Author: bugman
Date: Mon Jan 12 14:19:16 2009
New Revision: 8410
URL: http://svn.gna.org/viewcvs/relax?rev=8410&view=rev
Log:
Shifted __parse_pdb_record() from the Internal class to the MolContainer.
Modified:
branches/multi_structure/generic_fns/structure/internal.py
Modified: branches/multi_structure/generic_fns/structure/internal.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_structure/generic_fns/structure/internal.py?rev=8410&r1=8409&r2=8410&view=diff
==============================================================================
--- branches/multi_structure/generic_fns/structure/internal.py (original)
+++ branches/multi_structure/generic_fns/structure/internal.py Mon Jan 12
14:19:16 2009
@@ -374,161 +374,6 @@
# If records is not empty then there is only a single molecule, so
yield the lot.
if len(mol_records):
yield mol_num, mol_records
-
-
- def __parse_pdb_record(self, record):
- """Parse the PDB record string and return an array of the
corresponding atomic information.
-
- The format of the ATOM and HETATM records is::
-
__________________________________________________________________________________________
- | | | |
|
- | Columns | Data type | Field | Definition
|
-
|_________|______________|______________|________________________________________________|
- | | | |
|
- | 1 - 6 | Record name | "ATOM" |
|
- | 7 - 11 | Integer | serial | Atom serial number.
|
- | 13 - 16 | Atom | name | Atom name.
|
- | 17 | Character | altLoc | Alternate location
indicator. |
- | 18 - 20 | Residue name | resName | Residue name.
|
- | 22 | Character | chainID | Chain identifier.
|
- | 23 - 26 | Integer | resSeq | Residue sequence number.
|
- | 27 | AChar | iCode | Code for insertion of
residues. |
- | 31 - 38 | Real(8.3) | x | Orthogonal coordinates for
X in Angstroms. |
- | 39 - 46 | Real(8.3) | y | Orthogonal coordinates for
Y in Angstroms. |
- | 47 - 54 | Real(8.3) | z | Orthogonal coordinates for
Z in Angstroms. |
- | 55 - 60 | Real(6.2) | occupancy | Occupancy.
|
- | 61 - 66 | Real(6.2) | tempFactor | Temperature factor.
|
- | 73 - 76 | LString(4) | segID | Segment identifier,
left-justified. |
- | 77 - 78 | LString(2) | element | Element symbol,
right-justified. |
- | 79 - 80 | LString(2) | charge | Charge on the atom.
|
-
|_________|______________|______________|________________________________________________|
-
-
- The format of the TER record is::
-
__________________________________________________________________________________________
- | | | |
|
- | Columns | Data type | Field | Definition
|
-
|_________|______________|______________|________________________________________________|
- | | | |
|
- | 1 - 6 | Record name | "TER " |
|
- | 7 - 11 | Integer | serial | Serial number.
|
- | 18 - 20 | Residue name | resName | Residue name.
|
- | 22 | Character | chainID | Chain identifier.
|
- | 23 - 26 | Integer | resSeq | Residue sequence number.
|
- | 27 | AChar | iCode | Insertion code.
|
-
|_________|______________|______________|________________________________________________|
-
-
- The format of the CONECT record is::
-
__________________________________________________________________________________________
- | | | |
|
- | Columns | Data type | Field | Definition
|
-
|_________|______________|______________|________________________________________________|
- | | | |
|
- | 1 - 6 | Record name | "CONECT" |
|
- | 7 - 11 | Integer | serial | Atom serial number
|
- | 12 - 16 | Integer | serial | Serial number of bonded
atom |
- | 17 - 21 | Integer | serial | Serial number of bonded
atom |
- | 22 - 26 | Integer | serial | Serial number of bonded
atom |
- | 27 - 31 | Integer | serial | Serial number of bonded
atom |
- | 32 - 36 | Integer | serial | Serial number of hydrogen
bonded atom |
- | 37 - 41 | Integer | serial | Serial number of hydrogen
bonded atom |
- | 42 - 46 | Integer | serial | Serial number of salt
bridged atom |
- | 47 - 51 | Integer | serial | Serial number of hydrogen
bonded atom |
- | 52 - 56 | Integer | serial | Serial number of hydrogen
bonded atom |
- | 57 - 61 | Integer | serial | Serial number of salt
bridged atom |
-
|_________|______________|______________|________________________________________________|
-
-
- @param record: The single line PDB record.
- @type record: str
- @return: The list of atomic information, each element
corresponding to the PDB fields
- as defined in "Protein Data Bank Contents Guide:
Atomic Coordinate Entry
- Format Description" version 2.1 (draft), October 25,
1996.
- @rtype: list of str
- """
-
- # Initialise.
- fields = []
-
- # ATOM and HETATM records.
- if search('^ATOM', record) or search('^HETATM', record):
- # Split up the record.
- fields.append(record[0:6])
- fields.append(record[6:11])
- fields.append(record[12:16])
- fields.append(record[16])
- fields.append(record[17:20])
- fields.append(record[21])
- fields.append(record[22:26])
- fields.append(record[26])
- fields.append(record[30:38])
- fields.append(record[38:46])
- fields.append(record[46:54])
- fields.append(record[54:60])
- fields.append(record[60:66])
- fields.append(record[72:76])
- fields.append(record[76:78])
- fields.append(record[78:80])
-
- # Loop over the fields.
- for i in xrange(len(fields)):
- # Strip all whitespace.
- fields[i] = strip(fields[i])
-
- # Replace nothingness with None.
- if fields[i] == '':
- fields[i] = None
-
- # Convert strings to numbers.
- if fields[1]:
- fields[1] = int(fields[1])
- if fields[6]:
- fields[6] = int(fields[6])
- if fields[8]:
- fields[8] = float(fields[8])
- if fields[9]:
- fields[9] = float(fields[9])
- if fields[10]:
- fields[10] = float(fields[10])
- if fields[11]:
- fields[11] = float(fields[11])
- if fields[12]:
- fields[12] = float(fields[12])
-
- # CONECT records.
- if search('^CONECT', record):
- # Split up the record.
- fields.append(record[0:6])
- fields.append(record[6:11])
- fields.append(record[11:16])
- fields.append(record[16:21])
- fields.append(record[21:26])
- fields.append(record[26:31])
-
- # Loop over the fields.
- for i in xrange(len(fields)):
- # Strip all whitespace.
- fields[i] = strip(fields[i])
-
- # Replace nothingness with None.
- if fields[i] == '':
- fields[i] = None
-
- # Convert strings to numbers.
- if fields[1]:
- fields[1] = int(fields[1])
- if fields[2]:
- fields[2] = int(fields[2])
- if fields[3]:
- fields[3] = int(fields[3])
- if fields[4]:
- fields[4] = int(fields[4])
- if fields[5]:
- fields[5] = int(fields[5])
-
- # Return the atomic info.
- return fields
def __validate_data_arrays(self, struct):
@@ -1336,6 +1181,161 @@
self.z = []
+ def __parse_pdb_record(self, record):
+ """Parse the PDB record string and return an array of the
corresponding atomic information.
+
+ The format of the ATOM and HETATM records is::
+
__________________________________________________________________________________________
+ | | | |
|
+ | Columns | Data type | Field | Definition
|
+
|_________|______________|______________|________________________________________________|
+ | | | |
|
+ | 1 - 6 | Record name | "ATOM" |
|
+ | 7 - 11 | Integer | serial | Atom serial number.
|
+ | 13 - 16 | Atom | name | Atom name.
|
+ | 17 | Character | altLoc | Alternate location
indicator. |
+ | 18 - 20 | Residue name | resName | Residue name.
|
+ | 22 | Character | chainID | Chain identifier.
|
+ | 23 - 26 | Integer | resSeq | Residue sequence number.
|
+ | 27 | AChar | iCode | Code for insertion of
residues. |
+ | 31 - 38 | Real(8.3) | x | Orthogonal coordinates for
X in Angstroms. |
+ | 39 - 46 | Real(8.3) | y | Orthogonal coordinates for
Y in Angstroms. |
+ | 47 - 54 | Real(8.3) | z | Orthogonal coordinates for
Z in Angstroms. |
+ | 55 - 60 | Real(6.2) | occupancy | Occupancy.
|
+ | 61 - 66 | Real(6.2) | tempFactor | Temperature factor.
|
+ | 73 - 76 | LString(4) | segID | Segment identifier,
left-justified. |
+ | 77 - 78 | LString(2) | element | Element symbol,
right-justified. |
+ | 79 - 80 | LString(2) | charge | Charge on the atom.
|
+
|_________|______________|______________|________________________________________________|
+
+
+ The format of the TER record is::
+
__________________________________________________________________________________________
+ | | | |
|
+ | Columns | Data type | Field | Definition
|
+
|_________|______________|______________|________________________________________________|
+ | | | |
|
+ | 1 - 6 | Record name | "TER " |
|
+ | 7 - 11 | Integer | serial | Serial number.
