("reduced_score", &LoopCandidate::reduced_score)
.def_readwrite("torsion_score", &LoopCandidate::torsion_score)
.def_readwrite("packing_score", &LoopCandidate::packing_score)
.def_readwrite("hbond_score", &LoopCandidate::hbond_score)
- .def_readwrite("dssp_hbond_score", &LoopCandidate::dssp_hbond_score)
- .def_readwrite("stem_rmsd", &LoopCandidate::stem_rmsd)
+ .def_readwrite("ss_agreement_score", &LoopCandidate::ss_agreement_score)
+ .def_readwrite("combined_score", &LoopCandidate::combined_score)
.def_readwrite("bb_list", &LoopCandidate::bb_list)
;
- class_<LoopCandidates, LoopCandidatesPtr, boost::noncopyable>("LoopCandidates", init<const ost::mol::ResidueHandle&, const ost::mol::ResidueHandle&, const String&>())
+ class_<LoopCandidates, LoopCandidatesPtr, boost::noncopyable>("LoopCandidates", init<const String&>())
.def("FillFromDatabase",&LoopCandidates::FillFromDatabase,(arg("n_stem"),arg("c_stem"),arg("seq"),arg("frag_db"),arg("structure_db"),arg("extended_search")=false)).staticmethod("FillFromDatabase")
- .def("FillFromMonteCarloSampler",&FillFromMCInit,(arg("n_stem"),arg("c_stem"),arg("initial_bb"),arg("seq"),arg("num_loops"),arg("steps"),arg("sampler"),arg("closer"),arg("scorer"),arg("cooler")))
- .def("FillFromMonteCarloSampler",&FillFromMC,(arg("n_stem"),arg("c_stem"),arg("seq"),arg("num_loops"),arg("steps"),arg("sampler"),arg("closer"),arg("scorer"),arg("cooler"))).staticmethod("FillFromMonteCarloSampler")
- .def("ClusterCandidates",&LoopCandidates::ClusterCandidates)
- .def("ApplyCCD",&ApplyCCDWithSampler,(arg("torsion_sampler"),arg("max_iterations")=1000,arg("rmsd_cutoff")=0.1,arg("keep_non_converged")=false,arg("random_seed")=0))
- .def("ApplyCCD",&ApplyCCDWithoutSampler,(arg("max_iterations")=1000,arg("rmsd_cutoff")=0.1,arg("keep_non_converged")=false,arg("random_seed")=0))
- .def("ApplyCCD",&ApplyCCDWithAllSamplers,(arg("torsion_samplers"),arg("max_iterations")=1000,arg("rmsd_cutoff")=0.1,arg("keep_non_converged")=false,arg("random_seed")=0))
+ .def("FillFromMonteCarloSampler",&FillFromMCInit,(arg("initial_bb"),arg("seq"),arg("num_loops"),arg("steps"),arg("sampler"),arg("closer"),arg("scorer"),arg("cooler")))
+ .def("FillFromMonteCarloSampler",&FillFromMC,(arg("seq"),arg("num_loops"),arg("steps"),arg("sampler"),arg("closer"),arg("scorer"),arg("cooler"))).staticmethod("FillFromMonteCarloSampler")
+ .def("ClusterCandidates",&LoopCandidates::ClusterCandidates,(arg("max_rmsd"),arg("neglect_size_one")=true))
+ .def("ApplyCCD",&ApplyCCDWithSampler,(arg("n_stem"),arg("c_stem"),arg("torsion_sampler"),arg("max_iterations")=1000,arg("rmsd_cutoff")=0.1,arg("keep_non_converged")=false,arg("random_seed")=0))
+ .def("ApplyCCD",&ApplyCCDWithAllSamplers,(arg("n_stem"),arg("c_stem"),arg("torsion_samplers"),arg("max_iterations")=1000,arg("rmsd_cutoff")=0.1,arg("keep_non_converged")=false,arg("random_seed")=0))
+ .def("ApplyCCD",&ApplyCCDWithoutSampler,(arg("n_stem"),arg("c_stem"),arg("max_iterations")=1000,arg("rmsd_cutoff")=0.1,arg("keep_non_converged")=false))
.def("ApplyKIC",&LoopCandidates::ApplyKIC,(arg("pivot_one"),arg("pivot_two"),arg("pivot_three")))
- .def("ToEntity", &LoopCandidates::ToEntity,(arg("index")))
- .def("InsertInto", &LoopCandidates::InsertInto,(arg("entity"),arg("index")))
.def("GetAVGClashScore",&LoopCandidates::GetAVGClashScore)
.def("GetAVGCBetaScore",&LoopCandidates::GetAVGCBetaScore)
+ .def("GetAVGReducedScore",&LoopCandidates::GetAVGReducedScore)
.def("GetAVGTorsionScore",&LoopCandidates::GetAVGTorsionScore)
.def("GetAVGPackingScore",&LoopCandidates::GetAVGPackingScore)
.def("GetAVGHBondScore",&LoopCandidates::GetAVGHBondScore)
- .def("GetAVGDSSPHBondScore",&LoopCandidates::GetAVGDSSPHBondScore)
- .def("GetAVGStemRMSD",&LoopCandidates::GetAVGStemRMSD)
- .def("CalculateClashScores",&LoopCandidates::CalculateClashScores,(arg("chain_index")=0))
- .def("CalculateCBetaScores",&LoopCandidates::CalculateCBetaScores,(arg("chain_index")=0))
- .def("CalculateTorsionScores",&LoopCandidates::CalculateTorsionScores,(arg("chain_index")=0))
- .def("CalculateCBPackingScores",&LoopCandidates::CalculateCBPackingScores,(arg("chain_index")=0))
- .def("CalculateHBondScores",&LoopCandidates::CalculateHBondScores,(arg("chain_index")=0))
- .def("CalculateDSSPHBondScores",&LoopCandidates::CalculateDSSPHBondScores,(arg("chain_index")=0))
- .def("CalculateStemRMSD",&LoopCandidates::CalculateStemRMSD)
- .def("GetNStem",&LoopCandidates::GetNStem)
- .def("GetCStem",&LoopCandidates::GetCStem)
+ .def("GetAVGSSAgreementScore",&LoopCandidates::GetAVGSSAgreementScore)
+ .def("GetAVGCombinedScore",&LoopCandidates::GetAVGCombinedScore)
+ .def("CalculateClashScores",&LoopCandidates::CalculateClashScores,(arg("start_resnum"),arg("chain_index")=0))
+ .def("CalculateCBetaScores",&LoopCandidates::CalculateCBetaScores,(arg("start_resnum"),arg("chain_index")=0))
+ .def("CalculateReducedScores",&LoopCandidates::CalculateReducedScores,(arg("start_resnum"),arg("chain_index")))
+ .def("CalculateTorsionScores",&LoopCandidates::CalculateTorsionScores,(arg("start_resnum"),arg("chain_index")=0))
+ .def("CalculateCBPackingScores",&LoopCandidates::CalculateCBPackingScores,(arg("start_resnum"),arg("chain_index")=0))
+ .def("CalculateHBondScores",&LoopCandidates::CalculateHBondScores,(arg("start_resnum"),arg("chain_index")=0))
+ .def("CalculateSSAgreementScores",&LoopCandidates::CalculateSSAgreementScores,(arg("start_resnum"),arg("chain_index")=0))
+ .def("CalculateCombinedScores",&WrapCombinedScores,(arg("linear_weights"),arg("start_resnum"),arg("chain_index")=0))
.def("__iter__", iterator<LoopCandidates>())
.def("__len__", &LoopCandidates::size)
.def("__getitem__", lc_getitem,
diff --git a/loop/pymod/export_loop_score.cc b/loop/pymod/export_loop_score.cc
index 12b4ed32c50fea12ee5e55bc925106cea9784a1b..874516a5b2b6e92b09e58f61a2aecf75ea4be942 100644
--- a/loop/pymod/export_loop_score.cc
+++ b/loop/pymod/export_loop_score.cc
@@ -23,6 +23,19 @@ namespace{
p->Initialize(v);
}
+ void WrapSetPsipredPredictionSingle(BackboneLoopScorerPtr p, PsipredPredictionPtr pp){
+ p->SetPsipredPrediction(pp);
+ }
+
+ void WrapSetPsipredPredictionMulti(BackboneLoopScorerPtr p,
+ boost::python::list& pp){
+ std::vector<PsipredPredictionPtr> v_pp;
+ for(uint i = 0; i < boost::python::len(pp); ++i){
+ v_pp.push_back(boost::python::extract<PsipredPredictionPtr>(pp[i]));
+ }
+ p->SetPsipredPrediction(v_pp);
+ }
+
void SetEnvironment_env(BackboneLoopScorerPtr p, const ost::mol::EntityHandle& env){
p->SetEnvironment(env);
}
@@ -32,6 +45,12 @@ namespace{
p->SetEnvironment(bb_list,start_resnum,chain_index);
}
+ void SetEnvironment_bblist_resnum(BackboneLoopScorerPtr p, const promod3::loop::BackboneList& bb_list,
+ const ost::mol::ResNum& start_resnum, uint chain_index){
+ uint num = start_resnum.GetNum();
+ p->SetEnvironment(bb_list,num,chain_index);
+ }
+
void wrap_set_torsion_param(BackboneLoopScorerPtr p, const boost::python::list& l, uint bins){
std::vector<String> v;
for(uint i = 0; i < boost::python::len(l); ++i){
@@ -48,22 +67,30 @@ void export_loop_score()
.def("Save",&BackboneLoopScorer::Save,(arg("filename")))
.def("Initialize",&Initialize_string,(arg("seqres")))
.def("Initialize",&Initialize_string_list,(arg("seqres")))
+ .def("SetPsipredPrediction",&WrapSetPsipredPredictionSingle,(arg("psipred_prediction")))
+ .def("SetPsipredPrediction",&WrapSetPsipredPredictionMulti,(arg("psipred_predictions")))
.def("SetEnvironment",&SetEnvironment_env,(arg("env")))
.def("SetEnvironment",&SetEnvironment_bblist,(arg("bb_list"),arg("start_resnum"),arg("chain_index")=0))
+ .def("SetEnvironment",&SetEnvironment_bblist_resnum,(arg("bb_list"),arg("start_resnum"),arg("chain_index")=0))
.def("SetCBetaPotentialParameters",&BackboneLoopScorer::SetCBetaPotentialParameters,(arg("cbeta_cutoff"),arg("cbeta_bins"),arg("cbeta_seq_sep")))
+ .def("SetReducedPotentialParameters",&BackboneLoopScorer::SetReducedPotentialParameters,(arg("dist_cutoff"),arg("dist_bins"),arg("angle_bins"),arg("dihedral_bins"),arg("reduced_seq_sep")))
.def("SetTorsionPotentialParameters",&wrap_set_torsion_param,(arg("group_definitions"),arg("torsion_bins")))
.def("SetCBPackingPotentialParameters",&BackboneLoopScorer::SetCBPackingPotentialParameters,(arg("cb_packing_cutoff"),arg("cb_packing_max_count")))
.def("SetHBondPotentialParameters",&BackboneLoopScorer::SetHBondPotentialParameters,(arg("min_d"),arg("max_d"),arg("min_alpha"),arg("max_alpha"),arg("min_beta"),arg("max_beta"),arg("min_gamma"),arg("max_gamma"),arg("d_bins"),arg("alpha_bins"),arg("beta_bins"),arg("gamma_bins")))
+ .def("SetSSAgreementParameters",&BackboneLoopScorer::SetSSAgreementParameters)
.def("SetCBetaEnergy",&BackboneLoopScorer::SetCBetaEnergy,(arg("aa_one"),arg("aa_two"),arg("bin"),arg("energy")))
+ .def("SetReducedEnergy",&BackboneLoopScorer::SetReducedEnergy,(arg("aa_one"),arg("aa_two"),arg("dist_bin"),arg("alpha_bin"),arg("beta_bin"),arg("gamma_bin"),arg("energy")))
.def("SetTorsionEnergy",&BackboneLoopScorer::SetTorsionEnergy,(arg("group_identifier_idx"),arg("phi_bin"),arg("psi_bin"),arg("energy")))
.def("SetCBPackingEnergy",&BackboneLoopScorer::SetCBPackingEnergy,(arg("aa"),arg("count"),arg("energy")))
.def("SetHBondEnergy",&BackboneLoopScorer::SetHBondEnergy,(arg("state"),arg("d_bin"),arg("alpha_bin"),arg("beta_bin"),arg("gamma_bin")))
+ .def("SetSSAgreementScore",&BackboneLoopScorer::SetSSAgreementScore,(arg("psipred_state"),arg("psipred_confidence"),arg("dssp_state"),arg("score")))
.def("CalculateClashScore",&BackboneLoopScorer::CalculateClashScore,(arg("bb_list"),arg("start_resnum"),arg("chain_index")=0))
.def("CalculateCBetaScore",&BackboneLoopScorer::CalculateCBetaScore,(arg("bb_list"),arg("start_resnum"),arg("chain_index")=0))
+ .def("CalculateReducedScore",&BackboneLoopScorer::CalculateReducedScore,(arg("bb_list"),arg("start_resnum"),arg("chain_index")=0))
.def("CalculateTorsionScore",&BackboneLoopScorer::CalculateTorsionScore,(arg("bb_list"),arg("start_resnum"),arg("chain_index")=0))
.def("CalculateCBPackingScore",&BackboneLoopScorer::CalculateCBPackingScore,(arg("bb_list"),arg("start_resnum"),arg("chain_index")=0))
.def("CalculateHBondScore",&BackboneLoopScorer::CalculateHBondScore,(arg("bb_list"),arg("start_resnum"),arg("chain_index")=0))
- .def("CalculateDSSPHBondScore",&BackboneLoopScorer::CalculateDSSPHBondScore,(arg("bb_list"),arg("start_resnum"),arg("chain_index")=0))
+ .def("CalculateSSAgreementScore",&BackboneLoopScorer::CalculateSSAgreementScore,(arg("bb_list"),arg("start_resnum"),arg("chain_index")=0))
.def("TransOmegaTorsions",&BackboneLoopScorer::TransOmegaTorsions,(arg("bb_list"),arg("thresh")=20.0/180*M_PI,arg("allow_prepro_cis")=true))
;
diff --git a/loop/pymod/export_psipred_prediction.cc b/loop/pymod/export_psipred_prediction.cc
new file mode 100644
index 0000000000000000000000000000000000000000..55544e39bc6fa0a8f3882f0227cecd30579ba0b8
--- /dev/null
+++ b/loop/pymod/export_psipred_prediction.cc
@@ -0,0 +1,76 @@
+#include <boost/python.hpp>
+#include <boost/python/register_ptr_to_python.hpp>
+#include <boost/python/make_constructor.hpp>
+
+#include <promod3/loop/psipred_prediction.hh>
+
+using namespace promod3;
+using namespace promod3::loop;
+using namespace boost::python;
+
+
+namespace{
+
+ PsipredPredictionPtr WrapEmtpyConstructor(){
+ PsipredPredictionPtr p(new PsipredPrediction);
+ return p;
+ }
+
+ PsipredPredictionPtr WrapListConstructor(const boost::python::list& prediction,
+ const boost::python::list& confidence){
+
+ std::vector<char> v_prediction;
+ std::vector<int> v_confidence;
+
+ for(uint i = 0; i < boost::python::len(prediction); ++i){
+ v_prediction.push_back(boost::python::extract<char>(prediction[i]));
+ }
+
+ for(uint i = 0; i < boost::python::len(confidence); ++i){
+ v_confidence.push_back(boost::python::extract<int>(confidence[i]));
+ }
+
+ PsipredPredictionPtr p(new PsipredPrediction(v_prediction,v_confidence));
+ return p;
+ }
+
+ boost::python::list WrapGetPredictions(const PsipredPrediction& p){
+ std::vector<char> v_predictions = p.GetPredictions();
+ boost::python::list predictions;
+ for(std::vector<char>::iterator i = v_predictions.begin();
+ i != v_predictions.end(); ++i){
+ predictions.append(*i);
+ }
+ return predictions;
+ }
+
+ boost::python::list WrapGetConfidences(const PsipredPrediction& p){
+ std::vector<int> v_confidences = p.GetConfidences();
+ boost::python::list confidences;
+ for(std::vector<int>::iterator i = v_confidences.begin();
+ i != v_confidences.end(); ++i){
+ confidences.append(*i);
+ }
+ return confidences;
+ }
+}
+
+
+void export_PsipredPrediction(){
+
+ class_<PsipredPrediction> ("PsipredPrediction", no_init)
+ .def("__init__",make_constructor(&WrapEmtpyConstructor))
+ .def("__init__",make_constructor(&WrapListConstructor))
+ .def("FromHHM",&PsipredPrediction::FromHHM,(arg("filename"))).staticmethod("FromHHM")
+ .def("FromHoriz",&PsipredPrediction::FromHoriz,(arg("filename"))).staticmethod("FromHoriz")
+ .def("Extract",&PsipredPrediction::Extract,(arg("from"),arg("to")))
+ .def("Add",&PsipredPrediction::Add,(arg("prediction"),arg("confidence")))
+ .def("GetPrediction",&PsipredPrediction::GetPrediction,(arg("idx")))
+ .def("GetConfidence",&PsipredPrediction::GetConfidence,(arg("idx")))
+ .def("GetPredictions",&WrapGetPredictions)
+ .def("GetConfidences",&WrapGetConfidences)
+ .def("__len__",&PsipredPrediction::size)
+ ;
+
+ register_ptr_to_python<PsipredPredictionPtr>();
+}
diff --git a/loop/pymod/wrap_loop.cc b/loop/pymod/wrap_loop.cc
index daa0d4776a69a18b2f58e870fd3c121b600e87a6..23c98e48b00e2e8cc3c28eccbff803b346ce1bc4 100644
--- a/loop/pymod/wrap_loop.cc
+++ b/loop/pymod/wrap_loop.cc
@@ -11,6 +11,7 @@ void export_LoopObjectLoader();
void export_loop_score();
void export_LoopClosure();
void export_Fragger();
+void export_PsipredPrediction();
using namespace boost::python;
@@ -26,5 +27,6 @@ BOOST_PYTHON_MODULE(_loop)
export_loop_score();
export_LoopClosure();
export_Fragger();
+ export_PsipredPrediction();
}
diff --git a/loop/src/CMakeLists.txt b/loop/src/CMakeLists.txt
index 61b42a167bcebb074521cb193555d451f6ccb302..6550194a39f1556025ee67c693191692d072a8e9 100644
--- a/loop/src/CMakeLists.txt
+++ b/loop/src/CMakeLists.txt
@@ -19,11 +19,14 @@ ccd.hh
monte_carlo_cooler.hh
monte_carlo_scorer.hh
monte_carlo_closer.hh
-flame.hh
kic.hh
loop_object_loader.hh
backbone_relaxer.hh
dynamic_spatial_organizer.hh
+sec_struct.hh
+psipred_prediction.hh
+cluster.hh
+sidechain.hh
)
set(LOOP_SOURCES
@@ -40,10 +43,13 @@ ccd.cc
monte_carlo_scorer.cc
monte_carlo_cooler.cc
monte_carlo_closer.cc
-flame.cc
kic.cc
loop_object_loader.cc
backbone_relaxer.cc
+sec_struct.cc
+psipred_prediction.cc
+cluster.cc
+sidechain.cc
)
module(NAME loop HEADERS ${LOOP_HEADERS} SOURCES ${LOOP_SOURCES} DEPENDS_ON
diff --git a/loop/src/backbone.cc b/loop/src/backbone.cc
index 4461a286cf1d7da6037e22617c47051a34b80b60..b660a35dc3b887e7d78bbac60f3e17e65da5e8f7 100644
--- a/loop/src/backbone.cc
+++ b/loop/src/backbone.cc
@@ -409,16 +409,15 @@ ost::mol::EntityHandle BackboneList::ToEntity() const{
}
void BackboneList::InsertInto(ost::mol::ChainHandle& chain,
- uint n, uint c, bool remodel_cterminal_o) const{
+ uint start_resnum, bool remodel_cterminal_o) const{
- ost::mol::XCSEditor edi=chain.GetEntity().EditXCS(ost::mol::BUFFERED_EDIT);
+ ost::mol::ResNum num(start_resnum);
+ this->InsertInto(chain, num, remodel_cterminal_o);
+}
- if(n + this->size()-1 != c){
- std::stringstream ss;
- ss << "The provided residue numbers do not match with the length ";
- ss << "of the backbone to be inserted!";
- throw promod3::Error(ss.str());
- }
+void BackboneList::InsertInto(ost::mol::ChainHandle& chain,
+ const ost::mol::ResNum& start_resnum,
+ bool remodel_cterminal_o) const{
if(!chain.IsValid()){
std::stringstream ss;
@@ -426,8 +425,10 @@ void BackboneList::InsertInto(ost::mol::ChainHandle& chain,
throw promod3::Error(ss.str());
}
- ost::mol::ResNum n_num(n);
- ost::mol::ResNum c_num(c);
+ ost::mol::XCSEditor edi=chain.GetEntity().EditXCS(ost::mol::BUFFERED_EDIT);
+
+ ost::mol::ResNum n_num = start_resnum;
+ ost::mol::ResNum c_num = start_resnum + this->size() -1;
ost::mol::ResidueHandle before = chain.FindResidue(n_num);
ost::mol::ResidueHandle after = chain.FindResidue(c_num);
@@ -643,13 +644,6 @@ void BackboneList::InsertInto(ost::mol::ChainHandle& chain,
edi.ReorderResidues(chain);
}
-String BackboneList::GetSequence() const{
- String return_string(this->size(),'X');
- for(uint i = 0; i < this->size(); ++i){
- return_string[i] = bb_list_[i].one_letter_code;
- }
- return return_string;
-}
void BackboneList::SetSequence(const String& seq){
if(seq.size() != this->size()){
@@ -672,6 +666,14 @@ void BackboneList::SetSequence(const String& seq){
}
}
+String BackboneList::GetSequence() const{
+ String return_string(this->size(),'X');
+ for(uint i = 0; i < this->size(); ++i){
+ return_string[i] = bb_list_[i].one_letter_code;
+ }
+ return return_string;
+}
+
void BackboneList::ReconstructCBetaPositions(){
for(BackboneList::iterator i = this->begin(); i != this->end(); ++i){
promod3::core::ConstructCBetaPos(i->n_coord, i->ca_coord, i->c_coord,
diff --git a/loop/src/backbone.hh b/loop/src/backbone.hh
index de1ee76ae76686028f83baa91b01c7f011f41005..c88eccf4cd736984e1f2d4282979a3e00395ab7f 100644
--- a/loop/src/backbone.hh
+++ b/loop/src/backbone.hh
@@ -72,7 +72,11 @@ public:
ost::mol::EntityHandle ToEntity() const;
void InsertInto(ost::mol::ChainHandle& chain,
- uint n, uint c, bool remodel_cterminal_o = true) const;
+ uint start_resnum, bool remodel_cterminal_o = true) const;
+
+ void InsertInto(ost::mol::ChainHandle& chain,
+ const ost::mol::ResNum& start_resnum,
+ bool remodel_cterminal_o = true) const;
String GetSequence() const;
diff --git a/loop/src/backbone_loop_score.cc b/loop/src/backbone_loop_score.cc
index c10fa4d27b66ccbd17375f00e596c529e31a0253..682e3f4779f885cf0f02d472bcfbcc0e9ef6db2f 100644
--- a/loop/src/backbone_loop_score.cc
+++ b/loop/src/backbone_loop_score.cc
@@ -17,15 +17,6 @@ inline Real StericEnergy(Real d, Real rr){
return 57.273*(1.0-d/rr);
}
-inline Real DSSPHBondEnergy(const geom::Vec3& h_pos, const geom::Vec3& n_pos,
- const geom::Vec3& c_pos, const geom::Vec3& o_pos){
- Real on = 1.0/geom::Distance(o_pos,n_pos);
- Real ch = 1.0/geom::Distance(c_pos,h_pos);
- Real oh = 1.0/geom::Distance(o_pos,h_pos);
- Real cn = 1.0/geom::Distance(c_pos,n_pos);
- return 27.888 * (on+ch-oh-cn);
-}
-
inline int GetHBondState(Real phi, Real psi){
//check whether phi/psi pair is typical for
@@ -42,6 +33,29 @@ inline int GetHBondState(Real phi, Real psi){
return 0;
}
+inline int GetDSSPIdx(char dssp_state){
+ switch(dssp_state){
+ case 'H': return 0;
+ case 'E': return 1;
+ case 'C': return 2;
+ case 'G': return 3;
+ case 'B': return 4;
+ case 'S': return 5;
+ case 'T': return 6;
+ case 'I': return 7;
+ default: throw promod3::Error("Invalid dssp state observed!");
+ }
+}
+
+inline int GetPsipredIdx(char psipred_state){
+ switch(psipred_state){
+ case 'H': return 0;
+ case 'E': return 1;
+ case 'C': return 2;
+ default: throw promod3::Error("Invalid psipred state observed!");
+ }
+}
+
//calculates internal clash score, neglecting interactions from neighbouring residues
Real CalculateInternalClashScore(const promod3::loop::BackboneList& bb_list){
@@ -130,7 +144,9 @@ namespace promod3 { namespace loop {
BackboneLoopScorer::BackboneLoopScorer(): initialized_(false),
- cb_env_(10.0),
+ psipred_set_(false),
+ cb_env_(10.0),
+ reduced_env_(10.0),
clash_env_(6.0),
hbond_env_(10.0),
cbeta_seq_sep_(0),
@@ -138,6 +154,15 @@ BackboneLoopScorer::BackboneLoopScorer(): initialized_(false),
cbeta_cutoff_(0.0),
squared_cbeta_cutoff_(0.0),
cbeta_bin_size_(0.0),
+ reduced_seq_sep_(0),
+ reduced_dist_bins_(0),
+ reduced_angle_bins_(0),
+ reduced_dihedral_bins_(0),
+ reduced_distance_cutoff_(0.0),
+ reduced_squared_distance_cutoff_(0.0),
+ reduced_dist_bin_size_(0.0),
+ reduced_angle_bin_size_(0.0),
+ reduced_dihedral_bin_size_(0.0),
cb_packing_cutoff_(0.0),
squared_cb_packing_cutoff_(0.0),
cb_packing_max_count_(0.0),
@@ -162,19 +187,24 @@ BackboneLoopScorer::BackboneLoopScorer(): initialized_(false),
hb_beta_bins_(0),
hb_gamma_bins_(0),
cbeta_energies_(NULL),
+ reduced_energies_(NULL),
torsion_energies_(NULL),
cb_packing_energies_(NULL),
- hbond_energies_(NULL){ }
+ hbond_energies_(NULL),
+ ss_agreement_scores_(NULL){ }
BackboneLoopScorer::~BackboneLoopScorer(){
this->DeallocateCBeta();
+ this->DeallocateReduced();
this->DeallocateTorsion();
this->DeallocateCBPacking();
this->DeallocateHBond();
+ this->DeallocateSSAgreement();
if(initialized_){
for(uint i = 0; i < seqres_.size(); ++i){
delete [] cb_env_data_[i];
+ delete [] reduced_env_data_[i];
delete [] hbond_env_data_[i];
delete [] env_set_[i];
for(uint j = 0; j < seqres_[i].size(); ++j){
@@ -183,10 +213,12 @@ BackboneLoopScorer::~BackboneLoopScorer(){
delete [] clash_env_data_[i];
}
delete [] cb_env_data_;
+ delete [] reduced_env_data_;
delete [] clash_env_data_;
delete [] hbond_env_data_;
delete [] env_set_;
cb_env_.Clear();
+ reduced_env_.Clear();
clash_env_.Clear();
hbond_env_.Clear();
}
@@ -209,6 +241,16 @@ BackboneLoopScorerPtr BackboneLoopScorer::Load(const String& filename){
in_stream.read(reinterpret_cast<char*>(&p->squared_cbeta_cutoff_), sizeof(Real));
in_stream.read(reinterpret_cast<char*>(&p->cbeta_bin_size_), sizeof(Real));
+ in_stream.read(reinterpret_cast<char*>(&p->reduced_seq_sep_), sizeof(uint));
+ in_stream.read(reinterpret_cast<char*>(&p->reduced_dist_bins_), sizeof(uint));
+ in_stream.read(reinterpret_cast<char*>(&p->reduced_angle_bins_), sizeof(uint));
+ in_stream.read(reinterpret_cast<char*>(&p->reduced_dihedral_bins_), sizeof(uint));
+ in_stream.read(reinterpret_cast<char*>(&p->reduced_distance_cutoff_), sizeof(Real));
+ in_stream.read(reinterpret_cast<char*>(&p->reduced_squared_distance_cutoff_), sizeof(Real));
+ in_stream.read(reinterpret_cast<char*>(&p->reduced_dist_bin_size_), sizeof(Real));
+ in_stream.read(reinterpret_cast<char*>(&p->reduced_angle_bin_size_), sizeof(Real));
+ in_stream.read(reinterpret_cast<char*>(&p->reduced_dihedral_bin_size_), sizeof(Real));
+
in_stream.read(reinterpret_cast<char*>(&p->cb_packing_cutoff_), sizeof(Real));
in_stream.read(reinterpret_cast<char*>(&p->squared_cb_packing_cutoff_), sizeof(Real));
in_stream.read(reinterpret_cast<char*>(&p->cb_packing_max_count_), sizeof(Real));
@@ -261,6 +303,26 @@ BackboneLoopScorerPtr BackboneLoopScorer::Load(const String& filename){
}
}
}
+
+ }
+
+ if(p->reduced_dist_bins_ != 0){
+ p->AllocateReduced();
+ Real value;
+ for(int i = 0; i < ost::conop::XXX; ++i){
+ for(int j = 0; j < ost::conop::XXX; ++j){
+ for(uint k = 0; k < p->reduced_dist_bins_; ++k){
+ for(uint l = 0; l < p->reduced_angle_bins_; ++l){
+ for(uint m = 0; m < p->reduced_angle_bins_; ++m){
+ for(uint n = 0; n < p->reduced_dihedral_bins_; ++n){
+ in_stream.read(reinterpret_cast<char*>(&value),sizeof(Real));
+ p->reduced_energies_[i][j][k][l][m][n] = value;
+ }
+ }
+ }
+ }
+ }
+ }
}
if(p->num_torsion_bins_ != 0){
@@ -304,6 +366,21 @@ BackboneLoopScorerPtr BackboneLoopScorer::Load(const String& filename){
}
}
+ uint ss_agreement_present;
+ in_stream.read(reinterpret_cast<char*>(&ss_agreement_present),sizeof(uint));
+ if(ss_agreement_present == 1){
+ p->AllocateSSAgreement();
+ Real value;
+ for(uint i = 0; i < 8; ++i){
+ for(uint j = 0; j < 3; ++j){
+ for(uint k = 0; k < 10; ++k){
+ in_stream.read(reinterpret_cast<char*>(&value),sizeof(Real));
+ p->ss_agreement_scores_[i][j][k] = value;
+ }
+ }
+ }
+ }
+
in_stream.close();
return p;
}
@@ -317,6 +394,16 @@ void BackboneLoopScorer::Save(const String& filename){
out_stream.write(reinterpret_cast<char*>(&squared_cbeta_cutoff_), sizeof(Real));
out_stream.write(reinterpret_cast<char*>(&cbeta_bin_size_), sizeof(Real));
+ out_stream.write(reinterpret_cast<char*>(&reduced_seq_sep_), sizeof(uint));
+ out_stream.write(reinterpret_cast<char*>(&reduced_dist_bins_), sizeof(uint));
+ out_stream.write(reinterpret_cast<char*>(&reduced_angle_bins_), sizeof(uint));
+ out_stream.write(reinterpret_cast<char*>(&reduced_dihedral_bins_), sizeof(uint));
+ out_stream.write(reinterpret_cast<char*>(&reduced_distance_cutoff_), sizeof(Real));
+ out_stream.write(reinterpret_cast<char*>(&reduced_squared_distance_cutoff_), sizeof(Real));
+ out_stream.write(reinterpret_cast<char*>(&reduced_dist_bin_size_), sizeof(Real));
+ out_stream.write(reinterpret_cast<char*>(&reduced_angle_bin_size_), sizeof(Real));
+ out_stream.write(reinterpret_cast<char*>(&reduced_dihedral_bin_size_), sizeof(Real));
+
out_stream.write(reinterpret_cast<char*>(&cb_packing_cutoff_), sizeof(Real));
out_stream.write(reinterpret_cast<char*>(&squared_cb_packing_cutoff_), sizeof(Real));
out_stream.write(reinterpret_cast<char*>(&cb_packing_max_count_), sizeof(Real));
@@ -362,6 +449,22 @@ void BackboneLoopScorer::Save(const String& filename){
}
}
+ if(reduced_energies_ != NULL){
+ for(int i = 0; i < ost::conop::XXX; ++i){
+ for(int j = 0; j < ost::conop::XXX; ++j){
+ for(uint k = 0; k < reduced_dist_bins_; ++k){
+ for(uint l = 0; l < reduced_angle_bins_; ++l){
+ for(uint m = 0; m < reduced_angle_bins_; ++m){
+ for(uint n = 0; n < reduced_dihedral_bins_; ++n){
+ out_stream.write(reinterpret_cast<char*>(&reduced_energies_[i][j][k][l][m][n]),sizeof(Real));
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+
if(torsion_energies_ != NULL){
for(uint i = 0; i < num_torsion_groups_; ++i){
for(uint j = 0; j < num_torsion_bins_; ++j){
@@ -393,6 +496,23 @@ void BackboneLoopScorer::Save(const String& filename){
}
}
}
+
+ if(ss_agreement_scores_ != NULL){
+ uint ss_agreement_present = 1;
+ out_stream.write(reinterpret_cast<char*>(&ss_agreement_present),sizeof(uint));
+ for(uint i = 0; i < 8; ++i){
+ for(uint j = 0; j < 3; ++j){
+ for(uint k = 0; k < 10; ++k){
+ out_stream.write(reinterpret_cast<char*>(&ss_agreement_scores_[i][j][k]),sizeof(Real));
+ }
+ }
+ }
+ }
+ else{
+ uint ss_agreement_present = 0;
+ out_stream.write(reinterpret_cast<char*>(&ss_agreement_present),sizeof(uint));
+ }
+
out_stream.close();
}
@@ -410,6 +530,10 @@ void BackboneLoopScorer::SetCBetaPotentialParameters(Real cbeta_cutoff, uint cbe
throw promod3::Error("Number of bins must be nonzero!");
}
+ if(cbeta_seq_sep < 1){
+ throw promod3::Error("CBeta sequence separation must be at least 1!");
+ }
+
cbeta_seq_sep_ = cbeta_seq_sep;
cbeta_bins_ = cbeta_bins;
cbeta_cutoff_ = cbeta_cutoff;
@@ -420,6 +544,47 @@ void BackboneLoopScorer::SetCBetaPotentialParameters(Real cbeta_cutoff, uint cbe
this->AllocateCBeta();
}
+void BackboneLoopScorer::SetReducedPotentialParameters(Real dist_cutoff, uint dist_bins, uint angle_bins,
+ uint dihedral_bins, uint seq_sep){
+
+ //deallocate (nothing happens when reduced_energies_ is NULL)
+ this->DeallocateReduced();
+
+ if(dist_cutoff < 0.0){
+ throw promod3::Error("Reduced dist cutoff must not be negative!");
+ }
+
+ if(dist_bins == 0){
+ throw promod3::Error("Reduced dist bins must be nonzero!");
+ }
+
+ if(angle_bins == 0){
+ throw promod3::Error("Reduced angle bins must be nonzero!");
+ }
+
+ if(dihedral_bins == 0){
+ throw promod3::Error("Reduced dihedral bins must be nonzero!");
+ }
+
+ if(seq_sep == 0){
+ throw promod3::Error("Reduced seq_sep must be at least 1!");
+ }
+
+ reduced_seq_sep_ = seq_sep;
+ reduced_dist_bins_ = dist_bins;
+ reduced_angle_bins_ = angle_bins;
+ reduced_dihedral_bins_ = dihedral_bins;
+ reduced_distance_cutoff_ = dist_cutoff;
+ reduced_squared_distance_cutoff_ = reduced_distance_cutoff_ * reduced_distance_cutoff_;
+ reduced_dist_bin_size_ = reduced_distance_cutoff_ / reduced_dist_bins_;
+ reduced_angle_bin_size_ = M_PI / reduced_angle_bins_;
+ reduced_dihedral_bin_size_ = 2 * M_PI / reduced_dihedral_bins_;
+
+ //allocate reduced_energies_ according to previously extracted parameters
+ this->AllocateReduced();
+
+}
+
void BackboneLoopScorer::SetTorsionPotentialParameters(const std::vector<String>& group_definitions,
uint torsion_bins){
@@ -542,7 +707,7 @@ void BackboneLoopScorer::SetHBondPotentialParameters(Real hb_min_d, Real hb_max_
throw promod3::Error("hb_max_d must be larger than hb_min_d");
}
- if(hb_max_alpha_ <= hb_min_alpha){
+ if(hb_max_alpha <= hb_min_alpha){
throw promod3::Error("hb_max_alpha must be larger than hb_min_alpha");
}
@@ -575,9 +740,20 @@ void BackboneLoopScorer::SetHBondPotentialParameters(Real hb_min_d, Real hb_max_
this->AllocateHBond();
}
+void BackboneLoopScorer::SetSSAgreementParameters(){
+ //deallocate (nothing happens when hbond_energies_ is NULL)
+ this->DeallocateSSAgreement();
+ //allocate ss_agreement stuff with fixed parametrization
+ this->AllocateSSAgreement();
+}
+
void BackboneLoopScorer::SetCBetaEnergy(ost::conop::AminoAcid a,
- ost::conop::AminoAcid b,
- uint bin, Real e){
+ ost::conop::AminoAcid b,
+ uint bin, Real e){
+
+ if(cbeta_energies_ == NULL){
+ throw promod3::Error("You need to parametrize the cbeta potential before setting energies!");
+ }
if(a == ost::conop::XXX || b == ost::conop::XXX){
throw promod3::Error("Cannot set energy for invalid amino acid");
@@ -590,10 +766,49 @@ void BackboneLoopScorer::SetCBetaEnergy(ost::conop::AminoAcid a,
cbeta_energies_[a][b][bin] = e;
}
+void BackboneLoopScorer::SetReducedEnergy(ost::conop::AminoAcid a,
+ ost::conop::AminoAcid b,
+ uint dist_bin,
+ uint alpha_bin,
+ uint beta_bin,
+ uint gamma_bin,
+ Real e){
+
+ if(reduced_energies_ == NULL){
+ throw promod3::Error("You need to parametrize the reduced potential before setting energies!");
+ }
+
+ if(a == ost::conop::XXX || b == ost::conop::XXX){
+ throw promod3::Error("Cannot set energy for invalid amino acid");
+ }
+
+ if(dist_bin >= reduced_dist_bins_){
+ throw promod3::Error("Cannot set reduced energy for invalid dist bin");
+ }
+
+ if(alpha_bin >= reduced_angle_bins_){
+ throw promod3::Error("Cannot set reduced energy for invalid alpha bin");
+ }
+
+ if(beta_bin >= reduced_angle_bins_){
+ throw promod3::Error("Cannot set reduced energy for invalid beta bin");
+ }
+
+ if(gamma_bin >= reduced_dihedral_bins_){
+ throw promod3::Error("Cannot set reduced energy for invalid gamma bin");
+ }
+
+ reduced_energies_[a][b][dist_bin][alpha_bin][beta_bin][gamma_bin] = e;
+}
+
void BackboneLoopScorer::SetTorsionEnergy(uint group_id_idx,
uint phi_bin, uint psi_bin,
Real e){
+ if(torsion_energies_ == NULL){
+ throw promod3::Error("You need to parametrize the torsion potential before setting energies!");
+ }
+
if(group_id_idx >= num_torsion_groups_){
throw promod3::Error("Invalid torsion group identifier index!");
}
@@ -612,6 +827,10 @@ void BackboneLoopScorer::SetTorsionEnergy(uint group_id_idx,
void BackboneLoopScorer::SetCBPackingEnergy(ost::conop::AminoAcid aa,
uint count, Real e){
+ if(cb_packing_energies_ == NULL){
+ throw promod3::Error("You need to parametrize the packing potential before setting energies!");
+ }
+
if(aa == ost::conop::XXX){
throw promod3::Error("Cannot set energy for invalid amino acid!");
}
@@ -626,6 +845,10 @@ void BackboneLoopScorer::SetCBPackingEnergy(ost::conop::AminoAcid aa,
void BackboneLoopScorer::SetHBondEnergy(uint state, uint d_bin, uint alpha_bin,
uint beta_bin, uint gamma_bin, Real e){
+ if(hbond_energies_ == NULL){
+ throw promod3::Error("You need to parametrize the hbond potential before setting energies!");
+ }
+
if(state >= 3){
throw promod3::Error("Invalid state when setting energy for hbond potential!");
}
@@ -650,6 +873,21 @@ void BackboneLoopScorer::SetHBondEnergy(uint state, uint d_bin, uint alpha_bin,
}
+void BackboneLoopScorer::SetSSAgreementScore(char psipred_state, int psipred_confidence,
+ char dssp_state, Real score){
+
+ if(ss_agreement_scores_ == NULL){
+ throw promod3::Error("You need to parametrize the ss agreement term before setting scores!");
+ }
+
+ int psipred_idx = GetPsipredIdx(psipred_state);
+ int dssp_idx = GetDSSPIdx(dssp_state);
+ if(psipred_confidence < 0 || psipred_confidence > 9){
+ throw promod3::Error("Invalid psipred confidence observed!");
+ }
+ ss_agreement_scores_[dssp_idx][psipred_idx][psipred_confidence] = score;
+}
+
void BackboneLoopScorer::Initialize(const String& seqres){
std::vector<String> seqres_vec;
seqres_vec.push_back(seqres);
@@ -701,6 +939,7 @@ void BackboneLoopScorer::Initialize(const std::vector<String>& seqres){
if(initialized_){
for(uint i = 0; i < seqres_.size(); ++i){
delete [] cb_env_data_[i];
+ delete [] reduced_env_data_[i];
delete [] env_set_[i];
delete [] hbond_env_data_[i];
for(uint j = 0; j < seqres_[i].size(); ++j){
@@ -709,10 +948,12 @@ void BackboneLoopScorer::Initialize(const std::vector<String>& seqres){
delete [] clash_env_data_[i];
}
delete [] cb_env_data_;
+ delete [] reduced_env_data_;
delete [] clash_env_data_;
delete [] hbond_env_data_;
delete [] env_set_;
cb_env_.Clear();
+ reduced_env_.Clear();
clash_env_.Clear();
hbond_env_.Clear();
}
@@ -724,12 +965,14 @@ void BackboneLoopScorer::Initialize(const std::vector<String>& seqres){
//initialize the environment data
cb_env_data_ = new CBSpatialOrganizerItem*[seqres_.size()];
+ reduced_env_data_ = new ReducedSpatialOrganizerItem*[seqres_.size()];
clash_env_data_ = new ClashSpatialOrganizerItem**[seqres_.size()];
hbond_env_data_ = new HBondSpatialOrganizerItem*[seqres_.size()];
env_set_ = new bool*[seqres_.size()];
for(uint i = 0; i < seqres_.size(); ++i){
cb_env_data_[i] = new CBSpatialOrganizerItem[seqres_[i].size()];
+ reduced_env_data_[i] = new ReducedSpatialOrganizerItem[seqres_[i].size()];
clash_env_data_[i] = new ClashSpatialOrganizerItem*[seqres_[i].size()];
hbond_env_data_[i] = new HBondSpatialOrganizerItem[seqres_[i].size()];
env_set_[i] = new bool[seqres_[i].size()];
@@ -744,48 +987,133 @@ void BackboneLoopScorer::Initialize(const std::vector<String>& seqres){
}
//fill all data we already can into cb_env_data_
+ int actual_index = 0;
for(uint i = 0; i < seqres_.size(); ++i){
for(uint j = 0; j < seqres_[i].size(); ++j){
cb_env_data_[i][j].aa = seqres_[i][j];
- cb_env_data_[i][j].number = j+1;
- cb_env_data_[i][j].chain_index = i;
+ cb_env_data_[i][j].idx = actual_index;
+ ++actual_index;
+ }
+ }
+
+ //fill all data we already can into reduced_env_data_
+ actual_index = 0;
+ for(uint i = 0; i < seqres_.size(); ++i){
+ for(uint j = 0; j < seqres_[i].size(); ++j){
+ reduced_env_data_[i][j].aa = seqres_[i][j];
+ reduced_env_data_[i][j].idx = actual_index;
+ ++actual_index;
}
}
//fill all data we already can into clash_env_data_
+ actual_index = 0;
for(uint i = 0; i < seqres_.size(); ++i){
for(uint j = 0; j < seqres_[i].size(); ++j){
//N
clash_env_data_[i][j][0].radius = 1.3;
- clash_env_data_[i][j][0].number = j+1;
- clash_env_data_[i][j][0].chain_index = i;
+ clash_env_data_[i][j][0].idx = actual_index;
//CA
clash_env_data_[i][j][1].radius = 1.6;
- clash_env_data_[i][j][1].number = j+1;
- clash_env_data_[i][j][1].chain_index = i;
+ clash_env_data_[i][j][1].idx = actual_index;
//C
clash_env_data_[i][j][2].radius = 1.6;
- clash_env_data_[i][j][2].number = j+1;
- clash_env_data_[i][j][2].chain_index = i;
+ clash_env_data_[i][j][2].idx = actual_index;
//O
clash_env_data_[i][j][3].radius = 1.3;
- clash_env_data_[i][j][3].number = j+1;
- clash_env_data_[i][j][3].chain_index = i;
+ clash_env_data_[i][j][3].idx = actual_index;
//CB
clash_env_data_[i][j][4].radius = 1.6;
- clash_env_data_[i][j][4].number = j+1;
- clash_env_data_[i][j][4].chain_index = i;
+ clash_env_data_[i][j][4].idx = actual_index;
+ ++actual_index;
}
}
//fill all data we already can into hbond_env_data_
+ actual_index = 0;
for(uint i = 0; i < seqres_.size(); ++i){
for(uint j = 0; j < seqres_[i].size(); ++j){
- hbond_env_data_[i][j].number = j+1;
- hbond_env_data_[i][j].chain_index = i;
+ hbond_env_data_[i][j].idx = actual_index;
+ hbond_env_data_[i][j].is_proline = seqres_[i][j] == 'P';
+ ++actual_index;
}
}
+
+ //let's finally set the residue indices
+ residue_indices_.clear();
+ actual_index = 0;
+ for(uint i = 0; i < seqres_.size(); ++i){
+ residue_indices_.push_back(std::vector<int>());
+ for(uint j = 0; j < seqres_[i].size(); ++j){
+ residue_indices_[i].push_back(actual_index);
+ ++actual_index;
+ }
+ }
+
initialized_ = true;
+
+ psipred_pred_.clear();
+ psipred_conf_.clear();
+ psipred_set_ = false;
+}
+
+void BackboneLoopScorer::SetPsipredPrediction(PsipredPredictionPtr pp){
+ if(!initialized_){
+ throw promod3::Error("Cannot set psipred prediction if scorer is not initialized!");
+ }
+ if(seqres_.size() != 1){
+ String err = "Cannot set single psipred prediction for scorer being initialized ";
+ err += "with multiple chains!";
+ throw promod3::Error(err);
+ }
+ if(pp->size() != seqres_[0].size()){
+ String err = "Size of psipred prediction must be consistent with ";
+ err += "seqres you used to initialize the scorer!";
+ throw promod3::Error(err);
+ }
+ psipred_pred_.clear();
+ psipred_conf_.clear();
+
+ std::vector<int> pred;
+ for(uint i = 0; i < pp->size(); ++i){
+ pred.push_back(GetPsipredIdx(pp->GetPrediction(i)));
+ }
+ psipred_pred_.push_back(pred);
+ psipred_conf_.push_back(pp->GetConfidences());
+ psipred_set_ = true;
+}
+
+void BackboneLoopScorer::SetPsipredPrediction(std::vector<PsipredPredictionPtr>& pp){
+
+ if(!initialized_){
+ throw promod3::Error("Cannot set psipred prediction if scorer is not initialized!");
+ }
+ if(seqres_.size() != pp.size()){
+ String err = "Size of psipred predictions must be consistent with number ";
+ err += "of chains in scorer!";
+ throw promod3::Error(err);
+ }
+
+ for(uint i = 0; i < pp.size(); ++i){
+ if(seqres_[i].size() != pp[i]->size()){
+ String err = "Size of psipred predictions must be consistent with size ";
+ err += "seqres sequences in scorer!";
+ throw promod3::Error(err);
+ }
+ }
+
+ psipred_pred_.clear();
+ psipred_conf_.clear();
+
+ for(uint i = 0; i < pp.size(); ++i){
+ std::vector<int> pred;
+ for(uint j = 0; j < pp[i]->size(); ++j){
+ pred.push_back(GetPsipredIdx(pp[i]->GetPrediction(j)));
+ }
+ psipred_pred_.push_back(pred);
+ psipred_conf_.push_back(pp[i]->GetConfidences());
+ }
+ psipred_set_ = true;
}
void BackboneLoopScorer::SetEnvironment(const ost::mol::EntityHandle& env){
@@ -893,6 +1221,13 @@ void BackboneLoopScorer::SetEnvironment(const ost::mol::EntityHandle& env){
cb_env_data_[i][index].pos = cb_pos;
cb_env_.Reset(&cb_env_data_[i][index],old_pos,cb_pos);
+ //do reduced_env_
+ old_pos = reduced_env_data_[i][index].pos;
+ reduced_env_data_[i][index].pos = ca_pos;
+ reduced_env_data_[i][index].axis = geom::Normalize(ca_pos-n_pos) +
+ geom::Normalize(ca_pos-c_pos);
+ reduced_env_.Reset(&reduced_env_data_[i][index],old_pos,ca_pos);
+
//do clash_env_
//do N
@@ -935,6 +1270,12 @@ void BackboneLoopScorer::SetEnvironment(const ost::mol::EntityHandle& env){
cb_env_data_[i][index].pos = cb_pos;
cb_env_.Add(&cb_env_data_[i][index],cb_pos);
+ //do reduced_env_
+ reduced_env_data_[i][index].pos = ca_pos;
+ reduced_env_data_[i][index].axis = geom::Normalize(ca_pos-n_pos) +
+ geom::Normalize(ca_pos-c_pos);
+ reduced_env_.Add(&reduced_env_data_[i][index],ca_pos);
+
//do clash_env_
//do N
@@ -1000,7 +1341,7 @@ void BackboneLoopScorer::SetEnvironment(const ost::mol::EntityHandle& env){
states[i][j] = GetHBondState(phi,psi);
}
}
- //note, that last hydrogen is calculated with a wrong phi...
+ //note, that first hydrogen is calculated with a wrong phi...
