From e370363d123488e4ee3201f19b630a5858ebb33b Mon Sep 17 00:00:00 2001
From: Nathan Baker <nathanandrewbaker@gmail.com>
Date: Thu, 17 Dec 2020 16:33:51 -0800
Subject: [PATCH] Provide surface area output by residue type.

Fixes #3.
---
 CHANGELOG.md      |  6 ++++++
 osmolytes/main.py | 13 ++++++++++---
 setup.py          |  2 +-
 3 files changed, 17 insertions(+), 4 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 151ebb6..62df752 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,11 @@
 # osmolytes
 
+## 1.2.0 (17-Dec-2020)
+
+## Additions
+
+* Output surface area per residue type
+
 ## 1.1.1 (17-Dec-2020)
 
 ### Fixes
diff --git a/osmolytes/main.py b/osmolytes/main.py
index e60e566..4f5978b 100644
--- a/osmolytes/main.py
+++ b/osmolytes/main.py
@@ -6,7 +6,7 @@
 import osmolytes
 from osmolytes.pqr import parse_pqr_file, count_residues
 from osmolytes.sasa import SolventAccessibleSurface
-from osmolytes.energy import transfer_energy
+from osmolytes.energy import transfer_energy, get_folded_areas
 
 
 assert version_info > (3, 5)
@@ -96,8 +96,6 @@ def main(args=None):
     _LOGGER.info(f"Reading PQR input from {args.pqr_path}...")
     with open(args.pqr_path, "rt") as pqr_file:
         atoms = parse_pqr_file(pqr_file)
-    count_df = count_residues(atoms)
-    _LOGGER.info(f"Protein composition:\n{count_df}")
     _LOGGER.info(
         f"Constructing protein solvent-accessible surface with "
         f"solvent radius {args.solvent_radius} and {args.surface_points} "
@@ -109,6 +107,15 @@ def main(args=None):
         num_points=args.surface_points,
         xyz_path=args.surface_output,
     )
+    counts = count_residues(atoms)
+    areas = get_folded_areas(atoms, sas).rename(
+        {"sidechain": "sidechain areas", "backbone": "backbone areas"},
+        axis="columns"
+    )
+    areas["residue counts"] = counts
+    print(areas)
+    areas = areas[["residue counts", "sidechain areas", "backbone areas"]]
+    _LOGGER.info(f"Protein composition:\n{areas}")
     _LOGGER.info("Calculating transfer energies.")
     energy_df = transfer_energy(atoms, sas)
     _LOGGER.info(f"Detailed energies (kcal/mol/M):\n{energy_df.to_string()}")
diff --git a/setup.py b/setup.py
index 2aa2e92..bc56ca0 100644
--- a/setup.py
+++ b/setup.py
@@ -8,7 +8,7 @@
 
 setuptools.setup(
     name="osmolytes",
-    version="1.1.1",
+    version="1.2.0",
     description=(
         "This code attempts to predict the influence of osmolytes on protein "
         "stability"