Coor class

class pdb_manip_py.pdb_manip.Coor(coor_in=None, pdb_lines=None)

Topologie base on coordinates like pdb or gro.

The coor object containt a dictionnary of atoms indexed on the atom num and the crystal packing info.

Parameters

• atom_dict (dict) – dictionnary of atom

• crystal_pack (str) – crystal packing

Atom dictionnary parameters

Parameters

• field (str) – pdb field

• num (int) – atom number

• name (str) – atom name

• alter_loc (str) – atom number

• res_name (str) – residue name (3 letters)

• chain (str) – chain ID

• res_num (int) – residue number (based on pdb file)

• uniq_resid (int) – unique residue number

• insert_res (str) – atom number

• xyz – coordinate

• occ (float) – occupation

• beta (float) – beta flactor

Note

The atom num index in the dictionnary, is not the same as the atom_num field of the dictionnary.

Note

Files necessary for testing : ../test/input/1y0m.pdb, ../test/input/1rxz.pdb and ../test/input/4n1m.pdb. To do the unitary test, execute pdb_mani.py (-v for verbose mode)

Todo

Add an atom class ?

add_zinc_finger(ZN_pdb, cutoff=3.2)

Change protonation state of cysteins and histidine coordinating Zinc atoms. To do after correct_his_name and correct_cys_name, in order that protonation is recognize by pdb2gmx.

Example

>>> try: 
...   print("Start import")
...   from . import pdb2pqr
... except ImportError:
...   import pdb2pqr
Start import...
>>> TEST_OUT = str(getfixture('tmpdir'))
>>> show_log()
>>> # Read the pdb 1jd4 and keep only chain A
>>> input_pdb = Coor(os.path.join(TEST_PATH, '1jd4.pdb'))        
Succeed to read file ...1jd4.pdb ,  1586 atoms found
>>> chain_A = input_pdb.select_part_dict(selec_dict={'chain': ['A']})
>>> chain_A.write_pdb(os.path.join(TEST_OUT, '1jd4_A.pdb'))        
Succeed to save file ...1jd4_A.pdb
>>>
>>> # Compute protonation with pdb2pqr:
>>> pdb2pqr.compute_pdb2pqr(os.path.join(TEST_OUT, '1jd4_A.pdb'),os.path.join(TEST_OUT, '1jd4.pqr')) 
Succeed to read file ...1jd4_A.pdb ,  793 atoms found
Succeed to save file ...tmp_pdb2pqr.pdb
pdb2pqr30... --ff CHARMM --ffout CHARMM --keep-chain --titration-state-method=propka --with-ph=7.00...tmp_pdb2pqr.pdb ...1jd4.pqr
0
>>> prot_coor = Coor(os.path.join(TEST_OUT, '1jd4.pqr'))
Succeed to read file ...1jd4.pqr ,  1549 atoms found
>>> prot_coor.correct_cys_name() 
<...Coor object at 0x...
>>> prot_coor.correct_his_name() 
<...Coor object at 0x...
>>> prot_coor.correct_chain() 
Chain: A  Residue: 0 to 95
<...Coor object at 0x...
>>> ZN_index = prot_coor.get_index_selection({'name': ['ZN']})
>>> print(len(ZN_index))
0
>>> prot_coor.add_zinc_finger(os.path.join(TEST_OUT, '1jd4_A.pdb'))        
Succeed to read file ...1jd4_A.pdb ,  793 atoms found
Presence of 1 Zinc detected
change cystein residue(s) : [48, 51, 75]
change histidine residue(s) : [68]
True
>>> ZN_index = prot_coor.get_index_selection({'name': ['ZN']})
>>> print(len(ZN_index))
1

Note

This function seems useless. Since last version of pdb2pqr residue name seems correct.

align_principal_axis(axis=2, vector=[0, 0, 1], selec_dict={})

Align principal axis with index axis with vector.

Taken from: https://github.com/MDAnalysis/mdanalysis/blob/develop/package/MDAnalysis/core/topologyattrs.py

Parameters

• axis (int (Default 2)) – principal axis to align (0, 1, or 2)

• vector (list (Default z axis)) – vector to align

• selec_dict (dict, default={'name': ['CA']}) – selection dictionnary

Example

>>> show_log()
>>> prot_coor = Coor(os.path.join(TEST_PATH, '1y0m.pdb'))        
Succeed to read file ...1y0m.pdb ,  648 atoms found
>>> prot_coor.align_principal_axis()
Do a rotation of 66.43°
>>> prot_coor.align_principal_axis()
Do a rotation of 0.00°

static align_seq(seq_1, seq_2, gap_cost=-8, gap_extension=-2)

Align two amino acid sequences using the Waterman - Smith Algorithm.

Parameters

• seq_1 (str) – amino acid sequence 1

• seq_2 (str) – amino acid sequence 2

• gap_cost (int (Default -8)) – Gap cost

• gap_extension (int (Default -2)) – Gap extension cost

Returns

the two aligned sequences

Return type

str, str

Example

>>> seq_1 = 'AQDMVSPPPPIADEPLTVNTGIYLIECYSLDDKAETFKVNAFLSLSWKDRRLAFDPVRSGVRVKTYEPEAIWIPEIRFVNVENARDADVVDISVSPDGTVQYLERFSARVLSPLDFRRYPFDSQTLHIYLIVRSVDTRNIVLAVDLEKVGKNDDVFLTGWDIESFTAVVKPANFALEDRLESKLDYQLRISRQYFSYIPNIILPMLFILFISWTAFWSTSYEANVTLVVSTLIAHIAFNILVETNLPKTPYMTYTGAIIFMIYLFYFVAVIEVTVQHYLKVESQPARAASITRASRIAFPVVFLLANIILAFLFFGF'
>>> seq_2 = 'APSEFLDKLMGKVSGYDARIRPNFKGPPVNVTCNIFINSFGSIAETTMDYRVNIFLRQQWNDPRLAYSEYPDDSLDLDPSMLDSIWKPDLFFANEKGANFHEVTTDNKLLRISKNGNVLYSIRITLVLACPMDLKNFPMDVQTCIMQLESFGYTMNDLIFEWDEKGAVQVADGLTLPQFILKEEKDLRYCTKHYNTGKFTCIEARFHLERQMGYYLIQMYIPSLLIVILSWVSFWINMDAAPARVGLGITTVLTMTTQSSGSRASLPKVSYVKAIDIWMAVCLLFVFSALLEYAAVNFIARAGTKLFISRAKRIDTVSRVAFPLVFLIFNIFYWITYKLVPR'
>>> align_seq_1, align_seq_2 = Coor.align_seq(seq_1, seq_2)
>>> Coor.print_align_seq(align_seq_1, align_seq_2)        
-------------AQDMVSPPPPIADEPLTVNTGIYLIECYSLDDKAETFKVNAFLSLSWKDRRLAFDPVRS-GVRVKTY
             |   |   * |   *||*| |*|| |  *| | |  ||** **  |*|* ***||   | || |
APSEFLDKLMGKVSGYDARIRPNFKGPPVNVTCNIFINSFGSIAETTMDYRVNIFLRQQWNDPRLAYSEYPDDSLDLDPS