//I just don't care at this point...
promod3::core::ConstructAtomPos(current_item->c_pos,
current_item->pos,
@@ -1099,6 +1440,13 @@ void BackboneLoopScorer::SetEnvironment(const promod3::loop::BackboneList& bb_li
cb_env_data_[chain_index][index].pos = cb_pos;
cb_env_.Reset(&cb_env_data_[chain_index][index],old_pos,cb_pos);
+ //do reduced_env_
+ old_pos = reduced_env_data_[chain_index][index].pos;
+ reduced_env_data_[chain_index][index].pos = ca_pos;
+ reduced_env_data_[chain_index][index].axis = geom::Normalize(ca_pos-n_pos) +
+ geom::Normalize(ca_pos-c_pos);
+ reduced_env_.Reset(&reduced_env_data_[chain_index][index],old_pos,ca_pos);
+
//do clash_env_
//do N
@@ -1140,6 +1488,12 @@ void BackboneLoopScorer::SetEnvironment(const promod3::loop::BackboneList& bb_li
cb_env_data_[chain_index][index].pos = cb_pos;
cb_env_.Add(&cb_env_data_[chain_index][index],cb_pos);
+ //do reduced_env_
+ reduced_env_data_[chain_index][index].pos = ca_pos;
+ reduced_env_data_[chain_index][index].axis = geom::Normalize(ca_pos-n_pos) +
+ geom::Normalize(ca_pos-c_pos);
+ reduced_env_.Add(&reduced_env_data_[chain_index][index],ca_pos);
+
//do clash_env_
//do N
@@ -1256,10 +1610,58 @@ void BackboneLoopScorer::SetEnvironment(const promod3::loop::BackboneList& bb_li
}
}
+void BackboneLoopScorer::ClearEnvironment(uint start_resnum, uint num_residues,
+ uint chain_index){
+
+ if(chain_index >= seqres_.size()){
+ throw promod3::Error("Invalid chain index encountered when clearing environment!");
+ }
+
+ if(num_residues == 0){
+ throw promod3::Error("Num of residues to clear must be larger 0!");
+ }
+
+ uint end_resnum = start_resnum + num_residues - 1;
+ //in case of overflows(e.g. when user input is negative) start_resnum could be bigger end_resnum
+ if(start_resnum < 1 || end_resnum > seqres_[chain_index].size()){
+ throw promod3::Error("Invalid start residue number encountered when clearing environment!");
+ }
+
+ uint idx = start_resnum - 1;
+ uint num_clash_items;
+
+ for(uint i = 0; i < num_residues; ++i, ++idx){
+
+ env_set_[chain_index][idx] = false;
+
+ //remove cb env item in env
+ geom::Vec3 pos = cb_env_data_[chain_index][idx].pos;
+ cb_env_.Remove(&cb_env_data_[chain_index][idx],pos);
+
+ //remove hbond env item in env
+ pos = hbond_env_data_[chain_index][idx].pos;
+ hbond_env_.Remove(&hbond_env_data_[chain_index][idx],pos);
+
+ //remove reduced env item in env
+ pos = reduced_env_data_[chain_index][idx].pos;
+ reduced_env_.Remove(&reduced_env_data_[chain_index][idx],pos);
+
+ if(seqres_[chain_index][idx] == 'G') num_clash_items = 4;
+ else num_clash_items = 5;
+
+ for(uint j = 0; j < num_clash_items; ++j){
+ pos = clash_env_data_[chain_index][idx][j].pos;
+ clash_env_.Remove(&clash_env_data_[chain_index][idx][j],pos);
+ }
+ }
+}
+
Real BackboneLoopScorer::CalculateClashScore(const BackboneList& bb_list, uint start_resnum,
uint chain_index) const{
- if(bb_list.size() < 3){
+ int size = bb_list.size();
+
+ if(size < 3){
throw promod3::Error("Size of Backbone list must be at least 3!");
}
@@ -1271,7 +1673,7 @@ Real BackboneLoopScorer::CalculateClashScore(const BackboneList& bb_list, uint s
throw promod3::Error("Invalid chain index encountered when calculating backbone clash score!");
}
- uint end_resnum = start_resnum + bb_list.size() - 1;
+ uint end_resnum = start_resnum + size - 1;
//in case of overflows(e.g. when user input is negative) start_resnum could be bigger end_resnum
if(start_resnum < 1 || end_resnum > seqres_[chain_index].size()){
throw promod3::Error("Invalid start residue number encountered when calculating backbone clash score!");
@@ -1282,67 +1684,68 @@ Real BackboneLoopScorer::CalculateClashScore(const BackboneList& bb_list, uint s
Real clash_score = 0.0;
- //start resnum has at least value one... in this case we get the actual invalid
- //residue number 0... this has no effect on the result in the end...
- //also for neglect_end we could potentially get an invalid residue number.
- uint neglect_start = start_resnum-1;
- uint neglect_end = end_resnum+1;
+ //variables to figure out what interactions to the environment should be neglected later on...
+ int loop_start_idx = residue_indices_[chain_index][start_resnum-1];
+ int loop_end_idx = residue_indices_[chain_index][end_resnum-1];
+ int neglect_start = std::max(residue_indices_[chain_index][0],loop_start_idx-1);
+ int neglect_end = std::min(residue_indices_[chain_index].back(),loop_end_idx+1);
+
+ for(int i = 0; i < size; ++i){
- for(uint i = 0; i < bb_list.size(); ++i){
within_result = clash_env_.FindWithin(bb_list[i].n_coord, 2.9);
a = within_result.first;
for(uint j = 0; j < within_result.second; ++j) {
- if (neglect_start <= a[j].first->number && a[j].first->number <= neglect_end){
- if(a[j].first->chain_index == chain_index) continue;
+ if (a[j].first->idx < neglect_start || a[j].first->idx > neglect_end){
+ clash_score += StericEnergy(a[j].second,1.3+a[j].first->radius);
}
- clash_score += StericEnergy(a[j].second,1.3+a[j].first->radius);
}
+
within_result = clash_env_.FindWithin(bb_list[i].ca_coord, 3.2);
a = within_result.first;
for(uint j = 0; j < within_result.second; ++j) {
- if (neglect_start <= a[j].first->number && a[j].first->number <= neglect_end){
- if(a[j].first->chain_index == chain_index) continue;
+ if (a[j].first->idx < neglect_start || a[j].first->idx > neglect_end){
+ clash_score += StericEnergy(a[j].second,1.6+a[j].first->radius);
}
- clash_score += StericEnergy(a[j].second,1.6+a[j].first->radius);
}
+
within_result = clash_env_.FindWithin(bb_list[i].c_coord, 3.2);
a = within_result.first;
for(uint j = 0; j < within_result.second; ++j) {
- if (neglect_start <= a[j].first->number && a[j].first->number <= neglect_end){
- if(a[j].first->chain_index == chain_index) continue;
+ if (a[j].first->idx < neglect_start || a[j].first->idx > neglect_end){
+ clash_score += StericEnergy(a[j].second,1.6+a[j].first->radius);
}
- clash_score += StericEnergy(a[j].second,1.6+a[j].first->radius);
}
+
within_result = clash_env_.FindWithin(bb_list[i].o_coord, 2.9);
a = within_result.first;
for(uint j = 0; j < within_result.second; ++j) {
- if (neglect_start <= a[j].first->number && a[j].first->number <= neglect_end){
- if(a[j].first->chain_index == chain_index) continue;
- }
- clash_score += StericEnergy(a[j].second,1.3+a[j].first->radius);
+ if (a[j].first->idx < neglect_start || a[j].first->idx > neglect_end){
+ clash_score += StericEnergy(a[j].second,1.3+a[j].first->radius);
+ }
}
if(bb_list[i].aa != ost::conop::GLY){
within_result = clash_env_.FindWithin(bb_list[i].cb_coord, 3.2);
a = within_result.first;
for(uint j = 0; j < within_result.second; ++j) {
- if (neglect_start <= a[j].first->number && a[j].first->number <= neglect_end){
- if(a[j].first->chain_index == chain_index) continue;
+ if (a[j].first->idx < neglect_start || a[j].first->idx > neglect_end){
+ clash_score += StericEnergy(a[j].second,1.6+a[j].first->radius);
}
- clash_score += StericEnergy(a[j].second,1.6+a[j].first->radius);
}
}
}
clash_score += CalculateInternalClashScore(bb_list);
- clash_score /= bb_list.size();
+ clash_score /= size;
return clash_score;
}
Real BackboneLoopScorer::CalculateCBetaScore(const BackboneList& bb_list, uint start_resnum,
uint chain_index) const{
- if(bb_list.size() < 3){
+ int size = bb_list.size();
+
+ if(size < 3){
throw promod3::Error("Size of Backbone list must be at least 3!");
}
@@ -1354,7 +1757,7 @@ Real BackboneLoopScorer::CalculateCBetaScore(const BackboneList& bb_list, uint s
throw promod3::Error("Invalid chain index encountered when calculating cbeta score!");
}
- uint end_resnum = start_resnum + bb_list.size()-1;
+ uint end_resnum = start_resnum +size-1;
//in case of overflows(e.g. when user input is negative) start_resnum could be bigger end_resnum
if(start_resnum < 1 || end_resnum > seqres_[chain_index].size()){
throw promod3::Error("Invalid start residue number encountered when calculating cbeta score!");
@@ -1372,27 +1775,40 @@ Real BackboneLoopScorer::CalculateCBetaScore(const BackboneList& bb_list, uint s
Real cbeta_score = 0.0;
int counter = 0;
int max_bin = cbeta_bins_-1;
+
+ //let's precalculate the idx ranges we have to neglect
+ int loop_start_idx = residue_indices_[chain_index][start_resnum-1];
+ int loop_end_idx = residue_indices_[chain_index][end_resnum-1];
+ int min_idx_chain = residue_indices_[chain_index][0];
+ int max_idx_chain = residue_indices_[chain_index].back();
+ int seq_sep = static_cast<int>(cbeta_seq_sep_);
+ std::vector<int> start_neglect(size,loop_start_idx);
+ std::vector<int> end_neglect(size,loop_end_idx);
+ int neglect_range = seq_sep - 1;
+
+ for(int i = 0; i < neglect_range; ++i){
+ start_neglect[i] = std::max(min_idx_chain,start_neglect[i]-(neglect_range+i));
+ end_neglect[size-1-i] = std::min(max_idx_chain,end_neglect[i]+(neglect_range-i));
+ }
+
//let's go over every loop residue
- for(uint i = 0; i < bb_list.size(); ++i){
+ for(int i = 0; i < size; ++i){
within_result = cb_env_.FindWithin(bb_list[i].cb_coord, cbeta_cutoff_);
a = within_result.first;
for(uint j = 0; j < within_result.second; ++j){
- if(std::abs(static_cast<int>(a[j].first->number)-static_cast<int>(start_resnum+i)) < static_cast<int>(cbeta_seq_sep_) ||
- (a[j].first->number >= start_resnum && a[j].first->number <= end_resnum)){ //not considering any loop residues
- if(chain_index == a[j].first->chain_index){
- continue;
- }
+ if(a[j].first->idx < start_neglect[i] || a[j].first->idx > end_neglect[i]){
+ bin = std::min(static_cast<int>(a[j].second/cbeta_bin_size_),max_bin);
+ cbeta_score += cbeta_energies_[bb_list[i].aa][a[j].first->aa][bin];
+ ++counter;
}
- bin = std::min(static_cast<int>(a[j].second/cbeta_bin_size_),max_bin);
- cbeta_score += cbeta_energies_[bb_list[i].aa][a[j].first->aa][bin];
- ++counter;
}
}
+
//we do not have the loop internal interactions yet
//let's do first the interactions towards c_ter
- if(bb_list.size()>=cbeta_seq_sep_){
- for(uint i = 0; i < bb_list.size()-cbeta_seq_sep_; ++i){
- for(uint j = i+cbeta_seq_sep_; j < bb_list.size(); ++j){
+ if(size>=seq_sep){
+ for(int i = 0; i < size-seq_sep; ++i){
+ for(int j = i+seq_sep; j < size; ++j){
dist = geom::Length2(bb_list[i].cb_coord-bb_list[j].cb_coord);
if(dist >= squared_cbeta_cutoff_) continue;
dist = std::sqrt(dist);
@@ -1402,8 +1818,8 @@ Real BackboneLoopScorer::CalculateCBetaScore(const BackboneList& bb_list, uint s
}
}
//let's finally do the ones towards n_ter
- for(uint i = cbeta_seq_sep_; i < bb_list.size(); ++i){
- for(uint j = 0; j <= i-cbeta_seq_sep_; ++j){
+ for(int i = seq_sep; i < size; ++i){
+ for(int j = 0; j <= i-seq_sep; ++j){
dist = geom::Length2(bb_list[i].cb_coord-bb_list[j].cb_coord);
if(dist >= squared_cbeta_cutoff_) continue;
dist = std::sqrt(dist);
@@ -1417,14 +1833,154 @@ Real BackboneLoopScorer::CalculateCBetaScore(const BackboneList& bb_list, uint s
return cbeta_score;
}
+Real BackboneLoopScorer::CalculateReducedScore(const BackboneList& bb_list, uint start_resnum,
+ uint chain_index) const{
+
+ int size = bb_list.size();
+
+ if(size < 3){
+ throw promod3::Error("Size of Backbone list must be at least 3!");
+ }
+
+ if(!initialized_){
+ throw promod3::Error("Require Loop Scorer to be properly initialized before use!");
+ }
+
+ if(chain_index >= seqres_.size()){
+ throw promod3::Error("Invalid chain index encountered when calculating reduced score!");
+ }
+
+ uint end_resnum = start_resnum +size-1;
+ //in case of overflows(e.g. when user input is negative) start_resnum could be bigger end_resnum
+ if(start_resnum < 1 || end_resnum > seqres_[chain_index].size()){
+ throw promod3::Error("Invalid start residue number encountered when calculating reduced score!");
+ }
+
+ if(reduced_energies_ == NULL){
+ throw promod3::Error("Reduced potential needs to be attached to scorer to calculate according score!");
+ }
+
+ promod3::loop::DynamicSpatialOrganizer<ReducedSpatialOrganizerItem,geom::Vec3>::WithinResult within_result;
+ std::pair<ReducedSpatialOrganizerItem*,Real>* a;
+
+ Real reduced_score = 0.0;
+ Real dist;
+ Real alpha;
+ Real beta;
+ Real gamma;
+ int dist_bin;
+ int alpha_bin;
+ int beta_bin;
+ int gamma_bin;
+ int counter = 0;
+ int max_dist_bin = reduced_dist_bins_-1;
+ int max_angle_bin = reduced_angle_bins_-1;
+ int max_dihedral_bin = reduced_dihedral_bins_-1;
+
+ //let's precalculate the idx ranges we have to neglect
+ int loop_start_idx = residue_indices_[chain_index][start_resnum-1];
+ int loop_end_idx = residue_indices_[chain_index][end_resnum-1];
+ int min_idx_chain = residue_indices_[chain_index][0];
+ int max_idx_chain = residue_indices_[chain_index].back();
+ int seq_sep = static_cast<int>(reduced_seq_sep_);
+ std::vector<int> start_neglect(size,loop_start_idx);
+ std::vector<int> end_neglect(size,loop_end_idx);
+ int neglect_range = seq_sep - 1;
+
+ for(int i = 0; i < neglect_range; ++i){
+ start_neglect[i] = std::max(min_idx_chain,start_neglect[i]-(neglect_range+i));
+ end_neglect[size-1-i] = std::min(max_idx_chain,end_neglect[i]+(neglect_range-i));
+ }
+
+ geom::Vec3 bb_list_axis[size];
+ geom::Vec3 bb_list_ca_pos[size];
+ for(int i = 0; i < size; ++i){
+ bb_list_ca_pos[i] = bb_list[i].ca_coord;
+ bb_list_axis[i] = geom::Normalize(bb_list_ca_pos[i]-bb_list[i].n_coord) +
+ geom::Normalize(bb_list_ca_pos[i]-bb_list[i].c_coord);
+ }
+
+ //let's go over every loop residue
+ for(int i = 0; i < size; ++i){
+ within_result = reduced_env_.FindWithin(bb_list_ca_pos[i], reduced_distance_cutoff_);
+ a = within_result.first;
+ for(uint j = 0; j < within_result.second; ++j){
+ if(a[j].first->idx < start_neglect[i] || a[j].first->idx > end_neglect[i]){
+ dist_bin = std::min(static_cast<int>(a[j].second/reduced_dist_bin_size_),max_dist_bin);
+ alpha = geom::Angle(bb_list_axis[i],a[j].first->pos-bb_list_ca_pos[i]);
+ beta = geom::Angle(a[j].first->axis,bb_list_ca_pos[i]-a[j].first->pos);
+ gamma = geom::DihedralAngle(bb_list_ca_pos[i]+bb_list_axis[i], bb_list_ca_pos[i],
+ a[j].first->pos, a[j].first->pos+a[j].first->axis);
+ alpha_bin = std::min(static_cast<int>(alpha/reduced_angle_bin_size_), max_angle_bin);
+ beta_bin = std::min(static_cast<int>(beta/reduced_angle_bin_size_), max_angle_bin);
+ gamma_bin = std::min(static_cast<int>((gamma+M_PI)/reduced_dihedral_bin_size_), max_dihedral_bin);
+ reduced_score += reduced_energies_[bb_list[i].aa][a[j].first->aa][dist_bin][alpha_bin][beta_bin][gamma_bin];
+ ++counter;
+ }
+ }
+ }
+
+ //we do not have the loop internal interactions yet
+ //let's do first the interactions towards c_ter
+ if(size>=seq_sep){
+ for(int i = 0; i < size-seq_sep; ++i){
+ for(int j = i+seq_sep; j < size; ++j){
+ dist = geom::Length2(bb_list_ca_pos[i]-bb_list_ca_pos[j]);
+ if(dist >= reduced_squared_distance_cutoff_) continue;
+ dist = std::sqrt(dist);
+ alpha = geom::Angle(bb_list_axis[i],bb_list_ca_pos[j]-bb_list_ca_pos[i]);
+ beta = geom::Angle(bb_list_axis[j],bb_list_ca_pos[i]-bb_list_ca_pos[j]);
+ gamma = geom::DihedralAngle(bb_list_ca_pos[i] + bb_list_axis[i],
+ bb_list_ca_pos[i],
+ bb_list_ca_pos[j],
+ bb_list_ca_pos[j] + bb_list_axis[j]);
+ dist_bin = std::min(static_cast<int>(dist/reduced_dist_bin_size_),max_dist_bin);
+ alpha_bin = std::min(static_cast<int>(alpha/reduced_angle_bin_size_), max_angle_bin);
+ beta_bin = std::min(static_cast<int>(beta/reduced_angle_bin_size_), max_angle_bin);
+ gamma_bin = std::min(static_cast<int>((gamma+M_PI)/reduced_dihedral_bin_size_), max_dihedral_bin);
+ reduced_score += reduced_energies_[bb_list[i].aa][bb_list[j].aa][dist_bin][alpha_bin][beta_bin][gamma_bin];
+ ++counter;
+ }
+ }
+
+ //let's finally do the ones towards n_ter
+ for(int i = seq_sep; i < size; ++i){
+ for(int j = 0; j <= i-seq_sep; ++j){
+ dist = geom::Length2(bb_list_ca_pos[i]-bb_list_ca_pos[j]);
+ if(dist >= reduced_squared_distance_cutoff_) continue;
+ dist = std::sqrt(dist);
+ alpha = geom::Angle(bb_list_axis[i],bb_list_ca_pos[j]-bb_list_ca_pos[i]);
+ beta = geom::Angle(bb_list_axis[j],bb_list_ca_pos[i]-bb_list_ca_pos[j]);
+ gamma = geom::DihedralAngle(bb_list_ca_pos[i] + bb_list_axis[i],
+ bb_list_ca_pos[i],
+ bb_list_ca_pos[j],
+ bb_list_ca_pos[j] + bb_list_axis[j]);
+ dist_bin = std::min(static_cast<int>(dist/reduced_dist_bin_size_),max_dist_bin);
+ alpha_bin = std::min(static_cast<int>(alpha/reduced_angle_bin_size_), max_angle_bin);
+ beta_bin = std::min(static_cast<int>(beta/reduced_angle_bin_size_), max_angle_bin);
+ gamma_bin = std::min(static_cast<int>((gamma+M_PI)/reduced_dihedral_bin_size_), max_dihedral_bin);
+ reduced_score += reduced_energies_[bb_list[i].aa][bb_list[j].aa][dist_bin][alpha_bin][beta_bin][gamma_bin];
+ ++counter;
+ }
+ }
+ }
+
+ if(counter>0) reduced_score /= counter;
+ return reduced_score;
+
+ return 0.0;
+}
+
Real BackboneLoopScorer::CalculateTorsionScore(const BackboneList& bb_list, uint start_resnum,
uint chain_index) const{
- if(bb_list.size() < 3){
+ int size = bb_list.size();
+
+ if(size < 3){
throw promod3::Error("Size of Backbone list must be at least 3!");
}
- uint end_resnum = start_resnum + bb_list.size()-1;
+ uint end_resnum = start_resnum +size-1;
if(!initialized_){
throw promod3::Error("Require Loop Scorer to be properly initialized before use!");
}
@@ -1446,7 +2002,7 @@ Real BackboneLoopScorer::CalculateTorsionScore(const BackboneList& bb_list, uint
Real angle1, angle2;
uint bin1, bin2;
int torsion_group_index;
- for(uint i = 1; i < bb_list.size()-1; ++i){
+ for(int i = 1; i < size-1; ++i){
torsion_group_index = torsion_group_indices_[chain_index][start_resnum-1+i];
if(torsion_group_index == -1) continue;
angle1 = geom::DihedralAngle(bb_list[i-1].c_coord,bb_list[i].n_coord,
@@ -1484,7 +2040,7 @@ Real BackboneLoopScorer::CalculateTorsionScore(const BackboneList& bb_list, uint
torsion_group_index = torsion_group_indices_[chain_index][end_resnum-1];
if(torsion_group_index != -1){
//the data for the residues before and after get extracted from the hbond env data
- angle1 = bb_list.GetPhiTorsion(bb_list.size()-1);
+ angle1 = bb_list.GetPhiTorsion(size-1);
angle2 = geom::DihedralAngle(bb_list.back().n_coord,
bb_list.back().ca_coord,
bb_list.back().c_coord,
@@ -1505,7 +2061,9 @@ Real BackboneLoopScorer::CalculateTorsionScore(const BackboneList& bb_list, uint
Real BackboneLoopScorer::CalculateCBPackingScore(const BackboneList& bb_list, uint start_resnum,
uint chain_index) const{
- if(bb_list.size() < 3){
+ int size = bb_list.size();
+
+ if(size < 3){
throw promod3::Error("Size of Backbone list must be at least 3!");
}
@@ -1516,7 +2074,7 @@ Real BackboneLoopScorer::CalculateCBPackingScore(const BackboneList& bb_list, ui
if(chain_index >= seqres_.size()){
throw promod3::Error("Invalid chain index encountered when calculating cb packing score!");
}
- uint end_resnum = start_resnum + bb_list.size()-1;
+ uint end_resnum = start_resnum + size-1;
//in case of overflows(e.g. when user input is negative) start_resnum could be bigger end_resnum
if(start_resnum < 1 || end_resnum > seqres_[chain_index].size()){
throw promod3::Error("Invalid start residue number encountered when calculating cb packing score!");
@@ -1531,37 +2089,36 @@ Real BackboneLoopScorer::CalculateCBPackingScore(const BackboneList& bb_list, ui
uint counter;
Real packing_score = 0.0;
- //let's go over every loop residue (not including before and after)
- for(uint i = 0; i < bb_list.size(); ++i){
+ int loop_start_idx = residue_indices_[chain_index][start_resnum-1];
+ int loop_end_idx = residue_indices_[chain_index][end_resnum-1];
+ //let's go over every loop residue
+ for(int i = 0; i < size; ++i){
counter = 0;
//lets first search for other cb positions in the spatial organizer,
//neglecting all residue numbers from the loop
within_result = cb_env_.FindWithin(bb_list[i].cb_coord,cb_packing_cutoff_);
a = within_result.first;
for(uint j = 0; j < within_result.second; ++j){
- if(a[j].first->number >= start_resnum && a[j].first->number <= end_resnum){
- if(chain_index==a[j].first->chain_index){
- continue;
- }
- }
- ++counter;
+ if(a[j].first->idx < loop_start_idx || a[j].first->idx > loop_end_idx) ++counter;
}
//let's finally look for other residues within the cutoff in the loop
- for(uint j = 0; j < bb_list.size(); ++j){
+ for(int j = 0; j < size; ++j){
if(j == i) continue;
if(geom::Length2(bb_list[i].cb_coord-bb_list[j].cb_coord) < squared_cb_packing_cutoff_) ++counter;
}
packing_score += cb_packing_energies_[bb_list[i].aa][std::min(counter,cb_packing_max_count_)];
}
- packing_score /= bb_list.size();
+ packing_score /= size;
return packing_score;
}
Real BackboneLoopScorer::CalculateHBondScore(const BackboneList& bb_list, uint start_resnum,
uint chain_index) const{
- if(bb_list.size() < 3){
+ int size = bb_list.size();
+
+ if(size < 3){
throw promod3::Error("Size of Backbone list must be at least 3!");
}
@@ -1573,7 +2130,7 @@ Real BackboneLoopScorer::CalculateHBondScore(const BackboneList& bb_list, uint s
throw promod3::Error("Invalid chain index encountered when calculating hbond score!");
}
- uint end_resnum = start_resnum + bb_list.size()-1;
+ uint end_resnum = start_resnum + size-1;
//in case of overflows(e.g. when user input is negative) start_resnum could be bigger end_resnum
if(start_resnum < 1 || end_resnum > seqres_[chain_index].size()){
throw promod3::Error("Invalid start residue number encountered when calculating hbond score!");
@@ -1590,14 +2147,14 @@ Real BackboneLoopScorer::CalculateHBondScore(const BackboneList& bb_list, uint s
Real hbond_score = 0.0;
//note, that the n-terminal backbone hydrogen will be constructed below
- std::vector<geom::Vec3> h_positions(bb_list.size());
- for(uint i = 1; i < bb_list.size(); ++i){
+ std::vector<geom::Vec3> h_positions(size);
+ for(int i = 1; i < size; ++i){
Real phi = bb_list.GetPhiTorsion(i);
promod3::core::ConstructAtomPos(bb_list[i].c_coord,bb_list[i].ca_coord,
bb_list[i].n_coord,0.9970,2.0420,phi+M_PI,h_positions[i]);
}
- uint states[bb_list.size()];
+ uint states[size];
Real n_phi = -1.0472;
Real c_psi = -0.78540;
if(start_resnum > 1){
@@ -1623,9 +2180,9 @@ Real BackboneLoopScorer::CalculateHBondScore(const BackboneList& bb_list, uint s
bb_list[0].n_coord,0.9970,2.0420,n_phi+M_PI,h_positions[0]);
states[0] = GetHBondState(n_phi,bb_list.GetPsiTorsion(0));
- states[bb_list.size()-1] = GetHBondState(bb_list.GetPhiTorsion(bb_list.size()-1),c_psi);
+ states[size-1] = GetHBondState(bb_list.GetPhiTorsion(size-1),c_psi);
- for(uint i = 1; i < bb_list.size()-1; ++i){
+ for(int i = 1; i <size-1; ++i){
states[i] = GetHBondState(bb_list.GetPhiTorsion(i),
bb_list.GetPsiTorsion(i));
}
@@ -1649,13 +2206,23 @@ Real BackboneLoopScorer::CalculateHBondScore(const BackboneList& bb_list, uint s
states[0] = 0;
}
}
- if(states[bb_list.size()-1] == 2){
- if(next_state != 2 && states[bb_list.size()-2] != 2){
- states[bb_list.size()-1] = 0;
+ if(states[0] == 2){
+ if(prev_state != 2 && states[1] != 2){
+ states[0] = 0;
+ }
+ }
+ if(states[size-1] == 1){
+ if(next_state != 1 && states[size-2] != 1){
+ states[size-1] = 0;
+ }
+ }
+ if(states[size-1] == 2){
+ if(next_state != 2 && states[size-2] != 2){
+ states[size-1] = 0;
}
}
- for(uint i = 1; i < bb_list.size()-1; ++i){
+ for(int i = 1; i < size-1; ++i){
if(states[i] == 1){
if(states[i-1] == 1 || states[i+1] == 1) continue;
}
@@ -1667,69 +2234,82 @@ Real BackboneLoopScorer::CalculateHBondScore(const BackboneList& bb_list, uint s
//let's go over every loop residue
int state;
- for(uint i = 0; i < bb_list.size(); ++i){
- within_result = hbond_env_.FindWithin(bb_list[i].ca_coord, 8.0);
+ int loop_start_idx = residue_indices_[chain_index][start_resnum-1];
+ int loop_end_idx = residue_indices_[chain_index][end_resnum-1];
+ for(int i = 0; i < size; ++i){
+ within_result = hbond_env_.FindWithin(bb_list[i].ca_coord, 9.0);
a = within_result.first;
for(uint j = 0; j < within_result.second; ++j){
- if(a[j].first->number >= start_resnum && a[j].first->number <= end_resnum){ //not considering any loop residues
- if(chain_index == a[j].first->chain_index){
- continue;
- }
- }
- if(states[i] == a[j].first->state) state = states[i];
- else state = 0;
- //case of being donor for current bb item
- hbond_score += this->EvalHBondPotential(state,bb_list[i].n_coord,
- h_positions[i],
- a[j].first->pos,
- a[j].first->c_pos,
- a[j].first->o_pos);
+ if(a[j].first->idx < loop_start_idx || a[j].first->idx > loop_end_idx){
+ if(states[i] == a[j].first->state) state = states[i];
+ else state = 0;
- //case of being acceptor for current bb item
- hbond_score += this->EvalHBondPotential(state, a[j].first->n_pos,
- a[j].first->h_pos,
- bb_list[i].ca_coord,
- bb_list[i].c_coord,
- bb_list[i].o_coord);
+ //case of being donor for current bb item
+ if(bb_list[i].one_letter_code != 'P'){
+ hbond_score += this->EvalHBondPotential(state,bb_list[i].n_coord,
+ h_positions[i],
+ a[j].first->pos,
+ a[j].first->c_pos,
+ a[j].first->o_pos);
+ }
+
+ //case of being acceptor for current bb item
+ if(!a[j].first->is_proline){
+ hbond_score += this->EvalHBondPotential(state, a[j].first->n_pos,
+ a[j].first->h_pos,
+ bb_list[i].ca_coord,
+ bb_list[i].c_coord,
+ bb_list[i].o_coord);
+ }
+ }
}
}
//we do not have the loop internal interactions yet...
- for(uint i = 1; i < bb_list.size(); ++i){
- for(uint j = 0; j < i; ++j){
+ for(int i = 0; i < size; ++i){
+ for(int j = 0; j < size; ++j){
+
+ if(i == j) continue;
+
+ if(geom::Length2(bb_list[i].ca_coord-bb_list[j].ca_coord) > 81.0) continue;
if(states[i] == states[j]) state = states[i];
else state = 0;
//case of i being donor
- hbond_score += this->EvalHBondPotential(state,
- bb_list[i].n_coord,
- h_positions[i],
- bb_list[j].ca_coord,
- bb_list[j].c_coord,
- bb_list[j].o_coord);
+ if(bb_list[i].one_letter_code != 'P'){
+ hbond_score += this->EvalHBondPotential(state,
+ bb_list[i].n_coord,
+ h_positions[i],
+ bb_list[j].ca_coord,
+ bb_list[j].c_coord,
+ bb_list[j].o_coord);
+ }
//case of i being acceptor
- hbond_score += this->EvalHBondPotential(state,
- bb_list[j].n_coord,
- h_positions[j],
- bb_list[i].ca_coord,
- bb_list[i].c_coord,
- bb_list[i].o_coord);
+ if(bb_list[j].one_letter_code != 'P'){
+ hbond_score += this->EvalHBondPotential(state,
+ bb_list[j].n_coord,
+ h_positions[j],
+ bb_list[i].ca_coord,
+ bb_list[i].c_coord,
+ bb_list[i].o_coord);
+ }
}
}
- hbond_score /= bb_list.size();
+ hbond_score /= size;
return hbond_score;
}
+Real BackboneLoopScorer::CalculateSSAgreementScore(const BackboneList& bb_list, uint start_resnum,
+ uint chain_index) const{
-Real BackboneLoopScorer::CalculateDSSPHBondScore(const BackboneList& bb_list, uint start_resnum,
- uint chain_index) const{
+ int size = bb_list.size();
- if(bb_list.size() < 3){
+ if(size < 3){
throw promod3::Error("Size of Backbone list must be at least 3!");
}
@@ -1741,90 +2321,294 @@ Real BackboneLoopScorer::CalculateDSSPHBondScore(const BackboneList& bb_list, ui
throw promod3::Error("Invalid chain index encountered when calculating hbond score!");
}
- uint end_resnum = start_resnum + bb_list.size()-1;
+ if(ss_agreement_scores_ == NULL){
+ throw promod3::Error("SSAgreement scores must be attached to scorer to calculate according score!");
+ }
+
+ if(!psipred_set_){
+ throw promod3::Error("Psipred prediction must be set in scorer to calculate SSAgrement score!");
+ }
+
+ uint end_resnum = start_resnum + size-1;
//in case of overflows(e.g. when user input is negative) start_resnum could be bigger end_resnum
if(start_resnum < 1 || end_resnum > seqres_[chain_index].size()){
- throw promod3::Error("Invalid start residue number encountered when calculating hbond score!");
+ throw promod3::Error("Invalid start residue number encountered when calculating ss_agreement score!");
}
- promod3::loop::DynamicSpatialOrganizer<HBondSpatialOrganizerItem,geom::Vec3>::WithinResult within_result;
- std::pair<HBondSpatialOrganizerItem*,Real>* a;
+ //to assign the secondary structure as correct as possible we need to
+ //define margins to the left and right if the environment is correctly set there...
+ int start_idx = start_resnum-1;
+ int end_idx = end_resnum-1;
+ int max_left_margin = std::min(6,start_idx);
+ int max_right_margin = std::min(6,static_cast<int>(residue_indices_[chain_index].size())-1-end_idx);
+ int left_margin = 0;
+ int right_margin = 0;
- Real score;
- Real hbond_score = 0.0;
+ for(int i = 0; i < max_left_margin; ++i){
+ if(!env_set_[chain_index][start_idx-1-i]) break;
+ ++left_margin;
+ }
- std::vector<geom::Vec3> h_positions(bb_list.size());
- for(uint i = 1; i < bb_list.size(); ++i){
- Real phi = bb_list.GetPhiTorsion(i);
- promod3::core::ConstructAtomPos(bb_list[i].c_coord,bb_list[i].ca_coord,
- bb_list[i].n_coord,0.9970,2.0420,phi+M_PI,h_positions[i]);
+ for(int i = 0; i < max_right_margin; ++i){
+ if(!env_set_[chain_index][end_idx+1+i]) break;
+ ++right_margin;
}
- Real n_phi = -1.0472;
- if(start_resnum > 1){
- if(env_set_[chain_index][start_resnum-2]){
- n_phi = geom::DihedralAngle(hbond_env_data_[chain_index][start_resnum-2].c_pos,
- bb_list[0].n_coord,
- bb_list[0].ca_coord,
- bb_list[0].c_coord);
- }
+ int total_size = size + left_margin + right_margin;
+
+ std::vector<geom::Vec3> ca_positions(total_size, geom::Vec3(0,0,0));
+ std::vector<geom::Vec3> c_positions(total_size, geom::Vec3(0,0,0));
+ std::vector<geom::Vec3> o_positions(total_size, geom::Vec3(0,0,0));
+ std::vector<geom::Vec3> n_positions(total_size, geom::Vec3(0,0,0));
+ std::vector<geom::Vec3> h_positions(total_size, geom::Vec3(0,0,0));
+
+ //lets first fill everything from the left margin using hbond env
+ for(int i = 0; i < left_margin; ++i){
+ const HBondSpatialOrganizerItem& env_item = hbond_env_data_[chain_index][start_idx-left_margin+i];
+ ca_positions[i] = env_item.pos;
+ c_positions[i] = env_item.c_pos;
+ o_positions[i] = env_item.o_pos;
+ n_positions[i] = env_item.n_pos;
+ h_positions[i] = env_item.h_pos;
+ }
+ //lets fill everything from the right margin
+ for(int i = 0; i < right_margin; ++i){
+ const HBondSpatialOrganizerItem& env_item = hbond_env_data_[chain_index][end_idx+1+i];
+ ca_positions[left_margin+size+i] = env_item.pos;
+ c_positions[left_margin+size+i] = env_item.c_pos;
+ o_positions[left_margin+size+i] = env_item.o_pos;
+ n_positions[left_margin+size+i] = env_item.n_pos;
+ h_positions[left_margin+size+i] = env_item.h_pos;
+ }
+
+ //let's fill all positions from the bb_list except the hydrogen ones...
+ for(int i = 0; i < size; ++i){
+ const Backbone& bb_item = bb_list[i];
+ ca_positions[left_margin+i] = bb_item.ca_coord;
+ c_positions[left_margin+i] = bb_item.c_coord;
+ o_positions[left_margin+i] = bb_item.o_coord;
+ n_positions[left_margin+i] = bb_item.n_coord;
+ }
+
+ //we can finally calculate the h-positions, we do this the dirty dssp way
+ //(negative c-o vector of previous residue)
+ int first_h;
+ if(left_margin == 0) first_h = 1;
+ else first_h = 0;
+ for(int i = first_h; i < size; ++i){
+ geom::Vec3 dir = geom::Normalize(c_positions[left_margin+i-1]-
+ o_positions[left_margin+i-1]);
+ h_positions[left_margin+i] = n_positions[left_margin+i] + dir;
+ }
+
+ //if the first hbond is one, we have to construct a "dummy" h,
+ //note that there is no previous res in the env in this case...
+ if(first_h == 1){
+ promod3::core::ConstructAtomPos(c_positions[0],ca_positions[0],
+ n_positions[0],0.9970,2.0420,2.0944,h_positions[0]);
+
}
- promod3::core::ConstructAtomPos(bb_list[0].c_coord,bb_list[0].ca_coord,
- bb_list[0].n_coord,0.9970,2.0420,n_phi+M_PI,h_positions[0]);
+
+ std::vector<int> donor_for_one(total_size,-1);
+ std::vector<int> donor_for_two(total_size,-1);
+ std::vector<int> acceptor_for_one(total_size,-1);
+ std::vector<int> acceptor_for_two(total_size,-1);
+ std::vector<Real> donor_one_energies(total_size,std::numeric_limits<Real>::max());
+ std::vector<Real> donor_two_energies(total_size,std::numeric_limits<Real>::max());
+ std::vector<Real> acceptor_one_energies(total_size,std::numeric_limits<Real>::max());
+ std::vector<Real> acceptor_two_energies(total_size,std::numeric_limits<Real>::max());
+
+ int loop_start_idx = residue_indices_[chain_index][start_idx];
+ int loop_end_idx = residue_indices_[chain_index][end_idx];
+ int positions_start_idx = loop_start_idx-left_margin;
+ int positions_end_idx = loop_end_idx+right_margin;
+ int min_idx_chain = residue_indices_[chain_index][0];
+ int max_idx_chain = residue_indices_[chain_index].back();
+ //let's precalculate the idx ranges we have to neglect
+ std::vector<int> start_neglect(total_size,positions_start_idx);
+ std::vector<int> end_neglect(total_size,positions_end_idx);
+ for(int i = 0; i < 2; ++i){
+ start_neglect[i] = std::max(min_idx_chain,start_neglect[i]-(2+i));
+ end_neglect[total_size-1-i] = std::min(max_idx_chain,end_neglect[i]+(2-i));
+ }
- //let's go over every loop residue
- for(uint i = 0; i < bb_list.size(); ++i){
- within_result = hbond_env_.FindWithin(bb_list[i].ca_coord, 8.0);
+ //we have to know where the prolines are
+ bool prolines[total_size];
+ for(int i = 0; i < total_size; ++i){
+ prolines[i] = seqres_[chain_index][start_idx-left_margin+i] == ost::conop::PRO;
+ }
+
+ promod3::loop::DynamicSpatialOrganizer<HBondSpatialOrganizerItem,geom::Vec3>::WithinResult within_result;
+ std::pair<HBondSpatialOrganizerItem*,Real>* a;
+ Real e;
+ //let's start to fill the stuff from the env
+ for(int i = 0; i < total_size; ++i){
+ within_result = hbond_env_.FindWithin(ca_positions[i], 9.0);
a = within_result.first;
for(uint j = 0; j < within_result.second; ++j){
- if(a[j].first->number >= start_resnum && a[j].first->number <= end_resnum){ //not considering any loop residues
- if(chain_index == a[j].first->chain_index){
- continue;
+ if(a[j].first->idx < start_neglect[i] || a[j].first->idx > end_neglect[i]){
+
+ //i as acceptor
+ if(!a[j].first->is_proline && positions_start_idx + i < max_idx_chain && !(a[j].first->idx == min_idx_chain)){
+ e = DSSPHBondEnergy(a[j].first->h_pos, a[j].first->n_pos,
+ c_positions[i], o_positions[i]);
+
+ if(e < -0.5){
+ //it is an hbond... let's see, whether it is the best for i as acceptor
+ if(e < acceptor_two_energies[i]){
+ if(e < acceptor_one_energies[i]){
+ acceptor_two_energies[i] = acceptor_one_energies[i];
+ acceptor_for_two[i] = acceptor_for_one[i];
+ acceptor_one_energies[i] = e;
+ acceptor_for_one[i] = a[j].first->idx;
+ }
+ else{
+ acceptor_two_energies[i] = e;
+ acceptor_for_two[i] = a[j].first->idx;
+ }
+ }
+ }
+ }
+
+ //i as donor
+ if(!prolines[i] && positions_start_idx + i > min_idx_chain && a[j].first->idx < max_idx_chain){
+
+ e = DSSPHBondEnergy(h_positions[i],n_positions[i],
+ a[j].first->c_pos,a[j].first->o_pos);
+
+ if(e < -0.5){
+ //it is an hbond... let's see, whether it is the best for i as donor
+ if(e < donor_two_energies[i]){
+ if(e < donor_one_energies[i]){
+ donor_two_energies[i] = donor_one_energies[i];
+ donor_for_two[i] = donor_for_one[i];
+ donor_one_energies[i] = e;
+ donor_for_one[i] = a[j].first->idx;
+ }
+ else{
+ donor_two_energies[i] = e;
+ donor_for_two[i] = a[j].first->idx;
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+
+ //let's get the internal hbonds right...
+ for(int i = 0; i < total_size-3; ++i){
+ for(int j = i+3; j < total_size; ++j){
+ if(geom::Length2(ca_positions[i]-ca_positions[j]) < 81.0){
+ //i as acceptor ; j as donor
+ if(!prolines[j]){
+ e = DSSPHBondEnergy(h_positions[j],n_positions[j],
+ c_positions[i],o_positions[i]);
+
+ if(e < -0.5){
+ //it is an hbond... let's see, whether it is the best for i as acceptor
+ if(e < acceptor_two_energies[i]){
+ if(e < acceptor_one_energies[i]){
+ acceptor_two_energies[i] = acceptor_one_energies[i];
+ acceptor_for_two[i] = acceptor_for_one[i];
+ acceptor_one_energies[i] = e;
+ acceptor_for_one[i] = positions_start_idx + j;
+ }
+ else{
+ acceptor_two_energies[i] = e;
+ acceptor_for_two[i] = positions_start_idx + j;
+ }
+ }
+
+ //let's see, whether it is the best for j as donor
+ if(e < donor_two_energies[j]){
+ if(e < donor_one_energies[j]){
+ donor_two_energies[j] = donor_one_energies[j];
+ donor_for_two[j] = donor_for_one[j];
+ donor_one_energies[j] = e;
+ donor_for_one[j] = positions_start_idx + i;
+ }
+ else{
+ donor_two_energies[j] = e;
+ donor_for_two[j] = positions_start_idx + i;
+ }
+ }
+ }
+ }
+
+ //i as donor, j as acceptor
+ if(!prolines[i] && positions_start_idx + i > min_idx_chain && positions_start_idx + j < max_idx_chain){
+
+ e = DSSPHBondEnergy(h_positions[i],n_positions[i],
+ c_positions[j],o_positions[j]);
+
+ if(e < -0.5){
+ //it is an hbond... let's see, whether it is the best for i as donor
+ if(e < donor_two_energies[i]){
+ if(e < donor_one_energies[i]){
+ donor_two_energies[i] = donor_one_energies[i];
+ donor_for_two[i] = donor_for_one[i];
+ donor_one_energies[i] = e;
+ donor_for_one[i] = positions_start_idx + j;
+ }
+ else{
+ donor_two_energies[i] = e;
+ donor_for_two[i] = positions_start_idx + j;
+ }
+ }
+
+ //let's see, whether it is the best for j as acceptor
+ if(e < acceptor_two_energies[j]){
+ if(e < acceptor_one_energies[j]){
+ acceptor_two_energies[j] = acceptor_one_energies[j];
+ acceptor_for_two[j] = acceptor_for_one[j];
+ acceptor_one_energies[j] = e;
+ acceptor_for_one[j] = positions_start_idx + i;
+ }
+ else{
+ acceptor_two_energies[j] = e;
+ acceptor_for_two[j] = positions_start_idx + i;
+ }
+ }
+ }
}
}
- //case of being donor for current bb item
- score = DSSPHBondEnergy(h_positions[i],bb_list[i].n_coord,
- a[j].first->c_pos,a[j].first->o_pos);
- if(score < 0.0) hbond_score += score;
-
- //case of being acceptor for current bb item
- score = DSSPHBondEnergy(a[j].first->h_pos, a[j].first->n_pos,
- bb_list[i].c_coord, bb_list[i].o_coord);
- if(score < 0.0) hbond_score += score;
}
}
- //we do not have the loop internal interactions yet...
