Fix code style issues

Author: mdimura

FlexLabel/python/LabelLib_pymol.py

@@ -5,20 +5,20 @@
 
 # Usage example:
 # fetch 1BNA, async=0
-# remove solvent 
+# remove solvent
 # genAV('1BNA', '/1BNA/B/B/19/C5', allowed_sphere_radius=1.5)
 ## genAV('1BNA', '/1BNA/B/B/19/C5', linker_length=22.0, linker_diameter=3.0, dye_radius=4.0, disc_step=0.7, allowed_sphere_radius=2.0)
 def genAV(obstacles, attachment, linker_length=20.0, linker_diameter=2.0, dye_radius=3.5, disc_step=0.9, name=None, state=1, stripsc=True, allowed_sphere_radius=0.0, smoothSurf=True):
-  
+
   source = np.array(cmd.get_model(attachment, state).get_coord_list())
   if (source.shape[0]!=1):
     print('attachment selection must contain exactly one atom, selected: {}'.format(source.shape[0]))
     return
   source=source.reshape(3)
-  
+
   srcAt = cmd.get_model(attachment, state).atom[0]
   srcModelName = cmd.get_names('objects',0,attachment)[0]
-  
+
   obstacles = '(' + obstacles + ') and not (' + attachment + ')'
   if stripsc and isAA(srcAt.resn):
     obstacles += ' and not (' + srcModelName
@@ -27,7 +27,7 @@ def genAV(obstacles, attachment, linker_length=20.0, linker_diameter=2.0, dye_ra
     obstacles+=' and resi '+srcAt.resi+' and sidechain'+')'
   if allowed_sphere_radius > 0.0:
     obstacles+=' and not (({}) around {})'.format(attachment, allowed_sphere_radius)
-  
+
   xyzRT=np.zeros((1,4))
   nAtoms=cmd.count_atoms(obstacles)
   if nAtoms>0:
@@ -36,7 +36,7 @@ def genAV(obstacles, attachment, linker_length=20.0, linker_diameter=2.0, dye_ra
     xyzRT=np.zeros((nAtoms,4))
     for i,at in enumerate(atoms):
       xyzRT[i]=[at.coord[0],at.coord[1],at.coord[2],at.vdw]
-  
+
   av1=ll.dyeDensityAV1(xyzRT.T,source,linker_length, linker_diameter, dye_radius, disc_step)
   m=avToModel(av1)
   if len(m.atom)==0:
@@ -48,7 +48,7 @@ def genAV(obstacles, attachment, linker_length=20.0, linker_diameter=2.0, dye_ra
       name += srcAt.chain + '-'
     name +=  srcAt.resi + '-' + srcAt.name
   cmd.load_model(m, name)
-  
+
   if smoothSurf:
     surfName=name+'_surf'
     mapName=name+'_map'
@@ -68,7 +68,7 @@ def isAA(resn):
     return True
   return False
 
-def makeAtom(index, xyz, vdw, name='AV'):
+def makeAtom(index, xyz, vdw, name='AV', q=1.0):
     atom = chempy.Atom()
     atom.index = index
     atom.name = name
@@ -81,7 +81,7 @@ def makeAtom(index, xyz, vdw, name='AV'):
     atom.vdw=vdw
     atom.hetatm = False
     atom.b = 100
-    atom.q = 1
+    atom.q = q
     return atom
 
 def avToModel(av):
@@ -91,15 +91,14 @@ def avToModel(av):
 
   for i, p in enumerate(points.T):
     x, y, z, w = p
-    m.add_atom(makeAtom(i+1, [x, y, z], r))
+    m.add_atom(makeAtom(i+1, [x, y, z], r, q=w))
 