EPEAIWIPEIRFVNVENARDADVV----DISVSPDGTVQYLERFSARVLSPLDFRRYPFDSQTLHIYLIVRSVDTRNIVL
  ||** *|| *|* ||*|  |*|     | |* |*|* *  *||  |  *|*||||*|* **  | *   |   |||||
MLDSIWKPDLFFANEKGANFHEVTTDNKLLRISKNGNVLYSIRITLVLACPMDLKNFPMDVQTCIMQLESFGYTMNDLIF

AVDLEKVGKNDDVFLTGWDIESFTAVV-KPANFALEDRLESK---LDYQLRISRQYFSYIPNIILPMLFILFISWTAFW-
  * ** *  |     *  | |*     *  ||| |    |*   || |||||**   *| || |* *|*|||**||**
EWD-EK-GAVQ--VADGLTLPQFILKEEKDLRYCTKHYNTGKFTCIEARFHLERQMGYYLIQMYIPSLLIVILSWVSFWI

-STSYEANVTLVVSTLIAHIAFNILVETNLPKTPYMTYTGAIIFMIYLFYFVAVIEVTVQHYL-KVESQP--ARAASITR
   |  *|* * ||*|||  | |   |||***| *|      | |  ** * *||* || ||| || ||   |**  *
NMDAAPARVGLGITTVLTMTTQSSGSRASLPKVSYVKAIDIWMAVCLLFVFSALLEYAAVNFIARAGTKLFISRAKRIDT

ASRIAFPVVFLLANIILAFLFFGF-----
|**|***|***| **   * || |     
VSRVAFPLVFLIFNI---FYWITYKLVPR

align_seq_coor_to(atom_sel_2, chain_1=['A'], chain_2=['A'], back_names=['CA'], align=True, rmsd_flag=True, tmscore_flag=False)

Align 2 strucures, using a sequence alignement to determine which residue to align. Compute RMSD between two atom_dict Then return the RMSD value.

Parameters

• atom_sel_2 (dict) – atom dictionnary

• chain_1 (list) – list of chain

• chain_2 (list) – list of chain

Returns

rmsd and alignement index

Return type

float and list

Example

>>> prot_1_coor = Coor(os.path.join(TEST_PATH, '1jd4.pdb'))        
Succeed to read file ...1jd4.pdb ,  1586 atoms found
>>> prot_2_coor = Coor(os.path.join(TEST_PATH, '1dpx.pdb'))        
Succeed to read file ...1dpx.pdb ,  1192 atoms found
>>> rmsd, align_sel = prot_1_coor.align_seq_coor_to(prot_2_coor)        
------NYFPQYPEYAIETARLRTFEAWPRNLKQKPHQLAEAGFFYTGVGDRVRCFSCGGGLMDW-NDNDEPWEQHALWL
      |      |||||| *  ||  *      * ||  ||     ||   |       |   * **|  * ||| *  
KVFGRCELAAAMKRHGLDNYRGYSLGNW--VCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRN-LCN

SQCRFVKLMKGQLYIDTVAAKPV-------------------------------
  *    *|||||  || |** |                               
IPCS--ALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL

>>> print('RMSD = {:.2f} Å'.format(rmsd))
RMSD = 12.63 Å

align_to(atom_sel_2, selec_dict={'name': ['CA']}, index_list=None, rot_kabsch=True)

Align structure to an Coor object.

Parameters

• atom_sel_1 (dict) – atom dictionnary

• atom_sel_2 (dict) – atom dictionnary

• selec_dict (dict, default={'name': ['CA']}) – selection dictionnary

• rot_kabsch (bool, default=True) – method for rotation kabsh, if not quaternion

Example

>>> prot_coor = Coor(os.path.join(TEST_PATH, '1jd4.pdb'))        
Succeed to read file ...1jd4.pdb ,  1586 atoms found
>>> chain_A = prot_coor.select_part_dict(selec_dict={'chain': ['A']})
>>> chain_B = prot_coor.select_part_dict(selec_dict={'chain': ['B']})
>>> rmsd = chain_A.compute_rmsd_to(chain_B)
>>> print('RMSD before alignement is {:.2f} Å'.format(rmsd))
RMSD before alignement is 37.47 Å
>>> chain_A.align_to(chain_B)
>>> rmsd = chain_A.compute_rmsd_to(chain_B)
>>> print('RMSD after alignement is {:.2f} Å'.format(rmsd))
RMSD after alignement is 0.06 Å
>>> chain_A.align_to(chain_B)
>>> rmsd = chain_A.compute_rmsd_to(chain_B)
>>> print('RMSD after 2nd alignement is {:.2f} Å'.format(rmsd))
RMSD after 2nd alignement is 0.06 Å

static angle_vec(vec_a, vec_b)

Compute angle between two vectors.

Parameters

• vec_a (list) – vector

• vec_b (list) – vector

Returns

angle in radian

Return type

float

Example

>>> angle = Coor.angle_vec([1, 0, 0], [0, 1, 0])
>>> print('angle = {:.2f}'.format(np.degrees(angle)))
angle = 90.00
>>> angle = Coor.angle_vec([1, 0, 0], [1, 0, 0])
>>> print('angle = {:.2f}'.format(np.degrees(angle)))
angle = 0.00
>>> angle = Coor.angle_vec([1, 0, 0], [1, 1, 0])
>>> print('angle = {:.2f}'.format(np.degrees(angle)))
angle = 45.00
>>> angle = Coor.angle_vec([1, 0, 0], [-1, 0, 0])
>>> print('angle = {:.2f}'.format(np.degrees(angle)))
angle = 180.00

static atom_angle(atom_a, atom_b, atom_c)

Compute the anlge between 3 atoms.

Parameters

• atom_a (dict) – atom dictionnary

• atom_b (dict) – atom dictionnary

• atom_c (dict) – atom dictionnary

Returns

angle (degrees)

Return type

float

Example

>>> atom_1 = {'xyz': np.array([0.0, 0.0, 0.0])}
>>> atom_2 = {'xyz': np.array([0.0, 1.0, 0.0])}
>>> atom_3 = {'xyz': np.array([1.0, 1.0, 1.0])}
>>> Coor.atom_angle(atom_1, atom_2, atom_3)
90.0
>>> print('{:.3f}'.format(Coor.atom_angle(atom_1, atom_3, atom_2)))
35.264

static atom_dihed_angle(atom_a, atom_b, atom_c, atom_d)

Compute the dihedral anlge using 4 atoms.

Parameters

• atom_a (dict) – atom dictionnary

• atom_b (dict) – atom dictionnary

• atom_c (dict) – atom dictionnary

• atom_d (dict) – atom dictionnary

Returns

dihedral angle

Return type

float

Example

>>> atom_1 = {'xyz': np.array([0.0, -1.0, 0.0])}
>>> atom_2 = {'xyz': np.array([0.0, 0.0, 0.0])}
>>> atom_3 = {'xyz': np.array([1.0, 0.0, 0.0])}
>>> atom_4 = {'xyz': np.array([1.0, 1.0, 0.0])}
>>> atom_5 = {'xyz': np.array([1.0, -1.0, 0.0])}
>>> atom_6 = {'xyz': np.array([1.0, -1.0, 1.0])}
>>> angle_1 = Coor.atom_dihed_angle(atom_1, atom_2, atom_3, atom_4)
>>> print('{:.3f}'.format(angle_1))
180.000
>>> angle_2 = Coor.atom_dihed_angle(atom_1, atom_2, atom_3, atom_5)
>>> print('{:.3f}'.format(angle_2))
0.000
>>> angle_3 = Coor.atom_dihed_angle(atom_1, atom_2, atom_3, atom_6)
>>> print('{:.3f}'.format(angle_3))
-45.000

static atom_dist(atom_a, atom_b)

Compute the distance between 2 atoms.

Parameters

• atom_a (dict) – atom dictionnary

• atom_b (dict) – atom dictionnary

Returns

distance

Return type

float

Example

>>> atom_1 = {'xyz': np.array([0.0, 0.0, 0.0])}
>>> atom_2 = {'xyz': np.array([0.0, 1.0, 0.0])}
>>> atom_3 = {'xyz': np.array([1.0, 1.0, 1.0])}
>>> Coor.atom_dist(atom_1, atom_2)
1.0
>>> Coor.atom_dist(atom_1, atom_3)
1.7320508075688772

center_of_mass(selec_dict={})

Compute the center of mass of a selection Avoid using atoms with 2 letters atom name like NA Cl … If selection is empy, take all atoms.

Parameters

selec_dict (dict, default={}) – selection dictionnary

Example

>>> prot_coor = Coor(os.path.join(TEST_PATH, '1y0m.pdb'))        
Succeed to read file ...1y0m.pdb ,  648 atoms found
>>> com_1y0m = prot_coor.center_of_mass()
>>> print("x:{:.2f} y:{:.2f} z:{:.2f}".format(*com_1y0m))
x:16.01 y:0.45 z:8.57
>>> com_1y0m_ca = prot_coor.center_of_mass({'name': ['CA']})
>>> print("x:{:.2f} y:{:.2f} z:{:.2f}".format(*com_1y0m_ca))
x:15.95 y:0.72 z:8.96

Warning

Atom name must start with its type letter (H, C, N, O, P, S).

centroid(selec_dict={})

Compute the centroid of a selection If selection is empy, take all atoms.

Parameters

selec_dict (dict, default={}) – selection dictionnary

Example

>>> prot_coor = Coor(os.path.join(TEST_PATH, '1y0m.pdb'))        
Succeed to read file ...1y0m.pdb ,  648 atoms found
>>> com_1y0m = prot_coor.centroid()
>>> print("x:{:.2f} y:{:.2f} z:{:.2f}".format(*com_1y0m))
x:16.03 y:0.44 z:8.57
>>> com_1y0m_ca = prot_coor.centroid(selec_dict={'name': ['CA']})
>>> print("x:{:.2f} y:{:.2f} z:{:.2f}".format(*com_1y0m_ca))
x:15.95 y:0.72 z:8.96

change_index_pdb_field(index_list, change_dict)

Change all atom field of a part of coor object defined by index, the change is based on the change_dict dictionnary.

Parameters

• index_list (list) – list of atom index to change

• change_dict (dict) – change ditionnay eg. {“chain” : “A”}

Example

>>> prot_coor = Coor(os.path.join(TEST_PATH, '1y0m.pdb'))        
Succeed to read file ...1y0m.pdb ,  648 atoms found
>>> res_826_852 = prot_coor.get_index_selection({'res_num' :
... range(826,852)})
>>> prot_coor.change_index_pdb_field(index_list=res_826_852,
... change_dict={"chain" : "B"}) 
<...Coor object at ...>
>>> prot_seq = prot_coor.get_aa_seq()
>>> prot_seq == {'A': 'TFKSAVKALFDYKAQREDELTFTKSAIIQNVEKQD',
... 'B': 'GGWWRGDYGGKKQLWFPSNYVEEMIN'}
True

change_pdb_field(change_dict)

Change all atom field of a coor object, the change is based on the change_dict dictionnary.

Parameters

change_dict (dict) – change ditionnay eg. {“chain”: “A”}

Example

>>> prot_coor = Coor(os.path.join(TEST_PATH, '1y0m.pdb'))        
Succeed to read file ...1y0m.pdb ,  648 atoms found
>>> prot_coor.get_aa_seq()
{'A': 'TFKSAVKALFDYKAQREDELTFTKSAIIQNVEKQDGGWWRGDYGGKKQLWFPSNYVEEMIN'}
>>> prot_coor.change_pdb_field(change_dict = {"chain": "B"})        
<...Coor object at ...>
>>> prot_coor.get_aa_seq()
{'B': 'TFKSAVKALFDYKAQREDELTFTKSAIIQNVEKQDGGWWRGDYGGKKQLWFPSNYVEEMIN'}

compute_TMscore_to(atom_sel_2, ltarget, index_list=None)

Compute TMscore between two atom_dict Then return the TMscore.

Parameters

• atom_sel_1 (dict) – atom dictionnary

• atom_sel_2 (dict) – atom dictionnary

• selec_dict (dict, default={}) – selection dictionnary

Returns

TMscore

Return type

float

Ref: Y. Zhang, J. Skolnick, Scoring function for automated assessment of protein structure template quality, Proteins, 57: 702-710 (2004)

TMscore = max( 1/Ltarget * Sum(1/(1 + (di/do(Ltarget))**2 )) )

with Ltarget is length of model protein and: d0(Ltarget) = 1.24 * (Ltarget-15)**(1/3) - 1.8

compute_rmsd_to(atom_sel_2, selec_dict={'name': ['CA']}, index_list=None)

Compute RMSD between two atom_dict Then return the RMSD value.

Parameters

• atom_sel_1 (dict) – atom dictionnary

• atom_sel_2 (dict) – atom dictionnary

• selec_dict (dict, default={}) – selection dictionnary

Returns

RMSD

Return type

float

static concat_pdb(*pdb_in_files, pdb_out, check_file_out=True)

Concat a list of pdb files in one.

Parameters

• pdb_in_files (list) – list of pdb files

• pdb_out (dict) – atom dictionnary

Example

>>> TEST_OUT = str(getfixture('tmpdir'))
>>> Coor.concat_pdb(os.path.join(TEST_PATH, '1y0m.pdb'),
...                 os.path.join(TEST_PATH, '1rxz.pdb'),
...                 pdb_out = os.path.join(TEST_OUT, 'tmp_2.pdb'))         
Succeed to save concat file: ...tmp_2.pdb

correct_chain(Ca_cutoff=4.5)

Correct the chain ID’s of a coor object, by checking consecutive Calphas atoms distance. If the distance is higher than Ca_cutoff , the former atoms are considered as in a different chain.