- for(uint i = 1; i < bb_list.size(); ++i){
- for(uint j = 0; j < i; ++j){
- //case of i being donor
- score = DSSPHBondEnergy(h_positions[i],bb_list[i].n_coord,
- bb_list[j].c_coord, bb_list[j].o_coord);
- if(score < 0.0) hbond_score += score;
-
- //case of i being acceptor
- score = DSSPHBondEnergy(h_positions[j],bb_list[j].n_coord,
- bb_list[i].c_coord, bb_list[i].o_coord);
- if(score < 0.0) hbond_score += score;
-
- }
+
+ String ss;
+ RawEstimateSS(ca_positions, positions_start_idx, donor_for_one, donor_for_two,
+ acceptor_for_one, acceptor_for_two, ss);
+
+ int dssp_idx;
+ int psipred_idx;
+ int psipred_conf;
+ Real score = 0.0;
+ for(int i = 0; i < size; ++i){
+ dssp_idx = GetDSSPIdx(ss[left_margin+i]);
+ psipred_idx = psipred_pred_[chain_index][start_idx+i];
+ psipred_conf = psipred_conf_[chain_index][start_idx+i];
+ score += ss_agreement_scores_[dssp_idx][psipred_idx][psipred_conf];
}
- hbond_score /= bb_list.size();
- return hbond_score;
+ score /= size;
+ return score;
}
bool BackboneLoopScorer::TransOmegaTorsions(const BackboneList& bb_list,
Real thresh,
bool allow_prepro_cis) const{
- if(bb_list.size() < 3){
+ int size = bb_list.size();
+
+ if(size < 3){
throw promod3::Error("Size of Backbone list must be at least 3!");
}
Real angle;
- for(uint i = 0; i < bb_list.size()-1; ++i){
+ for(int i = 0; i < size-1; ++i){
angle = bb_list.GetOmegaTorsion(i);
if(std::abs(angle) < M_PI-thresh){
if(allow_prepro_cis && bb_list[i+1].aa == ost::conop::PRO){
@@ -1864,13 +2648,38 @@ void BackboneLoopScorer::AllocateCBeta(){
throw promod3::Error("Tried to allocate memory for cbeta term, but the memory is already allocated!");
}
cbeta_energies_ = new Real**[ost::conop::XXX];
- for (uint i = 0; i < ost::conop::XXX; ++i) {
+ for (uint i = 0; i < ost::conop::XXX; ++i){
cbeta_energies_[i] = new Real*[ost::conop::XXX];
for (uint j = 0; j < ost::conop::XXX; ++j){
cbeta_energies_[i][j] = new Real[cbeta_bins_];
memset(&cbeta_energies_[i][j][0],0,cbeta_bins_*sizeof(Real));
}
}
+
+}
+
+void BackboneLoopScorer::AllocateReduced(){
+ if(reduced_energies_ != NULL){
+ throw promod3::Error("Tried to allocate memory for reduced term, but the memory is already allocated!");
+ }
+ reduced_energies_ = new Real*****[ost::conop::XXX];
+ for (uint i = 0; i < ost::conop::XXX; ++i){
+ reduced_energies_[i] = new Real****[ost::conop::XXX];
+ for (uint j = 0; j < ost::conop::XXX; ++j){
+ reduced_energies_[i][j] = new Real***[reduced_dist_bins_];
+ for (uint k = 0; k < reduced_dist_bins_; ++k){
+ reduced_energies_[i][j][k] = new Real**[reduced_angle_bins_];
+ for(uint l = 0; l < reduced_angle_bins_; ++l){
+ reduced_energies_[i][j][k][l] = new Real*[reduced_angle_bins_];
+ for(uint m = 0; m < reduced_angle_bins_; ++m){
+ reduced_energies_[i][j][k][l][m] = new Real[reduced_dihedral_bins_];
+ memset(&reduced_energies_[i][j][k][l][m][0],0,reduced_dihedral_bins_*sizeof(Real));
+ }
+ }
+ }
+ }
+ }
+
}
void BackboneLoopScorer::AllocateCBPacking(){
@@ -1919,6 +2728,20 @@ void BackboneLoopScorer::AllocateHBond(){
}
}
+void BackboneLoopScorer::AllocateSSAgreement(){
+ if(ss_agreement_scores_ != NULL){
+ throw promod3::Error("Tried to allocate memory for ss agreement term, but the memory is already allocated!");
+ }
+ ss_agreement_scores_ = new Real**[8];
+ for (uint i = 0; i < 8; ++i) {
+ ss_agreement_scores_[i] = new Real*[3];
+ for (uint j = 0; j < 3; ++j){
+ ss_agreement_scores_[i][j] = new Real[10];
+ memset(&ss_agreement_scores_[i][j][0],0,10*sizeof(Real));
+ }
+ }
+}
+
void BackboneLoopScorer::DeallocateCBeta(){
if(cbeta_energies_ != NULL){
for (int i = 0; i < ost::conop::XXX; ++i) {
@@ -1932,6 +2755,28 @@ void BackboneLoopScorer::DeallocateCBeta(){
}
}
+void BackboneLoopScorer::DeallocateReduced(){
+ if(reduced_energies_ != NULL){
+ for (int i = 0; i < ost::conop::XXX; ++i) {
+ for (int j = 0; j < ost::conop::XXX; ++j){
+ for (uint k = 0; k < reduced_dist_bins_; ++k){
+ for (uint l = 0; l < reduced_angle_bins_; ++l){
+ for (uint m = 0; m < reduced_angle_bins_; ++m){
+ delete [] reduced_energies_[i][j][k][l][m];
+ }
+ delete [] reduced_energies_[i][j][k][l];
+ }
+ delete [] reduced_energies_[i][j][k];
+ }
+ delete [] reduced_energies_[i][j];
+ }
+ delete [] reduced_energies_[i];
+ }
+ delete [] reduced_energies_;
+ reduced_energies_ = NULL;
+ }
+}
+
void BackboneLoopScorer::DeallocateTorsion(){
if(torsion_energies_!=NULL){
for (uint i = 0; i < num_torsion_groups_; ++i) {
@@ -1974,4 +2819,19 @@ void BackboneLoopScorer::DeallocateHBond(){
}
}
+void BackboneLoopScorer::DeallocateSSAgreement(){
+ if(ss_agreement_scores_ != NULL){
+ for (int i = 0; i < 8; ++i) {
+ for (int j = 0; j < 3; ++j){
+ delete [] ss_agreement_scores_[i][j];
+ }
+ delete [] ss_agreement_scores_[i];
+ }
+ delete [] ss_agreement_scores_;
+ ss_agreement_scores_ = NULL;
+ }
+}
+
+
+
}}//ns
diff --git a/loop/src/backbone_loop_score.hh b/loop/src/backbone_loop_score.hh
index a6becc82f0f8ef2c78833aafcf36fe977bad7e93..d413b8e663b654be8364b448347920639e83f352 100644
--- a/loop/src/backbone_loop_score.hh
+++ b/loop/src/backbone_loop_score.hh
@@ -7,6 +7,8 @@
#include <ost/mol/view_op.hh>
#include <promod3/loop/backbone.hh>
#include <promod3/loop/dynamic_spatial_organizer.hh>
+#include <promod3/loop/sec_struct.hh>
+#include <promod3/loop/psipred_prediction.hh>
#include <boost/shared_ptr.hpp>
@@ -23,26 +25,34 @@ struct CBSpatialOrganizerItem{
CBSpatialOrganizerItem() { }
CBSpatialOrganizerItem(ost::conop::AminoAcid a,
- geom::Vec3& p, uint n,
- uint c_i): aa(a), pos(p), number(n),
- chain_index(c_i) { }
+ geom::Vec3& p, uint i): aa(a), pos(p), idx(i) { }
ost::conop::AminoAcid aa;
geom::Vec3 pos;
- uint number;
- uint chain_index;
+ int idx;
+};
+
+struct ReducedSpatialOrganizerItem{
+ ReducedSpatialOrganizerItem() { }
+
+ ReducedSpatialOrganizerItem(ost::conop::AminoAcid a,
+ geom::Vec3& p, geom::Vec3& ax,
+ uint i): aa(a), pos(p), axis(ax), idx(i) { }
+ ost::conop::AminoAcid aa;
+ geom::Vec3 pos;
+ geom::Vec3 axis;
+ int idx;
};
struct ClashSpatialOrganizerItem{
ClashSpatialOrganizerItem() { }
ClashSpatialOrganizerItem(Real r, const geom::Vec3& p,
- uint n, uint c_i): radius(r), pos(p),
- number(n), chain_index(c_i) { }
+ uint i): radius(r), pos(p),
+ idx(i) { }
Real radius;
geom::Vec3 pos;
- uint number;
- uint chain_index;
+ int idx;
};
struct HBondSpatialOrganizerItem{
@@ -50,11 +60,10 @@ struct HBondSpatialOrganizerItem{
HBondSpatialOrganizerItem(const geom::Vec3& p, const geom::Vec3& n,
const geom::Vec3& h, const geom::Vec3& c,
- const geom::Vec3& o, uint state, uint num,
+ const geom::Vec3& o, uint state, uint i,
uint c_i): pos(p), n_pos(n),
h_pos(h), c_pos(c),
- o_pos(o), number(num),
- chain_index(c_i) { }
+ o_pos(o), idx(i) { }
geom::Vec3 pos; //CA position of residue
geom::Vec3 n_pos; //donor N
@@ -62,21 +71,10 @@ struct HBondSpatialOrganizerItem{
geom::Vec3 c_pos; //acceptor C
geom::Vec3 o_pos; //acceptor O
uint state;
- uint number;
- uint chain_index;
+ int idx;
+ bool is_proline;
};
-struct HBondAcceptorSpatialOrganizerItem{
- HBondAcceptorSpatialOrganizerItem() { }
-
- HBondAcceptorSpatialOrganizerItem(const geom::Vec3& p, const geom::Vec3& c): pos(p),
- c_pos(c) { }
-
- geom::Vec3 pos; //acceptor oxygen
- geom::Vec3 c_pos; //carbon
-};
-
-
class BackboneLoopScorer{
public:
@@ -90,6 +88,9 @@ public:
void SetCBetaPotentialParameters(Real cbeta_cutoff, uint cbeta_bins, uint cbeta_seq_sep);
+ void SetReducedPotentialParameters(Real dist_cutoff, uint dist_bins, uint angle_bins,
+ uint dihedral_bins, uint seq_sep);
+
void SetTorsionPotentialParameters(const std::vector<String>& group_definitions,
uint torsion_bins);
@@ -102,8 +103,13 @@ public:
uint hb_d_bins, uint hb_alpha_bins,
uint hb_beta_bins, uint hb_gamma_bins);
+ void SetSSAgreementParameters();
+
void SetCBetaEnergy(ost::conop::AminoAcid a, ost::conop::AminoAcid b, uint bin, Real e);
+ void SetReducedEnergy(ost::conop::AminoAcid a, ost::conop::AminoAcid b,
+ uint dist_bin, uint alpha_bin, uint beta_bin, uint gamma_bin, Real e);
+
void SetTorsionEnergy(uint group_id_idx, uint phi_bin, uint psi_bin, Real e);
void SetCBPackingEnergy(ost::conop::AminoAcid aa, uint count, Real e);
@@ -111,32 +117,46 @@ public:
void SetHBondEnergy(uint state, uint d_bin, uint alpha_bin,
uint beta_bin, uint gamma_bin, Real e);
+ void SetSSAgreementScore(char psipred_state, int psipred_confidence,
+ char dssp_state, Real score);
+
void Initialize(const String& seqres);
void Initialize(const std::vector<String>& seqres);
+ void SetPsipredPrediction(PsipredPredictionPtr pp);
+
+ void SetPsipredPrediction(std::vector<PsipredPredictionPtr>& pp);
+
void SetEnvironment(const ost::mol::EntityHandle& env);
void SetEnvironment(const promod3::loop::BackboneList& bb_list, uint start_resnum,
uint chain_index = 0);
+ void ClearEnvironment(uint start_resnum, uint num_residues,
+ uint chain_index = 0);
+
Real CalculateClashScore(const BackboneList& bb_list, uint start_resnum,
- uint chain_index=0) const;
+ uint chain_index = 0) const;
Real CalculateCBetaScore(const BackboneList& bb_list, uint start_resnum,
- uint chain_index=0) const;
+ uint chain_index = 0) const;
+
+ Real CalculateReducedScore(const BackboneList& bb_list, uint start_resnum,
+ uint chain_index = 0) const;
Real CalculateTorsionScore(const BackboneList& bb_list, uint start_resnum,
- uint chain_index=0) const;
+ uint chain_index = 0) const;
Real CalculateCBPackingScore(const BackboneList& bb_list, uint start_resnum,
- uint chain_index=0) const;
+ uint chain_index = 0) const;
- Real CalculateHBondScore(const BackboneList& bb_list, uint start_resnum,
+ Real CalculateHBondScore(const BackboneList&
+ bb_list, uint start_resnum,
uint chain_index = 0) const;
- Real CalculateDSSPHBondScore(const BackboneList& bb_list, uint start_resnum,
- uint chain_index=0) const;
+ Real CalculateSSAgreementScore(const BackboneList& bb_list, uint start_resnum,
+ uint chain_index = 0) const;
bool TransOmegaTorsions(const BackboneList& bb_list,
Real thresh = 20.0/180*M_PI,
@@ -150,32 +170,46 @@ private:
void AllocateCBeta();
+ void AllocateReduced();
+
void AllocateCBPacking();
void AllocateTorsion();
void AllocateHBond();
+ void AllocateSSAgreement();
+
void DeallocateCBeta();
+ void DeallocateReduced();
+
void DeallocateCBPacking();
void DeallocateTorsion();
void DeallocateHBond();
+ void DeallocateSSAgreement();
+
//environment dependent data
bool initialized_;
std::vector<std::vector<ost::conop::AminoAcid> > seqres_;
+ std::vector<std::vector<int> > residue_indices_;
bool** env_set_;
CBSpatialOrganizerItem** cb_env_data_;
+ ReducedSpatialOrganizerItem** reduced_env_data_;
ClashSpatialOrganizerItem*** clash_env_data_;
HBondSpatialOrganizerItem** hbond_env_data_;
std::vector<std::vector<int> > torsion_group_indices_;
+ bool psipred_set_;
+ std::vector<std::vector<int> > psipred_pred_;
+ std::vector<std::vector<int> > psipred_conf_;
//the dynamic spatial organizer data objects, that directly depend on
- //cb_env_data_, clash_env_data_ and hbond_env_data_
+ //cb_env_data_, reduced_env_data_, clash_env_data_ and hbond_env_data_
promod3::loop::DynamicSpatialOrganizer<CBSpatialOrganizerItem,geom::Vec3> cb_env_;
+ promod3::loop::DynamicSpatialOrganizer<ReducedSpatialOrganizerItem,geom::Vec3> reduced_env_;
promod3::loop::DynamicSpatialOrganizer<ClashSpatialOrganizerItem,geom::Vec3> clash_env_;
promod3::loop::DynamicSpatialOrganizer<HBondSpatialOrganizerItem,geom::Vec3> hbond_env_;
@@ -186,6 +220,16 @@ private:
Real squared_cbeta_cutoff_;
Real cbeta_bin_size_;
+ uint reduced_seq_sep_;
+ uint reduced_dist_bins_;
+ uint reduced_angle_bins_;
+ uint reduced_dihedral_bins_;
+ Real reduced_distance_cutoff_;
+ Real reduced_squared_distance_cutoff_;
+ Real reduced_dist_bin_size_;
+ Real reduced_angle_bin_size_;
+ Real reduced_dihedral_bin_size_;
+
Real cb_packing_cutoff_;
Real squared_cb_packing_cutoff_;
uint cb_packing_max_count_;
@@ -212,10 +256,13 @@ private:
uint hb_beta_bins_;
uint hb_gamma_bins_;
+ //the scores
Real*** cbeta_energies_;
+ Real****** reduced_energies_;
Real*** torsion_energies_;
Real** cb_packing_energies_;
Real***** hbond_energies_;
+ Real*** ss_agreement_scores_;
};
}}//ns
diff --git a/loop/src/cluster.cc b/loop/src/cluster.cc
new file mode 100644
index 0000000000000000000000000000000000000000..66997a6b93b47dc49c303a410a0be3810aae7f58
--- /dev/null
+++ b/loop/src/cluster.cc
@@ -0,0 +1,83 @@
+#include <promod3/loop/cluster.hh>
+
+namespace promod3{ namespace loop{
+
+void Cluster::Merge(const Cluster& other){
+ for(std::vector<int>::const_iterator i = other.members.begin();
+ i != other.members.end(); ++i){
+ members.push_back(*i);
+ }
+}
+
+float Cluster::PairwiseDistanceAVG(const Cluster& other, float** dist_matrix){
+ float sum = 0.0;
+ for(std::vector<int>::const_iterator i = members.begin();
+ i != members.end(); ++i){
+ for(std::vector<int>::const_iterator j = other.members.begin();
+ j != other.members.end(); ++j){
+ sum += dist_matrix[*i][*j];
+ }
+ }
+ return sum / (members.size() * other.members.size());
+}
+
+float Cluster::PairwiseDistanceMAX(const Cluster& other, float** dist_matrix){
+ float max_dist = 0.0;
+ float current_dist;
+ for(std::vector<int>::const_iterator i = members.begin();
+ i != members.end(); ++i){
+ for(std::vector<int>::const_iterator j = other.members.begin();
+ j != other.members.end(); ++j){
+ current_dist = dist_matrix[*i][*j];
+ if(current_dist > max_dist) max_dist = current_dist;
+ }
+ }
+ return max_dist;
+}
+
+void DoClustering(float** dist_matrix, int num, float max_dist,
+ std::vector<std::vector<int> >& output){
+
+ //initialize every point as single cluster
+ std::vector<Cluster> clusters(num);
+ for(int i = 0; i < num; ++i){
+ clusters[i].members.push_back(i);
+ }
+
+ //always search for the closest distances and merge the according clusters
+ bool something_happened = true;
+ int num_clusters = num;
+ std::pair<int,int> pair_to_merge;
+ float min_distance;
+ float distance;
+
+ while(something_happened){
+ something_happened = false;
+ min_distance = std::numeric_limits<float>::max();
+
+ for(int i = 0; i < num_clusters; ++i){
+ for(int j = i + 1; j < num_clusters; ++j){
+ distance = clusters[i].PairwiseDistanceMAX(clusters[j], dist_matrix);
+ if(distance < min_distance){
+ pair_to_merge = std::make_pair(i,j);
+ min_distance = distance;
+ }
+ }
+ }
+
+ if(min_distance < max_dist){
+ clusters[pair_to_merge.first].Merge(clusters[pair_to_merge.second]);
+ clusters.erase(clusters.begin() + pair_to_merge.second);
+ something_happened = true;
+ --num_clusters;
+ }
+ }
+
+ //fill the output
+ output.clear();
+ for(unsigned int i = 0; i < clusters.size(); ++i){
+ output.push_back(clusters[i].members);
+ }
+}
+
+}} //ns
diff --git a/loop/src/cluster.hh b/loop/src/cluster.hh
new file mode 100644
index 0000000000000000000000000000000000000000..ae46de44f3a71aab5b6d9edb4d10c72764005eeb
--- /dev/null
+++ b/loop/src/cluster.hh
@@ -0,0 +1,29 @@
+#ifndef PROMOD_LOOP_CLUSTER_HH
+#define PROMOD_LOOP_CLUSTER_HH
+
+#include <vector>
+#include <limits>
+
+namespace promod3 { namespace loop {
+
+struct Cluster{
+
+ Cluster() { }
+
+ void Merge(const Cluster& other);
+
+ float PairwiseDistanceAVG(const Cluster& other, float** dist_matrix);
+
+ float PairwiseDistanceMAX(const Cluster& other, float** dist_matrix);
+
+ std::vector<int> members;
+
+};
+
+
+void DoClustering(float** dist_matrix, int num, float max_dist,
+ std::vector<std::vector<int> >& output);
+
+}} //ns
+
+#endif
diff --git a/loop/src/dynamic_spatial_organizer.hh b/loop/src/dynamic_spatial_organizer.hh
index ff02680610ca13ae5223e0daae139fef1a302f51..3b44311aec584b357fe621f4276b84bf3fabbb2f 100644
--- a/loop/src/dynamic_spatial_organizer.hh
+++ b/loop/src/dynamic_spatial_organizer.hh
@@ -94,9 +94,9 @@ public:
Index indx=gen_index(pos);
typename ItemMap::iterator i = map_.find(indx);
if(i != map_.end()){
- typename EntryMap::iterator j = i->find(reinterpret_cast<uintptr_t>(item));
- if(j != i->end()){
- i->erase(j);
+ typename EntryMap::iterator j = i->second.find(reinterpret_cast<uintptr_t>(item));
+ if(j != i->second.end()){
+ i->second.erase(j);
}
}
}
diff --git a/loop/src/flame.cc b/loop/src/flame.cc
deleted file mode 100644
index 181ffb146fc2306a480db3423243ab440b73aecb..0000000000000000000000000000000000000000
--- a/loop/src/flame.cc
+++ /dev/null
@@ -1,537 +0,0 @@
-/*===================================================================
- The standard implementation of FLAME data clustering algorithm.
-
- FLAME (Fuzzy clustering by Local Approximation of MEmberships)
- was first described in:
- "FLAME, a novel fuzzy clustering method for the analysis of DNA
- microarray data", BMC Bioinformatics, 2007, 8:3.
- Available from: http://www.biomedcentral.com/1471-2105/8/3
-
- Copyright(C) 2007, Fu Limin (phoolimin@gmail.com).
- All rights reserved.
-
- Permission is granted to anyone to use this software for any purpose,
- including commercial applications, and to alter it and redistribute it
- freely, subject to the following restrictions:
-
- 1. Redistributions of source code must retain the above copyright
- notice, this list of conditions and the following disclaimer.
- 2. The origin of this software must not be misrepresented; you must
- not claim that you wrote the original software. If you use this
- software in a product, an acknowledgment in the product
- documentation would be appreciated but is not required.
- 3. Altered source versions must be plainly marked as such, and must
- not be misrepresented as being the original software.
-
- This program is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-===================================================================*/
-
-#include"stdio.h"
-#include"stdlib.h"
-#include"string.h"
-#include"math.h"
-
-#include"flame.hh"
-
-namespace promod3{ namespace loop{ namespace flame{
-
-/* Quick Sort.
- * Adam Drozdek: Data Structures and Algorithms in C++, 2nd Edition.
- */
-void PartialQuickSort( IndexFloat *data, int first, int last, int part )
-{
- int lower=first+1, upper=last;
- float pivot;
- IndexFloat val;
- if( first >= last ) return;
- val = data[first];
- data[first] = data[ (first+last)/2 ];
- data[ (first+last)/2 ] = val;
- pivot = data[ first ].value;
-
- while( lower <= upper ){
- while( lower <= last && data[lower].value < pivot ) lower ++;
- while( pivot < data[upper].value ) upper --;
- if( lower < upper ){
- val = data[lower];
- data[lower] = data[upper];
- data[upper] = val;
- upper --;
- }
- lower ++;
- }
- val = data[first];
- data[first] = data[upper];
- data[upper] = val;
- if( first < upper-1 ) PartialQuickSort( data, first, upper-1, part );
- if( upper >= part ) return;
- if( upper+1 < last ) PartialQuickSort( data, upper+1, last, part );
-}
-
-const DistFunction basicDistFunctions[] =
-{
- Flame_Euclidean ,
- Flame_CosineDist ,
- Flame_PearsonDist ,
- Flame_UCPearsonDist ,
- Flame_SQPearsonDist ,
- Flame_DotProductDist ,
- Flame_CovarianceDist ,
- Flame_Manhattan
-};
-
-float Flame_Euclidean( float *x, float *y, int m )
-{
- float d = 0;
- int i;
- for(i=0; i<m; i++ ) d += ( x[i] - y[i] ) * ( x[i] - y[i] );
- return sqrt( d );
-}
-float Flame_Cosine( float *x, float *y, int m )
-{
- float r =0, x2 =0, y2 =0;
- int i;
- for(i=0; i<m; i++ ){
- r += x[i] * y[i];
- x2 += x[i] * x[i];
- y2 += y[i] * y[i];
- }
- return r / ( sqrt( x2 * y2 ) + EPSILON );
-}
-float Flame_Pearson( float *x, float *y, int m )
-{
- int i;
- float r, x2, y2, xavg, yavg;
- if( m ==0 ) return 0;
- xavg = yavg = 0;
- r = x2 = y2 = 0;
- for( i=0; i<m; i++ ){
- xavg += x[i];
- yavg += y[i];
- }
- xavg = xavg/m;
- yavg = yavg/m;
- for( i=0; i<m; i++ ){
- r += ( x[i] - xavg ) * ( y[i] - yavg );
- x2 += ( x[i] - xavg ) * ( x[i] - xavg );
- y2 += ( y[i] - yavg ) * ( y[i] - yavg );
- }
- return r / ( sqrt( x2 * y2 ) + EPSILON );
-}
-float Flame_UCPearson( float *x, float *y, int m )
-{
- int i;
- float r, x2, y2, xavg, yavg;
- if( m ==0 ) return 0;
- xavg = yavg = 0;
- r = x2 = y2 = 0;
- for( i=0; i<m; i++ ){
- xavg += x[i];
- yavg += y[i];
- }
- xavg = xavg/m;
- yavg = yavg/m;
- for( i=0; i<m; i++ ){
- r += x[i] * y[i];
- x2 += ( x[i] - xavg ) * ( x[i] - xavg );
- y2 += ( y[i] - yavg ) * ( y[i] - yavg );
- }
- return r / ( sqrt( x2 * y2 ) + EPSILON );
-}
-float Flame_SQPearson( float *x, float *y, int m )
-{
- int i;
- float r, x2, y2, xavg, yavg;
- if( m ==0 ) return 0;
- xavg = yavg = 0;
- r = x2 = y2 = 0;
- for( i=0; i<m; i++ ){
- xavg += x[i];
- yavg += y[i];
- }
- xavg = xavg/m;
- yavg = yavg/m;
- for( i=0; i<m; i++ ){
- r += ( x[i] - xavg ) * ( y[i] - yavg );
- x2 += ( x[i] - xavg ) * ( x[i] - xavg );
- y2 += ( y[i] - yavg ) * ( y[i] - yavg );
- }
- return r*r / ( x2 * y2 + EPSILON );
-}
-float Flame_DotProduct( float *x, float *y, int m )
-{
- int i;
- float r = 0;
- for(i=0; i<m; i++ ) r += x[i] * y[i];
- if( m == 0 ) return 0;
- return r / m;
-}
-float Flame_Covariance( float *x, float *y, int m )
-{
- int i;
- float r, x2, y2, xavg, yavg;
- if( m ==0 ) return 0;
- xavg = yavg = 0;
- r = x2 = y2 = 0;
- for( i=0; i<m; i++ ){
- xavg += x[i];
- yavg += y[i];
- }
- xavg = xavg/m;
- yavg = yavg/m;
- for( i=0; i<m; i++ ) r += ( x[i] - xavg ) * ( y[i] - yavg );
- if( m <= 1 ) return 0;
- return r / (m-1);
-}
-float Flame_Manhattan( float *x, float *y, int m )
-{
- float d = 0;
- int i;
- for(i=0; i<m; i++ ) d += fabs( x[i] - y[i] );
- return d;
-}
-float Flame_CosineDist( float *x, float *y, int m )
-{
- return 1-Flame_Cosine( x, y, m );
-}
-float Flame_PearsonDist( float *x, float *y, int m )
-{
- return 1-Flame_Pearson( x, y, m );
-}
-float Flame_UCPearsonDist( float *x, float *y, int m )
-{
- return 1-Flame_UCPearson( x, y, m );
-}
-float Flame_SQPearsonDist( float *x, float *y, int m )
-{
- return 1-Flame_SQPearson( x, y, m );
-}
-float Flame_DotProductDist( float *x, float *y, int m )
-{
- return 1-Flame_DotProduct( x, y, m );
-}
-float Flame_CovarianceDist( float *x, float *y, int m )
-{
- return 1-Flame_Covariance( x, y, m );
-}
-
-Flame* Flame_New()
-{
- Flame *self = (Flame*) malloc( sizeof(Flame) );
- memset( self, 0, sizeof(Flame) );
- return self;
-}
-void Flame_Clear( Flame *self )
-{
- int i;
- for(i=0; i<self->N; i++){
- free( self->graph[i] );
- free( self->dists[i] );
- free( self->weights[i] );
- free( self->fuzzyships[i] );
- }
- if( self->clusters ){
- for(i=0; i<=self->cso_count; i++){
- if( self->clusters[i].array ) free( self->clusters[i].array );
- }
- free( self->clusters );
- self->clusters = NULL;
- }
- if( self->graph ) free( self->graph );
- if( self->dists ) free( self->dists );
- if( self->nncounts ) free( self->nncounts );
- if( self->weights ) free( self->weights );
- if( self->fuzzyships ) free( self->fuzzyships );
- if( self->obtypes ) free( self->obtypes );
- self->graph = NULL;
- self->dists = NULL;
- self->nncounts = NULL;
- self->weights = NULL;
- self->obtypes = NULL;
- self->fuzzyships = NULL;
- self->N = self->K = self->KMAX = self->cso_count = 0;
-}
-
-/* If m==0, data is distance matrix. */
-void Flame_SetMatrix( Flame *self, float *data[], int n, int m )
-{
- int i, j, k;
- int MAX = sqrt( n ) + 10;
- IndexFloat *vals = (IndexFloat*) calloc( n, sizeof(IndexFloat) );
- if( MAX >= n ) MAX = n - 1;
-
- Flame_Clear( self );
- self->N = n;
- self->KMAX = MAX;
-
- self->graph = (int**) calloc( n, sizeof(int*) );
- self->dists = (float**) calloc( n, sizeof(float*) );
- self->weights = (float**) calloc( n, sizeof(float*) );
- self->nncounts = (int*) calloc( n, sizeof(int) );
- self->obtypes = (char*) calloc( n, sizeof(char) );
- self->fuzzyships = (float**) calloc( n, sizeof(float*) );
-
- for(i=0; i<n; i++){
- self->graph[i] = (int*) calloc( MAX, sizeof(int) );
- self->dists[i] = (float*) calloc( MAX, sizeof(float) );
- self->weights[i] = (float*) calloc( MAX, sizeof(float) );
- if( m ==0 ){
- /* data is distance matrix. */
- for(j=0; j<n; j++){
- vals[j].index = j;
- vals[j].value = data[i][j];
- }
- }else{
- /* data is raw data matrix. */
- for(j=0; j<n; j++){
- vals[j].index = j;
- vals[j].value = self->distfunc( data[i], data[j], m );
- }
- }
- PartialQuickSort( vals, 0, n-1, MAX+1 );
- /* Store MAX number of nearest neighbors. */
- for(j=0; j<MAX; j++){
- self->graph[i][j] = vals[j+1].index;
- self->dists[i][j] = vals[j+1].value;
- }
- }
- free( vals );
-}
-void Flame_SetDataMatrix( Flame *self, float *data[], int n, int m, int dt )
-{
- self->simtype = dt;
- if( dt >0 && dt < DST_NULL ) self->distfunc = basicDistFunctions[ dt-1 ];
- if( self->distfunc == NULL ) self->distfunc = basicDistFunctions[0];
- Flame_SetMatrix( self, data, n, m );
-}
-void Flame_SetDistMatrix( Flame *self, float *data[], int n )
-{
- Flame_SetMatrix( self, data, n, DST_USER );
-}
-void Flame_DefineSupports( Flame *self, int knn, float thd )
-{
- int i, j, k;
- int n = self->N;
- int kmax = self->KMAX;
- float **dists = self->dists;
- float *density = (float*) calloc( n, sizeof(float) );
- float d, sum, sum2, fmin, fmax = 0.0;
-
- if( knn > kmax ) knn = kmax;
- self->K = knn;
- for(i=0; i<n; i++){
- /* To include all the neighbors that have distances equal to the
- * distance of the most distant one of the K-Nearest Neighbors */
- k = knn;
- d = dists[i][knn-1];
- for(j=knn; j<kmax; j++) if( dists[i][j] == d ) k ++; else break;
- self->nncounts[i] = k;
-
- /* The definition of weights in this implementation is
- * different from the previous implementations where distances
- * or similarities often have to be transformed in some way.
- *
- * But in this definition, the weights are only dependent on
- * the ranking of distances of the neighbors, so it is more
- * robust against distance transformations. */
- sum = 0.5*k*(k+1.0);
- for(j=0; j<k; j++) self->weights[i][j] = (k-j) / sum;
-
- sum = 0.0;
- for(j=0; j<k; j++) sum += dists[i][j];
- density[i] = 1.0 / (sum + EPSILON);
- }
- sum = 0.0;
- sum2 = 0.0;
- for(i=0; i<n; i++){
- sum += density[i];
- sum2 += density[i] * density[i];
- }
- sum = sum / n;
- /* Density threshold for possible outliers. */
- thd = sum + thd * sqrt( sum2 / n - sum * sum );
-
- memset( self->obtypes, 0, n*sizeof(char) );
- self->cso_count = 0;
- for(i=0; i<n; i++){
- k = self->nncounts[i];
- fmax = 0.0;
- fmin = density[i] / density[ self->graph[i][0] ];
- for(j=1; j<k; j++){
- d = density[i] / density[ self->graph[i][j] ];
- if( d > fmax ) fmax = d;
- if( d < fmin ) fmin = d;
- /* To avoid defining neighboring objects or objects close
- * to an outlier as CSOs. */
- if( self->obtypes[ self->graph[i][j] ] ) fmin = 0.0;
- }
- if( fmin >= 1.0 ){
- self->cso_count ++;
- self->obtypes[i] = OBT_SUPPORT;
- }else if( fmax <= 1.0 && density[i] < thd ){
- self->obtypes[i] = OBT_OUTLIER;
- }
- }
- free( density );
-}
-void Flame_LocalApproximation( Flame *self, int steps, float epsilon )
-{
- int i, j, k, t, n = self->N, m = self->cso_count;
- float **fuzzyships = self->fuzzyships;
- float **fuzzyships2 = (float**)calloc( n, sizeof(float*) );
- char *obtypes = self->obtypes;
- char even = 0;
- double dev;
-
- k = 0;
- for(i=0; i<n; i++){
- fuzzyships[i] = (float*) realloc( fuzzyships[i], (m+1)*sizeof(float) );
- fuzzyships2[i] = (float*) calloc( m+1, sizeof(float) );
- memset( fuzzyships[i], 0, (m+1)*sizeof(float) );
- if( obtypes[i] == OBT_SUPPORT ){
- /* Full membership to the cluster represented by itself. */
- fuzzyships[i][k] = 1.0;
- fuzzyships2[i][k] = 1.0;
- k ++;
- }else if( obtypes[i] == OBT_OUTLIER ){
- /* Full membership to the outlier group. */
- fuzzyships[i][m] = 1.0;
- fuzzyships2[i][m] = 1.0;
- }else{
- /* Equal memberships to all clusters and the outlier group.
- * Random initialization does not change the results. */
- for(j=0; j<=m; j++)
- fuzzyships[i][j] = fuzzyships2[i][j] = 1.0/(m+1);
- }
- }
- for(t=0; t<steps; t++){
- dev = 0;
- for(i=0; i<n; i++){
- int knn = self->nncounts[i];
- int *ids = self->graph[i];
- float *wt = self->weights[i];
- float *fuzzy = fuzzyships[i];
- float **fuzzy2 = fuzzyships2;
- double sum = 0.0;
- if( self->obtypes[i] != OBT_NORMAL ) continue;
- if( even ){
- fuzzy = fuzzyships2[i];
- fuzzy2 = fuzzyships;
- }
- /* Update membership of an object by a linear combination of
- * the memberships of its nearest neighbors. */
- for(j=0; j<=m; j++){
- fuzzy[j] = 0.0;
- for(k=0; k<knn; k++) fuzzy[j] += wt[k] * fuzzy2[ ids[k] ][j];
- dev += (fuzzy[j] - fuzzy2[i][j]) * (fuzzy[j] - fuzzy2[i][j]);
- sum += fuzzy[j];
- }
- for(j=0; j<=m; j++) fuzzy[j] = fuzzy[j] / sum;
- }
- even = ! even;
- if( dev < epsilon ) break;
- }
- /* update the membership of all objects to remove clusters
- * that contains only the CSO. */
- for(i=0; i<n; i++){
- int knn = self->nncounts[i];
- int *ids = self->graph[i];
- float *wt = self->weights[i];
- float *fuzzy = fuzzyships[i];
- float **fuzzy2 = fuzzyships2;
- for(j=0; j<=m; j++){
- fuzzy[j] = 0.0;
- for(k=0; k<knn; k++) fuzzy[j] += wt[k] * fuzzy2[ ids[k] ][j];
- dev += (fuzzy[j] - fuzzy2[i][j]) * (fuzzy[j] - fuzzy2[i][j]);
- }
- }
- for(i=0; i<n; i++) free( fuzzyships2[i] );
- free( fuzzyships2 );
-}
-
-void IntArray_Push( IntArray *self, int value )
-{
- if( self->size >= self->bufsize ){
- self->bufsize += self->bufsize /10 + 10;
- self->array = (int*)realloc( self->array, self->bufsize*sizeof(int));
- }
- self->array[ self->size ] = value;
- self->size ++;
-}
-void Flame_MakeClusters( Flame *self, float thd )
-{
- int i, j, imax;
- int N = self->N;
- int C = self->cso_count+1;
- float fmax;
- float **fuzzyships = self->fuzzyships;
- IntArray *clust;
- IndexFloat *vals = (IndexFloat*) calloc( N, sizeof(IndexFloat) );
-
- /* Sort objects based on the "entropy" of fuzzy memberships. */
- for(i=0; i<N; i++){
- vals[i].index = i;
- vals[i].value = 0.0;
- for(j=0; j<C; j++){
- float fs = fuzzyships[i][j];
- if( fs > EPSILON ) vals[i].value -= fs * log( fs );
- }
- }
- PartialQuickSort( vals, 0, N-1, N );
-
- if( self->clusters ){
- for(i=0; i<C; i++)
- if( self->clusters[i].array ) free( self->clusters[i].array );
- free( self->clusters );
- }
- self->clusters = (IntArray*) calloc( C, sizeof(IntArray) );
- if( thd <0 || thd > 1.0 ){
- /* Assign each object to the cluster
- * in which it has the highest membership. */
- for(i=0; i<N; i++){
- int id = vals[i].index;
- fmax = 0;
- imax = -1;
- for(j=0; j<C; j++){
- if( fuzzyships[id][j] > fmax ){
- imax = j;
- fmax = fuzzyships[id][j];
- }
- }
- IntArray_Push( self->clusters + imax, id );
- }
- }else{
- /* Assign each object to all the clusters
- * in which it has membership higher than thd,
- * otherwise, assign it to the outlier group.*/
- for(i=0; i<N; i++){
- int id = vals[i].index;
- imax = -1;
- for(j=0; j<C; j++){
- if( fuzzyships[id][j] > thd || ( j == C-1 && imax <0 ) ){
- imax = j;
- clust = self->clusters + j;
- IntArray_Push( self->clusters + j, id );
- }
- }
- }
- }
- /* removing empty clusters */
- C = 0;
- for(i=0; i<self->cso_count; i++){
- if( self->clusters[i].size >0 ){
- self->clusters[C] = self->clusters[i];
- C ++;
- }
- }
- /* keep the outlier group, even if its empty */
- self->clusters[C] = self->clusters[self->cso_count];
- C ++;
- for(i=C; i<self->cso_count+1; i++) memset( self->clusters+i, 0, sizeof(IntArray) );
- self->count = C;
- free( vals );
-}
-
-}}}//ns
diff --git a/loop/src/flame.hh b/loop/src/flame.hh
deleted file mode 100644
index f68b74c2e6e99b4a70d026c4f30f23ddc654f15b..0000000000000000000000000000000000000000
--- a/loop/src/flame.hh
+++ /dev/null
@@ -1,190 +0,0 @@
-/*===================================================================
- The standard implementation of FLAME data clustering algorithm.
-
- FLAME (Fuzzy clustering by Local Approximation of MEmberships)
- was first described in:
- "FLAME, a novel fuzzy clustering method for the analysis of DNA
- microarray data", BMC Bioinformatics, 2007, 8:3.
- Available from: http://www.biomedcentral.com/1471-2105/8/3
-
- Copyright(C) 2007, Fu Limin (phoolimin@gmail.com).
- All rights reserved.
-
- Permission is granted to anyone to use this software for any purpose,
- including commercial applications, and to alter it and redistribute it
- freely, subject to the following restrictions:
-
- 1. Redistributions of source code must retain the above copyright
- notice, this list of conditions and the following disclaimer.
- 2. The origin of this software must not be misrepresented; you must
- not claim that you wrote the original software. If you use this
- software in a product, an acknowledgment in the product
- documentation would be appreciated but is not required.
- 3. Altered source versions must be plainly marked as such, and must
- not be misrepresented as being the original software.
-
- This program is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-===================================================================*/
-
-#ifndef __FLAME_H
-#define __FLAME_H
-
-/* Since data for clustering are usually noisy,
- * so it is not very necessary to have EPSILON extremely small.
- */
-
-namespace promod3{ namespace loop{ namespace flame{
-
-#define EPSILON 1E-9
-
-typedef struct IndexFloat IndexFloat;
-typedef struct Flame Flame;
-typedef struct IntArray IntArray;
-
-struct IntArray
-{
- int *array;
- int size;
- int bufsize;
-};
-
-/* For sorting and storing the orignal indices. */
-struct IndexFloat
-{
- int index;
- float value;
-};
-
-/* Sort until the smallest "part" items are sorted. */
-void PartialQuickSort( IndexFloat *data, int first, int last, int part );
-
-float Flame_Euclidean( float *x, float *y, int m );
-float Flame_Cosine( float *x, float *y, int m );
-float Flame_Pearson( float *x, float *y, int m );
-float Flame_UCPearson( float *x, float *y, int m );
-float Flame_SQPearson( float *x, float *y, int m );
-float Flame_DotProduct( float *x, float *y, int m );
-float Flame_Covariance( float *x, float *y, int m );
-float Flame_Manhattan( float *x, float *y, int m );
-float Flame_CosineDist( float *x, float *y, int m );
-float Flame_PearsonDist( float *x, float *y, int m );
-float Flame_UCPearsonDist( float *x, float *y, int m );
-float Flame_SQPearsonDist( float *x, float *y, int m );
-float Flame_DotProductDist( float *x, float *y, int m );
-float Flame_CovarianceDist( float *x, float *y, int m );
-
-enum DistSimTypes
-{
- DST_USER = 0,
- DST_EUCLID ,
- DST_COSINE ,
- DST_PEARSON ,
- DST_UC_PEARSON ,
- DST_SQ_PEARSON ,
- DST_DOT_PROD ,
- DST_COVARIANCE ,
- DST_MANHATTAN ,
- DST_NULL
-};
-typedef float (*DistFunction)( float *x, float *y, int m );
-
-extern const DistFunction basicDistFunctions[];
-
-enum FlameObjectTypes
-{
- OBT_NORMAL ,
- OBT_SUPPORT ,
- OBT_OUTLIER
-};
-
-struct Flame
-{
- int simtype;
-
- /* Number of objects */
- int N;
-
- /* Number of K-Nearest Neighbors */
- int K;
-
- /* Upper bound for K defined as: sqrt(N)+10 */
- int KMAX;
-
- /* Stores the KMAX nearest neighbors instead of K nearest neighbors
- * for each objects, so that when K is changed, weights and CSOs can be
- * re-computed without referring to the original data.
- */
- int **graph;
- /* Distances to the KMAX nearest neighbors. */
- float **dists;
-
- /* Nearest neighbor count.
- * it can be different from K if an object has nearest neighbors with
- * equal distance. */
- int *nncounts;
- float **weights;
-
- /* Number of identified Cluster Supporting Objects */
- int cso_count;
- char *obtypes;
-
- float **fuzzyships;
-
- /* Number of clusters including the outlier group */
- int count;
- /* The last one is the outlier group. */
- IntArray *clusters;
-
- DistFunction distfunc;
-};
-
-/* Create a structure for FLAME clustering, and set all fields to zero. */
-Flame* Flame_New();
-
-/* Free allocated memory, and set all fields to zero. */
-void Flame_Clear( Flame *self );
-
-/* Set a NxM data matrix, and compute distances of type T.
- *
- * If T==DST_USER or T>=DST_NULL, and Flame::distfunc member is set,
- * then Flame::distfunc is used to compute the distances;
- * Otherwise, Flame_Euclidean() is used. */
-void Flame_SetDataMatrix( Flame *self, float *data[], int N, int M, int T );
-
-/* Set a pre-computed NxN distance matrix. */
-void Flame_SetDistMatrix( Flame *self, float *data[], int N );
-
-/* Define knn-nearest neighbors for each object
- * and the Cluster Supporting Objects (CSO).
- *
- * The actual number of nearest neighbors could be large than knn,
- * if an object has neighbors of the same distances.
- *
- * Based on the distances of the neighbors, a density can be computed
- * for each object. Objects with local maximum density are defined as
- * CSOs. The initial outliers are defined as objects with local minimum
- * density which is less than mean( density ) + thd * stdev( density );
- */
-void Flame_DefineSupports( Flame *self, int knn, float thd );
-
-/* Local Approximation of fuzzy memberships.
- * Stopped after the maximum steps of iterations;
- * Or stopped when the overall membership difference between
- * two iterations become less than epsilon. */
-void Flame_LocalApproximation( Flame *self, int steps, float epsilon );
-
-/* Construct clusters.
- * If 0<thd<1:
- * each object is assigned to all clusters in which
- * it has membership higher than thd; if it can not be assigned
- * to any clusters, it is then assigned to the outlier group.