   MP = np.average(points[:3,:],axis=1,weights=points[3])
   if points.shape[1]>0:
     m.add_atom(makeAtom(points.shape[1]+1,list(MP),2.0,'AVmp'))
-  
+
   m.update_index()
   return m
 
 
 cmd.extend("genAV", genAV)
- 

FlexLabel/python/mdtraj_example.py

@@ -8,50 +8,49 @@
 import warnings
 
 # Prints inter-dye distance distribution histograms for each frame of a trajectory.
-# Labels are: donor at residue 2, acceptor at residue 27 
+# Labels are: donor at residue 2, acceptor at residue 27
 def main(args):
 	traj = md.load_pdb('http://www.rcsb.org/pdb/files/2EQQ.pdb')
-	
+
 	#strip sidechains of residues 2 and 27
 	idxs=traj.topology.select('name CB CA N C or not (resSeq 2 or resSeq 27)')
 	traj=traj.atom_slice(idxs)
-	
+
 	bins=np.linspace(0.0,80.0,41)
 	bin_centers=bins[:-1]+(bins[1]-bins[0])/2.0
-	
+
 	#get the index of donor and acceptor attachment atoms
 	donorAttIdx=traj.topology.select('name CB and resSeq 2')[0]
 	acceptorAttIdx=traj.topology.select('name CB and resSeq 27')[0]
-	
+
 	#print header
 	print('Frame#\t'+'A\t'.join('{:.1f}'.format(e) for e in bin_centers))
-	
+
 	for frIdx in range(traj.n_frames):
 		gridDonor=genAV(traj, frIdx, donorAttIdx, 20.0, 2.0, 3.5, 0.9, 0.3, 3.5+3.0)
 		gridAcceptor=genAV(traj, frIdx, acceptorAttIdx, 22.0, 2.0, 3.5, 0.9, 0.4, 3.5+3.0)
-		
+
 		donorVolSize=np.count_nonzero(np.array(gridDonor.grid) > 1.0)
 		accVolSize=np.count_nonzero(np.array(gridAcceptor.grid) > 1.0)
-		if donorVolSize==0 or accVolSize==0:	
+		if donorVolSize==0 or accVolSize==0:
 			continue
-		
+
 		distances=ll.sampleDistanceDistInv(gridDonor,gridAcceptor,1000000)
-		freq, bin_edges = np.histogram(distances,bins=bins)
+		freq, _ = np.histogram(distances,bins=bins)
 		print('{}\t'.format(frIdx)+'\t'.join(str(e) for e in freq))
-			
+
 
 # Converts mdtraj frame to xyzR array for LabelLib
 def xyzr(traj, frameId):
 	vdw=np.empty(traj.n_atoms)
 	for i,atom in enumerate(traj.topology.atoms):
 		vdw[i]=atom.element.radius
 	# For better performance `vdw` should be cached
-		
+
 	return np.column_stack([traj.xyz[frameId],vdw]).astype(np.float32).T*10.0
 
 #cvRadius does not include the dyeRadius, so one would typically set cvRadius=dyeR+const
 def genAV(traj, frameId, attachmentIdx, length, width, radius, resolution, cvFrac=None, cvRadius=0.0):
-	
 	atoms=xyzr(traj,frameId)
 	atoms[3,attachmentIdx]=0.0 #attachment atom should not be an obstacle
 	source=atoms[:3,attachmentIdx]
@@ -63,7 +62,7 @@ def genAV(traj, frameId, attachmentIdx, length, width, radius, resolution, cvFra
 	surfaceAtoms=np.vstack([atoms,labels])
 	surfaceAtoms[3]+=cvRadius
 	acv = ll.addWeights(av,surfaceAtoms)
-	
+
 	#reweight
 	acvarr=np.array(acv.grid)
 	volCV = np.count_nonzero(acvarr > 1.0)

FlexLabel/python/usage.py

@@ -16,8 +16,8 @@ def savePqrFromAtoms(fileName, atoms):
   with open(fileName, "w") as out:
     for i,at in enumerate(atoms.T):
       out.write(sz.format(i, i, at[0], at[1], at[2], 1.0, at[3]))
-    
-  
+
+
 atoms=np.array([
 [0.0, -4.0, 22.0, 1.5],
 [9.0, 0.0, 0.0, 3.0],
@@ -37,17 +37,17 @@ def savePqrFromAtoms(fileName, atoms):
 dye_radius_1 = 3.5
 simulation_grid_spaceing = 0.9
 av1 = ll.dyeDensityAV1(
-  atoms, source, 
-  linker_length, 
-  linker_width, 
-  dye_radius_1, 
+  atoms, source,
+  linker_length,
+  linker_width,
+  dye_radius_1,
   simulation_grid_spaceing
 )
 minLengthGrid = ll.minLinkerLength(
-  atoms, source, 
-  linker_length, 
-  linker_width, 
-  dye_radius_1, 
+  atoms, source,
+  linker_length,
+  linker_width,
+  dye_radius_1,
   simulation_grid_spaceing
 )
 