Parameters

Ca_cutoff (float, default=4.5) – cutoff for distances between Calphas atoms (X)

Example

>>> prot_coor = Coor(os.path.join(TEST_PATH, '1y0m.pdb'))        
Succeed to read file ...1y0m.pdb ,  648 atoms found
>>> res_810 = prot_coor.get_index_selection({'res_num': [810]})
>>> prot_coor = prot_coor.del_atom_index(index_list=res_810)
>>> prot_coor.get_aa_seq()
Residue A:THR:811 is not consecutive, there might be missing residues
{'A': 'TFKSAVKALFDYKAQREDE-TFTKSAIIQNVEKQDGGWWRGDYGGKKQLWFPSNYVEEMIN'}
>>> prot_coor.correct_chain() 
Chain: A  Residue: 0 to 18
Chain: B  Residue: 20 to 60
<...Coor object at ...>
>>> # As a residue is missing, Calphas after residue 18 is no
>>> # more consecutive

Note

This is specially usefull for pdb2gmx which cut the protein chains based on the chain ID’s.

correct_cys_name()

Correct the CYS resname from pdb2pqr

Example

>>> try: 
...   print("Start import")
...   from . import pdb2pqr
... except ImportError:
...   import pdb2pqr
Start import...
>>> TEST_OUT = str(getfixture('tmpdir'))
>>> # Compute protonation with pdb2pqr:
>>> pdb2pqr.compute_pdb2pqr(os.path.join(TEST_PATH, '1dpx.pdb'),os.path.join(TEST_OUT, '1dpx.pqr')) 
Succeed to read file ...1dpx.pdb ,  1192 atoms found
Succeed to save file ...tmp_pdb2pqr.pdb
pdb2pqr30... --ff CHARMM --ffout CHARMM --keep-chain --titration-state-method=propka --with-ph=7.00 ...tmp_pdb2pqr.pdb ...1dpx.pqr
0
>>> prot_coor = Coor(os.path.join(TEST_OUT, '1dpx.pqr'))
Succeed to read file ...1dpx.pqr ,  1960 atoms found
>>> Isu_index = prot_coor.get_index_selection({'res_name': ['DISU']})
>>> print(len(Isu_index))
16
>>> prot_coor.correct_cys_name() 
<...Coor object at 0x...
>>> Isu_index = prot_coor.get_index_selection({'res_name': ['DISU']})
>>> print(len(Isu_index))
0

correct_his_name()

Get his protonation state from pdb2pqr and replace HIS resname with HSE, HSD, HSP resname. To do after pdb2pqr, in order that protonation is recognize by pdb2gmx.

Example

>>> try: 
...   print("Start import")
...   from . import pdb2pqr
... except ImportError:
...   import pdb2pqr
Start import...
>>> TEST_OUT = str(getfixture('tmpdir'))
>>> # Compute protonation with pdb2pqr:
>>> pdb2pqr.compute_pdb2pqr(os.path.join(TEST_PATH, '4n1m.pdb'),os.path.join(TEST_OUT, '4n1m.pqr')) 
Succeed to read file ...4n1m.pdb ,  2530 atoms found
Succeed to save file ...tmp_pdb2pqr.pdb
pdb2pqr30... --ff CHARMM --ffout CHARMM --keep-chain --titration-state-method=propka --with-ph=7.00 ...tmp_pdb2pqr.pdb ...4n1m.pqr
0
>>> prot_coor = Coor(os.path.join(TEST_OUT, '4n1m.pqr')) 
Succeed to read file ...4n1m.pqr ,  2549 atoms found
>>> HSD_index = prot_coor.get_index_selection({'res_name': ['HSD'],'name': ['CA']})
>>> print(len(HSD_index))
4
>>> HSE_index = prot_coor.get_index_selection({'res_name': ['HSE'],'name': ['CA']})
>>> print(len(HSE_index))
0
>>> HSP_index = prot_coor.get_index_selection({'res_name': ['HSP'],'name': ['CA']})
>>> print(len(HSP_index))
1
>>> prot_coor.correct_his_name() 
<...Coor object at 0x...
>>> HIS_index = prot_coor.get_index_selection({'res_name': ['HIS'],'name': ['CA']})
>>> print(len(HIS_index))
0

Note

This function seems useless. Since last version of pdb2pqr residue name seems correct.

correct_ion_octa(ion_name_list, dist=0.9)

For specified ion, create an octahedral dummy model described by a set of 6 cationic dummy atoms connected around a central metal atom. From Duarte et al. J Phys Chem B 2014.

Parameters

ion_name (str) – name of metal present in .pdb to transform in octahedral dummy model

Example

>>> TEST_OUT = str(getfixture('tmpdir'))
>>> prot_coor = Coor(os.path.join(TEST_PATH, '1jd4.pdb'))        
Succeed to read file ...1jd4.pdb ,  1586 atoms found
>>> ion_index = prot_coor.get_index_selection({'res_name' : ['ZN']})
>>> print(len(ion_index))
2
>>> prot_coor.correct_ion_octa(['ZN']) 
<...Coor object at 0x...
>>> ion_index = prot_coor.get_index_selection({'res_name' : ['ZN']})
>>> print(len(ion_index))
14

correct_protonated_res()

Correct protonated residues names, to avoid a mix of residue names from pdb2pqr, like GLUP and GLU or ASPP and ASP. To do after pdb2pqr, in order that protonation is recognize by pdb2gmx.

Example

>>> try: 
...   print("Start import")
...   from . import pdb2pqr
... except ImportError:
...   import pdb2pqr
Start import...
>>> TEST_OUT = str(getfixture('tmpdir'))
>>> # Compute protonation with pdb2pqr:
>>> pdb2pqr.compute_pdb2pqr(os.path.join(TEST_PATH, '4n1m.pdb'),os.path.join(TEST_OUT, '4n1m.pqr'), ph=3.0) 
Succeed to read file ...4n1m.pdb ,  2530 atoms found
Succeed to save file ...tmp_pdb2pqr.pdb
pdb2pqr30... --ff CHARMM --ffout CHARMM --keep-chain --titration-state-method=propka --with-ph=3.00 ...tmp_pdb2pqr.pdb ...4n1m.pqr
0
>>> prot_coor = Coor(os.path.join(TEST_OUT, '4n1m.pqr')) 
Succeed to read file ...4n1m.pqr ,  2564 atoms found
>>> HSD_index = prot_coor.get_index_selection({'res_name': ['HSD'],'name': ['CA']})
>>> print(len(HSD_index))
0
>>> HSE_index = prot_coor.get_index_selection({'res_name': ['HSE'],'name': ['CA']})
>>> print(len(HSE_index))
0
>>> HSP_index = prot_coor.get_index_selection({'res_name': ['HSP'],'name': ['CA']})
>>> print(len(HSP_index))
5
>>> GLUP_index = prot_coor.get_index_selection({'res_name' : ['GLUP'],'name': ['CA']})
>>> print(len(GLUP_index))
0
>>> ASPP_index = prot_coor.get_index_selection({'res_name': ['ASPP'],'name': ['CA']})
>>> print(len(ASPP_index))
0
>>> prot_coor.correct_protonated_res() 
<...Coor object at 0x...
>>> GLUP_index = prot_coor.get_index_selection({'res_name': ['GLUP'],'name': ['CA']})
>>> print(len(GLUP_index))
9
>>> GLU_index = prot_coor.get_index_selection({'res_name': ['GLU'],'name': ['CA']})
>>> print(len(GLU_index))
3
>>> ASPP_index = prot_coor.get_index_selection({'res_name': ['ASPP'],'name': ['CA']})
>>> print(len(ASPP_index))
2
>>> ASP_index = prot_coor.get_index_selection({'res_name': ['ASP'],'name': ['CA']})
>>> print(len(ASP_index))
5

correct_water_name()