- * Else:
- * each object is assigned to the group (clusters/outlier group)
- * in which it has the highest membership. */
-void Flame_MakeClusters( Flame *self, float thd );
-
-}}}//ns
-
-#endif
diff --git a/loop/src/frag_db.cc b/loop/src/frag_db.cc
index 18f6f016db5a20b8f73e3168410b3274bd85b29c..bc446e8c1a34cd98834fdaad4781af78b7358fb1 100644
--- a/loop/src/frag_db.cc
+++ b/loop/src/frag_db.cc
@@ -109,8 +109,21 @@ void FragDB::SearchDB(const ost::mol::ResidueHandle& n_stem, const ost::mol::Res
uint frag_size, std::vector<FragmentInfo>& fragments,
bool extended_search){
-
std::pair<StemCoords,StemCoords> stems = this->StemCoordsFromResidues(n_stem, c_stem);
+ this->SearchDB(stems, frag_size, fragments, extended_search);
+}
+
+void FragDB::SearchDB(const Backbone& n_stem, const Backbone& c_stem,
+ uint frag_size, std::vector<FragmentInfo>& fragments,
+ bool extended_search){
+
+ std::pair<StemCoords,StemCoords> stems = this->StemCoordsFromBackbone(n_stem, c_stem);
+ this->SearchDB(stems, frag_size, fragments, extended_search);
+}
+
+void FragDB::SearchDB(const std::pair<StemCoords,StemCoords>& stems, uint frag_size,
+ std::vector<FragmentInfo>& fragments,
+ bool extended_search){
std::vector<StemPairGeom> stem_pairs = this->MakeStemPairGeom(stems.first, stems.second,
frag_size, extended_search);
@@ -196,6 +209,23 @@ std::pair<FragDB::StemCoords,FragDB::StemCoords> FragDB::StemCoordsFromResidues(
return std::make_pair(n_stem,c_stem);
}
+std::pair<FragDB::StemCoords,FragDB::StemCoords> FragDB::StemCoordsFromBackbone(const Backbone& n_bb,
+ const Backbone& c_bb){
+
+ FragDB::StemCoords n_stem;
+ FragDB::StemCoords c_stem;
+
+ n_stem.n_coord = n_bb.n_coord;
+ n_stem.ca_coord = n_bb.ca_coord;
+ n_stem.c_coord = n_bb.c_coord;
+
+ c_stem.n_coord = c_bb.n_coord;
+ c_stem.ca_coord = c_bb.ca_coord;
+ c_stem.c_coord = c_bb.c_coord;
+
+ return std::make_pair(n_stem,c_stem);
+}
+
std::pair<FragDB::StemCoords,FragDB::StemCoords> FragDB::StemCoordsFromPeptides(const Peptide& n_pep,
const Peptide& c_pep){
diff --git a/loop/src/frag_db.hh b/loop/src/frag_db.hh
index 5e38f5d77c194b0b5c70c8fa909b9ac867eb32e9..7d5156c67117a6651176da40259af225049520b8 100644
--- a/loop/src/frag_db.hh
+++ b/loop/src/frag_db.hh
@@ -61,6 +61,10 @@ public:
uint frag_size, std::vector<FragmentInfo>& fragments,
bool extended_search = false);
+ void SearchDB(const Backbone& n_stem, const Backbone& c_stem,
+ uint frag_size, std::vector<FragmentInfo>& fragments,
+ bool extended_search = false);
+
uint GetAngularBinSize() const { return angular_bin_size_; }
Real GetDistBinSize() const { return dist_bin_size_; }
@@ -81,13 +85,20 @@ public:
private:
+ void SearchDB(const std::pair<StemCoords,StemCoords>& stems, uint frag_size,
+ std::vector<FragmentInfo>& fragments,
+ bool extended_search);
+
FragDB(const FragDB& other) { };
std::pair<StemCoords,StemCoords> StemCoordsFromResidues(const ost::mol::ResidueHandle& n_res,
- const ost::mol::ResidueHandle& c_res);
+ const ost::mol::ResidueHandle& c_res);
+
+ std::pair<StemCoords,StemCoords> StemCoordsFromBackbone(const Backbone& n_bb,
+ const Backbone& c_bb);
std::pair<StemCoords,StemCoords> StemCoordsFromPeptides(const Peptide& n_pep,
- const Peptide& c_pep);
+ const Peptide& c_pep);
std::vector<StemPairGeom> MakeStemPairGeom(const FragDB::StemCoords& n_stem,
const FragDB::StemCoords& c_stem,
diff --git a/loop/src/fragger.cc b/loop/src/fragger.cc
index eac14b6298f83f15b75b678ff6f536a09bcdbd8e..02c0b94e47dc5c7494a3fe8c79bcb83fb075497c 100644
--- a/loop/src/fragger.cc
+++ b/loop/src/fragger.cc
@@ -152,7 +152,7 @@ void Fragger::AddSeqIDParameters(Real w){
score_types_.push_back(SeqID);
weights_.push_back(w);
subst_matrix_.push_back(ost::seq::alg::SubstWeightMatrix());
- psipred_prediction_.push_back(std::vector<char>());
+ psipred_prediction_.push_back(std::vector<int>());
psipred_confidence_.push_back(std::vector<int>());
t_sampler_.push_back(std::vector<TorsionSamplerPtr>());
t_sampler_indices_.push_back(std::vector<int>());
@@ -163,36 +163,25 @@ void Fragger::AddSeqSimParameters(Real w, ost::seq::alg::SubstWeightMatrix& subs
score_types_.push_back(SeqSim);
weights_.push_back(w);
subst_matrix_.push_back(subst_matrix);
- psipred_prediction_.push_back(std::vector<char>());
+ psipred_prediction_.push_back(std::vector<int>());
psipred_confidence_.push_back(std::vector<int>());
t_sampler_.push_back(std::vector<TorsionSamplerPtr>());
t_sampler_indices_.push_back(std::vector<int>());
profiles_.push_back(NULL);
}
-void Fragger::AddSSAgreeParameters(Real w, const std::vector<char>& p_p,
- const std::vector<int>& p_c){
+void Fragger::AddSSAgreeParameters(Real w, const PsipredPrediction& pp){
- if(p_p.size() != frag_sequence_.size()){
- throw promod3::Error("Length of psipred prediction must be consistent with fragment sequence!");
+ if(pp.size() != frag_sequence_.size()){
+ throw promod3::Error("Size of psipred prediction must be consistent with fragment sequence!");
}
- if(p_c.size() != frag_sequence_.size()){
- throw promod3::Error("Length of psipred confidence must be consistent with fragment sequence!");
- }
-
- for(std::vector<char>::const_iterator i = p_p.begin(),
- e = p_p.end(); i!=e; ++i){
- if(*i != 'H' && *i != 'E' && *i!='C'){
- throw promod3::Error("Every element in psipred prediction must be in ['H','E','C']!");
- }
- }
+ std::vector<int> p_p;
+ std::vector<int> p_c;
- for(std::vector<int>::const_iterator i = p_c.begin(),
- e = p_c.end(); i!=e; ++i){
- if(*i < 0 || *i > 9){
- throw promod3::Error("Every element in psipred confidence must be in range [0,9]!");
- }
+ for(uint i = 0; i < pp.size(); ++i){
+ p_p.push_back(GetPsipredIdx(pp.GetPrediction(i)));
+ p_c.push_back(pp.GetConfidence(i));
}
score_types_.push_back(SSAgree);
@@ -224,7 +213,7 @@ void Fragger::AddTorsionProbabilityParameters(Real w, const TorsionSamplerPtr t_
score_types_.push_back(TorsionProb);
weights_.push_back(w);
subst_matrix_.push_back(ost::seq::alg::SubstWeightMatrix());
- psipred_prediction_.push_back(std::vector<char>());
+ psipred_prediction_.push_back(std::vector<int>());
psipred_confidence_.push_back(std::vector<int>());
t_sampler_.push_back(v_t_s);
t_sampler_indices_.push_back(indices);
@@ -257,7 +246,7 @@ void Fragger::AddTorsionProbabilityParameters(Real w, const std::vector<TorsionS
score_types_.push_back(TorsionProb);
weights_.push_back(w);
subst_matrix_.push_back(ost::seq::alg::SubstWeightMatrix());
- psipred_prediction_.push_back(std::vector<char>());
+ psipred_prediction_.push_back(std::vector<int>());
psipred_confidence_.push_back(std::vector<int>());
t_sampler_.push_back(t_s);
t_sampler_indices_.push_back(indices);
@@ -271,7 +260,7 @@ void Fragger::AddSequenceProfileParameters(Real w, ost::seq::HMMPtr hmm){
score_types_.push_back(SequenceProfile);
weights_.push_back(w);
subst_matrix_.push_back(ost::seq::alg::SubstWeightMatrix());
- psipred_prediction_.push_back(std::vector<char>());
+ psipred_prediction_.push_back(std::vector<int>());
psipred_confidence_.push_back(std::vector<int>());
t_sampler_.push_back(std::vector<TorsionSamplerPtr>());
t_sampler_indices_.push_back(std::vector<int>());
@@ -306,7 +295,7 @@ void Fragger::AddStructureProfileParameters(Real w, ost::seq::HMMPtr hmm){
score_types_.push_back(StructureProfile);
weights_.push_back(w);
subst_matrix_.push_back(ost::seq::alg::SubstWeightMatrix());
- psipred_prediction_.push_back(std::vector<char>());
+ psipred_prediction_.push_back(std::vector<int>());
psipred_confidence_.push_back(std::vector<int>());
t_sampler_.push_back(std::vector<TorsionSamplerPtr>());
t_sampler_indices_.push_back(std::vector<int>());
@@ -586,7 +575,7 @@ void Fragger::GenerateSeqIDProfile(StructureDBPtr db, std::vector<Real>& profile
}
void Fragger::GenerateSSAgreementProfile(StructureDBPtr db, std::vector<Real>& profile, uint index,
- const std::vector<char>& predicted_ss,
+ const std::vector<int>& predicted_ss,
const std::vector<int>& confidence) const{
const std::vector<CoordInfo>& coord_toc = db->GetCoordToc();
@@ -600,25 +589,20 @@ void Fragger::GenerateSSAgreementProfile(StructureDBPtr db, std::vector<Real>& p
//let's precalculate as much as we can
std::vector<int> chain_dssp_states(chain_size);
- std::vector<int> seq_psipred_predictions(seq_size);
-
+
uint coord_index = coord_toc[index].offset;
for(uint i = 0; i < chain_size; ++i){
chain_dssp_states[i] = GetDSSPIdx(coords[coord_index].dssp_state);
++coord_index;
}
- for(uint i = 0; i < seq_size; ++i){
- seq_psipred_predictions[i] = GetPsipredIdx(predicted_ss[i]);
- }
-
Real score = 0.0;
Real factor = 1.0 / seq_size;
for(uint i = 0; i <= chain_size - seq_size; ++i){
score = 0.0;
for(uint j = 0; j < seq_size; ++j){
- score += ss_agreements[chain_dssp_states[i+j]][seq_psipred_predictions[j]][confidence[j]];
+ score += ss_agreements[chain_dssp_states[i+j]][predicted_ss[j]][confidence[j]];
}
profile.push_back(score*factor);
}
@@ -667,7 +651,6 @@ void Fragger::GenerateProfileProfile(StructureDBPtr db, std::vector<Real>& profi
Real** hmm) const{
const std::vector<CoordInfo>& coord_toc = db->GetCoordToc();
- const PagedArray<Peptide,4096>& coords = db->GetCoords();
profile.clear();
diff --git a/loop/src/fragger.hh b/loop/src/fragger.hh
index 63b75d7f39111ceffda65111a9e8ea09fdaa0dfe..cafc474499c183b5a0fd217a5ec0a316ea9e6f00 100644
--- a/loop/src/fragger.hh
+++ b/loop/src/fragger.hh
@@ -4,6 +4,7 @@
#include <promod3/loop/structure_db.hh>
#include <promod3/loop/backbone.hh>
#include <promod3/loop/torsion_sampler.hh>
+#include <promod3/loop/psipred_prediction.hh>
#include <ost/seq/hmm.hh>
#include <ost/conop/amino_acids.hh>
@@ -39,8 +40,7 @@ public:
void AddSeqSimParameters(Real w, ost::seq::alg::SubstWeightMatrix& subst_matrix);
- void AddSSAgreeParameters(Real w, const std::vector<char>& p_p,
- const std::vector<int>& p_c);
+ void AddSSAgreeParameters(Real w, const PsipredPrediction& pp);
void AddTorsionProbabilityParameters(Real w, TorsionSamplerPtr t_s,
const String& before, const String& after);
@@ -93,7 +93,7 @@ private:
uint index) const;
void GenerateSSAgreementProfile(StructureDBPtr db, std::vector<Real>& profile, uint index,
- const std::vector<char>& predicted_ss,
+ const std::vector<int>& predicted_ss,
const std::vector<int>& confidence) const;
void GenerateTorsionProbabilityProfile(StructureDBPtr db, std::vector<Real>& profile, uint index,
@@ -106,7 +106,7 @@ private:
//members holding stuff to calculate scores
std::vector<ost::seq::alg::SubstWeightMatrix> subst_matrix_;
- std::vector<std::vector<char> > psipred_prediction_;
+ std::vector<std::vector<int> > psipred_prediction_;
std::vector<std::vector<int> > psipred_confidence_;
std::vector<std::vector<TorsionSamplerPtr> > t_sampler_;
std::vector<std::vector<int> > t_sampler_indices_;
diff --git a/loop/src/loop_candidate.cc b/loop/src/loop_candidate.cc
index d107f4a57e3bb272304e5d3f0725dcc1344b3264..abf4b80277c82c00f865ec10e5f56759e26f6807 100644
--- a/loop/src/loop_candidate.cc
+++ b/loop/src/loop_candidate.cc
@@ -10,80 +10,7 @@ Real LoopCandidate::RMSD(const LoopCandidate& other){
return bb_list.RMSD(other.bb_list);
}
-LoopCandidates::LoopCandidates(const ost::mol::ResidueHandle& n_stem,
- const ost::mol::ResidueHandle& c_stem,
- const String& seq):
- n_stem_(n_stem),
- c_stem_(c_stem),
- sequence_(seq) {
-
- if(n_stem.GetOneLetterCode() != seq[0] ||
- c_stem.GetOneLetterCode() != seq[seq.size()-1]){
- throw promod3::Error("Amino acid identities from stem residues do not match with the provided sequence!");
- }
-
- int n_stem_num = n_stem.GetNumber().GetNum();
- int c_stem_num = c_stem.GetNumber().GetNum();
-
- if(c_stem_num - n_stem_num + 1 != static_cast<int>(seq.size())){
- throw promod3::Error("Difference in the stem residues numbers is inconsisten with the size of the provided sequence!");
- }
-}
-
-void LoopCandidates::InsertInto(ost::mol::EntityHandle& ent, uint index) const{
-
- if(index >= this->size()){
- throw promod3::Error("Index is out of bounds!");
- }
-
- if(!n_stem_.IsValid() && !c_stem_.IsValid()){
- std::stringstream ss;
- ss << "At least one of the stem residues must be valid when ";
- ss << "Inserting a loop candidate into an entity!";
- throw promod3::Error(ss.str());
- }
-
- ost::mol::ResNum n_num;
- ost::mol::ResNum c_num;
- ost::mol::ChainHandle chain;
- String chain_name;
-
- if(n_stem_.IsValid() && c_stem_.IsValid()){
- n_num = n_stem_.GetNumber();
- c_num = c_stem_.GetNumber();
- chain_name = n_stem_.GetChain().GetName();
- chain = ent.FindChain(chain_name);
- }
- else if(n_stem_.IsValid()){
- n_num = n_stem_.GetNumber();
- c_num = n_num + candidates_[index].size() - 1;
- chain_name = n_stem_.GetChain().GetName();
- chain = ent.FindChain(chain_name);
- }
- else{
- c_num = c_stem_.GetNumber();
- n_num = c_num - candidates_[index].size() + 1;
- chain_name = c_stem_.GetChain().GetName();
- chain = ent.FindChain(chain_name);
- }
-
- if(!chain.IsValid()){
- std::stringstream ss;
- ss << "Could not find required chain of name \"" <<chain_name;
- ss << "\" in ent to insert loop candidate!";
- throw promod3::Error(ss.str());
- }
-
- candidates_[index].bb_list.InsertInto(chain,n_num.GetNum(),c_num.GetNum());
-}
-
-
-ost::mol::EntityHandle LoopCandidates::ToEntity(uint index) const {
- if(index >= this->size()){
- throw promod3::Error("Index is out of bounds!");
- }
- return candidates_[index].bb_list.ToEntity();
-}
+LoopCandidates::LoopCandidates(const String& seq): sequence_(seq) { }
void LoopCandidates::Add(const LoopCandidate& candidate){
//we check, whether the length and the sequence are consistent
@@ -130,7 +57,7 @@ LoopCandidatesPtr LoopCandidates::FillFromDatabase(const ost::mol::ResidueHandle
StructureDBPtr structure_db,
bool extended_search){
- LoopCandidatesPtr candidates(new LoopCandidates(n_stem, c_stem, seq));
+ LoopCandidatesPtr candidates(new LoopCandidates(seq));
std::vector<FragmentInfo> fragments;
frag_db->SearchDB(n_stem,c_stem,seq.size(),fragments,extended_search);
@@ -159,16 +86,14 @@ LoopCandidatesPtr LoopCandidates::FillFromDatabase(const ost::mol::ResidueHandle
return candidates;
}
-LoopCandidatesPtr LoopCandidates::FillFromMonteCarloSampler(const ost::mol::ResidueHandle& n_stem,
- const ost::mol::ResidueHandle& c_stem,
- const String& seq,
+LoopCandidatesPtr LoopCandidates::FillFromMonteCarloSampler(const String& seq,
uint num_loops, uint steps,
MonteCarloSamplerPtr sampler,
MonteCarloCloserPtr closer,
MonteCarloScorerPtr scorer,
MonteCarloCoolerPtr cooler){
- LoopCandidatesPtr candidates(new LoopCandidates(n_stem,c_stem,seq));
+ LoopCandidatesPtr candidates(new LoopCandidates(seq));
for(uint i = 0; i < num_loops; ++i){
BackboneList new_backbone;
@@ -180,9 +105,7 @@ LoopCandidatesPtr LoopCandidates::FillFromMonteCarloSampler(const ost::mol::Resi
return candidates;
}
-LoopCandidatesPtr LoopCandidates::FillFromMonteCarloSampler(const ost::mol::ResidueHandle& n_stem,
- const ost::mol::ResidueHandle& c_stem,
- const BackboneList& initial_bb,
+LoopCandidatesPtr LoopCandidates::FillFromMonteCarloSampler(const BackboneList& initial_bb,
const String& seq,
uint num_loops, uint steps,
MonteCarloSamplerPtr sampler,
@@ -201,7 +124,7 @@ LoopCandidatesPtr LoopCandidates::FillFromMonteCarloSampler(const ost::mol::Resi
}
}
- LoopCandidatesPtr candidates(new LoopCandidates(n_stem,c_stem,seq));
+ LoopCandidatesPtr candidates(new LoopCandidates(seq));
for(uint i = 0; i < num_loops; ++i){
BackboneList new_backbone = initial_bb;
@@ -213,8 +136,12 @@ LoopCandidatesPtr LoopCandidates::FillFromMonteCarloSampler(const ost::mol::Resi
return candidates;
}
-void LoopCandidates::ApplyCCD(std::vector<TorsionSamplerPtr> torsion_sampler, int max_iterations, Real rmsd_cutoff, bool keep_non_converged, int random_seed){
- CCD closer(sequence_,n_stem_,c_stem_,torsion_sampler,max_iterations,rmsd_cutoff,random_seed);
+void LoopCandidates::ApplyCCD(const ost::mol::ResidueHandle& n_stem,
+ const ost::mol::ResidueHandle& c_stem,
+ std::vector<TorsionSamplerPtr> torsion_sampler,
+ int max_iterations, Real rmsd_cutoff,
+ bool keep_non_converged, int random_seed){
+ CCD closer(sequence_,n_stem,c_stem,torsion_sampler,max_iterations,rmsd_cutoff,random_seed);
for(LoopCandidateList::iterator i = this->begin(); i != this->end(); ){
if(!closer.Close(i->bb_list) && !keep_non_converged){
i = candidates_.erase(i);
@@ -224,8 +151,12 @@ void LoopCandidates::ApplyCCD(std::vector<TorsionSamplerPtr> torsion_sampler, in
}
}
-void LoopCandidates::ApplyCCD(TorsionSamplerPtr torsion_sampler, int max_iterations, Real rmsd_cutoff, bool keep_non_converged, int random_seed){
- CCD closer(sequence_,n_stem_,c_stem_,torsion_sampler,max_iterations,rmsd_cutoff,random_seed);
+void LoopCandidates::ApplyCCD(const ost::mol::ResidueHandle& n_stem,
+ const ost::mol::ResidueHandle& c_stem,
+ TorsionSamplerPtr torsion_sampler,
+ int max_iterations, Real rmsd_cutoff,
+ bool keep_non_converged, int random_seed){
+ CCD closer(sequence_,n_stem,c_stem,torsion_sampler,max_iterations,rmsd_cutoff,random_seed);
for(LoopCandidateList::iterator i = this->begin(); i != this->end(); ){
if(!closer.Close(i->bb_list) && !keep_non_converged){
i = candidates_.erase(i);
@@ -235,8 +166,11 @@ void LoopCandidates::ApplyCCD(TorsionSamplerPtr torsion_sampler, int max_iterati
}
}
-void LoopCandidates::ApplyCCD(int max_iterations, Real rmsd_cutoff, bool keep_non_converged, int random_seed){
- CCD closer(n_stem_,c_stem_,max_iterations,rmsd_cutoff);
+void LoopCandidates::ApplyCCD(const ost::mol::ResidueHandle& n_stem,
+ const ost::mol::ResidueHandle& c_stem,
+ int max_iterations, Real rmsd_cutoff,
+ bool keep_non_converged){
+ CCD closer(n_stem,c_stem,max_iterations,rmsd_cutoff);
for(LoopCandidateList::iterator i = this->begin(); i != this->end(); ){
if(!closer.Close(i->bb_list) && !keep_non_converged){
i = candidates_.erase(i);
@@ -246,10 +180,12 @@ void LoopCandidates::ApplyCCD(int max_iterations, Real rmsd_cutoff, bool keep_no
}
}
-void LoopCandidates::ApplyKIC(uint pivot_one, uint pivot_two, uint pivot_three){
+void LoopCandidates::ApplyKIC(const ost::mol::ResidueHandle& n_stem,
+ const ost::mol::ResidueHandle& c_stem,
+ uint pivot_one, uint pivot_two, uint pivot_three){
LoopCandidateList new_candidates;
- KIC closer(n_stem_, c_stem_);
+ KIC closer(n_stem, c_stem);
for(LoopCandidateList::iterator i = this->begin(); i != this->end(); ++i){
@@ -268,62 +204,63 @@ void LoopCandidates::ApplyKIC(uint pivot_one, uint pivot_two, uint pivot_three){
candidates_ = new_candidates;
}
-LoopCandidatesList LoopCandidates::ClusterCandidates(){
+LoopCandidatesList LoopCandidates::ClusterCandidates(Real max_dist,
+ bool neglect_size_one){
LoopCandidatesList return_list;
- uint num_loops = candidates_.size();
+ int num_loops = candidates_.size();
if(num_loops <= 1){
return_list.push_back(*this);
return return_list;
}
- Real** rmsd_matrix = NULL;
+ float** rmsd_matrix = NULL;
- rmsd_matrix = (Real**)malloc(num_loops*sizeof(Real*));
- for(uint i = 0; i < num_loops; ++i){
- rmsd_matrix[i] = (Real*)malloc(num_loops*sizeof(Real));
- memset(rmsd_matrix[i],0,num_loops*sizeof(Real));
+ rmsd_matrix = new float*[num_loops];
+ for(int i= 0; i < num_loops; ++i){
+ rmsd_matrix[i] = new float[num_loops];
+ }
+
+ //set diagonal elements to zero
+ for(int i = 0; i < num_loops; ++i){
+ rmsd_matrix[i][i] = 0.0;
}
Real rmsd;
- for(uint i = 0; i < num_loops; ++i){
- for(uint j = i+1; j < num_loops; ++j){
+ for(int i = 0; i < num_loops; ++i){
+ for(int j = i+1; j < num_loops; ++j){
rmsd = candidates_[i].CARMSD(candidates_[j]);
rmsd_matrix[i][j] = rmsd;
rmsd_matrix[j][i] = rmsd;
}
}
- flame::Flame* flame = flame::Flame_New();
- flame::Flame_SetDistMatrix(flame, rmsd_matrix, num_loops);
- flame::Flame_DefineSupports(flame,int(std::sqrt(candidates_.size())),-2.0);
- flame::Flame_LocalApproximation(flame, 500, 1e-6);
- flame::Flame_MakeClusters(flame,-1.0);
+ std::vector<std::vector<int> > clusters;
+ DoClustering(rmsd_matrix, num_loops, max_dist, clusters);
- for(int i = 0; i <= flame->cso_count; ++i){
- LoopCandidates new_candidates(n_stem_,c_stem_,sequence_);
+ for(uint i = 0; i < clusters.size(); ++i){
+ if(clusters[i].size() <= 1 && neglect_size_one) continue;
+ LoopCandidates new_candidates(sequence_);
return_list.push_back(new_candidates);
- for(int j = 0; j < flame->clusters[i].size; ++j){
- return_list.back().Add(candidates_[flame->clusters[i].array[j]]);
- }
+ for(uint j = 0; j < clusters[i].size(); ++j){
+ return_list.back().Add(candidates_[clusters[i][j]]);
+ }
}
- for(uint i = 0; i < num_loops; ++i){
- free(rmsd_matrix[i]);
+ for(int i = 0; i < num_loops; ++i){
+ delete [] rmsd_matrix[i];
}
- free(rmsd_matrix);
- flame::Flame_Clear(flame);
+ delete [] rmsd_matrix;
return return_list;
}
-void LoopCandidates::CalculateClashScores(int chain_index){
+void LoopCandidates::CalculateClashScores(uint start_resnum, uint chain_index){
if(!scorer_){
throw promod3::Error("Require a loop scorer to be attached to LoopCandidatesObject!");
}
Real clash_score;
- int start_resnum = n_stem_.GetNumber().GetNum();
for(LoopCandidateList::iterator i = this->begin();
i != this->end(); ++i){
@@ -332,12 +269,11 @@ void LoopCandidates::CalculateClashScores(int chain_index){
}
}
-void LoopCandidates::CalculateCBetaScores(int chain_index){
+void LoopCandidates::CalculateCBetaScores(uint start_resnum, uint chain_index){
if(!scorer_){
throw promod3::Error("Require a loop scorer to be attached to LoopCandidatesObject!");
}
Real cbeta_score;
- int start_resnum = n_stem_.GetNumber().GetNum();
for(LoopCandidateList::iterator i = this->begin();
i != this->end(); ++i){
@@ -346,12 +282,24 @@ void LoopCandidates::CalculateCBetaScores(int chain_index){
}
}
-void LoopCandidates::CalculateTorsionScores(int chain_index){
+void LoopCandidates::CalculateReducedScores(uint start_resnum, uint chain_index){
+ if(!scorer_){
+ throw promod3::Error("Require a loop scorer to be attached to LoopCandidatesObject!");
+ }
+ Real reduced_score;
+
+ for(LoopCandidateList::iterator i = this->begin();
+ i != this->end(); ++i){
+ reduced_score = scorer_->CalculateReducedScore(i->bb_list,start_resnum, chain_index);
+ i->reduced_score = reduced_score;
+ }
+}
+
+void LoopCandidates::CalculateTorsionScores(uint start_resnum, uint chain_index){
if(!scorer_){
throw promod3::Error("Require a loop scorer to be attached to LoopCandidatesObject!");
}
Real torsion_score;
- int start_resnum = n_stem_.GetNumber().GetNum();
for(LoopCandidateList::iterator i = this->begin();
i != this->end(); ++i){
@@ -360,12 +308,11 @@ void LoopCandidates::CalculateTorsionScores(int chain_index){
}
}
-void LoopCandidates::CalculateCBPackingScores(int chain_index){
+void LoopCandidates::CalculateCBPackingScores(uint start_resnum, uint chain_index){
if(!scorer_){
throw promod3::Error("Require a loop scorer to be attached to LoopCandidatesObject!");
}
Real packing_score;
- int start_resnum = n_stem_.GetNumber().GetNum();
for(LoopCandidateList::iterator i = this->begin();
i != this->end(); ++i){
@@ -374,12 +321,11 @@ void LoopCandidates::CalculateCBPackingScores(int chain_index){
}
}
-void LoopCandidates::CalculateHBondScores(int chain_index){
+void LoopCandidates::CalculateHBondScores(uint start_resnum, uint chain_index){
if(!scorer_){
throw promod3::Error("Require a loop scorer to be attached to LoopCandidatesObject!");
}
Real hbond_score;
- int start_resnum = n_stem_.GetNumber().GetNum();
for(LoopCandidateList::iterator i = this->begin();
i != this->end(); ++i){
@@ -388,45 +334,73 @@ void LoopCandidates::CalculateHBondScores(int chain_index){
}
}
-void LoopCandidates::CalculateDSSPHBondScores(int chain_index){
+void LoopCandidates::CalculateSSAgreementScores(uint start_resnum, uint chain_index){
if(!scorer_){
throw promod3::Error("Require a loop scorer to be attached to LoopCandidatesObject!");
}
- Real dssp_hbond_score;
- int start_resnum = n_stem_.GetNumber().GetNum();
+ Real ss_agreement_score;
for(LoopCandidateList::iterator i = this->begin();
i != this->end(); ++i){
- dssp_hbond_score = scorer_->CalculateDSSPHBondScore(i->bb_list,start_resnum, chain_index);
- i->dssp_hbond_score = dssp_hbond_score;
+ ss_agreement_score = scorer_->CalculateSSAgreementScore(i->bb_list,start_resnum, chain_index);
+ i->ss_agreement_score = ss_agreement_score;
}
}
-void LoopCandidates::CalculateStemRMSD(){
+void LoopCandidates::CalculateCombinedScores(const std::map<String,Real>& linear_weights,
+ uint start_resnum, uint chain_index){
- geom::Vec3 before_n_pos = n_stem_.FindAtom("N").GetPos();
- geom::Vec3 before_ca_pos = n_stem_.FindAtom("CA").GetPos();
- geom::Vec3 before_c_pos = n_stem_.FindAtom("C").GetPos();
- geom::Vec3 before_o_pos = n_stem_.FindAtom("O").GetPos();
- geom::Vec3 after_n_pos = c_stem_.FindAtom("N").GetPos();
- geom::Vec3 after_ca_pos = c_stem_.FindAtom("CA").GetPos();
- geom::Vec3 after_c_pos = c_stem_.FindAtom("C").GetPos();
- geom::Vec3 after_o_pos = c_stem_.FindAtom("O").GetPos();
- Real rmsd;
+ typedef Real (BackboneLoopScorer::*score_f_ptr)(const BackboneList&, uint, uint) const;
+ std::vector<std::pair<score_f_ptr, Real> > weights;
+ Real intercept = 0.0;
- for(LoopCandidateList::iterator i = candidates_.begin();
- i != candidates_.end(); ++i){
- rmsd = 0.0;
- rmsd += geom::Length2(before_n_pos-i->bb_list[0].n_coord);
- rmsd += geom::Length2(before_ca_pos-i->bb_list[0].ca_coord);
- rmsd += geom::Length2(before_c_pos-i->bb_list[0].c_coord);
- rmsd += geom::Length2(before_o_pos-i->bb_list[0].o_coord);
- rmsd += geom::Length2(after_n_pos-i->bb_list.back().n_coord);
- rmsd += geom::Length2(after_ca_pos-i->bb_list.back().ca_coord);
- rmsd += geom::Length2(after_c_pos-i->bb_list.back().c_coord);
- rmsd += geom::Length2(after_o_pos-i->bb_list.back().o_coord);
- i->stem_rmsd = std::sqrt(rmsd/8);
+ for(std::map<String, Real>::const_iterator i =linear_weights.begin();
+ i != linear_weights.end(); ++i){
+
+ if(i->first == "cbeta"){
+ weights.push_back(std::make_pair(&BackboneLoopScorer::CalculateCBetaScore,i->second));
+ }
+ else if(i->first == "clash"){
+ weights.push_back(std::make_pair(&BackboneLoopScorer::CalculateClashScore,i->second));
+ }
+ else if(i->first == "torsion"){
+ weights.push_back(std::make_pair(&BackboneLoopScorer::CalculateTorsionScore,i->second));
+ }
+ else if(i->first == "cb_packing"){
+ weights.push_back(std::make_pair(&BackboneLoopScorer::CalculateCBPackingScore,i->second));
+ }
+ else if(i->first == "hbond"){
+ weights.push_back(std::make_pair(&BackboneLoopScorer::CalculateHBondScore,i->second));
+ }
+ else if(i->first == "ss_agreement"){
+ weights.push_back(std::make_pair(&BackboneLoopScorer::CalculateSSAgreementScore,i->second));
+ }
+ else if(i->first == "reduced"){
+ weights.push_back(std::make_pair(&BackboneLoopScorer::CalculateReducedScore,i->second));
+ }
+ else if(i->first == "intercept"){
+ intercept = i->second;
+ }
+ else{
+ std::stringstream ss;
+ ss << "Invalid keyword in weight dictionary observed when Calculating combined score! ";
+ ss << "Valid keywords are: cbeta, clash, torsion, cb_packing, hbond, ss_agreement, reduced ";
+ ss << "and intercept.";
+ throw promod3::Error(ss.str());
+ }
+ }
+
+ Real score;
+ for(LoopCandidateList::iterator i = this->begin();
+ i != this->end(); ++i){
+ score = 0.0;
+ for(std::vector<std::pair<score_f_ptr, Real> >::iterator j = weights.begin();
+ j != weights.end(); ++j){
+ score += j->second * ((*scorer_).*(j->first))(i->bb_list,start_resnum,chain_index);
+ }
+ score += intercept;
+ i->combined_score = score;
}
}
@@ -446,6 +420,14 @@ Real LoopCandidates::GetAVGCBetaScore(){
return score/this->size();
}
+Real LoopCandidates::GetAVGReducedScore(){
+ Real score = 0.0;
+ for(LoopCandidateList::iterator i = this->begin(); i != this->end(); ++i){
+ score += i->reduced_score;
+ }
+ return score/this->size();
+}
+
Real LoopCandidates::GetAVGTorsionScore(){
Real score = 0.0;
for(LoopCandidateList::iterator i = this->begin(); i != this->end(); ++i){
@@ -470,20 +452,21 @@ Real LoopCandidates::GetAVGHBondScore(){
return score/this->size();
}
-Real LoopCandidates::GetAVGDSSPHBondScore(){
+Real LoopCandidates::GetAVGSSAgreementScore(){
Real score = 0.0;
for(LoopCandidateList::iterator i = this->begin(); i != this->end(); ++i){
- score += i->dssp_hbond_score;
+ score += i->ss_agreement_score;
}
return score/this->size();
}
-Real LoopCandidates::GetAVGStemRMSD(){
+Real LoopCandidates::GetAVGCombinedScore(){
Real score = 0.0;
for(LoopCandidateList::iterator i = this->begin(); i != this->end(); ++i){
- score += i->stem_rmsd;
+ score += i->combined_score;
}
return score/this->size();
}
+
}}
diff --git a/loop/src/loop_candidate.hh b/loop/src/loop_candidate.hh
index c0a127269c3297bd6382f8ff034b494f459b6b36..9e0bf4300c892367742ae06118d7fe9c7727b26a 100644
--- a/loop/src/loop_candidate.hh
+++ b/loop/src/loop_candidate.hh
@@ -4,7 +4,7 @@
#include <promod3/loop/backbone.hh>
#include <promod3/loop/frag_db.hh>
#include <promod3/loop/monte_carlo.hh>
-#include <promod3/loop/flame.hh>
+#include <promod3/loop/cluster.hh>
#include <promod3/loop/backbone_loop_score.hh>
#include <promod3/loop/ccd.hh>
#include <promod3/loop/kic.hh>
@@ -16,18 +16,15 @@ namespace promod3 { namespace loop {
struct LoopCandidate {
public:
LoopCandidate(const BackboneList& bb_list):
- clash_score(0.0), cbeta_score(0.0),
+ clash_score(0.0), cbeta_score(0.0), reduced_score(0.0),
torsion_score(0.0), packing_score(0.0), hbond_score(0.0),
- dssp_hbond_score(0.0), stem_rmsd(0.0), original_sequence(""),
- bb_list(bb_list)
- { }
+ ss_agreement_score(0.0),original_sequence(""), bb_list(bb_list) { }
LoopCandidate(const BackboneList& bb_list, const String& original_sequence,
const String& original_dssp_states):
clash_score(0.0), cbeta_score(0.0),
torsion_score(0.0), packing_score(0.0), hbond_score(0.0),
- dssp_hbond_score(0.0), stem_rmsd(0.0), original_sequence(original_sequence),
- original_dssp_states(original_dssp_states), bb_list(bb_list)
- { }
+ original_sequence(original_sequence),
+ original_dssp_states(original_dssp_states), bb_list(bb_list) { }
Real CARMSD(const LoopCandidate& other);
@@ -41,11 +38,12 @@ public:
Real clash_score;
Real cbeta_score;
+ Real reduced_score;
Real torsion_score;
Real packing_score;
Real hbond_score;
- Real dssp_hbond_score;
- Real stem_rmsd;
+ Real ss_agreement_score;
+ Real combined_score;
String original_sequence;
String original_dssp_states;
BackboneList bb_list;
@@ -58,9 +56,7 @@ typedef std::vector<LoopCandidates> LoopCandidatesList;
class LoopCandidates {
public:
- LoopCandidates(const ost::mol::ResidueHandle& n_stem,
- const ost::mol::ResidueHandle& c_stem,
- const String& seq);
+ LoopCandidates( const String& seq);
static LoopCandidatesPtr FillFromDatabase(const ost::mol::ResidueHandle& n_stem,
const ost::mol::ResidueHandle& c_stem,
@@ -69,9 +65,7 @@ public:
StructureDBPtr structure_db,
bool extended_search);
- static LoopCandidatesPtr FillFromMonteCarloSampler(const ost::mol::ResidueHandle& n_stem,
- const ost::mol::ResidueHandle& c_stem,
- const String& seq,
+ static LoopCandidatesPtr FillFromMonteCarloSampler(const String& seq,
uint num_loops,
uint steps,
MonteCarloSamplerPtr sampler,
@@ -79,9 +73,7 @@ public:
MonteCarloScorerPtr scorer,
MonteCarloCoolerPtr cooler);
- static LoopCandidatesPtr FillFromMonteCarloSampler(const ost::mol::ResidueHandle& n_stem,
- const ost::mol::ResidueHandle& c_stem,
- const BackboneList& initial_bb,
+ static LoopCandidatesPtr FillFromMonteCarloSampler(const BackboneList& initial_bb,
const String& seq,
uint num_loops,
uint steps,
@@ -91,22 +83,28 @@ public:
MonteCarloCoolerPtr cooler);
- void ApplyCCD(std::vector<TorsionSamplerPtr> torsion_sampler,
+ void ApplyCCD(const ost::mol::ResidueHandle& n_stem,
+ const ost::mol::ResidueHandle& c_stem,
+ std::vector<TorsionSamplerPtr> torsion_sampler,
int max_iterations = 1000, Real rmsd_cutoff = 0.1,
bool keep_non_converged = false, int random_seed=0);
- void ApplyCCD(TorsionSamplerPtr torsion_sampler, int max_iterations = 1000, Real rmsd_cutoff = 0.1,
- bool keep_non_converged = false, int random_seed=0);
-
- void ApplyCCD(int max_iterations = 1000, Real rmsd_cutoff = 0.1, bool keep_non_converged = false, int random_seed=0);
-
- void ApplyKIC(uint pivot_one, uint pivot_two, uint pivot_three);
+ void ApplyCCD(const ost::mol::ResidueHandle& n_stem,
+ const ost::mol::ResidueHandle& c_stem,
+ TorsionSamplerPtr torsion_sampler, int max_iterations = 1000,
+ Real rmsd_cutoff = 0.1, bool keep_non_converged = false,
+ int random_seed=0);
- LoopCandidatesList ClusterCandidates();
+ void ApplyCCD(const ost::mol::ResidueHandle& n_stem,
+ const ost::mol::ResidueHandle& c_stem,
+ int max_iterations = 1000, Real rmsd_cutoff = 0.1,
+ bool keep_non_converged = false);
- ost::mol::EntityHandle ToEntity(uint index) const;
+ void ApplyKIC(const ost::mol::ResidueHandle& n_stem,
+ const ost::mol::ResidueHandle& c_stem,
+ uint pivot_one, uint pivot_two, uint pivot_three);
- void InsertInto(ost::mol::EntityHandle& ent, uint index) const;
+ LoopCandidatesList ClusterCandidates(Real max_dist, bool neglect_size_one = true);
void Add(const LoopCandidate& candidate);
@@ -116,37 +114,38 @@ public:
void AttachScorer(BackboneLoopScorerPtr scorer) { scorer_ = scorer; }
- void CalculateClashScores(int chain_index = 0);
+ void CalculateClashScores(uint start_resnum, uint chain_index = 0);
- void CalculateCBetaScores(int chain_index = 0);
+ void CalculateCBetaScores(uint start_resnum, uint chain_index = 0);
- void CalculateTorsionScores(int chain_index = 0);
+ void CalculateReducedScores(uint start_resnum, uint chain_index = 0);
- void CalculateCBPackingScores(int chain_index = 0);
+ void CalculateTorsionScores(uint start_resnum, uint chain_index = 0);
- void CalculateHBondScores(int chain_index = 0);
+ void CalculateCBPackingScores(uint start_resnum, uint chain_index = 0);
- void CalculateDSSPHBondScores(int chain_index = 0);
+ void CalculateHBondScores(uint start_resnum, uint chain_index = 0);
- void CalculateStemRMSD();
+ void CalculateSSAgreementScores(uint start_resnum, uint chain_index = 0);
+
+ void CalculateCombinedScores(const std::map<String, Real>& linear_weights,
+ uint start_resnum, uint chain_index = 0);
Real GetAVGClashScore();
Real GetAVGCBetaScore();
+ Real GetAVGReducedScore();
+
Real GetAVGTorsionScore();
Real GetAVGPackingScore();
Real GetAVGHBondScore();
- Real GetAVGDSSPHBondScore();
-
- Real GetAVGStemRMSD();
-
- ost::mol::ResidueHandle GetNStem() { return n_stem_; }
+ Real GetAVGSSAgreementScore();
- ost::mol::ResidueHandle GetCStem() { return c_stem_; }
+ Real GetAVGCombinedScore();
size_t size() const { return candidates_.size(); }
@@ -182,8 +181,7 @@ public:
private:
- LoopCandidateList candidates_;
- ost::mol::ResidueHandle n_stem_, c_stem_;
+ LoopCandidateList candidates_;;
String sequence_;
BackboneLoopScorerPtr scorer_;
};
diff --git a/loop/src/monte_carlo_scorer.cc b/loop/src/monte_carlo_scorer.cc
index bf216b09ec6e7b702cbc7593df1e5576d49eda95..18e86101c40bf72a4ee08c3ba8e7a66522a634cf 100644
--- a/loop/src/monte_carlo_scorer.cc
+++ b/loop/src/monte_carlo_scorer.cc
@@ -28,16 +28,19 @@ LinearScorer::LinearScorer(BackboneLoopScorerPtr scorer, uint start_resnum, uint
else if(i->first == "hbond"){
weights_.push_back(std::make_pair(&BackboneLoopScorer::CalculateHBondScore,i->second));
}
- else if(i->first == "dssp_hbond"){
- weights_.push_back(std::make_pair(&BackboneLoopScorer::CalculateDSSPHBondScore,i->second));
- }
+ else if(i->first == "ss_agreement"){
+ weights_.push_back(std::make_pair(&BackboneLoopScorer::CalculateSSAgreementScore,i->second));
+ }
+ else if(i->first == "reduced"){
+ weights_.push_back(std::make_pair(&BackboneLoopScorer::CalculateReducedScore,i->second));
+ }
else if(i->first == "intercept"){
intercept_ = i->second;
}
else{
std::stringstream ss;
ss << "Invalid keyword in weight dictionary observed when setting up Linear Scorer! ";
- ss << "Valid keywords are: cbeta, clash, torsion, cb_packing, hbond, dssp_hbond ";
+ ss << "Valid keywords are: cbeta, clash, torsion, cb_packing, hbond, ss_agreement, reduced ";
ss << "and intercept.";
throw promod3::Error(ss.str());
}
diff --git a/loop/src/psipred_prediction.cc b/loop/src/psipred_prediction.cc
new file mode 100644
index 0000000000000000000000000000000000000000..00b3f460be3e9564c5d7eda160cbc9b31440ccb3
--- /dev/null
+++ b/loop/src/psipred_prediction.cc
@@ -0,0 +1,187 @@
+#include <promod3/loop/psipred_prediction.hh>
+
+namespace promod3{ namespace loop{
+
+PsipredPrediction::PsipredPrediction(const std::vector<char>& prediction,
+ const std::vector<int>& confidence){
+
+ //check input for validity
+ if(prediction.size() != confidence.size()){
+ throw promod3::Error("Size of psipred prediction and confidence is inconsistent!");
+ }
+
+ for(std::vector<char>::const_iterator i = prediction.begin();
+ i != prediction.end(); ++i){
+ if(!(*i == 'H' || *i == 'C' || *i == 'E')){
+ throw promod3::Error("Psipred prediction must be element of ['H','E','C']!");
+ }
+ }
+
+ for(std::vector<int>::const_iterator i = confidence.begin();
+ i != confidence.end(); ++i){
+ if((*i)<0 || (*i)>9){
+ throw promod3::Error("Psipred confidence must be in range [0,9]!");
+ }
+ }
+
+ prediction_ = prediction;
+ confidence_ = confidence;
+}
+
+PsipredPredictionPtr PsipredPrediction::Extract(uint from, uint to) const{
+
+ if(to <= from){
+ throw promod3::Error("'from' parameter must be smaller than 'to' parameter!");
+ }
+
+ if(to > this->size()){
+ throw promod3::Error("Try to access invalid range in PsipredPrediction!");
+ }
+
+ std::vector<char> pred;
+ std::vector<int> conf;
+
+ for(uint i = from; i < to; ++i){
+ pred.push_back(prediction_[i]);
+ conf.push_back(confidence_[i]);
+ }
+
+ PsipredPredictionPtr p(new PsipredPrediction(pred,conf));
+ return p;
+}
+
+void PsipredPrediction::Add(char prediction, int confidence){
+ if(!(prediction == 'H' || prediction == 'E' || prediction == 'C')){
+ throw promod3::Error("Psipred prediction must be in ['H','E','C']!");
+ }
+ if(confidence < 0 || confidence > 9){
+ throw promod3::Error("Psipred confidence must be in [0,9]!");
+ }
+ prediction_.push_back(prediction);
+ confidence_.push_back(confidence);
+}
+
+char PsipredPrediction::GetPrediction(uint idx) const{
+ if(idx >= this->size()){
+ throw promod3::Error("Invalid idx for getting psipred prediction!");
+ }
+
+ return prediction_[idx];
+}
+
+int PsipredPrediction::GetConfidence(uint idx) const{
+ if(idx >= this->size()){
+ throw promod3::Error("Invalid idx for getting psipred confidence!");
+ }
+ return confidence_[idx];
+}
+
+PsipredPredictionPtr PsipredPrediction::FromHHM(const String& filename){
+
+ std::vector<char> prediction;
+ std::vector<int> confidence;
+
+ boost::iostreams::filtering_stream<boost::iostreams::input> in;
+ std::ifstream stream(filename.c_str());
+ if(!stream){
+ throw std::runtime_error("Could not open file!");
+ }
+ if (filename.rfind(".gz") == filename.size()-3) {
+ in.push(boost::iostreams::gzip_decompressor());
+ }
+
+ bool in_sspred = false;
+ bool in_ssconf = false;
+
+ in.push(stream);
+ std::string line;
+ ost::StringRef sline;
+ while (std::getline(in, line)) {
+ sline=ost::StringRef(line.c_str(), line.length());
+ sline = sline.trim();
+ if (sline.empty()) continue;
+ if (sline == ost::StringRef("//", 2)) break;
+
+ if(sline.length() > 0 &&
+ sline[0] == '>'){
+ in_sspred = false;
+ in_ssconf = false;
+ }
+
+ if (sline.length() > 8 &&
+ sline.substr(0, 9)==ost::StringRef(">ss_pred ", 9)) {
+ in_sspred = true;
+ continue;
+ }
+
+ if (sline.length() > 8 &&
+ sline.substr(0, 9)==ost::StringRef(">ss_conf ", 9)) {
+ in_ssconf = true;
+ continue;
+ }
+
+ if(in_sspred){
+ for(uint i = 0; i < sline.size(); ++i){
+ prediction.push_back(sline[i]);
+ }
+ }
+
+ if(in_ssconf){
+ for(uint i = 0; i < sline.size(); ++i){
+ confidence.push_back(int(sline[i])-48); //note, that the number zero
+ //has number 48 in ascii...
+ }
+ }
+ }
+
+ PsipredPredictionPtr p(new PsipredPrediction(prediction,confidence));
+ return p;
+}
+
+PsipredPredictionPtr PsipredPrediction::FromHoriz(const String& filename){
+
+ std::vector<char> prediction;
+ std::vector<int> confidence;
+
+ boost::iostreams::filtering_stream<boost::iostreams::input> in;
+ std::ifstream stream(filename.c_str());
+ if(!stream){
+ throw std::runtime_error("Could not open file!");
+ }
+ if (filename.rfind(".gz") == filename.size()-3) {
+ in.push(boost::iostreams::gzip_decompressor());
+ }
+
+ in.push(stream);
+ std::string line;
+ ost::StringRef sline;
+ std::vector<ost::StringRef> split_sline;
+
+ while (std::getline(in, line)) {
+ sline=ost::StringRef(line.c_str(), line.length());
+ sline = sline.trim();
+ if (sline.empty()) continue;
+
+ split_sline = sline.split();
+
+ if(split_sline[0].str() == "Pred:" && split_sline.size() == 2){
+ String data = split_sline[1].str();
+ for(uint i = 0; i < data.size(); ++i){
+ prediction.push_back(data[i]);
+ }
+ }
+
+ if(split_sline[0].str() == "Conf:" && split_sline.size() == 2){
+ String data = split_sline[1].str();
+ for(uint i = 0; i < data.size(); ++i){
+ confidence.push_back(int(data[i])-48); //note, that the number zero
+ //has number 48 in ascii...
+ }
+ }
+ }
+
+ PsipredPredictionPtr p(new PsipredPrediction(prediction,confidence));
+ return p;
+}
+
+}} //ns
diff --git a/loop/src/psipred_prediction.hh b/loop/src/psipred_prediction.hh
new file mode 100644
index 0000000000000000000000000000000000000000..b7786813907d8d25c6c1534c066853fa221698d9
--- /dev/null
+++ b/loop/src/psipred_prediction.hh
@@ -0,0 +1,51 @@
+#ifndef PROMOD_LOOP_PSIPRED_PREDICTION_HH
+#define PROMOD_LOOP_PSIPRED_PREDICTION_HH
+
+#include <vector>
+#include <boost/shared_ptr.hpp>
+#include <ost/string_ref.hh>
+#include <promod3/core/message.hh>
+#include <fstream>
+#include <boost/iostreams/filter/gzip.hpp>
+#include <boost/iostreams/filtering_stream.hpp>
+
+namespace promod3 { namespace loop {
+
+class PsipredPrediction;
+typedef boost::shared_ptr<PsipredPrediction> PsipredPredictionPtr;
+
+class PsipredPrediction{
+
+public:
+
+ PsipredPrediction() {}
+
+ PsipredPrediction(const std::vector<char>& prediction,
+ const std::vector<int>& confidence);
+
+ static PsipredPredictionPtr FromHHM(const String& filename);
+
+ static PsipredPredictionPtr FromHoriz(const String& filename);
+
+ PsipredPredictionPtr Extract(uint from, uint to) const;
+
+ void Add(char prediction, int confidence);
+
+ char GetPrediction(uint idx) const;
+
+ int GetConfidence(uint idx) const;
+
+ std::vector<char> GetPredictions() const { return prediction_; }
+
+ std::vector<int> GetConfidences() const { return confidence_; }
+
+ size_t size() const { return prediction_.size(); }
+
+private:
+ std::vector<char> prediction_;
+ std::vector<int> confidence_;
+};
+
+}} //ns
+
+#endif
diff --git a/loop/src/sec_struct.cc b/loop/src/sec_struct.cc
new file mode 100644
index 0000000000000000000000000000000000000000..1bd43d87bd5db09b477e3a5b5183ef179d608534
--- /dev/null
+++ b/loop/src/sec_struct.cc
@@ -0,0 +1,405 @@
+#include <promod3/loop/sec_struct.hh>
+
+namespace promod3{ namespace loop{
+
+void RawEstimateSS(const std::vector<geom::Vec3>& ca_positions,
+ int start_idx,
+ const std::vector<int>& donor_for_one,
+ const std::vector<int>& donor_for_two,
+ const std::vector<int>& acceptor_for_one,
+ const std::vector<int>& acceptor_for_two,
+ String& ss_assignment){
+
+ int size = ca_positions.size();
+
+ if(size != static_cast<int>(donor_for_one.size())){
+ throw promod3::Error("Position and donor data are inconsistent for dssp calculation!");
+ }
+
+ if(size != static_cast<int>(donor_for_two.size())){
+ throw promod3::Error("Position and donor data are inconsistent for dssp calculation!");
+ }
+
+ if(size != static_cast<int>(acceptor_for_one.size())){
+ throw promod3::Error("Position and acceptor data are inconsistent for dssp calculation!");
+ }
+
+ if(size != static_cast<int>(acceptor_for_two.size())){
+ throw promod3::Error("Position and acceptor data are inconsistent for dssp calculation!");
+ }
+
+ if(size < 3){
+ throw promod3::Error("Size of input positions are too small!");
+ }
+
+ ss_assignment.assign(size,'C');
+
+ int bends[size];
+ int turn_3[size];
+ int turn_4[size];
+ int turn_5[size];
+ int para_bridge[size];
+ int antipara_bridge[size];
+
+ memset(bends,0,size*sizeof(int));
+ memset(turn_3,0,size*sizeof(int));
+ memset(turn_4,0,size*sizeof(int));
+ memset(turn_5,0,size*sizeof(int));
+ memset(para_bridge,0,size*sizeof(int));
+ memset(antipara_bridge,0,size*sizeof(int));
+
+ //let's first search for the bends, i.e. pieces with high curvature
+ Real angle;
+ for(int i = 2; i < size-2; ++i){
+ angle = geom::Angle(ca_positions[i]-ca_positions[i-2],
+ ca_positions[i+2]-ca_positions[i]);
+ if(angle > 1.2217) bends[i] = 1;
+ }
+
+ //let's search for turns
+ int three = start_idx + 3;
+ int four = start_idx + 4;
+ int five = start_idx + 5;
+ for(int i = 0; i < size; ++i, ++three, ++four, ++five){
+ if(acceptor_for_one[i] == four) turn_4[i] = 1;
+ if(acceptor_for_one[i] == three) turn_3[i] = 1;
+ if(acceptor_for_one[i] == five) turn_5[i] = 1;
+ if(acceptor_for_two[i] == four) turn_4[i] = 1;
+ if(acceptor_for_two[i] == three) turn_3[i] = 1;
+ if(acceptor_for_two[i] == five) turn_5[i] = 1;
+ }
+
+ //let's search for antiparallel beta bridges
+ for(int i = 0; i < size; ++i){
+ if(acceptor_for_one[i] != -1){
+ if(acceptor_for_one[i] == donor_for_one[i]) antipara_bridge[i] = 1;
+ if(acceptor_for_one[i] == donor_for_two[i]) antipara_bridge[i] = 1;
+ }
+ if(acceptor_for_two[i] != -1){
+ if(acceptor_for_two[i] == donor_for_one[i]) antipara_bridge[i] = 1;
+ if(acceptor_for_two[i] == donor_for_two[i]) antipara_bridge[i] = 1;
+ }
+ }
+
+ for(int i = 1; i < size-1; ++i){
+ if(donor_for_one[i+1] != -1){
+ if(donor_for_one[i+1] + 2 == acceptor_for_one[i-1]) antipara_bridge[i] = 1;
+ if(donor_for_one[i+1] + 2 == acceptor_for_two[i-1]) antipara_bridge[i] = 1;
+ }
+
+ if(donor_for_two[i+1] != -1){
+ if(donor_for_two[i+1] + 2 == acceptor_for_one[i-1]) antipara_bridge[i] = 1;
+ if(donor_for_two[i+1] + 2 == acceptor_for_two[i-1]) antipara_bridge[i] = 1;
+ }
+ }
+
+ //let's search for parallel beta bridges
+ for(int i = 1; i < size-1; ++i){
+ if(acceptor_for_one[i-1] != -1){
+ if(acceptor_for_one[i-1] == donor_for_one[i+1]) para_bridge[i] = 1;
+ if(acceptor_for_one[i-1] == donor_for_two[i+1]) para_bridge[i] = 1;
+ }
+ if(acceptor_for_two[i-1] != -1){
+ if(acceptor_for_two[i-1] == donor_for_one[i+1]) para_bridge[i] = 1;
+ if(acceptor_for_two[i-1] == donor_for_two[i+1]) para_bridge[i] = 1;
+ }
+ }
+
+ for(int i = 0; i < size; ++i){
+ if(donor_for_one[i] != -1){
+ if(donor_for_one[i] + 2 == acceptor_for_one[i]) para_bridge[i] = 1;
+ if(donor_for_one[i] + 2 == acceptor_for_two[i]) para_bridge[i] = 1;
+ }
+
+ if(donor_for_two[i] != -1){
+ if(donor_for_two[i] + 2 == acceptor_for_one[i]) para_bridge[i] = 1;
+ if(donor_for_two[i] + 2 == acceptor_for_two[i]) para_bridge[i] = 1;
+ }
+ }
+
+ //priority according to the dssp paper is: H,B,E,G,I,T,S
+ //we therefore start to assign from lowest to highest priority,
+ //potentially overwriting low priority elements
+
+ //do S
+ for(int i = 0; i < size; ++i){
+ if(bends[i]) ss_assignment[i] = 'S';
+ }
+
+ //do T
+ for(int i = 0; i < size - 2; ++i){
+ if(turn_3[i]){
+ ss_assignment[i+1] = 'T';
+ ss_assignment[i+2] = 'T';
+ }
+ }
+
+ for(int i = 0; i < size - 3; ++i){
+ if(turn_4[i]){
+ ss_assignment[i+1] = 'T';
+ ss_assignment[i+2] = 'T';
+ ss_assignment[i+3] = 'T';
+ }
+ }
+
+ for(int i = 0; i < size - 4; ++i){
+ if(turn_5[i]){
+ ss_assignment[i+1] = 'T';
+ ss_assignment[i+2] = 'T';
+ ss_assignment[i+3] = 'T';
+ ss_assignment[i+4] = 'T';
+ }
+ }
+
+ //let's do the helices... we use the bend arrays to fill helices
+ //and start with H, we then fill in G if there is no space occupied by H
+ //and finally I if there is nothing in that range occupied.
+ memset(bends,0,size*sizeof(int));
+ for(int i = 1; i < size-4; ++i){
+ if(turn_4[i-1] && turn_4[i]){
+ bends[i] = 1;
+ bends[i+1] = 1;
+ bends[i+2] = 1;
+ bends[i+3] = 1;
+ }
+ }
+
+ int start;
+ int end;
+ for(int i = 1; i < size-3; ++i){
+ if(turn_3[i-1] && turn_3[i]){
+ start = i;
+ end = i+3;
+ //let's search how long it continues...
+ while(true && end < size){
+ if(turn_3[end-3] && turn_3[end-2]){
+ ++end;
+ }
+ else break;
+ }
+ //check, whether there already is something in this range
+ bool empty = true;
+ for(int j = start; j < end; ++j){
+ if(bends[j]){
+ empty = false;
+ break;
+ }
+ }
+ if(empty){
+ //let's fill!
+ for(int j = start; j < end; ++j){
+ bends[j] = 2;
+ }
+ }
+ }
+ }
+
+ for(int i = 1; i < size-5; ++i){
+ if(turn_5[i-1] && turn_5[i]){
+ start = i;
+ end = i+5;
+ //let's search how long it continues...
+ while(true && end < size){
+ if(turn_5[end-5] && turn_5[end-4]){
+ ++end;
+ }
+ else break;
+ }
+ //check, whether there already is something in this range
+ bool empty = true;
+ for(int j = start; j < end; ++j){
+ if(bends[j]){
+ empty = false;
+ break;
+ }
+ }
+ if(empty){
+ //let's fill!
+ for(int j = start; j < end; ++j){
+ bends[j] = 3;
+ }
+ }
+ }
+ }
+
+ //do I
+ for(int i = 0; i < size; ++i){
+ if(bends[i] == 3) ss_assignment[i] = 'I';
+ }
+
+ //do G
+ for(int i = 0; i < size; ++i){
+ if(bends[i] == 2) ss_assignment[i] = 'G';
+ }
+
+ //do E
+ if(para_bridge[0]){
+ if(para_bridge[1]) ss_assignment[0] = 'E';
+ }
+ if(antipara_bridge[0]){
+ if(antipara_bridge[1]) ss_assignment[0] = 'E';
+ }
+
+ for(int i = 1; i < size - 1; ++i){
+ if(para_bridge[i]){
+ if(para_bridge[i-1] || para_bridge[i+1]) ss_assignment[i] = 'E';
+ }
+ if(antipara_bridge[i]){
+ if(antipara_bridge[i-1] || antipara_bridge[i+1]) ss_assignment[i] = 'E';
+ }
+ }
+
+ if(para_bridge[size-1]){
+ if(para_bridge[size-2]) ss_assignment[size-1] = 'E';
+ }
+ if(antipara_bridge[size-1]){
+ if(antipara_bridge[size-2]) ss_assignment[size-1] = 'E';
+ }
+
+ //do B
+ if(para_bridge[0]){
+ if(!para_bridge[1]) ss_assignment[0] = 'B';
+ }
+ if(antipara_bridge[0]){
+ if(!antipara_bridge[1]) ss_assignment[0] = 'B';
+ }
+
+ for(int i = 1; i < size-1; ++i){
+ if(para_bridge[i]){
+ if(!(para_bridge[i-1] || para_bridge[i+1])) ss_assignment[i] = 'B';
+ }
+ if(antipara_bridge[i]){
+ if(!(antipara_bridge[i-1] ||antipara_bridge[i+1])) ss_assignment[i] = 'B';
+ }
+ }
+
+ if(para_bridge[size-1]){
+ if(!para_bridge[size-2]) ss_assignment[size-1] = 'B';
+ }
+ if(antipara_bridge[size-1]){
+ if(!antipara_bridge[size-2]) ss_assignment[size-1] = 'B';
+ }
+
+ //do H
+ for(int i = 0; i < size; ++i){
+ if(bends[i] == 1) ss_assignment[i] = 'H';
+ }
+}
+
+void EstimateSS(const BackboneList& bb_list, String& ss_assignment){
+
+ int size = bb_list.size();
+
+ if(size == 0){
+ throw promod3::Error("Cannot estimate SS with empty BackboneList!");
+ }
+
+ std::vector<int> donor_for_one(size,-1);
+ std::vector<int> donor_for_two(size,-1);
+ std::vector<int> acceptor_for_one(size,-1);
+ std::vector<int> acceptor_for_two(size,-1);
+ std::vector<Real> donor_one_energies(size,std::numeric_limits<Real>::max());
+ std::vector<Real> donor_two_energies(size,std::numeric_limits<Real>::max());
+ std::vector<Real> acceptor_one_energies(size,std::numeric_limits<Real>::max());
+ std::vector<Real> acceptor_two_energies(size,std::numeric_limits<Real>::max());
+ std::vector<geom::Vec3> ca_positions(size,geom::Vec3(0,0,0));
+ std::vector<geom::Vec3> h_positions(size,geom::Vec3(0,0,0));
+
+ //first residue is expected not to be an hbond donor,
+ //we don't do anything for the first h_position...
+ ca_positions[0] = bb_list[0].ca_coord;
+
+ geom::Vec3 co_vec;
+ for(int i = 1; i < size; ++i){
+ ca_positions[i] = bb_list[i].ca_coord;
+ co_vec = geom::Normalize(bb_list[i-1].o_coord - bb_list[i-1].c_coord);
+ h_positions[i] = bb_list[i].n_coord - co_vec;
+ }
+
+ Real e;
+ for(int i = 0; i < size-3; ++i){
+ for(int j = i+3; j < size; ++j){
+ if(geom::Length2(ca_positions[i]-ca_positions[j]) < 81.0){
+ //i as acceptor ; j as donor
+ if(bb_list[j].one_letter_code != 'P'){
+ e = DSSPHBondEnergy(h_positions[j],bb_list[j].n_coord,
+ bb_list[i].c_coord,bb_list[i].o_coord);
+
+ if(e < -0.5){
+ //it is an hbond... let's see, whether it is the best for i as acceptor
+ if(e < acceptor_two_energies[i]){
+ if(e < acceptor_one_energies[i]){
+ acceptor_two_energies[i] = acceptor_one_energies[i];
+ acceptor_for_two[i] = acceptor_for_one[i];
+ acceptor_one_energies[i] = e;
+ acceptor_for_one[i] = j;
+ }
+ else{
+ acceptor_two_energies[i] = e;
+ acceptor_for_two[i] = j;
+ }
+ }
+
+ //let's see, whether it is the best for j as donor
+ if(e < donor_two_energies[j]){
+ if(e < donor_one_energies[j]){
+ donor_two_energies[j] = donor_one_energies[j];
+ donor_for_two[j] = donor_for_one[j];
+ donor_one_energies[j] = e;
+ donor_for_one[j] = i;
+ }
+ else{
+ donor_two_energies[j] = e;
+ donor_for_two[j] = i;
+ }
+ }
+ }
+ }
+
+ //i as donor, j as acceptor
+ // note, that the first residue is not considered for donor
+ // and last element not as acceptor
+ if(bb_list[i].one_letter_code != 'P' && i > 0 && j < size-1){
+
+ e = DSSPHBondEnergy(h_positions[i],bb_list[i].n_coord,
+ bb_list[j].c_coord,bb_list[j].o_coord);
+
+ if(e < -0.5){
+ //it is an hbond... let's see, whether it is the best for i as donor
+ if(e < donor_two_energies[i]){
+ if(e < donor_one_energies[i]){
+ donor_two_energies[i] = donor_one_energies[i];
+ donor_for_two[i] = donor_for_one[i];
+ donor_one_energies[i] = e;
+ donor_for_one[i] = j;
+ }
+ else{
+ donor_two_energies[i] = e;
+ donor_for_two[i] = j;
+ }
+ }
+
+ //let's see, whether it is the best for j as acceptor
+ if(e < acceptor_two_energies[j]){
+ if(e < acceptor_one_energies[j]){
+ acceptor_two_energies[j] = acceptor_one_energies[j];
+ acceptor_for_two[j] = acceptor_for_one[j];
+ acceptor_one_energies[j] = e;
+ acceptor_for_one[j] = i;
+ }
+ else{
+ acceptor_two_energies[j] = e;
+ acceptor_for_two[j] = i;
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+
+ RawEstimateSS(ca_positions, 0, donor_for_one, donor_for_two,
+ acceptor_for_one, acceptor_for_two, ss_assignment);
+}
+
+}} //ns
diff --git a/loop/src/sec_struct.hh b/loop/src/sec_struct.hh
new file mode 100644
index 0000000000000000000000000000000000000000..b808265bfe6869c5c0dbaa8ec8d88499512f2448
--- /dev/null
+++ b/loop/src/sec_struct.hh
@@ -0,0 +1,63 @@
+#ifndef PROMOD_LOOP_SEC_STRUCT_HH
+#define PROMOD_LOOP_SEC_STRUCT_HH
+
+#include <promod3/loop/backbone.hh>
+#include <algorithm>
+#include <limits>
+#include <math.h>
+
+namespace promod3 { namespace loop {
+
+inline Real DSSPHBondEnergy(const geom::Vec3& h_pos, const geom::Vec3& n_pos,
+ const geom::Vec3& c_pos, const geom::Vec3& o_pos){
+ Real on = 1.0/geom::Distance(o_pos,n_pos);
+ Real ch = 1.0/geom::Distance(c_pos,h_pos);
+ Real oh = 1.0/geom::Distance(o_pos,h_pos);
+ Real cn = 1.0/geom::Distance(c_pos,n_pos);
+ return 27.888 * (on+ch-oh-cn);
+}
+
+//Raw estimation of secondary structure
+//
+// This function is not intended for Python export, since the
+// input has to be prepared carefully. It basically estimates
+// the secondary structure based on the hydrogen pattern as
+// described for the dssp tool. Some simplifications lead to
+// same estimation for roughly 98-99 % of the residues.