|
+ | 18 - 20 | Residue name | resName | Residue name.
|
+ | 22 | Character | chainID | Chain identifier.
|
+ | 23 - 26 | Integer | resSeq | Residue sequence number.
|
+ | 27 | AChar | iCode | Insertion code.
|
+
|_________|______________|______________|________________________________________________|
+
+
+ The format of the CONECT record is::
+
__________________________________________________________________________________________
+ | | | |
|
+ | Columns | Data type | Field | Definition
|
+
|_________|______________|______________|________________________________________________|
+ | | | |
|
+ | 1 - 6 | Record name | "CONECT" |
|
+ | 7 - 11 | Integer | serial | Atom serial number
|
+ | 12 - 16 | Integer | serial | Serial number of bonded
atom |
+ | 17 - 21 | Integer | serial | Serial number of bonded
atom |
+ | 22 - 26 | Integer | serial | Serial number of bonded
atom |
+ | 27 - 31 | Integer | serial | Serial number of bonded
atom |
+ | 32 - 36 | Integer | serial | Serial number of hydrogen
bonded atom |
+ | 37 - 41 | Integer | serial | Serial number of hydrogen
bonded atom |
+ | 42 - 46 | Integer | serial | Serial number of salt
bridged atom |
+ | 47 - 51 | Integer | serial | Serial number of hydrogen
bonded atom |
+ | 52 - 56 | Integer | serial | Serial number of hydrogen
bonded atom |
+ | 57 - 61 | Integer | serial | Serial number of salt
bridged atom |
+
|_________|______________|______________|________________________________________________|
+
+
+ @param record: The single line PDB record.
+ @type record: str
+ @return: The list of atomic information, each element
corresponding to the PDB fields
+ as defined in "Protein Data Bank Contents Guide:
Atomic Coordinate Entry
+ Format Description" version 2.1 (draft), October 25,
1996.
+ @rtype: list of str
+ """
+
+ # Initialise.
+ fields = []
+
+ # ATOM and HETATM records.
+ if search('^ATOM', record) or search('^HETATM', record):
+ # Split up the record.
+ fields.append(record[0:6])
+ fields.append(record[6:11])
+ fields.append(record[12:16])
+ fields.append(record[16])
+ fields.append(record[17:20])
+ fields.append(record[21])
+ fields.append(record[22:26])
+ fields.append(record[26])
+ fields.append(record[30:38])
+ fields.append(record[38:46])
+ fields.append(record[46:54])
+ fields.append(record[54:60])
+ fields.append(record[60:66])
+ fields.append(record[72:76])
+ fields.append(record[76:78])
+ fields.append(record[78:80])
+
+ # Loop over the fields.
+ for i in xrange(len(fields)):
+ # Strip all whitespace.
+ fields[i] = strip(fields[i])
+
+ # Replace nothingness with None.
+ if fields[i] == '':
+ fields[i] = None
+
+ # Convert strings to numbers.
+ if fields[1]:
+ fields[1] = int(fields[1])
+ if fields[6]:
+ fields[6] = int(fields[6])
+ if fields[8]:
+ fields[8] = float(fields[8])
+ if fields[9]:
+ fields[9] = float(fields[9])
+ if fields[10]:
+ fields[10] = float(fields[10])
+ if fields[11]:
+ fields[11] = float(fields[11])
+ if fields[12]:
+ fields[12] = float(fields[12])
+
+ # CONECT records.
+ if search('^CONECT', record):
+ # Split up the record.
+ fields.append(record[0:6])
+ fields.append(record[6:11])
+ fields.append(record[11:16])
+ fields.append(record[16:21])
+ fields.append(record[21:26])
+ fields.append(record[26:31])
+
+ # Loop over the fields.
+ for i in xrange(len(fields)):
+ # Strip all whitespace.
+ fields[i] = strip(fields[i])
+
+ # Replace nothingness with None.
+ if fields[i] == '':
+ fields[i] = None
+
+ # Convert strings to numbers.
+ if fields[1]:
+ fields[1] = int(fields[1])
+ if fields[2]:
+ fields[2] = int(fields[2])
+ if fields[3]:
+ fields[3] = int(fields[3])
+ if fields[4]:
+ fields[4] = int(fields[4])
+ if fields[5]:
+ fields[5] = int(fields[5])
+
+ # Return the atomic info.
+ return fields
+
+
def atom_add(self, pdb_record=None, atom_num=None, atom_name=None,
res_name=None, chain_id=None, res_num=None, pos=[None, None, None],
segment_id=None, element=None):
"""Method for adding an atom to the structural data object.
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