Correct the water resname from pdb2pqr

Example

>>> try: 
...   print("Start import")
...   from . import pdb2pqr
... except ImportError:
...   import pdb2pqr
Start import...
>>> TEST_OUT = str(getfixture('tmpdir'))
>>> prot_coor = Coor(os.path.join(TEST_PATH, '1dpx.pdb'))        
Succeed to read file ...1dpx.pdb ,  1192 atoms found
>>> prot_coor.water_to_ATOM() 
<...Coor object at 0x...
>>> prot_coor.write_pdb(os.path.join(TEST_OUT, '1dpx_water.pdb'))        
Succeed to save file ...1dpx_water.pdb
>>> # Compute protonation with pdb2pqr:
>>> pdb2pqr.compute_pdb2pqr(
... os.path.join(TEST_OUT, '1dpx_water.pdb'),
... os.path.join(TEST_OUT, '1dpx_water.pqr')) 
Succeed to read file ...1dpx_water.pdb ,  1192 atoms found
Succeed to save file ...tmp_pdb2pqr.pdb
pdb2pqr30... --ff CHARMM --ffout CHARMM --keep-chain --titration-state-method=propka --with-ph=7.00...tmp_pdb2pqr.pdb ...1dpx_water.pqr
0
>>> prot_coor = Coor(os.path.join(
... TEST_OUT, '1dpx_water.pqr')) 
Succeed to read file ...1dpx_water.pqr ,  2492 atoms found
>>> water_index = prot_coor.get_index_selection(
... {'res_name': ['TP3M'], 'name': ['OH2']})
>>> print(len(water_index))
177

cryst_convert(format_out='pdb')

PDB format: https://www.wwpdb.org/documentation/file-format-content/format33/sect8.html

Gro to pdb: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2008-May/033944.html

https://en.wikipedia.org/wiki/Fractional_coordinates

>>> prot_coor = Coor()
>>> prot_coor.read_file(os.path.join(TEST_PATH, '1y0m.gro'))        
Succeed to read file ...1y0m.gro ,  648 atoms found
>>> prot_coor.cryst_convert(format_out='pdb')
'CRYST1   28.748   30.978   29.753  90.00  92.12  90.00 P 1           1\n'
>>> prot_coor = Coor()
>>> prot_coor.read_file(os.path.join(TEST_PATH, '1y0m.pdb'))        
Succeed to read file ...1y0m.pdb ,  648 atoms found
>>> prot_coor.cryst_convert(format_out='gro')
'   2.87480   3.09780   2.97326   0.00000   0.00000   0.00000   0.00000  -0.11006   0.00000\n'

del_atom_index(index_list)

Delete atoms of a coor object defined by their index.

Parameters

index_list (list) – list of atom index to delete

Example

>>> prot_coor = Coor(os.path.join(TEST_PATH, '1y0m.pdb'))        
Succeed to read file ...1y0m.pdb ,  648 atoms found
>>> prot_coor.get_aa_seq()
{'A': 'TFKSAVKALFDYKAQREDELTFTKSAIIQNVEKQDGGWWRGDYGGKKQLWFPSNYVEEMIN'}
>>> res_810_852 = prot_coor.get_index_selection({'res_num': range(810,852)})
>>> prot_coor.del_atom_index(index_list=res_810_852)        
<...Coor object at ...>
>>> prot_coor.get_aa_seq()
{'A': 'TFKSAVKALFDYKAQREDE'}

dist_under_index(atom_sel_2, cutoff=10.0)

Check is distance between atoms of self.coor is under cutoff with atoms of group 1. Then return list of index of atoms of self.coor under ctuoff ditance.

Parameters

• atom_sel_1 (dict) – atom dictionnary

• atom_sel_2 (dict) – atom dictionnary

• cutoff (float, default=10.0) – distance cutoff

Returns

array of index

Return type

np.array

get_PDB(pdb_ID, out_file=None, check_file_out=True)

Get a pdb file from the PDB using its ID and return a Coor object.

Parameters

• pdb_ID (str) – Protein Data Bank structure ID

• out_file (str, optional, default=None) – path of the pdb file to save

• check_file_out (bool, optional, default=True) – flag to check or not if file has already been created. If the file is present then the command break.

Example

>>> show_log()
>>> TEST_OUT = str(getfixture('tmpdir'))
>>> prot_coor = Coor()
>>> prot_coor.get_PDB('3EAM', os.path.join(TEST_OUT, '3eam.pdb'))        
Succeed to read file ...3eam.pdb ,  13505 atoms found

get_aa_DL_seq(gap_in_seq=True)

Get the amino acid sequence from a coor object. if amino acid is in D form it will be in lower case.

L or D form is determined using CA-N-C-CB angle Angle should take values around +34° and −34° for L- and D-amino acid residues.

Reference: https://onlinelibrary.wiley.com/doi/full/10.1002/prot.10320

Returns

dictionnary of sequence indexed by the chain ID

Return type

dict

Example

>>> prot_coor = Coor(os.path.join(TEST_PATH, '1y0m.pdb'))        
Succeed to read file ...1y0m.pdb ,  648 atoms found
>>> prot_coor.get_aa_DL_seq()
{'A': 'TFKSAVKALFDYKAQREDELTFTKSAIIQNVEKQDGGWWRGDYGGKKQLWFPSNYVEEMIN'}
>>> prot_coor = Coor(os.path.join(TEST_PATH, '6be9_frame_0.pdb'))        
Succeed to read file ...6be9_frame_0.pdb ,  104 atoms found
>>> prot_coor.get_aa_DL_seq()
Residue K2 is in D form
Residue N6 is in D form
Residue P7 is in D form
{'A': 'TkNDTnp'}

Warning

If atom chains are not arranged sequentialy (A,A,A,B,B,A,A,A …), the first atom seq will be overwritten by the last one.

get_aa_num()

Get the amino acid number of a coor object.

Returns

Number of residues

Return type

int

Example

>>> prot_coor = Coor(os.path.join(TEST_PATH, '1y0m.pdb'))        
Succeed to read file ...1y0m.pdb ,  648 atoms found
>>> prot_coor.get_aa_num()
61

Note

Only count Ca atoms, this may not be the best choice ?

get_aa_seq(gap_in_seq=True)

Get the amino acid sequence from a coor object.

Returns

dictionnary of sequence indexed by the chain ID

Return type

dict

Example

>>> prot_coor = Coor(os.path.join(TEST_PATH, '1y0m.pdb'))        
Succeed to read file ...1y0m.pdb ,  648 atoms found
>>> prot_coor.get_aa_seq()
{'A': 'TFKSAVKALFDYKAQREDELTFTKSAIIQNVEKQDGGWWRGDYGGKKQLWFPSNYVEEMIN'}

Warning

If atom chains are not arranged sequentialy (A,A,A,B,B,A,A,A …), the first atom seq will be overwritten by the last one.

get_array(field='xyz', index_list=None)

Convert atom dict as a numpy array.