+// Please note, that there is absolutely no handling of chain
+// breaks!
+//
+// The idea is, that secondary structure estimation can be performed
+// for a small stretch in the environment of a full structure.
+// ca_positions contains the CA-positions of this stretch.
+// Every residue is considered to serve as donor/acceptor
+// for two other residues (note, that Proline cannot be a donor,
+// you have to consider that in the input data!!).
+// This acceptor/donor information is
+// given in the other four vectors. donor_for_one[i] means,
+// that residue i of the stretch is donor for the corresponding
+// entry, where a value of -1 means that i is NOT a donor at all.
+// The entry indices are based on the residue index in
+// the full structure. For the proper positioning of the stretch
+// in the full structure, the parameter start_idx is used.
+//
+//
+// Some points to consider when preparing the input data:
+// Only check for hbonds of residue i beginning at i+3
+// => at least 3 residue apart... Only consider HBonds
+// with DSSPHBondEnergy < -0.5
+
+
+void RawEstimateSS(const std::vector<geom::Vec3>& ca_positions,
+ int start_idx,
+ const std::vector<int>& donor_for_one,
+ const std::vector<int>& donor_for_two,
+ const std::vector<int>& acceptor_for_one,
+ const std::vector<int>& acceptor_for_two,
+ String& ss_assignment);
+
+void EstimateSS(const BackboneList& bb_list, String& ss_assignment);
+
+}} //ns
+
+#endif
diff --git a/loop/src/sidechain.cc b/loop/src/sidechain.cc
new file mode 100644
index 0000000000000000000000000000000000000000..fc7982bc5a51acda0af9ebcd3119bc1e752100bb
--- /dev/null
+++ b/loop/src/sidechain.cc
@@ -0,0 +1,16 @@
+#include <promod3/loop/sidechain.hh>
+
+namespace promod3 { namespace loop {
+
+
+Sidechain::Sidechain(uint num_heavy_atoms, uint num_hydrogens){
+ heavy_atom_positions_ = new geom::Vec3[num_heavy_atoms];
+ hydrogen_positions_ = new geom::Vec3[num_hydrogens];
+}
+
+Sidechain::~Sidechain(){
+ delete [] heavy_atom_positions_;
+ delete [] hydrogen_positions_;
+}
+
+}} //ns
diff --git a/loop/src/sidechain.hh b/loop/src/sidechain.hh
new file mode 100644
index 0000000000000000000000000000000000000000..7a63b37196210d02f2b4b4f24667e19cf2075b7b
--- /dev/null
+++ b/loop/src/sidechain.hh
@@ -0,0 +1,44 @@
+#ifndef PROMOD_LOOP_SIDECHAIN_HH
+#define PROMOD_LOOP_SIDECHAIN_HH
+
+#include <boost/shared_ptr.hpp>
+
+#include <promod3/sidechain/rotamer.hh>
+#include <promod3/sidechain/frame.hh>
+#include <promod3/loop/backbone.hh>
+
+
+
+namespace promod3 { namespace loop {
+
+class Sidechain;
+typedef boost::shared_ptr<Sidechain> SidechainPtr;
+
+class Sidechain{
+
+public:
+
+ Sidechain(uint num_heavy_atoms, uint num_hydrogens);
+
+ virtual ~Sidechain();
+
+ virtual void FillPositions(const promod3::sidechain::RRMRotamer& rot) = 0;
+
+ virtual void FillPositions(const promod3::sidechain::FRMRotamer& rot) = 0;
+
+ virtual void FillPositions(const promod3::sidechain::FrameResidue& frame_res) = 0;
+
+ virtual void FillPositions(const ost::mol::ResidueHandle& res) = 0;
+
+ virtual void ConstructHydrogens(const Backbone& bb) = 0;
+
+ virtual void SetResiduePositions(const ost::mol::ResidueHandle& res) = 0;
+
+protected:
+ geom::Vec3* heavy_atom_positions_;
+ geom::Vec3* hydrogen_positions_;
+};
+
+}} //ns
+
+#endif
diff --git a/loop/src/structure_db.cc b/loop/src/structure_db.cc
index 8a63ffd5dd2423415ec077a159754d7f0ecc7246..a136e90e1dfbdbb1efbdc563986fa5ba8b3f5e43 100644
--- a/loop/src/structure_db.cc
+++ b/loop/src/structure_db.cc
@@ -808,9 +808,7 @@ ost::seq::HMMPtr StructureDB::GenerateStructureProfile(const BackboneList& bb_li
Real frequencies[20];
for(uint i = 0; i < bb_list_size; ++i){
//sum up a value of one for every position
- //std::cerr<<"look at new column "<<i<<std::endl;
memset(frequencies,0,sizeof(Real)*20);
- //std::cerr<<"number of letters: "<<close_sequences[i].size()<<std::endl;
for(uint j = 0; j < close_sequences[i].size(); ++j){
int idx = ost::seq::HMMColumn::GetIndex(close_sequences[i][j]);
if(idx != -1) frequencies[idx] += 1.0;
@@ -827,9 +825,7 @@ ost::seq::HMMPtr StructureDB::GenerateStructureProfile(const BackboneList& bb_li
ost::seq::HMMColumn actual_col;
actual_col.SetOneLetterCode(bb_list[i].one_letter_code);
Real* hmm_col_data = actual_col.freqs_begin();
- //std::cerr<<"final frequencies: "<<std::endl;
for(uint j = 0; j < 20; ++j){
- //std::cerr<<j<<" "<<frequencies[j]<<std::endl;
hmm_col_data[j] = frequencies[j];
}
return_hmm->push_back(actual_col);
diff --git a/loop/tests/CMakeLists.txt b/loop/tests/CMakeLists.txt
index 846838f7fa9152dab8ef6b36ef9bc5ae0265b996..7b2d6138caabe9acb69af2ae3e6dd3ef2b989aaf 100644
--- a/loop/tests/CMakeLists.txt
+++ b/loop/tests/CMakeLists.txt
@@ -3,12 +3,16 @@ set(LOOP_UNIT_TESTS
test_torsion_sampler.cc
test_loop_closing.cc
test_loop_score.cc
+ test_psipred_prediction.cc
+ test_ss_assignment.cc
tests.cc
)
set(LOOP_TEST_DATA
data/4nyk.pdb
data/3DEFA.pdb
+ data/1akyA.horiz
+ data/1A88A.hhm
)
promod3_unittest(MODULE loop
diff --git a/loop/tests/data/1A88A.hhm b/loop/tests/data/1A88A.hhm
new file mode 100644
index 0000000000000000000000000000000000000000..eb3dc68c20708835ecc19322b6cf46e9bb1066e3
--- /dev/null
+++ b/loop/tests/data/1A88A.hhm
@@ -0,0 +1,869 @@
+HHsearch 1.5
+NAME 9ec8ef8344f0798f4d5e69635f049d78
+FAM
+FILE 9ec8ef8344f0798f4d5e69635f049d78
+COM /import/bc2/soft/app/hhsuite/2.0.16/Linux/bin/hhmake -i <118 characters> -o <118 characters>
+DATE Fri Sep 6 18:12:11 2013
+LENG 275 match states, 275 columns in multiple alignment
+FILT 141 out of 1335 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100)
+NEFF 11.1
+SEQ
+>ss_pred PSIPRED predicted secondary structure
+CEEEECCCCEEEEEEECCCCCCEEEEECCCCCCHHHHHHHHHHHHHCCCEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCEEEEEECHHHH
+HHHHHHHHCCHHHCCEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
+HHHCCCHHHHHHHCCCCEEEEEECCCCCCCHHHHHHHHHHHCCCCEEEEECCCCCCHHHHCHHHHHHHHHHHHHC
+>ss_conf PSIPRED confidence values
+9599149928999981588998699989999977799999999986898899966899899999988899999999999999981999869999888899
+9999998638011138999878761000133354323278999999998764899998631211110134310102789999999863110688999999
+751012677885389998999958998669899999999848998899989998644552999999999999849
+>Consensus
+xxxxxxxgxxlxxxxxgxxxxxxivllHGxxxxxxxxxxxxxxlxxxxxxvxxxDxxGxGxSxxxxxxxxxxxxxxdlxxxlxxlxxxxxxlvGhSxGgx
+xxxxxxaxxxxxxixxlvlxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+xxxxxxxxxxlxxixxPxlxixgxxDxxxxxxxxxxxxxxxxxxxxxxxxxxxgHxxxxxxxxxxxxxixxflxx
+>9ec8ef8344f0798f4d5e69635f049d78
+GTVTTSDGTNIFYKDWGPRDGLPVVFHHGWPLSADDWDNQMLFFLSHGYRVIAHDRRGHGRSDQPSTGHDMDTYAADVAALTEALDLRGAVHIGHSTGGG
+EVARYVARAEPGRVAKAVLVSAVPPVMVKSDTNPDGLPLEVFDEFRAALAANRAQFYIDVPSGPFYGFNREGATVSQGLIDHWWLQGMMGAANAHYECIA
+AFSETDFTDDLKRIDVPVLVAHGTDDQVVPYADAAPKSAELLANATLKSYEGLPHGMLSTHPEVLNPDLLAFVKS
+>gi|68171462|ref|ZP_00544849.1| Alpha/beta hydrolase fold [Ehrlichia chaffeensis str. Sapulpa]gi|88658364|ref|YP_507044.1| putative hydrolase [Ehrlichia chaffeensis str. Arkansas]gi|67999123|gb|EAM85786.1| Alpha/beta hydrolase fold [Ehrlichia chaffeensis str. Sapulpa]gi|88599821|gb|ABD45290.1| putative hydrolase [Ehrlichia chaffeensis str. Arkansas]
+-LNISHLQeKFIMHYNYTnSPSSNYLICVHGITRNSRDFDYLANILS-SDYKIICPDIVGRGKSSWLEDySlYNYLTYCKSIIYLLKHLKIDKVDFLGTS
+MGGIIGMYLAAYFP-NLINKLIINDIG----------PA-IKVSALEKISKHINinpifNTIteaEIYIKKLLC-NF-S-IDQEDHWQHIIKHSIIQNPN
+-KTYSLAVDPkigiafNKEINCIKdtdawtIWDIWEKIQSRILVIRGSLSNILTKTTL-NKMLLSKQYIDFIEYPNIGHAPALMSNNQIQD-IRNWLL-
+>gi|254240840|ref|ZP_04934162.1| hypothetical protein PA2G_01514 [Pseudomonas aeruginosa 2192]gi|126194218|gb|EAZ58281.1| hypothetical protein PA2G_01514 [Pseudomonas aeruginosa 2192]
+--------------------------------------------LPAWLAVRPVELPGRGARMAEPLQTDLASLAQQLARELHDEVrQGPYAMLGHSLGA
+LlacEVLYALRELGCPTPLGFFACGTAAP-SRRAEY-DRG-FAEP---------KSDAELIADLR--------DLQGTPEEVLGNRELMSLTLPILRADF
+LLCGSYRHQ----RRPPLACPIRTLGGRED-KASEEQLLAWAEETRSGFGLELFDGG-HFFIHQREAEVLAVVE-----
+>gi|302776726|ref|XP_002971512.1| hypothetical protein SELMODRAFT_172238 [Selaginella moellendorffii]gi|300160644|gb|EFJ27261.1| hypothetical protein SELMODRAFT_172238 [Selaginella moellendorffii]
+-------------------------------------KYLVSRVRNIGWHTVVFNSRGCSdspvTSPKFYSASFTEDLRQVVRFVAYRFPESRIYAVGWS
+LGANILVRYLGQ--EGEnciLSGAVSLCNPFDLVVADEDFRKGFNNiydkSLATSLRTIFRKHA--ALFEEIGG---EYNIPLAANAKTVRqfDEGLTRV
+SFGYRSVD----EYYADASSSKSIEHVKVPLFCIQAANDPIAP---------------------------------------------
+#
+NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665
+HMM A C D E F G H I K L M N P Q R S T V W Y
+ M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D
+ 0 * * 0 * 0 * * * *
+G 1 * * * * * 996 * * * * 1972 * * * * 2037 * * * * 1
+ 0 * * * * * * 2838 0 0
+
+T 2 * * * 4056 2327 * 3938 4866 4909 4125 * * 5124 5031 4063 3499 3185 * * 2102 2
+ 0 * * * * * * 8843 0 0
+
+V 3 4516 * * * 2079 * 4638 2746 5558 2395 * * * 5598 4583 5711 5415 3414 4653 3634 3
+ 31 5572 * 0 * * * 9738 1000 0
+
+T 4 4266 5829 4140 3808 4129 * 4958 4342 3207 3808 4854 5787 4700 5006 4810 3598 3075 3246 * 5689 4
+ 0 * * * * * * 9990 0 0
+
+T 5 4422 * 4539 3793 5000 5201 5971 4250 4012 3393 5911 4082 5927 * * 2983 2021 4411 * 4567 5
+ 88 5975 4521 1000 1000 * * 10168 1001 0
+
+S 6 3445 5077 5977 4405 4547 4332 4952 * 4124 4192 6128 3516 3157 6066 4448 2532 5050 4017 6285 5235 6
+ 66 5049 6080 1575 590 602 1552 10235 1197 1351
+
+D 7 3610 * 1385 5187 6206 3282 * * 5130 * * 3046 4664 3438 4669 4757 5547 * * 6324 7
+ 39 6171 6274 0 * 969 1032 10301 1023 1190
+
+G 8 5073 * 4335 4295 * 865 5280 * 4941 5475 6222 4347 5459 6494 5279 3672 5248 6271 * * 8
+ 104 4046 6755 1700 530 1022 979 10424 1672 1176
+
+T 9 4066 4947 4822 4456 4942 4082 4392 4837 4777 2700 4800 6361 6500 4834 3924 5323 4201 2707 6593 4073 9
+ 108 5395 4373 1224 806 1096 910 10560 1187 1160
+
+N 10 6685 * 3739 3811 6229 5536 6484 5478 2895 3902 6497 3684 4800 4763 2764 3491 3273 3972 * 6738 10
+ 74 4605 6774 2429 296 810 1219 10607 1710 1721
+
+I 11 * * * * 4611 * 5003 2159 * 1346 4480 * 6531 5624 * 5596 4253 2918 6620 5708 11
+ 44 5662 6559 1613 571 1433 667 10709 1170 1386
+
+F 12 3223 6690 5669 5641 3443 4945 2361 6623 4694 6638 * 5366 6299 6637 3245 3348 3785 5006 6437 3325 12
+ 52 4807 * 384 2098 1541 608 10737 1449 1363
+
+Y 13 4015 5630 5477 * 3374 4169 5607 5215 * 4239 6410 5702 * 6319 * 5442 6665 3159 3755 1393 13
+ 82 4877 5548 1239 795 * 0 10778 1404 1176
+
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+ 13 6808 * 0 * 885 1125 11123 1000 1177
+
+E 263 3753 * 2587 1814 * 6704 4526 6939 3430 5385 * 5013 5260 3198 4308 4571 5460 5969 * * 263
+ 44 5908 6202 2400 303 * 0 11134 1213 1000
+
+V 264 2987 * 4360 2556 5373 4814 6876 3851 3312 3689 * 4611 5329 3343 4328 5119 4668 4986 6899 5858 264
+ 11 7012 * 0 * 587 1580 11134 1166 1344
+
+L 265 5895 5938 * * 2231 6837 6803 3675 * 2699 7259 * 6866 6892 5697 6787 3866 1915 6604 3210 265
+ 22 * 6037 1000 1000 0 * 11092 1000 1000
+
+N 266 2247 * 5992 5894 4812 4600 6816 4305 6690 4387 5068 2914 * 4774 4270 4077 3648 3530 * 3529 266
+ 23 7013 6995 3700 115 0 * 11041 1000 1152
+
+P 267 3024 * 3044 2691 * 5845 5700 5179 3404 * 6844 3966 4559 2831 3513 4300 5346 5400 * * 267
+ 23 6738 7218 1585 585 0 * 11028 1019 1000
+
+D 268 2600 5791 3739 3661 5744 4737 4477 3526 5210 3128 6922 5809 6844 3972 3993 4884 4723 4183 5238 5709 268
+ 13 6762 * 2807 222 * 0 11025 1000 1000
+
+L 269 4181 6481 * * 3988 * 6708 1665 * 1887 4755 * * * * * 5623 2390 * 5192 269
+ 26 5810 * 1357 714 * 0 10939 1180 1000
+
+L 270 4146 * 3826 3591 5757 4446 6764 3312 3445 2254 6633 4416 * 4881 3214 5715 4385 5790 6536 5651 270
+ 0 * * * * * 0 10939 0 1000
+
+A 271 3523 * 2805 2564 * 5299 * 6639 3727 4903 6533 3562 6634 3894 3248 3141 4715 5838 * 6733 271
+ 14 * 6699 * * * 0 10890 0 1000
+
+F 272 3917 5018 6827 * 938 * 6529 4662 * 4367 * * * * * * 4968 5594 2439 4789 272
+ 0 * * 2322 322 0 * 10808 1000 1163
+
+V 273 4599 5452 6385 * 3697 * * 1990 * 1137 4956 6476 * 6372 6514 6534 4867 5114 * * 273
+ 36 5349 * 2411 300 * * 10640 1192 0
+
+K 274 3763 6333 3453 3017 6339 3835 5302 6307 3384 4725 6189 3835 5389 3163 3534 3676 4346 6371 * * 274
+ 112 3747 * 2000 415 * * 10532 1024 0
+
+S 275 2375 * 3914 * * 4008 * * 2405 * * * * 3017 4171 3063 2387 * * * 275
+ 0 * * 0 * * * 6498 0 0
+
+//
diff --git a/loop/tests/data/1akyA.horiz b/loop/tests/data/1akyA.horiz
new file mode 100644
index 0000000000000000000000000000000000000000..1564e9eccda74130990c1eee14010c1a554f3edc
--- /dev/null
+++ b/loop/tests/data/1akyA.horiz
@@ -0,0 +1,25 @@
+# PSIPRED HFORMAT (PSIPRED V3.2)
+
+Conf: 960499976999993515779998829960155289999998299434999999763999
+Pred: CCCEEEEECCCCCCCCCHHHHHHHHHCCCCCCHHHHHHHHHHCCCHHHHHHHHHHHCCCC
+ AA: ESIRMVLIGPPGAGKGTQAPNLQERFHAAHLATGDMLRSQIAKGTQLGLEAKKIMDQGGL
+ 10 20 30 40 50 60
+
+
+Conf: 628999999999741499987770111899998989999999997299976799984396
+Pred: CHHHHHHHHHHHHHHCCCCCCCCEEECCCCCCHHHHHHHHHHHHHCCCCCCEEEEEECCH
+ AA: VSDDIMVNMIKDELTNNPACKNGFILDGFPRTIPQAEKLDQMLKEQGTPLEKAIELKVDD
+ 70 80 90 100 110 120
+
+
+Conf: 899999754532379996232012799878877787976321589999999999999995
+Pred: HHHHHHHHCCCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHH
+ AA: ELLVARITGRLIHPASGRSYHKIFNPPKEDMKDDVTGEALVQRSDDNADALKKRLAAYHA
+ 130 140 150 160 170 180
+
+
+Conf: 05046999966197788307999578999999973459
+Pred: CCCHHHHHHHHCCCEEEECCCCCHHHHHHHHHHHHCCC
+ AA: QTEPIVDFYKKTGIWAGVDASQPPATVWADILNKLGKN
+ 190 200 210
+
diff --git a/loop/tests/test_loop_score.cc b/loop/tests/test_loop_score.cc
index 3d2c46eb96d60aca901dcaaf62132ff2909a4aa3..88cab4c4631badbe111fcd553b328de402d1ba4c 100644
--- a/loop/tests/test_loop_score.cc
+++ b/loop/tests/test_loop_score.cc
@@ -14,8 +14,6 @@ BOOST_AUTO_TEST_SUITE( loop );
using namespace promod3::loop;
-
-
BOOST_AUTO_TEST_CASE(test_loop_score_set_env){
//load an entity to test...
@@ -87,10 +85,13 @@ BOOST_AUTO_TEST_CASE(test_loop_score_potential_terms){
bb_list.push_back(new_bb);
}
- //check whether error gets thrown when no potentials are set
+ //check whether error gets thrown when no scores are set
BOOST_CHECK_THROW(scorer.CalculateCBetaScore(bb_list,214,0),promod3::Error);
BOOST_CHECK_THROW(scorer.CalculateCBPackingScore(bb_list,214,0),promod3::Error);
BOOST_CHECK_THROW(scorer.CalculateTorsionScore(bb_list,214,0),promod3::Error);
+ BOOST_CHECK_THROW(scorer.CalculateReducedScore(bb_list,214,0),promod3::Error);
+ BOOST_CHECK_THROW(scorer.CalculateHBondScore(bb_list,214,0),promod3::Error);
+ BOOST_CHECK_THROW(scorer.CalculateSSAgreementScore(bb_list,214,0),promod3::Error);
//load scorer with properly set potentials
promod3::loop::BackboneLoopScorerPtr standard_scorer = LoadBackboneLoopScorer();
@@ -101,17 +102,45 @@ BOOST_AUTO_TEST_CASE(test_loop_score_potential_terms){
BOOST_CHECK_THROW(standard_scorer->CalculateCBetaScore(bb_list,214,1),promod3::Error);
BOOST_CHECK_THROW(standard_scorer->CalculateCBPackingScore(bb_list,214,1),promod3::Error);
BOOST_CHECK_THROW(standard_scorer->CalculateTorsionScore(bb_list,214,1),promod3::Error);
+ BOOST_CHECK_THROW(standard_scorer->CalculateReducedScore(bb_list,214,1),promod3::Error);
+ BOOST_CHECK_THROW(standard_scorer->CalculateClashScore(bb_list,214,1),promod3::Error);
+ BOOST_CHECK_THROW(standard_scorer->CalculateHBondScore(bb_list,214,1),promod3::Error);
+ BOOST_CHECK_THROW(standard_scorer->CalculateSSAgreementScore(bb_list,214,1),promod3::Error);
+
BOOST_CHECK_THROW(standard_scorer->CalculateCBetaScore(bb_list,214,-1),promod3::Error);
BOOST_CHECK_THROW(standard_scorer->CalculateCBPackingScore(bb_list,214,-1),promod3::Error);
BOOST_CHECK_THROW(standard_scorer->CalculateTorsionScore(bb_list,214,-1),promod3::Error);
+ BOOST_CHECK_THROW(standard_scorer->CalculateReducedScore(bb_list,214,-1),promod3::Error);
+ BOOST_CHECK_THROW(standard_scorer->CalculateClashScore(bb_list,214,-1),promod3::Error);
+ BOOST_CHECK_THROW(standard_scorer->CalculateHBondScore(bb_list,214,-1),promod3::Error);
+ BOOST_CHECK_THROW(standard_scorer->CalculateSSAgreementScore(bb_list,214,-1),promod3::Error);
+
//invalid residues
BOOST_CHECK_THROW(standard_scorer->CalculateCBetaScore(bb_list,1000,0),promod3::Error);
BOOST_CHECK_THROW(standard_scorer->CalculateCBPackingScore(bb_list,1000,0),promod3::Error);
BOOST_CHECK_THROW(standard_scorer->CalculateTorsionScore(bb_list,1000,0),promod3::Error);
+ BOOST_CHECK_THROW(standard_scorer->CalculateReducedScore(bb_list,1000,0),promod3::Error);
+ BOOST_CHECK_THROW(standard_scorer->CalculateClashScore(bb_list,1000,0),promod3::Error);
+ BOOST_CHECK_THROW(standard_scorer->CalculateHBondScore(bb_list,1000,0),promod3::Error);
+ BOOST_CHECK_THROW(standard_scorer->CalculateSSAgreementScore(bb_list,1000,0),promod3::Error);
+
+ BOOST_CHECK_THROW(standard_scorer->CalculateCBetaScore(bb_list,0,0),promod3::Error);
+ BOOST_CHECK_THROW(standard_scorer->CalculateCBPackingScore(bb_list,0,0),promod3::Error);
+ BOOST_CHECK_THROW(standard_scorer->CalculateTorsionScore(bb_list,0,0),promod3::Error);
+ BOOST_CHECK_THROW(standard_scorer->CalculateReducedScore(bb_list,0,0),promod3::Error);
+ BOOST_CHECK_THROW(standard_scorer->CalculateClashScore(bb_list,0,0),promod3::Error);
+ BOOST_CHECK_THROW(standard_scorer->CalculateHBondScore(bb_list,0,0),promod3::Error);
+ BOOST_CHECK_THROW(standard_scorer->CalculateSSAgreementScore(bb_list,0,0),promod3::Error);
+
BOOST_CHECK_THROW(standard_scorer->CalculateCBetaScore(bb_list,-1,0),promod3::Error);
BOOST_CHECK_THROW(standard_scorer->CalculateCBPackingScore(bb_list,-1,0),promod3::Error);
BOOST_CHECK_THROW(standard_scorer->CalculateTorsionScore(bb_list,-1,0),promod3::Error);
+ BOOST_CHECK_THROW(standard_scorer->CalculateReducedScore(bb_list,-1,0),promod3::Error);
+ BOOST_CHECK_THROW(standard_scorer->CalculateClashScore(bb_list,-1,0),promod3::Error);
+ BOOST_CHECK_THROW(standard_scorer->CalculateHBondScore(bb_list,-1,0),promod3::Error);
+ BOOST_CHECK_THROW(standard_scorer->CalculateSSAgreementScore(bb_list,-1,0),promod3::Error);
+
//we check the energy calculation after saving/loading, so this is tested as well...
standard_scorer->Save("test_loop_scorer.dat");
@@ -120,14 +149,56 @@ BOOST_AUTO_TEST_CASE(test_loop_score_potential_terms){
loaded_scorer->Initialize(seqres);
loaded_scorer->SetEnvironment(test_ent);
+ //generate a psipred object and attach it to the scorer to calculate the
+ //ss_agreement score
+ String psipred_ss = "CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCCCHHHHHHH";
+ psipred_ss += "HHCCCCCCCCCCCCEEEEEEEEEEECCCEEEEEEECCCCCCCCCHHHHHHHHHHHHHCCCC";
+ psipred_ss += "CCEEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCCCCCCHHHHHHH";
+ psipred_ss += "HHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCEEECCCCCEECCCCHHHHHHHHHHHH";
+ psipred_ss += "HHHHHCCCCCCCCHHHHHHCCCCC";
+
+ int psipred_conf[] = {9,6,4,0,3,4,1,3,1,1,4,6,7,7,8,9,9,9,9,9,9,9,9,9,9,9,9,9,
+ 8,8,6,1,5,8,8,7,2,8,9,9,9,8,8,9,9,9,9,8,8,9,9,9,9,9,9,9,
+ 6,7,8,7,6,5,3,3,5,6,6,7,5,4,6,8,8,8,9,9,9,9,8,4,1,8,6,6,
+ 8,9,9,9,9,7,9,9,8,4,0,1,2,2,0,3,7,9,9,9,9,9,9,9,9,8,6,3,
+ 3,4,7,9,9,8,8,9,9,9,9,8,4,7,8,6,6,5,5,4,7,7,9,9,9,9,9,9,
+ 9,9,9,9,8,3,4,2,4,5,7,8,5,8,9,9,9,9,8,6,0,0,1,7,7,4,4,4,
+ 6,8,9,9,9,9,9,9,8,7,9,9,9,9,9,9,9,9,9,7,3,3,0,0,0,1,1,2,
+ 2,1,1,3,5,8,6,5,8,9,8,6,2,4,5,2,3,5,5,6,8,8,6,3,0,0,7,7,
+ 7,2,5,8,9,9,9,9,9,9,9,9,9,9,9,9,9,8,2,7,9,9,6,3,3,1,7,7,
+ 7,7,7,5,3,0,2,4,7,9};
+
+ std::vector<char> v_psipred_ss;
+ std::vector<int> v_psipred_conf;
+
+ for(int i = 0; i < 262; ++i){
+ v_psipred_ss.push_back(psipred_ss[i]);
+ v_psipred_conf.push_back(psipred_conf[i]);
+ }
+
+ PsipredPredictionPtr psipred_prediction(new PsipredPrediction(v_psipred_ss,v_psipred_conf));
+ loaded_scorer->SetPsipredPrediction(psipred_prediction);
+ //let's calculate the scores
Real cb_score = loaded_scorer->CalculateCBetaScore(bb_list,214,0);
Real cb_packing_score = loaded_scorer->CalculateCBPackingScore(bb_list,214,0);
Real torsion_score = loaded_scorer->CalculateTorsionScore(bb_list,214,0);
-
- BOOST_CHECK_CLOSE(cb_score,0.00311393,Real(1e-3));
- BOOST_CHECK_CLOSE(cb_packing_score,-0.657945,Real(1e-3));
- BOOST_CHECK_CLOSE(torsion_score,-0.143922,Real(1e-3));
+ Real hbond_score = loaded_scorer->CalculateHBondScore(bb_list,214,0);
+ Real ss_agreement_score = loaded_scorer->CalculateSSAgreementScore(bb_list,214,0);
+ Real reduced_score = loaded_scorer->CalculateReducedScore(bb_list,214,0);
+ Real clash_score = loaded_scorer->CalculateClashScore(bb_list,214,0);
+
+
+ //the following target values have been calculated externally from promod
+ //with qmean and should be the reference, since the qmean potentials are quiet
+ //well tested
+ BOOST_CHECK_CLOSE(cb_score,-0.00178876915015,Real(1e-3));
+ BOOST_CHECK_CLOSE(cb_packing_score,-0.657944619656,Real(1e-3));
+ BOOST_CHECK_CLOSE(torsion_score,-0.143922114538,Real(1e-3));
+ BOOST_CHECK_CLOSE(hbond_score,-0.79220325417,Real(1e-3));
+ BOOST_CHECK_CLOSE(ss_agreement_score,0.566874,Real(1e-3));
+ BOOST_CHECK_CLOSE(reduced_score,-0.0734949707985,Real(1e-3));
+ BOOST_CHECK_CLOSE(clash_score,0.0,Real(1e-3));
}
diff --git a/loop/tests/test_psipred_prediction.cc b/loop/tests/test_psipred_prediction.cc
new file mode 100644
index 0000000000000000000000000000000000000000..7053e5a1dc6eaf2f60ab062fca6765b0d13e632e
--- /dev/null
+++ b/loop/tests/test_psipred_prediction.cc
@@ -0,0 +1,158 @@
+#include <promod3/loop/psipred_prediction.hh>
+#include <promod3/core/message.hh>
+#define BOOST_TEST_DYN_LINK
+#include <boost/test/unit_test.hpp>
+#include <boost/test/auto_unit_test.hpp>
+
+BOOST_AUTO_TEST_SUITE( loop );
+using namespace promod3::loop;
+
+BOOST_AUTO_TEST_CASE(test_loading_from_hhm){
+
+ PsipredPredictionPtr p = PsipredPrediction::FromHHM("data/1A88A.hhm");
+
+ String expected_prediction = "CEEEECCCCEEEEEEECCCCCCEEEEECCCCCCHHHHHHHHHHHHH";
+ expected_prediction += "CCCEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCEEEEEECHH";
+ expected_prediction += "HHHHHHHHHHCCHHHCCEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHH";
+ expected_prediction += "HHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH";
+ expected_prediction += "HCCCHHHHHHHCCCCEEEEEECCCCCCCHHHHHHHHHHHCCCCEEEEECCCC";
+ expected_prediction += "CCHHHHCHHHHHHHHHHHHHC";
+
+ int expected_confidence[] = {9,5,9,9,1,4,9,9,2,8,9,9,9,9,8,1,5,8,8,9,9,8,6,9,
+ 9,9,8,9,9,9,9,9,7,7,7,9,9,9,9,9,9,9,9,9,8,6,8,9,
+ 8,8,9,9,9,6,6,8,9,9,8,9,9,9,9,9,9,8,8,8,9,9,9,9,
+ 9,9,9,9,9,9,9,9,9,9,9,8,1,9,9,9,8,6,9,9,9,9,8,8,
+ 8,8,9,9,9,9,9,9,9,9,8,6,3,8,0,1,1,1,3,8,9,9,9,8,
+ 7,8,7,6,1,0,0,0,1,3,3,3,5,4,3,2,3,2,7,8,9,9,9,9,
+ 9,9,9,9,8,7,6,4,8,9,9,9,9,8,6,3,1,2,1,1,1,1,0,1,
+ 3,4,3,1,0,1,0,2,7,8,9,9,9,9,9,9,9,8,6,3,1,1,0,6,
+ 8,8,9,9,9,9,9,9,7,5,1,0,1,2,6,7,7,8,8,5,3,8,9,9,
+ 9,8,9,9,9,9,5,8,9,9,8,6,6,9,8,9,9,9,9,9,9,9,9,8,
+ 4,8,9,9,8,8,9,9,9,8,9,9,9,8,6,4,4,5,5,2,9,9,9,9,
+ 9,9,9,9,9,9,9,9,8,4,9};
+
+ BOOST_CHECK(p->size() == expected_prediction.size());
+
+ for(uint i = 0; i < expected_prediction.size(); ++i){
+ BOOST_CHECK(expected_prediction[i] == p->GetPrediction(i));
+ BOOST_CHECK(expected_confidence[i] == p->GetConfidence(i));
+ }
+}
+
+BOOST_AUTO_TEST_CASE(test_loading_from_horiz){
+
+ PsipredPredictionPtr p = PsipredPrediction::FromHoriz("data/1akyA.horiz");
+
+ String expected_prediction = "CCCEEEEECCCCCCCCCHHHHHHHHHCCCCCCHHHHHHHHHHCCCH";
+ expected_prediction += "HHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCCCCCEEECCCCCCHHHHHH";
+ expected_prediction += "HHHHHHHCCCCCCEEEEEECCHHHHHHHHHCCCCCCCCCCEEECCCCCCCCC";
+ expected_prediction += "CCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHCCCEEEECCCC";
+ expected_prediction += "CHHHHHHHHHHHHCCC";
+
+ int expected_confidence[] = {9,6,0,4,9,9,9,7,6,9,9,9,9,9,3,5,1,5,7,7,9,9,9,8,
+ 8,2,9,9,6,0,1,5,5,2,8,9,9,9,9,9,9,8,2,9,9,4,3,4,
+ 9,9,9,9,9,9,7,6,3,9,9,9,6,2,8,9,9,9,9,9,9,9,9,9,
+ 7,4,1,4,9,9,9,8,7,7,7,0,1,1,1,8,9,9,9,9,8,9,8,9,
+ 9,9,9,9,9,9,9,9,7,2,9,9,9,7,6,7,9,9,9,8,4,3,9,6,
+ 8,9,9,9,9,9,7,5,4,5,3,2,3,7,9,9,9,6,2,3,2,0,1,2,
+ 7,9,9,8,7,8,8,7,7,7,8,7,9,7,6,3,2,1,5,8,9,9,9,9,
+ 9,9,9,9,9,9,9,9,9,9,9,5,0,5,0,4,6,9,9,9,9,6,6,1,
+ 9,7,7,8,8,3,0,7,9,9,9,5,7,8,9,9,9,9,9,9,9,7,3,4,
+ 5,9};
+
+ BOOST_CHECK(p->size() == expected_prediction.size());
+
+ for(uint i = 0; i < expected_prediction.size(); ++i){
+ BOOST_CHECK(expected_prediction[i] == p->GetPrediction(i));
+ BOOST_CHECK(expected_confidence[i] == p->GetConfidence(i));
+ }
+}
+
+BOOST_AUTO_TEST_CASE(test_init){
+
+
+ std::vector<char> invalid_pred;
+ std::vector<int> invalid_conf_one;
+ std::vector<int> invalid_conf_two;
+ std::vector<char> valid_pred;
+ std::vector<int> valid_conf;
+ std::vector<char> long_pred;
+
+ invalid_pred.push_back('H');
+ invalid_pred.push_back('X');
+ invalid_conf_one.push_back(4);
+ invalid_conf_one.push_back(-1);
+ invalid_conf_two.push_back(4);
+ invalid_conf_two.push_back(10);
+ valid_pred.push_back('C');
+ valid_pred.push_back('E');
+ valid_conf.push_back(1);
+ valid_conf.push_back(2);
+ long_pred.push_back('E');
+ long_pred.push_back('C');
+ long_pred.push_back('H');
+
+ BOOST_CHECK_THROW(PsipredPrediction(invalid_pred,valid_conf),promod3::Error);
+ BOOST_CHECK_THROW(PsipredPrediction(valid_pred,invalid_conf_one),promod3::Error);
+ BOOST_CHECK_THROW(PsipredPrediction(valid_pred,invalid_conf_two),promod3::Error);
+ BOOST_CHECK_THROW(PsipredPrediction(long_pred,valid_conf),promod3::Error);
+ BOOST_CHECK_NO_THROW(PsipredPrediction(valid_pred,valid_conf));
+}
+
+BOOST_AUTO_TEST_CASE(test_remaining_stuff){
+
+ std::vector<char> pred;
+ std::vector<int> conf;
+
+ pred.push_back('H');
+ pred.push_back('E');
+ pred.push_back('C');
+ pred.push_back('E');
+
+ conf.push_back(9);
+ conf.push_back(2);
+ conf.push_back(3);
+ conf.push_back(5);
+
+ PsipredPrediction p(pred,conf);
+
+ //check, whether the add functionality throws the expected exceptions
+ BOOST_CHECK(p.size() == 4);
+ BOOST_CHECK_THROW(p.Add('X',4),promod3::Error);
+ BOOST_CHECK_THROW(p.Add('H',-1),promod3::Error);
+ BOOST_CHECK_THROW(p.Add('H',10),promod3::Error);
+ BOOST_CHECK_NO_THROW(p.Add('H',5));
+
+ //Check, wether the Getter functions properly check the indices
+ BOOST_CHECK_THROW(p.GetPrediction(-1),promod3::Error);
+ BOOST_CHECK_THROW(p.GetPrediction(10),promod3::Error);
+
+ BOOST_CHECK_THROW(p.GetConfidence(-1),promod3::Error);
+ BOOST_CHECK_THROW(p.GetConfidence(10),promod3::Error);
+
+ //check the size function
+ BOOST_CHECK(p.size() == 5);
+
+ //lets see whether the expected stuff is filled in...
+ String expected_pred = "HECEH";
+ int expected_conf[] = {9,2,3,5,5};
+
+ for(int i = 0; i < 5; ++i){
+ BOOST_CHECK(expected_pred[i] == p.GetPrediction(i));
+ BOOST_CHECK(expected_conf[i] == p.GetConfidence(i));
+ }
+
+ //Check, whether the extract function does the right thing
+ BOOST_CHECK_THROW(p.Extract(1,1),promod3::Error);
+ BOOST_CHECK_THROW(p.Extract(1,10),promod3::Error);
+ BOOST_CHECK_THROW(p.Extract(3,1),promod3::Error);
+
+ PsipredPredictionPtr p_two = p.Extract(1,3);
+ BOOST_CHECK(p_two->size() == 2);
+ BOOST_CHECK(p_two->GetPrediction(0) == 'E');
+ BOOST_CHECK(p_two->GetPrediction(1) == 'C');
+ BOOST_CHECK(p_two->GetConfidence(0) == 2);
+ BOOST_CHECK(p_two->GetConfidence(1) == 3);
+}
+
+BOOST_AUTO_TEST_SUITE_END();
diff --git a/loop/tests/test_ss_assignment.cc b/loop/tests/test_ss_assignment.cc
new file mode 100644
index 0000000000000000000000000000000000000000..3a922811e06e00d5342c43759646cfdc1c717d1c
--- /dev/null
+++ b/loop/tests/test_ss_assignment.cc
@@ -0,0 +1,50 @@
+#include <promod3/loop/sec_struct.hh>
+#include <promod3/core/message.hh>
+#define BOOST_TEST_DYN_LINK
+#include <boost/test/unit_test.hpp>
+#include <boost/test/auto_unit_test.hpp>
+
+#include <ost/io/mol/pdb_reader.hh>
+#include <ost/conop/heuristic.hh>
+#include <ost/mol/builder.hh>
+
+BOOST_AUTO_TEST_SUITE( loop );
+
+using namespace promod3::loop;
+
+BOOST_AUTO_TEST_CASE(test_ss_assignment){
+
+ //load an entity to test...
+ String pdb_name = "data/3DEFA.pdb";
+
+ ost::io::PDBReader reader(pdb_name, ost::io::IOProfile());
+ ost::mol::EntityHandle test_ent = ost::mol::CreateEntity();
+ reader.Import(test_ent);
+
+ ost::conop::ProcessorPtr processor(new ost::conop::HeuristicProcessor(false,true,true,true,ost::conop::CONOP_SILENT));
+ processor->Process(test_ent);
+
+ ost::mol::ResidueHandleList res_list = test_ent.GetResidueList();
+
+ String sequence(res_list.size(),'X');
+
+ for(uint i = 0; i < res_list.size(); ++i){
+ sequence[i] = res_list[i].GetOneLetterCode();
+ }
+
+ BackboneList bb_list(sequence,res_list);
+
+ String ss_estimate;
+ EstimateSS(bb_list,ss_estimate);
+
+ String expected_output = "CBCHHHHTSCHHHHHHHHHHHHHHHHTTCCEEEEEEEECTTSSHHHHHHH";
+ expected_output += "HHTSCCSCCCSSCCSCCCEEEEEBETTEEEEEEECCCSEETTEECHHHHHHHHHHT";
+ expected_output += "TTCEECEEEEEEESSCSCCCHHHHHHHHHHHHHHCGGGGGGEEEEEECTTCCCSTT";
+ expected_output += "CCHHHHHHHHHHHHHHHHHHHHTCCHHHHHHHCCEEEECCCCTTCCBCTTSCEECT";
+ expected_output += "TSCBHHHHHHHHHHHHHTSCSCCEEC";
+
+ BOOST_CHECK(ss_estimate == expected_output);
+}
+
+
+BOOST_AUTO_TEST_SUITE_END();
diff --git a/modelling/pymod/_closegaps.py b/modelling/pymod/_closegaps.py
index 2a13fc64d96874d22f603078e5489716742c1261..65ff9bf5390736187c7a5090e914ae46e77a5f56 100644
--- a/modelling/pymod/_closegaps.py
+++ b/modelling/pymod/_closegaps.py
@@ -121,16 +121,17 @@ def CloseSmallDeletions(mhandle, scorer, extension_steps=9, clash_thresh=1.0,
# gather residues for backbone relaxation, check that we get a
# bunch of actual residues, otherwise jump to next extension
res_list = list()
- current_resnum = current_gap.before.GetNumber()
- after_resnum = current_gap.after.GetNumber()
+ n_stem_resnum = current_gap.before.GetNumber()
+ c_stem_resnum = current_gap.after.GetNumber()
+ idx = 0
found_residues = True
- while current_resnum <= after_resnum:
- res = current_chain.FindResidue(current_resnum)
+ while n_stem_resnum + idx <= c_stem_resnum:
+ res = current_chain.FindResidue(n_stem_resnum+idx)
if not res.IsValid():
found_residues = False
break
res_list.append(res)
- current_resnum += 1
+ idx += 1
if not found_residues:
continue
# backbone relaxation, for now we allow 300 steps or stop at
@@ -141,7 +142,7 @@ def CloseSmallDeletions(mhandle, scorer, extension_steps=9, clash_thresh=1.0,
# check for clashes
score = scorer.CalculateClashScore(\
bb_list,
- current_gap.before.GetNumber().GetNum(),
+ n_stem_resnum.GetNum(),
current_chain_index)
# if there is no clash and potential energy is low enough we
# just solved a gap, delete it and update the scorer for the
@@ -152,11 +153,10 @@ def CloseSmallDeletions(mhandle, scorer, extension_steps=9, clash_thresh=1.0,
ost.LogInfo("Closed: %s by relaxing %s" % \
(mhandle.gaps[current_gap_index], current_gap))
chain = current_gap.before.GetChain()
- bb_list.InsertInto(chain, current_gap.before.GetNumber().GetNum(),
- current_gap.after.GetNumber().GetNum())
- scorer.SetEnvironment(\
- bb_list,
- current_gap.before.GetNumber().GetNum())
+ bb_list.InsertInto(chain, n_stem_resnum,
+ current_chain_index)
+ scorer.SetEnvironment(bb_list, n_stem_resnum,
+ current_chain_index)
modelling.ClearGaps(mhandle, current_gap)
success = True
break
@@ -452,7 +452,8 @@ def FillLoopsByDatabase(mhandle, scorer, fragment_db, structure_db,
# try to close loops
try:
#pylint: disable=broad-except
- candidates.ApplyCCD(torsion_sampler)
+ candidates.ApplyCCD(actual_gap.before, actual_gap.after,
+ torsion_sampler)
except Exception:
# ccd requires the residues before and after the stems
# to be valid, it could be that we extend too much...
@@ -490,20 +491,14 @@ def FillLoopsByDatabase(mhandle, scorer, fragment_db, structure_db,
frame_backbone_list[i] = frame_backbone
actual_res_num += 1
- overall_before_residue = actual_chain.FindResidue(
- ost.mol.ResNum(min_before_resnum))
- overall_after_residue = actual_chain.FindResidue(
- ost.mol.ResNum(max_after_resnum))
- final_loop_candidates = loop.LoopCandidates(overall_before_residue,
- overall_after_residue,
- frame_seq)
+ final_loop_candidates = loop.LoopCandidates(frame_seq)
##################################
# prepare loop candidates for scoring
##################################
back_mapper = list()
for i, loop_candidates in enumerate(actual_candidates):
- start_index = loop_candidates.GetNStem().GetNumber().GetNum()\
+ start_index = actual_extended_gaps[i].before.GetNumber().GetNum()\
- min_before_resnum
for j, loop_candidate in enumerate(loop_candidates):
actual_frame_backbone_list = frame_backbone_list
@@ -513,11 +508,16 @@ def FillLoopsByDatabase(mhandle, scorer, fragment_db, structure_db,
back_mapper.append((i, j))
final_loop_candidates.AttachScorer(scorer)
- final_loop_candidates.CalculateClashScores(actual_chain_idx)
- final_loop_candidates.CalculateCBetaScores(actual_chain_idx)
- final_loop_candidates.CalculateTorsionScores(actual_chain_idx)
- final_loop_candidates.CalculateCBPackingScores(actual_chain_idx)
- final_loop_candidates.CalculateHBondScores(actual_chain_idx)
+ final_loop_candidates.CalculateClashScores(min_before_resnum,
+ actual_chain_idx)
+ final_loop_candidates.CalculateCBetaScores(min_before_resnum,
+ actual_chain_idx)
+ final_loop_candidates.CalculateTorsionScores(min_before_resnum,
+ actual_chain_idx)
+ final_loop_candidates.CalculateCBPackingScores(min_before_resnum,
+ actual_chain_idx)
+ final_loop_candidates.CalculateHBondScores(min_before_resnum,
+ actual_chain_idx)
##################################
# compare scores
@@ -546,13 +546,12 @@ def FillLoopsByDatabase(mhandle, scorer, fragment_db, structure_db,
idx_a = back_mapper[optimal_candidate][0]
idx_b = back_mapper[optimal_candidate][1]
# update model
- actual_candidates[idx_a].InsertInto(mhandle.model, idx_b)
- # update scorer
+ start_resnum = actual_extended_gaps[idx_a].before.GetNumber()
bb_list = actual_candidates[idx_a][idx_b].bb_list
- scorer.SetEnvironment(\
- bb_list,
- actual_candidates[idx_a].GetNStem().GetNumber().GetNum(),
- actual_chain_idx)
+ bb_list.InsertInto(mhandle.model.chains[actual_chain_idx],
+ start_resnum, actual_chain_idx)
+ # update scorer
+ scorer.SetEnvironment(bb_list, start_resnum, actual_chain_idx)
ost.LogInfo("Resolved %s by filling %s (%d candidates)" % \
(str(gap_orig),
str(actual_extended_gaps[idx_a]),
@@ -679,8 +678,9 @@ def FillLoopsByMonteCarlo(mhandle, scorer, torsion_sampler, max_loops_to_search=
weights["cbeta"]=5.0
weights["cb_packing"]=1.0
weights["clash"]=0.05
- mc_scorer = loop.LinearScorer(scorer, actual_gap.before.GetNumber().GetNum(),
- actual_chain_idx, weights)
+ mc_scorer = loop.LinearScorer(
+ scorer, actual_gap.before.GetNumber().GetNum(),
+ actual_chain_idx, weights)
mc_cooler = loop.ExponentialCooler(200,100,0.9)
except:
@@ -692,9 +692,8 @@ def FillLoopsByMonteCarlo(mhandle, scorer, torsion_sampler, max_loops_to_search=
try:
ost.LogVerbose("Firing MC for " + str(actual_gap))
candidates = loop.LoopCandidates.FillFromMonteCarloSampler(
- actual_gap.before, actual_gap.after, actual_gap.full_seq,
- mc_num_loops, mc_steps, mc_sampler, mc_closer,
- mc_scorer, mc_cooler)
+ actual_gap.full_seq, mc_num_loops, mc_steps, mc_sampler,
+ mc_closer, mc_scorer, mc_cooler)
except RuntimeError:
# monte carlo cannot be initialized when the stems are too far apart
# => we need further loop extension
@@ -736,20 +735,14 @@ def FillLoopsByMonteCarlo(mhandle, scorer, torsion_sampler, max_loops_to_search=
frame_backbone_list[i] = frame_backbone
actual_res_num += 1
- overall_before_residue = actual_chain.FindResidue(
- ost.mol.ResNum(min_before_resnum))
- overall_after_residue = actual_chain.FindResidue(
- ost.mol.ResNum(max_after_resnum))
- final_loop_candidates = loop.LoopCandidates(overall_before_residue,
- overall_after_residue,
- frame_seq)
+ final_loop_candidates = loop.LoopCandidates(frame_seq)
##################################
# prepare loop candidates for scoring (NOTE: identical to DB)
##################################
back_mapper = list()
for i, loop_candidates in enumerate(actual_candidates):
- start_index = loop_candidates.GetNStem().GetNumber().GetNum()\
+ start_index = actual_extended_gaps[i].before.GetNumber().GetNum()\
- min_before_resnum
for j, loop_candidate in enumerate(loop_candidates):
actual_frame_backbone_list = frame_backbone_list
@@ -759,11 +752,16 @@ def FillLoopsByMonteCarlo(mhandle, scorer, torsion_sampler, max_loops_to_search=
back_mapper.append((i,j))
final_loop_candidates.AttachScorer(scorer)
- final_loop_candidates.CalculateClashScores(actual_chain_idx)
- final_loop_candidates.CalculateCBetaScores(actual_chain_idx)
- final_loop_candidates.CalculateTorsionScores(actual_chain_idx)
- final_loop_candidates.CalculateCBPackingScores(actual_chain_idx)
- final_loop_candidates.CalculateHBondScores(actual_chain_idx)
+ final_loop_candidates.CalculateClashScores(min_before_resnum,
+ actual_chain_idx)
+ final_loop_candidates.CalculateCBetaScores(min_before_resnum,
+ actual_chain_idx)
+ final_loop_candidates.CalculateTorsionScores(min_before_resnum,
+ actual_chain_idx)
+ final_loop_candidates.CalculateCBPackingScores(min_before_resnum,
+ actual_chain_idx)
+ final_loop_candidates.CalculateHBondScores(min_before_resnum,
+ actual_chain_idx)
##################################
# compare scores (NOTE: can be made identical to DB)
@@ -790,13 +788,12 @@ def FillLoopsByMonteCarlo(mhandle, scorer, torsion_sampler, max_loops_to_search=
idx_a = back_mapper[optimal_candidate][0]
idx_b = back_mapper[optimal_candidate][1]
# update model
- actual_candidates[idx_a].InsertInto(mhandle.model, idx_b)
- # update scorer
+ start_resnum = actual_extended_gaps[idx_a].before.GetNumber()
bb_list = actual_candidates[idx_a][idx_b].bb_list
- scorer.SetEnvironment(\
- bb_list,
- actual_candidates[idx_a].GetNStem().GetNumber().GetNum(),
- actual_chain_idx)
+ bb_list.InsertInto(mhandle.model.chains[actual_chain_idx],
+ start_resnum, actual_chain_idx)
+ # update scorer
+ scorer.SetEnvironment(bb_list, start_resnum, actual_chain_idx)
ost.LogInfo("Resolved %s by filling %s (%d candidates)" % \
(str(gap_orig),
str(actual_extended_gaps[idx_a]),
diff --git a/modelling/tests/data/1crn_build.pdb b/modelling/tests/data/1crn_build.pdb
index d6442a5c2894ec0706359d4fa291e898dfda9372..bb62cfddebfbc5c7a47e00c6ffb148db65269993 100644
--- a/modelling/tests/data/1crn_build.pdb
+++ b/modelling/tests/data/1crn_build.pdb
@@ -1,329 +1,329 @@
-ATOM 1 N THR A 1 17.055 14.170 3.573 1.00 13.79 N
-ATOM 2 CA THR A 1 16.959 12.877 4.362 1.00 10.80 C
-ATOM 3 C THR A 1 15.697 12.787 5.169 1.00 9.19 C
-ATOM 4 O THR A 1 15.243 13.804 5.681 1.00 9.85 O
-ATOM 5 CB THR A 1 18.166 12.761 5.287 1.00 13.02 C
-ATOM 6 OG1 THR A 1 19.334 12.714 4.477 1.00 15.06 O
-ATOM 7 CG2 THR A 1 18.168 11.511 6.185 1.00 14.23 C
-ATOM 8 N THR A 2 15.087 11.587 5.299 1.00 7.81 N
-ATOM 9 CA THR A 2 13.820 11.412 6.003 1.00 8.31 C
-ATOM 10 C THR A 2 14.029 10.685 7.315 1.00 5.80 C
-ATOM 11 O THR A 2 14.692 9.651 7.385 1.00 6.94 O
-ATOM 12 CB THR A 2 12.739 10.686 5.199 1.00 10.32 C
-ATOM 13 OG1 THR A 2 13.137 9.383 4.796 1.00 12.81 O
-ATOM 14 CG2 THR A 2 12.465 11.458 3.905 1.00 11.90 C
-ATOM 15 N CYS A 3 13.474 11.234 8.407 1.00 5.24 N
-ATOM 16 CA CYS A 3 13.656 10.729 9.760 1.00 5.39 C
-ATOM 17 C CYS A 3 12.287 10.480 10.370 1.00 4.45 C
-ATOM 18 O CYS A 3 11.412 11.336 10.260 1.00 6.54 O
-ATOM 19 CB CYS A 3 14.388 11.771 10.640 1.00 5.99 C
-ATOM 20 SG CYS A 3 15.945 12.381 9.926 1.00 7.01 S
-ATOM 21 N CYS A 4 12.030 9.320 11.002 1.00 3.90 N
-ATOM 22 CA CYS A 4 10.699 8.968 11.472 1.00 4.24 C
-ATOM 23 C CYS A 4 10.678 8.737 12.981 1.00 3.72 C
-ATOM 24 O CYS A 4 11.673 8.282 13.542 1.00 5.30 O
-ATOM 25 CB CYS A 4 10.172 7.709 10.747 1.00 4.41 C
-ATOM 26 SG CYS A 4 9.837 8.008 8.982 1.00 0.00 S
-ATOM 27 N PRO A 5 9.596 9.037 13.704 1.00 3.96 N
-ATOM 28 CA PRO A 5 9.577 8.975 15.169 1.00 4.25 C
-ATOM 29 C PRO A 5 9.323 7.570 15.685 1.00 4.96 C
-ATOM 30 O PRO A 5 9.411 7.342 16.888 1.00 7.44 O
-ATOM 31 CB PRO A 5 8.381 9.880 15.518 1.00 5.11 C
-ATOM 32 CG PRO A 5 7.412 9.673 14.352 1.00 5.24 C
-ATOM 33 CD PRO A 5 8.369 9.637 13.167 1.00 5.20 C
-ATOM 34 N SER A 6 8.941 6.616 14.820 1.00 4.83 N
-ATOM 35 CA SER A 6 8.656 5.263 15.240 1.00 4.45 C
-ATOM 36 C SER A 6 8.756 4.363 14.030 1.00 4.99 C
-ATOM 37 O SER A 6 8.707 4.809 12.883 1.00 4.61 O
-ATOM 38 CB SER A 6 7.276 5.075 15.952 1.00 5.05 C
-ATOM 39 OG SER A 6 6.156 5.097 15.056 1.00 6.39 O
-ATOM 40 N ILE A 7 8.881 3.045 14.263 1.00 4.94 N
-ATOM 41 CA ILE A 7 8.882 2.013 13.237 1.00 6.33 C
-ATOM 42 C ILE A 7 7.579 1.986 12.435 1.00 5.32 C
-ATOM 43 O ILE A 7 7.585 1.876 11.212 1.00 6.85 O
-ATOM 44 CB ILE A 7 9.219 0.673 13.893 1.00 8.43 C
-ATOM 45 CG1 ILE A 7 10.712 0.677 14.316 1.00 9.78 C
-ATOM 46 CG2 ILE A 7 8.907 -0.511 12.951 1.00 11.70 C
-ATOM 47 CD1 ILE A 7 11.132 -0.542 15.147 1.00 9.92 C
-ATOM 48 N VAL A 8 6.416 2.161 13.101 1.00 5.02 N
-ATOM 49 CA VAL A 8 5.109 2.266 12.452 1.00 6.93 C
-ATOM 50 C VAL A 8 5.037 3.440 11.486 1.00 5.39 C
-ATOM 51 O VAL A 8 4.580 3.314 10.350 1.00 6.30 O
-ATOM 52 CB VAL A 8 4.003 2.393 13.502 1.00 9.64 C
-ATOM 53 CG1 VAL A 8 2.648 2.815 12.893 1.00 13.85 C
-ATOM 54 CG2 VAL A 8 3.839 1.037 14.211 1.00 11.97 C
-ATOM 55 N ALA A 9 5.555 4.610 11.905 1.00 3.73 N
-ATOM 56 CA ALA A 9 5.647 5.795 11.081 1.00 3.56 C
-ATOM 57 C ALA A 9 6.500 5.603 9.826 1.00 4.13 C
-ATOM 58 O ALA A 9 6.095 5.955 8.718 1.00 4.36 O
-ATOM 59 CB ALA A 9 6.210 6.922 11.958 1.00 4.80 C
-ATOM 60 N ARG A 10 7.678 4.958 9.958 1.00 3.73 N
-ATOM 61 CA ARG A 10 8.513 4.576 8.830 1.00 3.38 C
-ATOM 62 C ARG A 10 7.866 3.588 7.867 1.00 3.47 C
-ATOM 63 O ARG A 10 7.937 3.750 6.648 1.00 4.67 O
-ATOM 64 CB ARG A 10 9.853 3.989 9.334 1.00 3.95 C
-ATOM 65 CG ARG A 10 10.844 3.550 8.228 1.00 4.55 C
-ATOM 66 CD ARG A 10 11.291 4.651 7.257 1.00 5.89 C
-ATOM 67 NE ARG A 10 12.180 5.560 8.027 1.00 6.20 N
-ATOM 68 CZ ARG A 10 12.841 6.605 7.523 1.00 7.52 C
-ATOM 69 NH1 ARG A 10 12.702 6.977 6.257 1.00 10.68 N
-ATOM 70 NH2 ARG A 10 13.639 7.298 8.322 1.00 9.48 N
-ATOM 71 N SER A 11 7.188 2.544 8.378 1.00 5.19 N
-ATOM 72 CA SER A 11 6.460 1.589 7.548 1.00 4.60 C
-ATOM 73 C SER A 11 5.335 2.226 6.751 1.00 4.84 C
-ATOM 74 O SER A 11 5.209 2.007 5.547 1.00 5.84 O
-ATOM 75 CB SER A 11 5.874 0.431 8.385 1.00 5.91 C
-ATOM 76 OG SER A 11 6.941 -0.341 8.934 1.00 8.38 O
-ATOM 77 N ASN A 12 4.535 3.105 7.393 1.00 3.54 N
-ATOM 78 CA ASN A 12 3.522 3.916 6.733 1.00 4.57 C
-ATOM 79 C ASN A 12 4.112 4.876 5.697 1.00 4.14 C
-ATOM 80 O ASN A 12 3.562 5.043 4.610 1.00 5.52 O
-ATOM 81 CB ASN A 12 2.696 4.717 7.773 1.00 6.42 C
-ATOM 82 CG ASN A 12 1.866 3.763 8.625 1.00 8.25 C
-ATOM 83 OD1 ASN A 12 1.605 2.614 8.272 1.00 12.72 O
-ATOM 84 ND2 ASN A 12 1.395 4.260 9.791 1.00 9.92 N
-ATOM 85 N PHE A 13 5.277 5.504 5.985 1.00 3.43 N
-ATOM 86 CA PHE A 13 6.007 6.342 5.039 1.00 3.49 C
-ATOM 87 C PHE A 13 6.391 5.602 3.763 1.00 3.40 C
-ATOM 88 O PHE A 13 6.166 6.085 2.656 1.00 4.07 O
-ATOM 89 CB PHE A 13 7.297 6.904 5.711 1.00 5.48 C
-ATOM 90 CG PHE A 13 8.035 7.860 4.818 1.00 5.57 C
-ATOM 91 CD1 PHE A 13 9.142 7.418 4.074 1.00 6.99 C
-ATOM 92 CD2 PHE A 13 7.583 9.177 4.662 1.00 6.52 C
-ATOM 93 CE1 PHE A 13 9.772 8.277 3.167 1.00 8.20 C
-ATOM 94 CE2 PHE A 13 8.223 10.049 3.773 1.00 6.34 C
-ATOM 95 CZ PHE A 13 9.307 9.591 3.017 1.00 6.84 C
-ATOM 96 N ASN A 14 6.947 4.387 3.894 1.00 3.64 N
-ATOM 97 CA ASN A 14 7.350 3.575 2.763 1.00 4.31 C
-ATOM 98 C ASN A 14 6.172 3.168 1.873 1.00 3.98 C
-ATOM 99 O ASN A 14 6.250 3.277 0.652 1.00 6.22 O
-ATOM 100 CB ASN A 14 8.155 2.347 3.258 1.00 5.81 C
-ATOM 101 CG ASN A 14 9.490 2.800 3.853 1.00 6.82 C
-ATOM 102 OD1 ASN A 14 9.983 3.911 3.657 1.00 9.43 O
-ATOM 103 ND2 ASN A 14 10.141 1.885 4.607 1.00 8.21 N
-ATOM 104 N VAL A 15 5.021 2.765 2.459 1.00 3.76 N
-ATOM 105 CA VAL A 15 3.782 2.519 1.715 1.00 3.98 C
-ATOM 106 C VAL A 15 3.248 3.762 1.014 1.00 3.80 C
-ATOM 107 O VAL A 15 2.864 3.722 -0.154 1.00 4.85 O
-ATOM 108 CB VAL A 15 2.697 1.918 2.606 1.00 4.71 C
-ATOM 109 CG1 VAL A 15 1.356 1.767 1.854 1.00 6.67 C
-ATOM 110 CG2 VAL A 15 3.174 0.534 3.079 1.00 6.26 C
-ATOM 111 N CYS A 16 3.271 4.926 1.690 1.00 3.79 N
-ATOM 112 CA CYS A 16 2.892 6.211 1.123 1.00 3.54 C
-ATOM 113 C CYS A 16 3.722 6.595 -0.101 1.00 3.48 C
-ATOM 114 O CYS A 16 3.213 7.158 -1.070 1.00 4.63 O
-ATOM 115 CB CYS A 16 2.985 7.298 2.227 1.00 4.58 C
-ATOM 116 SG CYS A 16 2.400 8.945 1.711 1.00 0.00 S
-ATOM 117 N ARG A 17 5.029 6.278 -0.088 1.00 3.99 N
-ATOM 118 CA ARG A 17 5.940 6.527 -1.186 1.00 3.83 C
-ATOM 119 C ARG A 17 5.816 5.581 -2.379 1.00 3.79 C
-ATOM 120 O ARG A 17 6.274 5.931 -3.465 1.00 5.39 O
-ATOM 121 CB ARG A 17 7.399 6.499 -0.659 1.00 4.11 C
-ATOM 122 CG ARG A 17 7.757 7.715 0.220 1.00 4.69 C
-ATOM 123 CD ARG A 17 7.914 9.031 -0.550 1.00 5.10 C
-ATOM 124 NE ARG A 17 9.204 8.932 -1.303 1.00 4.71 N
-ATOM 125 CZ ARG A 17 9.509 9.606 -2.418 1.00 5.28 C
-ATOM 126 NH1 ARG A 17 8.619 10.341 -3.078 1.00 6.67 N
-ATOM 127 NH2 ARG A 17 10.763 9.546 -2.865 1.00 6.41 N
-ATOM 128 N LEU A 18 5.163 4.403 -2.251 1.00 4.70 N
-ATOM 129 CA LEU A 18 4.982 3.452 -3.352 1.00 5.46 C
-ATOM 130 C LEU A 18 4.297 4.004 -4.615 1.00 5.13 C
-ATOM 131 O LEU A 18 4.811 3.721 -5.696 1.00 5.55 O
-ATOM 132 CB LEU A 18 4.206 2.176 -2.907 1.00 6.47 C
-ATOM 133 CG LEU A 18 4.966 1.173 -2.018 1.00 7.43 C
-ATOM 134 CD1 LEU A 18 3.997 0.071 -1.562 1.00 8.70 C
-ATOM 135 CD2 LEU A 18 6.158 0.530 -2.741 1.00 9.39 C
-ATOM 136 N PRO A 19 3.212 4.786 -4.630 1.00 4.28 N
-ATOM 137 CA PRO A 19 2.696 5.374 -5.865 1.00 5.38 C
-ATOM 138 C PRO A 19 3.519 6.551 -6.369 1.00 6.30 C
-ATOM 139 O PRO A 19 3.170 7.112 -7.404 1.00 9.62 O
-ATOM 140 CB PRO A 19 1.245 5.770 -5.544 1.00 5.87 C
-ATOM 141 CG PRO A 19 1.129 5.806 -4.016 1.00 6.47 C
-ATOM 142 CD PRO A 19 2.286 4.946 -3.506 1.00 6.45 C
-ATOM 143 N GLY A 20 4.588 6.976 -5.663 1.00 4.94 N
-ATOM 144 CA GLY A 20 5.419 8.095 -6.096 1.00 5.39 C
-ATOM 145 C GLY A 20 5.077 9.407 -5.451 1.00 5.03 C
-ATOM 146 O GLY A 20 5.637 10.440 -5.811 1.00 7.34 O
-ATOM 147 N THR A 21 4.166 9.407 -4.456 1.00 4.10 N
-ATOM 148 CA THR A 21 3.758 10.568 -3.659 1.00 3.94 C
-ATOM 149 C THR A 21 4.943 11.387 -3.140 1.00 3.96 C
-ATOM 150 O THR A 21 5.888 10.785 -2.614 1.00 5.82 O
-ATOM 151 CB THR A 21 2.919 10.159 -2.456 1.00 4.13 C
-ATOM 152 OG1 THR A 21 1.883 9.279 -2.862 1.00 5.45 O
-ATOM 153 CG2 THR A 21 2.253 11.354 -1.745 1.00 5.41 C
-ATOM 154 N PRO A 22 5.013 12.720 -3.270 1.00 5.04 N
-ATOM 155 CA PRO A 22 6.092 13.539 -2.719 1.00 4.69 C
-ATOM 156 C PRO A 22 6.439 13.279 -1.266 1.00 4.19 C
-ATOM 157 O PRO A 22 5.540 13.036 -0.460 1.00 4.47 O
-ATOM 158 CB PRO A 22 5.635 14.989 -2.938 1.00 7.12 C
-ATOM 159 CG PRO A 22 4.668 14.910 -4.121 1.00 7.03 C
-ATOM 160 CD PRO A 22 4.006 13.544 -3.946 1.00 4.90 C
-ATOM 161 N GLU A 23 7.732 13.369 -0.889 1.00 5.16 N
-ATOM 162 CA GLU A 23 8.161 13.178 0.485 1.00 5.31 C
-ATOM 163 C GLU A 23 7.497 14.128 1.464 1.00 4.11 C
-ATOM 164 O GLU A 23 7.125 13.714 2.551 1.00 5.11 O
-ATOM 165 CB GLU A 23 9.699 13.264 0.646 1.00 6.16 C
-ATOM 166 CG GLU A 23 10.443 12.076 -0.005 1.00 7.48 C
-ATOM 167 CD GLU A 23 11.918 11.974 0.381 1.00 9.40 C
-ATOM 168 OE1 GLU A 23 12.483 12.943 0.944 1.00 10.40 O
-ATOM 169 OE2 GLU A 23 12.466 10.870 0.122 1.00 13.32 O
-ATOM 170 N ALA A 24 7.285 15.410 1.109 1.00 4.56 N
-ATOM 171 CA ALA A 24 6.612 16.370 1.966 1.00 4.49 C
-ATOM 172 C ALA A 24 5.173 16.007 2.340 1.00 4.10 C
-ATOM 173 O ALA A 24 4.771 16.101 3.497 1.00 5.64 O
-ATOM 174 CB ALA A 24 6.626 17.725 1.239 1.00 5.80 C
-ATOM 175 N ILE A 25 4.372 15.542 1.357 1.00 0.00 N
-ATOM 176 CA ILE A 25 3.023 15.032 1.584 1.00 0.00 C
-ATOM 177 C ILE A 25 3.033 13.748 2.391 1.00 0.00 C
-ATOM 178 O ILE A 25 2.258 13.574 3.324 1.00 0.00 O
-ATOM 179 CB ILE A 25 2.274 14.810 0.267 1.00 0.00 C
-ATOM 180 CG1 ILE A 25 2.068 16.167 -0.444 1.00 0.00 C
-ATOM 181 CG2 ILE A 25 0.909 14.114 0.507 1.00 0.00 C
-ATOM 182 CD1 ILE A 25 1.532 16.038 -1.873 1.00 0.00 C
-ATOM 183 N CYS A 26 3.924 12.791 2.080 1.00 0.00 N
-ATOM 184 CA CYS A 26 4.003 11.593 2.894 1.00 0.00 C
-ATOM 185 C CYS A 26 4.520 11.796 4.297 1.00 0.00 C
-ATOM 186 O CYS A 26 3.931 11.284 5.242 1.00 0.00 O
-ATOM 187 CB CYS A 26 4.881 10.517 2.224 1.00 0.00 C
-ATOM 188 SG CYS A 26 4.020 9.793 0.824 1.00 0.00 S
-ATOM 189 N ALA A 27 5.629 12.536 4.475 1.00 0.00 N
-ATOM 190 CA ALA A 27 6.383 12.536 5.709 1.00 0.00 C
-ATOM 191 C ALA A 27 5.594 13.018 6.901 1.00 0.00 C
-ATOM 192 O ALA A 27 5.400 12.278 7.856 1.00 0.00 O
-ATOM 193 CB ALA A 27 7.661 13.392 5.556 1.00 0.00 C
-ATOM 194 N THR A 28 5.017 14.227 6.827 1.00 0.00 N
-ATOM 195 CA THR A 28 4.317 14.839 7.956 1.00 0.00 C
-ATOM 196 C THR A 28 3.119 14.027 8.418 1.00 0.00 C
-ATOM 197 O THR A 28 2.887 13.839 9.611 1.00 0.00 O
-ATOM 198 CB THR A 28 3.883 16.267 7.635 1.00 0.00 C
-ATOM 199 OG1 THR A 28 5.028 17.056 7.339 1.00 0.00 O
-ATOM 200 CG2 THR A 28 3.178 16.921 8.833 1.00 0.00 C
-ATOM 201 N TYR A 29 2.334 13.469 7.481 1.00 0.00 N
-ATOM 202 CA TYR A 29 1.128 12.728 7.803 1.00 0.00 C
-ATOM 203 C TYR A 29 1.396 11.298 8.263 1.00 0.00 C
-ATOM 204 O TYR A 29 0.546 10.659 8.879 1.00 0.00 O
-ATOM 205 CB TYR A 29 0.188 12.706 6.576 1.00 0.00 C
-ATOM 206 CG TYR A 29 -0.392 14.075 6.319 1.00 0.00 C
-ATOM 207 CD1 TYR A 29 0.240 14.973 5.445 1.00 0.00 C
-ATOM 208 CD2 TYR A 29 -1.608 14.457 6.912 1.00 0.00 C
-ATOM 209 CE1 TYR A 29 -0.346 16.203 5.125 1.00 0.00 C
-ATOM 210 CE2 TYR A 29 -2.201 15.691 6.599 1.00 0.00 C
-ATOM 211 CZ TYR A 29 -1.573 16.556 5.693 1.00 0.00 C
-ATOM 212 OH TYR A 29 -2.177 17.775 5.332 1.00 0.00 O
-ATOM 213 N THR A 30 2.605 10.761 8.031 1.00 0.00 N
-ATOM 214 CA THR A 30 2.999 9.466 8.583 1.00 0.00 C
-ATOM 215 C THR A 30 3.781 9.652 9.871 1.00 0.00 C
-ATOM 216 O THR A 30 4.102 8.687 10.554 1.00 0.00 O
-ATOM 217 CB THR A 30 3.818 8.634 7.597 1.00 0.00 C
-ATOM 218 OG1 THR A 30 5.010 9.290 7.198 1.00 0.00 O
-ATOM 219 CG2 THR A 30 2.989 8.381 6.319 1.00 0.00 C
-ATOM 220 N GLY A 31 4.046 10.915 10.269 1.00 0.00 N
-ATOM 221 CA GLY A 31 4.737 11.308 11.504 1.00 0.00 C
-ATOM 222 C GLY A 31 6.147 11.792 11.263 1.00 0.00 C
-ATOM 223 O GLY A 31 6.792 12.401 12.124 1.00 0.00 O
-ATOM 224 N CYS A 32 6.707 11.440 10.107 1.00 4.30 N
-ATOM 225 CA CYS A 32 8.077 11.673 9.715 1.00 4.89 C
-ATOM 226 C CYS A 32 8.445 13.103 9.303 1.00 5.50 C
-ATOM 227 O CYS A 32 7.607 13.949 9.003 1.00 5.82 O
-ATOM 228 CB CYS A 32 8.476 10.711 8.578 1.00 4.66 C
-ATOM 229 SG CYS A 32 8.059 8.978 8.956 1.00 0.00 S
-ATOM 230 N ILE A 33 9.759 13.413 9.269 1.00 6.02 N
-ATOM 231 CA ILE A 33 10.249 14.736 8.900 1.00 5.24 C
-ATOM 232 C ILE A 33 11.293 14.632 7.807 1.00 5.16 C
-ATOM 233 O ILE A 33 11.911 13.586 7.600 1.00 7.19 O
-ATOM 234 CB ILE A 33 10.816 15.522 10.086 1.00 5.49 C
-ATOM 235 CG1 ILE A 33 12.043 14.825 10.721 1.00 6.85 C
-ATOM 236 CG2 ILE A 33 9.671 15.720 11.104 1.00 6.45 C
-ATOM 237 CD1 ILE A 33 12.736 15.658 11.806 1.00 8.94 C
-ATOM 238 N ILE A 34 11.519 15.741 7.076 1.00 5.52 N
-ATOM 239 CA ILE A 34 12.549 15.860 6.054 1.00 6.82 C
-ATOM 240 C ILE A 34 13.561 16.856 6.572 1.00 6.92 C
-ATOM 241 O ILE A 34 13.213 17.966 6.969 1.00 9.22 O
-ATOM 242 CB ILE A 34 12.026 16.370 4.709 1.00 8.11 C
-ATOM 243 CG1 ILE A 34 10.932 15.434 4.158 1.00 9.59 C
-ATOM 244 CG2 ILE A 34 13.182 16.504 3.683 1.00 9.73 C
-ATOM 245 CD1 ILE A 34 10.162 16.057 2.995 1.00 13.41 C
-ATOM 246 N ILE A 35 14.852 16.480 6.588 1.00 7.06 N
-ATOM 247 CA ILE A 35 15.928 17.368 6.993 1.00 7.52 C
-ATOM 248 C ILE A 35 16.911 17.541 5.835 1.00 6.63 C
-ATOM 249 O ILE A 35 17.043 16.627 5.007 1.00 7.90 O
-ATOM 250 CB ILE A 35 16.647 16.907 8.262 1.00 8.07 C
-ATOM 251 CG1 ILE A 35 17.337 15.534 8.098 1.00 9.41 C
-ATOM 252 CG2 ILE A 35 15.625 16.905 9.421 1.00 9.46 C
-ATOM 253 CD1 ILE A 35 18.260 15.190 9.270 1.00 9.85 C
-ATOM 254 N PRO A 36 17.610 18.681 5.706 1.00 8.07 N
-ATOM 255 CA PRO A 36 18.634 18.864 4.679 1.00 8.78 C
-ATOM 256 C PRO A 36 19.873 18.018 4.929 1.00 8.31 C
-ATOM 257 O PRO A 36 20.505 17.583 3.971 1.00 9.09 O
-ATOM 258 CB PRO A 36 18.955 20.374 4.681 1.00 9.67 C
-ATOM 259 CG PRO A 36 18.263 20.995 5.906 1.00 10.15 C
-ATOM 260 CD PRO A 36 17.371 19.898 6.494 1.00 9.53 C
-ATOM 261 N GLY A 37 20.255 17.799 6.205 1.00 8.48 N
-ATOM 262 CA GLY A 37 21.404 16.976 6.583 1.00 9.20 C
-ATOM 263 C GLY A 37 21.174 15.485 6.488 1.00 10.41 C
-ATOM 264 O GLY A 37 20.158 15.010 5.994 1.00 12.06 O
-ATOM 265 N ALA A 38 22.131 14.681 6.985 1.00 9.24 N
-ATOM 266 CA ALA A 38 22.041 13.229 6.948 1.00 9.24 C
-ATOM 267 C ALA A 38 21.922 12.593 8.325 1.00 9.60 C
-ATOM 268 O ALA A 38 21.787 11.379 8.452 1.00 13.65 O
-ATOM 269 CB ALA A 38 23.292 12.681 6.238 1.00 10.43 C
-ATOM 270 N THR A 39 21.924 13.409 9.391 1.00 8.70 N
-ATOM 271 CA THR A 39 22.001 12.917 10.762 1.00 9.46 C
-ATOM 272 C THR A 39 20.681 13.188 11.430 1.00 8.32 C
-ATOM 273 O THR A 39 20.370 14.321 11.790 1.00 9.89 O
-ATOM 274 CB THR A 39 23.102 13.595 11.579 1.00 10.72 C
-ATOM 275 OG1 THR A 39 24.336 13.513 10.879 1.00 11.66 O
-ATOM 276 CG2 THR A 39 23.307 12.895 12.931 1.00 11.81 C
-ATOM 277 N CYS A 40 19.840 12.151 11.593 1.00 7.64 N
-ATOM 278 CA CYS A 40 18.561 12.278 12.269 1.00 8.05 C
-ATOM 279 C CYS A 40 18.703 12.511 13.781 1.00 7.63 C
-ATOM 280 O CYS A 40 19.602 11.926 14.390 1.00 9.64 O
-ATOM 281 CB CYS A 40 17.675 11.038 12.000 1.00 7.80 C
-ATOM 282 SG CYS A 40 17.232 10.850 10.242 1.00 7.30 S
-ATOM 283 N PRO A 41 17.894 13.344 14.445 1.00 8.00 N
-ATOM 284 CA PRO A 41 17.918 13.482 15.902 1.00 8.96 C
-ATOM 285 C PRO A 41 17.362 12.258 16.624 1.00 9.06 C
-ATOM 286 O PRO A 41 16.726 11.403 16.012 1.00 8.82 O
-ATOM 287 CB PRO A 41 17.061 14.731 16.151 1.00 10.39 C
-ATOM 288 CG PRO A 41 16.047 14.729 15.005 1.00 10.99 C
-ATOM 289 CD PRO A 41 16.846 14.167 13.830 1.00 10.49 C
-ATOM 290 N GLY A 42 17.599 12.144 17.951 1.00 7.55 N
-ATOM 291 CA GLY A 42 17.294 10.935 18.721 1.00 8.00 C
-ATOM 292 C GLY A 42 15.838 10.634 18.980 1.00 7.22 C
-ATOM 293 O GLY A 42 15.493 9.521 19.364 1.00 8.41 O
-ATOM 294 N ASP A 43 14.945 11.604 18.754 1.00 5.54 N
-ATOM 295 CA ASP A 43 13.508 11.479 18.868 1.00 5.85 C
-ATOM 296 C ASP A 43 12.858 11.199 17.510 1.00 5.87 C
-ATOM 297 O ASP A 43 11.667 10.909 17.403 1.00 7.29 O
-ATOM 298 CB ASP A 43 12.945 12.766 19.537 1.00 6.72 C
-ATOM 299 CG ASP A 43 13.339 14.080 18.863 1.00 8.59 C
-ATOM 300 OD1 ASP A 43 14.399 14.135 18.183 1.00 9.59 O
-ATOM 301 OD2 ASP A 43 12.584 15.063 19.060 1.00 11.45 O
-ATOM 302 N TYR A 44 13.675 11.175 16.441 1.00 5.22 N
-ATOM 303 CA TYR A 44 13.270 10.780 15.106 1.00 5.56 C
-ATOM 304 C TYR A 44 14.262 9.745 14.605 1.00 4.61 C
-ATOM 305 O TYR A 44 14.914 9.899 13.575 1.00 6.04 O
-ATOM 306 CB TYR A 44 13.186 11.958 14.104 1.00 5.41 C
-ATOM 307 CG TYR A 44 12.012 12.845 14.406 1.00 5.34 C
-ATOM 308 CD1 TYR A 44 12.103 13.885 15.345 1.00 6.59 C
-ATOM 309 CD2 TYR A 44 10.793 12.640 13.737 1.00 5.94 C
-ATOM 310 CE1 TYR A 44 10.994 14.698 15.620 1.00 5.97 C
-ATOM 311 CE2 TYR A 44 9.683 13.451 14.008 1.00 5.17 C
-ATOM 312 CZ TYR A 44 9.785 14.478 14.952 1.00 5.96 C
-ATOM 313 OH TYR A 44 8.659 15.282 15.216 1.00 8.60 O
-ATOM 314 N ALA A 45 14.395 8.643 15.360 1.00 4.76 N
-ATOM 315 CA ALA A 45 15.467 7.680 15.218 1.00 5.89 C
-ATOM 316 C ALA A 45 15.167 6.501 14.296 1.00 6.67 C
-ATOM 317 O ALA A 45 15.962 5.565 14.193 1.00 7.56 O
-ATOM 318 CB ALA A 45 15.739 7.116 16.627 1.00 6.82 C
-ATOM 319 N ASN A 46 14.014 6.506 13.612 1.00 5.80 N
-ATOM 320 CA ASN A 46 13.586 5.407 12.777 1.00 6.15 C
-ATOM 321 C ASN A 46 13.305 5.864 11.329 1.00 6.61 C
-ATOM 322 O ASN A 46 13.555 7.041 10.956 1.00 7.18 O
-ATOM 323 CB ASN A 46 12.283 4.789 13.338 1.00 7.27 C
-ATOM 324 CG ASN A 46 12.481 4.240 14.742 1.00 7.98 C
-ATOM 325 OD1 ASN A 46 11.771 4.587 15.685 1.00 11.00 O
-ATOM 326 ND2 ASN A 46 13.439 3.301 14.905 1.00 10.32 N
-ATOM 327 OXT ASN A 46 12.803 5.019 10.541 1.00 0.00 O
+ATOM 1 N THR A 1 17.052 14.174 3.574 1.00 13.79 N
+ATOM 2 CA THR A 1 16.951 12.881 4.364 1.00 10.80 C
+ATOM 3 C THR A 1 15.689 12.789 5.177 1.00 9.19 C
+ATOM 4 O THR A 1 15.237 13.807 5.689 1.00 9.85 O
+ATOM 5 CB THR A 1 18.164 12.766 5.283 1.00 13.02 C
+ATOM 6 OG1 THR A 1 19.334 12.715 4.478 1.00 15.06 O
+ATOM 7 CG2 THR A 1 18.170 11.509 6.175 1.00 14.23 C
+ATOM 8 N THR A 2 15.080 11.588 5.312 1.00 7.81 N
+ATOM 9 CA THR A 2 13.810 11.412 6.010 1.00 8.31 C
+ATOM 10 C THR A 2 14.012 10.684 7.323 1.00 5.80 C
+ATOM 11 O THR A 2 14.661 9.642 7.391 1.00 6.94 O
+ATOM 12 CB THR A 2 12.734 10.690 5.193 1.00 10.32 C
+ATOM 13 OG1 THR A 2 13.124 9.387 4.781 1.00 12.81 O
+ATOM 14 CG2 THR A 2 12.464 11.473 3.904 1.00 11.90 C
+ATOM 15 N CYS A 3 13.467 11.238 8.419 1.00 5.24 N
+ATOM 16 CA CYS A 3 13.653 10.742 9.776 1.00 5.39 C
+ATOM 17 C CYS A 3 12.289 10.504 10.403 1.00 4.45 C
+ATOM 18 O CYS A 3 11.428 11.381 10.332 1.00 6.54 O
+ATOM 19 CB CYS A 3 14.409 11.786 10.637 1.00 5.99 C
+ATOM 20 SG CYS A 3 15.971 12.359 9.904 1.00 7.01 S
+ATOM 21 N CYS A 4 12.020 9.328 11.007 1.00 3.90 N
+ATOM 22 CA CYS A 4 10.692 8.963 11.473 1.00 4.24 C
+ATOM 23 C CYS A 4 10.653 8.765 12.990 1.00 3.72 C
+ATOM 24 O CYS A 4 11.636 8.317 13.571 1.00 5.30 O
+ATOM 25 CB CYS A 4 10.210 7.673 10.770 1.00 4.41 C
+ATOM 26 SG CYS A 4 9.834 7.941 9.013 1.00 0.00 S
+ATOM 27 N PRO A 5 9.559 9.092 13.691 1.00 3.96 N
+ATOM 28 CA PRO A 5 9.500 9.032 15.155 1.00 4.25 C
+ATOM 29 C PRO A 5 9.250 7.623 15.665 1.00 4.96 C
+ATOM 30 O PRO A 5 9.301 7.394 16.870 1.00 7.44 O
+ATOM 31 CB PRO A 5 8.291 9.932 15.476 1.00 5.11 C
+ATOM 32 CG PRO A 5 7.360 9.737 14.279 1.00 5.24 C
+ATOM 33 CD PRO A 5 8.351 9.701 13.123 1.00 5.20 C
+ATOM 34 N SER A 6 8.912 6.667 14.785 1.00 4.83 N
+ATOM 35 CA SER A 6 8.658 5.302 15.196 1.00 4.45 C
+ATOM 36 C SER A 6 8.772 4.377 14.002 1.00 4.99 C
+ATOM 37 O SER A 6 8.750 4.798 12.846 1.00 4.61 O
+ATOM 38 CB SER A 6 7.291 5.092 15.927 1.00 5.05 C
+ATOM 39 OG SER A 6 6.156 5.079 15.051 1.00 6.39 O
+ATOM 40 N ILE A 7 8.884 3.059 14.258 1.00 4.94 N
+ATOM 41 CA ILE A 7 8.878 2.011 13.244 1.00 6.33 C
+ATOM 42 C ILE A 7 7.570 1.972 12.448 1.00 5.32 C
+ATOM 43 O ILE A 7 7.573 1.843 11.226 1.00 6.85 O
+ATOM 44 CB ILE A 7 9.220 0.670 13.899 1.00 8.43 C
+ATOM 45 CG1 ILE A 7 10.714 0.675 14.322 1.00 9.78 C
+ATOM 46 CG2 ILE A 7 8.917 -0.516 12.953 1.00 11.70 C
+ATOM 47 CD1 ILE A 7 11.132 -0.546 15.153 1.00 9.92 C
+ATOM 48 N VAL A 8 6.406 2.155 13.111 1.00 5.02 N
+ATOM 49 CA VAL A 8 5.098 2.256 12.461 1.00 6.93 C
+ATOM 50 C VAL A 8 5.032 3.426 11.490 1.00 5.39 C
+ATOM 51 O VAL A 8 4.574 3.298 10.354 1.00 6.30 O
+ATOM 52 CB VAL A 8 3.993 2.383 13.513 1.00 9.64 C
+ATOM 53 CG1 VAL A 8 2.634 2.799 12.905 1.00 13.85 C
+ATOM 54 CG2 VAL A 8 3.839 1.027 14.226 1.00 11.97 C
+ATOM 55 N ALA A 9 5.562 4.592 11.902 1.00 3.73 N
+ATOM 56 CA ALA A 9 5.693 5.765 11.068 1.00 3.56 C
+ATOM 57 C ALA A 9 6.563 5.549 9.824 1.00 4.13 C
+ATOM 58 O ALA A 9 6.189 5.912 8.708 1.00 4.36 O
+ATOM 59 CB ALA A 9 6.276 6.887 11.942 1.00 4.80 C
+ATOM 60 N ARG A 10 7.730 4.889 9.970 1.00 3.73 N
+ATOM 61 CA ARG A 10 8.560 4.481 8.846 1.00 3.38 C
+ATOM 62 C ARG A 10 7.914 3.476 7.895 1.00 3.47 C
+ATOM 63 O ARG A 10 8.009 3.612 6.676 1.00 4.67 O
+ATOM 64 CB ARG A 10 9.915 3.924 9.344 1.00 3.95 C
+ATOM 65 CG ARG A 10 10.909 3.510 8.229 1.00 4.55 C
+ATOM 66 CD ARG A 10 11.322 4.627 7.257 1.00 5.89 C
+ATOM 67 NE ARG A 10 12.192 5.554 8.026 1.00 6.20 N
+ATOM 68 CZ ARG A 10 12.848 6.604 7.529 1.00 7.52 C
+ATOM 69 NH1 ARG A 10 12.715 6.986 6.265 1.00 10.68 N
+ATOM 70 NH2 ARG A 10 13.641 7.295 8.333 1.00 9.48 N
+ATOM 71 N SER A 11 7.210 2.449 8.409 1.00 5.19 N
+ATOM 72 CA SER A 11 6.484 1.490 7.580 1.00 4.60 C
+ATOM 73 C SER A 11 5.381 2.126 6.757 1.00 4.84 C
+ATOM 74 O SER A 11 5.272 1.887 5.553 1.00 5.84 O
+ATOM 75 CB SER A 11 5.875 0.348 8.422 1.00 5.91 C
+ATOM 76 OG SER A 11 6.933 -0.431 8.979 1.00 8.38 O
+ATOM 77 N ASN A 12 4.587 3.029 7.368 1.00 3.54 N
+ATOM 78 CA ASN A 12 3.603 3.847 6.680 1.00 4.57 C
+ATOM 79 C ASN A 12 4.236 4.770 5.629 1.00 4.14 C
+ATOM 80 O ASN A 12 3.663 4.982 4.564 1.00 5.52 O
+ATOM 81 CB ASN A 12 2.766 4.672 7.696 1.00 6.42 C
+ATOM 82 CG ASN A 12 1.918 3.747 8.562 1.00 8.25 C
+ATOM 83 OD1 ASN A 12 1.637 2.598 8.228 1.00 12.72 O
+ATOM 84 ND2 ASN A 12 1.446 4.272 9.716 1.00 9.92 N
+ATOM 85 N PHE A 13 5.454 5.316 5.882 1.00 3.43 N
+ATOM 86 CA PHE A 13 6.199 6.127 4.919 1.00 3.49 C
+ATOM 87 C PHE A 13 6.521 5.390 3.631 1.00 3.40 C
+ATOM 88 O PHE A 13 6.267 5.889 2.535 1.00 4.07 O
+ATOM 89 CB PHE A 13 7.524 6.648 5.555 1.00 5.48 C
+ATOM 90 CG PHE A 13 8.244 7.611 4.660 1.00 5.57 C
+ATOM 91 CD1 PHE A 13 9.417 7.205 4.019 1.00 6.99 C
+ATOM 92 CD2 PHE A 13 7.716 8.882 4.387 1.00 6.52 C
+ATOM 93 CE1 PHE A 13 10.037 8.031 3.082 1.00 8.20 C
+ATOM 94 CE2 PHE A 13 8.364 9.746 3.491 1.00 6.34 C
+ATOM 95 CZ PHE A 13 9.511 9.302 2.823 1.00 6.84 C
+ATOM 96 N ASN A 14 7.048 4.161 3.748 1.00 3.64 N
+ATOM 97 CA ASN A 14 7.433 3.329 2.627 1.00 4.31 C
+ATOM 98 C ASN A 14 6.227 2.958 1.758 1.00 3.98 C
+ATOM 99 O ASN A 14 6.291 3.071 0.538 1.00 6.22 O
+ATOM 100 CB ASN A 14 8.248 2.110 3.146 1.00 5.81 C
+ATOM 101 CG ASN A 14 9.555 2.608 3.774 1.00 6.82 C
+ATOM 102 OD1 ASN A 14 10.043 3.709 3.526 1.00 9.43 O
+ATOM 103 ND2 ASN A 14 10.187 1.768 4.629 1.00 8.21 N
+ATOM 104 N VAL A 15 5.070 2.602 2.368 1.00 3.76 N
+ATOM 105 CA VAL A 15 3.798 2.407 1.665 1.00 3.98 C
+ATOM 106 C VAL A 15 3.271 3.662 0.978 1.00 3.80 C
+ATOM 107 O VAL A 15 2.864 3.630 -0.182 1.00 4.85 O
+ATOM 108 CB VAL A 15 2.715 1.865 2.600 1.00 4.71 C
+ATOM 109 CG1 VAL A 15 1.353 1.732 1.878 1.00 6.67 C
+ATOM 110 CG2 VAL A 15 3.167 0.485 3.108 1.00 6.26 C
+ATOM 111 N CYS A 16 3.303 4.825 1.659 1.00 3.79 N
+ATOM 112 CA CYS A 16 2.897 6.114 1.110 1.00 3.54 C
+ATOM 113 C CYS A 16 3.721 6.536 -0.103 1.00 3.48 C
+ATOM 114 O CYS A 16 3.207 7.106 -1.065 1.00 4.63 O
+ATOM 115 CB CYS A 16 2.961 7.184 2.233 1.00 4.58 C
+ATOM 116 SG CYS A 16 2.261 8.815 1.808 1.00 0.00 S
+ATOM 117 N ARG A 17 5.033 6.245 -0.087 1.00 3.99 N
+ATOM 118 CA ARG A 17 5.939 6.511 -1.185 1.00 3.83 C
+ATOM 119 C ARG A 17 5.817 5.572 -2.386 1.00 3.79 C
+ATOM 120 O ARG A 17 6.266 5.939 -3.470 1.00 5.39 O
+ATOM 121 CB ARG A 17 7.398 6.495 -0.662 1.00 4.11 C
+ATOM 122 CG ARG A 17 7.751 7.718 0.212 1.00 4.69 C
+ATOM 123 CD ARG A 17 7.902 9.037 -0.554 1.00 5.10 C
+ATOM 124 NE ARG A 17 9.194 8.943 -1.308 1.00 4.71 N
+ATOM 125 CZ ARG A 17 9.499 9.612 -2.424 1.00 5.28 C
+ATOM 126 NH1 ARG A 17 8.607 10.335 -3.096 1.00 6.67 N
+ATOM 127 NH2 ARG A 17 10.761 9.564 -2.858 1.00 6.41 N
+ATOM 128 N LEU A 18 5.175 4.383 -2.270 1.00 4.70 N
+ATOM 129 CA LEU A 18 4.986 3.439 -3.376 1.00 5.46 C
+ATOM 130 C LEU A 18 4.291 3.996 -4.635 1.00 5.13 C
+ATOM 131 O LEU A 18 4.803 3.719 -5.717 1.00 5.55 O
+ATOM 132 CB LEU A 18 4.207 2.162 -2.930 1.00 6.47 C
+ATOM 133 CG LEU A 18 4.965 1.160 -2.035 1.00 7.43 C
+ATOM 134 CD1 LEU A 18 4.002 0.060 -1.562 1.00 8.70 C
+ATOM 135 CD2 LEU A 18 6.164 0.515 -2.745 1.00 9.39 C
+ATOM 136 N PRO A 19 3.199 4.773 -4.650 1.00 4.28 N
+ATOM 137 CA PRO A 19 2.686 5.374 -5.882 1.00 5.38 C
+ATOM 138 C PRO A 19 3.516 6.549 -6.386 1.00 6.30 C
+ATOM 139 O PRO A 19 3.156 7.125 -7.409 1.00 9.62 O
+ATOM 140 CB PRO A 19 1.232 5.768 -5.558 1.00 5.87 C
+ATOM 141 CG PRO A 19 1.126 5.808 -4.029 1.00 6.47 C
+ATOM 142 CD PRO A 19 2.266 4.916 -3.531 1.00 6.45 C
+ATOM 143 N GLY A 20 4.600 6.960 -5.696 1.00 4.94 N
+ATOM 144 CA GLY A 20 5.447 8.064 -6.138 1.00 5.39 C
+ATOM 145 C GLY A 20 5.108 9.397 -5.530 1.00 5.03 C
+ATOM 146 O GLY A 20 5.706 10.412 -5.879 1.00 7.34 O
+ATOM 147 N THR A 21 4.154 9.430 -4.579 1.00 4.10 N
+ATOM 148 CA THR A 21 3.748 10.589 -3.779 1.00 3.94 C
+ATOM 149 C THR A 21 4.926 11.404 -3.230 1.00 3.96 C
+ATOM 150 O THR A 21 5.864 10.792 -2.702 1.00 5.82 O
+ATOM 151 CB THR A 21 2.874 10.168 -2.604 1.00 4.13 C
+ATOM 152 OG1 THR A 21 1.821 9.334 -3.052 1.00 5.45 O
+ATOM 153 CG2 THR A 21 2.220 11.361 -1.879 1.00 5.41 C
+ATOM 154 N PRO A 22 4.999 12.742 -3.327 1.00 5.04 N
