Commit c6e18071 authored by Fabrice  ALLAIN's avatar Fabrice ALLAIN

Pdbstat distance type functionnal

parent 998a96f1
......@@ -72,26 +72,20 @@ hb_dplus: 0.5
; use all, heavy atms or from a minimized
; list (CA, CB, SC) for contribution list for
; each distance restraint
; pair_product : True, False [True]
; Define if there is more than one contribution
; per atom type. If True, compute pairwise
; product between contribution lists of the 2
; residues. Otherwise, pair_list will be a
; atoms_type : all, heavy, min [min]
; use all, heavy atms or from a minimized
; list (CA, CB, SC) for contribution list for
; each distance restraint
; contributions_type : same, allvsall, onevsall [same]
; By default contributions list will be a
; simple list between atoms of the same type
; (CA-CA, CB-CB, ...)
; ambiguous_distance_restraint : True, False [False]
; Generate Ambiguous Distance Restraints.
; Otherwise, each distance restraints will have
; only one contribution (unambiguous distance
; restraints)
; ambiguous_distance_type : min, deff [min]
; compute Deff or min distance as target
; distance if reference structure given
; ambiguous_restraint_type : allvsall, onevsall [allvsall]
; generate one ADR for all contribution pairs or
; one ADR foreach atom in first res against all
; the others in second res defined by
; contribution list
; (CA-CA, CB-CB, ...). Otherwise, compute
; pairwise product between contribution
; lists of the 2 residues (onevsall and
; allvsall). In the case of ADR, onevsall will
; generate one ADR for all contribution pairs
; between an atom of the first residue against
; all the other atoms in the second residue
; distance_type : fixed, pdbstat, distfile [fixed]
; Define distance use for target distance. By
; default the target distance is fixed by
......@@ -100,22 +94,25 @@ hb_dplus: 0.5
; (not yet implemented) or given by the user can
; be used.
; pdbdistance_level : ss, res,
; groupby_method : mean, min [min]
; groupby_method : mean, min, deff [min]
; If a distance map is used for setting distance
; target, define if we use min or mean distance
; values at residu level.
; target, define if we use min, mean or deff
; distance on all the possible values.
; ambiguous_distance_restraint : True, False [False]
; Generate Ambiguous Distance Restraints.
; Otherwise, each distance restraints will have
; only one contribution (unambiguous distance
; restraints)
native_reliable: False
evfold_weight: False
neighborhood_contact: False
pair_list: min
pair_product: True
ambiguous_distance_restraint: False
ambiguous_restraint_type: onevsall
ambiguous_distance_type: min
deffpow: 6
atoms_type: min
contributions_type: same
distance_type: fixed
pdbdistance_level: ss
groupby_method: min
deffpow: 6
pdbdistance_level: ss
ambiguous_distance_restraint: False
; Parameters below used only when distance_type is set to "fixed"
restraint_distance: 2.5
lower_bound: 1.0
......
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......@@ -61,6 +61,19 @@ class SsList(object):
else:
return []
@property
def sequence(self):
"""
Returns
-------
"""
if self.ss_matrix:
return [_ for _ in zip(*self.ss_matrix)[2]]
else:
return []
def check_filetype(self, filename):
"""
......
......@@ -936,10 +936,10 @@ class ProteinMap(Map):
if scoremap is not None:
score = scoremap.iat[(int(contact[0]) - offset,
int(contact[1]) - offset)]
outfile.write("%d %d %.4f" %
outfile.write("%d %d %.4f\n" %
(contact[0], contact[1], score))
else:
outfile.write("%d %d" % (contact[0], contact[1]))
outfile.write("%d %d\n" % (contact[0], contact[1]))
class ResAtmMap(ProteinMap):
......
......@@ -849,8 +849,10 @@ class MapFileListReader(object):
if os.path.exists(filepath):
# TODO: check_type functionstr
LOG.debug("Adding %s file to watchlist", maptypes[i])
if maptypes[i].lower() == "pdb" and \
os.path.splitext(filepath)[1][1:] == "pdb":
if (maptypes[i].lower() == "pdb" and
os.path.splitext(filepath)[1][1:] == "pdb") or (
maptypes[i].lower() == "distfile" and
os.path.splitext(filepath)[1][1:] == "pdb"):
self.maps.append(PDBFile(filepath))
else:
self.maps.append(ContactMapFile(filepath,
......
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