Parameters

• field (str (Default='xyz')) – field to extract

• index_list (list (Default=None)) – list of index to extract

Returns

coordinates array

Return type

np.array

Example

>>> prot_coor = Coor(os.path.join(TEST_PATH, '1y0m.pdb'))        
Succeed to read file ...1y0m.pdb ,  648 atoms found
>>> coor_array = prot_coor.get_array()
>>> print(coor_array[1:4])
[[-0.971  9.213 12.734]
 [-0.185  7.901 12.631]
 [ 0.456  7.524 13.61 ]]
>>> coor_array = prot_coor.get_array(field='name')
>>> print(coor_array[1:4])
['CA' 'C' 'O']

get_attribute_selection(selec_dict={}, attribute='uniq_resid', index_list=None)

Select atom of a coor object based on the change_dict dictionnary. Return the list of unique attribute of the selected atoms.

Parameters

selec_dict (dict) – select ditionnay eg. {“chain”: [“A”,”G”]}

Returns

list of atom index

Return type

list of int

Example

>>> prot_coor = Coor(os.path.join(TEST_PATH, '1y0m.pdb'))        
Succeed to read file ...1y0m.pdb ,  648 atoms found
>>> prot_coor.get_attribute_selection({'res_num': [826,827]},attribute='uniq_resid')
[35, 36]

get_box_dim(selec_dict={})

Compute the x, y, z dimension of a selection

Parameters

selec_dict (dict, default={}) – selection dictionnary

Example

>>> prot_coor = Coor(os.path.join(TEST_PATH, '1y0m.pdb'))        
Succeed to read file ...1y0m.pdb ,  648 atoms found
>>> box_1y0m = prot_coor.get_box_dim()
>>> print("x:{:.2f} y:{:.2f} z:{:.2f}".format(*box_1y0m))
x:39.14 y:29.36 z:31.19

Warning

Atom name must start with its type letter (H, C, N, O, P, S).

get_center_residue(selec_dict={'res_name': ['GLY', 'HIS', 'HSP', 'HSE', 'HSD', 'HIP', 'HIE', 'HID', 'ARG', 'LYS', 'ASP', 'ASPP', 'GLU', 'GLUP', 'SER', 'THR', 'ASN', 'GLN', 'CYS', 'SEC', 'PRO', 'ALA', 'ILE', 'PHE', 'TYR', 'TRP', 'VAL', 'LEU', 'MET', 'DA5', 'DA3', 'DAN', 'DA', 'DT5', 'DT3', 'DTN', 'DT', 'DC5', 'DC3', 'DCN', 'DC', 'DG5', 'DG3', 'DGN', 'DG', 'RA5', 'RA3', 'RAN', 'RA', 'RU5', 'RU3', 'RUN', 'RU', 'RC5', 'RC3', 'RCN', 'RC', 'RG5', 'RG3', 'RGN', 'RG']}, field='res_num')

Find the closet residue to protein center of mass. Return the residue index.

Parameters

selec_res_list (list, default={'res_name': PROTEIN_RES}) – selection residue

>>> prot_coor = Coor(os.path.join(TEST_PATH, '1y0m.pdb'))        
Succeed to read file ...1y0m.pdb ,  648 atoms found
>>> center_res = prot_coor.get_center_residue()
Minimal distance to protein COM is 3.00 Å with residue "res_num": 841
>>> print("Center residue is {:d}".format(center_res))
Center residue is 841

get_common_atom(atom_sel_2, chain_1=['A'], chain_2=['A'], back_names=['C', 'N', 'O', 'CA'])

Get atom selection in common for two atom_dict based on sequence alignement.

get_gro_structure_string()

Return a coor object as a pdb string.

Example

>>> prot_coor = Coor()
>>> prot_coor.read_pdb(os.path.join(TEST_PATH, '1y0m.pdb'))        
Succeed to read file ...1y0m.pdb ,  648 atoms found
>>> gro_str = prot_coor.get_gro_structure_string()
>>> print('Number of caracters: {}'.format(len(gro_str)))
Number of caracters: 29283

get_index_dist_between(atom_sel_2, cutoff_min=0, cutoff_max=10)

Check is distance between atoms of self.atom_dict is under cutoff with the atoms of group 1. Then return list of index of atoms of self.coor under cutoff ditance.

Parameters

• atom_sel_1 (dict) – atom dictionnary

• atom_sel_2 (dict) – atom dictionnary

• cutoff_min (float, default=0.0) – maximum distance cutoff

• cutoff_max (float, default=10.0) – minimum distance cutoff

Example

>>> prot_coor = Coor(os.path.join(TEST_PATH, '1y0m.pdb'))        
Succeed to read file ...1y0m.pdb ,  648 atoms found
>>> res_810 = prot_coor.select_part_dict({'res_num': [810]})
>>> close_r810 = prot_coor.get_index_dist_between(
... res_810, cutoff_min=3, cutoff_max=5)
>>> print(len(close_r810))
65

get_index_selection(selec_dict)

Select atom of a coor object based on the change_dict dictionnary. Return the list of index of selected atoms.

Parameters

selec_dict (dict) – select ditionnay eg. {“chain”: [“A”,”G”]}

Returns

list of atom index

Return type

list of int

Example

>>> prot_coor = Coor(os.path.join(TEST_PATH, '1y0m.pdb'))        
Succeed to read file ...1y0m.pdb ,  648 atoms found
>>> prot_coor.get_index_selection({'res_num': [826,827]})
[297, 298, 299, 300, 301, 302, 303, 304]

get_mass_array()

Extract mass of each atom_dict and return it as an numpy array Avoid using atoms with 2 letters atom name like NA Cl …

Returns

mass array

Return type

np.array

Example

>>> prot_coor = Coor(os.path.join(TEST_PATH, '1y0m.pdb'))        
Succeed to read file ...1y0m.pdb ,  648 atoms found
>>> mass_1y0m = prot_coor.get_mass_array()
>>> print("Mass of 10 first atoms: {}".format(mass_1y0m[:10]))
Mass of 10 first atoms: [7 6 6 8 6 8 6 7 6 6]
>>> prot_coor_ca = prot_coor.select_part_dict({'name': ['CA']})
>>> mass_1y0m_ca = prot_coor_ca.get_mass_array()
>>> print("Mass of 10 first atoms: {}".format(mass_1y0m_ca[:10]))
Mass of 10 first atoms: [6 6 6 6 6 6 6 6 6 6]

get_max_size()

Get maximum size of a molecule.

Example

>>> prot_coor = Coor(os.path.join(TEST_PATH, '1y0m.pdb'))        
Succeed to read file ...1y0m.pdb ,  648 atoms found
>>> print('Maximum size without alignment is {:.2f} Å'.format(
... np.ceil(prot_coor.get_box_dim()).max()))
Maximum size without alignment is 40.00 Å
>>> max_size = prot_coor.get_max_size()
Do a rotation of 66.43°
>>> print('Maximum size is {:.2f} Å'.format(max_size))
Maximum size is 43.00 Å

get_pqr_structure_string()

Return a coor object as a pqr string.

Example

>>> prot_coor = Coor()
>>> prot_coor.read_pdb(os.path.join(TEST_PATH, '1y0m.pdb'))        
Succeed to read file ...1y0m.pdb ,  648 atoms found
>>> pqr_str = prot_coor.get_pqr_structure_string()
>>> print('Number of caracters: {}'.format(len(pqr_str)))
Number of caracters: 46728

get_structure_string()

Return a coor object as a pdb string.

