From 1621caa93ca2984a2a4c93a54b30fc005bb94d36 Mon Sep 17 00:00:00 2001
From: James Graham <J.A.Graham@soton.ac.uk>
Date: Thu, 8 Sep 2016 16:52:14 +0100
Subject: [PATCH] Added simulation time to Frame Fixes graphs from GROMACS
tools analysing output XTCs
---
pycgtool/frame.py | 6 +++++-
pycgtool/mapping.py | 1 +
2 files changed, 6 insertions(+), 1 deletion(-)
diff --git a/pycgtool/frame.py b/pycgtool/frame.py
index f7d0c83..eee0ac4 100644
--- a/pycgtool/frame.py
+++ b/pycgtool/frame.py
@@ -135,6 +135,7 @@ class Frame:
"""
self.residues = []
self.number = frame_start - 1
+ self.time = 0
self.numframes = 0
self.natoms = 0
self.box = np.zeros(3, dtype=np.float32)
@@ -249,6 +250,7 @@ class Frame:
i += 1
self.number += 1
+ self.time = xtc_frame.time[0]
self.box = xtc_frame.unitcell_lengths[0]
return True
# IndexError - run out of xtc frames
@@ -274,6 +276,7 @@ class Frame:
atom.coords = self.xtc.x[i]
i += 1
self.number += 1
+ self.time = self.xtc.time
self.box = np.diag(self.xtc.box)[0:3] / 10
@@ -303,13 +306,14 @@ class Frame:
xyz[0][i] = atom.coords
i += 1
+ time = np.array([self.time], dtype=np.float32)
step = np.array([self.number], dtype=np.int32)
box = np.zeros((1, 3, 3), dtype=np.float32)
for i in range(3):
box[0][i][i] = self.box[i]
- self._xtc_buffer.write(xyz, step=step, box=box)
+ self._xtc_buffer.write(xyz, time=time, step=step, box=box)
def _parse_gro(self, filename):
"""
diff --git a/pycgtool/mapping.py b/pycgtool/mapping.py
index 8a72f45..e93a010 100644
--- a/pycgtool/mapping.py
+++ b/pycgtool/mapping.py
@@ -175,6 +175,7 @@ class Mapping:
aa_residues = list(aa_residues)
cgframe = self._cg_frame_setup(aa_residues, frame.name)
+ cgframe.time = frame.time
cgframe.number = frame.number
cgframe.box = frame.box
--
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