FlexLabel/src/FlexLabel.cxx

@@ -61,7 +61,7 @@ class Grid3DExt final : public Grid3D
 			std::numeric_limits<int>::max();
 	}
 
-	Grid3DExt(const Grid3D &grid) : Grid3D(grid)
+	explicit Grid3DExt(const Grid3D &grid) : Grid3D(grid)
 	{
 		originAdj = Vec4f(originXYZ).array() - 0.5f * discStep;
 		originAdj[3] = 0.0f;
@@ -104,7 +104,7 @@ class Grid3DExt final : public Grid3D
 private:
 	Eigen::Vector4f originAdj; // originXYZ - discStep*0.5
 	Eigen::Array4i shape4i;
-	float devNull;
+	float devNull = 0.0f;
 
 	Eigen::Array4i getIjk(const Eigen::Vector4f &xyz);
 
@@ -154,9 +154,8 @@ std::vector<Grid3DExt::edge_t> Grid3DExt::essentialNeighbours()
 	allowedDist << 1.0f, 2.0f, 3.0f, 5.0f, 6.0f;
 	allowedDist = allowedDist.cwiseSqrt() * discStep;
 	std::vector<edge_t> edges;
-	float minDiff;
 	for (const edge_t &e : fullList) {
-		minDiff = (allowedDist.array() - e.r).cwiseAbs().minCoeff();
+		float minDiff = (allowedDist.array() - e.r).cwiseAbs().minCoeff();
 		if (minDiff < discStep * 0.01f) {
 			edges.push_back(e);
 		}
@@ -257,10 +256,9 @@ void Grid3DExt::excludeConcentricSpheres(const Eigen::Matrix4Xf &xyzR,
 	const float l2out = std::pow(maxL + maxRclash, 2.0f);
 
 	Vector4f at;
-	float rAt;
 	for (int iAtom = 0; iAtom < xyzR.cols(); ++iAtom) {
 		at = xyzR.col(iAtom);
-		rAt = at[3];
+		float rAt = at[3];
 		at[3] = 0.0f;
 		const float dist2 = (center - at).squaredNorm();
 		if (dist2 > l2out) {
@@ -594,7 +592,7 @@ double meanDistanceInv(const Grid3D &g1, const Grid3D &g2,
 }
 
 std::vector<float> sampleDistanceDistInv(const Grid3D &g1, const Grid3D &g2,
-	const unsigned nsamples)
+					 const unsigned nsamples)
 {
 	// Draw distances using Inverse transform sampling
 
@@ -636,13 +634,12 @@ double meanEfficiencyUniform(const Grid3D &g1, const Grid3D &g2, const float R0,
 	const unsigned size2 = p2.cols();
 
 	double totalW = 0.0;
-	double e = 0., w;
-	unsigned i, j;
+	double e = 0.;
 	Eigen::Vector4f tmp;
 	for (unsigned s = 0; s < nsamples; s++) {
-		i = rng(size1);
-		j = rng(size2);
-		w = p1(3, i) * p2(3, j);
+		unsigned i = rng(size1);
+		unsigned j = rng(size2);
+		double w = p1(3, i) * p2(3, j);
 		totalW += w;
 		tmp = p1.col(i) - p2.col(j);
 		tmp[3] = 0.0f;
@@ -664,13 +661,12 @@ double meanDistanceUniform(const Grid3D &g1, const Grid3D &g2,
 	const unsigned size2 = p2.cols();
 
 	double totalW = 0.0;
-	double r = 0., w;
-	unsigned i, j;
+	double r = 0.;
 	Eigen::Vector4f tmp;
 	for (unsigned s = 0; s < nsamples; s++) {
-		i = rng(size1);
-		j = rng(size2);
-		w = p1(3, i) * p2(3, j);
+		unsigned i = rng(size1);
+		unsigned j = rng(size2);
+		double w = p1(3, i) * p2(3, j);
 		totalW += w;
 		tmp = p1.col(i) - p2.col(j);
 		tmp[3] = 0.0f;