Example

>>> prot_coor = Coor()
>>> prot_coor.read_pdb(os.path.join(TEST_PATH, '1y0m.pdb'))        
Succeed to read file ...1y0m.pdb ,  648 atoms found
>>> pdb_str = prot_coor.get_structure_string()
>>> print('Number of caracters: {}'.format(len(pdb_str)))
Number of caracters: 51264

insert_mol(pdb_out, out_folder, mol_chain, mol_num, check_file_out=True, prot_atom_name=['CA'], sol_res_name=['SOL'], sol_atom_name=['OW'])

Insert molecules defined by chain ID mol_chain in a water solvant. Check which water molecules are within cutoff_prot_off=12.0 X and cutoff_prot_in=15.0 X of protein and peptide C alpha atoms. Move the molecules to be inserted at the position of water molecules. Then delete all water molecules within cutoff_water_clash=1.2 X of the inserted molecule atoms.

Parameters

• pdb_out (str) – name of output pdb file

• out_folder (str) – path of the ouput directory

• mol_chain (str) – chain ID of the molecule to be inserted,

• mol_num (int) – Number of molecule to be inserted,

• check_file_out (bool, optional, default=True) – flag to check or not if file has already been created. If the file is present then the command break.

Warning

self.atom_dict file must contain alredy a concatenated system with a ligand (chain: mol_chain) and a solvated system. Molecules to insert should have different residue number or at least non consecutive.

static kabsch(coor_1, coor_2)

Source: https://github.com/charnley/rmsd/blob/master/rmsd/ calculate_rmsd.py Using the Kabsch algorithm with two sets of paired point P and Q, centered around the centroid. Each vector set is represented as an NxD matrix, where D is the the dimension of the space.

The algorithm works in three steps: - a centroid translation of P and Q (assumed done before this function call) - the computation of a covariance matrix C - computation of the optimal rotation matrix U For more info see http://en.wikipedia.org/wiki/Kabsch_algorithm

Parameters

• coor_1 (np.array) – coordinates array of size (N, D), where N is points and D is dimension.

• coor_2 (np.array) – coordinates array of size (N, D), where N is points and D is dimension.

Returns

rotation matrix

Return type

np.array of size (D, D)

static makeQ(r1, r2, r3, r4=0)

Source: https://github.com/charnley/rmsd/blob/master/rmsd/ calculate_rmsd.py matrix involved in quaternion rotation

static makeW(r1, r2, r3, r4=0)

Source: https://github.com/charnley/rmsd/blob/master/rmsd/ calculate_rmsd.py matrix involved in quaternion rotation

make_peptide(sequence, pdb_out, check_file_out=True)

Create a linear peptide structure.

Parameters

• sequence (str) – peptide sequence

• pdb_out (str) – name of output pdb file

• check_file_out (bool, optional, default=True) – flag to check or not if file has already been created. If the file is present then the command break.

moment_inertia()

Tensor moment of inertia relative to center of mass.

Taken from: https://github.com/MDAnalysis/mdanalysis/blob/develop/package/MDAnalysis/core/topologyattrs.py

Returns

tensor matrix 3*3

Return type

np.array

Example

>>> prot_coor = Coor(os.path.join(TEST_PATH, '1y0m.pdb'))        
Succeed to read file ...1y0m.pdb ,  648 atoms found
>>> tensor = prot_coor.moment_inertia()
>>> print(tensor)
[[343695.37614973  31289.34303697  40416.71166176]
 [ 31289.34303697 478561.60329129  -9443.32698326]
 [ 40416.71166176  -9443.32698326 413840.08602987]]

parse_gro_lines(gro_lines)

Parse a gro file and return atom informations as a dictionnary indexed on the atom num.

Parameters

gro_in (list of str) – lines to parse

Example

>>> prot_coor = Coor()
>>> f = open(os.path.join(TEST_PATH, '1y0m.gro'))
>>> lines = f.readlines()
>>> prot_coor.parse_gro_lines(lines)
>>> prot_coor.num
648

parse_pdb_lines(pdb_lines, pqr_format=False)

Parse the pdb lines and return atom informations as a dictionnary indexed on the atom num. The fonction can also read pqr files if specified with pqr_format = True, it will only change the column format of beta and occ factors.

Parameters

pdb_lines (list of str) – lines to parse

Example

>>> prot_coor = Coor()
>>> f = open(os.path.join(TEST_PATH, '1y0m.pdb'))
>>> lines = f.readlines()
>>> prot_coor.parse_pdb_lines(lines)
>>> prot_coor.num
648

plot_pseudo_3D(c_field=None, cmap='gist_rainbow', line_w=1.5, chainbreak=5.0, sel={'name': ['CA']}, fig_size=(7, 7))

Plot alpha Carbon trace of protein in pseudo 3D.

Inspired from Colab fold plot_pseudo_3D() function from sokrypton https://github.com/sokrypton/ColabFold

Parameters

• c_field (str (Default=None or 'index')) – field used to color figure

• cmap (str (Default="gist_rainbow")) – Color map

• line_w (flt (Default=1.5)) – Line width

• chainbreak (flt (Default=5.0)) – Distance for chain break (in Å)

• sel (dict (Default={'name': ['CA']})) – selection to plot

• fig_size (tupple (Default=(7, 7))) – Figure size

Returns

matplotlib ax

Return type

ax

Example

principal_axis()

Calculate the principal axes from the moment of inertia.

Taken from: https://github.com/MDAnalysis/mdanalysis/blob/develop/ package/MDAnalysis/core/topologyattrs.py

Returns

3 principal axis

Return type

list of np.array

Example

>>> prot_coor = Coor(os.path.join(TEST_PATH, '1y0m.pdb'))        
Succeed to read file ...1y0m.pdb ,  648 atoms found
>>> princ_axis = prot_coor.principal_axis()
>>> print(princ_axis)
[[-0.21318784 -0.97697417  0.00850932]
 [ 0.39228202 -0.07761763  0.91656441]
 [-0.89479929  0.19873844  0.39979654]]

static quaternion_rotate(X, Y)

Source: https://github.com/charnley/rmsd/blob/master/rmsd/ calculate_rmsd.py Calculate the rotation

Parameters

• coor_1 (np.array) – coordinates array of size (N, D), where N is points and D is dimension.

• coor_2 (np.array) – coordinates array of size (N, D), where N is points and D is dimension.

Returns

rotation matrix

Return type

np.array of size (D, D)

static quaternion_transform(r)

Source: https://github.com/charnley/rmsd/blob/master/rmsd/ calculate_rmsd.py Get optimal rotation note: translation will be zero when the centroids of each molecule are the same.

read_file(file_in)

Read a pdb file and return atom informations as a dictionnary indexed on the atom num. The fonction can also read pqr files if specified with pqr_format = True, it will only change the column format of beta and occ factors.

Parameters

• pdb_in (str) – path of the pdb file to read

• pqr_format (bool, default=False) – Flag for .pqr file format reading.

