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fixing bug from issue #50 #51

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Mar 30, 2018
Merged

fixing bug from issue #50 #51

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16 changes: 9 additions & 7 deletions PyContact/core/ContactAnalyzer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -354,8 +354,8 @@ def analyze_psf_dcd_grid(self, psf, dcd, cutoff, hbondcutoff, hbondcutangle, sel
# pass positions and distance to cython
natoms1 = len(sel1.atoms)
natoms2 = len(sel2.atoms)
pos1 = np.reshape(sel1.positions, (1, natoms1 * 3))
pos2 = np.reshape(sel2.positions, (1, natoms2 * 3))
pos1 = np.array(np.reshape(sel1.positions, (1, natoms1 * 3)), dtype=np.float64)
pos2 = np.array(np.reshape(sel2.positions, (1, natoms2 * 3)), dtype=np.float64)
xyz1 = np.array(pos1, dtype=np.float32)
xyz2 = np.array(pos2, dtype=np.float32)
# 2d array with index of atom1 being the index of the first dimension
Expand Down Expand Up @@ -383,7 +383,9 @@ def analyze_psf_dcd_grid(self, psf, dcd, cutoff, hbondcutoff, hbondcutangle, sel
continue
# distance = distarray[idx1, idx2]
# weight = self.weight_function(distance)
distance = np.linalg.norm(pos1[0][3*idx1:3*idx1+3] - pos2[0][3*idx2:3*idx2+3])
dvec = pos1[0][3*idx1:3*idx1+3] - pos2[0][3*idx2:3*idx2+3]
distance = np.sqrt(dvec.dot(dvec))
# print(dvec, distance, dvec.dtype)
# if (distance - distarray[idx1, idx2]) > 0.001:
# print("Error in distance calculations!")
# return
Expand Down Expand Up @@ -454,8 +456,8 @@ def analyze_psf_dcd_grid(self, psf, dcd, cutoff, hbondcutoff, hbondcutangle, sel
dist = np.linalg.norm(pos1[0][3*conv_hatom:3*conv_hatom+3] - pos2[0][3*idx2:3*idx2+3])
if (dist <= hbondcutoff):
donorPosition = sel1.positions[idx1]
hydrogenPosition = sel1.positions[conv_hatom]
acceptorPosition = sel2.positions[idx2]
hydrogenPosition = np.array(sel1.positions[conv_hatom], dtype=np.float64)
acceptorPosition = np.array(sel2.positions[idx2], dtype=np.float64)
v1 = hydrogenPosition - acceptorPosition
v2 = hydrogenPosition - donorPosition
v1norm = np.linalg.norm(v1)
Expand Down Expand Up @@ -483,8 +485,8 @@ def analyze_psf_dcd_grid(self, psf, dcd, cutoff, hbondcutoff, hbondcutangle, sel
dist = np.linalg.norm(pos1[0][3*idx1:3*idx1+3] - pos2[0][3*conv_hatom:3*conv_hatom+3])
if (dist <= hbondcutoff):
donorPosition = sel2.positions[idx2]
hydrogenPosition = sel2.positions[conv_hatom]
acceptorPosition = sel1.positions[idx1]
hydrogenPosition = np.array(sel2.positions[conv_hatom], dtype=np.float64)
acceptorPosition = np.array(sel1.positions[idx1], dtype=np.float64)
v1 = hydrogenPosition - acceptorPosition
v2 = hydrogenPosition - donorPosition
v1norm = np.linalg.norm(v1)
Expand Down
15 changes: 8 additions & 7 deletions PyContact/core/multi_trajectory.py
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Original file line number Diff line number Diff line change
Expand Up @@ -71,8 +71,8 @@ def loop_trajectory_grid(sel1c, sel2c, indices1, indices2, config, suppl, selfIn
currentFrameContacts = []
natoms1 = len(s1)
natoms2 = len(s2)
pos1 = np.reshape(s1, (1, natoms1 * 3))
pos2 = np.reshape(s2, (1, natoms2 * 3))
pos1 = np.array(np.reshape(s1, (1, natoms1 * 3)), dtype=np.float64)
pos2 = np.array(np.reshape(s2, (1, natoms2 * 3)), dtype=np.float64)
xyz1 = np.array(pos1, dtype=np.float32)
xyz2 = np.array(pos2, dtype=np.float32)
# 2d array with index of atom1 being the index of the first dimension
Expand All @@ -96,7 +96,8 @@ def loop_trajectory_grid(sel1c, sel2c, indices1, indices2, config, suppl, selfIn
continue
# distance = distarray[idx1, idx2]
# weight = weight_function(distance)
distance = np.linalg.norm(pos1[0][3*idx1:3*idx1+3] - pos2[0][3*idx2:3*idx2+3])
dvec = pos1[0][3*idx1:3*idx1+3] - pos2[0][3*idx2:3*idx2+3]
distance = np.sqrt(dvec.dot(dvec))
# if (distance - distarray[idx1, idx2]) > 0.001:
# print("Error in distance calculations!")
# return
Expand Down Expand Up @@ -165,8 +166,8 @@ def loop_trajectory_grid(sel1c, sel2c, indices1, indices2, config, suppl, selfIn
dist = np.linalg.norm(pos1[0][3*conv_hatom:3*conv_hatom+3] - pos2[0][3*idx2:3*idx2+3])
if (dist <= hbondcutoff):
donorPosition = s1[idx1]
hydrogenPosition = s1[conv_hatom]
acceptorPosition = s2[idx2]
hydrogenPosition = np.array(s1[conv_hatom], dtype=np.float64)
acceptorPosition = np.array(s2[idx2], dtype=np.float64)
v1 = hydrogenPosition - acceptorPosition
v2 = hydrogenPosition - donorPosition
v1norm = np.linalg.norm(v1)
Expand Down Expand Up @@ -194,8 +195,8 @@ def loop_trajectory_grid(sel1c, sel2c, indices1, indices2, config, suppl, selfIn
dist = np.linalg.norm(pos1[0][3*idx1:3*idx1+3] - pos2[0][3*conv_hatom:3*conv_hatom+3])
if (dist <= hbondcutoff):
donorPosition = s2[idx2]
hydrogenPosition = s2[conv_hatom]
acceptorPosition = s1[idx1]
hydrogenPosition = np.array(s2[conv_hatom], dtype=np.float64)
acceptorPosition = np.array(s1[idx1], dtype=np.float64)
v1 = hydrogenPosition - acceptorPosition
v2 = hydrogenPosition - donorPosition
v1norm = np.linalg.norm(v1)
Expand Down
6 changes: 5 additions & 1 deletion PyContact/gui/Canvas.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@
from PyQt5.QtCore import QSize, QRect
from PyQt5.QtCore import pyqtSignal, QObject
import numpy as np
import math