README.md

@@ -5,7 +5,6 @@
 [![Anaconda-Server Version](https://anaconda.org/tpeulen/labellib/badges/version.svg)](https://anaconda.org/tpeulen/labellib)
 [![Anaconda-Server Downloads](https://anaconda.org/tpeulen/labellib/badges/downloads.svg)](https://anaconda.org/tpeulen/labellib)
 
-
 ## General description
 LabelLib is a low-level C++ library for the simulation of small probes flexibly coupled to biomolecules for the 
 development of higher-level applications and libraries. LabelLib can calculate the distribution of flexible labels 
@@ -20,7 +19,6 @@ probe are approximated by a tube and soft sphere, respectively. Details are prov
 [![DOI for citing FPS](https://img.shields.io/badge/DOI-10.1038%2Fnmeth.2222-blue.svg)](https://doi.org/10.1038/nmeth.2222)
 [![DOI for citing FPS](https://img.shields.io/badge/DOI-10.1021%2Fja105725e-blue.svg)](https://doi.org/10.1021/ja105725e).
 
-
 ![dsDNA and an AV surface][2]
 
 LabelLib is a library for programmers and provides APIs for C/C++ and Python. Furthermore, LabelLib can be integrated 
@@ -46,10 +44,9 @@ MD-simulations and the development of Python scripts handling FRET-based structu
 structural modeling. FPS can calculate accessible volumes (AVs), screen a set of structural models against experimental 
 observables, and can generate new structural models by rigid-body docking using experimental FRET data.
 
+## Building and installation
 
-# Building and installation
-
-## C++ shared library
+### C++ shared library
 
 C++ shared library can be installed from source with cmake:
 ```bash
@@ -66,7 +63,7 @@ cmake .. && make package
 sudo dpkg -i FlexLabel-*-Linux.deb
 ```
 
-## Python bindings
+### Python bindings
 
 Python bindings can be be either installed via pip or conda. Installation of the C++ library is not necessary for this.
 The python binding can be installed via pip using the following command:
@@ -78,12 +75,11 @@ The python bindings can be installed via conda using the following command:
 conda install -c tpeulen labellib
 ```
 
+## Usage
 
-# Usage
-
-## Pymol
+### Pymol
 
-To access the functionality of LabelLib in PyMOL two basic prerequisites need to be fulfilled:
+To access the functionality of LabelLib in [PyMOL][1] two basic prerequisites need to be fulfilled:
   1) LabelLib needs to be installed in the Python installation used by PyMOL
   2) The file [LabelLib_pymol.py](FlexLabel/python/LabelLib_pymol.py) needs to be downloaded and executed from 
   PyMOL's command line interace. 
@@ -116,7 +112,7 @@ As a result you should see something like this:
 
 More extended examples of `genAV()` usage can be found in [LabelLib_pymol.py](FlexLabel/python/LabelLib_pymol.py).
 
-## C++
+### C++
 
 C++ usage example can be found in [testFlexLabel.cxx](FlexLabel/test/testFlexLabel.cxx). Your own software could be 
 compiled like this:
@@ -128,7 +124,7 @@ g++ -std=c++14 -O3 -o FlexLabelTest testFlexLabel.cxx -lFlexLabel
 Possible output:
 > AV calculation took: 20.783 ms
 
-## Python
+### Python
 
 The LabelLib can be used from python as shown below in a code example.
 LabelLib requires the Cartesian-coordinates, xyz, and van der Waals radii, vdW, of the biomolecule the label is 
@@ -163,7 +159,7 @@ grid3d = np.array(grid).reshape(shape, order='F')
 ```
 Another usage example is available in [usage.py](FlexLabel/python/usage.py)
 
-# Citation
+## Citation
 If you have used LabelLib in a scientific publication, we would appreciate citations to the following paper: 
 [![DOI for citing LabelLib](https://img.shields.io/badge/DOI-10.1016%2Fj.sbi.2016.11.012-blue.svg)](https://doi.org/10.1016/j.sbi.2016.11.012)
 > Dimura, M., Peulen, T.O., Hanke, C.A., Prakash, A., Gohlke, H. and Seidel, C.A., 2016. Quantitative FRET studies and integrative modeling unravel the structure and dynamics of biomolecular systems. Current opinion in structural biology, 40, pp.163-185.