Example

>>> prot_coor = Coor()
>>> prot_coor.read_file(os.path.join(TEST_PATH, '1y0m.pdb'))        
Succeed to read file ...1y0m.pdb ,  648 atoms found
>>> prot_coor.read_file(os.path.join(TEST_PATH, '1y0m.gro'))        
Succeed to read file ...1y0m.gro ,  648 atoms found

read_pdb(pdb_in, pqr_format=False)

Read a pdb file and return atom informations as a dictionnary indexed on the atom num. The fonction can also read pqr files if specified with pqr_format = True, it will only change the column format of beta and occ factors.

Parameters

• pdb_in (str) – path of the pdb file to read

• pqr_format (bool, default=False) – Flag for .pqr file format reading.

Example

>>> prot_coor = Coor()
>>> prot_coor.read_pdb(os.path.join(TEST_PATH, '1y0m.pdb'))        
Succeed to read file ...1y0m.pdb ,  648 atoms found

remove_alter_position()

Remove alternative position.

Example

>>> prot_coor = Coor(os.path.join(TEST_PATH, '4n1m.pdb'))        
Succeed to read file ...4n1m.pdb ,  2530 atoms found
>>> print('Atom num = {}'.format(prot_coor.num))
Atom num = 2530
>>> prot_coor.remove_alter_position()
>>> print('Atom num = {}'.format(prot_coor.num))
Atom num = 2475

rotation_angle(tau_x, tau_y, tau_z)

Compute coordinates of a system after a rotation on x, y and z axis.

Parameters

• tau_x (float) – angle of rotation (degrees) on the x axis

• tau_y (float) – angle of rotation (degrees) on the y axis

• tau_z (float) – angle of rotation (degrees) on the z axis

Example

>>> prot_coor = Coor(os.path.join(TEST_PATH, '1y0m.pdb'))        
Succeed to read file ...1y0m.pdb ,  648 atoms found
>>> com_1y0m = prot_coor.center_of_mass()
>>> print("x:{:.2f} y:{:.2f} z:{:.2f}".format(*com_1y0m))
x:16.01 y:0.45 z:8.57
>>> prot_coor.rotation_angle(90, 90, 90)
>>> com_1y0m = prot_coor.center_of_mass()
>>> print("x:{:.2f} y:{:.2f} z:{:.2f}".format(*com_1y0m))        
x:9.98 y:-4.03 z:-14.63

select_from_index(index_list)

Select atom of a coor object from an atom index list. Return a new coor object.

Parameters

index_list (list) – list of index eg. [0, 4]

Returns

a new coor object

Return type

coor

Example

>>> prot_coor = Coor(os.path.join(TEST_PATH, '1y0m.pdb'))        
Succeed to read file ...1y0m.pdb ,  648 atoms found
>>> index_list = prot_coor.get_index_selection({'res_num': [826,827]})
>>> index_list
[297, 298, 299, 300, 301, 302, 303, 304]
>>> prot_sel = prot_coor.select_from_index(index_list)
>>> len(prot_sel.atom_dict) == len(index_list)
True

select_part_dict(selec_dict)

Select atom of a coor object defined, the selection is based on the change_dict dictionnary. Return a new coor object.

Parameters

selec_dict (dict) – change ditionnay eg. {“chain” : [“A”,”G”]}

Returns

a new coor object

Return type

coor

Example

>>> prot_coor = Coor(os.path.join(TEST_PATH, '1y0m.pdb'))        
Succeed to read file ...1y0m.pdb ,  648 atoms found
>>> prot_coor.get_aa_num()
61
>>> prot_20_coor = prot_coor.select_part_dict(selec_dict={'res_num': list(range(791,800))})
>>> prot_20_coor.get_aa_seq()
{'A': 'TFKSAVKAL'}
>>> prot_20_coor.get_aa_num()
9
>>> prot_N_atom = prot_coor.select_part_dict(selec_dict={'name': ['ZN']})
>>> # WARNING using selec_dict = {'name': 'ZN'} will
>>> # give you 61 residues !!
>>> print(prot_N_atom.num)
0
>>> # Select only protein atoms
>>> print(prot_coor.num)
648
>>> prot_only = prot_coor.select_part_dict(selec_dict={'res_name': PROTEIN_RES})
>>> print(prot_only.num)
526

translate(vector)

Translate all atoms of a coor object by a given vector

Parameters

vector (list) – 3d translation vector

Example

>>> prot_coor = Coor(os.path.join(TEST_PATH, '1y0m.pdb'))        
Succeed to read file ...1y0m.pdb ,  648 atoms found
>>> com_1y0m = prot_coor.center_of_mass()
>>> print("x:{:.2f} y:{:.2f} z:{:.2f}".format(*com_1y0m))
x:16.01 y:0.45 z:8.57
>>> prot_coor.translate(-com_1y0m)
>>> com_1y0m = prot_coor.center_of_mass()
>>> print("x:{:.2f} y:{:.2f} z:{:.2f}".format(*com_1y0m))
x:-0.00 y:0.00 z:0.00

property view

Return a nglview object to be view in a jupyter notebook.

Example:

>>> TEST_OUT = str(getfixture('tmpdir'))
>>> prot_coor = Coor()
>>> prot_coor.get_PDB('3EAM', os.path.join(TEST_OUT, '3eam.pdb'))
Succeed to read file ...3eam.pdb ,  13505 atoms found
>>> view = prot_coor.view 
>>> view 

water_to_ATOM()

Change HETATM field of water to ATOM, as pdb2pqr only use ATOM field.

Example

>>> try: 
...   print("Start import")
...   from . import pdb2pqr
... except ImportError:
...   import pdb2pqr
Start import...
>>> prot_coor = Coor(os.path.join(TEST_PATH, '1dpx.pdb'))        
Succeed to read file ...1dpx.pdb ,  1192 atoms found
>>> hetatm_index = prot_coor.get_index_selection({'field': ['HETATM']})
>>> print(len(hetatm_index))
179
>>> prot_coor.water_to_ATOM() 
<...Coor object at 0x...
>>> hetatm_index = prot_coor.get_index_selection({'field': ['HETATM']})
>>> print(len(hetatm_index))
2
>>> water_index = prot_coor.get_index_selection({'res_name': ['HOH']})
>>> print(len(water_index))
177

write_pdb(pdb_out, check_file_out=True)

Write a pdb file.

Parameters

• pdb_out (str) – path of the pdb file to write

• check_file_out (bool, optional, default=True) – flag to check or not if file has already been created. If the file is present then the command break.

Example

>>> TEST_OUT = str(getfixture('tmpdir'))
>>> prot_coor = Coor(os.path.join(TEST_PATH, '1y0m.pdb'))        
Succeed to read file ...1y0m.pdb ,  648 atoms found
>>> prot_coor.write_pdb(os.path.join(TEST_OUT, 'tmp.pdb'))        
Succeed to save file ...tmp.pdb

write_pqr(pqr_out, check_file_out=True)

Write a pdb file.

Parameters

• pdb_out (str) – path of the pdb file to write

• check_file_out (bool, optional, default=True) – flag to check or not if file has already been created. If the file is present then the command break.

Example

>>> TEST_OUT = str(getfixture('tmpdir'))
>>> prot_coor = Coor(os.path.join(TEST_PATH, '1y0m.pdb'))        
Succeed to read file ...1y0m.pdb ,  648 atoms found
>>> prot_coor.write_pdb(os.path.join(TEST_OUT, 'tmp.pdb'))        
Succeed to save file ...tmp.pdb