from ..core.ContactFilters import *
from .LabelView import LabelView
Expand Down Expand Up @@ -195,9 +196,12 @@ def renderContact(self, generator):
alpha = merged_score * self.alphaFactor
if alpha > 255:
alpha = 255
if math.isnan(alpha):
alpha = 255
if self.colorScheme == ColorScheme.bbsc:
# pass
p.setBrush(QColor(bbScColor[0], bbScColor[1], bbScColor[2], alpha))
p.setBrush(QColor(bbScColor[0], bbScColor[1], bbScColor[2],
alpha))
elif self.colorScheme == ColorScheme.custom:
color = QColor(self.customColor)
color.setAlpha(alpha)
Expand Down
4 changes: 2 additions & 2 deletions PyContact/gui/VMDControlPanel.py
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Original file line number Diff line number Diff line change
Expand Up @@ -121,7 +121,7 @@ def initUI(self):
self.fancyPrepared = False
self.setLayout(self.grid)
self.setWindowTitle("VMD Control Panel")
self.resize(640, 144)
self.resize(640, 444)
self.grid.setGeometry(QtCore.QRect(10, 10, 621, 431))

self.startButton = QPushButton("Start VMD")
Expand Down Expand Up @@ -289,7 +289,7 @@ def pushConnectVMD(self):
def pushStartVMD(self):
self.startButton.setEnabled(False)
self.stopButton.setEnabled(True)
# self.commandButton.setEnabled(True)
self.commandButton.setEnabled(True)
response = self.vmd.start()
if response == -1:
self.connectButton.setEnabled(True)
Expand Down