Commit 1cf6e97f authored by fabrice's avatar fabrice

Bug fixe: wrong atom list when pair_list set to all (add terminal atoms)

parent 8d077988
This diff is collapsed.
No preview for this file type
......@@ -80,7 +80,7 @@ class AriaEcContactMap(object):
# Use only position filter
# self.filter(fo.mapdict, fo.filetype, fo.contactlist,
# self.protein, clashlist=fo.clashlist,
# protname=self.protname,
# outprefix=self.outprefix,
# outdir=self.settings.outdir, mapfilters="pos")
self.allresmap[(fo.filename, fo.filetype)] = fo.mapdict
......
No preview for this file type
No preview for this file type
......@@ -54,7 +54,7 @@ class AriaEcSetup:
# -------------------------------------------------------------------- #
self.outprefix = get_filename(self.settings.setup.args.get("seq",
None))
self.converter.protname = self.outprefix
self.converter.outprefix = self.outprefix
# ------------------------- Load sequence ---------------------------- #
self.protein.set_aa_sequence(self.settings.setup.args.get("seq", None))
# -------------- Load secondary structure prediction ----------------- #
......@@ -69,7 +69,7 @@ class AriaEcSetup:
# ---------------------------- Processing ---------------------------- #
# -------------------------------------------------------------------- #
# TODO: write submatrix in a file
# TODO: change read method in reader to __call__ ?
# TODO: change read method in reader to __call__
# -------------------------- contact maps ---------------------------- #
self.reader.read(self.settings.setup.args.get("infiles"),
filetypelist=self.settings.setup.args.get("contact_types"),
......@@ -142,7 +142,8 @@ class AriaEcSetup:
# ----------------------------- SEQ file ----------------------------- #
self.protein.write_seq(os.path.join(self.settings.infra.get("others", ''),
self.outprefix + ".seq"))
# Load aria molecule object from generated seq file
self.converter.load_molecule(self.protein.seqfile_path)
# --------------------------- TBL restraints ------------------------- #
# Setting contact number limit for hbmap
n_hb = int(len(self.protein.aa_sequence.sequence) *
......@@ -159,16 +160,16 @@ class AriaEcSetup:
self.allresmap, self.targetmap)
# --------------------------- XML SEQ file --------------------------- #
seq_file = self.converter.write_xmlseq(self.protein.seqfile_path)
xmlseq_file = self.converter.write_xmlseq()
# ---------------------- ARIA XML project file ----------------------- #
aria_template = self.settings.main.config["ariaproject_template"] if \
self.settings.main.config["ariaproject_template"] and \
os.path.exists(self.settings.main.config["ariaproject_template"])\
else None
self.converter.write_project(aria_template,
seq_file, dist_files, tbl_files,
desc="_".join(sorted(self.allresmap.keys())))
self.converter.write_ariaproject(aria_template,
xmlseq_file, dist_files, tbl_files,
desc="_".join(sorted(self.allresmap.keys())))
# ------------------------------ others ------------------------------ #
self.write_optional_files()
......
No preview for this file type
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment