Jamesk add LRA app again with fixed tests

docs/apps/prody/lra.rst

@@ -0,0 +1,104 @@
+.. _prody-lra:
+
+prody lra
+====================
+
+Usage
+--------------------
+
+Running :command:`prody lra -h` displays::
+
+  usage: prody lra [-h] [--quiet] [--examples] [-n INT] [-s SEL] [-a] [-o PATH]
+                   [-e] [-r] [-u] [-q] [-v] [-z] [-t STR] [-j] [-p STR] [-f STR]
+                   [-d STR] [-x STR] [-A] [-R] [-Q] [-J STR] [-F STR] [-D INT]
+                   [-W FLOAT] [-H FLOAT] [--psf PSF | --pdb PDB] [--aligned]
+                   dcd
+
+  positional arguments:
+    dcd                   file in DCD or PDB format
+
+  optional arguments:
+    -h, --help            show this help message and exit
+    --quiet               suppress info messages to stderr
+    --examples            show usage examples and exit
+    --psf PSF             PSF filename
+    --pdb PDB             PDB filename
+    --aligned             trajectory is already aligned
+
+  parameters:
+    -n INT, --number-of-modes INT
+                          number of non-zero eigenvectors (modes) to calculate
+                          (default: 1, note difference here)
+    -s SEL, --select SEL  atom selection (default: "protein and name CA or
+                          nucleic and name P C4' C2")
+
+  output:
+    -a, --all-output      write all outputs
+    -o PATH, --output-dir PATH
+                          output directory (default: .)
+    -e, --eigenvs         write eigenvalues/vectors
+    -r, --cross-correlations
+                          write cross-correlations
+    -u, --heatmap         write cross-correlations heatmap file
+    -q, --square-fluctuations
+                          write square-fluctuations
+    -v, --covariance      write covariance matrix
+    -z, --npz             write compressed ProDy data file
+    -t STR, --extend STR  write NMD file for the model extended to "backbone"
+                          ("bb") or "all" atoms of the residue, model must have
+                          one node per residue
+    -j, --projection      write projections onto LR modes
+
+    -i, --
+
+  output options:
+    -p STR, --file-prefix STR
+                          output file prefix (default: pdb_lra)
+    -f STR, --number-format STR
+                          number output format (default: %12g)
+    -d STR, --delimiter STR
+                          number delimiter (default: " ")
+    -x STR, --extension STR
+                          numeric file extension (default: .txt)
+
+  figures:
+    -A, --all-figures     save all figures
+    -R, --cross-correlations-figure
+                          save cross-correlations figure
+    -Q, --square-fluctuations-figure
+                          save square-fluctuations figure
+    -J STR, --projection-figure STR
+                          save projections onto specified subspaces, e.g. "1,2"
+                          for projections onto PCs 1 and 2; "1,2 1,3" for
+                          projections onto PCs 1,2 and 1, 3; "1 1,2,3" for
+                          projections onto PCs 1 and 1, 2, 3
+
+  figure options:
+    -F STR, --figure-format STR
+                          pdf (default: pdf)
+    -D INT, --dpi INT     figure resolution (dpi) (default: 300)
+    -W FLOAT, --width FLOAT
+                          figure width (inch) (default: 8.0)
+    -H FLOAT, --height FLOAT
+                          figure height (inch) (default: 6.0)
+
+Examples
+--------------------
+
+Running :command:`prody lra --examples` displays::
+
+  This command performs logistic regression analysis (LRA) calculations for 
+  given multi-model PDB structure or DCD format trajectory file and outputs 
+  results in NMD format.  If a PDB identifier is given, structure file will be
+  downloaded from the PDB FTP server.  DCD files may be accompanied with
+  PDB or PSF files to enable atoms selections.
+
+  Fetch pdb 2k39, perform LRA calculations, and output NMD file:
+
+    $ prody lra 2k39
+
+  Fetch pdb 2k39 and perform calculations for backbone of residues up to
+  71, and save all output and figure files:
+
+    $ prody lra 2k39 --select "backbone and resnum < 71" -a -A
+

docs/reference/apps/prody_lra.rst

@@ -0,0 +1,6 @@
+LRA Application
+===============
+
+.. automodule:: prody.apps.prody_apps.prody_lra
+   :members:
+   :undoc-members:

environment.yml

@@ -11,7 +11,7 @@ dependencies:
   - numpy
   - pyparsing<=3.1.1
   - scipy
-  - matplotlib # REQUIRED: Prevents import errors and allows font caching
+  - matplotlib # REQUIRED: Prevents import errors and allows font caching and app outputs
   - nose
   - pytest
   - pytest-timeout  # Added here for caching
@@ -20,9 +20,10 @@ dependencies:
   - mdtraj
   - openmm
   - clustalw
-
+  - scikit-learn
+  - kmedoids
+
   # Pip packages
   - pip
   - pip:
     - mmtf-python
-    - scikit-learn

prody/apps/prody_apps/__init__.py

@@ -27,7 +27,7 @@
 
 PRODY_APPS = ['anm', 'gnm', 'pca', 'eda', 'align', 'blast', 'biomol',
                   'catdcd', 'contacts', 'fetch', 'select', 'energy', 
-                  'clustenm', 'rtb']
+                  'clustenm', 'rtb', 'lra']
 
 __all__ = ['prody_main']
 

prody/apps/prody_apps/nmaoptions.py

@@ -49,13 +49,14 @@
            'addNMAFigures', 'addNMAFigureOptions']
 
 
-def addNMAParameters(parser, include_nproc=True):
+def addNMAParameters(parser, include_nproc=True, include_nmodes=True):
 
     parser = parser.add_argument_group('parameters')
 
-    parser.add_argument('-n', '--number-of-modes', dest='nmodes', type=int,
-        default=DEFAULTS['nmodes'], metavar='INT',
-        help=HELPTEXT['nmodes'] + ' (default: %(default)s)')
+    if include_nmodes:
+        parser.add_argument('-n', '--number-of-modes', dest='nmodes', type=int,
+            default=DEFAULTS['nmodes'], metavar='INT',
+            help=HELPTEXT['nmodes'] + ' (default: %(default)s)')
 
     parser.add_argument('-s', '--select', dest='select', type=str,
         default=DEFAULTS['select'], metavar='STR',