+ATOM 155 CA PRO A 22 6.089 13.542 -2.768 1.00 4.69 C
+ATOM 156 C PRO A 22 6.446 13.263 -1.317 1.00 4.19 C
+ATOM 157 O PRO A 22 5.553 12.987 -0.514 1.00 4.47 O
+ATOM 158 CB PRO A 22 5.638 14.999 -2.961 1.00 7.12 C
+ATOM 159 CG PRO A 22 4.681 14.943 -4.153 1.00 7.03 C
+ATOM 160 CD PRO A 22 3.993 13.590 -3.976 1.00 4.90 C
+ATOM 161 N GLU A 23 7.739 13.376 -0.935 1.00 5.16 N
+ATOM 162 CA GLU A 23 8.169 13.194 0.441 1.00 5.31 C
+ATOM 163 C GLU A 23 7.496 14.148 1.410 1.00 4.11 C
+ATOM 164 O GLU A 23 7.078 13.729 2.474 1.00 5.11 O
+ATOM 165 CB GLU A 23 9.707 13.273 0.616 1.00 6.16 C
+ATOM 166 CG GLU A 23 10.449 12.081 -0.029 1.00 7.48 C
+ATOM 167 CD GLU A 23 11.913 11.943 0.386 1.00 9.40 C
+ATOM 168 OE1 GLU A 23 12.492 12.886 0.971 1.00 10.40 O
+ATOM 169 OE2 GLU A 23 12.439 10.827 0.117 1.00 13.32 O
+ATOM 170 N ALA A 24 7.308 15.438 1.067 1.00 4.56 N
+ATOM 171 CA ALA A 24 6.621 16.397 1.921 1.00 4.49 C
+ATOM 172 C ALA A 24 5.180 16.031 2.297 1.00 4.10 C
+ATOM 173 O ALA A 24 4.756 16.198 3.440 1.00 5.64 O
+ATOM 174 CB ALA A 24 6.636 17.764 1.211 1.00 5.80 C
+ATOM 175 N ILE A 25 4.394 15.501 1.339 1.00 0.00 N
+ATOM 176 CA ILE A 25 3.048 15.002 1.590 1.00 0.00 C
+ATOM 177 C ILE A 25 3.061 13.730 2.432 1.00 0.00 C
+ATOM 178 O ILE A 25 2.372 13.615 3.444 1.00 0.00 O
+ATOM 179 CB ILE A 25 2.313 14.812 0.255 1.00 0.00 C
+ATOM 180 CG1 ILE A 25 2.102 16.205 -0.397 1.00 0.00 C
+ATOM 181 CG2 ILE A 25 0.963 14.078 0.443 1.00 0.00 C
+ATOM 182 CD1 ILE A 25 1.586 16.177 -1.843 1.00 0.00 C
+ATOM 183 N CYS A 26 3.904 12.748 2.059 1.00 0.00 N
+ATOM 184 CA CYS A 26 4.028 11.492 2.777 1.00 0.00 C
+ATOM 185 C CYS A 26 4.679 11.528 4.128 1.00 0.00 C
+ATOM 186 O CYS A 26 4.192 10.866 5.031 1.00 0.00 O
+ATOM 187 CB CYS A 26 4.785 10.458 1.933 1.00 0.00 C
+ATOM 188 SG CYS A 26 3.688 9.746 0.705 1.00 0.00 S
+ATOM 189 N ALA A 27 5.778 12.279 4.333 1.00 0.00 N
+ATOM 190 CA ALA A 27 6.493 12.310 5.592 1.00 0.00 C
+ATOM 191 C ALA A 27 5.591 12.834 6.695 1.00 0.00 C
+ATOM 192 O ALA A 27 5.400 12.218 7.736 1.00 0.00 O
+ATOM 193 CB ALA A 27 7.764 13.180 5.435 1.00 0.00 C
+ATOM 194 N THR A 28 4.893 13.937 6.394 1.00 0.00 N
+ATOM 195 CA THR A 28 3.923 14.572 7.274 1.00 0.00 C
+ATOM 196 C THR A 28 2.741 13.674 7.621 1.00 0.00 C
+ATOM 197 O THR A 28 2.339 13.603 8.779 1.00 0.00 O
+ATOM 198 CB THR A 28 3.412 15.893 6.700 1.00 0.00 C
+ATOM 199 OG1 THR A 28 4.497 16.775 6.442 1.00 0.00 O
+ATOM 200 CG2 THR A 28 2.489 16.602 7.704 1.00 0.00 C
+ATOM 201 N TYR A 29 2.175 12.909 6.654 1.00 0.00 N
+ATOM 202 CA TYR A 29 1.080 11.970 6.896 1.00 0.00 C
+ATOM 203 C TYR A 29 1.428 10.870 7.911 1.00 0.00 C
+ATOM 204 O TYR A 29 0.593 10.382 8.666 1.00 0.00 O
+ATOM 205 CB TYR A 29 0.624 11.324 5.544 1.00 0.00 C
+ATOM 206 CG TYR A 29 -0.635 10.499 5.709 1.00 0.00 C
+ATOM 207 CD1 TYR A 29 -1.850 11.143 5.992 1.00 0.00 C
+ATOM 208 CD2 TYR A 29 -0.606 9.091 5.669 1.00 0.00 C
+ATOM 209 CE1 TYR A 29 -3.007 10.401 6.264 1.00 0.00 C
+ATOM 210 CE2 TYR A 29 -1.766 8.345 5.940 1.00 0.00 C
+ATOM 211 CZ TYR A 29 -2.964 9.005 6.243 1.00 0.00 C
+ATOM 212 OH TYR A 29 -4.135 8.277 6.531 1.00 0.00 O
+ATOM 213 N THR A 30 2.697 10.436 7.917 1.00 0.00 N
+ATOM 214 CA THR A 30 3.176 9.274 8.649 1.00 0.00 C
+ATOM 215 C THR A 30 3.831 9.697 9.960 1.00 0.00 C
+ATOM 216 O THR A 30 4.153 8.869 10.809 1.00 0.00 O
+ATOM 217 CB THR A 30 4.159 8.500 7.763 1.00 0.00 C
+ATOM 218 OG1 THR A 30 5.287 9.281 7.382 1.00 0.00 O
+ATOM 219 CG2 THR A 30 3.434 8.105 6.459 1.00 0.00 C
+ATOM 220 N GLY A 31 4.004 11.024 10.173 1.00 0.00 N
+ATOM 221 CA GLY A 31 4.606 11.660 11.347 1.00 0.00 C
+ATOM 222 C GLY A 31 6.090 11.917 11.212 1.00 0.00 C
+ATOM 223 O GLY A 31 6.743 12.404 12.129 1.00 0.00 O
+ATOM 224 N CYS A 32 6.681 11.555 10.065 1.00 4.30 N
+ATOM 225 CA CYS A 32 8.085 11.715 9.748 1.00 4.89 C
+ATOM 226 C CYS A 32 8.454 13.116 9.288 1.00 5.50 C
+ATOM 227 O CYS A 32 7.612 13.924 8.912 1.00 5.82 O
+ATOM 228 CB CYS A 32 8.560 10.707 8.666 1.00 4.66 C
+ATOM 229 SG CYS A 32 8.095 8.986 9.047 1.00 0.00 S
+ATOM 230 N ILE A 33 9.760 13.441 9.302 1.00 6.02 N
+ATOM 231 CA ILE A 33 10.248 14.755 8.913 1.00 5.24 C
+ATOM 232 C ILE A 33 11.287 14.639 7.813 1.00 5.16 C
+ATOM 233 O ILE A 33 11.891 13.587 7.601 1.00 7.19 O
+ATOM 234 CB ILE A 33 10.819 15.544 10.091 1.00 5.49 C
+ATOM 235 CG1 ILE A 33 12.042 14.839 10.724 1.00 6.85 C
+ATOM 236 CG2 ILE A 33 9.676 15.751 11.111 1.00 6.45 C
+ATOM 237 CD1 ILE A 33 12.741 15.661 11.811 1.00 8.94 C
+ATOM 238 N ILE A 34 11.519 15.747 7.079 1.00 5.52 N
+ATOM 239 CA ILE A 34 12.549 15.859 6.058 1.00 6.82 C
+ATOM 240 C ILE A 34 13.565 16.851 6.576 1.00 6.92 C
+ATOM 241 O ILE A 34 13.220 17.961 6.972 1.00 9.22 O
+ATOM 242 CB ILE A 34 12.028 16.369 4.711 1.00 8.11 C
+ATOM 243 CG1 ILE A 34 10.930 15.435 4.162 1.00 9.59 C
+ATOM 244 CG2 ILE A 34 13.185 16.501 3.685 1.00 9.73 C
+ATOM 245 CD1 ILE A 34 10.156 16.056 3.000 1.00 13.41 C
+ATOM 246 N ILE A 35 14.855 16.472 6.592 1.00 7.06 N
+ATOM 247 CA ILE A 35 15.930 17.361 6.996 1.00 7.52 C
+ATOM 248 C ILE A 35 16.911 17.537 5.836 1.00 6.63 C
+ATOM 249 O ILE A 35 17.044 16.619 5.015 1.00 7.90 O
+ATOM 250 CB ILE A 35 16.652 16.899 8.263 1.00 8.07 C
+ATOM 251 CG1 ILE A 35 17.337 15.523 8.103 1.00 9.41 C
+ATOM 252 CG2 ILE A 35 15.631 16.897 9.423 1.00 9.46 C
+ATOM 253 CD1 ILE A 35 18.260 15.183 9.277 1.00 9.85 C
+ATOM 254 N PRO A 36 17.607 18.682 5.698 1.00 8.07 N
+ATOM 255 CA PRO A 36 18.634 18.863 4.674 1.00 8.78 C
+ATOM 256 C PRO A 36 19.871 18.014 4.931 1.00 8.31 C
+ATOM 257 O PRO A 36 20.493 17.561 3.975 1.00 9.09 O
+ATOM 258 CB PRO A 36 18.953 20.375 4.670 1.00 9.67 C
+ATOM 259 CG PRO A 36 18.270 20.996 5.902 1.00 10.15 C
+ATOM 260 CD PRO A 36 17.370 19.900 6.484 1.00 9.53 C
+ATOM 261 N GLY A 37 20.258 17.805 6.207 1.00 8.48 N
+ATOM 262 CA GLY A 37 21.401 16.977 6.592 1.00 9.20 C
+ATOM 263 C GLY A 37 21.174 15.486 6.493 1.00 10.41 C
+ATOM 264 O GLY A 37 20.154 15.010 6.007 1.00 12.06 O
+ATOM 265 N ALA A 38 22.138 14.679 6.975 1.00 9.24 N
+ATOM 266 CA ALA A 38 22.048 13.226 6.937 1.00 9.24 C
+ATOM 267 C ALA A 38 21.924 12.592 8.317 1.00 9.60 C
+ATOM 268 O ALA A 38 21.779 11.380 8.448 1.00 13.65 O
+ATOM 269 CB ALA A 38 23.301 12.675 6.231 1.00 10.43 C
+ATOM 270 N THR A 39 21.936 13.409 9.384 1.00 8.70 N
+ATOM 271 CA THR A 39 22.006 12.918 10.757 1.00 9.46 C
+ATOM 272 C THR A 39 20.684 13.190 11.422 1.00 8.32 C
+ATOM 273 O THR A 39 20.371 14.325 11.774 1.00 9.89 O
+ATOM 274 CB THR A 39 23.098 13.598 11.584 1.00 10.72 C
+ATOM 275 OG1 THR A 39 24.337 13.528 10.894 1.00 11.66 O
+ATOM 276 CG2 THR A 39 23.300 12.891 12.934 1.00 11.81 C
+ATOM 277 N CYS A 40 19.843 12.153 11.591 1.00 7.64 N
+ATOM 278 CA CYS A 40 18.566 12.277 12.270 1.00 8.05 C
+ATOM 279 C CYS A 40 18.707 12.523 13.782 1.00 7.63 C
+ATOM 280 O CYS A 40 19.612 11.951 14.392 1.00 9.64 O
+ATOM 281 CB CYS A 40 17.691 11.026 12.008 1.00 7.80 C
+ATOM 282 SG CYS A 40 17.247 10.823 10.250 1.00 7.30 S
+ATOM 283 N PRO A 41 17.893 13.350 14.448 1.00 8.00 N
+ATOM 284 CA PRO A 41 17.916 13.489 15.905 1.00 8.96 C
+ATOM 285 C PRO A 41 17.356 12.265 16.627 1.00 9.06 C
+ATOM 286 O PRO A 41 16.729 11.408 16.008 1.00 8.82 O
+ATOM 287 CB PRO A 41 17.059 14.740 16.150 1.00 10.39 C
+ATOM 288 CG PRO A 41 16.041 14.730 15.007 1.00 10.99 C
+ATOM 289 CD PRO A 41 16.842 14.169 13.833 1.00 10.49 C
+ATOM 290 N GLY A 42 17.582 12.149 17.957 1.00 7.55 N
+ATOM 291 CA GLY A 42 17.287 10.932 18.720 1.00 8.00 C
+ATOM 292 C GLY A 42 15.834 10.626 18.991 1.00 7.22 C
+ATOM 293 O GLY A 42 15.500 9.515 19.390 1.00 8.41 O
+ATOM 294 N ASP A 43 14.934 11.587 18.754 1.00 5.54 N
+ATOM 295 CA ASP A 43 13.499 11.469 18.872 1.00 5.85 C
+ATOM 296 C ASP A 43 12.848 11.189 17.514 1.00 5.87 C
+ATOM 297 O ASP A 43 11.658 10.897 17.409 1.00 7.29 O
+ATOM 298 CB ASP A 43 12.948 12.770 19.528 1.00 6.72 C
+ATOM 299 CG ASP A 43 13.364 14.078 18.851 1.00 8.59 C
+ATOM 300 OD1 ASP A 43 14.431 14.115 18.179 1.00 9.59 O
+ATOM 301 OD2 ASP A 43 12.624 15.073 19.035 1.00 11.45 O
+ATOM 302 N TYR A 44 13.664 11.169 16.443 1.00 5.22 N
+ATOM 303 CA TYR A 44 13.258 10.777 15.107 1.00 5.56 C
+ATOM 304 C TYR A 44 14.250 9.745 14.602 1.00 4.61 C
+ATOM 305 O TYR A 44 14.893 9.899 13.567 1.00 6.04 O
+ATOM 306 CB TYR A 44 13.179 11.959 14.108 1.00 5.41 C
+ATOM 307 CG TYR A 44 12.005 12.848 14.406 1.00 5.34 C
+ATOM 308 CD1 TYR A 44 12.093 13.887 15.346 1.00 6.59 C
+ATOM 309 CD2 TYR A 44 10.790 12.643 13.731 1.00 5.94 C
+ATOM 310 CE1 TYR A 44 10.982 14.701 15.615 1.00 5.97 C
+ATOM 311 CE2 TYR A 44 9.679 13.453 13.999 1.00 5.17 C
+ATOM 312 CZ TYR A 44 9.775 14.480 14.942 1.00 5.96 C
+ATOM 313 OH TYR A 44 8.649 15.285 15.201 1.00 8.60 O
+ATOM 314 N ALA A 45 14.393 8.645 15.361 1.00 4.76 N
+ATOM 315 CA ALA A 45 15.464 7.683 15.215 1.00 5.89 C
+ATOM 316 C ALA A 45 15.162 6.500 14.300 1.00 6.67 C
+ATOM 317 O ALA A 45 15.948 5.556 14.215 1.00 7.56 O
+ATOM 318 CB ALA A 45 15.746 7.121 16.623 1.00 6.82 C
+ATOM 319 N ASN A 46 14.016 6.508 13.604 1.00 5.80 N
+ATOM 320 CA ASN A 46 13.591 5.409 12.769 1.00 6.15 C
+ATOM 321 C ASN A 46 13.325 5.866 11.320 1.00 6.61 C
+ATOM 322 O ASN A 46 13.563 7.051 10.958 1.00 7.18 O
+ATOM 323 CB ASN A 46 12.283 4.791 13.320 1.00 7.27 C
+ATOM 324 CG ASN A 46 12.469 4.228 14.720 1.00 7.98 C
+ATOM 325 OD1 ASN A 46 11.740 4.544 15.659 1.00 11.00 O
+ATOM 326 ND2 ASN A 46 13.441 3.305 14.887 1.00 10.32 N
+ATOM 327 OXT ASN A 46 12.841 5.020 10.525 1.00 0.00 O
TER 328 ASN A 46
END
diff --git a/modelling/tests/data/1crn_final.pdb b/modelling/tests/data/1crn_final.pdb
index a07e6e5353cb9bcb7841f63f7345ae85fbce4852..34120cd7a69d5e787eb42d88db930733ce51cd15 100644
--- a/modelling/tests/data/1crn_final.pdb
+++ b/modelling/tests/data/1crn_final.pdb
@@ -1,329 +1,329 @@
-ATOM 1 N THR A 1 17.054 14.171 3.574 1.00 13.79 N
-ATOM 2 CA THR A 1 16.956 12.878 4.361 1.00 10.80 C
-ATOM 3 C THR A 1 15.694 12.787 5.170 1.00 9.19 C
-ATOM 4 O THR A 1 15.240 13.804 5.683 1.00 9.85 O
-ATOM 5 CB THR A 1 18.164 12.763 5.286 1.00 13.02 C
-ATOM 6 OG1 THR A 1 19.333 12.720 4.476 1.00 15.06 O
-ATOM 7 CG2 THR A 1 18.169 11.510 6.180 1.00 14.23 C
-ATOM 8 N THR A 2 15.084 11.587 5.299 1.00 7.81 N
-ATOM 9 CA THR A 2 13.816 11.412 6.002 1.00 8.31 C
-ATOM 10 C THR A 2 14.023 10.683 7.313 1.00 5.80 C
-ATOM 11 O THR A 2 14.680 9.644 7.380 1.00 6.94 O
-ATOM 12 CB THR A 2 12.736 10.688 5.193 1.00 10.32 C
-ATOM 13 OG1 THR A 2 13.134 9.386 4.786 1.00 12.81 O
-ATOM 14 CG2 THR A 2 12.462 11.464 3.902 1.00 11.90 C
-ATOM 15 N CYS A 3 13.473 11.234 8.407 1.00 5.24 N
-ATOM 16 CA CYS A 3 13.656 10.729 9.760 1.00 5.39 C
-ATOM 17 C CYS A 3 12.287 10.484 10.372 1.00 4.45 C
-ATOM 18 O CYS A 3 11.413 11.341 10.265 1.00 6.54 O
-ATOM 19 CB CYS A 3 14.390 11.771 10.639 1.00 5.99 C
-ATOM 20 SG CYS A 3 15.949 12.375 9.925 1.00 7.01 S
-ATOM 21 N CYS A 4 12.028 9.323 11.004 1.00 3.90 N
-ATOM 22 CA CYS A 4 10.696 8.971 11.472 1.00 4.24 C
-ATOM 23 C CYS A 4 10.675 8.740 12.981 1.00 3.72 C
-ATOM 24 O CYS A 4 11.669 8.278 13.542 1.00 5.30 O
-ATOM 25 CB CYS A 4 10.174 7.709 10.748 1.00 4.41 C
-ATOM 26 SG CYS A 4 9.843 8.005 8.982 1.00 0.00 S
-ATOM 27 N PRO A 5 9.594 9.045 13.706 1.00 3.96 N
-ATOM 28 CA PRO A 5 9.574 8.974 15.169 1.00 4.25 C
-ATOM 29 C PRO A 5 9.321 7.566 15.681 1.00 4.96 C
-ATOM 30 O PRO A 5 9.405 7.339 16.886 1.00 7.44 O
-ATOM 31 CB PRO A 5 8.385 9.883 15.525 1.00 5.11 C
-ATOM 32 CG PRO A 5 7.412 9.677 14.365 1.00 5.24 C
-ATOM 33 CD PRO A 5 8.361 9.644 13.174 1.00 5.20 C
-ATOM 34 N SER A 6 8.942 6.610 14.817 1.00 4.83 N
-ATOM 35 CA SER A 6 8.656 5.258 15.239 1.00 4.45 C
-ATOM 36 C SER A 6 8.755 4.359 14.029 1.00 4.99 C
-ATOM 37 O SER A 6 8.704 4.806 12.882 1.00 4.61 O
-ATOM 38 CB SER A 6 7.275 5.074 15.951 1.00 5.05 C
-ATOM 39 OG SER A 6 6.154 5.096 15.055 1.00 6.39 O
-ATOM 40 N ILE A 7 8.881 3.041 14.260 1.00 4.94 N
-ATOM 41 CA ILE A 7 8.880 2.010 13.233 1.00 6.33 C
-ATOM 42 C ILE A 7 7.575 1.982 12.433 1.00 5.32 C
-ATOM 43 O ILE A 7 7.580 1.867 11.209 1.00 6.85 O
-ATOM 44 CB ILE A 7 9.219 0.669 13.889 1.00 8.43 C
-ATOM 45 CG1 ILE A 7 10.712 0.675 14.316 1.00 9.78 C
-ATOM 46 CG2 ILE A 7 8.911 -0.515 12.948 1.00 11.70 C
-ATOM 47 CD1 ILE A 7 11.131 -0.544 15.149 1.00 9.92 C
-ATOM 48 N VAL A 8 6.413 2.162 13.098 1.00 5.02 N
-ATOM 49 CA VAL A 8 5.106 2.268 12.451 1.00 6.93 C
-ATOM 50 C VAL A 8 5.035 3.444 11.486 1.00 5.39 C
-ATOM 51 O VAL A 8 4.574 3.319 10.351 1.00 6.30 O
-ATOM 52 CB VAL A 8 4.001 2.393 13.502 1.00 9.64 C
-ATOM 53 CG1 VAL A 8 2.644 2.810 12.895 1.00 13.85 C
-ATOM 54 CG2 VAL A 8 3.843 1.036 14.213 1.00 11.97 C
-ATOM 55 N ALA A 9 5.556 4.612 11.904 1.00 3.73 N
-ATOM 56 CA ALA A 9 5.651 5.797 11.080 1.00 3.56 C
-ATOM 57 C ALA A 9 6.503 5.603 9.825 1.00 4.13 C
-ATOM 58 O ALA A 9 6.099 5.956 8.717 1.00 4.36 O
-ATOM 59 CB ALA A 9 6.218 6.923 11.958 1.00 4.80 C
-ATOM 60 N ARG A 10 7.680 4.956 9.957 1.00 3.73 N
-ATOM 61 CA ARG A 10 8.515 4.572 8.829 1.00 3.38 C
-ATOM 62 C ARG A 10 7.867 3.584 7.866 1.00 3.47 C
-ATOM 63 O ARG A 10 7.939 3.746 6.647 1.00 4.67 O
-ATOM 64 CB ARG A 10 9.854 3.986 9.335 1.00 3.95 C
-ATOM 65 CG ARG A 10 10.848 3.548 8.232 1.00 4.55 C
-ATOM 66 CD ARG A 10 11.295 4.648 7.258 1.00 5.89 C
-ATOM 67 NE ARG A 10 12.182 5.559 8.028 1.00 6.20 N
-ATOM 68 CZ ARG A 10 12.844 6.604 7.526 1.00 7.52 C
-ATOM 69 NH1 ARG A 10 12.707 6.980 6.261 1.00 10.68 N
-ATOM 70 NH2 ARG A 10 13.642 7.294 8.328 1.00 9.48 N
-ATOM 71 N SER A 11 7.186 2.541 8.375 1.00 5.19 N
-ATOM 72 CA SER A 11 6.457 1.587 7.545 1.00 4.60 C
-ATOM 73 C SER A 11 5.333 2.226 6.749 1.00 4.84 C
-ATOM 74 O SER A 11 5.209 2.009 5.543 1.00 5.84 O
-ATOM 75 CB SER A 11 5.870 0.429 8.382 1.00 5.91 C
-ATOM 76 OG SER A 11 6.937 -0.345 8.928 1.00 8.38 O
-ATOM 77 N ASN A 12 4.535 3.104 7.391 1.00 3.54 N
-ATOM 78 CA ASN A 12 3.523 3.918 6.732 1.00 4.57 C
-ATOM 79 C ASN A 12 4.115 4.877 5.698 1.00 4.14 C
-ATOM 80 O ASN A 12 3.563 5.047 4.611 1.00 5.52 O
-ATOM 81 CB ASN A 12 2.698 4.718 7.773 1.00 6.42 C
-ATOM 82 CG ASN A 12 1.868 3.763 8.626 1.00 8.25 C
-ATOM 83 OD1 ASN A 12 1.608 2.613 8.274 1.00 12.72 O
-ATOM 84 ND2 ASN A 12 1.396 4.261 9.791 1.00 9.92 N
-ATOM 85 N PHE A 13 5.281 5.504 5.985 1.00 3.43 N
-ATOM 86 CA PHE A 13 6.010 6.341 5.037 1.00 3.49 C
-ATOM 87 C PHE A 13 6.392 5.599 3.762 1.00 3.40 C
-ATOM 88 O PHE A 13 6.165 6.082 2.654 1.00 4.07 O
-ATOM 89 CB PHE A 13 7.300 6.904 5.708 1.00 5.48 C
-ATOM 90 CG PHE A 13 8.037 7.860 4.814 1.00 5.57 C
-ATOM 91 CD1 PHE A 13 9.150 7.417 4.081 1.00 6.99 C
-ATOM 92 CD2 PHE A 13 7.584 9.176 4.647 1.00 6.52 C
-ATOM 93 CE1 PHE A 13 9.780 8.269 3.168 1.00 8.20 C
-ATOM 94 CE2 PHE A 13 8.231 10.043 3.758 1.00 6.34 C
-ATOM 95 CZ PHE A 13 9.315 9.581 3.004 1.00 6.84 C
-ATOM 96 N ASN A 14 6.947 4.384 3.893 1.00 3.64 N
-ATOM 97 CA ASN A 14 7.351 3.572 2.762 1.00 4.31 C
-ATOM 98 C ASN A 14 6.173 3.165 1.871 1.00 3.98 C
-ATOM 99 O ASN A 14 6.252 3.279 0.650 1.00 6.22 O
-ATOM 100 CB ASN A 14 8.156 2.345 3.258 1.00 5.81 C
-ATOM 101 CG ASN A 14 9.487 2.798 3.861 1.00 6.82 C
-ATOM 102 OD1 ASN A 14 9.980 3.912 3.674 1.00 9.43 O
-ATOM 103 ND2 ASN A 14 10.139 1.880 4.610 1.00 8.21 N
-ATOM 104 N VAL A 15 5.022 2.759 2.455 1.00 3.76 N
-ATOM 105 CA VAL A 15 3.781 2.513 1.713 1.00 3.98 C
-ATOM 106 C VAL A 15 3.247 3.756 1.012 1.00 3.80 C
-ATOM 107 O VAL A 15 2.860 3.716 -0.155 1.00 4.85 O
-ATOM 108 CB VAL A 15 2.697 1.915 2.607 1.00 4.71 C
-ATOM 109 CG1 VAL A 15 1.354 1.763 1.858 1.00 6.67 C
-ATOM 110 CG2 VAL A 15 3.174 0.532 3.085 1.00 6.26 C
-ATOM 111 N CYS A 16 3.271 4.921 1.688 1.00 3.79 N
-ATOM 112 CA CYS A 16 2.893 6.207 1.122 1.00 3.54 C
-ATOM 113 C CYS A 16 3.723 6.592 -0.102 1.00 3.48 C
-ATOM 114 O CYS A 16 3.213 7.155 -1.071 1.00 4.63 O
-ATOM 115 CB CYS A 16 2.985 7.293 2.226 1.00 4.58 C
-ATOM 116 SG CYS A 16 2.414 8.945 1.706 1.00 0.00 S
-ATOM 117 N ARG A 17 5.030 6.276 -0.088 1.00 3.99 N
-ATOM 118 CA ARG A 17 5.942 6.526 -1.185 1.00 3.83 C
-ATOM 119 C ARG A 17 5.817 5.581 -2.379 1.00 3.79 C
-ATOM 120 O ARG A 17 6.272 5.933 -3.465 1.00 5.39 O
-ATOM 121 CB ARG A 17 7.400 6.499 -0.656 1.00 4.11 C
-ATOM 122 CG ARG A 17 7.758 7.717 0.223 1.00 4.69 C
-ATOM 123 CD ARG A 17 7.912 9.034 -0.545 1.00 5.10 C
-ATOM 124 NE ARG A 17 9.202 8.937 -1.300 1.00 4.71 N
-ATOM 125 CZ ARG A 17 9.506 9.609 -2.418 1.00 5.28 C
-ATOM 126 NH1 ARG A 17 8.614 10.338 -3.083 1.00 6.67 N
-ATOM 127 NH2 ARG A 17 10.762 9.554 -2.859 1.00 6.41 N
-ATOM 128 N LEU A 18 5.163 4.401 -2.253 1.00 4.70 N
-ATOM 129 CA LEU A 18 4.980 3.452 -3.355 1.00 5.46 C
-ATOM 130 C LEU A 18 4.292 4.004 -4.616 1.00 5.13 C
-ATOM 131 O LEU A 18 4.806 3.720 -5.698 1.00 5.55 O
-ATOM 132 CB LEU A 18 4.206 2.174 -2.910 1.00 6.47 C
-ATOM 133 CG LEU A 18 4.968 1.173 -2.017 1.00 7.43 C
-ATOM 134 CD1 LEU A 18 4.002 0.071 -1.556 1.00 8.70 C
-ATOM 135 CD2 LEU A 18 6.161 0.529 -2.738 1.00 9.39 C
-ATOM 136 N PRO A 19 3.208 4.786 -4.632 1.00 4.28 N
-ATOM 137 CA PRO A 19 2.691 5.375 -5.867 1.00 5.38 C
-ATOM 138 C PRO A 19 3.515 6.552 -6.371 1.00 6.30 C
-ATOM 139 O PRO A 19 3.161 7.117 -7.402 1.00 9.62 O
-ATOM 140 CB PRO A 19 1.239 5.769 -5.546 1.00 5.87 C
-ATOM 141 CG PRO A 19 1.128 5.814 -4.018 1.00 6.47 C
-ATOM 142 CD PRO A 19 2.280 4.945 -3.510 1.00 6.45 C
-ATOM 143 N GLY A 20 4.588 6.971 -5.668 1.00 4.94 N
-ATOM 144 CA GLY A 20 5.421 8.088 -6.100 1.00 5.39 C
-ATOM 145 C GLY A 20 5.081 9.403 -5.456 1.00 5.03 C
-ATOM 146 O GLY A 20 5.649 10.433 -5.813 1.00 7.34 O
-ATOM 147 N THR A 21 4.164 9.407 -4.466 1.00 4.10 N
-ATOM 148 CA THR A 21 3.759 10.567 -3.667 1.00 3.94 C
-ATOM 149 C THR A 21 4.944 11.388 -3.146 1.00 3.96 C
-ATOM 150 O THR A 21 5.889 10.786 -2.619 1.00 5.82 O
-ATOM 151 CB THR A 21 2.920 10.157 -2.463 1.00 4.13 C
-ATOM 152 OG1 THR A 21 1.883 9.280 -2.872 1.00 5.45 O
-ATOM 153 CG2 THR A 21 2.256 11.352 -1.752 1.00 5.41 C
-ATOM 154 N PRO A 22 5.013 12.721 -3.275 1.00 5.04 N
-ATOM 155 CA PRO A 22 6.090 13.540 -2.721 1.00 4.69 C
-ATOM 156 C PRO A 22 6.439 13.280 -1.268 1.00 4.19 C
-ATOM 157 O PRO A 22 5.541 13.035 -0.461 1.00 4.47 O
-ATOM 158 CB PRO A 22 5.630 14.990 -2.940 1.00 7.12 C
-ATOM 159 CG PRO A 22 4.670 14.910 -4.129 1.00 7.03 C
-ATOM 160 CD PRO A 22 4.008 13.543 -3.955 1.00 4.90 C
-ATOM 161 N GLU A 23 7.732 13.375 -0.891 1.00 5.16 N
-ATOM 162 CA GLU A 23 8.163 13.184 0.484 1.00 5.31 C
-ATOM 163 C GLU A 23 7.499 14.132 1.463 1.00 4.11 C
-ATOM 164 O GLU A 23 7.125 13.716 2.550 1.00 5.11 O
-ATOM 165 CB GLU A 23 9.702 13.264 0.646 1.00 6.16 C
-ATOM 166 CG GLU A 23 10.442 12.076 -0.009 1.00 7.48 C
-ATOM 167 CD GLU A 23 11.915 11.959 0.380 1.00 9.40 C
-ATOM 168 OE1 GLU A 23 12.486 12.915 0.961 1.00 10.40 O
-ATOM 169 OE2 GLU A 23 12.456 10.856 0.105 1.00 13.32 O
-ATOM 170 N ALA A 24 7.288 15.415 1.110 1.00 4.56 N
-ATOM 171 CA ALA A 24 6.611 16.374 1.966 1.00 4.49 C
-ATOM 172 C ALA A 24 5.170 16.008 2.335 1.00 4.10 C
-ATOM 173 O ALA A 24 4.766 16.103 3.492 1.00 5.64 O
-ATOM 174 CB ALA A 24 6.629 17.729 1.240 1.00 5.80 C
-ATOM 175 N ILE A 25 4.372 15.541 1.351 1.00 0.00 N
-ATOM 176 CA ILE A 25 3.024 15.030 1.578 1.00 0.00 C
-ATOM 177 C ILE A 25 3.036 13.747 2.388 1.00 0.00 C
-ATOM 178 O ILE A 25 2.260 13.576 3.323 1.00 0.00 O
-ATOM 179 CB ILE A 25 2.273 14.811 0.262 1.00 0.00 C
-ATOM 180 CG1 ILE A 25 2.067 16.170 -0.447 1.00 0.00 C
-ATOM 181 CG2 ILE A 25 0.907 14.117 0.502 1.00 0.00 C
-ATOM 182 CD1 ILE A 25 1.529 16.047 -1.877 1.00 0.00 C
-ATOM 183 N CYS A 26 3.927 12.791 2.081 1.00 0.00 N
-ATOM 184 CA CYS A 26 4.009 11.594 2.899 1.00 0.00 C
-ATOM 185 C CYS A 26 4.529 11.797 4.300 1.00 0.00 C
-ATOM 186 O CYS A 26 3.941 11.279 5.246 1.00 0.00 O
-ATOM 187 CB CYS A 26 4.889 10.519 2.232 1.00 0.00 C
-ATOM 188 SG CYS A 26 4.040 9.792 0.827 1.00 0.00 S
-ATOM 189 N ALA A 27 5.634 12.538 4.483 1.00 0.00 N
-ATOM 190 CA ALA A 27 6.384 12.544 5.719 1.00 0.00 C
-ATOM 191 C ALA A 27 5.589 13.026 6.910 1.00 0.00 C
-ATOM 192 O ALA A 27 5.397 12.287 7.867 1.00 0.00 O
-ATOM 193 CB ALA A 27 7.658 13.402 5.567 1.00 0.00 C
-ATOM 194 N THR A 28 5.010 14.234 6.834 1.00 0.00 N
-ATOM 195 CA THR A 28 4.305 14.851 7.959 1.00 0.00 C
-ATOM 196 C THR A 28 3.107 14.039 8.415 1.00 0.00 C
-ATOM 197 O THR A 28 2.869 13.859 9.611 1.00 0.00 O
-ATOM 198 CB THR A 28 3.873 16.280 7.639 1.00 0.00 C
-ATOM 199 OG1 THR A 28 5.017 17.068 7.334 1.00 0.00 O
-ATOM 200 CG2 THR A 28 3.176 16.939 8.839 1.00 0.00 C
-ATOM 201 N TYR A 29 2.331 13.470 7.478 1.00 0.00 N
-ATOM 202 CA TYR A 29 1.126 12.728 7.800 1.00 0.00 C
-ATOM 203 C TYR A 29 1.393 11.299 8.262 1.00 0.00 C
-ATOM 204 O TYR A 29 0.542 10.661 8.880 1.00 0.00 O
-ATOM 205 CB TYR A 29 0.183 12.708 6.575 1.00 0.00 C
-ATOM 206 CG TYR A 29 -0.394 14.078 6.320 1.00 0.00 C
-ATOM 207 CD1 TYR A 29 0.240 14.979 5.450 1.00 0.00 C
-ATOM 208 CD2 TYR A 29 -1.612 14.459 6.909 1.00 0.00 C
-ATOM 209 CE1 TYR A 29 -0.344 16.213 5.136 1.00 0.00 C
-ATOM 210 CE2 TYR A 29 -2.204 15.693 6.597 1.00 0.00 C
-ATOM 211 CZ TYR A 29 -1.573 16.563 5.699 1.00 0.00 C
-ATOM 212 OH TYR A 29 -2.178 17.782 5.341 1.00 0.00 O
-ATOM 213 N THR A 30 2.602 10.759 8.031 1.00 0.00 N
-ATOM 214 CA THR A 30 2.995 9.465 8.585 1.00 0.00 C
-ATOM 215 C THR A 30 3.786 9.652 9.869 1.00 0.00 C
-ATOM 216 O THR A 30 4.098 8.696 10.569 1.00 0.00 O
-ATOM 217 CB THR A 30 3.810 8.627 7.603 1.00 0.00 C
-ATOM 218 OG1 THR A 30 5.004 9.277 7.201 1.00 0.00 O
-ATOM 219 CG2 THR A 30 2.980 8.371 6.329 1.00 0.00 C
-ATOM 220 N GLY A 31 4.060 10.915 10.258 1.00 0.00 N
-ATOM 221 CA GLY A 31 4.734 11.314 11.500 1.00 0.00 C
-ATOM 222 C GLY A 31 6.140 11.801 11.258 1.00 0.00 C
-ATOM 223 O GLY A 31 6.791 12.410 12.125 1.00 0.00 O
-ATOM 224 N CYS A 32 6.709 11.446 10.113 1.00 4.30 N
-ATOM 225 CA CYS A 32 8.082 11.671 9.731 1.00 4.89 C
-ATOM 226 C CYS A 32 8.442 13.104 9.313 1.00 5.50 C
-ATOM 227 O CYS A 32 7.599 13.952 9.020 1.00 5.82 O
-ATOM 228 CB CYS A 32 8.477 10.713 8.585 1.00 4.66 C
-ATOM 229 SG CYS A 32 8.066 8.980 8.957 1.00 0.00 S
-ATOM 230 N ILE A 33 9.756 13.416 9.272 1.00 6.02 N
-ATOM 231 CA ILE A 33 10.249 14.737 8.902 1.00 5.24 C
-ATOM 232 C ILE A 33 11.292 14.632 7.809 1.00 5.16 C
-ATOM 233 O ILE A 33 11.908 13.583 7.603 1.00 7.19 O
-ATOM 234 CB ILE A 33 10.816 15.522 10.088 1.00 5.49 C
-ATOM 235 CG1 ILE A 33 12.042 14.825 10.725 1.00 6.85 C
-ATOM 236 CG2 ILE A 33 9.671 15.725 11.105 1.00 6.45 C
-ATOM 237 CD1 ILE A 33 12.736 15.657 11.809 1.00 8.94 C
-ATOM 238 N ILE A 34 11.521 15.741 7.079 1.00 5.52 N
-ATOM 239 CA ILE A 34 12.549 15.860 6.058 1.00 6.82 C
-ATOM 240 C ILE A 34 13.563 16.855 6.575 1.00 6.92 C
-ATOM 241 O ILE A 34 13.217 17.965 6.971 1.00 9.22 O
-ATOM 242 CB ILE A 34 12.028 16.370 4.712 1.00 8.11 C
-ATOM 243 CG1 ILE A 34 10.933 15.436 4.161 1.00 9.59 C
-ATOM 244 CG2 ILE A 34 13.184 16.503 3.685 1.00 9.73 C
-ATOM 245 CD1 ILE A 34 10.163 16.060 2.998 1.00 13.41 C
-ATOM 246 N ILE A 35 14.854 16.477 6.590 1.00 7.06 N
-ATOM 247 CA ILE A 35 15.930 17.365 6.994 1.00 7.52 C
-ATOM 248 C ILE A 35 16.912 17.539 5.836 1.00 6.63 C
-ATOM 249 O ILE A 35 17.045 16.622 5.010 1.00 7.90 O
-ATOM 250 CB ILE A 35 16.650 16.903 8.263 1.00 8.07 C
-ATOM 251 CG1 ILE A 35 17.336 15.529 8.101 1.00 9.41 C
-ATOM 252 CG2 ILE A 35 15.627 16.901 9.422 1.00 9.46 C
-ATOM 253 CD1 ILE A 35 18.260 15.186 9.274 1.00 9.85 C
-ATOM 254 N PRO A 36 17.608 18.681 5.702 1.00 8.07 N
-ATOM 255 CA PRO A 36 18.634 18.862 4.678 1.00 8.78 C
-ATOM 256 C PRO A 36 19.872 18.015 4.930 1.00 8.31 C
-ATOM 257 O PRO A 36 20.498 17.571 3.972 1.00 9.09 O
-ATOM 258 CB PRO A 36 18.953 20.373 4.676 1.00 9.67 C
-ATOM 259 CG PRO A 36 18.266 20.994 5.904 1.00 10.15 C
-ATOM 260 CD PRO A 36 17.370 19.899 6.490 1.00 9.53 C
-ATOM 261 N GLY A 37 20.256 17.801 6.207 1.00 8.48 N
+ATOM 1 N THR A 1 17.052 14.173 3.575 1.00 13.79 N
+ATOM 2 CA THR A 1 16.953 12.879 4.364 1.00 10.80 C
+ATOM 3 C THR A 1 15.693 12.789 5.176 1.00 9.19 C
+ATOM 4 O THR A 1 15.240 13.808 5.685 1.00 9.85 O
+ATOM 5 CB THR A 1 18.161 12.760 5.286 1.00 13.02 C
+ATOM 6 OG1 THR A 1 19.334 12.709 4.486 1.00 15.06 O
+ATOM 7 CG2 THR A 1 18.169 11.511 6.183 1.00 14.23 C
+ATOM 8 N THR A 2 15.084 11.589 5.311 1.00 7.81 N
+ATOM 9 CA THR A 2 13.816 11.413 6.012 1.00 8.31 C
+ATOM 10 C THR A 2 14.022 10.686 7.325 1.00 5.80 C
+ATOM 11 O THR A 2 14.679 9.648 7.395 1.00 6.94 O
+ATOM 12 CB THR A 2 12.738 10.690 5.200 1.00 10.32 C
+ATOM 13 OG1 THR A 2 13.128 9.386 4.790 1.00 12.81 O
+ATOM 14 CG2 THR A 2 12.469 11.465 3.907 1.00 11.90 C
+ATOM 15 N CYS A 3 13.469 11.238 8.419 1.00 5.24 N
+ATOM 16 CA CYS A 3 13.654 10.741 9.774 1.00 5.39 C
+ATOM 17 C CYS A 3 12.291 10.501 10.399 1.00 4.45 C
+ATOM 18 O CYS A 3 11.430 11.378 10.325 1.00 6.54 O
+ATOM 19 CB CYS A 3 14.406 11.785 10.639 1.00 5.99 C
+ATOM 20 SG CYS A 3 15.966 12.368 9.908 1.00 7.01 S
+ATOM 21 N CYS A 4 12.022 9.326 11.003 1.00 3.90 N
+ATOM 22 CA CYS A 4 10.694 8.962 11.470 1.00 4.24 C
+ATOM 23 C CYS A 4 10.654 8.765 12.985 1.00 3.72 C
+ATOM 24 O CYS A 4 11.638 8.318 13.568 1.00 5.30 O
+ATOM 25 CB CYS A 4 10.206 7.673 10.769 1.00 4.41 C
+ATOM 26 SG CYS A 4 9.829 7.938 9.013 1.00 0.00 S
+ATOM 27 N PRO A 5 9.561 9.088 13.685 1.00 3.96 N
+ATOM 28 CA PRO A 5 9.499 9.033 15.149 1.00 4.25 C
+ATOM 29 C PRO A 5 9.253 7.626 15.662 1.00 4.96 C
+ATOM 30 O PRO A 5 9.314 7.398 16.868 1.00 7.44 O
+ATOM 31 CB PRO A 5 8.288 9.930 15.467 1.00 5.11 C
+ATOM 32 CG PRO A 5 7.360 9.738 14.268 1.00 5.24 C
+ATOM 33 CD PRO A 5 8.355 9.700 13.117 1.00 5.20 C
+ATOM 34 N SER A 6 8.911 6.669 14.786 1.00 4.83 N
+ATOM 35 CA SER A 6 8.659 5.305 15.199 1.00 4.45 C
+ATOM 36 C SER A 6 8.773 4.379 14.008 1.00 4.99 C
+ATOM 37 O SER A 6 8.749 4.802 12.850 1.00 4.61 O
+ATOM 38 CB SER A 6 7.292 5.093 15.929 1.00 5.05 C
+ATOM 39 OG SER A 6 6.157 5.081 15.050 1.00 6.39 O
+ATOM 40 N ILE A 7 8.884 3.062 14.263 1.00 4.94 N
+ATOM 41 CA ILE A 7 8.880 2.016 13.248 1.00 6.33 C
+ATOM 42 C ILE A 7 7.574 1.977 12.449 1.00 5.32 C
+ATOM 43 O ILE A 7 7.580 1.854 11.227 1.00 6.85 O
+ATOM 44 CB ILE A 7 9.219 0.673 13.900 1.00 8.43 C
+ATOM 45 CG1 ILE A 7 10.713 0.677 14.321 1.00 9.78 C
+ATOM 46 CG2 ILE A 7 8.911 -0.511 12.955 1.00 11.70 C
+ATOM 47 CD1 ILE A 7 11.133 -0.544 15.151 1.00 9.92 C
+ATOM 48 N VAL A 8 6.409 2.155 13.113 1.00 5.02 N
+ATOM 49 CA VAL A 8 5.102 2.253 12.461 1.00 6.93 C
+ATOM 50 C VAL A 8 5.037 3.423 11.490 1.00 5.39 C
+ATOM 51 O VAL A 8 4.578 3.293 10.354 1.00 6.30 O
+ATOM 52 CB VAL A 8 3.995 2.383 13.511 1.00 9.64 C
+ATOM 53 CG1 VAL A 8 2.639 2.807 12.902 1.00 13.85 C
+ATOM 54 CG2 VAL A 8 3.835 1.028 14.224 1.00 11.97 C
+ATOM 55 N ALA A 9 5.563 4.590 11.902 1.00 3.73 N
+ATOM 56 CA ALA A 9 5.687 5.763 11.069 1.00 3.56 C
+ATOM 57 C ALA A 9 6.556 5.548 9.827 1.00 4.13 C
+ATOM 58 O ALA A 9 6.179 5.905 8.711 1.00 4.36 O
+ATOM 59 CB ALA A 9 6.264 6.885 11.942 1.00 4.80 C
+ATOM 60 N ARG A 10 7.725 4.893 9.972 1.00 3.73 N
+ATOM 61 CA ARG A 10 8.555 4.491 8.846 1.00 3.38 C
+ATOM 62 C ARG A 10 7.910 3.488 7.897 1.00 3.47 C
+ATOM 63 O ARG A 10 8.003 3.624 6.676 1.00 4.67 O
+ATOM 64 CB ARG A 10 9.909 3.932 9.342 1.00 3.95 C
+ATOM 65 CG ARG A 10 10.899 3.516 8.225 1.00 4.55 C
+ATOM 66 CD ARG A 10 11.314 4.633 7.256 1.00 5.89 C
+ATOM 67 NE ARG A 10 12.188 5.556 8.026 1.00 6.20 N
+ATOM 68 CZ ARG A 10 12.844 6.606 7.526 1.00 7.52 C
+ATOM 69 NH1 ARG A 10 12.708 6.981 6.261 1.00 10.68 N
+ATOM 70 NH2 ARG A 10 13.638 7.300 8.327 1.00 9.48 N
+ATOM 71 N SER A 11 7.210 2.460 8.408 1.00 5.19 N
+ATOM 72 CA SER A 11 6.485 1.501 7.580 1.00 4.60 C
+ATOM 73 C SER A 11 5.380 2.135 6.759 1.00 4.84 C
+ATOM 74 O SER A 11 5.267 1.892 5.557 1.00 5.84 O
+ATOM 75 CB SER A 11 5.880 0.357 8.422 1.00 5.91 C
+ATOM 76 OG SER A 11 6.939 -0.419 8.981 1.00 8.38 O
+ATOM 77 N ASN A 12 4.586 3.037 7.371 1.00 3.54 N
+ATOM 78 CA ASN A 12 3.597 3.850 6.684 1.00 4.57 C
+ATOM 79 C ASN A 12 4.229 4.770 5.632 1.00 4.14 C
+ATOM 80 O ASN A 12 3.652 4.979 4.565 1.00 5.52 O
+ATOM 81 CB ASN A 12 2.759 4.673 7.701 1.00 6.42 C
+ATOM 82 CG ASN A 12 1.911 3.747 8.567 1.00 8.25 C
+ATOM 83 OD1 ASN A 12 1.629 2.600 8.230 1.00 12.72 O
+ATOM 84 ND2 ASN A 12 1.441 4.271 9.722 1.00 9.92 N
+ATOM 85 N PHE A 13 5.444 5.321 5.882 1.00 3.43 N
+ATOM 86 CA PHE A 13 6.194 6.136 4.923 1.00 3.49 C
+ATOM 87 C PHE A 13 6.522 5.401 3.640 1.00 3.40 C
+ATOM 88 O PHE A 13 6.270 5.901 2.543 1.00 4.07 O
+ATOM 89 CB PHE A 13 7.509 6.662 5.565 1.00 5.48 C
+ATOM 90 CG PHE A 13 8.230 7.626 4.670 1.00 5.57 C
+ATOM 91 CD1 PHE A 13 9.402 7.223 4.022 1.00 6.99 C
+ATOM 92 CD2 PHE A 13 7.700 8.896 4.411 1.00 6.52 C
+ATOM 93 CE1 PHE A 13 10.014 8.055 3.090 1.00 8.20 C
+ATOM 94 CE2 PHE A 13 8.350 9.772 3.530 1.00 6.34 C
+ATOM 95 CZ PHE A 13 9.481 9.323 2.839 1.00 6.84 C
+ATOM 96 N ASN A 14 7.044 4.174 3.756 1.00 3.64 N
+ATOM 97 CA ASN A 14 7.428 3.346 2.633 1.00 4.31 C
+ATOM 98 C ASN A 14 6.223 2.974 1.765 1.00 3.98 C
+ATOM 99 O ASN A 14 6.287 3.081 0.545 1.00 6.22 O
+ATOM 100 CB ASN A 14 8.242 2.129 3.152 1.00 5.81 C
+ATOM 101 CG ASN A 14 9.551 2.624 3.774 1.00 6.82 C
+ATOM 102 OD1 ASN A 14 10.043 3.725 3.521 1.00 9.43 O
+ATOM 103 ND2 ASN A 14 10.184 1.784 4.623 1.00 8.21 N
+ATOM 104 N VAL A 15 5.066 2.621 2.378 1.00 3.76 N
+ATOM 105 CA VAL A 15 3.797 2.421 1.672 1.00 3.98 C
+ATOM 106 C VAL A 15 3.271 3.675 0.984 1.00 3.80 C
+ATOM 107 O VAL A 15 2.866 3.640 -0.178 1.00 4.85 O
+ATOM 108 CB VAL A 15 2.713 1.874 2.600 1.00 4.71 C
+ATOM 109 CG1 VAL A 15 1.354 1.740 1.872 1.00 6.67 C
+ATOM 110 CG2 VAL A 15 3.168 0.491 3.100 1.00 6.26 C
+ATOM 111 N CYS A 16 3.301 4.838 1.664 1.00 3.79 N
+ATOM 112 CA CYS A 16 2.895 6.123 1.112 1.00 3.54 C
+ATOM 113 C CYS A 16 3.720 6.540 -0.103 1.00 3.48 C
+ATOM 114 O CYS A 16 3.206 7.107 -1.066 1.00 4.63 O
+ATOM 115 CB CYS A 16 2.959 7.195 2.230 1.00 4.58 C
+ATOM 116 SG CYS A 16 2.251 8.818 1.798 1.00 0.00 S
+ATOM 117 N ARG A 17 5.031 6.246 -0.088 1.00 3.99 N
+ATOM 118 CA ARG A 17 5.936 6.512 -1.187 1.00 3.83 C
+ATOM 119 C ARG A 17 5.817 5.572 -2.385 1.00 3.79 C
+ATOM 120 O ARG A 17 6.269 5.938 -3.468 1.00 5.39 O
+ATOM 121 CB ARG A 17 7.396 6.495 -0.666 1.00 4.11 C
+ATOM 122 CG ARG A 17 7.751 7.716 0.209 1.00 4.69 C
+ATOM 123 CD ARG A 17 7.905 9.034 -0.559 1.00 5.10 C
+ATOM 124 NE ARG A 17 9.197 8.936 -1.308 1.00 4.71 N
+ATOM 125 CZ ARG A 17 9.503 9.609 -2.425 1.00 5.28 C
+ATOM 126 NH1 ARG A 17 8.614 10.341 -3.089 1.00 6.67 N
+ATOM 127 NH2 ARG A 17 10.761 9.552 -2.866 1.00 6.41 N
+ATOM 128 N LEU A 18 5.173 4.385 -2.266 1.00 4.70 N
+ATOM 129 CA LEU A 18 4.988 3.441 -3.371 1.00 5.46 C
+ATOM 130 C LEU A 18 4.297 3.996 -4.631 1.00 5.13 C
+ATOM 131 O LEU A 18 4.812 3.718 -5.713 1.00 5.55 O
+ATOM 132 CB LEU A 18 4.207 2.166 -2.926 1.00 6.47 C
+ATOM 133 CG LEU A 18 4.963 1.162 -2.034 1.00 7.43 C
+ATOM 134 CD1 LEU A 18 3.996 0.062 -1.566 1.00 8.70 C
+ATOM 135 CD2 LEU A 18 6.162 0.520 -2.747 1.00 9.39 C
+ATOM 136 N PRO A 19 3.206 4.773 -4.647 1.00 4.28 N
+ATOM 137 CA PRO A 19 2.693 5.374 -5.878 1.00 5.38 C
+ATOM 138 C PRO A 19 3.520 6.549 -6.383 1.00 6.30 C
+ATOM 139 O PRO A 19 3.165 7.118 -7.411 1.00 9.62 O
+ATOM 140 CB PRO A 19 1.240 5.768 -5.554 1.00 5.87 C
+ATOM 141 CG PRO A 19 1.129 5.800 -4.025 1.00 6.47 C
+ATOM 142 CD PRO A 19 2.275 4.919 -3.526 1.00 6.45 C
+ATOM 143 N GLY A 20 4.599 6.967 -5.686 1.00 4.94 N
+ATOM 144 CA GLY A 20 5.442 8.073 -6.130 1.00 5.39 C
+ATOM 145 C GLY A 20 5.102 9.404 -5.519 1.00 5.03 C
+ATOM 146 O GLY A 20 5.693 10.422 -5.872 1.00 7.34 O
+ATOM 147 N THR A 21 4.157 9.429 -4.558 1.00 4.10 N
+ATOM 148 CA THR A 21 3.747 10.592 -3.765 1.00 3.94 C
+ATOM 149 C THR A 21 4.925 11.403 -3.218 1.00 3.96 C
+ATOM 150 O THR A 21 5.862 10.791 -2.690 1.00 5.82 O
+ATOM 151 CB THR A 21 2.876 10.175 -2.591 1.00 4.13 C
+ATOM 152 OG1 THR A 21 1.830 9.329 -3.028 1.00 5.45 O
+ATOM 153 CG2 THR A 21 2.221 11.363 -1.861 1.00 5.41 C
+ATOM 154 N PRO A 22 4.999 12.740 -3.319 1.00 5.04 N
+ATOM 155 CA PRO A 22 6.091 13.539 -2.762 1.00 4.69 C
+ATOM 156 C PRO A 22 6.446 13.262 -1.313 1.00 4.19 C
+ATOM 157 O PRO A 22 5.551 12.990 -0.510 1.00 4.47 O
+ATOM 158 CB PRO A 22 5.644 14.997 -2.957 1.00 7.12 C
+ATOM 159 CG PRO A 22 4.679 14.941 -4.143 1.00 7.03 C
+ATOM 160 CD PRO A 22 3.992 13.588 -3.964 1.00 4.90 C
+ATOM 161 N GLU A 23 7.738 13.370 -0.931 1.00 5.16 N
+ATOM 162 CA GLU A 23 8.167 13.188 0.444 1.00 5.31 C
+ATOM 163 C GLU A 23 7.493 14.141 1.412 1.00 4.11 C
+ATOM 164 O GLU A 23 7.076 13.723 2.476 1.00 5.11 O
+ATOM 165 CB GLU A 23 9.703 13.273 0.618 1.00 6.16 C
+ATOM 166 CG GLU A 23 10.449 12.081 -0.024 1.00 7.48 C
+ATOM 167 CD GLU A 23 11.916 11.960 0.385 1.00 9.40 C
+ATOM 168 OE1 GLU A 23 12.491 12.919 0.955 1.00 10.40 O
+ATOM 169 OE2 GLU A 23 12.449 10.845 0.134 1.00 13.32 O
+ATOM 170 N ALA A 24 7.304 15.431 1.065 1.00 4.56 N
+ATOM 171 CA ALA A 24 6.621 16.391 1.921 1.00 4.49 C
+ATOM 172 C ALA A 24 5.181 16.026 2.300 1.00 4.10 C
+ATOM 173 O ALA A 24 4.760 16.189 3.446 1.00 5.64 O
+ATOM 174 CB ALA A 24 6.633 17.758 1.211 1.00 5.80 C
+ATOM 175 N ILE A 25 4.394 15.498 1.342 1.00 0.00 N
+ATOM 176 CA ILE A 25 3.048 14.999 1.592 1.00 0.00 C
+ATOM 177 C ILE A 25 3.063 13.721 2.425 1.00 0.00 C
+ATOM 178 O ILE A 25 2.374 13.609 3.439 1.00 0.00 O
+ATOM 179 CB ILE A 25 2.315 14.813 0.256 1.00 0.00 C
+ATOM 180 CG1 ILE A 25 2.106 16.205 -0.396 1.00 0.00 C
+ATOM 181 CG2 ILE A 25 0.968 14.075 0.441 1.00 0.00 C
+ATOM 182 CD1 ILE A 25 1.591 16.171 -1.842 1.00 0.00 C
+ATOM 183 N CYS A 26 3.900 12.738 2.044 1.00 0.00 N
+ATOM 184 CA CYS A 26 4.017 11.484 2.760 1.00 0.00 C
+ATOM 185 C CYS A 26 4.663 11.511 4.108 1.00 0.00 C
+ATOM 186 O CYS A 26 4.166 10.856 5.015 1.00 0.00 O
+ATOM 187 CB CYS A 26 4.774 10.456 1.922 1.00 0.00 C
+ATOM 188 SG CYS A 26 3.686 9.742 0.700 1.00 0.00 S
+ATOM 189 N ALA A 27 5.768 12.251 4.302 1.00 0.00 N
+ATOM 190 CA ALA A 27 6.485 12.285 5.562 1.00 0.00 C
+ATOM 191 C ALA A 27 5.597 12.815 6.671 1.00 0.00 C
+ATOM 192 O ALA A 27 5.416 12.207 7.723 1.00 0.00 O
+ATOM 193 CB ALA A 27 7.757 13.156 5.411 1.00 0.00 C
+ATOM 194 N THR A 28 4.900 13.915 6.374 1.00 0.00 N
+ATOM 195 CA THR A 28 3.941 14.548 7.262 1.00 0.00 C
+ATOM 196 C THR A 28 2.763 13.650 7.617 1.00 0.00 C
+ATOM 197 O THR A 28 2.370 13.577 8.777 1.00 0.00 O
+ATOM 198 CB THR A 28 3.430 15.867 6.695 1.00 0.00 C
+ATOM 199 OG1 THR A 28 4.519 16.744 6.448 1.00 0.00 O
+ATOM 200 CG2 THR A 28 2.505 16.576 7.695 1.00 0.00 C
+ATOM 201 N TYR A 29 2.188 12.890 6.652 1.00 0.00 N
+ATOM 202 CA TYR A 29 1.092 11.953 6.893 1.00 0.00 C
+ATOM 203 C TYR A 29 1.450 10.851 7.898 1.00 0.00 C
+ATOM 204 O TYR A 29 0.619 10.357 8.658 1.00 0.00 O
+ATOM 205 CB TYR A 29 0.627 11.317 5.543 1.00 0.00 C
+ATOM 206 CG TYR A 29 -0.631 10.495 5.714 1.00 0.00 C
+ATOM 207 CD1 TYR A 29 -1.844 11.140 5.999 1.00 0.00 C
+ATOM 208 CD2 TYR A 29 -0.603 9.088 5.676 1.00 0.00 C
+ATOM 209 CE1 TYR A 29 -3.002 10.399 6.268 1.00 0.00 C
+ATOM 210 CE2 TYR A 29 -1.763 8.343 5.945 1.00 0.00 C
+ATOM 211 CZ TYR A 29 -2.961 9.003 6.245 1.00 0.00 C
+ATOM 212 OH TYR A 29 -4.134 8.276 6.526 1.00 0.00 O
+ATOM 213 N THR A 30 2.716 10.423 7.904 1.00 0.00 N
+ATOM 214 CA THR A 30 3.193 9.261 8.634 1.00 0.00 C
+ATOM 215 C THR A 30 3.853 9.685 9.941 1.00 0.00 C
+ATOM 216 O THR A 30 4.161 8.862 10.791 1.00 0.00 O
+ATOM 217 CB THR A 30 4.182 8.494 7.759 1.00 0.00 C
+ATOM 218 OG1 THR A 30 5.301 9.279 7.374 1.00 0.00 O
+ATOM 219 CG2 THR A 30 3.475 8.099 6.458 1.00 0.00 C
+ATOM 220 N GLY A 31 4.006 11.011 10.161 1.00 0.00 N
+ATOM 221 CA GLY A 31 4.604 11.641 11.336 1.00 0.00 C
+ATOM 222 C GLY A 31 6.090 11.890 11.209 1.00 0.00 C
+ATOM 223 O GLY A 31 6.737 12.382 12.130 1.00 0.00 O
+ATOM 224 N CYS A 32 6.679 11.570 10.053 1.00 4.30 N
+ATOM 225 CA CYS A 32 8.086 11.718 9.747 1.00 4.89 C
+ATOM 226 C CYS A 32 8.454 13.114 9.283 1.00 5.50 C
+ATOM 227 O CYS A 32 7.612 13.925 8.913 1.00 5.82 O
+ATOM 228 CB CYS A 32 8.564 10.705 8.671 1.00 4.66 C
+ATOM 229 SG CYS A 32 8.099 8.989 9.053 1.00 0.00 S
+ATOM 230 N ILE A 33 9.758 13.438 9.290 1.00 6.02 N
+ATOM 231 CA ILE A 33 10.248 14.752 8.909 1.00 5.24 C
+ATOM 232 C ILE A 33 11.287 14.640 7.811 1.00 5.16 C
+ATOM 233 O ILE A 33 11.894 13.589 7.601 1.00 7.19 O
+ATOM 234 CB ILE A 33 10.819 15.542 10.089 1.00 5.49 C
+ATOM 235 CG1 ILE A 33 12.043 14.838 10.721 1.00 6.85 C
+ATOM 236 CG2 ILE A 33 9.676 15.745 11.110 1.00 6.45 C
+ATOM 237 CD1 ILE A 33 12.740 15.662 11.808 1.00 8.94 C
+ATOM 238 N ILE A 34 11.518 15.747 7.076 1.00 5.52 N
+ATOM 239 CA ILE A 34 12.548 15.860 6.055 1.00 6.82 C
+ATOM 240 C ILE A 34 13.562 16.853 6.573 1.00 6.92 C
+ATOM 241 O ILE A 34 13.216 17.963 6.969 1.00 9.22 O
+ATOM 242 CB ILE A 34 12.026 16.368 4.709 1.00 8.11 C
+ATOM 243 CG1 ILE A 34 10.930 15.433 4.159 1.00 9.59 C
+ATOM 244 CG2 ILE A 34 13.182 16.502 3.683 1.00 9.73 C
+ATOM 245 CD1 ILE A 34 10.157 16.054 2.997 1.00 13.41 C
+ATOM 246 N ILE A 35 14.853 16.476 6.590 1.00 7.06 N
+ATOM 247 CA ILE A 35 15.927 17.365 6.995 1.00 7.52 C
+ATOM 248 C ILE A 35 16.910 17.539 5.837 1.00 6.63 C
+ATOM 249 O ILE A 35 17.041 16.621 5.013 1.00 7.90 O
+ATOM 250 CB ILE A 35 16.649 16.904 8.262 1.00 8.07 C
+ATOM 251 CG1 ILE A 35 17.338 15.530 8.100 1.00 9.41 C
+ATOM 252 CG2 ILE A 35 15.627 16.902 9.422 1.00 9.46 C
+ATOM 253 CD1 ILE A 35 18.261 15.187 9.273 1.00 9.85 C
+ATOM 254 N PRO A 36 17.609 18.681 5.702 1.00 8.07 N
+ATOM 255 CA PRO A 36 18.635 18.864 4.677 1.00 8.78 C
+ATOM 256 C PRO A 36 19.874 18.016 4.929 1.00 8.31 C
+ATOM 257 O PRO A 36 20.501 17.575 3.972 1.00 9.09 O
+ATOM 258 CB PRO A 36 18.954 20.375 4.676 1.00 9.67 C
+ATOM 259 CG PRO A 36 18.267 20.996 5.905 1.00 10.15 C
+ATOM 260 CD PRO A 36 17.373 19.898 6.489 1.00 9.53 C
+ATOM 261 N GLY A 37 20.257 17.801 6.206 1.00 8.48 N
ATOM 262 CA GLY A 37 21.402 16.976 6.587 1.00 9.20 C
-ATOM 263 C GLY A 37 21.173 15.485 6.489 1.00 10.41 C
-ATOM 264 O GLY A 37 20.155 15.010 5.999 1.00 12.06 O
-ATOM 265 N ALA A 38 22.135 14.680 6.979 1.00 9.24 N
-ATOM 266 CA ALA A 38 22.045 13.228 6.942 1.00 9.24 C
-ATOM 267 C ALA A 38 21.924 12.592 8.321 1.00 9.60 C
-ATOM 268 O ALA A 38 21.783 11.379 8.449 1.00 13.65 O
-ATOM 269 CB ALA A 38 23.297 12.678 6.234 1.00 10.43 C
-ATOM 270 N THR A 39 21.931 13.409 9.387 1.00 8.70 N
-ATOM 271 CA THR A 39 22.003 12.917 10.760 1.00 9.46 C
-ATOM 272 C THR A 39 20.682 13.188 11.426 1.00 8.32 C
-ATOM 273 O THR A 39 20.369 14.322 11.783 1.00 9.89 O
-ATOM 274 CB THR A 39 23.100 13.597 11.581 1.00 10.72 C
-ATOM 275 OG1 THR A 39 24.336 13.521 10.885 1.00 11.66 O
-ATOM 276 CG2 THR A 39 23.303 12.893 12.932 1.00 11.81 C
-ATOM 277 N CYS A 40 19.840 12.152 11.591 1.00 7.64 N
-ATOM 278 CA CYS A 40 18.563 12.278 12.269 1.00 8.05 C
-ATOM 279 C CYS A 40 18.705 12.517 13.781 1.00 7.63 C
-ATOM 280 O CYS A 40 19.608 11.938 14.390 1.00 9.64 O
-ATOM 281 CB CYS A 40 17.680 11.035 12.004 1.00 7.80 C
-ATOM 282 SG CYS A 40 17.233 10.842 10.247 1.00 7.30 S
-ATOM 283 N PRO A 41 17.893 13.346 14.446 1.00 8.00 N
-ATOM 284 CA PRO A 41 17.917 13.485 15.903 1.00 8.96 C
-ATOM 285 C PRO A 41 17.359 12.262 16.626 1.00 9.06 C
-ATOM 286 O PRO A 41 16.727 11.405 16.011 1.00 8.82 O
-ATOM 287 CB PRO A 41 17.061 14.735 16.150 1.00 10.39 C
-ATOM 288 CG PRO A 41 16.045 14.729 15.006 1.00 10.99 C
-ATOM 289 CD PRO A 41 16.844 14.168 13.831 1.00 10.49 C
-ATOM 290 N GLY A 42 17.591 12.148 17.954 1.00 7.55 N
-ATOM 291 CA GLY A 42 17.291 10.934 18.720 1.00 8.00 C
-ATOM 292 C GLY A 42 15.836 10.630 18.985 1.00 7.22 C
-ATOM 293 O GLY A 42 15.495 9.518 19.377 1.00 8.41 O
-ATOM 294 N ASP A 43 14.941 11.596 18.754 1.00 5.54 N
-ATOM 295 CA ASP A 43 13.504 11.475 18.870 1.00 5.85 C
-ATOM 296 C ASP A 43 12.856 11.193 17.511 1.00 5.87 C
-ATOM 297 O ASP A 43 11.665 10.901 17.405 1.00 7.29 O
-ATOM 298 CB ASP A 43 12.946 12.768 19.532 1.00 6.72 C
-ATOM 299 CG ASP A 43 13.352 14.079 18.857 1.00 8.59 C
-ATOM 300 OD1 ASP A 43 14.416 14.127 18.181 1.00 9.59 O
-ATOM 301 OD2 ASP A 43 12.603 15.067 19.048 1.00 11.45 O
-ATOM 302 N TYR A 44 13.673 11.173 16.443 1.00 5.22 N
-ATOM 303 CA TYR A 44 13.270 10.779 15.107 1.00 5.56 C
-ATOM 304 C TYR A 44 14.263 9.746 14.604 1.00 4.61 C
-ATOM 305 O TYR A 44 14.912 9.900 13.573 1.00 6.04 O
-ATOM 306 CB TYR A 44 13.186 11.959 14.106 1.00 5.41 C
-ATOM 307 CG TYR A 44 12.011 12.846 14.407 1.00 5.34 C
-ATOM 308 CD1 TYR A 44 12.101 13.885 15.347 1.00 6.59 C
-ATOM 309 CD2 TYR A 44 10.794 12.642 13.735 1.00 5.94 C
-ATOM 310 CE1 TYR A 44 10.991 14.698 15.620 1.00 5.97 C
-ATOM 311 CE2 TYR A 44 9.684 13.453 14.005 1.00 5.17 C
-ATOM 312 CZ TYR A 44 9.783 14.479 14.951 1.00 5.96 C
-ATOM 313 OH TYR A 44 8.656 15.281 15.214 1.00 8.60 O
-ATOM 314 N ALA A 45 14.398 8.643 15.360 1.00 4.76 N
-ATOM 315 CA ALA A 45 15.468 7.679 15.216 1.00 5.89 C
-ATOM 316 C ALA A 45 15.166 6.498 14.298 1.00 6.67 C
-ATOM 317 O ALA A 45 15.957 5.556 14.205 1.00 7.56 O
-ATOM 318 CB ALA A 45 15.744 7.117 16.626 1.00 6.82 C
-ATOM 319 N ASN A 46 14.017 6.506 13.608 1.00 5.80 N
-ATOM 320 CA ASN A 46 13.588 5.407 12.773 1.00 6.15 C
-ATOM 321 C ASN A 46 13.309 5.866 11.326 1.00 6.61 C
-ATOM 322 O ASN A 46 13.556 7.045 10.958 1.00 7.18 O
-ATOM 323 CB ASN A 46 12.284 4.789 13.331 1.00 7.27 C
-ATOM 324 CG ASN A 46 12.476 4.235 14.733 1.00 7.98 C
-ATOM 325 OD1 ASN A 46 11.756 4.568 15.674 1.00 11.00 O
-ATOM 326 ND2 ASN A 46 13.442 3.303 14.897 1.00 10.32 N
-ATOM 327 OXT ASN A 46 12.809 5.022 10.536 1.00 0.00 O
+ATOM 263 C GLY A 37 21.174 15.486 6.491 1.00 10.41 C
+ATOM 264 O GLY A 37 20.157 15.011 5.999 1.00 12.06 O
+ATOM 265 N ALA A 38 22.134 14.680 6.981 1.00 9.24 N
+ATOM 266 CA ALA A 38 22.043 13.228 6.943 1.00 9.24 C
+ATOM 267 C ALA A 38 21.922 12.594 8.323 1.00 9.60 C
+ATOM 268 O ALA A 38 21.784 11.380 8.453 1.00 13.65 O
+ATOM 269 CB ALA A 38 23.295 12.679 6.234 1.00 10.43 C
+ATOM 270 N THR A 39 21.928 13.411 9.389 1.00 8.70 N
+ATOM 271 CA THR A 39 22.003 12.918 10.760 1.00 9.46 C
+ATOM 272 C THR A 39 20.684 13.190 11.427 1.00 8.32 C
+ATOM 273 O THR A 39 20.372 14.325 11.782 1.00 9.89 O
+ATOM 274 CB THR A 39 23.100 13.596 11.580 1.00 10.72 C
+ATOM 275 OG1 THR A 39 24.336 13.518 10.885 1.00 11.66 O
+ATOM 276 CG2 THR A 39 23.303 12.894 12.932 1.00 11.81 C
+ATOM 277 N CYS A 40 19.843 12.153 11.594 1.00 7.64 N
+ATOM 278 CA CYS A 40 18.565 12.277 12.270 1.00 8.05 C
+ATOM 279 C CYS A 40 18.704 12.517 13.782 1.00 7.63 C
+ATOM 280 O CYS A 40 19.605 11.937 14.392 1.00 9.64 O
+ATOM 281 CB CYS A 40 17.684 11.031 12.004 1.00 7.80 C
+ATOM 282 SG CYS A 40 17.245 10.833 10.245 1.00 7.30 S
+ATOM 283 N PRO A 41 17.893 13.347 14.447 1.00 8.00 N
+ATOM 284 CA PRO A 41 17.917 13.484 15.903 1.00 8.96 C
+ATOM 285 C PRO A 41 17.360 12.260 16.624 1.00 9.06 C
+ATOM 286 O PRO A 41 16.727 11.406 16.008 1.00 8.82 O
+ATOM 287 CB PRO A 41 17.060 14.734 16.150 1.00 10.39 C
+ATOM 288 CG PRO A 41 16.045 14.730 15.006 1.00 10.99 C
+ATOM 289 CD PRO A 41 16.845 14.167 13.833 1.00 10.49 C
+ATOM 290 N GLY A 42 17.593 12.145 17.952 1.00 7.55 N
+ATOM 291 CA GLY A 42 17.292 10.933 18.720 1.00 8.00 C
+ATOM 292 C GLY A 42 15.837 10.632 18.984 1.00 7.22 C
+ATOM 293 O GLY A 42 15.498 9.519 19.374 1.00 8.41 O
+ATOM 294 N ASP A 43 14.940 11.597 18.753 1.00 5.54 N
+ATOM 295 CA ASP A 43 13.505 11.475 18.870 1.00 5.85 C
+ATOM 296 C ASP A 43 12.853 11.194 17.512 1.00 5.87 C
+ATOM 297 O ASP A 43 11.662 10.906 17.408 1.00 7.29 O
+ATOM 298 CB ASP A 43 12.946 12.768 19.533 1.00 6.72 C
+ATOM 299 CG ASP A 43 13.348 14.081 18.858 1.00 8.59 C
+ATOM 300 OD1 ASP A 43 14.411 14.127 18.181 1.00 9.59 O
+ATOM 301 OD2 ASP A 43 12.600 15.070 19.050 1.00 11.45 O
+ATOM 302 N TYR A 44 13.668 11.170 16.441 1.00 5.22 N
+ATOM 303 CA TYR A 44 13.259 10.777 15.107 1.00 5.56 C
+ATOM 304 C TYR A 44 14.250 9.744 14.603 1.00 4.61 C
+ATOM 305 O TYR A 44 14.895 9.898 13.569 1.00 6.04 O
+ATOM 306 CB TYR A 44 13.179 11.957 14.106 1.00 5.41 C
+ATOM 307 CG TYR A 44 12.007 12.847 14.404 1.00 5.34 C
+ATOM 308 CD1 TYR A 44 12.096 13.886 15.343 1.00 6.59 C
+ATOM 309 CD2 TYR A 44 10.790 12.641 13.733 1.00 5.94 C
+ATOM 310 CE1 TYR A 44 10.986 14.700 15.614 1.00 5.97 C
+ATOM 311 CE2 TYR A 44 9.679 13.451 14.003 1.00 5.17 C
+ATOM 312 CZ TYR A 44 9.778 14.480 14.945 1.00 5.96 C
+ATOM 313 OH TYR A 44 8.653 15.286 15.205 1.00 8.60 O
+ATOM 314 N ALA A 45 14.390 8.644 15.361 1.00 4.76 N
+ATOM 315 CA ALA A 45 15.463 7.684 15.218 1.00 5.89 C
+ATOM 316 C ALA A 45 15.163 6.504 14.299 1.00 6.67 C
+ATOM 317 O ALA A 45 15.957 5.565 14.203 1.00 7.56 O
+ATOM 318 CB ALA A 45 15.740 7.120 16.626 1.00 6.82 C
+ATOM 319 N ASN A 46 14.012 6.507 13.611 1.00 5.80 N
+ATOM 320 CA ASN A 46 13.586 5.411 12.773 1.00 6.15 C
+ATOM 321 C ASN A 46 13.322 5.867 11.321 1.00 6.61 C
+ATOM 322 O ASN A 46 13.563 7.047 10.952 1.00 7.18 O
+ATOM 323 CB ASN A 46 12.282 4.790 13.330 1.00 7.27 C
+ATOM 324 CG ASN A 46 12.473 4.235 14.734 1.00 7.98 C
+ATOM 325 OD1 ASN A 46 11.756 4.566 15.677 1.00 11.00 O
+ATOM 326 ND2 ASN A 46 13.438 3.300 14.896 1.00 10.32 N
+ATOM 327 OXT ASN A 46 12.834 5.019 10.528 1.00 0.00 O
TER 328 ASN A 46
END
diff --git a/modelling/tests/data/1crn_rec.pdb b/modelling/tests/data/1crn_rec.pdb
index e78f6224eed82852786a737f9494605e2fdb3755..ff82efa903ff5647b49d6c22bfaa77734d532221 100644
--- a/modelling/tests/data/1crn_rec.pdb
+++ b/modelling/tests/data/1crn_rec.pdb
@@ -167,50 +167,50 @@ ATOM 166 CG GLU A 23 10.440 12.093 0.063 1.00 7.48 C
ATOM 167 CD GLU A 23 11.941 12.170 0.391 1.00 9.40 C
ATOM 168 OE1 GLU A 23 12.416 13.225 0.681 1.00 10.40 O
ATOM 169 OE2 GLU A 23 12.539 11.070 0.292 1.00 13.32 O
-ATOM 170 N ALA A 24 7.206 15.339 0.972 1.00 4.56 N
-ATOM 171 CA ALA A 24 6.625 16.316 1.907 1.00 4.49 C
-ATOM 172 C ALA A 24 5.206 15.933 2.351 1.00 4.10 C
-ATOM 173 O ALA A 24 4.867 16.052 3.523 1.00 5.64 O
-ATOM 174 CB ALA A 24 6.585 17.662 1.246 1.00 5.80 C
-ATOM 175 N ILE A 25 4.400 15.462 1.405 1.00 0.00 N
-ATOM 176 CA ILE A 25 3.013 15.077 1.697 1.00 0.00 C
-ATOM 177 C ILE A 25 2.949 13.799 2.532 1.00 0.00 C
-ATOM 178 O ILE A 25 2.149 13.704 3.465 1.00 0.00 O
-ATOM 179 CB ILE A 25 2.276 14.865 0.408 1.00 0.00 C
-ATOM 180 N CYS A 26 3.801 12.828 2.191 1.00 0.00 N
-ATOM 181 CA CYS A 26 3.820 11.519 2.858 1.00 0.00 C
-ATOM 182 C CYS A 26 4.443 11.568 4.247 1.00 0.00 C
-ATOM 183 O CYS A 26 3.895 10.981 5.191 1.00 0.00 O
-ATOM 184 CB CYS A 26 4.593 10.553 2.011 1.00 0.00 C
-ATOM 185 N ALA A 27 5.577 12.255 4.371 1.00 0.00 N
-ATOM 186 CA ALA A 27 6.381 12.218 5.600 1.00 0.00 C
-ATOM 187 C ALA A 27 5.720 12.806 6.859 1.00 0.00 C
-ATOM 188 O ALA A 27 5.714 12.148 7.900 1.00 0.00 O
-ATOM 189 CB ALA A 27 7.654 12.970 5.347 1.00 0.00 C
-ATOM 190 N THR A 28 5.158 14.043 6.781 1.00 0.00 N
-ATOM 191 CA THR A 28 4.495 14.590 7.965 1.00 0.00 C
-ATOM 192 C THR A 28 3.288 13.781 8.406 1.00 0.00 C
-ATOM 193 O THR A 28 3.207 13.408 9.584 1.00 0.00 O
-ATOM 194 CB THR A 28 4.056 15.994 7.669 1.00 0.00 C
-ATOM 195 N TYR A 29 2.381 13.481 7.483 1.00 0.00 N
-ATOM 196 CA TYR A 29 1.150 12.736 7.809 1.00 0.00 C
-ATOM 197 C TYR A 29 1.442 11.314 8.293 1.00 0.00 C
-ATOM 198 O TYR A 29 0.559 10.652 8.849 1.00 0.00 O
-ATOM 199 CB TYR A 29 0.279 12.671 6.590 1.00 0.00 C
-ATOM 200 N THR A 30 2.676 10.862 8.093 1.00 0.00 N
-ATOM 201 CA THR A 30 3.102 9.534 8.547 1.00 0.00 C
-ATOM 202 C THR A 30 3.922 9.620 9.845 1.00 0.00 C
-ATOM 203 O THR A 30 4.406 8.609 10.339 1.00 0.00 O
-ATOM 204 CB THR A 30 3.931 8.885 7.478 1.00 0.00 C
-ATOM 205 N GLY A 31 4.092 10.832 10.363 1.00 0.00 N
-ATOM 206 CA GLY A 31 4.903 11.062 11.544 1.00 0.00 C
-ATOM 207 C GLY A 31 6.393 11.105 11.251 1.00 0.00 C
-ATOM 208 O GLY A 31 7.221 10.693 12.071 1.00 0.00 O
-ATOM 209 N CYS A 32 6.755 11.608 10.078 1.00 4.30 N
-ATOM 210 CA CYS A 32 8.167 11.695 9.659 1.00 4.89 C
-ATOM 211 C CYS A 32 8.465 13.129 9.146 1.00 5.50 C
-ATOM 212 O CYS A 32 7.601 13.916 8.762 1.00 5.82 O
-ATOM 213 CB CYS A 32 8.411 10.688 8.583 1.00 4.66 C
+ATOM 170 N ALA A 24 7.184 15.340 0.984 1.00 4.56 N
+ATOM 171 CA ALA A 24 6.630 16.325 1.910 1.00 4.49 C
+ATOM 172 C ALA A 24 5.224 15.922 2.335 1.00 4.10 C
+ATOM 173 O ALA A 24 4.841 16.076 3.489 1.00 5.64 O
+ATOM 174 CB ALA A 24 6.590 17.671 1.249 1.00 5.80 C
+ATOM 175 N ILE A 25 4.450 15.401 1.376 1.00 0.00 N
+ATOM 176 CA ILE A 25 3.092 14.965 1.629 1.00 0.00 C
+ATOM 177 C ILE A 25 3.062 13.609 2.333 1.00 0.00 C
+ATOM 178 O ILE A 25 2.371 13.438 3.344 1.00 0.00 O
+ATOM 179 CB ILE A 25 2.352 14.864 0.328 1.00 0.00 C
+ATOM 180 N CYS A 26 3.813 12.637 1.816 1.00 0.00 N
+ATOM 181 CA CYS A 26 3.822 11.305 2.416 1.00 0.00 C
+ATOM 182 C CYS A 26 4.463 11.271 3.789 1.00 0.00 C
+ATOM 183 O CYS A 26 3.868 10.786 4.744 1.00 0.00 O
+ATOM 184 CB CYS A 26 4.568 10.370 1.510 1.00 0.00 C
+ATOM 185 N ALA A 27 5.693 11.780 3.893 1.00 0.00 N
+ATOM 186 CA ALA A 27 6.413 11.794 5.153 1.00 0.00 C
+ATOM 187 C ALA A 27 5.608 12.397 6.310 1.00 0.00 C
+ATOM 188 O ALA A 27 5.543 11.812 7.398 1.00 0.00 O
+ATOM 189 CB ALA A 27 7.677 12.584 4.979 1.00 0.00 C
+ATOM 190 N THR A 28 4.988 13.552 6.073 1.00 0.00 N
+ATOM 191 CA THR A 28 4.196 14.207 7.124 1.00 0.00 C
+ATOM 192 C THR A 28 3.020 13.328 7.533 1.00 0.00 C
+ATOM 193 O THR A 28 2.658 13.279 8.714 1.00 0.00 O
+ATOM 194 CB THR A 28 3.687 15.525 6.622 1.00 0.00 C
+ATOM 195 N TYR A 29 2.415 12.636 6.571 1.00 0.00 N
+ATOM 196 CA TYR A 29 1.299 11.759 6.889 1.00 0.00 C
+ATOM 197 C TYR A 29 1.753 10.591 7.751 1.00 0.00 C
+ATOM 198 O TYR A 29 0.989 10.063 8.559 1.00 0.00 O
+ATOM 199 CB TYR A 29 0.696 11.238 5.618 1.00 0.00 C
+ATOM 200 N THR A 30 3.002 10.172 7.592 1.00 0.00 N
+ATOM 201 CA THR A 30 3.538 9.056 8.363 1.00 0.00 C
+ATOM 202 C THR A 30 4.131 9.513 9.681 1.00 0.00 C
+ATOM 203 O THR A 30 4.622 8.696 10.464 1.00 0.00 O
+ATOM 204 CB THR A 30 4.598 8.364 7.559 1.00 0.00 C
+ATOM 205 N GLY A 31 4.097 10.820 9.941 1.00 0.00 N
+ATOM 206 CA GLY A 31 4.647 11.345 11.171 1.00 0.00 C
+ATOM 207 C GLY A 31 6.147 11.478 11.136 1.00 0.00 C
+ATOM 208 O GLY A 31 6.797 11.474 12.181 1.00 0.00 O
+ATOM 209 N CYS A 32 6.705 11.609 9.935 1.00 4.30 N
+ATOM 210 CA CYS A 32 8.165 11.744 9.774 1.00 4.89 C
+ATOM 211 C CYS A 32 8.488 13.127 9.150 1.00 5.50 C
+ATOM 212 O CYS A 32 7.704 14.003 9.062 1.00 5.82 O
+ATOM 213 CB CYS A 32 8.662 10.640 8.894 1.00 4.66 C
ATOM 214 N ILE A 33 9.793 13.410 9.173 1.00 6.02 N
ATOM 215 CA ILE A 33 10.280 14.760 8.823 1.00 5.24 C
ATOM 216 C ILE A 33 11.346 14.658 7.743 1.00 5.16 C
diff --git a/modelling/tests/data/1crn_sc.pdb b/modelling/tests/data/1crn_sc.pdb
index 1bc10793e2bd3b935c6d09b8d60d057855accc46..45fb2b2d0974b048005efa8fc863ed3bcd3d9edb 100644
--- a/modelling/tests/data/1crn_sc.pdb
+++ b/modelling/tests/data/1crn_sc.pdb
@@ -167,66 +167,66 @@ ATOM 166 CG GLU A 23 10.440 12.093 0.063 1.00 7.48 C
ATOM 167 CD GLU A 23 11.941 12.170 0.391 1.00 9.40 C
ATOM 168 OE1 GLU A 23 12.416 13.225 0.681 1.00 10.40 O
ATOM 169 OE2 GLU A 23 12.539 11.070 0.292 1.00 13.32 O
-ATOM 170 N ALA A 24 7.206 15.339 0.972 1.00 4.56 N
-ATOM 171 CA ALA A 24 6.625 16.316 1.907 1.00 4.49 C
-ATOM 172 C ALA A 24 5.206 15.933 2.351 1.00 4.10 C
-ATOM 173 O ALA A 24 4.867 16.052 3.523 1.00 5.64 O
-ATOM 174 CB ALA A 24 6.585 17.662 1.246 1.00 5.80 C
-ATOM 175 N ILE A 25 4.400 15.462 1.405 1.00 0.00 N
-ATOM 176 CA ILE A 25 3.013 15.077 1.697 1.00 0.00 C
-ATOM 177 C ILE A 25 2.949 13.799 2.532 1.00 0.00 C
-ATOM 178 O ILE A 25 2.149 13.704 3.465 1.00 0.00 O
-ATOM 179 CB ILE A 25 2.276 14.865 0.408 1.00 0.00 C
-ATOM 180 CG1 ILE A 25 2.083 16.162 -0.418 1.00 0.00 C
-ATOM 181 CG2 ILE A 25 0.958 14.073 0.562 1.00 0.00 C
-ATOM 182 CD1 ILE A 25 1.575 15.925 -1.850 1.00 0.00 C
-ATOM 183 N CYS A 26 3.801 12.828 2.191 1.00 0.00 N
-ATOM 184 CA CYS A 26 3.820 11.519 2.858 1.00 0.00 C
-ATOM 185 C CYS A 26 4.443 11.568 4.247 1.00 0.00 C
-ATOM 186 O CYS A 26 3.895 10.981 5.191 1.00 0.00 O
-ATOM 187 CB CYS A 26 4.593 10.553 2.011 1.00 0.00 C
-ATOM 188 SG CYS A 26 3.768 10.129 0.427 1.00 0.00 S
-ATOM 189 N ALA A 27 5.577 12.255 4.371 1.00 0.00 N
-ATOM 190 CA ALA A 27 6.381 12.218 5.600 1.00 0.00 C
-ATOM 191 C ALA A 27 5.720 12.806 6.859 1.00 0.00 C
-ATOM 192 O ALA A 27 5.714 12.148 7.900 1.00 0.00 O
-ATOM 193 CB ALA A 27 7.654 12.970 5.347 1.00 0.00 C
-ATOM 194 N THR A 28 5.158 14.043 6.781 1.00 0.00 N
-ATOM 195 CA THR A 28 4.495 14.590 7.965 1.00 0.00 C
-ATOM 196 C THR A 28 3.288 13.781 8.406 1.00 0.00 C
-ATOM 197 O THR A 28 3.207 13.408 9.584 1.00 0.00 O
-ATOM 198 CB THR A 28 4.056 15.994 7.669 1.00 0.00 C
-ATOM 199 OG1 THR A 28 5.156 16.850 7.373 1.00 0.00 O
-ATOM 200 CG2 THR A 28 3.217 16.676 8.755 1.00 0.00 C
-ATOM 201 N TYR A 29 2.381 13.481 7.483 1.00 0.00 N
-ATOM 202 CA TYR A 29 1.150 12.736 7.809 1.00 0.00 C
-ATOM 203 C TYR A 29 1.442 11.314 8.293 1.00 0.00 C
-ATOM 204 O TYR A 29 0.559 10.652 8.849 1.00 0.00 O
-ATOM 205 CB TYR A 29 0.279 12.671 6.590 1.00 0.00 C
-ATOM 206 CG TYR A 29 -0.340 14.004 6.236 1.00 0.00 C
-ATOM 207 CD1 TYR A 29 0.250 14.806 5.281 1.00 0.00 C
-ATOM 208 CD2 TYR A 29 -1.494 14.418 6.869 1.00 0.00 C
-ATOM 209 CE1 TYR A 29 -0.323 16.041 4.953 1.00 0.00 C
-ATOM 210 CE2 TYR A 29 -2.067 15.653 6.541 1.00 0.00 C
-ATOM 211 CZ TYR A 29 -1.494 16.461 5.595 1.00 0.00 C
-ATOM 212 OH TYR A 29 -2.067 17.696 5.267 1.00 0.00 O
-ATOM 213 N THR A 30 2.676 10.862 8.093 1.00 0.00 N
-ATOM 214 CA THR A 30 3.102 9.534 8.547 1.00 0.00 C
-ATOM 215 C THR A 30 3.922 9.620 9.845 1.00 0.00 C
-ATOM 216 O THR A 30 4.406 8.609 10.339 1.00 0.00 O
-ATOM 217 CB THR A 30 3.931 8.885 7.478 1.00 0.00 C
-ATOM 218 OG1 THR A 30 5.105 9.636 7.178 1.00 0.00 O
-ATOM 219 CG2 THR A 30 3.213 8.599 6.155 1.00 0.00 C
-ATOM 220 N GLY A 31 4.092 10.832 10.363 1.00 0.00 N
-ATOM 221 CA GLY A 31 4.903 11.062 11.544 1.00 0.00 C
-ATOM 222 C GLY A 31 6.393 11.105 11.251 1.00 0.00 C
-ATOM 223 O GLY A 31 7.221 10.693 12.071 1.00 0.00 O
-ATOM 224 N CYS A 32 6.755 11.608 10.078 1.00 4.30 N
-ATOM 225 CA CYS A 32 8.167 11.695 9.659 1.00 4.89 C
-ATOM 226 C CYS A 32 8.465 13.129 9.146 1.00 5.50 C
-ATOM 227 O CYS A 32 7.601 13.916 8.762 1.00 5.82 O
-ATOM 228 CB CYS A 32 8.411 10.688 8.583 1.00 4.66 C
-ATOM 229 SG CYS A 32 8.094 8.955 9.101 1.00 0.00 S
+ATOM 170 N ALA A 24 7.184 15.340 0.984 1.00 4.56 N
+ATOM 171 CA ALA A 24 6.630 16.325 1.910 1.00 4.49 C
+ATOM 172 C ALA A 24 5.224 15.922 2.335 1.00 4.10 C
+ATOM 173 O ALA A 24 4.841 16.076 3.489 1.00 5.64 O
+ATOM 174 CB ALA A 24 6.590 17.671 1.249 1.00 5.80 C
+ATOM 175 N ILE A 25 4.450 15.401 1.376 1.00 0.00 N
+ATOM 176 CA ILE A 25 3.092 14.965 1.629 1.00 0.00 C
+ATOM 177 C ILE A 25 3.062 13.609 2.333 1.00 0.00 C
+ATOM 178 O ILE A 25 2.371 13.438 3.344 1.00 0.00 O
+ATOM 179 CB ILE A 25 2.352 14.864 0.328 1.00 0.00 C
+ATOM 180 CG1 ILE A 25 2.149 16.228 -0.379 1.00 0.00 C
+ATOM 181 CG2 ILE A 25 1.039 14.053 0.415 1.00 0.00 C
+ATOM 182 CD1 ILE A 25 1.640 16.116 -1.826 1.00 0.00 C
+ATOM 183 N CYS A 26 3.813 12.637 1.816 1.00 0.00 N
+ATOM 184 CA CYS A 26 3.822 11.305 2.416 1.00 0.00 C
+ATOM 185 C CYS A 26 4.463 11.271 3.789 1.00 0.00 C
+ATOM 186 O CYS A 26 3.868 10.786 4.744 1.00 0.00 O
+ATOM 187 CB CYS A 26 4.568 10.370 1.510 1.00 0.00 C
+ATOM 188 SG CYS A 26 3.716 10.041 -0.082 1.00 0.00 S
+ATOM 189 N ALA A 27 5.693 11.780 3.893 1.00 0.00 N
+ATOM 190 CA ALA A 27 6.413 11.794 5.153 1.00 0.00 C
+ATOM 191 C ALA A 27 5.608 12.397 6.310 1.00 0.00 C
+ATOM 192 O ALA A 27 5.543 11.812 7.398 1.00 0.00 O
+ATOM 193 CB ALA A 27 7.677 12.584 4.979 1.00 0.00 C
+ATOM 194 N THR A 28 4.988 13.552 6.073 1.00 0.00 N
+ATOM 195 CA THR A 28 4.196 14.207 7.124 1.00 0.00 C
+ATOM 196 C THR A 28 3.020 13.328 7.533 1.00 0.00 C
+ATOM 197 O THR A 28 2.658 13.279 8.714 1.00 0.00 O
+ATOM 198 CB THR A 28 3.687 15.525 6.622 1.00 0.00 C
+ATOM 199 OG1 THR A 28 4.746 16.413 6.274 1.00 0.00 O
+ATOM 200 CG2 THR A 28 2.740 16.279 7.562 1.00 0.00 C
+ATOM 201 N TYR A 29 2.415 12.636 6.571 1.00 0.00 N
+ATOM 202 CA TYR A 29 1.299 11.759 6.889 1.00 0.00 C
+ATOM 203 C TYR A 29 1.753 10.591 7.751 1.00 0.00 C
+ATOM 204 O TYR A 29 0.989 10.063 8.559 1.00 0.00 O
+ATOM 205 CB TYR A 29 0.696 11.238 5.618 1.00 0.00 C
+ATOM 206 CG TYR A 29 -0.580 10.461 5.846 1.00 0.00 C
+ATOM 207 CD1 TYR A 29 -1.759 11.132 6.101 1.00 0.00 C
+ATOM 208 CD2 TYR A 29 -0.566 9.082 5.800 1.00 0.00 C
+ATOM 209 CE1 TYR A 29 -2.942 10.412 6.313 1.00 0.00 C
+ATOM 210 CE2 TYR A 29 -1.749 8.363 6.012 1.00 0.00 C
+ATOM 211 CZ TYR A 29 -2.928 9.013 6.266 1.00 0.00 C
+ATOM 212 OH TYR A 29 -4.110 8.294 6.478 1.00 0.00 O
+ATOM 213 N THR A 30 3.002 10.172 7.592 1.00 0.00 N
+ATOM 214 CA THR A 30 3.538 9.056 8.363 1.00 0.00 C
+ATOM 215 C THR A 30 4.131 9.513 9.681 1.00 0.00 C
+ATOM 216 O THR A 30 4.622 8.696 10.464 1.00 0.00 O
+ATOM 217 CB THR A 30 4.598 8.364 7.559 1.00 0.00 C
+ATOM 218 OG1 THR A 30 5.684 9.231 7.243 1.00 0.00 O
+ATOM 219 CG2 THR A 30 4.130 7.712 6.254 1.00 0.00 C
+ATOM 220 N GLY A 31 4.097 10.820 9.941 1.00 0.00 N
+ATOM 221 CA GLY A 31 4.647 11.345 11.171 1.00 0.00 C
+ATOM 222 C GLY A 31 6.147 11.478 11.136 1.00 0.00 C
+ATOM 223 O GLY A 31 6.797 11.474 12.181 1.00 0.00 O
+ATOM 224 N CYS A 32 6.705 11.609 9.935 1.00 4.30 N
+ATOM 225 CA CYS A 32 8.165 11.744 9.774 1.00 4.89 C
+ATOM 226 C CYS A 32 8.488 13.127 9.150 1.00 5.50 C
+ATOM 227 O CYS A 32 7.704 14.003 9.062 1.00 5.82 O
+ATOM 228 CB CYS A 32 8.662 10.640 8.894 1.00 4.66 C
+ATOM 229 SG CYS A 32 8.352 8.959 9.564 1.00 0.00 S
ATOM 230 N ILE A 33 9.793 13.410 9.173 1.00 6.02 N
ATOM 231 CA ILE A 33 10.280 14.760 8.823 1.00 5.24 C
ATOM 232 C ILE A 33 11.346 14.658 7.743 1.00 5.16 C
diff --git a/modelling/tests/test_pipeline.py b/modelling/tests/test_pipeline.py
index 38d6475e8a64be38979b4cbe8260928c2d182b2d..83d6e647c384f46a334aa8b870029c5fbb1b1a9b 100644
--- a/modelling/tests/test_pipeline.py
+++ b/modelling/tests/test_pipeline.py
@@ -27,6 +27,8 @@ from ost import io, mol
# io.SaveAlignment(aln, "data/1crn.fasta")
################################################################
# Code to generate reference solutions:
+# -> these files must be carefully (!!) updated each time
+# parts of the pipeline change!
################################################################
# from ost import io
# from promod3 import loop,modelling
diff --git a/scripts/loop/backbone_scorer/cb_pot.dat b/scripts/loop/backbone_scorer/cb_pot.dat
deleted file mode 100644
index 6c9b2d2a0e3ed27145bbea120dec091732c4524d..0000000000000000000000000000000000000000
Binary files a/scripts/loop/backbone_scorer/cb_pot.dat and /dev/null differ
diff --git a/scripts/loop/backbone_scorer/cbeta_pot.dat b/scripts/loop/backbone_scorer/cbeta_pot.dat
new file mode 100644
index 0000000000000000000000000000000000000000..1c7b7a480c35b3e0e1a7690116bf2baad550ce12
Binary files /dev/null and b/scripts/loop/backbone_scorer/cbeta_pot.dat differ
diff --git a/scripts/loop/backbone_scorer/create_loop_scorer.py b/scripts/loop/backbone_scorer/create_loop_scorer.py
index 681dfdc037b1dd6ed962be9d29055d5c0e1a7c48..597675d341d2aad25d94a05fe0e741b55d14ce37 100644
--- a/scripts/loop/backbone_scorer/create_loop_scorer.py
+++ b/scripts/loop/backbone_scorer/create_loop_scorer.py
@@ -12,12 +12,14 @@ has to be adjusted accordingly for different needs
"""
cb_packing_pot = CBPackingPotential.Load("cb_packing_pot.dat")
-cbeta_pot = CBetaPotential.Load("cb_pot.dat")
+cb_pot = CBetaPotential.Load("cbeta_pot.dat")
+reduced_pot = ReducedPotential.Load("reduced_pot.dat")
torsion_pot = TorsionPotential.Load("torsion_pot.dat")
hbond_pot = HBondPotential.Load("hbond_pot.dat")
cb_packing_opts = cb_packing_pot.GetOptions()
-cbeta_opts = cbeta_pot.GetOptions()
+cb_opts = cb_pot.GetOptions()
+reduced_opts = reduced_pot.GetOptions()
torsion_opts = torsion_pot.GetOptions()
hbond_opts = hbond_pot.GetOptions()
@@ -27,6 +29,8 @@ for item in torsion_opts.group_identifier:
#check whether the provided potentials are parametrized in a way
#promod can use them
+
+#check torsion
if torsion_opts.number_of_bins[0] != 1:
raise ValueError("Require torsion potential only looking at central phi/psi angles!")
if torsion_opts.number_of_bins[1] != 1:
@@ -38,9 +42,34 @@ if torsion_opts.number_of_bins[5] != 1:
if torsion_opts.number_of_bins[2] != torsion_opts.number_of_bins[3]:
raise ValueError("Require same amount of phi and psi bin for central amino acid")
-if cbeta_opts.lower_cutoff != 0.0:
+
+#check cbeta interaction
+if cb_opts.lower_cutoff != 0.0:
raise ValueError("Require lower cutoff in cbeta potential to be zero in cbeta potential")
+if cb_opts.number_of_bins < 1:
+ raise ValueError("Number of dist bins in cbeta potential must be >= 1")
+
+if cb_opts.sequence_sep < 1:
+ raise ValueError("Sequence separation in cbeta potential must be >= 1")
+
+#check reduced
+if reduced_opts.lower_cutoff != 0.0:
+ raise ValueError("Require lower cutoff in reduced potential to be zero in reduced potential")
+
+if reduced_opts.num_dist_bins < 1:
+ raise ValueError("Number of dist bins in reduced potential must be >= 1")
+
+if reduced_opts.num_angle_bins < 1:
+ raise ValueError("Number of angle bins in reduced potential must be >= 1")
+
+if reduced_opts.num_dihedral_bins < 1:
+ raise ValueError("Number of dihedral bins in reduced potential must be >= 1")
+
+if reduced_opts.sequence_sep < 1:
+ raise ValueError("Sequence separation in reduced potential must be >= 1")
+
+#check cb packing
if(cb_packing_opts.bin_size != 1):
raise ValueError("Expect bin size of cb packing potential to be 1!");
@@ -52,7 +81,8 @@ loop_scorer = loop.BackboneLoopScorer()
#let's set the parameters
loop_scorer.SetCBPackingPotentialParameters(cb_packing_opts.cutoff,cb_packing_opts.max_counts)
-loop_scorer.SetCBetaPotentialParameters(cbeta_opts.upper_cutoff, cbeta_opts.number_of_bins, cbeta_opts.sequence_sep)
+loop_scorer.SetCBetaPotentialParameters(cb_opts.upper_cutoff, cb_opts.number_of_bins, cb_opts.sequence_sep)
+loop_scorer.SetReducedPotentialParameters(reduced_opts.upper_cutoff,reduced_opts.num_dist_bins,reduced_opts.num_angle_bins,reduced_opts.num_dihedral_bins,reduced_opts.sequence_sep)
loop_scorer.SetTorsionPotentialParameters(torsion_group_identifiers,torsion_opts.number_of_bins[3])
loop_scorer.SetHBondPotentialParameters(hbond_opts.d_min, hbond_opts.d_max,
hbond_opts.alpha_min, hbond_opts.alpha_max,
@@ -61,19 +91,42 @@ loop_scorer.SetHBondPotentialParameters(hbond_opts.d_min, hbond_opts.d_max,
hbond_opts.d_bins, hbond_opts.alpha_bins,
hbond_opts.beta_bins, hbond_opts.gamma_bins)
-
#fill cbeta potential
-cbeta_bin_size = cbeta_opts.upper_cutoff / cbeta_opts.number_of_bins
+cbeta_bin_size = cb_opts.upper_cutoff / cb_opts.number_of_bins
for i in range(ost.conop.XXX):
aa_one = ost.conop.AminoAcid(i)
for j in range(ost.conop.XXX):
aa_two = ost.conop.AminoAcid(j)
d = 0.001
- for actual_bin in range(cbeta_opts.number_of_bins):
- e = cbeta_pot.GetEnergy(aa_one,aa_two,d)
+ for actual_bin in range(cb_opts.number_of_bins):
+ e = cb_pot.GetEnergy(aa_one,aa_two,d)
loop_scorer.SetCBetaEnergy(aa_one,aa_two,actual_bin,e)
d += cbeta_bin_size
+#fill reduced
+reduced_dist_bin_size = reduced_opts.upper_cutoff / reduced_opts.num_dist_bins
+reduced_angle_bin_size = np.pi / reduced_opts.num_angle_bins
+reduced_dihedral_bin_size = 2 * np.pi / reduced_opts.num_dihedral_bins
+
+for i in range(ost.conop.XXX):
+ aa_one = ost.conop.AminoAcid(i)
+ for j in range(ost.conop.XXX):
+ aa_two = ost.conop.AminoAcid(j)
+ dist = 0.001
+ for k in range(reduced_opts.num_dist_bins):
+ alpha = 0.001
+ for l in range(reduced_opts.num_angle_bins):
+ beta = 0.001
+ for m in range(reduced_opts.num_angle_bins):
+ gamma = -np.pi + 0.001
+ for n in range(reduced_opts.num_dihedral_bins):
+ e = reduced_pot.GetEnergy(aa_one,aa_two,dist,alpha,beta,gamma)
+ loop_scorer.SetReducedEnergy(aa_one,aa_two,k,l,m,n,e)
+ gamma += reduced_dihedral_bin_size
+ beta += reduced_angle_bin_size
+ alpha += reduced_angle_bin_size
+ dist += reduced_dist_bin_size
+
#fill torsion potential
torsion_angles = list()
for i in range(6):
@@ -122,5 +175,21 @@ for i in range(3):
alpha += alpha_bin_size
d += d_bin_size
+#fill ss_agreement
+psipred_states = ['H','E','C']
+psipred_confidences = [0,1,2,3,4,5,6,7,8,9]
+dssp_states = ['H','E','C','G','B','S','T','I']
+
+qmean_ss_agreement = SSAgreement()
+
+loop_scorer.SetSSAgreementParameters()
+for p_s in psipred_states:
+ for p_c in psipred_confidences:
+ for d_s in dssp_states:
+ score = qmean_ss_agreement.LogOddScore(d_s,p_s,p_c)
+ loop_scorer.SetSSAgreementScore(p_s,p_c,d_s,score)
+
+
+
loop_scorer.Save("super_awesome_loop_scorer.dat")
diff --git a/scripts/loop/backbone_scorer/hbond_pot.dat b/scripts/loop/backbone_scorer/hbond_pot.dat
index 6986e10fc7d816c629e35557e5541ac20ad8f152..82b4a959624a2797c4d8a69554f410b865dc8b1a 100644
Binary files a/scripts/loop/backbone_scorer/hbond_pot.dat and b/scripts/loop/backbone_scorer/hbond_pot.dat differ
diff --git a/scripts/loop/backbone_scorer/reduced_pot.dat b/scripts/loop/backbone_scorer/reduced_pot.dat
new file mode 100644
index 0000000000000000000000000000000000000000..04443ad6e044b75563a6a99df2bc597e84f78a7f
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diff --git a/scripts/loop/backbone_scorer/super_awesome_loop_scorer.dat b/scripts/loop/backbone_scorer/super_awesome_loop_scorer.dat
new file mode 100644
index 0000000000000000000000000000000000000000..2d787a1dd00166fcac6b78c1fbcbbc4a95cd7bc4
Binary files /dev/null and b/scripts/loop/backbone_scorer/super_awesome_loop_scorer.dat differ